[{"month":"03","department":[{"_id":"DaZi"}],"publisher":"Public Library of Science","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pgen.1002512"}],"scopus_import":"1","status":"public","language":[{"iso":"eng"}],"date_published":"2012-03-22T00:00:00Z","doi":"10.1371/journal.pgen.1002512","extern":"1","intvolume":"         8","volume":8,"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"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.","lang":"eng"}],"article_type":"original","publication_status":"published","article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","_id":"9499","year":"2012","date_created":"2021-06-07T11:07:56Z","pmid":1,"title":"EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development","external_id":{"pmid":["22457632"]},"article_number":"e1002512","issue":"3","author":[{"full_name":"Kim, Sang Yeol","first_name":"Sang Yeol","last_name":"Kim"},{"last_name":"Lee","first_name":"Jungeun","full_name":"Lee, Jungeun"},{"last_name":"Eshed-Williams","first_name":"Leor","full_name":"Eshed-Williams, Leor"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel"},{"full_name":"Sung, Z. Renee","first_name":"Z. Renee","last_name":"Sung"}],"citation":{"short":"S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (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>.","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.","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>"},"date_updated":"2021-12-14T08:31:14Z","oa":1,"publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"publication":"PLoS Genetics","day":"22"},{"status":"public","language":[{"iso":"eng"}],"date_published":"2012-04-01T00:00:00Z","doi":"10.1016/j.gde.2012.01.007","extern":"1","intvolume":"        22","volume":22,"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"04","publisher":"Elsevier","department":[{"_id":"DaZi"}],"page":"132-138","scopus_import":"1","title":"Regulation of biological accuracy, precision, and memory by plant chromatin organization","external_id":{"pmid":["22336527"]},"issue":"2","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>.","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.","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>.","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>","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>","short":"J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138."},"date_updated":"2021-12-14T08:32:38Z","author":[{"full_name":"Huff, Jason T.","first_name":"Jason T.","last_name":"Huff"},{"last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"}],"publication_identifier":{"issn":["0959-437X"]},"publication":"Current Opinion in Genetics and Development","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"}],"article_type":"review","publication_status":"published","article_processing_charge":"No","oa_version":"None","quality_controlled":"1","_id":"9528","year":"2012","date_created":"2021-06-08T08:58:52Z","pmid":1},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","volume":77,"intvolume":"        77","extern":"1","doi":"10.1101/sqb.2012.77.014944","date_published":"2012-12-18T00:00:00Z","language":[{"iso":"eng"}],"status":"public","scopus_import":"1","page":"147-154","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/sqb.2012.77.014944"}],"department":[{"_id":"DaZi"}],"publisher":"Cold Spring Harbor Laboratory Press","month":"12","day":"18","publication":"Cold Spring Harbor Symposia on Quantitative Biology","publication_identifier":{"issn":["0091-7451"],"eissn":["1943-4456"]},"oa":1,"citation":{"short":"D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative Biology 77 (2012) 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.","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>","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>.","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."},"author":[{"last_name":"Coleman-Derr","first_name":"D.","full_name":"Coleman-Derr, D."},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman"}],"date_updated":"2021-12-14T08:33:09Z","title":"DNA methylation, H2A.Z, and the regulation of constitutive expression","external_id":{"pmid":["23250988"]},"pmid":1,"date_created":"2021-06-08T13:01:23Z","year":"2012","_id":"9535","quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"No","publication_status":"published","article_type":"review","abstract":[{"lang":"eng","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."}]},{"_id":"9755","year":"2012","date_created":"2021-07-30T08:39:13Z","abstract":[{"lang":"eng","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”)."