[{"year":"2012","_id":"5745","ec_funded":1,"date_created":"2018-12-18T13:01:46Z","series_title":"LNCS","file":[{"access_level":"open_access","creator":"dernst","checksum":"68415837a315de3cc4d120f6019d752c","content_type":"application/pdf","file_size":465502,"date_updated":"2020-07-14T12:47:10Z","file_name":"2012_ATVA_Gupta.pdf","file_id":"5746","date_created":"2018-12-18T13:07:35Z","relation":"main_file"}],"publication_status":"published","oa_version":"None","article_processing_charge":"No","quality_controlled":"1","citation":{"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 <i>Automated Technology for Verification and Analysis</i>, 7561:107–21. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">https://doi.org/10.1007/978-3-642-33386-6_10</a>.","ieee":"A. Gupta, “Improved Single Pass Algorithms for Resolution Proof Reduction,” in <i>Automated Technology for Verification and Analysis</i>, vol. 7561, Berlin, Heidelberg: Springer Berlin Heidelberg, 2012, pp. 107–121.","apa":"Gupta, A. (2012). Improved Single Pass Algorithms for Resolution Proof Reduction. In <i>Automated Technology for Verification and Analysis</i> (Vol. 7561, pp. 107–121). Berlin, Heidelberg: Springer Berlin Heidelberg. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">https://doi.org/10.1007/978-3-642-33386-6_10</a>","ama":"Gupta A. Improved Single Pass Algorithms for Resolution Proof Reduction. In: <i>Automated Technology for Verification and Analysis</i>. Vol 7561. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg; 2012:107-121. doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">10.1007/978-3-642-33386-6_10</a>","mla":"Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.” <i>Automated Technology for Verification and Analysis</i>, vol. 7561, Springer Berlin Heidelberg, 2012, pp. 107–21, doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">10.1007/978-3-642-33386-6_10</a>.","short":"A. Gupta, in:, Automated Technology for Verification and Analysis, Springer Berlin Heidelberg, Berlin, Heidelberg, 2012, pp. 107–121."},"author":[{"first_name":"Ashutosh","last_name":"Gupta","full_name":"Gupta, Ashutosh"}],"date_updated":"2023-09-05T14:15:29Z","publication":"Automated Technology for Verification and Analysis","publication_identifier":{"issn":["0302-9743"],"isbn":["9783642333859","9783642333866"],"eissn":["1611-3349"]},"oa":1,"project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7"}],"title":"Improved Single Pass Algorithms for Resolution Proof Reduction","has_accepted_license":"1","conference":{"name":"ATVA 2012","start_date":"2012-10-03","location":"Thiruvananthapuram, Kerala, India","end_date":"2012-10-06"},"page":"107-121","place":"Berlin, Heidelberg","publisher":"Springer Berlin Heidelberg","department":[{"_id":"ToHe"}],"volume":7561,"pubrep_id":"180","type":"book_chapter","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-07-14T12:47:10Z","language":[{"iso":"eng"}],"status":"public","doi":"10.1007/978-3-642-33386-6_10","date_published":"2012-01-01T00:00:00Z","intvolume":"      7561","ddc":["005"]},{"intvolume":"         8","date_published":"2012-01-01T00:00:00Z","language":[{"iso":"eng"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":8,"isi":1,"main_file_link":[{"url":"http://mi.mathnet.ru/eng/jmag525","open_access":"1"}],"publisher":"B. Verkin Institute for Low Temperature Physics and Engineering","department":[{"_id":"HeEd"}],"month":"01","acknowledgement":"This work is supported by the Austrian Science Fund (FWF), Project P22025-N18.\r\n","scopus_import":"1","page":"63-78","issue":"1","title":"Elementary solutions of the Bernstein problem on two intervals","external_id":{"isi":["000301173600004"]},"day":"01","publication_identifier":{"issn":["1812-9471"]},"publication":"Journal of Mathematical Physics, Analysis, Geometry","oa":1,"date_updated":"2023-10-16T09:41:31Z","author":[{"last_name":"Pausinger","first_name":"Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","full_name":"Pausinger, Florian","orcid":"0000-0002-8379-3768"}],"citation":{"mla":"Pausinger, Florian. “Elementary Solutions of the Bernstein Problem on Two Intervals.” <i>Journal of Mathematical Physics, Analysis, Geometry</i>, vol. 8, no. 1, B. Verkin Institute for Low Temperature Physics and Engineering, 2012, pp. 63–78.","ieee":"F. Pausinger, “Elementary solutions of the Bernstein problem on two intervals,” <i>Journal of Mathematical Physics, Analysis, Geometry</i>, vol. 8, no. 1. B. Verkin Institute for Low Temperature Physics and Engineering, pp. 63–78, 2012.","ama":"Pausinger F. Elementary solutions of the Bernstein problem on two intervals. <i>Journal of Mathematical Physics, Analysis, Geometry</i>. 2012;8(1):63-78.","apa":"Pausinger, F. (2012). Elementary solutions of the Bernstein problem on two intervals. <i>Journal of Mathematical Physics, Analysis, Geometry</i>. B. Verkin Institute for Low Temperature Physics and Engineering.","chicago":"Pausinger, Florian. “Elementary Solutions of the Bernstein Problem on Two Intervals.” <i>Journal of Mathematical Physics, Analysis, Geometry</i>. B. Verkin Institute for Low Temperature Physics and Engineering, 2012.","ista":"Pausinger F. 2012. Elementary solutions of the Bernstein problem on two intervals. Journal of Mathematical Physics, Analysis, Geometry. 8(1), 63–78.","short":"F. Pausinger, Journal of Mathematical Physics, Analysis, Geometry 8 (2012) 63–78."},"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"No","publication_status":"published","article_type":"original","abstract":[{"text":"First we note that the best polynomial approximation to vertical bar x vertical bar on the set, which consists of an interval on the positive half-axis and a point on the negative half-axis, can be given by means of the classical Chebyshev polynomials. Then we explore the cases when a solution of the related problem on two intervals can be given in elementary functions.","lang":"eng"}],"date_created":"2019-06-27T08:16:56Z","year":"2012","_id":"6588"},{"type":"journal_article","volume":337,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2012-09-14T00:00:00Z","doi":"10.1126/science.1224839","status":"public","language":[{"iso":"eng"}],"extern":"1","intvolume":"       337","ddc":["580"],"page":"1360-1364","scopus_import":"1","month":"09","publisher":"American Association for the Advancement of Science","department":[{"_id":"DaZi"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/"}],"date_updated":"2021-12-14T08:28:51Z","citation":{"chicago":"Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” <i>Science</i>. American Association for the Advancement of Science, 2012. <a href=\"https://doi.org/10.1126/science.1224839\">https://doi.org/10.1126/science.1224839</a>.","ista":"Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 337(6100), 1360–1364.","mla":"Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” <i>Science</i>, vol. 337, no. 6100, American Association for the Advancement of Science, 2012, pp. 1360–64, doi:<a href=\"https://doi.org/10.1126/science.1224839\">10.1126/science.1224839</a>.","apa":"Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1224839\">https://doi.org/10.1126/science.1224839</a>","ieee":"C. A. Ibarra <i>et al.</i>, “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes,” <i>Science</i>, vol. 337, no. 6100. American Association for the Advancement of Science, pp. 1360–1364, 2012.","ama":"Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. <i>Science</i>. 2012;337(6100):1360-1364. doi:<a href=\"https://doi.org/10.1126/science.1224839\">10.1126/science.1224839</a>","short":"C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H. Tamaru, D. Zilberman, Science 337 (2012) 1360–1364."},"author":[{"last_name":"Ibarra","first_name":"Christian A.","full_name":"Ibarra, Christian A."},{"first_name":"Xiaoqi","last_name":"Feng","full_name":"Feng, Xiaoqi"},{"full_name":"Schoft, Vera K.","last_name":"Schoft","first_name":"Vera K."},{"last_name":"Hsieh","first_name":"Tzung-Fu","full_name":"Hsieh, Tzung-Fu"},{"full_name":"Uzawa, Rie","first_name":"Rie","last_name":"Uzawa"},{"full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues","first_name":"Jessica A."