[{"day":"23","article_processing_charge":"No","month":"03","department":[{"_id":"GaTk"}],"author":[{"last_name":"Friedlander","full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar"},{"first_name":"Avraham E.","last_name":"Mayo","full_name":"Mayo, Avraham E."},{"full_name":"Tlusty, Tsvi","last_name":"Tlusty","first_name":"Tsvi"},{"first_name":"Uri","last_name":"Alon","full_name":"Alon, Uri"}],"type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9718","date_published":"2015-03-23T00:00:00Z","date_created":"2021-07-26T08:35:23Z","oa_version":"Published Version","year":"2015","date_updated":"2025-09-23T08:43:16Z","status":"public","doi":"10.1371/journal.pcbi.1004055.s001","related_material":{"record":[{"id":"1827","status":"public","relation":"used_in_publication"}]},"title":"Supporting information text","publisher":"Public Library of Science","citation":{"ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">10.1371/journal.pcbi.1004055.s001</a>.","mla":"Friedlander, Tamar, et al. <i>Supporting Information Text</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">10.1371/journal.pcbi.1004055.s001</a>.","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information text.” Public Library of Science, 2015.","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Supporting Information Text.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">https://doi.org/10.1371/journal.pcbi.1004055.s001</a>.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., &#38; Alon, U. (2015). Supporting information text. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">https://doi.org/10.1371/journal.pcbi.1004055.s001</a>","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Supporting information text. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">10.1371/journal.pcbi.1004055.s001</a>"}},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.cj910"}],"citation":{"short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, (2015).","ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria. 2015. doi:<a href=\"https://doi.org/10.5061/dryad.cj910\">10.5061/dryad.cj910</a>","apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &#38; Hall, A. R. (2015). Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria. Dryad. <a href=\"https://doi.org/10.5061/dryad.cj910\">https://doi.org/10.5061/dryad.cj910</a>","ista":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2015. Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria, Dryad, <a href=\"https://doi.org/10.5061/dryad.cj910\">10.5061/dryad.cj910</a>.","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria.” Dryad, 2015.","chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Data from: Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Non-Mutator Bacteria.” Dryad, 2015. <a href=\"https://doi.org/10.5061/dryad.cj910\">https://doi.org/10.5061/dryad.cj910</a>.","mla":"Wielgoss, Sébastien, et al. <i>Data from: Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Non-Mutator Bacteria</i>. Dryad, 2015, doi:<a href=\"https://doi.org/10.5061/dryad.cj910\">10.5061/dryad.cj910</a>."},"related_material":{"record":[{"relation":"used_in_publication","id":"5749","status":"public"}]},"title":"Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria","abstract":[{"lang":"eng","text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance."}],"publisher":"Dryad","oa":1,"date_updated":"2026-04-29T05:57:01Z","status":"public","doi":"10.5061/dryad.cj910","oa_version":"Published Version","year":"2015","_id":"9719","date_published":"2015-12-21T00:00:00Z","date_created":"2021-07-26T08:44:04Z","month":"12","department":[{"_id":"CaGu"}],"author":[{"full_name":"Wielgoss, Sébastien","last_name":"Wielgoss","first_name":"Sébastien"},{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346"},{"last_name":"Bischofberger","full_name":"Bischofberger, Anna M.","first_name":"Anna M."},{"first_name":"Alex R.","full_name":"Hall, Alex R.","last_name":"Hall"}],"type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"21","article_processing_charge":"No"},{"article_processing_charge":"No","day":"01","month":"06","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"author":[{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","orcid":"0000-0003-2012-9947","full_name":"Symonova, Olga","last_name":"Symonova"},{"last_name":"Topp","full_name":"Topp, Christopher","first_name":"Christopher"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"date_published":"2015-06-01T00:00:00Z","_id":"9737","date_created":"2021-07-28T06:20:13Z","oa_version":"Published Version","year":"2015","date_updated":"2025-09-23T08:30:43Z","status":"public","doi":"10.1371/journal.pone.0127657.s001","related_material":{"record":[{"relation":"used_in_publication","id":"1793","status":"public"}]},"publisher":"Public Library of Science","title":"Root traits computed by DynamicRoots for the maize root shown in fig 2","citation":{"chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">https://doi.org/10.1371/journal.pone.0127657.s001</a>.","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “Root traits computed by DynamicRoots for the maize root shown in fig 2.” Public Library of Science, 2015.","mla":"Symonova, Olga, et al. <i>Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">10.1371/journal.pone.0127657.s001</a>.","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. Root traits computed by DynamicRoots for the maize root shown in fig 2, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">10.1371/journal.pone.0127657.s001</a>.","ama":"Symonova O, Topp C, Edelsbrunner H. Root traits computed by DynamicRoots for the maize root shown in fig 2. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">10.1371/journal.pone.0127657.s001</a>","apa":"Symonova, O., Topp, C., &#38; Edelsbrunner, H. (2015). Root traits computed by DynamicRoots for the maize root shown in fig 2. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">https://doi.org/10.1371/journal.pone.0127657.s001</a>","short":"O. Symonova, C. Topp, H. Edelsbrunner, (2015)."}},{"status":"public","date_updated":"2025-09-29T11:42:25Z","doi":"10.5061/dryad.7kc79","oa":1,"related_material":{"record":[{"id":"2161","status":"public","relation":"used_in_publication"}]},"publisher":"Dryad","abstract":[{"lang":"eng","text":"Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects."}],"title":"Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant","main_file_link":[{"url":"https://doi.org/10.5061/dryad.7kc79","open_access":"1"}],"citation":{"mla":"Westhus, Claudia, et al. <i>Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant</i>. Dryad, 2015, doi:<a href=\"https://doi.org/10.5061/dryad.7kc79\">10.5061/dryad.7kc79</a>.","ieee":"C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer, “Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant.” Dryad, 2015.","chicago":"Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie Doums, and Sylvia Cremer. “Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant.” Dryad, 2015. <a href=\"https://doi.org/10.5061/dryad.7kc79\">https://doi.org/10.5061/dryad.7kc79</a>.","ista":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2015. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant, Dryad, <a href=\"https://doi.org/10.5061/dryad.7kc79\">10.5061/dryad.7kc79</a>.","apa":"Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., &#38; Cremer, S. (2015). Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Dryad. <a href=\"https://doi.org/10.5061/dryad.7kc79\">https://doi.org/10.5061/dryad.7kc79</a>","ama":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. 2015. doi:<a href=\"https://doi.org/10.5061/dryad.7kc79\">10.5061/dryad.7kc79</a>","short":"C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, (2015)."},"article_processing_charge":"No","day":"09","month":"07","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Claudia","full_name":"Westhus, Claudia","last_name":"Westhus"},{"last_name":"Ugelvig","full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tourdot, Edouard","last_name":"Tourdot","first_name":"Edouard"},{"first_name":"Jürgen","full_name":"Heinze, Jürgen","last_name":"Heinze"},{"full_name":"Doums, Claudie","last_name":"Doums","first_name":"Claudie"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"department":[{"_id":"SyCr"}],"date_published":"2015-07-09T00:00:00Z","_id":"9742","date_created":"2021-07-28T08:52:53Z","oa_version":"Published Version","year":"2015"},{"doi":"10.1371/journal.pbio.1002299.s008","date_updated":"2025-09-23T09:58:54Z","status":"public","title":"Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs","publisher":"Public Library of Science","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1619"}]},"citation":{"ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">10.1371/journal.pbio.1002299.s008</a>.","mla":"Chevereau, Guillaume, et al. <i>Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">10.1371/journal.pbio.1002299.s008</a>.","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">https://doi.org/10.1371/journal.pbio.1002299.s008</a>.","ieee":"G. Chevereau <i>et al.</i>, “Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs.” Public Library of Science, 2015.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., &#38; Bollenbach, M. T. (2015). Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">https://doi.org/10.1371/journal.pbio.1002299.s008</a>","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">10.1371/journal.pbio.1002299.s008</a>"},"day":"18","article_processing_charge":"No","department":[{"_id":"ToBo"}],"author":[{"last_name":"Chevereau","full_name":"Chevereau, Guillaume","first_name":"Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87"},{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","orcid":"0000-0002-2519-8004","last_name":"Lukacisinova","full_name":"Lukacisinova, Marta"},{"first_name":"Tugce","full_name":"Batur, Tugce","last_name":"Batur"},{"last_name":"Guvenek","full_name":"Guvenek, Aysegul","first_name":"Aysegul"},{"first_name":"Dilay Hazal","full_name":"Ayhan, Dilay Hazal","last_name":"Ayhan"},{"last_name":"Toprak","full_name":"Toprak, Erdal","first_name":"Erdal"},{"orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","month":"11","date_created":"2021-08-03T07:05:16Z","_id":"9765","date_published":"2015-11-18T00:00:00Z","year":"2015","oa_version":"Published Version"},{"citation":{"ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Description of the agent based simulations. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">https://doi.org/10.1371/journal.pone.0126907.s003</a>","short":"B. Trubenova, S. Novak, R. Hager, (2015).","ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015.","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">https://doi.org/10.1371/journal.pone.0126907.s003</a>.","mla":"Trubenova, Barbora, et al. <i>Description of the Agent Based Simulations</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>.","ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>."},"title":"Description of the agent based simulations","publisher":"Public Library of Science","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1809"}]},"date_updated":"2025-09-23T09:21:54Z","status":"public","doi":"10.1371/journal.pone.0126907.s003","year":"2015","oa_version":"Published Version","date_created":"2021-08-05T12:55:20Z","_id":"9772","date_published":"2015-05-18T00:00:00Z","department":[{"_id":"NiBa"}],"author":[{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967"},{"last_name":"Novak","full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"},{"first_name":"Reinmar","last_name":"Hager","full_name":"Hager, Reinmar"}],"type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"05","day":"18","article_processing_charge":"No"},{"date_updated":"2025-09-23T08:43:16Z","status":"public","doi":"10.1371/journal.pcbi.1004055.s002","citation":{"mla":"Friedlander, Tamar, et al. <i>Evolutionary Simulation Code</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">10.1371/journal.pcbi.1004055.s002</a>.","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015.","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary Simulation Code.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">https://doi.org/10.1371/journal.pcbi.1004055.s002</a>.","ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">10.1371/journal.pcbi.1004055.s002</a>.","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., &#38; Alon, U. (2015). Evolutionary simulation code. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">https://doi.org/10.1371/journal.pcbi.1004055.s002</a>","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">10.1371/journal.pcbi.1004055.s002</a>","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015)."},"related_material":{"record":[{"relation":"used_in_publication","id":"1827","status":"public"}]},"publisher":"Public Library of Science","title":"Evolutionary simulation code","month":"03","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"GaTk"}],"author":[{"first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar","last_name":"Friedlander"},{"first_name":"Avraham E.","full_name":"Mayo, Avraham E.","last_name":"Mayo"},{"full_name":"Tlusty, Tsvi","last_name":"Tlusty","first_name":"Tsvi"},{"first_name":"Uri","last_name":"Alon","full_name":"Alon, Uri"}],"article_processing_charge":"No","day":"23","oa_version":"Published Version","year":"2015","date_published":"2015-03-23T00:00:00Z","_id":"9773","date_created":"2021-08-05T12:58:07Z"},{"language":[{"iso":"eng"}],"oa_version":"Submitted Version","page":"180 - 197","pubrep_id":"336","department":[{"_id":"ToHe"}],"author":[{"last_name":"Cerny","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"},{"full_name":"Clarke, Edmund","last_name":"Clarke","first_name":"Edmund"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun"},{"first_name":"Leonid","last_name":"Ryzhyk","full_name":"Ryzhyk, Leonid"},{"last_name":"Samanta","full_name":"Samanta, Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","first_name":"Roopsha"},{"first_name":"Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4409-8487","full_name":"Tarrach, Thorsten","last_name":"Tarrach"}],"conference":{"start_date":"2015-07-18","location":"San Francisco, CA, United States","end_date":"2015-07-24","name":"CAV: Computer Aided Verification"},"publication_status":"published","isi":1,"month":"07","volume":9207,"scopus_import":"1","intvolume":"      9207","ddc":["000"],"citation":{"apa":"Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., &#38; Tarrach, T. (2015). From non-preemptive to preemptive scheduling using synchronization synthesis. Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-319-21668-3_11\">https://doi.org/10.1007/978-3-319-21668-3_11</a>","ama":"Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. 