[{"file_date_updated":"2021-12-01T14:38:08Z","oa_version":"Submitted Version","article_processing_charge":"No","title":"Stimfit: A fast visualization and analysis environment for cellular neurophysiology","publication_status":"published","article_type":"original","publication_identifier":{"issn":["0013-5585"],"eissn":["1862-278X"]},"doi":"10.1515/bmt-2013-4181","_id":"10396","file":[{"creator":"schloegl","file_id":"10397","content_type":"application/pdf","checksum":"cdfc5339b530a25d6079f7223f0b1f16","success":1,"access_level":"open_access","file_name":"Schloegl_Abstract-BMT2013.pdf","date_updated":"2021-12-01T14:38:08Z","file_size":149825,"date_created":"2021-12-01T14:38:08Z","relation":"main_file"}],"date_created":"2021-12-01T14:35:35Z","conference":{"start_date":"2013-09-19","location":"Graz, Austria","name":"BMT: Biomedizinische Technik ","end_date":"2013-09-21"},"abstract":[{"lang":"eng","text":"Stimfit is a free cross-platform software package for viewing and analyzing electrophysiological data. It supports most standard file types for cellular neurophysiology and other biomedical formats. Its analysis algorithms have been used and validated in several experimental laboratories. Its embedded Python scripting interface makes Stimfit highly extensible and customizable."}],"article_number":"000010151520134181","year":"2013","citation":{"short":"A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering / Biomedizinische Technik 58 (2013).","apa":"Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., &#38; Guzman, S. J. (2013). Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. Graz, Austria: De Gruyter. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>","chicago":"Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>. De Gruyter, 2013. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>.","mla":"Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>.","ama":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. 2013;58(SI-1-Track-G). doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>","ieee":"A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A fast visualization and analysis environment for cellular neurophysiology,” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G. De Gruyter, 2013.","ista":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181."},"oa":1,"volume":58,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl"},{"last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"},{"last_name":"Schmidt-Hieber","first_name":"C.","full_name":"Schmidt-Hieber, C."},{"full_name":"Guzman, S. J.","first_name":"S. J.","last_name":"Guzman"}],"publication":"Biomedical Engineering / Biomedizinische Technik","date_updated":"2021-12-02T12:51:12Z","department":[{"_id":"PeJo"}],"intvolume":"        58","quality_controlled":"1","day":"01","has_accepted_license":"1","issue":"SI-1-Track-G","date_published":"2013-08-01T00:00:00Z","external_id":{"pmid":["24042795"]},"type":"journal_article","publisher":"De Gruyter","pmid":1,"status":"public","month":"08","keyword":["biomedical engineering","data analysis","free software"],"language":[{"iso":"eng"}],"ddc":["005","610"]},{"quality_controlled":"1","day":"28","page":"193-205","issue":"1","type":"journal_article","external_id":{"pmid":["23540698"]},"date_published":"2013-03-28T00:00:00Z","pmid":1,"publisher":"Elsevier","status":"public","month":"03","extern":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","oa_version":"Published Version","publication_status":"published","title":"The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"article_type":"original","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2013.02.033","open_access":"1"}],"doi":"10.1016/j.cell.2013.02.033","date_created":"2021-06-04T12:23:28Z","_id":"9459","abstract":[{"text":"Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Here, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromatic sequences preferentially require DDM1 for DNA methylation and that this preference depends on linker histone H1. RdDM is instead inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together, DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway.","lang":"eng"}],"citation":{"short":"A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K. Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205.","apa":"Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>","chicago":"Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>.","mla":"Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>, vol. 153, no. 1, Elsevier, 2013, pp. 193–205, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>.","ama":"Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. 2013;153(1):193-205. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>","ieee":"A. Zemach <i>et al.</i>, “The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin,” <i>Cell</i>, vol. 153, no. 1. Elsevier, pp. 193–205, 2013.","ista":"Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 153(1), 193–205."},"year":"2013","volume":153,"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Zemach","first_name":"Assaf","full_name":"Zemach, Assaf"},{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung","last_name":"Hsieh"},{"first_name":"Devin","last_name":"Coleman-Derr","full_name":"Coleman-Derr, Devin"},{"full_name":"Eshed-Williams, Leor","last_name":"Eshed-Williams","first_name":"Leor"},{"full_name":"Thao, Ka","first_name":"Ka","last_name":"Thao"},{"last_name":"Harmer","first_name":"Stacey L.","full_name":"Harmer, Stacey L."},{"first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"date_updated":"2021-12-14T08:25:35Z","publication":"Cell","department":[{"_id":"DaZi"}],"intvolume":"       153"},{"quality_controlled":"1","day":"07","page":"7934-7939","issue":"19","type":"journal_article","date_published":"2013-05-07T00:00:00Z","external_id":{"pmid":["23613580"]},"pmid":1,"publisher":"National Academy of Sciences","status":"public","month":"05","extern":"1","keyword":["Multidisciplinary"],"language":[{"iso":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","publication_status":"published","title":"Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"article_type":"original","scopus_import":"1","doi":"10.1073/pnas.1306164110","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1306164110","open_access":"1"}],"date_created":"2021-06-07T07:31:02Z","_id":"9481","abstract":[{"text":"Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo, exhibits extensive localized DNA demethylation on maternally inherited chromosomes. Demethylation mediates parent-of-origin–specific (imprinted) gene expression but is apparently unnecessary for the extensive accumulation of maternally biased small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation is generally parent-of-origin specific is unknown. Imprinted expression of sRNA also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing of the Kitaake rice cultivar that enabled us to show that localized hypomethylation in rice endosperm occurs solely on the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small class II (cut-and-paste) transposable elements, those in endosperm are more uniformly derived, including sequences from other transposon classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that localized hypomethylation of maternal endosperm DNA is conserved in flowering plants.","lang":"eng"}],"citation":{"mla":"Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7934–39, doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>.","chicago":"Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>.","apa":"Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald, P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>","short":"J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110 (2013) 7934–7939.","ista":"Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. 110(19), 7934–7939.","ieee":"J. A. Rodrigues <i>et al.