[{"intvolume":"         8","year":"2012","external_id":{"pmid":["23071449"]},"publication_status":"published","oa":1,"scopus_import":"1","article_type":"original","month":"10","extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pgen.1002988"}],"date_created":"2021-06-07T10:55:27Z","department":[{"_id":"DaZi"}],"quality_controlled":"1","title":"Deposition of histone variant H2A.Z within gene bodies regulates responsive genes","pmid":1,"citation":{"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>.","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.","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>.","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>","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>","short":"D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012).","ista":"Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988."},"publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"article_number":"e1002988","_id":"9497","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1371/journal.pgen.1002988","article_processing_charge":"No","volume":8,"language":[{"iso":"eng"}],"date_published":"2012-10-11T00:00:00Z","status":"public","abstract":[{"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.","lang":"eng"}],"publication":"PLoS Genetics","issue":"10","oa_version":"Published Version","type":"journal_article","author":[{"full_name":"Coleman-Derr, Devin","last_name":"Coleman-Derr","first_name":"Devin"},{"last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"publisher":"Public Library of Science","day":"11","date_updated":"2021-12-14T08:29:57Z"},{"oa_version":"Published Version","issue":"3","publication":"PLoS Genetics","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."}],"status":"public","language":[{"iso":"eng"}],"date_published":"2012-03-22T00:00:00Z","volume":8,"doi":"10.1371/journal.pgen.1002512","article_processing_charge":"No","date_updated":"2021-12-14T08:31:14Z","day":"22","publisher":"Public Library of Science","author":[{"first_name":"Sang Yeol","full_name":"Kim, Sang Yeol","last_name":"Kim"},{"first_name":"Jungeun","last_name":"Lee","full_name":"Lee, Jungeun"},{"full_name":"Eshed-Williams, Leor","last_name":"Eshed-Williams","first_name":"Leor"},{"full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"},{"first_name":"Z. Renee","full_name":"Sung, Z. Renee","last_name":"Sung"}],"type":"journal_article","month":"03","oa":1,"article_type":"original","scopus_import":"1","publication_status":"published","external_id":{"pmid":["22457632"]},"year":"2012","intvolume":"         8","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9499","article_number":"e1002512","publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"pmid":1,"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>.","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.","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>.","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>","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>","short":"S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012).","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."},"title":"EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development","department":[{"_id":"DaZi"}],"quality_controlled":"1","date_created":"2021-06-07T11:07:56Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pgen.1002512"}],"extern":"1"},{"oa_version":"None","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"}],"status":"public","issue":"2","publication":"Current Opinion in Genetics and Development","date_published":"2012-04-01T00:00:00Z","language":[{"iso":"eng"}],"page":"132-138","article_processing_charge":"No","doi":"10.1016/j.gde.2012.01.007","volume":22,"date_updated":"2021-12-14T08:32:38Z","author":[{"full_name":"Huff, Jason T.","last_name":"Huff","first_name":"Jason T."},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman"}],"publisher":"Elsevier","type":"journal_article","month":"04","publication_status":"published","article_type":"review","scopus_import":"1","external_id":{"pmid":["22336527"]},"year":"2012","intvolume":"        22","_id":"9528","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["0959-437X"]},"pmid":1,"citation":{"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>.","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.","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>.","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.","short":"J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138.","ama":"Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. <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>","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>"},"date_created":"2021-06-08T08:58:52Z","extern":"1","title":"Regulation of biological accuracy, precision, and memory by plant chromatin organization","department":[{"_id":"DaZi"}],"quality_controlled":"1"},{"year":"2012","external_id":{"pmid":["23250988"]},"intvolume":"        77","month":"12","publication_status":"published","scopus_import":"1","oa":1,"article_type":"review","pmid":1,"citation":{"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>","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>","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.","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>.","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.","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>."},"extern":"1","main_file_link":[{"url":"https://doi.org/10.1101/sqb.2012.77.014944","open_access":"1"}],"date_created":"2021-06-08T13:01:23Z","department":[{"_id":"DaZi"}],"quality_controlled":"1","title":"DNA methylation, H2A.Z, and the regulation of constitutive expression","_id":"9535","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"eissn":["1943-4456"],"issn":["0091-7451"]},"date_published":"2012-12-18T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1101/sqb.2012.77.014944","article_processing_charge":"No","page":"147-154","volume":77,"oa_version":"Published Version","status":"public","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"}],"publication":"Cold Spring Harbor Symposia on Quantitative Biology","author":[{"full_name":"Coleman-Derr, D.","last_name":"Coleman-Derr","first_name":"D."},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel"}],"publisher":"Cold Spring Harbor Laboratory Press","type":"journal_article","date_updated":"2021-12-14T08:33:09Z","day":"18"},{"day":"27","_id":"9755","date_updated":"2025-09-30T07:50:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.sv37s"}],"date_created":"2021-07-30T08:39:13Z","type":"research_data_reference","title":"Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies","department":[{"_id":"SyCr"}],"citation":{"ieee":"M. Konrad <i>et al.