},{"full_name":"Zemach, Assaf","first_name":"Assaf","last_name":"Zemach"},{"full_name":"Chumak, Nina","first_name":"Nina","last_name":"Chumak"},{"full_name":"Machlicova, Adriana","last_name":"Machlicova","first_name":"Adriana"},{"first_name":"Toshiro","last_name":"Nishimura","full_name":"Nishimura, Toshiro"},{"first_name":"Denisse","last_name":"Rojas","full_name":"Rojas, Denisse"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"full_name":"Tamaru, Hisashi","last_name":"Tamaru","first_name":"Hisashi"},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"}],"day":"14","oa":1,"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication":"Science","title":"Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes","external_id":{"pmid":["22984074"]},"has_accepted_license":"1","issue":"6100","pmid":1,"date_created":"2021-06-04T07:51:31Z","_id":"9451","year":"2012","publication_status":"published","article_type":"original","abstract":[{"text":"The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations.","lang":"eng"}],"quality_controlled":"1","article_processing_charge":"No","oa_version":"Published Version"},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pgen.1002988"}],"month":"10","department":[{"_id":"DaZi"}],"publisher":"Public Library of Science","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","volume":8,"extern":"1","intvolume":"         8","date_published":"2012-10-11T00:00:00Z","doi":"10.1371/journal.pgen.1002988","status":"public","language":[{"iso":"eng"}],"date_created":"2021-06-07T10:55:27Z","pmid":1,"_id":"9497","year":"2012","quality_controlled":"1","article_processing_charge":"No","oa_version":"Published Version","article_type":"original","publication_status":"published","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."}],"day":"11","oa":1,"publication":"PLoS Genetics","publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"author":[{"full_name":"Coleman-Derr, Devin","last_name":"Coleman-Derr","first_name":"Devin"},{"last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"}],"date_updated":"2021-12-14T08:29:57Z","citation":{"chicago":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” <i>PLoS Genetics</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pgen.1002988\">https://doi.org/10.1371/journal.pgen.1002988</a>.","ista":"Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988.","mla":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” <i>PLoS Genetics</i>, vol. 8, no. 10, e1002988, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002988\">10.1371/journal.pgen.1002988</a>.","ama":"Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. <i>PLoS Genetics</i>. 2012;8(10). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002988\">10.1371/journal.pgen.1002988</a>","ieee":"D. Coleman-Derr and D. Zilberman, “Deposition of histone variant H2A.Z within gene bodies regulates responsive genes,” <i>PLoS Genetics</i>, vol. 8, no. 10. Public Library of Science, 2012.","apa":"Coleman-Derr, D., &#38; Zilberman, D. (2012). Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1002988\">https://doi.org/10.1371/journal.pgen.1002988</a>","short":"D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012)."},"issue":"10","article_number":"e1002988","external_id":{"pmid":["23071449"]},"title":"Deposition of histone variant H2A.Z within gene bodies regulates responsive genes"},{"oa_version":"Published Version","article_processing_charge":"No","quality_controlled":"1","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."}],"publication_status":"published","article_type":"original","year":"2012","_id":"9499","date_created":"2021-06-07T11:07:56Z","pmid":1,"issue":"3","article_number":"e1002512","external_id":{"pmid":["22457632"]},"title":"EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development","publication":"PLoS Genetics","publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"oa":1,"day":"22","date_updated":"2021-12-14T08:31:14Z","citation":{"mla":"Kim, Sang Yeol, et al. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” <i>PLoS Genetics</i>, vol. 8, no. 3, e1002512, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002512\">10.1371/journal.pgen.1002512</a>.","ama":"Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. <i>PLoS Genetics</i>. 2012;8(3). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002512\">10.1371/journal.pgen.1002512</a>","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,” <i>PLoS Genetics</i>, vol. 8, no. 3. Public Library of Science, 2012.","apa":"Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., &#38; Sung, Z. R. (2012). EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1002512\">https://doi.org/10.1371/journal.pgen.1002512</a>","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.” <i>PLoS Genetics</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pgen.1002512\">https://doi.org/10.1371/journal.pgen.1002512</a>.","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.","short":"S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012)."},"author":[{"first_name":"Sang Yeol","last_name":"Kim","full_name":"Kim, Sang Yeol"},{"first_name":"Jungeun","last_name":"Lee","full_name":"Lee, Jungeun"},{"full_name":"Eshed-Williams, Leor","last_name":"Eshed-Williams","first_name":"Leor"},{"last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"},{"first_name":"Z. Renee","last_name":"Sung","full_name":"Sung, Z. Renee"}],"main_file_link":[{"url":"https://doi.org/10.1371/journal.pgen.1002512","open_access":"1"}],"department":[{"_id":"DaZi"}],"publisher":"Public Library of Science","month":"03","scopus_import":"1","intvolume":"         8","extern":"1","language":[{"iso":"eng"}],"status":"public","doi":"10.1371/journal.pgen.1002512","date_published":"2012-03-22T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":8,"type":"journal_article"},{"scopus_import":"1","page":"132-138","month":"04","publisher":"Elsevier","department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","volume":22,"extern":"1","intvolume":"        22","date_published":"2012-04-01T00:00:00Z","doi":"10.1016/j.gde.2012.01.007","status":"public","language":[{"iso":"eng"}],"date_created":"2021-06-08T08:58:52Z","pmid":1,"_id":"9528","year":"2012","quality_controlled":"1","article_processing_charge":"No","oa_version":"None","publication_status":"published","article_type":"review","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"}],"publication":"Current Opinion in Genetics and Development","publication_identifier":{"issn":["0959-437X"]},"date_updated":"2021-12-14T08:32:38Z","citation":{"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.","chicago":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">https://doi.org/10.1016/j.gde.2012.01.007</a>.","apa":"Huff, J. T., &#38; Zilberman, D. (2012). Regulation of biological accuracy, precision, and memory by plant chromatin organization. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">https://doi.org/10.1016/j.gde.2012.01.007</a>","ieee":"J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision, and memory by plant chromatin organization,” <i>Current Opinion in Genetics and Development</i>, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.","ama":"Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. <i>Current Opinion in Genetics and Development</i>. 2012;22(2):132-138. doi:<a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">10.1016/j.gde.2012.01.007</a>","mla":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” <i>Current Opinion in Genetics and Development</i>, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:<a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">10.1016/j.gde.2012.01.007</a>.","short":"J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138."},"author":[{"first_name":"Jason T.","last_name":"Huff","full_name":"Huff, Jason T."