</i>, “Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19. National Academy of Sciences, pp. 7934–7939, 2013.","ama":"Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2013;110(19):7934-7939. doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>"},"year":"2013","volume":110,"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Rodrigues, Jessica A.","first_name":"Jessica A.","last_name":"Rodrigues"},{"last_name":"Ruan","first_name":"Randy","full_name":"Ruan, Randy"},{"full_name":"Nishimura, Toshiro","last_name":"Nishimura","first_name":"Toshiro"},{"full_name":"Sharma, Manoj K.","last_name":"Sharma","first_name":"Manoj K."},{"last_name":"Sharma","first_name":"Rita","full_name":"Sharma, Rita"},{"last_name":"Ronald","first_name":"Pamela C","full_name":"Ronald, Pamela C"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"date_updated":"2021-12-14T08:26:44Z","publication":"Proceedings of the National Academy of Sciences","department":[{"_id":"DaZi"}],"intvolume":"       110"},{"quality_controlled":"1","page":"215-225","day":"11","issue":"3","type":"journal_article","date_published":"2013-02-11T00:00:00Z","external_id":{"pmid":["23410937"]},"pmid":1,"publisher":"Elsevier","month":"02","status":"public","language":[{"iso":"eng"}],"extern":"1","publication_status":"published","title":"A conversation across generations: Soma-germ cell crosstalk in plants","oa_version":"Published Version","article_processing_charge":"No","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2013.01.014"}],"doi":"10.1016/j.devcel.2013.01.014","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"article_type":"review","date_created":"2021-06-08T06:14:50Z","_id":"9520","citation":{"ama":"Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ cell crosstalk in plants. <i>Developmental Cell</i>. 2013;24(3):215-225. doi:<a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">10.1016/j.devcel.2013.01.014</a>","ieee":"X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations: Soma-germ cell crosstalk in plants,” <i>Developmental Cell</i>, vol. 24, no. 3. Elsevier, pp. 215–225, 2013.","ista":"Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225.","mla":"Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” <i>Developmental Cell</i>, vol. 24, no. 3, Elsevier, 2013, pp. 215–25, doi:<a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">10.1016/j.devcel.2013.01.014</a>.","apa":"Feng, X., Zilberman, D., &#38; Dickinson, H. (2013). A conversation across generations: Soma-germ cell crosstalk in plants. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">https://doi.org/10.1016/j.devcel.2013.01.014</a>","short":"X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225.","chicago":"Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” <i>Developmental Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">https://doi.org/10.1016/j.devcel.2013.01.014</a>."},"year":"2013","abstract":[{"lang":"eng","text":"Plants undergo alternation of generation in which reproductive cells develop in the plant body (\"sporophytic generation\") and then differentiate into a multicellular gamete-forming \"gametophytic generation.\" Different populations of helper cells assist in this transgenerational journey, with somatic tissues supporting early development and single nurse cells supporting gametogenesis. New data reveal a two-way relationship between early reproductive cells and their helpers involving complex epigenetic and signaling networks determining cell number and fate. Later, the egg cell plays a central role in specifying accessory cells, whereas in both gametophytes, companion cells contribute non-cell-autonomously to the epigenetic landscape of the gamete genomes."}],"volume":24,"oa":1,"author":[{"orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","last_name":"Feng"},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel"},{"full_name":"Dickinson, Hugh","last_name":"Dickinson","first_name":"Hugh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"date_updated":"2023-05-08T11:00:59Z","publication":"Developmental Cell","intvolume":"        24"},{"abstract":[{"lang":"eng","text":"Cooperative behavior, where one individual incurs a cost to help another, is a wide spread phenomenon. Here we study direct reciprocity in the context of the alternating Prisoner's Dilemma. We consider all strategies that can be implemented by one and two-state automata. We calculate the payoff matrix of all pairwise encounters in the presence of noise. We explore deterministic selection dynamics with and without mutation. Using different error rates and payoff values, we observe convergence to a small number of distinct equilibria. Two of them are uncooperative strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium is mixed and represents a cooperative alliance of several strategies, dominated by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent has cooperated; it defects once when the opponent has defected, but subsequently Forgiver attempts to re-establish cooperation even if the opponent has defected again. Forgiver is not an evolutionarily stable strategy, but the alliance, which it rules, is asymptotically stable. For a wide range of parameter values the most commonly observed outcome is convergence to the mixed equilibrium, dominated by Forgiver. Our results show that although forgiving might incur a short-term loss it can lead to a long-term gain. Forgiveness facilitates stable cooperation in the presence of exploitation and noise."}],"year":"2013","citation":{"ista":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating prisoner’s dilemma , Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">10.1371/journal.pone.0080814.s001</a>.","ieee":"B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma .” Public Library of Science, 2013.","ama":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating prisoner’s dilemma . 2013. doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">10.1371/journal.pone.0080814.s001</a>","mla":"Zagorsky, Benjamin, et al. <i>Forgiver Triumphs in Alternating Prisoner’s Dilemma </i>. Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">10.1371/journal.pone.0080814.s001</a>.","short":"B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, (2013).","apa":"Zagorsky, B., Reiter, J., Chatterjee, K., &#38; Nowak, M. (2013). Forgiver triumphs in alternating prisoner’s dilemma . Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">https://doi.org/10.1371/journal.pone.0080814.s001</a>","chicago":"Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">https://doi.org/10.1371/journal.pone.0080814.s001</a>."},"_id":"9749","date_created":"2021-07-28T15:45:07Z","day":"12","doi":"10.1371/journal.pone.0080814.s001","article_processing_charge":"No","oa_version":"Published Version","title":"Forgiver triumphs in alternating prisoner's dilemma ","status":"public","date_updated":"2023-02-23T10:34:39Z","month":"12","department":[{"_id":"KrCh"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","author":[{"full_name":"Zagorsky, Benjamin","first_name":"Benjamin","last_name":"Zagorsky"},{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","first_name":"Johannes","last_name":"Reiter"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"related_material":{"record":[{"id":"2247","relation":"used_in_publication","status":"public"}]},"date_published":"2013-12-12T00:00:00Z","type":"research_data_reference"},{"department":[{"_id":"CaGu"}],"month":"03","date_updated":"2023-10-18T06:43:22Z","status":"public","type":"research_data_reference","date_published":"2013-03-21T00:00:00Z","related_material":{"record":[{"id":"2853","relation":"used_in_publication","status":"public"}]},"oa":1,"author":[{"last_name":"Refardt","first_name":"Dominik","full_name":"Refardt, Dominik"},{"first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"last_name":"Kümmerli","first_name":"Rolf","full_name":"Kümmerli, Rolf"}],"publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-07-30T08:08:09Z","_id":"9751","citation":{"ista":"Refardt D, Bergmiller T, Kümmerli R. 2013. Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection, Dryad, <a href=\"https://doi.org/10.5061/dryad.b1q2n\">10.5061/dryad.b1q2n</a>.","ieee":"D. Refardt, T. Bergmiller, and R. Kümmerli, “Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection.” Dryad, 2013.","ama":"Refardt D, Bergmiller T, Kümmerli R. Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection. 