2015;9207:180-197. doi:<a href=\"https://doi.org/10.1007/978-3-319-21668-3_11\">10.1007/978-3-319-21668-3_11</a>","short":"P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, 9207 (2015) 180–197.","mla":"Cerny, Pavol, et al. <i>From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis</i>. Vol. 9207, Springer, 2015, pp. 180–97, doi:<a href=\"https://doi.org/10.1007/978-3-319-21668-3_11\">10.1007/978-3-319-21668-3_11</a>.","chicago":"Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” Lecture Notes in Computer Science. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-21668-3_11\">https://doi.org/10.1007/978-3-319-21668-3_11</a>.","ieee":"P. Cerny <i>et al.</i>, “From non-preemptive to preemptive scheduling using synchronization synthesis,” vol. 9207. Springer, pp. 180–197, 2015.","ista":"Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2015. From non-preemptive to preemptive scheduling using synchronization synthesis. 9207, 180–197."},"OA_type":"green","has_accepted_license":"1","related_material":{"record":[{"id":"1338","status":"public","relation":"later_version"},{"status":"public","id":"1130","relation":"dissertation_contains"}]},"alternative_title":["LNCS"],"ec_funded":1,"OA_place":"repository","publist_id":"5398","year":"2015","file_date_updated":"2025-06-26T07:12:35Z","date_created":"2018-12-11T11:53:42Z","_id":"1729","external_id":{"isi":["000491470400011"]},"date_published":"2015-07-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"conference","day":"01","article_processing_charge":"No","series_title":"Lecture Notes in Computer Science","quality_controlled":"1","title":"From non-preemptive to preemptive scheduling using synchronization synthesis","abstract":[{"text":"We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of such sequences produced under a non-preemptive scheduler. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and rules for inserting synchronization. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient, and, since it does not require explicit specifications, is more practical than the conventional approach based on user-provided assertions.","lang":"eng"}],"publisher":"Springer","file":[{"file_name":"IST-2015-336-v1+1_long_version.pdf","date_created":"2018-12-12T10:08:53Z","relation":"main_file","file_size":481922,"creator":"system","access_level":"open_access","file_id":"4715","content_type":"application/pdf","checksum":"6ff58ac220e2f20cb001ba35d4924495","date_updated":"2025-06-26T07:12:35Z"}],"oa":1,"status":"public","doi":"10.1007/978-3-319-21668-3_11","date_updated":"2026-04-09T10:54:00Z","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}]},{"page":"587 - 620","oa_version":"Preprint","language":[{"iso":"eng"}],"volume":53,"month":"04","isi":1,"publication_status":"published","author":[{"first_name":"Éric","full_name":"Colin De Verdière, Éric","last_name":"Colin De Verdière"},{"full_name":"Hubard, Alfredo","last_name":"Hubard","first_name":"Alfredo"},{"first_name":"Arnaud N","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","full_name":"De Mesmay, Arnaud N","last_name":"De Mesmay"}],"department":[{"_id":"UlWa"}],"intvolume":"        53","scopus_import":"1","issue":"3","citation":{"ama":"Colin De Verdière É, Hubard A, de Mesmay AN. Discrete systolic inequalities and decompositions of triangulated surfaces. <i>Discrete &#38; Computational Geometry</i>. 2015;53(3):587-620. doi:<a href=\"https://doi.org/10.1007/s00454-015-9679-9\">10.1007/s00454-015-9679-9</a>","apa":"Colin De Verdière, É., Hubard, A., &#38; de Mesmay, A. N. (2015). Discrete systolic inequalities and decompositions of triangulated surfaces. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-015-9679-9\">https://doi.org/10.1007/s00454-015-9679-9</a>","short":"É. Colin De Verdière, A. Hubard, A.N. de Mesmay, Discrete &#38; Computational Geometry 53 (2015) 587–620.","chicago":"Colin De Verdière, Éric, Alfredo Hubard, and Arnaud N de Mesmay. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00454-015-9679-9\">https://doi.org/10.1007/s00454-015-9679-9</a>.","ieee":"É. Colin De Verdière, A. Hubard, and A. N. de Mesmay, “Discrete systolic inequalities and decompositions of triangulated surfaces,” <i>Discrete &#38; Computational Geometry</i>, vol. 53, no. 3. Springer, pp. 587–620, 2015.","mla":"Colin De Verdière, Éric, et al. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” <i>Discrete &#38; Computational Geometry</i>, vol. 53, no. 3, Springer, 2015, pp. 587–620, doi:<a href=\"https://doi.org/10.1007/s00454-015-9679-9\">10.1007/s00454-015-9679-9</a>.","ista":"Colin De Verdière É, Hubard A, de Mesmay AN. 2015. Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete &#38; Computational Geometry. 53(3), 587–620."