},{"first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"issue":"2","external_id":{"pmid":["22336527"]},"title":"Regulation of biological accuracy, precision, and memory by plant chromatin organization"},{"month":"12","publisher":"Cold Spring Harbor Laboratory Press","department":[{"_id":"DaZi"}],"main_file_link":[{"url":"https://doi.org/10.1101/sqb.2012.77.014944","open_access":"1"}],"page":"147-154","scopus_import":"1","date_published":"2012-12-18T00:00:00Z","doi":"10.1101/sqb.2012.77.014944","status":"public","language":[{"iso":"eng"}],"extern":"1","intvolume":"        77","type":"journal_article","volume":77,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_type":"review","publication_status":"published","abstract":[{"text":"The most well-studied function of DNA methylation in eukaryotic cells is the transcriptional silencing of genes and transposons. More recent results showed that many eukaryotes methylate the bodies of genes as well and that this methylation correlates with transcriptional activity rather than repression. The purpose of gene body methylation remains mysterious, but is potentially related to the histone variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and other investigators have shown that this relationship is likely to be the result of an ancient but unknown mechanism by which DNA methylation prevents the incorporation of H2A.Z. Recently, we discovered strong correlations between the presence of H2A.Z within gene bodies, the degree to which a gene's expression varies across tissue types or environmental conditions, and transcriptional misregulation in an h2a.z mutant. We propose that one basal function of gene body methylation is the establishment of constitutive expression patterns within housekeeping genes by excluding H2A.Z from their bodies.","lang":"eng"}],"quality_controlled":"1","article_processing_charge":"No","oa_version":"Published Version","pmid":1,"date_created":"2021-06-08T13:01:23Z","_id":"9535","year":"2012","external_id":{"pmid":["23250988"]},"title":"DNA methylation, H2A.Z, and the regulation of constitutive expression","citation":{"short":"D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative Biology 77 (2012) 147–154.","ista":"Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 77, 147–154.","chicago":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Cold Spring Harbor Laboratory Press, 2012. <a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">https://doi.org/10.1101/sqb.2012.77.014944</a>.","apa":"Coleman-Derr, D., &#38; Zilberman, D. (2012). DNA methylation, H2A.Z, and the regulation of constitutive expression. <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">https://doi.org/10.1101/sqb.2012.77.014944</a>","ieee":"D. Coleman-Derr and D. Zilberman, “DNA methylation, H2A.Z, and the regulation of constitutive expression,” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012.","ama":"Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of constitutive expression. <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. 2012;77:147-154. doi:<a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">10.1101/sqb.2012.77.014944</a>","mla":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 77, Cold Spring Harbor Laboratory Press, 2012, pp. 147–54, doi:<a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">10.1101/sqb.2012.77.014944</a>."},"author":[{"last_name":"Coleman-Derr","first_name":"D.","full_name":"Coleman-Derr, D."},{"last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"date_updated":"2021-12-14T08:33:09Z","day":"18","oa":1,"publication_identifier":{"eissn":["1943-4456"],"issn":["0091-7451"]},"publication":"Cold Spring Harbor Symposia on Quantitative Biology"},{"article_processing_charge":"No","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5061/dryad.sv37s","open_access":"1"}],"abstract":[{"text":"Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”).","lang":"eng"}],"month":"09","publisher":"Dryad","department":[{"_id":"SyCr"}],"related_material":{"record":[{"id":"3242","status":"public","relation":"used_in_publication"}]},"_id":"9755","year":"2012","date_created":"2021-07-30T08:39:13Z","status":"public","title":"Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies","date_published":"2012-09-27T00:00:00Z","doi":"10.5061/dryad.sv37s","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"27","date_updated":"2023-02-23T11:18:41Z","author":[{"last_name":"Konrad","first_name":"Matthias","full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Meghan","last_name":"Vyleta","full_name":"Vyleta, Meghan","id":"418901AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Theis","first_name":"Fabian","full_name":"Theis, Fabian"},{"last_name":"Stock","first_name":"Miriam","full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Klatt","first_name":"Martina","full_name":"Klatt, Martina","id":"E60F29C6-E9AE-11E9-AF6E-D190C7302F38"},{"full_name":"Drescher, Verena","first_name":"Verena","last_name":"Drescher"},{"first_name":"Carsten","last_name":"Marr","full_name":"Marr, Carsten"},{"full_name":"Ugelvig, Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","last_name":"Ugelvig","first_name":"Line V"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia"}],"citation":{"short":"M. Konrad, M. Vyleta, F. Theis, M. Stock, M. Klatt, V. Drescher, C. Marr, L.V. Ugelvig, S. Cremer, (2012).","ista":"Konrad M, Vyleta M, Theis F, Stock M, Klatt M, Drescher V, Marr C, Ugelvig LV, Cremer S. 2012. Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies, Dryad, <a href=\"https://doi.org/10.5061/dryad.sv37s\">10.5061/dryad.sv37s</a>.","chicago":"Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Martina Klatt, Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer. “Data from: Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” Dryad, 2012. <a href=\"https://doi.org/10.5061/dryad.sv37s\">https://doi.org/10.5061/dryad.sv37s</a>.","apa":"Konrad, M., Vyleta, M., Theis, F., Stock, M., Klatt, M., Drescher, V., … Cremer, S. (2012). Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. Dryad. <a href=\"https://doi.org/10.5061/dryad.sv37s\">https://doi.org/10.5061/dryad.sv37s</a>","ama":"Konrad M, Vyleta M, Theis F, et al. Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. 2012. doi:<a href=\"https://doi.org/10.5061/dryad.sv37s\">10.5061/dryad.sv37s</a>","ieee":"M. Konrad <i>et al.</i>, “Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies.” Dryad, 2012.","mla":"Konrad, Matthias, et al. <i>Data from: Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies</i>. Dryad, 2012, doi:<a href=\"https://doi.org/10.5061/dryad.sv37s\">10.5061/dryad.sv37s</a>."},"type":"research_data_reference"},{"_id":"9757","year":"2012","date_created":"2021-07-30T12:31:31Z","article_processing_charge":"No","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5061/dryad.61649","open_access":"1"}],"abstract":[{"text":"To fight infectious diseases, host immune defences are employed at multiple levels. Sanitary behaviour, such as pathogen avoidance and removal, acts as a first line of defence to prevent infection [1] before activation of the physiological immune system. Insect societies have evolved a wide range of collective hygiene measures and intensive health care towards pathogen-exposed group members [2]. One of the most common behaviours is allogrooming, in which nestmates remove infectious particles from the body surfaces of exposed individuals [3]. Here we show that, in invasive garden ants, grooming of fungus-exposed brood is effective beyond the sheer mechanical removal of fungal conidiospores as it also includes chemical disinfection through the application of poison produced by the ants themselves. Formic acid is the main active component of the poison. It inhibits fungal growth of conidiospores remaining on the brood surface after grooming and also those collected in the mouth of the grooming ant. This dual function is achieved by uptake of the poison droplet into the mouth through acidopore self-grooming and subsequent application onto the infectious brood via brood grooming. This extraordinary behaviour extends current understanding of grooming and the establishment of social immunity in insect societies.","lang":"eng"}],"month":"12","publisher":"Dryad","related_material":{"record":[{"relation":"used_in_publication","id":"2926","status":"public"}]},"department":[{"_id":"SyCr"}],"oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"14","author":[{"full_name":"Tragust, Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","last_name":"Tragust","first_name":"Simon"},{"id":"479DDAAC-E9CD-11E9-9B5F-82450873F7A1","full_name":"Mitteregger, Barbara","last_name":"Mitteregger","first_name":"Barbara"},{"full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","first_name":"Vanessa","last_name":"Barone"},{"full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Konrad"},{"first_name":"Line V","last_name":"Ugelvig","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data_reference","date_updated":"2023-02-23T11:04:28Z","citation":{"apa":"Tragust, S., Mitteregger, B., Barone, V., Konrad, M., Ugelvig, L. V., &#38; Cremer, S. (2012). Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Dryad. <a href=\"https://doi.org/10.5061/dryad.61649\">https://doi.org/10.5061/dryad.61649</a>","ama":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. 2012. doi:<a href=\"https://doi.org/10.5061/dryad.61649\">10.5061/dryad.61649</a>","ieee":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer, “Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison.” Dryad, 2012.","mla":"Tragust, Simon, et al. <i>Data from: Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison</i>. Dryad, 2012, doi:<a href=\"https://doi.org/10.5061/dryad.61649\">10.5061/dryad.61649</a>.","ista":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. 2012. Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison, Dryad, <a href=\"https://doi.org/10.5061/dryad.61649\">10.5061/dryad.61649</a>.","chicago":"Tragust, Simon, Barbara Mitteregger, Vanessa Barone, Matthias Konrad, Line V Ugelvig, and Sylvia Cremer. “Data from: Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” Dryad, 2012. <a href=\"https://doi.org/10.5061/dryad.61649\">https://doi.org/10.5061/dryad.61649</a>.","short":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer, (2012)."},"status":"public","title":"Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison","date_published":"2012-12-14T00:00:00Z","doi":"10.5061/dryad.61649"},{"status":"public","title":"Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates","date_published":"2012-11-14T00:00:00Z","doi":"10.5061/dryad.274b1","type":"research_data_reference","citation":{"short":"S. Aeschbacher, A. Futschik, M. Beaumont, (2012).","ista":"Aeschbacher S, Futschik A, Beaumont M. 2012. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates, Dryad, <a href=\"https://doi.org/10.5061/dryad.274b1\">10.5061/dryad.274b1</a>.","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates.” Dryad, 2012. <a href=\"https://doi.org/10.5061/dryad.274b1\">https://doi.org/10.5061/dryad.274b1</a>.","ama":"Aeschbacher S, Futschik A, Beaumont M. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. 2012. doi:<a href=\"https://doi.org/10.5061/dryad.274b1\">10.5061/dryad.274b1</a>","apa":"Aeschbacher, S., Futschik, A., &#38; Beaumont, M. (2012). Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. Dryad. <a href=\"https://doi.org/10.5061/dryad.274b1\">https://doi.org/10.5061/dryad.274b1</a>","ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates.” Dryad, 2012.","mla":"Aeschbacher, Simon, et al. <i>Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates</i>. Dryad, 2012, doi:<a href=\"https://doi.org/10.5061/dryad.274b1\">10.5061/dryad.274b1</a>."},"date_updated":"2023-02-23T11:05:19Z","author":[{"full_name":"Aeschbacher, Simon","id":"2D35326E-F248-11E8-B48F-1D18A9856A87","last_name":"Aeschbacher","first_name":"Simon"},{"first_name":"Andreas","last_name":"Futschik","full_name":"Futschik, Andreas"},{"first_name":"Mark","last_name":"Beaumont","full_name":"Beaumont, Mark"}],"oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"14","abstract":[{"lang":"eng","text":"We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction."}],"month":"11","publisher":"Dryad","related_material":{"record":[{"status":"public","id":"2944","relation":"used_in_publication"}]},"department":[{"_id":"NiBa"}],"article_processing_charge":"No","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.274b1"}],"_id":"9758","year":"2012","date_created":"2021-07-30T12:36:39Z"},{"oa_version":"None","article_processing_charge":"No","quality_controlled":"1","abstract":[{"lang":"eng","text":"This paper presents a method to create a model of an articulated object using the planar motion in an initialization video. The model consists of rigid parts connected by points of articulation. The rigid parts are described by the positions of salient feature-points tracked throughout the video. Following a filtering step that identifies points that belong to different objects, rigid parts are found by a grouping process in a graph pyramid. Valid articulation points are selected by verifying multiple hypotheses for each pair of parts."}],"publication_status":"published","year":"2011","_id":"10907","date_created":"2022-03-21T08:08:35Z","series_title":"LNIP","title":"Spatio-temporal extraction of articulated models in a graph pyramid","publication":"Graph-Based Representations in Pattern Recognition","publication_identifier":{"issn":["0302-9743"],"isbn":["9783642208430"],"eissn":["1611-3349"],"eisbn":["9783642208447"]},"day":"01","date_updated":"2023-09-05T14:10:15Z","citation":{"short":"N.M. Artner, A. Ion, W.G. Kropatsch, in:, X. Jiang, M. Ferrer, A. Torsello (Eds.), Graph-Based Representations in Pattern Recognition, Springer, Berlin, Heidelberg, 2011, pp. 215–224.","ieee":"N. M. Artner, A. Ion, and W. G. Kropatsch, “Spatio-temporal extraction of articulated models in a graph pyramid,” in <i>Graph-Based Representations in Pattern Recognition</i>, Münster, Germany, 2011, vol. 6658, pp. 215–224.","ama":"Artner NM, Ion A, Kropatsch WG. Spatio-temporal extraction of articulated models in a graph pyramid. In: Jiang X, Ferrer M, Torsello A, eds. <i>Graph-Based Representations in Pattern Recognition</i>. Vol 6658. LNIP. Berlin, Heidelberg: Springer; 2011:215-224. doi:<a href=\"https://doi.org/10.1007/978-3-642-20844-7_22\">10.1007/978-3-642-20844-7_22</a>","apa":"Artner, N. M., Ion, A., &#38; Kropatsch, W. G. (2011). Spatio-temporal extraction of articulated models in a graph pyramid. In X. Jiang, M. Ferrer, &#38; A. Torsello (Eds.), <i>Graph-Based Representations in Pattern Recognition</i> (Vol. 6658, pp. 215–224). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-20844-7_22\">https://doi.org/10.1007/978-3-642-20844-7_22</a>","mla":"Artner, Nicole M., et al. “Spatio-Temporal Extraction of Articulated Models in a Graph Pyramid.” <i>Graph-Based Representations in Pattern Recognition</i>, edited by Xiaoyi Jiang et al., vol. 6658, Springer, 2011, pp. 215–24, doi:<a href=\"https://doi.org/10.1007/978-3-642-20844-7_22\">10.1007/978-3-642-20844-7_22</a>.","ista":"Artner NM, Ion A, Kropatsch WG. 2011. Spatio-temporal extraction of articulated models in a graph pyramid. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNIP, LNCS, vol. 6658, 215–224.","chicago":"Artner, Nicole M., Adrian Ion, and Walter G. Kropatsch. “Spatio-Temporal Extraction of Articulated Models in a Graph Pyramid.” In <i>Graph-Based Representations in Pattern Recognition</i>, edited by Xiaoyi Jiang, Miquel Ferrer, and Andrea Torsello, 6658:215–24. LNIP. Berlin, Heidelberg: Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-20844-7_22\">https://doi.org/10.1007/978-3-642-20844-7_22</a>."},"author":[{"last_name":"Artner","first_name":"Nicole M.","full_name":"Artner, Nicole M."},{"id":"29F89302-F248-11E8-B48F-1D18A9856A87","full_name":"Ion, Adrian","last_name":"Ion","first_name":"Adrian"},{"last_name":"Kropatsch","first_name":"Walter G.","full_name":"Kropatsch, Walter G."}],"department":[{"_id":"HeEd"}],"publisher":"Springer","editor":[{"full_name":"Jiang, Xiaoyi","first_name":"Xiaoyi","last_name":"Jiang"},{"last_name":"Ferrer","first_name":"Miquel","full_name":"Ferrer, Miquel"},{"first_name":"Andrea","last_name":"Torsello","full_name":"Torsello, Andrea"}],"month":"06","scopus_import":"1","place":"Berlin, Heidelberg","acknowledgement":"This work has been partially supported by the Austrian Science Fund under grants S9103-N13 and P18716-N13.","conference":{"end_date":"2011-05-20","start_date":"2011-05-18","location":"Münster, Germany","name":"GbRPR: Graph-based Representations in Pattern Recognition"},"page":"215-224","intvolume":"      6658","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"status":"public","doi":"10.1007/978-3-642-20844-7_22","date_published":"2011-06-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":6658,"type":"conference"},{"conference":{"end_date":"2011-12-14","location":"Granada, Spain","start_date":"2011-12-12","name":"NIPS: Neural Information Processing Systems"},"date_created":"2018-12-11T12:01:45Z","year":"2011","scopus_import":1,"_id":"3163","publication_status":"published","related_material":{"record":[{"status":"public","id":"3322","relation":"later_version"}]},"publisher":"Neural Information Processing Systems","department":[{"_id":"ChLa"}],"month":"12","abstract":[{"text":"We study multi-label prediction for structured output sets, a problem that occurs, for example, in object detection in