2013. doi:<a href=\"https://doi.org/10.5061/dryad.b1q2n\">10.5061/dryad.b1q2n</a>","apa":"Refardt, D., Bergmiller, T., &#38; Kümmerli, R. (2013). Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection. Dryad. <a href=\"https://doi.org/10.5061/dryad.b1q2n\">https://doi.org/10.5061/dryad.b1q2n</a>","short":"D. Refardt, T. Bergmiller, R. Kümmerli, (2013).","chicago":"Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” Dryad, 2013. <a href=\"https://doi.org/10.5061/dryad.b1q2n\">https://doi.org/10.5061/dryad.b1q2n</a>.","mla":"Refardt, Dominik, et al. <i>Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection</i>. Dryad, 2013, doi:<a href=\"https://doi.org/10.5061/dryad.b1q2n\">10.5061/dryad.b1q2n</a>."},"year":"2013","abstract":[{"text":"High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation.","lang":"eng"}],"title":"Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection","article_processing_charge":"No","oa_version":"Published Version","doi":"10.5061/dryad.b1q2n","main_file_link":[{"url":"https://doi.org/10.5061/dryad.b1q2n","open_access":"1"}],"day":"21"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","author":[{"full_name":"Hearn, Jack","last_name":"Hearn","first_name":"Jack"},{"full_name":"Stone, Graham","first_name":"Graham","last_name":"Stone"},{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"last_name":"Lohse","first_name":"Konrad","full_name":"Lohse, Konrad"},{"full_name":"Bunnefeld, Lynsey","first_name":"Lynsey","last_name":"Bunnefeld"}],"oa":1,"related_material":{"record":[{"id":"2170","relation":"used_in_publication","status":"public"}]},"date_published":"2013-10-01T00:00:00Z","type":"research_data_reference","status":"public","date_updated":"2023-02-23T10:31:17Z","month":"10","department":[{"_id":"NiBa"}],"day":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.r3r60"}],"doi":"10.5061/dryad.r3r60","oa_version":"Published Version","article_processing_charge":"No","title":"Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies","abstract":[{"lang":"eng","text":"Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate among recent, non-equilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model, and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources."}],"year":"2013","citation":{"apa":"Hearn, J., Stone, G., Barton, N. H., Lohse, K., &#38; Bunnefeld, L. (2013). Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. Dryad. <a href=\"https://doi.org/10.5061/dryad.r3r60\">https://doi.org/10.5061/dryad.r3r60</a>","chicago":"Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies.” Dryad, 2013. <a href=\"https://doi.org/10.5061/dryad.r3r60\">https://doi.org/10.5061/dryad.r3r60</a>.","short":"J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013).","mla":"Hearn, Jack, et al. <i>Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies</i>. Dryad, 2013, doi:<a href=\"https://doi.org/10.5061/dryad.r3r60\">10.5061/dryad.r3r60</a>.","ama":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. 2013. doi:<a href=\"https://doi.org/10.5061/dryad.r3r60\">10.5061/dryad.r3r60</a>","ieee":"J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies.” Dryad, 2013.","ista":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies, Dryad, <a href=\"https://doi.org/10.5061/dryad.r3r60\">10.5061/dryad.r3r60</a>."},"_id":"9754","date_created":"2021-07-30T08:31:22Z"},{"publication_status":"published","title":"Defining the selectivity of processes along the auxin response chain: A study using auxin analogues","article_processing_charge":"No","oa_version":"Published Version","scopus_import":"1","doi":"10.1111/nph.12437","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/nph.12437"}],"acknowledgement":"The authors thank Dr Christian Luschnig (University of Natural Resources and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds and, last but not least, to Dr David Morris for critical reading of the manuscript. We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance. This work was supported by the Grant Agency of the Czech Republic (P305/11/0797 to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European Research Council starting independent research grant ERC-2011-StG-20101109-PSDP (to J.F.).","article_type":"original","date_created":"2018-12-11T11:57:41Z","_id":"2443","citation":{"mla":"Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>, vol. 200, no. 4, Wiley, 2013, pp. 1034–48, doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>.","apa":"Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová, E. (2013). Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>","chicago":"Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>.","short":"S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek, E. Zažímalová, New Phytologist 200 (2013) 1034–1048.","ama":"Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. 2013;200(4):1034-1048. doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>","ieee":"S. Simon <i>et al.</i>, “Defining the selectivity of processes along the auxin response chain: A study using auxin analogues,” <i>New Phytologist</i>, vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.","ista":"Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová E. 2013. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 200(4), 1034–1048."},"year":"2013","abstract":[{"text":"The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery.","lang":"eng"}],"volume":200,"oa":1,"author":[{"last_name":"Simon","first_name":"Sibu","full_name":"Simon, Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741"},{"first_name":"Martin","last_name":"Kubeš","full_name":"Kubeš, Martin"},{"full_name":"Baster, Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","last_name":"Baster","first_name":"Pawel"},{"full_name":"Robert, Stéphanie","first_name":"Stéphanie","last_name":"Robert"},{"last_name":"Dobrev","first_name":"Petre","full_name":"Dobrev, Petre"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"das_tickbox":"1","ec_funded":1,"date_updated":"2026-06-18T07:49:41Z","publication":"New Phytologist","intvolume":"       200","quality_controlled":"1","page":"1034 - 1048","day":"01","issue":"4","project":[{"name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300"}],"type":"journal_article","date_published":"2013-12-01T00:00:00Z","publisher":"Wiley","month":"12","publist_id":"4460","status":"public","ddc":["580"],"language":[{"iso":"eng"}]},{"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Ła̧Cki","first_name":"Jakub","full_name":"Ła̧Cki, Jakub"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","series_title":"Lecture Notes in Computer Science","volume":8044,"oa":1,"arxiv":1,"intvolume":"      8044","das_tickbox":"1","department":[{"_id":"KrCh"}],"ec_funded":1,"date_updated":"2026-06-18T07:50:03Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.0084"}],"doi":"10.1007/978-3-642-39799-8_36","title":"Faster algorithms for Markov decision processes with low treewidth","publication_status":"published","article_processing_charge":"No","oa_version":"Preprint","citation":{"mla":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. <i>Faster Algorithms for Markov Decision Processes with Low Treewidth</i>. Vol. 8044, Springer, 2013, pp. 543–58, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">10.1007/978-3-642-39799-8_36</a>.","short":"K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558.","chicago":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">https://doi.org/10.1007/978-3-642-39799-8_36</a>.","apa":"Chatterjee, K., &#38; Ła̧Cki, J. (2013). Faster algorithms for Markov decision processes with low treewidth. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">https://doi.org/10.1007/978-3-642-39799-8_36</a>","ama":"Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with low treewidth. 2013;8044:543-558. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">10.1007/978-3-642-39799-8_36</a>","ista":"Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes with low treewidth. 8044, 543–558.","ieee":"K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013."