}],"month":"09","publisher":"Dryad","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"3242"}]},"department":[{"_id":"SyCr"}],"article_processing_charge":"No","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5061/dryad.sv37s","open_access":"1"}],"author":[{"full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Konrad"},{"id":"418901AA-F248-11E8-B48F-1D18A9856A87","full_name":"Vyleta, Meghan","last_name":"Vyleta","first_name":"Meghan"},{"first_name":"Fabian","last_name":"Theis","full_name":"Theis, Fabian"},{"first_name":"Miriam","last_name":"Stock","id":"42462816-F248-11E8-B48F-1D18A9856A87","full_name":"Stock, Miriam"},{"full_name":"Klatt, Martina","id":"E60F29C6-E9AE-11E9-AF6E-D190C7302F38","first_name":"Martina","last_name":"Klatt"},{"last_name":"Drescher","first_name":"Verena","full_name":"Drescher, Verena"},{"full_name":"Marr, Carsten","first_name":"Carsten","last_name":"Marr"},{"last_name":"Ugelvig","first_name":"Line V","full_name":"Ugelvig, Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"}],"date_updated":"2023-02-23T11:18:41Z","citation":{"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>.","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>.","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>.","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>","ieee":"M. Konrad <i>et al.</i>, “Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies.” Dryad, 2012.","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>","short":"M. Konrad, M. Vyleta, F. Theis, M. Stock, M. Klatt, V. Drescher, C. Marr, L.V. Ugelvig, S. Cremer, (2012)."},"type":"research_data_reference","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"27","title":"Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies","status":"public","date_published":"2012-09-27T00:00:00Z","doi":"10.5061/dryad.sv37s"},{"type":"research_data_reference","citation":{"short":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer, (2012).","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>.","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.","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>","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>."},"author":[{"first_name":"Simon","last_name":"Tragust","full_name":"Tragust, Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Barbara","last_name":"Mitteregger","id":"479DDAAC-E9CD-11E9-9B5F-82450873F7A1","full_name":"Mitteregger, 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"},{"last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"date_updated":"2023-02-23T11:04:28Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"day":"14","status":"public","title":"Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison","doi":"10.5061/dryad.61649","date_published":"2012-12-14T00:00:00Z","year":"2012","_id":"9757","date_created":"2021-07-30T12:31:31Z","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"}],"publisher":"Dryad","related_material":{"record":[{"id":"2926","status":"public","relation":"used_in_publication"}]},"department":[{"_id":"SyCr"}],"month":"12","oa_version":"Published Version","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5061/dryad.61649","open_access":"1"}]},{"year":"2012","_id":"9758","date_created":"2021-07-30T12:36:39Z","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."}],"related_material":{"record":[{"relation":"used_in_publication","id":"2944","status":"public"}]},"publisher":"Dryad","department":[{"_id":"NiBa"}],"month":"11","oa_version":"Published Version","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.274b1"}],"type":"research_data_reference","date_updated":"2023-02-23T11:05:19Z","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>.","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>","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.","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>.","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)."},"author":[{"id":"2D35326E-F248-11E8-B48F-1D18A9856A87","full_name":"Aeschbacher, Simon","first_name":"Simon","last_name":"Aeschbacher"},{"full_name":"Futschik, Andreas","first_name":"Andreas","last_name":"Futschik"},{"full_name":"Beaumont, Mark","last_name":"Beaumont","first_name":"Mark"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"day":"14","status":"public","title":"Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates","doi":"10.5061/dryad.274b1","date_published":"2012-11-14T00:00:00Z"},{"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","oa_version":"None","article_processing_charge":"No","quality_controlled":"1","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","author":[{"last_name":"Artner","first_name":"Nicole M.","full_name":"Artner, Nicole M."},{"first_name":"Adrian","last_name":"Ion","id":"29F89302-F248-11E8-B48F-1D18A9856A87","full_name":"Ion, Adrian"},{"first_name":"Walter G.","last_name":"Kropatsch","full_name":"Kropatsch, Walter G."}],"date_updated":"2023-09-05T14:10:15Z","citation":{"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>.","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.","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>","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>","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>.","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."