images, secondary structure prediction in computational biology, and graph matching with symmetries. Conventional multilabel classification techniques are typically not applicable in this situation, because they require explicit enumeration of the label set, which is infeasible in case of structured outputs. Relying on techniques originally designed for single-label structured prediction, in particular structured support vector machines, results in reduced prediction accuracy, or leads to infeasible optimization problems. In this work we derive a maximum-margin training formulation for multi-label structured prediction that remains computationally tractable while achieving high prediction accuracy. It also shares most beneficial properties with single-label maximum-margin approaches, in particular formulation as a convex optimization problem, efficient working set training, and PAC-Bayesian generalization bounds.","lang":"eng"}],"quality_controlled":"1","oa_version":"None","author":[{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert"}],"citation":{"ieee":"C. Lampert, “Maximum margin multi-label structured prediction,” presented at the NIPS: Neural Information Processing Systems, Granada, Spain, 2011.","apa":"Lampert, C. (2011). Maximum margin multi-label structured prediction. Presented at the NIPS: Neural Information Processing Systems, Granada, Spain: Neural Information Processing Systems.","ama":"Lampert C. Maximum margin multi-label structured prediction. In: Neural Information Processing Systems; 2011.","mla":"Lampert, Christoph. <i>Maximum Margin Multi-Label Structured Prediction</i>. Neural Information Processing Systems, 2011.","ista":"Lampert C. 2011. Maximum margin multi-label structured prediction. NIPS: Neural Information Processing Systems.","chicago":"Lampert, Christoph. “Maximum Margin Multi-Label Structured Prediction.” Neural Information Processing Systems, 2011.","short":"C. Lampert, in:, Neural Information Processing Systems, 2011."},"type":"conference","date_updated":"2023-10-17T11:47:35Z","day":"01","publist_id":"3522","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_published":"2011-12-01T00:00:00Z","language":[{"iso":"eng"}],"status":"public","title":"Maximum margin multi-label structured prediction"},{"type":"conference","author":[{"full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","first_name":"Ashutosh"},{"full_name":"Popeea, Corneliu","last_name":"Popeea","first_name":"Corneliu"},{"last_name":"Rybalchenko","first_name":"Andrey","full_name":"Rybalchenko, Andrey"}],"citation":{"short":"A. Gupta, C. Popeea, A. Rybalchenko, in:, H. Yang (Ed.), Springer, 2011, pp. 188–203.","mla":"Gupta, Ashutosh, et al. <i>Solving Recursion-Free Horn Clauses over LI+UIF</i>. Edited by Hongseok Yang, vol. 7078, Springer, 2011, pp. 188–203, doi:<a href=\"https://doi.org/10.1007/978-3-642-25318-8_16\">10.1007/978-3-642-25318-8_16</a>.","apa":"Gupta, A., Popeea, C., &#38; Rybalchenko, A. (2011). Solving recursion-free Horn clauses over LI+UIF. In H. Yang (Ed.) (Vol. 7078, pp. 188–203). Presented at the APLAS: Asian Symposium on Programming Languages and Systems, Kenting, Taiwan: Springer. <a href=\"https://doi.org/10.1007/978-3-642-25318-8_16\">https://doi.org/10.1007/978-3-642-25318-8_16</a>","ieee":"A. Gupta, C. Popeea, and A. Rybalchenko, “Solving recursion-free Horn clauses over LI+UIF,” presented at the APLAS: Asian Symposium on Programming Languages and Systems, Kenting, Taiwan, 2011, vol. 7078, pp. 188–203.","ama":"Gupta A, Popeea C, Rybalchenko A. Solving recursion-free Horn clauses over LI+UIF. In: Yang H, ed. Vol 7078. Springer; 2011:188-203. doi:<a href=\"https://doi.org/10.1007/978-3-642-25318-8_16\">10.1007/978-3-642-25318-8_16</a>","chicago":"Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Solving Recursion-Free Horn Clauses over LI+UIF.” edited by Hongseok Yang, 7078:188–203. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-25318-8_16\">https://doi.org/10.1007/978-3-642-25318-8_16</a>.","ista":"Gupta A, Popeea C, Rybalchenko A. 2011. Solving recursion-free Horn clauses over LI+UIF. APLAS: Asian Symposium on Programming Languages and Systems, LNCS, vol. 7078, 188–203."},"date_updated":"2021-01-12T07:42:15Z","volume":7078,"day":"05","publist_id":"3383","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-642-25318-8_16","date_published":"2011-12-05T00:00:00Z","language":[{"iso":"eng"}],"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"}],"status":"public","title":"Solving recursion-free Horn clauses over LI+UIF","alternative_title":["LNCS"],"intvolume":"      7078","conference":{"location":"Kenting, Taiwan","start_date":"2011-12-05","name":"APLAS: Asian Symposium on Programming Languages and Systems","end_date":"2011-12-07"},"page":"188 - 203","ec_funded":1,"date_created":"2018-12-11T12:02:20Z","year":"2011","_id":"3264","publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"}],"editor":[{"full_name":"Yang, Hongseok","first_name":"Hongseok","last_name":"Yang"}],"month":"12","abstract":[{"lang":"eng","text":"Verification of programs with procedures, multi-threaded programs, and higher-order functional programs can be effectively au- tomated using abstraction and refinement schemes that rely on spurious counterexamples for abstraction discovery. The analysis of counterexam- ples can be automated by a series of interpolation queries, or, alterna- tively, as a constraint solving query expressed by a set of recursion free Horn clauses. (A set of interpolation queries can be formulated as a single constraint over Horn clauses with linear dependency structure between the unknown relations.) In this paper we present an algorithm for solving recursion free Horn clauses over a combined theory of linear real/rational arithmetic and uninterpreted functions. Our algorithm performs resolu- tion to deal with the clausal structure and relies on partial solutions to deal with (non-local) instances of functionality axioms."}],"quality_controlled":"1","oa_version":"None"},{"month":"12","publisher":"Neural Information Processing Systems Foundation","publication_status":"published","department":[{"_id":"HeEd"}],"abstract":[{"text":"We present a joint image segmentation and labeling model (JSL) which, given a bag of figure-ground segment hypotheses extracted at multiple image locations and scales, constructs a joint probability distribution over both the compatible image interpretations (tilings or image segmentations) composed from those segments, and over their labeling into categories. The process of drawing samples from the joint distribution can be interpreted as first sampling tilings, modeled as maximal cliques, from a graph connecting spatially non-overlapping segments in the bag [1], followed by sampling labels for those segments, conditioned on the choice of a particular tiling. We learn the segmentation and labeling parameters jointly, based on Maximum Likelihood with a novel Incremental Saddle Point estimation procedure. The partition function over tilings and labelings is increasingly more accurately approximated by including incorrect configurations that a not-yet-competent model rates probable during learning. We show that the proposed methodologymatches the current state of the art in the Stanford dataset [2], as well as in VOC2010, where 41.7% accuracy on the test set is achieved.","lang":"eng"}],"quality_controlled":"1","oa_version":"None","conference":{"end_date":"2011-12-14","start_date":"2011-12-12","name":"NIPS: Neural Information Processing Systems","location":"Granada, Spain"},"page":"1827 - 1835","date_created":"2018-12-11T12:02:21Z","_id":"3266","scopus_import":1,"year":"2011","date_published":"2011-12-01T00:00:00Z","title":"Probabilistic joint image segmentation and labeling","status":"public","language":[{"iso":"eng"}],"intvolume":"        24","date_updated":"2021-01-12T07:42:15Z","type":"conference","citation":{"short":"A. Ion, J. Carreira, C. Sminchisescu, in:, NIPS Proceedings, Neural Information Processing Systems Foundation, 2011, pp. 1827–1835.","mla":"Ion, Adrian, et al. “Probabilistic Joint Image Segmentation and Labeling.” <i>NIPS Proceedings</i>, vol. 24, Neural Information Processing Systems Foundation, 2011, pp. 1827–35.","apa":"Ion, A., Carreira, J., &#38; Sminchisescu, C. (2011). Probabilistic joint image segmentation and labeling. In <i>NIPS Proceedings</i> (Vol. 24, pp. 1827–1835). Granada, Spain: Neural Information Processing Systems Foundation.","ieee":"A. Ion, J. Carreira, and C. Sminchisescu, “Probabilistic joint image segmentation and labeling,” in <i>NIPS Proceedings</i>, Granada, Spain, 2011, vol. 24, pp. 1827–1835.","ama":"Ion A, Carreira J, Sminchisescu C. Probabilistic joint image segmentation and labeling. In: <i>NIPS Proceedings</i>. Vol 24. Neural Information Processing Systems Foundation; 2011:1827-1835.","chicago":"Ion, Adrian, Joao Carreira, and Cristian Sminchisescu. “Probabilistic Joint Image Segmentation and Labeling.” In <i>NIPS Proceedings</i>, 24:1827–35. Neural Information Processing Systems Foundation, 2011.","ista":"Ion A, Carreira J, Sminchisescu C. 2011. Probabilistic joint image segmentation and labeling. NIPS Proceedings. NIPS: Neural Information Processing Systems vol. 24, 1827–1835."