</i>, “Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies.” Dryad, 2012.","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>.","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>.","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>.","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>","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>"},"publisher":"Dryad","author":[{"full_name":"Konrad, Matthias","last_name":"Konrad","first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vyleta","full_name":"Vyleta, Meghan","first_name":"Meghan","id":"418901AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Theis","full_name":"Theis, Fabian","first_name":"Fabian"},{"last_name":"Stock","full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam"},{"first_name":"Martina","id":"E60F29C6-E9AE-11E9-AF6E-D190C7302F38","full_name":"Klatt, Martina","last_name":"Klatt"},{"last_name":"Drescher","full_name":"Drescher, Verena","first_name":"Verena"},{"last_name":"Marr","full_name":"Marr, Carsten","first_name":"Carsten"},{"last_name":"Ugelvig","full_name":"Ugelvig, Line V","first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883"},{"full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"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"}],"status":"public","oa":1,"month":"09","oa_version":"Published Version","doi":"10.5061/dryad.sv37s","article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"3242"}]},"year":"2012","date_published":"2012-09-27T00:00:00Z"},{"day":"14","_id":"9757","date_updated":"2025-09-30T08:15:49Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.61649"}],"date_created":"2021-07-30T12:31:31Z","title":"Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison","department":[{"_id":"SyCr"}],"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>","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>.","short":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer, (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>.","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>.","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."},"publisher":"Dryad","author":[{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Tragust, Simon","last_name":"Tragust"},{"first_name":"Barbara","id":"479DDAAC-E9CD-11E9-9B5F-82450873F7A1","last_name":"Mitteregger","full_name":"Mitteregger, Barbara"},{"full_name":"Barone, Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","orcid":"0000-0003-2676-3367"},{"last_name":"Konrad","full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V","last_name":"Ugelvig","full_name":"Ugelvig, Line V"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"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"}],"status":"public","oa":1,"month":"12","oa_version":"Published Version","doi":"10.5061/dryad.61649","article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2926"}]},"year":"2012","date_published":"2012-12-14T00:00:00Z"},{"year":"2012","date_published":"2012-11-14T00:00:00Z","doi":"10.5061/dryad.274b1","article_processing_charge":"No","related_material":{"record":[{"id":"2944","relation":"used_in_publication","status":"public"}]},"month":"11","oa_version":"Published Version","status":"public","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."}],"oa":1,"publisher":"Dryad","author":[{"full_name":"Aeschbacher, Simon","last_name":"Aeschbacher","id":"2D35326E-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Andreas","last_name":"Futschik","full_name":"Futschik, Andreas"},{"last_name":"Beaumont","full_name":"Beaumont, Mark","first_name":"Mark"}],"citation":{"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>.","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>.","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.","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>","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>","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>.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, (2012)."},"type":"research_data_reference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.274b1"}],"date_created":"2021-07-30T12:36:39Z","department":[{"_id":"NiBa"}],"title":"Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates","_id":"9758","date_updated":"2025-09-29T13:25:35Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"14"},{"oa":1,"article_type":"original","scopus_import":"1","publication_status":"published","ddc":["500"],"acknowledgement":"This work is supported by the Austrian Science Fund (FWF), Project P22025-N18.\r\n","month":"01","intvolume":"         8","year":"2012","external_id":{"isi":["000301173600004"]},"OA_place":"publisher","publication_identifier":{"issn":["1812-9471"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6588","department":[{"_id":"HeEd"}],"quality_controlled":"1","title":"Elementary solutions of the Bernstein problem on two intervals","main_file_link":[{"url":"https://www.mathnet.ru/eng/jmag525","open_access":"1"}],"date_created":"2019-06-27T08:16:56Z","citation":{"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.","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.","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.","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.","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."},"publication":"Journal of Mathematical Physics, Analysis, Geometry","issue":"1","status":"public","corr_author":"1","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"}],"oa_version":"Published Version","volume":8,"article_processing_charge":"No","page":"63-78","date_published":"2012-01-01T00:00:00Z","language":[{"iso":"eng"}],"day":"01","isi":1,"date_updated":"2026-06-18T19:08:51Z","type":"journal_article","author":[{"last_name":"Pausinger","full_name":"Pausinger, Florian","orcid":"0000-0002-8379-3768","first_name":"Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87"}],"publisher":"B. Verkin Institute for Low Temperature Physics and Engineering"},{"month":"12","scopus_import":"1","oa":1,"acknowledgement":"We thank Eyal Flato (Plataine Ltd.) for raising the offset-deconstruction problem in connection with wood cutting. We also thank Tim Bretl (UIUC) for suggesting the digital-pen offset-deconstruction problem. This work has been supported in part by the Israel Science Foundation (grant no. 1102/11), by the German–Israeli Foundation (grant no. 969/07), by the Hermann Minkowski–Minerva Center for Geometry at Tel Aviv University, and by the EU Project under Contract No. 255827 (CGL—Computational Geometry Learning).\r\n","publication_status":"published","external_id":{"arxiv":["1109.2158"],"isi":["000311503200006"]},"arxiv":1,"year":"2012","related_material":{"record":[{"id":"3329","status":"public","relation":"earlier_version"}]},"intvolume":"        48","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"3115","publist_id":"3584","citation":{"mla":"Berberich, Eric, et al. “Deconstructing Approximate Offsets.” <i>Discrete &#38; Computational Geometry</i>, vol. 48, no. 4, Springer, 2012, pp. 964–89, doi:<a href=\"https://doi.org/10.1007/s00454-012-9441-5\">10.1007/s00454-012-9441-5</a>.","chicago":"Berberich, Eric, Dan Halperin, Michael Kerber, and Roza Pogalnikova. “Deconstructing Approximate Offsets.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2012. <a href=\"https://doi.org/10.1007/s00454-012-9441-5\">https://doi.org/10.1007/s00454-012-9441-5</a>.","ieee":"E. Berberich, D. Halperin, M. Kerber, and R. Pogalnikova, “Deconstructing approximate offsets,” <i>Discrete &#38; Computational Geometry</i>, vol. 48, no. 4. Springer, pp. 964–989, 2012.","ama":"Berberich E, Halperin D, Kerber M, Pogalnikova R. Deconstructing approximate offsets. <i>Discrete &#38; Computational Geometry</i>. 2012;48(4):964-989. doi:<a href=\"https://doi.org/10.1007/s00454-012-9441-5\">10.1007/s00454-012-9441-5</a>","apa":"Berberich, E., Halperin, D., Kerber, M., &#38; Pogalnikova, R. (2012). Deconstructing approximate offsets. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-012-9441-5\">https://doi.org/10.1007/s00454-012-9441-5</a>","ista":"Berberich E, Halperin D, Kerber M, Pogalnikova R. 2012. Deconstructing approximate offsets. Discrete &#38; Computational Geometry. 48(4), 964–989.","short":"E. Berberich, D. Halperin, M. Kerber, R. Pogalnikova, Discrete &#38; Computational Geometry 48 (2012) 964–989."},"title":"Deconstructing approximate offsets","quality_controlled":"1","department":[{"_id":"HeEd"}],"date_created":"2018-12-11T12:01:28Z","main_file_link":[{"url":"http://arxiv.org/abs/1109.2158","open_access":"1"}],"oa_version":"Preprint","issue":"4","publication":"Discrete & Computational Geometry","abstract":[{"lang":"eng","text":"We consider the offset-deconstruction problem: Given a polygonal shape Q with n vertices, can it be expressed, up to a tolerance ε in Hausdorff distance, as the Minkowski sum of another polygonal shape P with a disk of fixed radius? If it does, we also seek a preferably simple-looking solution P; then, P's offset constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We give an O(nlogn)-time exact decision algorithm that handles any polygonal shape, assuming the real-RAM model of computation. A variant of the algorithm, which we have implemented using the cgal library, is based on rational arithmetic and answers the same deconstruction problem up to an uncertainty parameter δ its running time additionally depends on δ. If the input shape is found to be approximable, this algorithm also computes an approximate solution for the problem. It also allows us to solve parameter-optimization problems induced by the offset-deconstruction problem. For convex shapes, the complexity of the exact decision algorithm drops to O(n), which is also the time required to compute a solution P with at most one more vertex than a vertex-minimal one."}],"corr_author":"1","status":"public","date_published":"2012-12-01T00:00:00Z","language":[{"iso":"eng"}],"volume":48,"page":"964 - 989","article_processing_charge":"No","doi":"10.1007/s00454-012-9441-5","date_updated":"2025-09-30T08:01:36Z","day":"01","isi":1,"publisher":"Springer","author":[{"first_name":"Eric","last_name":"Berberich","full_name":"Berberich, Eric"},{"last_name":"Halperin","full_name":"Halperin, Dan","first_name":"Dan"},{"full_name":"Kerber, Michael","last_name":"Kerber","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","orcid":"0000-0002-8030-9299"},{"first_name":"Roza","full_name":"Pogalnikova, Roza","last_name":"Pogalnikova"}],"type":"journal_article"},{"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1006.1990"}],"date_created":"2018-12-11T12:01:29Z","title":"Minimizing a sum of submodular functions","quality_controlled":"1","department":[{"_id":"VlKo"}],"citation":{"ieee":"V. Kolmogorov, “Minimizing a sum of submodular functions,” <i>Discrete Applied Mathematics</i>, vol. 160, no. 15. Elsevier, pp. 2246–2258, 2012.","chicago":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” <i>Discrete Applied Mathematics</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.dam.2012.05.025\">https://doi.org/10.1016/j.dam.2012.05.025</a>.","mla":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” <i>Discrete Applied Mathematics</i>, vol. 160, no. 15, Elsevier, 2012, pp. 2246–58, doi:<a href=\"https://doi.org/10.1016/j.dam.2012.05.025\">10.1016/j.dam.2012.05.025</a>.","short":"V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 2246–2258.","ista":"Kolmogorov V. 2012. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 160(15), 2246–2258.","ama":"Kolmogorov V. Minimizing a sum of submodular functions. <i>Discrete Applied Mathematics</i>. 2012;160(15):2246-2258. doi:<a href=\"https://doi.org/10.1016/j.dam.2012.05.025\">10.1016/j.dam.2012.05.025</a>","apa":"Kolmogorov, V. (2012). Minimizing a sum of submodular functions. <i>Discrete Applied Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.dam.2012.05.025\">https://doi.org/10.1016/j.dam.2012.05.025</a>"},"publist_id":"3582","_id":"3117","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       160","external_id":{"isi":["000308052600017"]},"year":"2012","publication_status":"published","oa":1,"scopus_import":"1","month":"10","type":"journal_article","publisher":"Elsevier","author":[{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"}],"isi":1,"day":"01","date_updated":"2025-09-30T08:01:04Z","page":"2246 - 2258","doi":"10.1016/j.dam.2012.05.025","article_processing_charge":"No","volume":160,"language":[{"iso":"eng"}],"date_published":"2012-10-01T00:00:00Z","abstract":[{"text":"We consider the problem of minimizing a function represented as a sum of submodular terms. We assume each term allows an efficient computation of exchange capacities. This holds, for example, for terms depending on a small number of variables, or for certain cardinality-dependent terms. A naive application of submodular minimization algorithms would not exploit the existence of specialized exchange capacity subroutines for individual terms. To overcome this, we cast the problem as a submodular flow (SF) problem in an auxiliary graph in such a way that applying most existing SF algorithms would rely only on these subroutines. We then explore in more detail Iwata's capacity scaling approach for submodular flows (Iwata 1997 [19]). In particular, we show how to improve its complexity in the case when the function contains cardinality-dependent terms.","lang":"eng"}],"corr_author":"1","status":"public","issue":"15","publication":"Discrete Applied Mathematics","oa_version":"Preprint"},{"oa_version":"Submitted Version","status":"public","corr_author":"1","abstract":[{"text":"We present a method for recovering a temporally coherent, deforming triangle mesh with arbitrarily changing topology from an incoherent sequence of static closed surfaces. We solve this problem using the surface geometry alone, without any prior information like surface templates or velocity fields. Our system combines a proven strategy for triangle mesh improvement, a robust multi-resolution non-rigid registration routine, and a reliable technique for changing surface mesh topology. We also introduce a novel topological constraint enforcement algorithm to ensure that the output and input always have similar topology. We apply our technique to a series of diverse input data from video reconstructions, physics simulations, and artistic morphs. The structured output of our algorithm allows us to efficiently track information like colors and displacement maps, recover velocity information, and solve PDEs on the mesh as a post process.","lang":"eng"}],"publication":"ACM Transactions on Graphics","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:46:00Z","file_id":"5359","file_name":"IST-2016-602-v1+1_topoReg.pdf","file_size":44538518,"creator":"system","content_type":"application/pdf","checksum":"1e219c5bf4e5552c1290c62eefa5cd60","date_created":"2018-12-12T10:18:37Z","relation":"main_file"}],"issue":"4","file_date_updated":"2020-07-14T12:46:00Z","pubrep_id":"602","language":[{"iso":"eng"}],"date_published":"2012-07-01T00:00:00Z","doi":"10.1145/2185520.2185549","article_processing_charge":"No","volume":31,"date_updated":"2025-09-30T08:00:23Z","isi":1,"day":"01","publisher":"ACM","author":[{"orcid":"0000-0002-4417-3224","first_name":"Morten","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","full_name":"Bojsen-Hansen, Morten","last_name":"Bojsen-Hansen"},{"first_name":"Hao","full_name":"Li, Hao","last_name":"Li"},{"orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","last_name":"Wojtan"}],"type":"journal_article","month":"07","ddc":["000"],"acknowledgement":"This work is supported by the SNF fellowship PBEZP2-134464.