},"publication":"Graph-Based Representations in Pattern Recognition","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783642208430"],"eisbn":["9783642208447"]},"day":"01","publisher":"Springer","department":[{"_id":"HeEd"}],"editor":[{"last_name":"Jiang","first_name":"Xiaoyi","full_name":"Jiang, Xiaoyi"},{"last_name":"Ferrer","first_name":"Miquel","full_name":"Ferrer, Miquel"},{"full_name":"Torsello, Andrea","last_name":"Torsello","first_name":"Andrea"}],"month":"06","conference":{"end_date":"2011-05-20","name":"GbRPR: Graph-based Representations in Pattern Recognition","location":"Münster, Germany","start_date":"2011-05-18"},"page":"215-224","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.","language":[{"iso":"eng"}],"status":"public","doi":"10.1007/978-3-642-20844-7_22","date_published":"2011-06-01T00:00:00Z","intvolume":"      6658","alternative_title":["LNCS"],"volume":6658,"type":"conference","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"month":"12","publisher":"Neural Information Processing Systems","related_material":{"record":[{"id":"3322","status":"public","relation":"later_version"}]},"publication_status":"published","department":[{"_id":"ChLa"}],"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","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","_id":"3163","year":"2011","scopus_import":1,"date_published":"2011-12-01T00:00:00Z","title":"Maximum margin multi-label structured prediction","status":"public","language":[{"iso":"eng"}],"citation":{"short":"C. Lampert, in:, 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.","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."},"author":[{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"date_updated":"2023-10-17T11:47:35Z","type":"conference","publist_id":"3522","day":"01","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"date_updated":"2021-01-12T07:42:15Z","type":"conference","citation":{"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.","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>.","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>","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>","short":"A. Gupta, C. Popeea, A. Rybalchenko, in:, H. Yang (Ed.), Springer, 2011, pp. 188–203."},"author":[{"full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","last_name":"Gupta"},{"last_name":"Popeea","first_name":"Corneliu","full_name":"Popeea, Corneliu"},{"last_name":"Rybalchenko","first_name":"Andrey","full_name":"Rybalchenko, Andrey"}],"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":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"title":"Solving recursion-free Horn clauses over LI+UIF","status":"public","intvolume":"      7078","alternative_title":["LNCS"],"conference":{"end_date":"2011-12-07","start_date":"2011-12-05","name":"APLAS: Asian Symposium on Programming Languages and Systems","location":"Kenting, Taiwan"},"page":"188 - 203","date_created":"2018-12-11T12:02:20Z","ec_funded":1,"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"},{"date_published":"2011-12-01T00:00:00Z","title":"Probabilistic joint image segmentation and labeling","status":"public","language":[{"iso":"eng"}],"intvolume":"        24","type":"conference","citation":{"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.","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.","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.","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.","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.","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.","short":"A. Ion, J. Carreira, C. Sminchisescu, in:, NIPS Proceedings, Neural Information Processing Systems Foundation, 2011, pp. 1827–1835."},"author":[{"id":"29F89302-F248-11E8-B48F-1D18A9856A87","full_name":"Ion, Adrian","last_name":"Ion","first_name":"Adrian"},{"first_name":"Joao","last_name":"Carreira","full_name":"Carreira, Joao"},{"first_name":"Cristian","last_name":"Sminchisescu","full_name":"Sminchisescu, Cristian"}],"date_updated":"2021-01-12T07:42:15Z","volume":24,"publist_id":"3381","day":"01","publication":"NIPS Proceedings","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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","page":"1827 - 1835","conference":{"location":"Granada, Spain","name":"NIPS: Neural Information Processing Systems","start_date":"2011-12-12","end_date":"2011-12-14"},"date_created":"2018-12-11T12:02:21Z","_id":"3266","scopus_import":1,"year":"2011"},{"author":[{"last_name":"Chen","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao"},{"full_name":"Freedman, Daniel","first_name":"Daniel","last_name":"Freedman"}],"citation":{"short":"C. Chen, D. Freedman, Discrete &#38; Computational Geometry 45 (2011) 425–448.","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>","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.","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>","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>.","ista":"Chen C, Freedman D. 2011. Hardness results for homology localization. Discrete &#38; Computational Geometry. 45(3), 425–448.","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>."