},"author":[{"first_name":"Adrian","last_name":"Ion","full_name":"Ion, Adrian","id":"29F89302-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Carreira","first_name":"Joao","full_name":"Carreira, Joao"},{"full_name":"Sminchisescu, Cristian","last_name":"Sminchisescu","first_name":"Cristian"}],"volume":24,"publist_id":"3381","day":"01","publication":"NIPS Proceedings","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Discrete & Computational Geometry","day":"14","publist_id":"3379","volume":45,"citation":{"short":"C. Chen, D. Freedman, Discrete &#38; Computational Geometry 45 (2011) 425–448.","mla":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” <i>Discrete &#38; Computational Geometry</i>, vol. 45, no. 3, Springer, 2011, pp. 425–48, doi:<a href=\"https://doi.org/10.1007/s00454-010-9322-8\">10.1007/s00454-010-9322-8</a>.","apa":"Chen, C., &#38; Freedman, D. (2011). Hardness results for homology localization. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-010-9322-8\">https://doi.org/10.1007/s00454-010-9322-8</a>","ieee":"C. Chen and D. Freedman, “Hardness results for homology localization,” <i>Discrete &#38; Computational Geometry</i>, vol. 45, no. 3. Springer, pp. 425–448, 2011.","ama":"Chen C, Freedman D. Hardness results for homology localization. <i>Discrete &#38; Computational Geometry</i>. 2011;45(3):425-448. doi:<a href=\"https://doi.org/10.1007/s00454-010-9322-8\">10.1007/s00454-010-9322-8</a>","chicago":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/s00454-010-9322-8\">https://doi.org/10.1007/s00454-010-9322-8</a>.","ista":"Chen C, Freedman D. 2011. Hardness results for homology localization. Discrete &#38; Computational Geometry. 45(3), 425–448."},"date_updated":"2023-02-21T16:07:10Z","author":[{"first_name":"Chao","last_name":"Chen","full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Freedman","first_name":"Daniel","full_name":"Freedman, Daniel"}],"type":"journal_article","issue":"3","intvolume":"        45","language":[{"iso":"eng"}],"status":"public","title":"Hardness results for homology localization","doi":"10.1007/s00454-010-9322-8","date_published":"2011-01-14T00:00:00Z","scopus_import":1,"year":"2011","_id":"3267","date_created":"2018-12-11T12:02:21Z","page":"425 - 448","oa_version":"None","quality_controlled":"1","abstract":[{"text":"We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We study the problem with different measures: volume, diameter and radius. For volume, that is, the 1-norm of a cycle, two main results are presented. First, we prove that the problem is NP-hard to approximate within any constant factor. Second, we prove that for homology of dimension two or higher, the problem is NP-hard to approximate even when the Betti number is O(1). The latter result leads to the inapproximability of the problem of computing the nonbounding cycle with the smallest volume and computing cycles representing a homology basis with the minimal total volume. As for the other two measures defined by pairwise geodesic distance, diameter and radius, we show that the localization problem is NP-hard for diameter but is polynomial for radius. Our work is restricted to homology over the ℤ2 field.","lang":"eng"}],"department":[{"_id":"HeEd"}],"related_material":{"record":[{"status":"public","id":"10909","relation":"earlier_version"}]},"publication_status":"published","publisher":"Springer","month":"01"},{"main_file_link":[{"url":"http://www.cs.cmu.edu/%7Eshengyu/download/egsr2011_paper.pdf","open_access":"1"}],"month":"07","publisher":"Wiley-Blackwell","department":[{"_id":"HeEd"}],"scopus_import":1,"page":"1261 - 1268","intvolume":"        30","status":"public","language":[{"iso":"eng"}],"date_published":"2011-07-19T00:00:00Z","doi":"10.1111/j.1467-8659.2011.01985.x","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":30,"type":"journal_article","article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","abstract":[{"text":"The unintentional scattering of light between neighboring surfaces in complex projection environments increases the brightness and decreases the contrast, disrupting the appearance of the desired imagery. To achieve satisfactory projection results, the inverse problem of global illumination must be solved to cancel this secondary scattering. In this paper, we propose a global illumination cancellation method that minimizes the perceptual difference between the desired imagery and the actual total illumination in the resulting physical environment. Using Gauss-Newton and active set methods, we design a fast solver for the bound constrained nonlinear least squares problem raised by the perceptual error metrics. Our solver is further accelerated with a CUDA implementation and multi-resolution method to achieve 1–2 fps for problems with approximately 3000 variables. We demonstrate the global illumination cancellation algorithm with our multi-projector system. Results show that our method preserves the color fidelity of the desired imagery significantly better than previous methods.","lang":"eng"}],"article_type":"original","publication_status":"published","_id":"3269","year":"2011","date_created":"2018-12-11T12:02:22Z","issue":"4","title":"Perceptual global illumination cancellation in complex projection environments","oa":1,"publication":"Computer Graphics Forum","publist_id":"3377","day":"19","author":[{"full_name":"Sheng, Yu","first_name":"Yu","last_name":"Sheng"},{"full_name":"Cutler, Barbara","first_name":"Barbara","last_name":"Cutler"},{"first_name":"Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao"},{"full_name":"Nasman, Joshua","last_name":"Nasman","first_name":"Joshua"}],"citation":{"ista":"Sheng Y, Cutler B, Chen C, Nasman J. 2011. Perceptual global illumination cancellation in complex projection environments. Computer Graphics Forum. 30(4), 1261–1268.","chicago":"Sheng, Yu, Barbara Cutler, Chao Chen, and Joshua Nasman. “Perceptual Global Illumination Cancellation in Complex Projection Environments.” <i>Computer Graphics Forum</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">https://doi.org/10.1111/j.1467-8659.2011.01985.x</a>.","ieee":"Y. Sheng, B. Cutler, C. Chen, and J. Nasman, “Perceptual global illumination cancellation in complex projection environments,” <i>Computer Graphics Forum</i>, vol. 30, no. 4. Wiley-Blackwell, pp. 1261–1268, 2011.","apa":"Sheng, Y., Cutler, B., Chen, C., &#38; Nasman, J. (2011). Perceptual global illumination cancellation in complex projection environments. <i>Computer Graphics Forum</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">https://doi.org/10.1111/j.1467-8659.2011.01985.x</a>","ama":"Sheng Y, Cutler B, Chen C, Nasman J. Perceptual global illumination cancellation in complex projection environments. <i>Computer Graphics Forum</i>. 2011;30(4):1261-1268. doi:<a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">10.1111/j.1467-8659.2011.01985.x</a>","mla":"Sheng, Yu, et al. “Perceptual Global Illumination Cancellation in Complex Projection Environments.” <i>Computer Graphics Forum</i>, vol. 30, no. 4, Wiley-Blackwell, 2011, pp. 1261–68, doi:<a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">10.1111/j.1467-8659.2011.01985.x</a>.","short":"Y. Sheng, B. Cutler, C. Chen, J. Nasman, Computer Graphics Forum 30 (2011) 1261–1268."