},"year":"2013","abstract":[{"lang":"eng","text":"We consider two core algorithmic problems for probabilistic verification: the maximal end-component decomposition and the almost-sure reachability set computation for Markov decision processes (MDPs). For MDPs with treewidth k, we present two improved static algorithms for both the problems that run in time O(n·k 2.38·2k ) and O(m·logn· k), respectively, where n is the number of states and m is the number of edges, significantly improving the previous known O(n·k·√n· k) bound for low treewidth. We also present decremental algorithms for both problems for MDPs with constant treewidth that run in amortized logarithmic time, which is a huge improvement over the previously known algorithms that require amortized linear time."}],"conference":{"start_date":"2013-07-13","end_date":"2013-07-19","name":"CAV: Computer Aided Verification","location":"St. Petersburg, Russia"},"date_created":"2018-12-11T11:57:42Z","_id":"2444","publisher":"Springer","type":"conference","external_id":{"arxiv":["1304.0084"]},"date_published":"2013-07-01T00:00:00Z","ddc":["000"],"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"month":"07","publist_id":"4459","status":"public","page":"543 - 558","day":"01","quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}]},{"volume":2,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2022-03-21T12:15:29Z","publication":"Plants","department":[{"_id":"JiFr"}],"intvolume":"         2","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2022-03-21T12:12:56Z","publication_status":"published","title":"Calcium: The missing link in auxin action","publication_identifier":{"issn":["2223-7747"]},"article_type":"original","scopus_import":"1","doi":"10.3390/plants2040650","file":[{"checksum":"fb4ff2e820e344e253c9197544610be6","file_id":"10916","creator":"dernst","content_type":"application/pdf","file_size":670188,"relation":"main_file","date_updated":"2022-03-21T12:12:56Z","date_created":"2022-03-21T12:12:56Z","file_name":"2013_Plants_Vanneste.pdf","access_level":"open_access","success":1}],"date_created":"2022-03-21T07:13:49Z","_id":"10895","abstract":[{"text":"Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. ","lang":"eng"}],"citation":{"ieee":"S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” <i>Plants</i>, vol. 2, no. 4. MDPI, pp. 650–675, 2013.","ista":"Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants. 2(4), 650–675.","ama":"Vanneste S, Friml J. Calcium: The missing link in auxin action. <i>Plants</i>. 2013;2(4):650-675. doi:<a href=\"https://doi.org/10.3390/plants2040650\">10.3390/plants2040650</a>","mla":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” <i>Plants</i>, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:<a href=\"https://doi.org/10.3390/plants2040650\">10.3390/plants2040650</a>.","chicago":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” <i>Plants</i>. MDPI, 2013. <a href=\"https://doi.org/10.3390/plants2040650\">https://doi.org/10.3390/plants2040650</a>.","apa":"Vanneste, S., &#38; Friml, J. (2013). Calcium: The missing link in auxin action. <i>Plants</i>. MDPI. <a href=\"https://doi.org/10.3390/plants2040650\">https://doi.org/10.3390/plants2040650</a>","short":"S. Vanneste, J. Friml, Plants 2 (2013) 650–675."},"year":"2013","type":"journal_article","date_published":"2013-10-21T00:00:00Z","external_id":{"pmid":["27137397"]},"pmid":1,"publisher":"MDPI","status":"public","month":"10","keyword":["Plant Science","Ecology","Ecology","Evolution","Behavior and Systematics"],"ddc":["580"],"language":[{"iso":"eng"}],"quality_controlled":"1","day":"21","page":"650-675","license":"https://creativecommons.org/licenses/by/3.0/","has_accepted_license":"1","tmp":{"short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"issue":"4"},{"quality_controlled":"1","page":"182-183","day":"01","project":[{"call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems"}],"date_published":"2013-06-01T00:00:00Z","type":"conference","publisher":"Springer Nature","month":"06","status":"public","language":[{"iso":"eng"}],"title":"Persistent homology in image processing","publication_status":"published","article_processing_charge":"No","oa_version":"None","doi":"10.1007/978-3-642-38221-5_19","scopus_import":"1","acknowledgement":"This research is partially supported by the European Science Foundation (ESF) under the Research Network Programme, the European Union under the Toposys Project FP7-ICT-318493-STREP, the Russian Government under the Mega Project 11.G34.31.0053.","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783642382215"],"isbn":["9783642382208"],"eissn":["1611-3349"]},"conference":{"end_date":"2013-05-17","location":"Vienna, Austria","name":"GbRPR: Graph-based Representations in Pattern Recognition","start_date":"2013-05-15"},"_id":"10897","date_created":"2022-03-21T07:30:33Z","year":"2013","place":"Berlin, Heidelberg","citation":{"mla":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” <i>Graph-Based Representations in Pattern Recognition</i>, vol. 7877, Springer Nature, 2013, pp. 182–83, doi:<a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">10.1007/978-3-642-38221-5_19</a>.","chicago":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” In <i>Graph-Based Representations in Pattern Recognition</i>, 7877:182–83. LNCS. Berlin, Heidelberg: Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">https://doi.org/10.1007/978-3-642-38221-5_19</a>.","apa":"Edelsbrunner, H. (2013). Persistent homology in image processing. In <i>Graph-Based Representations in Pattern Recognition</i> (Vol. 7877, pp. 182–183). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">https://doi.org/10.1007/978-3-642-38221-5_19</a>","short":"H. Edelsbrunner, in:, Graph-Based Representations in Pattern Recognition, Springer Nature, Berlin, Heidelberg, 2013, pp. 182–183.","ama":"Edelsbrunner H. Persistent homology in image processing. In: <i>Graph-Based Representations in Pattern Recognition</i>. Vol 7877. LNCS. Berlin, Heidelberg: Springer Nature; 2013:182-183. doi:<a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">10.1007/978-3-642-38221-5_19</a>","ieee":"H. Edelsbrunner, “Persistent homology in image processing,” in <i>Graph-Based Representations in Pattern Recognition</i>, Vienna, Austria, 2013, vol. 7877, pp. 182–183.","ista":"Edelsbrunner H. 2013. Persistent homology in image processing. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNCS vol. 7877, 182–183."},"abstract":[{"lang":"eng","text":"Taking images is an efficient way to collect data about the physical world. It can be done fast and in exquisite detail. By definition, image processing is the field that concerns itself with the computation aimed at harnessing the information contained in images [10]. This talk is concerned with topological information. Our main thesis is that persistent homology [5] is a useful method to quantify and summarize topological information, building a bridge that connects algebraic topology with applications. We provide supporting evidence for this thesis by touching upon four technical developments in the overlap between persistent homology and image processing."}],"series_title":"LNCS","volume":7877,"author":[{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"HeEd"}],"publication":"Graph-Based Representations in Pattern Recognition","ec_funded":1,"date_updated":"2023-09-05T15:10:20Z","intvolume":"      7877"},{"year":"2013","article_number":"17","citation":{"ama":"Haas A, Lippautz M, Henzinger TA, et al. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In: <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. ACM Press; 2013. doi:<a href=\"https://doi.org/10.1145/2482767.2482789\">10.1145/2482767.2482789</a>","ieee":"A. Haas <i>et al.</i>, “Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation,” in <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>, Ischia, Italy, 2013, no. 5.","ista":"Haas A, Lippautz M, Henzinger TA, Payer H, Sokolova A, Kirsch CM, Sezgin A. 2013. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. CF: Conference on Computing Frontiers, 17.","apa":"Haas, A., Lippautz, M., Henzinger, T. A., Payer, H., Sokolova, A., Kirsch, C. M., &#38; Sezgin, A. (2013). Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. Ischia, Italy: ACM Press. <a href=\"https://doi.org/10.1145/2482767.2482789\">https://doi.org/10.1145/2482767.2482789</a>","chicago":"Haas, Andreas, Michael Lippautz, Thomas A Henzinger, Hannes Payer, Ana Sokolova, Christoph M. Kirsch, and Ali Sezgin. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” In <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. ACM Press, 2013. <a href=\"https://doi.org/10.1145/2482767.2482789\">https://doi.org/10.1145/2482767.2482789</a>.","short":"A. Haas, M. Lippautz, T.A. Henzinger, H. Payer, A. Sokolova, C.M. Kirsch, A. Sezgin, in:, Proceedings of the ACM International Conference on Computing Frontiers - CF ’13, ACM Press, 2013.","mla":"Haas, Andreas, et al. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>, no. 5, 17, ACM Press, 2013, doi:<a href=\"https://doi.org/10.1145/2482767.2482789\">10.1145/2482767.2482789</a>."},"abstract":[{"lang":"eng","text":"A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered."}],"issue":"5","conference":{"location":"Ischia, Italy","name":"CF: Conference on Computing Frontiers","end_date":"2013-05-16","start_date":"2013-05-14"},"_id":"10898","date_created":"2022-03-21T07:33:22Z","doi":"10.1145/2482767.2482789","scopus_import":"1","day":"01","publication_identifier":{"isbn":["978-145032053-5"]},"publication_status":"published","title":"Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation","quality_controlled":"1","article_processing_charge":"No","oa_version":"None","language":[{"iso":"eng"}],"month":"05","department":[{"_id":"ToHe"}],"status":"public","publication":"Proceedings of the ACM International Conference on Computing Frontiers - CF '13","date_updated":"2022-06-21T08:01:19Z","publisher":"ACM Press","author":[{"last_name":"Haas","first_name":"Andreas","full_name":"Haas, Andreas"},{"first_name":"Michael","last_name":"Lippautz","full_name":"Lippautz, Michael"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Payer, Hannes","last_name":"Payer","first_name":"Hannes"},{"last_name":"Sokolova","first_name":"Ana","full_name":"Sokolova, Ana"},{"first_name":"Christoph M.","last_name":"Kirsch","full_name":"Kirsch, Christoph M."},{"last_name":"Sezgin","first_name":"Ali","full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2013-05-01T00:00:00Z","type":"conference"},{"quality_controlled":"1","publication_status":"published","title":"Differentiation","article_processing_charge":"No","oa_version":"None","scopus_import":"1","edition":"2","doi":"10.1016/b978-0-12-384719-5.00031-9","page":"508-515","day":"01","publication_identifier":{"isbn":["978-0-12-384720-1"]},"date_created":"2022-03-21T07:46:22Z","_id":"10899","citation":{"chicago":"Barton, Nicholas H. “Differentiation.” In <i>Encyclopedia of Biodiversity</i>, 2nd ed., 508–15. Elsevier, 2013. <a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">https://doi.org/10.1016/b978-0-12-384719-5.00031-9</a>.","short":"N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515.","apa":"Barton, N. H. (2013). Differentiation. In <i>Encyclopedia of Biodiversity</i> (2nd ed., pp. 508–515). Elsevier. <a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">https://doi.org/10.1016/b978-0-12-384719-5.00031-9</a>","mla":"Barton, Nicholas H. “Differentiation.” <i>Encyclopedia of Biodiversity</i>, 2nd ed., Elsevier, 2013, pp. 508–15, doi:<a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">10.1016/b978-0-12-384719-5.00031-9</a>.","ista":"Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515.","ieee":"N. H. Barton, “Differentiation,” in <i>Encyclopedia of Biodiversity</i>, 2nd ed., Elsevier, 2013, pp. 508–515.","ama":"Barton NH. Differentiation. In: <i>Encyclopedia of Biodiversity</i>. 2nd ed. Elsevier; 2013:508-515. doi:<a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">10.1016/b978-0-12-384719-5.00031-9</a>"},"year":"2013","type":"book_chapter","date_published":"2013-01-01T00:00:00Z","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"month":"01","date_updated":"2022-06-20T09:18:06Z","publication":"Encyclopedia of Biodiversity","status":"public","language":[{"iso":"eng"}],"keyword":["Adaptive landscape","Cline","Coalescent process","Gene flow","Hybrid zone","Local adaptation","Natural selection","Neutral theory","Population structure","Speciation"]},{"month":"04","status":"public","language":[{"iso":"eng"}],"alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","external_id":{"pmid":["23625502"]},"date_published":"2013-04-03T00:00:00Z","pmid":1,"publisher":"Humana Press","quality_controlled":"1","page":"215-226","day":"03","department":[{"_id":"MiSi"}],"date_updated":"2023-09-05T13:15:33Z","publication":"Chemokines","intvolume":"      1013","series_title":"MIMB","volume":1013,"author":[{"first_name":"Michele","last_name":"Weber","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","full_name":"Weber, Michele"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","editor":[{"last_name":"Cardona","first_name":"Astrid","full_name":"Cardona, Astrid"},{"first_name":"Eroboghene","last_name":"Ubogu","full_name":"Ubogu, Eroboghene"}],"date_created":"2022-03-21T07:47:41Z","_id":"10900","citation":{"ama":"Weber M, Sixt MK. Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Cardona A, Ubogu E, eds. <i>Chemokines</i>. Vol 1013. MIMB. Totowa, NJ: Humana Press; 2013:215-226. doi:<a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">10.1007/978-1-62703-426-5_14</a>","ieee":"M. Weber and M. K. Sixt, “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations,” in <i>Chemokines</i>, vol. 1013, A. Cardona and E. Ubogu, Eds. Totowa, NJ: Humana Press, 2013, pp. 215–226.","ista":"Weber M, Sixt MK. 2013.Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Chemokines. Methods in Molecular Biology, vol. 1013, 215–226.","short":"M. Weber, M.K. Sixt, in:, A. Cardona, E. Ubogu (Eds.), Chemokines, Humana Press, Totowa, NJ, 2013, pp. 215–226.","chicago":"Weber, Michele, and Michael K Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” In <i>Chemokines</i>, edited by Astrid Cardona and Eroboghene Ubogu, 1013:215–26. MIMB. Totowa, NJ: Humana Press, 2013. <a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">https://doi.org/10.1007/978-1-62703-426-5_14</a>.","apa":"Weber, M., &#38; Sixt, M. K. (2013). Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In A. Cardona &#38; E. Ubogu (Eds.), <i>Chemokines</i> (Vol. 1013, pp. 215–226). Totowa, NJ: Humana Press. <a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">https://doi.org/10.1007/978-1-62703-426-5_14</a>","mla":"Weber, Michele, and Michael K. Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” <i>Chemokines</i>, edited by Astrid Cardona and Eroboghene Ubogu, vol. 1013, Humana Press, 2013, pp. 215–26, doi:<a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">10.1007/978-1-62703-426-5_14</a>."},"year":"2013","place":"Totowa, NJ","abstract":[{"text":"Leukocyte migration through the interstitial space is crucial for the maintenance of tolerance and immunity. The main cues for leukocyte trafficking are chemokines thought to directionally guide these cells towards their targets. However, model systems that facilitate quantification of chemokine-guided leukocyte migration in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted mouse ears that allows the visualization of chemokine-dependent dendritic cell (DC) motility in the dermal interstitium in real time. We present methods for the preparation of mouse ear sheets and their use in multidimensional confocal imaging experiments to monitor and analyze the directional migration of fluorescently labelled DCs through the dermis and into afferent lymphatic vessels. The assay provides a more physiological approach to study leukocyte migration than in vitro three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen gels and transwell assays.","lang":"eng"}],"publication_status":"published","title":"Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations","article_processing_charge":"No","oa_version":"None","scopus_import":"1","doi":"10.1007/978-1-62703-426-5_14","acknowledgement":"We would like to thank Alexander Eichner and Ingrid de Vries for discussion and critical reading of the manuscript, and Mary Frank for assistance