},"date_updated":"2023-02-21T16:07:10Z","type":"journal_article","volume":45,"publist_id":"3379","day":"14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Discrete & Computational Geometry","date_published":"2011-01-14T00:00:00Z","doi":"10.1007/s00454-010-9322-8","status":"public","title":"Hardness results for homology localization","language":[{"iso":"eng"}],"intvolume":"        45","issue":"3","page":"425 - 448","date_created":"2018-12-11T12:02:21Z","_id":"3267","scopus_import":1,"year":"2011","month":"01","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10909"}]},"publisher":"Springer","publication_status":"published","department":[{"_id":"HeEd"}],"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"}],"quality_controlled":"1","oa_version":"None"},{"main_file_link":[{"open_access":"1","url":"http://www.cs.cmu.edu/%7Eshengyu/download/egsr2011_paper.pdf"}],"month":"07","publisher":"Wiley-Blackwell","department":[{"_id":"HeEd"}],"scopus_import":1,"page":"1261 - 1268","intvolume":"        30","date_published":"2011-07-19T00:00:00Z","doi":"10.1111/j.1467-8659.2011.01985.x","status":"public","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":30,"quality_controlled":"1","article_processing_charge":"No","oa_version":"Published Version","article_type":"original","publication_status":"published","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"}],"date_created":"2018-12-11T12:02:22Z","_id":"3269","year":"2011","issue":"4","title":"Perceptual global illumination cancellation in complex projection environments","publist_id":"3377","day":"19","oa":1,"publication":"Computer Graphics Forum","date_updated":"2021-01-12T07:42:16Z","citation":{"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>.","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.","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>","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>","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>.","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.","short":"Y. Sheng, B. Cutler, C. Chen, J. Nasman, Computer Graphics Forum 30 (2011) 1261–1268."},"author":[{"last_name":"Sheng","first_name":"Yu","full_name":"Sheng, Yu"},{"last_name":"Cutler","first_name":"Barbara","full_name":"Cutler, Barbara"},{"full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chao"},{"full_name":"Nasman, Joshua","first_name":"Joshua","last_name":"Nasman"}]},{"date_published":"2011-01-01T00:00:00Z","language":[{"iso":"eng"}],"title":"Persistent homology computation with a twist","status":"public","day":"01","publist_id":"3376","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"conference","citation":{"mla":"Chen, Chao, and Michael Kerber. <i>Persistent Homology Computation with a Twist</i>. TU Dortmund, 2011, pp. 197–200.","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.","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.","ama":"Chen C, Kerber M. Persistent homology computation with a twist. In: TU Dortmund; 2011:197-200.","chicago":"Chen, Chao, and Michael Kerber. “Persistent Homology Computation with a Twist,” 197–200. TU Dortmund, 2011.","ista":"Chen C, Kerber M. 2011. Persistent homology computation with a twist. EuroCG: European Workshop on Computational Geometry, 197–200.","short":"C. Chen, M. Kerber, in:, TU Dortmund, 2011, pp. 197–200."},"author":[{"full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chao"},{"orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","full_name":"Kerber, Michael","last_name":"Kerber","first_name":"Michael"}],"date_updated":"2021-01-12T07:42:17Z","quality_controlled":"1","oa_version":"None","publisher":"TU Dortmund","publication_status":"published","department":[{"_id":"HeEd"}],"month":"01","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"}],"date_created":"2018-12-11T12:02:22Z","year":"2011","_id":"3270","page":"197 - 200","conference":{"end_date":"2011-03-30","name":"EuroCG: European Workshop on Computational Geometry","start_date":"2011-03-28","location":"Morschach, Switzerland"}},{"day":"14","publist_id":"3375","publication":"Topological Methods in Data Analysis and Visualization II","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","date_updated":"2021-01-12T07:42:18Z","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.","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>.","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>."},"author":[{"first_name":"Hubert","last_name":"Wagner","full_name":"Wagner, Hubert"},{"full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","last_name":"Chen"},{"full_name":"Vuçini, Erald","first_name":"Erald","last_name":"Vuçini"}],"alternative_title":["Theory, Algorithms, and Applications"],"doi":"10.1007/978-3-642-23175-9_7","date_published":"2011-11-14T00:00:00Z","language":[{"iso":"eng"}],"title":"Efficient computation of persistent homology for cubical data","status":"public","date_created":"2018-12-11T12:02:23Z","year":"2011","scopus_import":1,"_id":"3271","page":"91 - 106","quality_controlled":"1","oa_version":"None","publisher":"Springer","department":[{"_id":"HeEd"}],"publication_status":"published","month":"11","editor":[{"first_name":"Ronald","last_name":"Peikert","full_name":"Peikert, Ronald"},{"full_name":"Hauser, Helwig","last_name":"Hauser","first_name":"Helwig"},{"last_name":"Carr","first_name":"Hamish","full_name":"Carr, Hamish"},{"first_name":"Raphael","last_name":"Fuchs","full_name":"Fuchs, Raphael"}],"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.","apa":"Maître, J.