\r\nWe would like to thank Xiaochen Hu for implementing mesh con- version tools, Duygu Ceylan for helping with the rendering, and Art Tevs for the human performance data comparison. We also thank Nils Thuerey and Christopher Batty for helpful discussions. ","publication_status":"published","article_type":"original","oa":1,"scopus_import":"1","alternative_title":["SIGGRAPH"],"year":"2012","external_id":{"isi":["000308250300029"]},"intvolume":"        31","_id":"3118","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3581","article_number":"53","has_accepted_license":"1","citation":{"ista":"Bojsen-Hansen M, Li H, Wojtan C. 2012. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 31(4), 53.","short":"M. Bojsen-Hansen, H. Li, C. Wojtan, ACM Transactions on Graphics 31 (2012).","ama":"Bojsen-Hansen M, Li H, Wojtan C. Tracking surfaces with evolving topology. <i>ACM Transactions on Graphics</i>. 2012;31(4). doi:<a href=\"https://doi.org/10.1145/2185520.2185549\">10.1145/2185520.2185549</a>","apa":"Bojsen-Hansen, M., Li, H., &#38; Wojtan, C. (2012). Tracking surfaces with evolving topology. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2185520.2185549\">https://doi.org/10.1145/2185520.2185549</a>","chicago":"Bojsen-Hansen, Morten, Hao Li, and Chris Wojtan. “Tracking Surfaces with Evolving Topology.” <i>ACM Transactions on Graphics</i>. ACM, 2012. <a href=\"https://doi.org/10.1145/2185520.2185549\">https://doi.org/10.1145/2185520.2185549</a>.","ieee":"M. Bojsen-Hansen, H. Li, and C. Wojtan, “Tracking surfaces with evolving topology,” <i>ACM Transactions on Graphics</i>, vol. 31, no. 4. ACM, 2012.","mla":"Bojsen-Hansen, Morten, et al. “Tracking Surfaces with Evolving Topology.” <i>ACM Transactions on Graphics</i>, vol. 31, no. 4, 53, ACM, 2012, doi:<a href=\"https://doi.org/10.1145/2185520.2185549\">10.1145/2185520.2185549</a>."},"date_created":"2018-12-11T12:01:29Z","department":[{"_id":"ChWo"}],"quality_controlled":"1","title":"Tracking surfaces with evolving topology"},{"type":"conference","publisher":"ACM","author":[{"first_name":"Karthik","last_name":"Raveendran","full_name":"Raveendran, Karthik"},{"first_name":"Nils","last_name":"Thuerey","full_name":"Thuerey, Nils"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","last_name":"Wojtan","full_name":"Wojtan, Christopher J"},{"last_name":"Turk","full_name":"Turk, Greg","first_name":"Greg"}],"day":"29","date_updated":"2023-02-23T11:13:07Z","page":"255 - 264","file_date_updated":"2020-07-14T12:46:00Z","pubrep_id":"600","language":[{"iso":"eng"}],"date_published":"2012-07-29T00:00:00Z","status":"public","abstract":[{"text":"We present an approach for artist-directed animation of liquids using multiple levels of control over the simulation, ranging from the overall tracking of desired shapes to highly detailed secondary effects such as dripping streams, separating sheets of fluid, surface waves and ripples. The first portion of our technique is a volume preserving morph that allows the animator to produce a plausible fluid-like motion from a sparse set of control meshes. By rasterizing the resulting control meshes onto the simulation grid, the mesh velocities act as boundary conditions during the projection step of the fluid simulation. We can then blend this motion together with uncontrolled fluid velocities to achieve a more relaxed control over the fluid that captures natural inertial effects. Our method can produce highly detailed liquid surfaces with control over sub-grid details by using a mesh-based surface tracker on top of a coarse grid-based fluid simulation. We can create ripples and waves on the fluid surface attracting the surface mesh to the control mesh with spring-like forces and also by running a wave simulation over the surface mesh. Our video results demonstrate how our control scheme can be used to create animated characters and shapes that are made of water.\r\n","lang":"eng"}],"file":[{"file_size":4939370,"creator":"system","file_name":"IST-2016-600-v1+1_ControllingLiquids_Preprint.pdf","file_id":"4877","date_updated":"2020-07-14T12:46:00Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"babda64c24cf90a4d05ae86d712bed08","date_created":"2018-12-12T10:11:23Z"}],"publication":"Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation","conference":{"name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","start_date":"2012-07-29","location":"Aire-la-Ville, Switzerland","end_date":"2012-07-31"},"oa_version":"Submitted Version","date_created":"2018-12-11T12:01:30Z","department":[{"_id":"ChWo"}],"quality_controlled":"1","title":"Controlling liquids using meshes","has_accepted_license":"1","citation":{"mla":"Raveendran, Karthik, et al. “Controlling Liquids Using Meshes.” <i>Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation</i>, ACM, 2012, pp. 255–64.","chicago":"Raveendran, Karthik, Nils Thuerey, Chris Wojtan, and Greg Turk. “Controlling Liquids Using Meshes.” In <i>Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation</i>, 255–64. ACM, 2012.","ieee":"K. Raveendran, N. Thuerey, C. Wojtan, and G. Turk, “Controlling liquids using meshes,” in <i>Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation</i>, Aire-la-Ville, Switzerland, 2012, pp. 255–264.","ama":"Raveendran K, Thuerey N, Wojtan C, Turk G. Controlling liquids using meshes. In: <i>Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation</i>. ACM; 2012:255-264.","apa":"Raveendran, K., Thuerey, N., Wojtan, C., &#38; Turk, G. (2012). Controlling liquids using meshes. In <i>Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation</i> (pp. 255–264). Aire-la-Ville, Switzerland: ACM.","ista":"Raveendran K, Thuerey N, Wojtan C, Turk G. 2012. Controlling liquids using meshes. Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 255–264.","short":"K. Raveendran, N. Thuerey, C. Wojtan, G. Turk, in:, Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–264."},"publist_id":"3580","_id":"3119","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"url":"http://dl.acm.org/citation.cfm?id=2422393","relation":"table_of_contents"}]},"year":"2012","acknowledgement":"This work was partially funded by NSF grants CCF-0811485 and IIS-1130934. We would like to thank Scanline VFX for additional funding. We would like to thank Jie Tan as well as our anonymous reviewers for their useful suggestions and feedback.","publication_status":"published","ddc":["000"],"oa":1,"scopus_import":1,"month":"07"},{"oa_version":"Preprint","publication":"Compositio Mathematica","issue":"4","status":"public","abstract":[{"lang":"eng","text":"We introduce a strategy based on Kustin-Miller unprojection that allows us to construct many hundreds of Gorenstein codimension 4 ideals with 9 × 16 resolutions (that is, nine equations and sixteen first syzygies). Our two basic games are called Tom and Jerry; the main application is the biregular construction of most of the anticanonically polarised Mori Fano 3-folds of Altinok's thesis. There are 115 cases whose numerical data (in effect, the Hilbert series) allow a Type I projection. In every case, at least one Tom and one Jerry construction works, providing at least two deformation families of quasismooth Fano 3-folds having the same numerics but different topology. © 2012 Copyright Foundation Compositio Mathematica."