with the recording of videos and images in Fig. 1. M.S. is supported through funding from the German Research Foundation (DFG). M.W. acknowledges the Alexander von Humboldt Foundation for funding.","publication_identifier":{"issn":["1064-3745"],"eissn":["1940-6029"],"isbn":["9781627034258"],"eisbn":["9781627034265"]}},{"publisher":"Springer Nature","date_published":"2013-04-15T00:00:00Z","type":"conference","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"month":"04","status":"public","page":"214-225","day":"15","quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Siddhesh","last_name":"Chaubal","full_name":"Chaubal, Siddhesh"},{"last_name":"Rubin","first_name":"Sasha","full_name":"Rubin, Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","series_title":"LNCS","volume":7810,"intvolume":"      7810","department":[{"_id":"KrCh"}],"publication":"7th International Conference on Language and Automata Theory and Applications","ec_funded":1,"date_updated":"2023-09-05T15:10:38Z","doi":"10.1007/978-3-642-37064-9_20","scopus_import":"1","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783642370649"],"isbn":["9783642370632"],"eissn":["1611-3349"]},"acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award. Thanks to Gabriele Puppis for suggesting the problem of identifying a deterministic transducer to compute the optimal cost, and to Martin Chmelik for his comments on the introduction.","publication_status":"published","title":"How to travel between languages","article_processing_charge":"No","oa_version":"None","year":"2013","place":"Berlin, Heidelberg","citation":{"mla":"Chatterjee, Krishnendu, et al. “How to Travel between Languages.” <i>7th International Conference on Language and Automata Theory and Applications</i>, vol. 7810, Springer Nature, 2013, pp. 214–25, doi:<a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">10.1007/978-3-642-37064-9_20</a>.","apa":"Chatterjee, K., Chaubal, S., &#38; Rubin, S. (2013). How to travel between languages. In <i>7th International Conference on Language and Automata Theory and Applications</i> (Vol. 7810, pp. 214–225). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">https://doi.org/10.1007/978-3-642-37064-9_20</a>","chicago":"Chatterjee, Krishnendu, Siddhesh Chaubal, and Sasha Rubin. “How to Travel between Languages.” In <i>7th International Conference on Language and Automata Theory and Applications</i>, 7810:214–25. LNCS. Berlin, Heidelberg: Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">https://doi.org/10.1007/978-3-642-37064-9_20</a>.","short":"K. Chatterjee, S. Chaubal, S. Rubin, in:, 7th International Conference on Language and Automata Theory and Applications, Springer Nature, Berlin, Heidelberg, 2013, pp. 214–225.","ista":"Chatterjee K, Chaubal S, Rubin S. 2013. How to travel between languages. 7th International Conference on Language and Automata Theory and Applications. LATA: Conference on Language and Automata Theory and ApplicationsLNCS, LNCS, vol. 7810, 214–225.","ieee":"K. Chatterjee, S. Chaubal, and S. Rubin, “How to travel between languages,” in <i>7th International Conference on Language and Automata Theory and Applications</i>, Bilbao, Spain, 2013, vol. 7810, pp. 214–225.","ama":"Chatterjee K, Chaubal S, Rubin S. How to travel between languages. In: <i>7th International Conference on Language and Automata Theory and Applications</i>. Vol 7810. LNCS. Berlin, Heidelberg: Springer Nature; 2013:214-225. doi:<a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">10.1007/978-3-642-37064-9_20</a>"},"abstract":[{"lang":"eng","text":"We consider how to edit strings from a source language so that the edited strings belong to a target language, where the languages are given as deterministic finite automata. Non-streaming (or offline) transducers perform edits given the whole source string. We show that the class of deterministic one-pass transducers with registers along with increment and min operation suffices for computing optimal edit distance, whereas the same class of transducers without the min operation is not sufficient. Streaming (or online) transducers perform edits as the letters of the source string are received. We present a polynomial time algorithm for the partial-repair problem that given a bound α asks for the construction of a deterministic streaming transducer (if one exists) that ensures that the ‘maximum fraction’ η of the strings of the source language are edited, within cost α, to the target language."}],"conference":{"name":"LATA: Conference on Language and Automata Theory and Applications","location":"Bilbao, Spain","end_date":"2013-04-05","start_date":"2013-04-02"},"_id":"10902","date_created":"2022-03-21T07:56:21Z"},{"conference":{"start_date":"2013-01-23","end_date":"2013-01-25","name":"POPL: Principles of Programming Languages","location":"Rome, Italy"},"_id":"2181","file":[{"checksum":"adf465e70948f4e80e48057524516456","creator":"system","file_id":"5086","content_type":"application/pdf","date_updated":"2020-07-14T12:45:31Z","date_created":"2018-12-12T10:14:33Z","file_size":294689,"relation":"main_file","file_name":"IST-2014-198-v1+1_popl128-henzinger-clean.pdf","access_level":"open_access"}],"date_created":"2018-12-11T11:56:11Z","year":"2013","citation":{"ama":"Henzinger TA, Kirsch C, Payer H, Sezgin A, Sokolova A. Quantitative relaxation of concurrent data structures. In: <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>. ACM; 2013:317-328. doi:<a href=\"https://doi.org/10.1145/2429069.2429109\">10.1145/2429069.2429109</a>","ieee":"T. A. Henzinger, C. Kirsch, H. Payer, A. Sezgin, and A. Sokolova, “Quantitative relaxation of concurrent data structures,” in <i>Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language</i>, Rome, Italy, 2013, pp. 317–328.","ista":"Henzinger TA, Kirsch C, Payer H, Sezgin A, Sokolova A. 2013. Quantitative relaxation of concurrent data structures. Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language. POPL: Principles of Programming Languages, 317–328.","chicago":"Henzinger, Thomas A, Christoph Kirsch, Hannes Payer, Ali Sezgin, and Ana Sokolova. “Quantitative Relaxation of Concurrent Data Structures.” In <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>, 317–28. ACM, 2013. <a href=\"https://doi.org/10.1145/2429069.2429109\">https://doi.org/10.1145/2429069.2429109</a>.","apa":"Henzinger, T. A., Kirsch, C., Payer, H., Sezgin, A., &#38; Sokolova, A. (2013). Quantitative relaxation of concurrent data structures. In <i>Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language</i> (pp. 317–328). Rome, Italy: ACM. <a href=\"https://doi.org/10.1145/2429069.2429109\">https://doi.org/10.1145/2429069.2429109</a>","short":"T.A. Henzinger, C. Kirsch, H. Payer, A. Sezgin, A. Sokolova, in:, Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, ACM, 2013, pp. 317–328.","mla":"Henzinger, Thomas A., et al. “Quantitative Relaxation of Concurrent Data Structures.” <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>, ACM, 2013, pp. 317–28, doi:<a href=\"https://doi.org/10.1145/2429069.2429109\">10.1145/2429069.2429109</a>."},"abstract":[{"lang":"eng","text":"There is a trade-off between performance and correctness in implementing concurrent data structures. Better performance may be achieved at the expense of relaxing correctness, by redefining the semantics of data structures. We address such a redefinition of data structure semantics and present a systematic and formal framework for obtaining new data structures by quantitatively relaxing existing ones. We view a data structure as a sequential specification S containing all &quot;legal&quot; sequences over an alphabet of method calls. Relaxing the data structure corresponds to defining a distance from any sequence over the alphabet to the sequential specification: the k-relaxed sequential specification contains all sequences over the alphabet within distance k from the original specification. In contrast to other existing work, our relaxations are semantic (distance in terms of data structure states). As an instantiation of our framework, we present two simple yet generic relaxation schemes, called out-of-order and stuttering relaxation, along with several ways of computing distances. We show that the out-of-order relaxation, when further instantiated to stacks, queues, and priority queues, amounts to tolerating bounded out-of-order behavior, which cannot be captured by a purely syntactic relaxation (distance in terms of sequence manipulation, e.g. edit distance). We give concurrent implementations of relaxed data structures and demonstrate that bounded relaxations provide the means for trading correctness for performance in a controlled way. The relaxations are monotonic which further highlights the trade-off: increasing k increases the number of permitted sequences, which as we demonstrate can lead to better performance. Finally, since a relaxed stack or queue also implements a pool, we actually have new concurrent pool implementations that outperform the state-of-the-art ones."