-L. (2011). <i>Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors</i>. Institute of Science and Technology Austria.","ama":"Maître J-L. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. 2011.","ieee":"J.-L. Maître, “Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors,” Institute of Science and Technology Austria, 2011.","mla":"Maître, Jean-Léon. <i>Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors</i>. 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.","chicago":"Maître, Jean-Léon. “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","orcid":"0000-0002-3688-1474","full_name":"Maître, Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87"}],"supervisor":[{"last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"publist_id":"3373","day":"12","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"date_published":"2011-12-12T00:00:00Z","status":"public","title":"Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"]},{"supervisor":[{"first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"}],"citation":{"short":"K. Schumann, The Role of Chemotactic Gradients in Dendritic Cell Migration, 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.","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.","ieee":"K. Schumann, “The role of chemotactic gradients in dendritic cell migration,” Institute of Science and Technology Austria, 2011.","mla":"Schumann, Kathrin. <i>The Role of Chemotactic Gradients in Dendritic Cell Migration</i>. Institute of Science and Technology Austria, 2011."},"date_updated":"2023-09-07T11:31:48Z","author":[{"full_name":"Schumann, Kathrin","id":"F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F","first_name":"Kathrin","last_name":"Schumann"}],"publication_identifier":{"issn":["2663-337X"]},"oa":1,"day":"01","publist_id":"3371","title":"The role of chemotactic gradients in dendritic cell migration","has_accepted_license":"1","year":"2011","_id":"3275","date_created":"2018-12-11T12:02:24Z","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","file_size":4487708,"content_type":"application/pdf","checksum":"e69eee6252660f0b694a2ea8923ddc72"},{"file_id":"9175","date_created":"2021-02-22T11:24:30Z","relation":"main_file","success":1,"file_name":"2011_Thesis_Schumann_noS.pdf","date_updated":"2021-02-22T11:24:30Z","file_size":4313127,"content_type":"application/pdf","checksum":"71727d63f424b5b446f68f4b87ecadc0","access_level":"open_access","creator":"dernst"}],"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. "}],"publication_status":"published","oa_version":"Published Version","article_processing_charge":"No","pubrep_id":"11","type":"dissertation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2021-02-22T11:24:30Z","language":[{"iso":"eng"}],"status":"public","date_published":"2011-03-01T00:00:00Z","alternative_title":["ISTA Thesis"],"ddc":["570","579"],"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. ","department":[{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","month":"03","degree_awarded":"PhD"},{"author":[{"first_name":"Verena","last_name":"Ruprecht","full_name":"Ruprecht, Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4088-8633"},{"full_name":"Axmann, Markus","first_name":"Markus","last_name":"Axmann"},{"id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","full_name":"Wieser, Stefan","orcid":"0000-0002-2670-2217","first_name":"Stefan","last_name":"Wieser"},{"full_name":"Schuetz, Gerhard","first_name":"Gerhard","last_name":"Schuetz"}],"type":"journal_article","citation":{"ista":"Ruprecht V, Axmann M, Wieser S, Schuetz G. 2011. What can we learn from single molecule trajectories? Current Protein &#38; Peptide Science. 12(8), 714–724.","chicago":"Ruprecht, Verena, Markus Axmann, Stefan Wieser, and Gerhard Schuetz. “What Can We Learn from Single Molecule Trajectories?” <i>Current Protein &#38; Peptide Science</i>. Bentham Science Publishers, 2011. <a href=\"https://doi.org/10.2174/138920311798841753\">https://doi.org/10.2174/138920311798841753</a>.","ama":"Ruprecht V, Axmann M, Wieser S, Schuetz G. What can we learn from single molecule trajectories? <i>Current Protein &#38; Peptide Science</i>. 2011;12(8):714-724. doi:<a href=\"https://doi.org/10.2174/138920311798841753\">10.2174/138920311798841753</a>","ieee":"V. Ruprecht, M. Axmann, S. Wieser, and G. Schuetz, “What can we learn from single molecule trajectories?,” <i>Current Protein &#38; Peptide Science</i>, vol. 12, no. 8. Bentham Science Publishers, pp. 714–724, 2011.","apa":"Ruprecht, V., Axmann, M., Wieser, S., &#38; Schuetz, G. (2011). What can we learn from single molecule trajectories? <i>Current Protein &#38; Peptide Science</i>. Bentham Science Publishers. <a href=\"https://doi.org/10.2174/138920311798841753\">https://doi.org/10.2174/138920311798841753</a>","mla":"Ruprecht, Verena, et al. “What Can We Learn from Single Molecule Trajectories?” <i>Current Protein &#38; Peptide Science</i>, vol. 12, no. 8, Bentham Science Publishers, 2011, pp. 714–24, doi:<a href=\"https://doi.org/10.2174/138920311798841753\">10.2174/138920311798841753</a>.","short":"V. Ruprecht, M. Axmann, S. Wieser, G. Schuetz, Current Protein &#38; Peptide Science 12 (2011) 714–724."