},"year":"2015","publist_id":"5397","date_published":"2015-04-02T00:00:00Z","external_id":{"isi":["000353895200006"],"arxiv":["1408.4036"]},"_id":"1730","date_created":"2018-12-11T11:53:42Z","publication":"Discrete & Computational Geometry","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","article_processing_charge":"No","day":"02","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1408.4036"}],"publisher":"Springer","abstract":[{"text":"How much cutting is needed to simplify the topology of a surface? We provide bounds for several instances of this question, for the minimum length of topologically non-trivial closed curves, pants decompositions, and cut graphs with a given combinatorial map in triangulated combinatorial surfaces (or their dual cross-metric counterpart). Our work builds upon Riemannian systolic inequalities, which bound the minimum length of non-trivial closed curves in terms of the genus and the area of the surface. We first describe a systematic way to translate Riemannian systolic inequalities to a discrete setting, and vice-versa. This implies a conjecture by Przytycka and Przytycki (Graph structure theory. Contemporary Mathematics, vol. 147, 1993), a number of new systolic inequalities in the discrete setting, and the fact that a theorem of Hutchinson on the edge-width of triangulated surfaces and Gromov’s systolic inequality for surfaces are essentially equivalent. We also discuss how these proofs generalize to higher dimensions. Then we focus on topological decompositions of surfaces. Relying on ideas of Buser, we prove the existence of pants decompositions of length O(g^(3/2)n^(1/2)) for any triangulated combinatorial surface of genus g with n triangles, and describe an O(gn)-time algorithm to compute such a decomposition. Finally, we consider the problem of embedding a cut graph (or more generally a cellular graph) with a given combinatorial map on a given surface. Using random triangulations, we prove (essentially) that, for any choice of a combinatorial map, there are some surfaces on which any cellular embedding with that combinatorial map has length superlinear in the number of triangles of the triangulated combinatorial surface. There is also a similar result for graphs embedded on polyhedral triangulations.","lang":"eng"}],"title":"Discrete systolic inequalities and decompositions of triangulated surfaces","quality_controlled":"1","oa":1,"doi":"10.1007/s00454-015-9679-9","status":"public","date_updated":"2025-09-23T08:27:38Z","arxiv":1},{"ec_funded":1,"related_material":{"record":[{"id":"3856","status":"public","relation":"earlier_version"}]},"corr_author":"1","citation":{"ieee":"K. Chatterjee, L. Doyen, H. Gimbert, and T. A. Henzinger, “Randomness for free,” <i>Information and Computation</i>, vol. 245, no. 12. Elsevier, pp. 3–16, 2015.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Thomas A Henzinger. “Randomness for Free.” <i>Information and Computation</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.ic.2015.06.003\">https://doi.org/10.1016/j.ic.2015.06.003</a>.","mla":"Chatterjee, Krishnendu, et al. “Randomness for Free.” <i>Information and Computation</i>, vol. 245, no. 12, Elsevier, 2015, pp. 3–16, doi:<a href=\"https://doi.org/10.1016/j.ic.2015.06.003\">10.1016/j.ic.2015.06.003</a>.","ista":"Chatterjee K, Doyen L, Gimbert H, Henzinger TA. 2015. Randomness for free. Information and Computation. 245(12), 3–16.","ama":"Chatterjee K, Doyen L, Gimbert H, Henzinger TA. Randomness for free. <i>Information and Computation</i>. 2015;245(12):3-16. doi:<a href=\"https://doi.org/10.1016/j.ic.2015.06.003\">10.1016/j.ic.2015.06.003</a>","apa":"Chatterjee, K., Doyen, L., Gimbert, H., &#38; Henzinger, T. A. (2015). Randomness for free. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2015.06.003\">https://doi.org/10.1016/j.ic.2015.06.003</a>","short":"K. Chatterjee, L. Doyen, H. Gimbert, T.A. Henzinger, Information and Computation 245 (2015) 3–16."},"issue":"12","language":[{"iso":"eng"}],"page":"3 - 16","oa_version":"Preprint","intvolume":"       245","scopus_import":"1","publication_status":"published","isi":1,"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"},{"last_name":"Gimbert","full_name":"Gimbert, Hugo","first_name":"Hugo"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"month":"12","volume":245,"publisher":"Elsevier","quality_controlled":"1","title":"Randomness for free","abstract":[{"lang":"eng","text":"We consider two-player zero-sum games on graphs. These games can be classified on the basis of the information of the players and on the mode of interaction between them. On the basis of information the classification is as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided complete-observation (one player has complete observation); and (c) complete-observation (both players have complete view of the game). On the basis of mode of interaction we have the following classification: (a) concurrent (both players interact simultaneously); and (b) turn-based (both players interact in turn). The two sources of randomness in these games are randomness in transition function and randomness in strategies. In general, randomized strategies are more powerful than deterministic strategies, and randomness in transitions gives more general classes of games. In this work we present a complete characterization for the classes of games where randomness is not helpful in: (a) the transition function probabilistic transition can be simulated by deterministic transition); and (b) strategies (pure strategies