}],"language":[{"iso":"eng"}],"date_published":"2012-07-01T00:00:00Z","volume":148,"doi":"10.1112/S0010437X11007226","article_processing_charge":"No","page":"1171 - 1194","date_updated":"2025-09-30T07:59:55Z","day":"01","isi":1,"author":[{"first_name":"Gavin","full_name":"Brown, Gavin","last_name":"Brown"},{"first_name":"Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8030-9299","last_name":"Kerber","full_name":"Kerber, Michael"},{"full_name":"Reid, Miles","last_name":"Reid","first_name":"Miles"}],"publisher":"Cambridge University Press","type":"journal_article","month":"07","oa":1,"scopus_import":"1","publication_status":"published","acknowledgement":"This research is supported by the Korean Government WCU Grant R33-2008-000-10101-0.","year":"2012","external_id":{"arxiv":["1009.4313"],"isi":["000307176400007"]},"arxiv":1,"intvolume":"       148","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"3120","publist_id":"3579","citation":{"ista":"Brown G, Kerber M, Reid M. 2012. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 148(4), 1171–1194.","short":"G. Brown, M. Kerber, M. Reid, Compositio Mathematica 148 (2012) 1171–1194.","apa":"Brown, G., Kerber, M., &#38; Reid, M. (2012). Fano 3 folds in codimension 4 Tom and Jerry Part I. <i>Compositio Mathematica</i>. Cambridge University Press. <a href=\"https://doi.org/10.1112/S0010437X11007226\">https://doi.org/10.1112/S0010437X11007226</a>","ama":"Brown G, Kerber M, Reid M. Fano 3 folds in codimension 4 Tom and Jerry Part I. <i>Compositio Mathematica</i>. 2012;148(4):1171-1194. doi:<a href=\"https://doi.org/10.1112/S0010437X11007226\">10.1112/S0010437X11007226</a>","chicago":"Brown, Gavin, Michael Kerber, and Miles Reid. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” <i>Compositio Mathematica</i>. Cambridge University Press, 2012. <a href=\"https://doi.org/10.1112/S0010437X11007226\">https://doi.org/10.1112/S0010437X11007226</a>.","ieee":"G. Brown, M. Kerber, and M. Reid, “Fano 3 folds in codimension 4 Tom and Jerry Part I,” <i>Compositio Mathematica</i>, vol. 148, no. 4. Cambridge University Press, pp. 1171–1194, 2012.","mla":"Brown, Gavin, et al. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” <i>Compositio Mathematica</i>, vol. 148, no. 4, Cambridge University Press, 2012, pp. 1171–94, doi:<a href=\"https://doi.org/10.1112/S0010437X11007226\">10.1112/S0010437X11007226</a>."},"quality_controlled":"1","department":[{"_id":"HeEd"}],"title":"Fano 3 folds in codimension 4 Tom and Jerry Part I","date_created":"2018-12-11T12:01:30Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1009.4313"}]},{"publist_id":"3578","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"3121","department":[{"_id":"PeJo"}],"quality_controlled":"1","title":"Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA","date_created":"2018-12-11T12:01:30Z","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431448/"}],"citation":{"mla":"Williams, Courtney, et al. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” <i>Nature Neuroscience</i>, vol. 15, no. 9, Nature Publishing Group, 2012, pp. 1195–97, doi:<a href=\"https://doi.org/10.1038/nn.3162\">10.1038/nn.3162</a>.","ieee":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, and S. Smith, “Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA,” <i>Nature Neuroscience</i>, vol. 15, no. 9. Nature Publishing Group, pp. 1195–1197, 2012.","chicago":"Williams, Courtney, Wenyan Chen, Chia Lee, Daniel Yaeger, Nicholas Vyleta, and Stephen Smith. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2012. <a href=\"https://doi.org/10.1038/nn.3162\">https://doi.org/10.1038/nn.3162</a>.","apa":"Williams, C., Chen, W., Lee, C., Yaeger, D., Vyleta, N., &#38; Smith, S. (2012). Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.3162\">https://doi.org/10.1038/nn.3162</a>","ama":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. <i>Nature Neuroscience</i>. 2012;15(9):1195-1197. doi:<a href=\"https://doi.org/10.1038/nn.3162\">10.1038/nn.3162</a>","short":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, S. Smith, Nature Neuroscience 15 (2012) 1195–1197.","ista":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. 2012. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 15(9), 1195–1197."},"pmid":1,"scopus_import":"1","oa":1,"publication_status":"published","acknowledgement":"The work was supported by the US National Institutes of Health (DA027110 and GM097433) and OCTRI. C.W. and N.P.V. were supported by a grant from the National Heart, Lung, and Blood Institute (T32HL033808).\r\nWe thank M. Andresen and K. Khodakhah for helpful comments. ","month":"09","intvolume":"        15","year":"2012","external_id":{"pmid":["22842148"],"isi":["000308072600008"]},"day":"01","isi":1,"date_updated":"2025-09-30T07:59:27Z","type":"journal_article","publisher":"Nature Publishing Group","author":[{"full_name":"Williams, Courtney","last_name":"Williams","first_name":"Courtney"},{"first_name":"Wenyan","full_name":"Chen, Wenyan","last_name":"Chen"},{"first_name":"Chia","full_name":"Lee, Chia","last_name":"Lee"},{"first_name":"Daniel","last_name":"Yaeger","full_name":"Yaeger, Daniel"},{"id":"36C4978E-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas","last_name":"Vyleta","full_name":"Vyleta, Nicholas"},{"last_name":"Smith","full_name":"Smith, Stephen","first_name":"Stephen"}],"publication":"Nature Neuroscience","issue":"9","status":"public","abstract":[{"lang":"eng","text":"Voltage-activated Ca(2+) channels (VACCs) mediate Ca(2+) influx to trigger action potential-evoked neurotransmitter release, but the mechanism by which Ca(2+) regulates spontaneous transmission is unclear. We found that VACCs are the major physiological triggers for spontaneous release at mouse neocortical inhibitory synapses. Moreover, despite the absence of a synchronizing action potential, we found that spontaneous fusion of a GABA-containing vesicle required the activation of multiple tightly coupled VACCs of variable type."}],"oa_version":"Submitted Version","volume":15,"article_processing_charge":"No","doi":"10.1038/nn.3162","page":"1195 - 1197","language":[{"iso":"eng"}],"date_published":"2012-09-01T00:00:00Z"},{"date_created":"2018-12-11T12:01:31Z","title":"Disassortative mating and the maintenance of sexual polymorphism in painted maple","quality_controlled":"1","department":[{"_id":"NiBa"}],"citation":{"mla":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” <i>Molecular Ecology</i>, vol. 21, no. 15, Wiley-Blackwell, 2012, pp. 3640–43, doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2012.05643.x\">10.1111/j.1365-294X.2012.05643.x</a>.","ieee":"D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual polymorphism in painted maple,” <i>Molecular Ecology</i>, vol. 21, no. 15. Wiley-Blackwell, pp. 3640–3643, 2012.","chicago":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” <i>Molecular Ecology</i>. Wiley-Blackwell, 2012. <a href=\"https://doi.org/10.1111/j.1365-294X.2012.05643.x\">https://doi.org/10.1111/j.1365-294X.2012.05643.x</a>.","apa":"Field, D., &#38; Barrett, S. (2012). Disassortative mating and the maintenance of sexual polymorphism in painted maple. <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-294X.2012.05643.x\">https://doi.org/10.1111/j.1365-294X.2012.05643.x</a>","ama":"Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism in painted maple. <i>Molecular Ecology</i>. 