},"date_updated":"2021-01-12T07:42:24Z","volume":12,"publist_id":"3358","day":"01","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication":"Current Protein & Peptide Science","date_published":"2011-12-01T00:00:00Z","doi":"10.2174/138920311798841753","title":"What can we learn from single molecule trajectories?","status":"public","language":[{"iso":"eng"}],"intvolume":"        12","issue":"8","page":"714 - 724","date_created":"2018-12-11T12:02:28Z","_id":"3287","scopus_import":1,"year":"2011","month":"12","publisher":"Bentham Science Publishers","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"publication_status":"published","abstract":[{"text":"Diffusing membrane constituents are constantly exposed to a variety of forces that influence their stochastic path. Single molecule experiments allow for resolving trajectories at extremely high spatial and temporal accuracy, thereby offering insights into en route interactions of the tracer. In this review we discuss approaches to derive information about the underlying processes, based on single molecule tracking experiments. In particular, we focus on a new versatile way to analyze single molecule diffusion in the absence of a full analytical treatment. The method is based on comprehensive comparison of an experimental data set against the hypothetical outcome of multiple experiments performed on the computer. Since Monte Carlo simulations can be easily and rapidly performed even on state-of-the-art PCs, our method provides a simple way for testing various - even complicated - diffusion models. We describe the new method in detail, and show the applicability on two specific examples: firstly, kinetic rate constants can be derived for the transient interaction of mobile membrane proteins; secondly, residence time and corral size can be extracted for confined diffusion.","lang":"eng"}],"quality_controlled":"1","oa_version":"None"},{"issue":"7","has_accepted_license":"1","title":"Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens","oa":1,"publication":"PLoS One","publist_id":"3357","day":"22","citation":{"short":"M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011).","chicago":"Smutny, Michael, Selwin Wu, Guillermo Gomez, Sabine Mangold, Alpha Yap, and Nicholas Hamilton. “Multicomponent Analysis of Junctional Movements Regulated by Myosin II Isoforms at the Epithelial Zonula Adherens.” <i>PLoS One</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pone.0022458\">https://doi.org/10.1371/journal.pone.0022458</a>.","ista":"Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. 2011. Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. PLoS One. 6(7).","mla":"Smutny, Michael, et al. “Multicomponent Analysis of Junctional Movements Regulated by Myosin II Isoforms at the Epithelial Zonula Adherens.” <i>PLoS One</i>, vol. 6, no. 7, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pone.0022458\">10.1371/journal.pone.0022458</a>.","ama":"Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. <i>PLoS One</i>. 2011;6(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0022458\">10.1371/journal.pone.0022458</a>","apa":"Smutny, M., Wu, S., Gomez, G., Mangold, S., Yap, A., &#38; Hamilton, N. (2011). Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0022458\">https://doi.org/10.1371/journal.pone.0022458</a>","ieee":"M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, and N. Hamilton, “Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens,” <i>PLoS One</i>, vol. 6, no. 7. Public Library of Science, 2011."},"date_updated":"2021-01-12T07:42:25Z","author":[{"last_name":"Smutny","first_name":"Michael","orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wu","first_name":"Selwin","full_name":"Wu, Selwin"},{"full_name":"Gomez, Guillermo","last_name":"Gomez","first_name":"Guillermo"},{"full_name":"Mangold, Sabine","first_name":"Sabine","last_name":"Mangold"},{"full_name":"Yap, Alpha","last_name":"Yap","first_name":"Alpha"},{"last_name":"Hamilton","first_name":"Nicholas","full_name":"Hamilton, Nicholas"}],"oa_version":"Published Version","quality_controlled":"1","abstract":[{"text":"The zonula adherens (ZA) of epithelial cells is a site of cell-cell adhesion where cellular forces are exerted and resisted. Increasing evidence indicates that E-cadherin adhesion molecules at the ZA serve to sense force applied on the junctions and coordinate cytoskeletal responses to those forces. Efforts to understand the role that cadherins play in mechanotransduction have been limited by the lack of assays to measure the impact of forces on the ZA. In this