},"date_updated":"2021-01-12T07:42:16Z"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","day":"01","publist_id":"3376","type":"conference","citation":{"apa":"Chen, C., &#38; Kerber, M. (2011). Persistent homology computation with a twist (pp. 197–200). Presented at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland: TU Dortmund.","ieee":"C. Chen and M. Kerber, “Persistent homology computation with a twist,” presented at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland, 2011, pp. 197–200.","ama":"Chen C, Kerber M. Persistent homology computation with a twist. In: TU Dortmund; 2011:197-200.","mla":"Chen, Chao, and Michael Kerber. <i>Persistent Homology Computation with a Twist</i>. TU Dortmund, 2011, pp. 197–200.","ista":"Chen C, Kerber M. 2011. Persistent homology computation with a twist. EuroCG: European Workshop on Computational Geometry, 197–200.","chicago":"Chen, Chao, and Michael Kerber. “Persistent Homology Computation with a Twist,” 197–200. TU Dortmund, 2011.","short":"C. Chen, M. Kerber, in:, TU Dortmund, 2011, pp. 197–200."},"date_updated":"2021-01-12T07:42:17Z","author":[{"full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chao"},{"id":"36E4574A-F248-11E8-B48F-1D18A9856A87","full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","first_name":"Michael","last_name":"Kerber"}],"language":[{"iso":"eng"}],"status":"public","title":"Persistent homology computation with a twist","date_published":"2011-01-01T00:00:00Z","year":"2011","_id":"3270","date_created":"2018-12-11T12:02:22Z","page":"197 - 200","conference":{"end_date":"2011-03-30","name":"EuroCG: European Workshop on Computational Geometry","start_date":"2011-03-28","location":"Morschach, Switzerland"},"oa_version":"None","quality_controlled":"1","abstract":[{"text":"The persistence diagram of a filtered simplicial com- plex is usually computed by reducing the boundary matrix of the complex. We introduce a simple op- timization technique: by processing the simplices of the complex in decreasing dimension, we can “kill” columns (i.e., set them to zero) without reducing them. This technique completely avoids reduction on roughly half of the columns. We demonstrate that this idea significantly improves the running time of the reduction algorithm in practice. We also give an output-sensitive complexity analysis for the new al- gorithm which yields to sub-cubic asymptotic bounds under certain assumptions.","lang":"eng"}],"publication_status":"published","publisher":"TU Dortmund","department":[{"_id":"HeEd"}],"month":"01"},{"publist_id":"3375","day":"14","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication":"Topological Methods in Data Analysis and Visualization II","type":"book_chapter","citation":{"short":"H. Wagner, C. Chen, E. Vuçini, in:, R. Peikert, H. Hauser, H. Carr, R. Fuchs (Eds.), Topological Methods in Data Analysis and Visualization II, Springer, 2011, pp. 91–106.","ama":"Wagner H, Chen C, Vuçini E. Efficient computation of persistent homology for cubical data. In: Peikert R, Hauser H, Carr H, Fuchs R, eds. <i>Topological Methods in Data Analysis and Visualization II</i>. Springer; 2011:91-106. doi:<a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">10.1007/978-3-642-23175-9_7</a>","ieee":"H. Wagner, C. Chen, and E. Vuçini, “Efficient computation of persistent homology for cubical data,” in <i>Topological Methods in Data Analysis and Visualization II</i>, R. Peikert, H. Hauser, H. Carr, and R. Fuchs, Eds. Springer, 2011, pp. 91–106.","apa":"Wagner, H., Chen, C., &#38; Vuçini, E. (2011). Efficient computation of persistent homology for cubical data. In R. Peikert, H. Hauser, H. Carr, &#38; R. Fuchs (Eds.), <i>Topological Methods in Data Analysis and Visualization II</i> (pp. 91–106). Springer. <a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">https://doi.org/10.1007/978-3-642-23175-9_7</a>","mla":"Wagner, Hubert, et al. “Efficient Computation of Persistent Homology for Cubical Data.” <i>Topological Methods in Data Analysis and Visualization II</i>, edited by Ronald Peikert et al., Springer, 2011, pp. 91–106, doi:<a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">10.1007/978-3-642-23175-9_7</a>.","ista":"Wagner H, Chen C, Vuçini E. 2011.Efficient computation of persistent homology for cubical data. In: Topological Methods in Data Analysis and Visualization II. Theory, Algorithms, and Applications, , 91–106.","chicago":"Wagner, Hubert, Chao Chen, and Erald Vuçini. “Efficient Computation of Persistent Homology for Cubical Data.” In <i>Topological Methods in Data Analysis and Visualization II</i>, edited by Ronald Peikert, Helwig Hauser, Hamish Carr, and Raphael Fuchs, 91–106. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">https://doi.org/10.1007/978-3-642-23175-9_7</a>."},"date_updated":"2021-01-12T07:42:18Z","author":[{"full_name":"Wagner, Hubert","first_name":"Hubert","last_name":"Wagner"},{"full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","last_name":"Chen"},{"full_name":"Vuçini, Erald","last_name":"Vuçini","first_name":"Erald"}],"alternative_title":["Theory, Algorithms, and Applications"],"date_published":"2011-11-14T00:00:00Z","doi":"10.1007/978-3-642-23175-9_7","title":"Efficient computation of persistent homology for cubical data","status":"public","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:02:23Z","_id":"3271","year":"2011","scopus_import":1,"page":"91 - 106","quality_controlled":"1","oa_version":"None","editor":[{"full_name":"Peikert, Ronald","first_name":"Ronald","last_name":"Peikert"},{"full_name":"Hauser, Helwig","last_name":"Hauser","first_name":"Helwig"},{"full_name":"Carr, Hamish","first_name":"Hamish","last_name":"Carr"},{"full_name":"Fuchs, Raphael","last_name":"Fuchs","first_name":"Raphael"}],"month":"11","publication_status":"published","publisher":"Springer","department":[{"_id":"HeEd"}],"abstract":[{"text":"In this paper we present an efficient framework for computation of persis- tent homology of cubical data in arbitrary dimensions. An existing algorithm using simplicial complexes is adapted to the setting of cubical complexes. The proposed approach enables efficient application of persistent homology in domains where the data is naturally given in a cubical form. By avoiding triangulation of the data, we significantly reduce the size of the complex. We also present a data-structure de- signed to compactly store and quickly manipulate cubical complexes. By means of numerical experiments, we show high speed and memory efficiency of our ap- proach. We compare our framework to other available implementations, showing its superiority. Finally, we report performance on selected 3D and 4D data-sets.","lang":"eng"}]},{"date_created":"2018-12-11T12:02:23Z","_id":"3273","year":"2011","month":"12","publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","degree_awarded":"PhD","oa_version":"None","type":"dissertation","citation":{"short":"J.-L. Maître, Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors, Institute of Science and Technology Austria, 2011.","chicago":"Maître, Jean-Léon. “Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors.” Institute of Science and Technology Austria, 2011.","ista":"Maître J-L. 2011. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. Institute of Science and Technology Austria.","mla":"Maître, Jean-Léon. <i>Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors</i>. Institute of Science and Technology Austria, 2011.","ama":"Maître J-L. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. 2011.","apa":"Maître, J.-L. (2011). <i>Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors</i>. Institute of Science and Technology Austria.","ieee":"J.-L. Maître, “Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors,” Institute of Science and Technology Austria, 2011."},"date_updated":"2023-09-07T11:30:16Z","author":[{"last_name":"Maître","first_name":"Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","full_name":"Maître, Jean-Léon","orcid":"0000-0002-3688-1474"}],"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"publist_id":"3373","day":"12","publication_identifier":{"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2011-12-12T00:00:00Z","title":"Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors","status":"public","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"]},{"month":"03","department":[{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","page":"141","acknowledgement":"I would like to express my sincere gratitude to the following people who made with their continuous support and encouragement this thesis possible: First, I want to thank Prof. Dr. Michael Sixt for his excellent supervision and mentoring, especially for the nice, relaxed working atmosphere, a lot of brilliant ideas and the freedom to work in my own way.