2012;21(15):3640-3643. doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2012.05643.x\">10.1111/j.1365-294X.2012.05643.x</a>","short":"D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643.","ista":"Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643."},"publist_id":"3577","_id":"3122","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        21","external_id":{"isi":["000306478800002"]},"year":"2012","publication_status":"published","scopus_import":"1","month":"08","type":"journal_article","publisher":"Wiley-Blackwell","author":[{"last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barrett, Spencer","last_name":"Barrett","first_name":"Spencer"}],"isi":1,"day":"01","date_updated":"2025-09-30T07:58:59Z","page":"3640 - 3643","doi":"10.1111/j.1365-294X.2012.05643.x","article_processing_charge":"No","volume":21,"date_published":"2012-08-01T00:00:00Z","language":[{"iso":"eng"}],"corr_author":"1","abstract":[{"text":"Since Darwin's pioneering research on plant reproductive biology (e.g. Darwin 1877), understanding the mechanisms maintaining the diverse sexual strategies of plants has remained an important challenge for evolutionary biologists. In some species, populations are sexually polymorphic and contain two or more mating morphs (sex phenotypes). Differences in morphology or phenology among the morphs influence patterns of non-random mating. In these populations, negative frequency-dependent selection arising from disassortative (intermorph) mating is usually required for the evolutionary maintenance of sexual polymorphism, but few studies have demonstrated the required patterns of non-random mating. In the current issue of Molecular Ecology, Shang (2012) make an important contribution to our understanding of how disassortative mating influences sex phenotype ratios in Acer pictum subsp. mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They monitored sex expression in 97 adults and used paternity analysis of open-pollinated seed to examine disassortative mating among three sex phenotypes. Using a deterministic 'pollen transfer' model, Shang et al. present convincing evidence that differences in the degree of disassortative mating in progeny arrays of the sex phenotypes can explain their uneven frequencies in the adult population. This study provides a useful example of how the deployment of genetic markers, demographic monitoring and modelling can be integrated to investigate the maintenance of sexual diversity in plants. ","lang":"eng"}],"status":"public","issue":"15","publication":"Molecular Ecology","oa_version":"None"},{"day":"01","isi":1,"date_updated":"2025-09-30T07:58:32Z","type":"conference","publisher":"Wiley","author":[{"first_name":"Jihun","last_name":"Yu","full_name":"Yu, Jihun"},{"orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","last_name":"Wojtan"},{"first_name":"Greg","last_name":"Turk","full_name":"Turk, Greg"},{"full_name":"Yap, Chee","last_name":"Yap","first_name":"Chee"}],"issue":"2","file":[{"checksum":"acb325dd1e31859bedd30e013f61d0b9","date_created":"2018-12-12T10:14:39Z","relation":"main_file","file_size":5740527,"creator":"system","access_level":"open_access","file_id":"5092","date_updated":"2020-07-14T12:46:00Z","file_name":"IST-2016-601-v1+1_meshSPH.pdf","content_type":"application/pdf"}],"publication":"Computer Graphics Forum","abstract":[{"text":"We introduce the idea of using an explicit triangle mesh to track the air/fluid interface in a smoothed particle hydrodynamics (SPH) simulator. Once an initial surface mesh is created, this mesh is carried forward in time using nearby particle velocities to advect the mesh vertices. The mesh connectivity remains mostly unchanged across time-steps; it is only modified locally for topology change events or for the improvement of triangle quality. In order to ensure that the surface mesh does not diverge from the underlying particle simulation, we periodically project the mesh surface onto an implicit surface defined by the physics simulation. The mesh surface gives us several advantages over previous SPH surface tracking techniques. We demonstrate a new method for surface tension calculations that clearly outperforms the state of the art in SPH surface tension for computer graphics. We also demonstrate a method for tracking detailed surface information (like colors) that is less susceptible to numerical diffusion than competing techniques. Finally, our temporally-coherent surface mesh allows us to simulate high-resolution surface wave dynamics without being limited by the particle resolution of the SPH simulation.","lang":"eng"}],"status":"public","oa_version":"Submitted Version","conference":{"start_date":"2012-05-13","location":"Cagliari, Sardinia, Italy","name":"EUROGRAPHICS: Conference on European Association for Computer Graphics","end_date":"2012-05-18"},"volume":31,"page":"815 - 824","article_processing_charge":"No","doi":"10.1111/j.1467-8659.2012.03062.x","date_published":"2012-05-01T00:00:00Z","language":[{"iso":"eng"}],"pubrep_id":"601","file_date_updated":"2020-07-14T12:46:00Z","publist_id":"3576","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"3123","title":"Explicit mesh surfaces for particle based fluids","quality_controlled":"1","department":[{"_id":"ChWo"}],"date_created":"2018-12-11T12:01:31Z","citation":{"ista":"Yu J, Wojtan C, Turk G, Yap C. 2012. Explicit mesh surfaces for particle based fluids. Computer Graphics Forum. EUROGRAPHICS: Conference on European Association for Computer Graphics, Eurographics, vol. 31, 815–824.","short":"J. Yu, C. Wojtan, G. Turk, C. Yap, in:, Computer Graphics Forum, Wiley, 2012, pp. 815–824.","apa":"Yu, J., Wojtan, C., Turk, G., &#38; Yap, C. (2012). Explicit mesh surfaces for particle based fluids. In <i>Computer Graphics Forum</i> (Vol. 31, pp. 815–824). Cagliari, Sardinia, Italy: Wiley. <a href=\"https://doi.org/10.1111/j.1467-8659.2012.03062.x\">https://doi.org/10.1111/j.1467-8659.2012.03062.x</a>","ama":"Yu J, Wojtan C, Turk G, Yap C. Explicit mesh surfaces for particle based fluids. In: <i>Computer Graphics Forum</i>. Vol 31. Wiley; 2012:815-824. doi:<a href=\"https://doi.org/10.1111/j.1467-8659.2012.03062.x\">10.1111/j.1467-8659.2012.03062.x</a>","chicago":"Yu, Jihun, Chris Wojtan, Greg Turk, and Chee Yap. “Explicit Mesh Surfaces for Particle Based Fluids.” In <i>Computer Graphics Forum</i>, 31:815–24. Wiley, 2012. <a href=\"https://doi.org/10.1111/j.1467-8659.2012.03062.x\">https://doi.org/10.1111/j.1467-8659.2012.03062.x</a>.","ieee":"J. Yu, C. Wojtan, G. Turk, and C. Yap, “Explicit mesh surfaces for particle based fluids,” in <i>Computer Graphics Forum</i>, Cagliari, Sardinia, Italy, 2012, vol. 31, no. 2, pp. 815–824.","mla":"Yu, Jihun, et al. “Explicit Mesh Surfaces for Particle Based Fluids.” <i>Computer Graphics Forum</i>, vol. 31, no. 2, Wiley, 2012, pp. 815–24, doi:<a href=\"https://doi.org/10.1111/j.1467-8659.2012.03062.x\">10.1111/j.1467-8659.2012.03062.x</a>."