study we used 4D imaging of GFP-tagged E-cadherin to analyse the movement of the ZA. Junctions in confluent epithelial monolayers displayed prominent movements oriented orthogonal (perpendicular) to the ZA itself. Two components were identified in these movements: a relatively slow unidirectional (translational) component that could be readily fitted by least-squares regression analysis, upon which were superimposed more rapid oscillatory movements. Myosin IIB was a dominant factor responsible for driving the unilateral translational movements. In contrast, frequency spectrum analysis revealed that depletion of Myosin IIA increased the power of the oscillatory movements. This implies that Myosin IIA may serve to dampen oscillatory movements of the ZA. This extends our recent analysis of Myosin II at the ZA to demonstrate that Myosin IIA and Myosin IIB make distinct contributions to junctional movement at the ZA.","lang":"eng"}],"file":[{"checksum":"57a5eb11dd05241c48c44f492b3ec3ac","content_type":"application/pdf","file_size":1984567,"creator":"dernst","access_level":"open_access","file_name":"2011_PLOS_Smutny.PDF","date_created":"2019-05-10T10:51:43Z","relation":"main_file","file_id":"6399","date_updated":"2020-07-14T12:46:06Z"}],"publication_status":"published","_id":"3288","year":"2011","date_created":"2018-12-11T12:02:28Z","ddc":["570"],"intvolume":"         6","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"date_published":"2011-07-22T00:00:00Z","doi":"10.1371/journal.pone.0022458","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:46:06Z","volume":6,"type":"journal_article","month":"07","publisher":"Public Library of Science","department":[{"_id":"CaHe"}],"acknowledgement":"his work was funded by the National Health and Medical Research Council (NHMRC) of Australia. M.S. was an Erwin Schroedinger postdoctoral fellow of the Austrian Science Fund (FWF), S.K.W. is supported by a UQ International Research Tuition Award and Research Scholarship, S.M .by an ANZ Trustees PhD Scholarship. A.S.Y. is a Research Fellow of the NHMRC. Confocal imaging was performed at the Australian Cancer Research Foundation (ACRF) Cancer Biology Imaging Centre at the Institute for Molecular Bioscience, established with the generous support of the ACRF."},{"page":"977 - 987","scopus_import":1,"month":"11","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/","open_access":"1"}],"type":"journal_article","volume":189,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_published":"2011-11-01T00:00:00Z","doi":"10.1534/genetics.111.129569","status":"public","language":[{"iso":"eng"}],"intvolume":"       189","date_created":"2018-12-11T12:02:29Z","ec_funded":1,"_id":"3290","year":"2011","publication_status":"published","abstract":[{"lang":"eng","text":"Analysis of genomic data requires an efficient way to calculate likelihoods across very large numbers of loci. We describe a general method for finding the distribution of genealogies: we allow migration between demes, splitting of demes [as in the isolation-with-migration (IM) model], and recombination between linked loci. These processes are described by a set of linear recursions for the generating function of branch lengths. Under the infinite-sites model, the probability of any configuration of mutations can be found by differentiating this generating function. Such calculations are feasible for small numbers of sampled genomes: as an example, we show how the generating function can be derived explicitly for three genes under the two-deme IM model. This derivation is done automatically, using Mathematica. Given data from a large number of unlinked and nonrecombining blocks of sequence, these results can be used to find maximum-likelihood estimates of model parameters by tabulating the probabilities of all relevant mutational configurations and then multiplying across loci. The feasibility of the method is demonstrated by applying it to simulated data and to a data set previously analyzed by Wang and Hey (2010) consisting of 26,141 loci sampled from Drosophila simulans and D. melanogaster. Our results suggest that such likelihood calculations are scalable to genomic data as long as the numbers of sampled individuals and mutations per sequence block are small."}],"quality_controlled":"1","oa_version":"Submitted Version","date_updated":"2021-01-12T07:42:26Z","author":[{"full_name":"Lohse, Konrad","first_name":"Konrad","last_name":"Lohse"},{"full_name":"Harrison, Richard","last_name":"Harrison","first_name":"Richard"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"citation":{"short":"K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987.","chicago":"Lohse, Konrad, Richard Harrison, and Nicholas H Barton. “A General Method for Calculating Likelihoods under the Coalescent Process.” <i>Genetics</i>. Genetics Society of America, 2011. <a href=\"https://doi.org/10.1534/genetics.111.129569\">https://doi.org/10.1534/genetics.111.129569</a>.","ista":"Lohse K, Harrison R, Barton NH. 2011. A general method for calculating likelihoods under the coalescent process. Genetics. 