\r\n\r\nProf. Dr. Reinhard Fässler for his constant support of the Sixt lab and for providing excellent working conditions. \r\n\r\nProf. Dr. Sanjiv Luther and Prof. Dr. Tobias Bollenbach for agreeing to be member of my thesis committee and to evaluate my work.\r\n\r\nDr. Walther Göhring, Carmen Schmitz, the Recombinant Protein Production core facility and the animal care takers for providing the “infrastructure” for this thesis. \r\n\r\nProf. Dr. Daniel Legler, Markus Bruckner and Dr. Julien Polleux for very fruitful collaborations and discussions.\r\n\r\nMy labmates for their help, a lot of discussions and to make the Sixt lab to a convenient place to work : Karin Hirsch, Tim Lämmeramnn, Holger Pflicke, Jörg Renkawitz, Michele Weber and Alexander Eichner All members of the Department of Molecular Medicine for their help. Especially I want to thank Sarah Schmidt, Karin Hirsch and Raphael Ruppert for their friendship, nice chats and their uncensored point of view. ","date_published":"2011-03-01T00:00:00Z","status":"public","language":[{"iso":"eng"}],"ddc":["570","579"],"alternative_title":["ISTA Thesis"],"type":"dissertation","pubrep_id":"11","file_date_updated":"2021-02-22T11:24:30Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","abstract":[{"lang":"eng","text":"Chemokines organize immune cell trafficking by inducing either directed (tactic) or random (kinetic) migration and by activating integrins in order to support surface adhesion (haptic). Beyond that the same chemokines can establish clearly defined functional areas in secondary lymphoid organs. Until now it is unclear how chemokines can fulfill such diverse functions. One decisive prerequisite to explain these capacities is to know how chemokines are presented in tissue. In theory chemokines could occur either soluble or immobilized, and could be distributed either homogenously or as a concentration gradient. To dissect if and how the presenting mode of chemokines influences immune cells, I tested the response of dendritic cells (DCs) to differentially displayed chemokines. DCs are antigen presenting cells that reside in the periphery and migrate into draining lymph nodes (LNs) once exposed to inflammatory stimuli to activate naïve T cells. DCs are guided to and within the LN by the chemokine receptor CCR7, which has two ligands, the chemokines CCL19 and CCL21. Both CCR7 ligands are expressed by fibroblastic reticular cells in the LN, but differ in their ability to bind to heparan sulfate residues. CCL21 has a highly charged C-terminal extension, which mediates binding to anionic surfaces, whereas CCL19 is lacking such residues and likely distributes as a soluble molecule. This study shows that surface-bound CCL21 causes random, haptokinetic DC motility, which is confined to the chemokine coated area by insideout activation of β2 integrins that mediate cell binding to the surface. CCL19 on the other hand forms concentration gradients which trigger directional, chemotactic movement, but no surface adhesion. In addition DCs can actively manipulate this system by recruiting and activating serine proteases on their surfaces, which create - by proteolytically removing the adhesive C-terminus - a solubilized variant of CCL21 that functionally resembles CCL19. By generating a CCL21 concentration gradient DCs establish a positive feedback loop to recruit further DCs from the periphery to the CCL21 coated region. In addition DCs can sense chemotactic gradients as well as immobilized haptokinetic fields at the same time and integrate these signals. The result is chemotactically biased haptokinesis - directional migration confined to a chemokine coated track or area - which could explain the dynamic but spatially tightly controlled swarming leukocyte locomotion patterns that have been observed in lymphatic organs by intravital microscopists. The finding that DCs can approach soluble cues in a non-adhesive manner while they attach to surfaces coated with immobilized cues raises the question how these cells transmit intracellular forces to the environment, especially in the non-adherent migration mode. In order to migrate, cells have to generate and transmit force to the extracellular substrate. Force transmission is the prerequisite to procure an expansion of the leading edge and a forward motion of the whole cell body. In the current conceptions actin polymerization at the leading edge is coupled to extracellular ligands via the integrin family of transmembrane receptors, which allows the transmission of intracellular force. Against the paradigm of force transmission during migration, leukocytes, like DCs, are able to migrate in threedimensional environments without using integrin transmembrane receptors (Lämmermann et al., 2008). This reflects the biological function of leukocytes, as they can invade almost all tissues, whereby their migration has to be independent from the extracellular environment. How the cells can achieve this is unclear. For this study I examined DC migration in a defined threedimensional environment and highlighted actin-dynamics with the probe Lifeact-GFP. The result was that chemotactic DCs can switch between integrin-dependent and integrin- independent locomotion and can thereby adapt to the adhesive properties of their environment. If the cells are able to couple their actin cytoskeleton to the substrate, actin polymerization is entirely converted into protrusion. Without coupling the actin cortex undergoes slippage and retrograde actin flow can be observed. But retrograde actin flow can be completely compensated by higher actin polymerization rate keeping the migration velocity and the shape of the cells unaltered. Mesenchymal cells like fibroblast cannot balance the loss of adhesive interaction, cannot protrude into open space and, therefore, strictly depend on integrinmediated force coupling. This leukocyte specific phenomenon of “adaptive force transmission” endows these cells with the unique ability to transit and invade almost every type of tissue. "}],"file":[{"date_updated":"2020-07-14T12:46:06Z","relation":"main_file","date_created":"2019-03-26T08:12:21Z","file_id":"6177","file_name":"2011_Thesis_Kathrin_Schumann.pdf","creator":"dernst","access_level":"closed","content_type":"application/pdf","file_size":4487708,"checksum":"e69eee6252660f0b694a2ea8923ddc72"},{"date_updated":"2021-02-22T11:24:30Z","file_id":"9175","success":1,"date_created":"2021-02-22T11:24:30Z","relation":"main_file","file_name":"2011_Thesis_Schumann_noS.pdf","access_level":"open_access","creator":"dernst","file_size":4313127,"content_type":"application/pdf","checksum":"71727d63f424b5b446f68f4b87ecadc0"}],"article_processing_charge":"No","oa_version":"Published Version","date_created":"2018-12-11T12:02:24Z","_id":"3275","year":"2011","title":"The role of chemotactic gradients in dendritic cell migration","has_accepted_license":"1","date_updated":"2023-09-07T11:31:48Z","citation":{"short":"K. Schumann, The Role of Chemotactic Gradients in Dendritic Cell Migration, Institute of Science and Technology Austria, 2011.","ieee":"K. Schumann, “The role of chemotactic gradients in dendritic cell migration,” Institute of Science and Technology Austria, 2011.","apa":"Schumann, K. (2011). <i>The role of chemotactic gradients in dendritic cell migration</i>. Institute of Science and Technology Austria.","ama":"Schumann K. The role of chemotactic gradients in dendritic cell migration. 2011.","mla":"Schumann, Kathrin. <i>The Role of Chemotactic Gradients in Dendritic Cell Migration</i>. Institute of Science and Technology Austria, 2011.","ista":"Schumann K. 2011. The role of chemotactic gradients in dendritic cell migration. Institute of Science and Technology Austria.","chicago":"Schumann, Kathrin. “The Role of Chemotactic Gradients in Dendritic Cell Migration.” Institute of Science and Technology Austria, 2011."},"author":[{"id":"F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F","full_name":"Schumann, Kathrin","first_name":"Kathrin","last_name":"Schumann"}],"supervisor":[{"last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"publist_id":"3371","day":"01","oa":1,"publication_identifier":{"issn":["2663-337X"]}}]