},"has_accepted_license":"1","alternative_title":["Eurographics"],"scopus_import":"1","oa":1,"publication_status":"published","ddc":["000"],"acknowledgement":"This work was funded by NSF grant IIS-1017014 and CCF- 0917093.","month":"05","intvolume":"        31","external_id":{"isi":["000306182500009"]},"year":"2012"},{"year":"2012","related_material":{"record":[{"id":"5396","status":"public","relation":"later_version"}]},"month":"06","oa":1,"alternative_title":["Inferning 2012"],"ddc":["000"],"publication_status":"published","has_accepted_license":"1","citation":{"ama":"Korc F, Kolmogorov V, Lampert C. Approximating marginals using discrete energy minimization. In: ICML; 2012.","apa":"Korc, F., Kolmogorov, V., &#38; Lampert, C. (2012). Approximating marginals using discrete energy minimization. Presented at the ICML: International Conference on Machine Learning, Edinburgh, Scotland: ICML.","short":"F. Korc, V. Kolmogorov, C. Lampert, in:, ICML, 2012.","ista":"Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete energy minimization. ICML: International Conference on Machine Learning, Inferning 2012, .","mla":"Korc, Filip, et al. <i>Approximating Marginals Using Discrete Energy Minimization</i>. ICML, 2012.","ieee":"F. Korc, V. Kolmogorov, and C. Lampert, “Approximating marginals using discrete energy minimization,” presented at the ICML: International Conference on Machine Learning, Edinburgh, Scotland, 2012.","chicago":"Korc, Filip, Vladimir Kolmogorov, and Christoph Lampert. “Approximating Marginals Using Discrete Energy Minimization.” ICML, 2012."},"department":[{"_id":"ChLa"},{"_id":"VlKo"}],"quality_controlled":"1","title":"Approximating marginals using discrete energy minimization","date_created":"2018-12-11T12:01:31Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3124","publist_id":"3575","pubrep_id":"565","file_date_updated":"2020-07-14T12:46:00Z","date_published":"2012-06-30T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"Submitted Version","conference":{"end_date":"2012-07-01","name":"ICML: International Conference on Machine Learning","start_date":"2012-06-26","location":"Edinburgh, Scotland"},"file":[{"file_size":305836,"creator":"system","file_name":"IST-2016-565-v1+1_DM-inferning2012.pdf","file_id":"4889","date_updated":"2020-07-14T12:46:00Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:11:34Z","checksum":"3d0d4246548c736857302aadb2ff5d15"}],"status":"public","corr_author":"1","abstract":[{"text":"We consider the problem of inference in a graphical model with binary variables. While in theory it is arguably preferable to compute marginal probabilities, in practice researchers often use MAP inference due to the availability of efficient discrete optimization algorithms. We bridge the gap between the two approaches by introducing the Discrete Marginals technique in which approximate marginals are obtained by minimizing an objective function with unary and pairwise terms over a discretized domain. This allows the use of techniques originally developed for MAP-MRF inference and learning. We explore two ways to set up the objective function - by discretizing the Bethe free energy and by learning it from training data. Experimental results show that for certain types of graphs a learned function can outperform the Bethe approximation. We also establish a link between the Bethe free energy and submodular functions.\r\n","lang":"eng"}],"author":[{"last_name":"Korc","full_name":"Korc, Filip","first_name":"Filip","id":"476A2FD6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert"}],"publisher":"ICML","type":"conference","date_updated":"2024-10-09T20:54:48Z","day":"30"},{"intvolume":"      7576","year":"2012","alternative_title":["LNCS"],"scopus_import":1,"oa":1,"publication_status":"published","ddc":["000"],"month":"10","title":"Augmented attribute representations","quality_controlled":"1","department":[{"_id":"ChLa"}],"date_created":"2018-12-11T12:01:32Z","citation":{"ieee":"V. Sharmanska, N. Quadrianto, and C. Lampert, “Augmented attribute representations,” presented at the ECCV: European Conference on Computer Vision, Florence, Italy, 2012, vol. 7576, no. PART 5, pp. 242–255.","chicago":"Sharmanska, Viktoriia, Novi Quadrianto, and Christoph Lampert. “Augmented Attribute Representations,” 7576:242–55. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33715-4_18\">https://doi.org/10.1007/978-3-642-33715-4_18</a>.","mla":"Sharmanska, Viktoriia, et al. <i>Augmented Attribute Representations</i>. Vol. 7576, no. PART 5, Springer, 2012, pp. 242–55, doi:<a href=\"https://doi.org/10.1007/978-3-642-33715-4_18\">10.1007/978-3-642-33715-4_18</a>.","short":"V. Sharmanska, N. Quadrianto, C. Lampert, in:, Springer, 2012, pp. 242–255.","ista":"Sharmanska V, Quadrianto N, Lampert C. 2012. Augmented attribute representations. ECCV: European Conference on Computer Vision, LNCS, vol. 7576, 242–255.","apa":"Sharmanska, V., Quadrianto, N., &#38; Lampert, C. (2012). Augmented attribute representations (Vol. 7576, pp. 242–255). Presented at the ECCV: European Conference on Computer Vision, Florence, Italy: Springer. <a href=\"https://doi.org/10.1007/978-3-642-33715-4_18\">https://doi.org/10.1007/978-3-642-33715-4_18</a>","ama":"Sharmanska V, Quadrianto N, Lampert C. Augmented attribute representations. In: Vol 7576. Springer; 2012:242-255. doi:<a href=\"https://doi.org/10.1007/978-3-642-33715-4_18\">10.1007/978-3-642-33715-4_18</a>"},"has_accepted_license":"1","publist_id":"3574","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3125","volume":7576,"page":"242 - 255","doi":"10.1007/978-3-642-33715-4_18","article_processing_charge":"No","date_published":"2012-10-01T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:00Z","issue":"PART 5","file":[{"file_id":"7861","date_updated":"2020-07-14T12:46:00Z","file_name":"2012_ECCV_Sharmanska.pdf","access_level":"open_access","creator":"dernst","file_size":6073897,"content_type":"application/pdf","relation":"main_file","date_created":"2020-05-15T12:29:04Z","checksum":"bccdbe0663780d25a1e0524002b2d896"}],"abstract":[{"text":"We propose a new learning method to infer a mid-level feature representation that combines the advantage of semantic attribute representations with the higher expressive power of non-semantic features. The idea lies in augmenting an existing attribute-based representation with additional dimensions for which an autoencoder model is coupled with a large-margin principle. This construction allows a smooth transition between the zero-shot regime with no training example, the unsupervised regime with training examples but without class labels, and the supervised regime with training examples and with class labels. The resulting optimization problem can be solved efficiently, because several of the necessity steps have closed-form solutions. Through extensive experiments we show that the augmented representation achieves better results in terms of object categorization accuracy than the semantic representation alone.","lang":"eng"}],"status":"public","oa_version":"Submitted Version","conference":{"name":"ECCV: European Conference on Computer Vision","start_date":"2012-10-07","location":"Florence, Italy","end_date":"2012-10-13"},"type":"conference","author":[{"id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","first_name":"Viktoriia","orcid":"0000-0003-0192-9308","last_name":"Sharmanska","full_name":"Sharmanska, Viktoriia"},{"last_name":"Quadrianto","full_name":"Quadrianto, Novi","first_name":"Novi"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"}],"publisher":"Springer","day":"01","date_updated":"2023-02-23T11:13:25Z"},{"publisher":"Springer","author":[{"first_name":"Andreas","full_name":"Müller, Andreas","last_name":"Müller"},{"last_name":"Nowozin","full_name":"Nowozin, Sebastian","first_name":"Sebastian"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert"}],"citation":{"chicago":"Müller, Andreas, Sebastian Nowozin, and Christoph Lampert. “Information Theoretic Clustering Using Minimal Spanning Trees,” 7476:205–15. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-32717-9_21\">https://doi.org/10.1007/978-3-642-32717-9_21</a>.","ieee":"A. Müller, S. Nowozin, and C. Lampert, “Information theoretic clustering using minimal spanning trees,” presented at the DAGM: German Association For Pattern Recognition, Graz, Austria, 2012, vol. 7476, pp. 205–215.","mla":"Müller, Andreas, et al. <i>Information Theoretic Clustering Using Minimal Spanning Trees</i>. Vol. 7476, Springer, 2012, pp. 205–15, doi:<a href=\"https://doi.org/10.1007/978-3-642-32717-9_21\">10.1007/978-3-642-32717-9_21</a>.","ista":"Müller A, Nowozin S, Lampert C. 2012. Information theoretic clustering using minimal spanning trees. DAGM: German Association For Pattern Recognition, LNCS, vol. 7476, 205–215.","short":"A. Müller, S. Nowozin, C. Lampert, in:, Springer, 2012, pp. 205–215.","apa":"Müller, A., Nowozin, S., &#38; Lampert, C. (2012). Information theoretic clustering using minimal spanning trees (Vol. 7476, pp. 205–215). Presented at the DAGM: German Association For Pattern Recognition, Graz, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-642-32717-9_21\">https://doi.org/10.1007/978-3-642-32717-9_21</a>","ama":"Müller A, Nowozin S, Lampert C. Information theoretic clustering using minimal spanning trees. In: Vol 7476. Springer; 2012:205-215. doi:<a href=\"https://doi.org/10.1007/978-3-642-32717-9_21\">10.1007/978-3-642-32717-9_21</a>"},"date_created":"2018-12-11T12:01:32Z","type":"conference","department":[{"_id":"ChLa"}],"quality_controlled":"1","title":"Information theoretic clustering using minimal spanning trees","_id":"3126","date_updated":"2021-01-12T07:41:14Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"14","publist_id":"3573","year":"2012","language":[{"iso":"eng"}],"date_published":"2012-08-14T00:00:00Z","doi":"10.1007/978-3-642-32717-9_21","intvolume":"      7476","page":"205 - 215","volume":7476,"month":"08","conference":{"end_date":"2012-08-31","start_date":"2012-08-28","location":"Graz, Austria","name":"DAGM: German Association For Pattern Recognition"},"oa_version":"None","status":"public","publication_status":"published","abstract":[{"text":"In this work we propose a new information-theoretic clustering algorithm that infers cluster memberships by direct optimization of a non-parametric mutual information estimate between data distribution and cluster assignment. Although the optimization objective has a solid theoretical foundation it is hard to optimize. We propose an approximate optimization formulation that leads to an efficient algorithm with low runtime complexity. The algorithm has a single free parameter, the number of clusters to find. We demonstrate superior performance on several synthetic and real datasets.\r\n","lang":"eng"}],"scopus_import":1,"alternative_title":["LNCS"]},{"oa":1,"publication":"Proceedings of the 29th International Conference on Machine Learning","scopus_import":"1","abstract":[{"text":"When searching for characteristic subpatterns in potentially noisy graph data, it appears self-evident that having multiple observations would be better than having just one. However, it turns out that the inconsistencies introduced when different graph instances have different edge sets pose a serious challenge. In this work we address this challenge for the problem of finding maximum weighted cliques.\r\n    We introduce the concept of most persistent soft-clique. This is subset of vertices, that 1) is almost fully or at least densely connected, 2) occurs in all or almost all graph instances, and 3) has the maximum weight. We present a measure of clique-ness, that essentially counts the number of edge missing to make a subset of vertices into a clique. With this measure, we show that the problem of finding the most persistent soft-clique problem can be cast either as: a) a max-min two person game optimization problem, or b) a min-min soft margin optimization problem. Both formulations lead to the same solution when using a partial Lagrangian method to solve the optimization problems. By experiments on synthetic data and on real social network data, we show that the proposed method is able to reliably find soft cliques in graph data, even if that is distorted by random noise or unreliable observations.","lang":"eng"}],"publication_status":"published","status":"public","oa_version":"Preprint","conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2012-06-26","location":"Edinburgh, United Kingdom","end_date":"2012-07-01"},"month":"06","page":"211-218","article_processing_charge":"No","date_published":"2012-06-01T00:00:00Z","language":[{"iso":"eng"}],"arxiv":1,"external_id":{"arxiv":["1206.4652"]},"year":"2012","publist_id":"3572","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-11T08:09:42Z","_id":"3127","title":"The most persistent soft-clique in a set of sampled graphs","quality_controlled":"1","department":[{"_id":"ChLa"},{"_id":"HeEd"}],"type":"conference","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1206.4652"}],"date_created":"2018-12-11T12:01:33Z","citation":{"ama":"Quadrianto N, Lampert C, Chen C. The most persistent soft-clique in a set of sampled graphs. In: <i>Proceedings of the 29th International Conference on Machine Learning</i>. ML Research Press; 2012:211-218.","apa":"Quadrianto, N., Lampert, C., &#38; Chen, C. (2012). The most persistent soft-clique in a set of sampled graphs. In <i>Proceedings of the 29th International Conference on Machine Learning</i> (pp. 211–218). Edinburgh, United Kingdom: ML Research Press.","short":"N. Quadrianto, C. Lampert, C. Chen, in:, Proceedings of the 29th International Conference on Machine Learning, ML Research Press, 2012, pp. 211–218.","ista":"Quadrianto N, Lampert C, Chen C. 2012. The most persistent soft-clique in a set of sampled graphs. Proceedings of the 29th International Conference on Machine Learning. ICML: International Conference on Machine Learning, 211–218.","mla":"Quadrianto, Novi, et al. “The Most Persistent Soft-Clique in a Set of Sampled Graphs.” <i>Proceedings of the 29th International Conference on Machine Learning</i>, ML Research Press, 2012, pp. 211–18.","ieee":"N. Quadrianto, C. Lampert, and C. Chen, “The most persistent soft-clique in a set of sampled graphs,” in <i>Proceedings of the 29th International Conference on Machine Learning</i>, Edinburgh, United Kingdom, 2012, pp. 211–218.","chicago":"Quadrianto, Novi, Christoph Lampert, and Chao Chen. “The Most Persistent Soft-Clique in a Set of Sampled Graphs.” In <i>Proceedings of the 29th International Conference on Machine Learning</i>, 211–18. ML Research Press, 2012."},"publisher":"ML Research Press","author":[{"first_name":"Novi","last_name":"Quadrianto","full_name":"Quadrianto, Novi"},{"full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"full_name":"Chen, Chao","last_name":"Chen","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"}]}]