}],"publication_status":"published","title":"Quantitative relaxation of concurrent data structures","file_date_updated":"2020-07-14T12:45:31Z","oa_version":"Submitted Version","doi":"10.1145/2429069.2429109","scopus_import":1,"acknowledgement":" and an Elise Richter Fellowship (Austrian Science Fund V00125). ","publication_identifier":{"isbn":["978-1-4503-1832-7"]},"department":[{"_id":"ToHe"}],"publication":"Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language","date_updated":"2023-02-21T16:06:49Z","ec_funded":1,"oa":1,"related_material":{"record":[{"id":"10901","status":"deleted","relation":"later_version"}]},"author":[{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Kirsch","first_name":"Christoph","full_name":"Kirsch, Christoph"},{"first_name":"Hannes","last_name":"Payer","full_name":"Payer, Hannes"},{"first_name":"Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","full_name":"Sezgin, Ali"},{"full_name":"Sokolova, Ana","last_name":"Sokolova","first_name":"Ana"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","project":[{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF"}],"pubrep_id":"198","quality_controlled":"1","page":"317 - 328","day":"01","month":"01","status":"public","publist_id":"4801","language":[{"iso":"eng"}],"ddc":["000","004"],"date_published":"2013-01-01T00:00:00Z","type":"conference","publisher":"ACM"},{"abstract":[{"text":"We propose a general framework for abstraction with respect to quantitative properties, such as worst-case execution time, or power consumption. Our framework provides a systematic way for counter-example guided abstraction refinement for quantitative properties. The salient aspect of the framework is that it allows anytime verification, that is, verification algorithms that can be stopped at any time (for example, due to exhaustion of memory), and report approximations that improve monotonically when the algorithms are given more time. We instantiate the framework with a number of quantitative abstractions and refinement schemes, which differ in terms of how much quantitative information they keep from the original system. We introduce both state-based and trace-based quantitative abstractions, and we describe conditions that define classes of quantitative properties for which the abstractions provide over-approximations. We give algorithms for evaluating the quantitative properties on the abstract systems. We present algorithms for counter-example based refinements for quantitative properties for both state-based and segment-based abstractions. We perform a case study on worst-case execution time of executables to evaluate the anytime verification aspect and the quantitative abstractions we proposed.","lang":"eng"}],"citation":{"ama":"Cerny P, Henzinger TA, Radhakrishna A. Quantitative abstraction refinement. In: <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>. ACM; 2013:115-128. doi:<a href=\"https://doi.org/10.1145/2429069.2429085\">10.1145/2429069.2429085</a>","ista":"Cerny P, Henzinger TA, Radhakrishna A. 2013. Quantitative abstraction refinement. Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language. POPL: Principles of Programming Languages, 115–128.","ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Quantitative abstraction refinement,” in <i>Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language</i>, Rome, Italy, 2013, pp. 115–128.","mla":"Cerny, Pavol, et al. “Quantitative Abstraction Refinement.” <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>, ACM, 2013, pp. 115–28, doi:<a href=\"https://doi.org/10.1145/2429069.2429085\">10.1145/2429069.2429085</a>.","apa":"Cerny, P., Henzinger, T. A., &#38; Radhakrishna, A. (2013). Quantitative abstraction refinement. In <i>Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language</i> (pp. 115–128). Rome, Italy: ACM. <a href=\"https://doi.org/10.1145/2429069.2429085\">https://doi.org/10.1145/2429069.2429085</a>","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, in:, Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, ACM, 2013, pp. 115–128.","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Quantitative Abstraction Refinement.” In <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>, 115–28. ACM, 2013. <a href=\"https://doi.org/10.1145/2429069.2429085\">https://doi.org/10.1145/2429069.2429085</a>."},"year":"2013","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF"}],"date_created":"2018-12-11T11:56:11Z","_id":"2182","conference":{"location":"Rome, Italy","name":"POPL: Principles of Programming Languages","end_date":"2013-01-25","start_date":"2013-07-23"},"day":"01","scopus_import":1,"page":"115 - 128","doi":"10.1145/2429069.2429085","oa_version":"None","quality_controlled":"1","publication_status":"published","title":"Quantitative abstraction refinement","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:55:50Z","ec_funded":1,"publist_id":"4800","publication":"Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language","status":"public","department":[{"_id":"ToHe"}],"month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","first_name":"Pavol","last_name":"Cerny"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","first_name":"Arjun","last_name":"Radhakrishna"}],"publisher":"ACM","type":"conference","date_published":"2013-01-01T00:00:00Z"},{"publication_status":"published","title":"Recognizing straight skeletons and Voronoi diagrams and reconstructing their input","quality_controlled":"1","oa_version":"None","page":"37 - 46","doi":"10.1109/ISVD.2013.11","scopus_import":1,"publication_identifier":{"eisbn":["978-0-7695-5037-4 "]},"day":"01","conference":{"name":"ISVD: Voronoi Diagrams in Science and Engineering","location":"St. Petersburg, Russia","end_date":"2013-07-10","start_date":"2013-07-08"},"_id":"2209","date_created":"2018-12-11T11:56:20Z","year":"2013","citation":{"ama":"Biedl T, Held M, Huber S. Recognizing straight skeletons and Voronoi diagrams and reconstructing their input. In: IEEE; 2013:37-46. doi:<a href=\"https://doi.org/10.1109/ISVD.2013.11\">10.1109/ISVD.2013.11</a>","ieee":"T. Biedl, M. Held, and S. Huber, “Recognizing straight skeletons and Voronoi diagrams and reconstructing their input,” presented at the ISVD: Voronoi Diagrams in Science and Engineering, St. Petersburg, Russia, 2013, pp. 37–46.","ista":"Biedl T, Held M, Huber S. 2013. Recognizing straight skeletons and Voronoi diagrams and reconstructing their input. ISVD: Voronoi Diagrams in Science and Engineering, 2013 10th International Symposium on Voronoi Diagrams in Science and Engineering (ISVD 2013) , , 37–46.","mla":"Biedl, Therese, et al. <i>Recognizing Straight Skeletons and Voronoi Diagrams and Reconstructing Their Input</i>. IEEE, 2013, pp. 37–46, doi:<a href=\"https://doi.org/10.1109/ISVD.2013.11\">10.1109/ISVD.2013.11</a>.","chicago":"Biedl, Therese, Martin Held, and Stefan Huber. “Recognizing Straight Skeletons and Voronoi Diagrams and Reconstructing Their Input,” 37–46. IEEE, 2013. <a href=\"https://doi.org/10.1109/ISVD.2013.11\">https://doi.org/10.1109/ISVD.2013.11</a>.","short":"T. Biedl, M. Held, S. Huber, in:, IEEE, 2013, pp. 37–46.","apa":"Biedl, T., Held, M., &#38; Huber, S. (2013). Recognizing straight skeletons and Voronoi diagrams and reconstructing their input (pp. 37–46). Presented at the ISVD: Voronoi Diagrams in Science and Engineering, St. Petersburg, Russia: IEEE. <a href=\"https://doi.org/10.1109/ISVD.2013.11\">https://doi.org/10.1109/ISVD.2013.11</a>"},"abstract":[{"text":"A straight skeleton is a well-known geometric structure, and several algorithms exist to construct the straight skeleton for a given polygon or planar straight-line graph. In this paper, we ask the reverse question: Given the straight skeleton (in form of a planar straight-line graph, with some rays to infinity), can we reconstruct a planar straight-line graph for which this was the straight skeleton? We show how to reduce this problem to the problem of finding a line that intersects a set of convex polygons. We can find these convex polygons and all such lines in $O(nlog n)$ time in the Real RAM computer model, where $n$ denotes the number of edges of the input graph. We also explain how our approach can be used for recognizing Voronoi diagrams of points, thereby completing a partial solution provided by Ash and Bolker in 1985.