189(3), 977–987.","mla":"Lohse, Konrad, et al. “A General Method for Calculating Likelihoods under the Coalescent Process.” <i>Genetics</i>, vol. 189, no. 3, Genetics Society of America, 2011, pp. 977–87, doi:<a href=\"https://doi.org/10.1534/genetics.111.129569\">10.1534/genetics.111.129569</a>.","ieee":"K. Lohse, R. Harrison, and N. H. Barton, “A general method for calculating likelihoods under the coalescent process,” <i>Genetics</i>, vol. 189, no. 3. Genetics Society of America, pp. 977–987, 2011.","ama":"Lohse K, Harrison R, Barton NH. A general method for calculating likelihoods under the coalescent process. <i>Genetics</i>. 2011;189(3):977-987. doi:<a href=\"https://doi.org/10.1534/genetics.111.129569\">10.1534/genetics.111.129569</a>","apa":"Lohse, K., Harrison, R., &#38; Barton, N. H. (2011). A general method for calculating likelihoods under the coalescent process. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.111.129569\">https://doi.org/10.1534/genetics.111.129569</a>"},"publist_id":"3355","day":"01","oa":1,"publication":"Genetics","title":"A general method for calculating likelihoods under the coalescent process","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"issue":"3"},{"publication_status":"published","file":[{"date_updated":"2020-07-14T12:46:06Z","file_name":"IST-2016-599-v1+1_meshyFluidsCourseSIGGRAPH2011.pdf","file_id":"5018","relation":"main_file","date_created":"2018-12-12T10:13:34Z","access_level":"open_access","creator":"system","checksum":"8d508ad7c82f50978acbaa4170ee0a75","content_type":"application/pdf","file_size":34672096}],"abstract":[{"lang":"eng","text":"Animating detailed liquid surfaces has always been a challenge for computer graphics researchers and visual effects artists. Over the past few years, researchers in this field have focused on mesh-based surface tracking to synthesize extremely detailed liquid surfaces as efficiently as possible. This course provides a solid understanding of the steps required to create a fluid simulator with a mesh-based liquid surface.\r\n\r\nThe course begins with an overview of several existing liquid-surface-tracking techniques and the pros and cons of each method. Then it explains how to embed a triangle mesh into a finite-difference-based fluid simulator and describes several methods for allowing the liquid surface to merge together or break apart. The final section showcases the benefits and further applications of a mesh-based liquid surface, highlighting state-of-the-art methods for tracking colors and textures, maintaining liquid volume, preserving small surface features, and simulating realistic surface-tension waves."}],"quality_controlled":"1","oa_version":"Published Version","date_created":"2018-12-11T12:02:31Z","year":"2011","_id":"3297","title":"Liquid simulation with mesh-based surface tracking","has_accepted_license":"1","article_number":"8","date_updated":"2023-02-23T11:21:02Z","author":[{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"},{"first_name":"Matthias","last_name":"Müller Fischer","full_name":"Müller Fischer, Matthias"},{"full_name":"Brochu, Tyson","last_name":"Brochu","first_name":"Tyson"}],"citation":{"ista":"Wojtan C, Müller Fischer M, Brochu T. 2011. Liquid simulation with mesh-based surface tracking. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, 8.","chicago":"Wojtan, Chris, Matthias Müller Fischer, and Tyson Brochu. “Liquid Simulation with Mesh-Based Surface Tracking.” ACM, 2011. <a href=\"https://doi.org/10.1145/2037636.2037644\">https://doi.org/10.1145/2037636.2037644</a>.","ama":"Wojtan C, Müller Fischer M, Brochu T. Liquid simulation with mesh-based surface tracking. In: ACM; 2011. doi:<a href=\"https://doi.org/10.1145/2037636.2037644\">10.1145/2037636.2037644</a>","ieee":"C. Wojtan, M. Müller Fischer, and T. Brochu, “Liquid simulation with mesh-based surface tracking,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Vancouver, BC, Canada, 2011.","apa":"Wojtan, C., Müller Fischer, M., &#38; Brochu, T. (2011). Liquid simulation with mesh-based surface tracking. Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Vancouver, BC, Canada: ACM. <a href=\"https://doi.org/10.1145/2037636.2037644\">https://doi.org/10.1145/2037636.2037644</a>","mla":"Wojtan, Chris, et al. <i>Liquid Simulation with Mesh-Based Surface Tracking</i>. 8, ACM, 2011, doi:<a href=\"https://doi.org/10.1145/2037636.2037644\">10.1145/2037636.2037644</a>.","short":"C. Wojtan, M. Müller Fischer, T. Brochu, in:, ACM, 2011."},"day":"07","publist_id":"3344","oa":1,"department":[{"_id":"ChWo"}],"publisher":"ACM","month":"08","conference":{"end_date":"2011-08-11","start_date":"2011-08-07","location":"Vancouver, BC, Canada","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"scopus_import":1,"doi":"10.1145/2037636.2037644","date_published":"2011-08-07T00:00:00Z","language":[{"iso":"eng"}],"status":"public","ddc":["000"],"pubrep_id":"599","type":"conference","file_date_updated":"2020-07-14T12:46:06Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"}]