\r\n","lang":"eng"}],"date_published":"2013-12-01T00:00:00Z","type":"conference","publisher":"IEEE","author":[{"full_name":"Biedl, Therese","first_name":"Therese","last_name":"Biedl"},{"first_name":"Martin","last_name":"Held","full_name":"Held, Martin"},{"last_name":"Huber","first_name":"Stefan","full_name":"Huber, Stefan","orcid":"0000-0002-8871-5814","id":"4700A070-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","department":[{"_id":"HeEd"}],"status":"public","date_updated":"2021-01-12T06:56:00Z","publist_id":"4763","language":[{"iso":"eng"}],"alternative_title":["2013 10th International Symposium on Voronoi Diagrams in Science and Engineering (ISVD 2013) "]},{"day":"01","page":"95 - 98","main_file_link":[{"url":"http://www.ibr.cs.tu-bs.de/alg/eurocg13/booklet_eurocg13.pdf","open_access":"1"}],"oa_version":"Submitted Version","publication_status":"published","title":"Reconstructing polygons from embedded straight skeletons","abstract":[{"lang":"eng","text":"A straight skeleton is a well-known geometric structure, and several algorithms exist to construct the straight skeleton for a given polygon. In this paper, we ask the reverse question: Given the straight skeleton (in form of a tree with a drawing in the plane, but with the exact position of the leaves unspecified), can we reconstruct the polygon? We show that in most cases there exists at most one polygon; in the remaining case there is an infinite number of polygons determined by one angle that can range in an interval. We can find this (set of) polygon(s) in linear time in the Real RAM computer model."}],"year":"2013","citation":{"mla":"Biedl, Therese, et al. “Reconstructing Polygons from Embedded Straight Skeletons.” <i>29th European Workshop on Computational Geometry</i>, TU Braunschweig, 2013, pp. 95–98.","apa":"Biedl, T., Held, M., &#38; Huber, S. (2013). Reconstructing polygons from embedded straight skeletons. In <i>29th European Workshop on Computational Geometry</i> (pp. 95–98). Braunschweig, Germany: TU Braunschweig.","chicago":"Biedl, Therese, Martin Held, and Stefan Huber. “Reconstructing Polygons from Embedded Straight Skeletons.” In <i>29th European Workshop on Computational Geometry</i>, 95–98. TU Braunschweig, 2013.","short":"T. Biedl, M. Held, S. Huber, in:, 29th European Workshop on Computational Geometry, TU Braunschweig, 2013, pp. 95–98.","ieee":"T. Biedl, M. Held, and S. Huber, “Reconstructing polygons from embedded straight skeletons,” in <i>29th European Workshop on Computational Geometry</i>, Braunschweig, Germany, 2013, pp. 95–98.","ista":"Biedl T, Held M, Huber S. 2013. Reconstructing polygons from embedded straight skeletons. 29th European Workshop on Computational Geometry. EuroCG: European Workshop on Computational Geometry, 95–98.","ama":"Biedl T, Held M, Huber S. Reconstructing polygons from embedded straight skeletons. In: <i>29th European Workshop on Computational Geometry</i>. TU Braunschweig; 2013:95-98."},"_id":"2210","date_created":"2018-12-11T11:56:21Z","conference":{"name":"EuroCG: European Workshop on Computational Geometry","location":"Braunschweig, Germany","end_date":"2013-03-20","start_date":"2013-03-17"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"TU Braunschweig","author":[{"first_name":"Therese","last_name":"Biedl","full_name":"Biedl, Therese"},{"first_name":"Martin","last_name":"Held","full_name":"Held, Martin"},{"last_name":"Huber","first_name":"Stefan","full_name":"Huber, Stefan","orcid":"0000-0002-8871-5814","id":"4700A070-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"date_published":"2013-03-01T00:00:00Z","type":"conference","language":[{"iso":"eng"}],"publication":"29th European Workshop on Computational Geometry","status":"public","date_updated":"2021-01-12T06:56:00Z","publist_id":"4762","month":"03","department":[{"_id":"HeEd"}]},{"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"ddc":["000"],"status":"public","publist_id":"4724","month":"01","publisher":"Springer","date_published":"2013-01-14T00:00:00Z","type":"conference","has_accepted_license":"1","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"}],"day":"14","page":"173 - 181","quality_controlled":"1","intvolume":"      8312","date_updated":"2020-08-11T10:09:42Z","department":[{"_id":"ToHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Blanc, Régis","first_name":"Régis","last_name":"Blanc"},{"last_name":"Gupta","first_name":"Ashutosh","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kovács, Laura","first_name":"Laura","last_name":"Kovács"},{"first_name":"Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard"}],"oa":1,"volume":8312,"series_title":"Lecture Notes in Computer Science","abstract":[{"text":"We describe new extensions of the Vampire theorem prover for computing tree interpolants. These extensions generalize Craig interpolation in Vampire, and can also be used to derive sequence interpolants. We evaluated our implementation on a large number of examples over the theory of linear integer arithmetic and integer-indexed arrays, with and without quantifiers. When compared to other methods, our experiments show that some examples could only be solved by our implementation.","lang":"eng"}],"year":"2013","citation":{"short":"R. Blanc, A. Gupta, L. Kovács, B. Kragl, 8312 (2013) 173–181.","apa":"Blanc, R., Gupta, A., Kovács, L., &#38; Kragl, B. (2013). Tree interpolation in Vampire. Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Stellenbosch, South Africa: Springer. <a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">https://doi.org/10.1007/978-3-642-45221-5_13</a>","chicago":"Blanc, Régis, Ashutosh Gupta, Laura Kovács, and Bernhard Kragl. “Tree Interpolation in Vampire.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">https://doi.org/10.1007/978-3-642-45221-5_13</a>.","mla":"Blanc, Régis, et al. <i>Tree Interpolation in Vampire</i>. Vol. 8312, Springer, 2013, pp. 173–81, doi:<a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">10.1007/978-3-642-45221-5_13</a>.","ama":"Blanc R, Gupta A, Kovács L, Kragl B. Tree interpolation in Vampire. 2013;8312:173-181. doi:<a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">10.1007/978-3-642-45221-5_13</a>","ista":"Blanc R, Gupta A, Kovács L, Kragl B. 2013. Tree interpolation in Vampire. 8312, 173–181.","ieee":"R. Blanc, A. Gupta, L. Kovács, and B. Kragl, “Tree interpolation in Vampire,” vol. 8312. Springer, pp. 173–181, 2013."},"_id":"2237","date_created":"2018-12-11T11:56:29Z","file":[{"file_id":"7858","creator":"dernst","content_type":"application/pdf","checksum":"9cebaafca032e6769d273f393305c705","file_name":"2013_LPAR_Blanc.pdf","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:45:34Z","file_size":279206,"date_created":"2020-05-15T11:10:40Z"}],"conference":{"start_date":"2013-12-14","end_date":"2013-12-19","location":"Stellenbosch, South Africa","name":"LPAR: Logic for Programming, Artificial Intelligence, and Reasoning"},"doi":"10.1007/978-3-642-45221-5_13","scopus_import":1,"file_date_updated":"2020-07-14T12:45:34Z","oa_version":"Submitted Version","article_processing_charge":"No","publication_status":"published","title":"Tree interpolation in Vampire"}]