are as powerful as randomized strategies). As consequence of our characterization we obtain new undecidability results for these games. "}],"main_file_link":[{"url":"http://arxiv.org/abs/1006.0673","open_access":"1"}],"arxiv":1,"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques","grant_number":"215543"},{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems","grant_number":"214373","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"date_updated":"2025-09-23T10:32:00Z","status":"public","doi":"10.1016/j.ic.2015.06.003","oa":1,"date_created":"2018-12-11T11:53:42Z","date_published":"2015-12-01T00:00:00Z","_id":"1731","external_id":{"isi":["000368899100002"],"arxiv":["1006.0673"]},"year":"2015","publist_id":"5395","article_processing_charge":"No","day":"01","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Information and Computation"},{"language":[{"iso":"eng"}],"page":"325 - 330","oa_version":"Preprint","publication_status":"published","department":[{"_id":"KrCh"}],"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Chmelik, Martin","last_name":"Chmelik","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gupta","full_name":"Gupta, Raghav","first_name":"Raghav"},{"first_name":"Ayush","full_name":"Kanodia, Ayush","last_name":"Kanodia"}],"conference":{"name":"ICRA: International Conference on Robotics and Automation","end_date":"2015-05-30","start_date":"2015-05-26","location":"Seattle, WA, United States"},"month":"01","scopus_import":1,"citation":{"short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, IEEE, 2015, pp. 325–330.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., &#38; Kanodia, A. (2015). Qualitative analysis of POMDPs with temporal logic specifications for robotics applications (pp. 325–330). Presented at the ICRA: International Conference on Robotics and Automation, Seattle, WA, United States: IEEE. <a href=\"https://doi.org/10.1109/ICRA.2015.7139019\">https://doi.org/10.1109/ICRA.2015.7139019</a>","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. In: IEEE; 2015:325-330. doi:<a href=\"https://doi.org/10.1109/ICRA.2015.7139019\">10.1109/ICRA.2015.7139019</a>","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. ICRA: International Conference on Robotics and Automation, 325–330.","mla":"Chatterjee, Krishnendu, et al. <i>Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications</i>. IEEE, 2015, pp. 325–30, doi:<a href=\"https://doi.org/10.1109/ICRA.2015.7139019\">10.1109/ICRA.2015.7139019</a>.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Qualitative analysis of POMDPs with temporal logic specifications for robotics applications,” presented at the ICRA: International Conference on Robotics and Automation, Seattle, WA, United States, 2015, pp. 325–330.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications,” 325–30. IEEE, 2015. <a href=\"https://doi.org/10.1109/ICRA.2015.7139019\">https://doi.org/10.1109/ICRA.2015.7139019</a>."},"ec_funded":1,"related_material":{"record":[{"id":"5424","status":"public","relation":"earlier_version"},{"id":"5426","status":"public","relation":"earlier_version"}]},"year":"2015","publist_id":"5394","date_created":"2018-12-11T11:53:43Z","date_published":"2015-01-01T00:00:00Z","_id":"1732","external_id":{"arxiv":["1409.3360"]},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","main_file_link":[{"url":"http://arxiv.org/abs/1409.3360","open_access":"1"}],"publisher":"IEEE","title":"Qualitative analysis of POMDPs with temporal logic specifications for robotics applications","quality_controlled":"1","abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs), that are a standard framework for robotics applications to model uncertainties present in the real world, with temporal logic specifications. All temporal logic specifications in linear-time temporal logic (LTL) can be expressed as parity objectives. We study the qualitative analysis problem for POMDPs with parity objectives that asks whether there is a controller (policy) to ensure that the objective holds with probability 1 (almost-surely). While the qualitative analysis of POMDPs with parity objectives is undecidable, recent results show that when restricted to finite-memory policies the problem is EXPTIME-complete. While the problem is intractable in theory, we present a practical approach to solve the qualitative analysis problem. We designed several heuristics to deal with the exponential complexity, and have used our implementation on a number of well-known POMDP examples for robotics applications. Our results provide the first practical approach to solve the qualitative analysis of robot motion planning with LTL properties in the presence of uncertainty.","lang":"eng"}],"oa":1,"arxiv":1,"project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"}],"doi":"10.1109/ICRA.2015.7139019","status":"public","date_updated":"2023-02-23T12:25:52Z"},{"year":"2015","publist_id":"5391","date_created":"2018-12-11T11:53:43Z","date_published":"2015-05-01T00:00:00Z","external_id":{"isi":["000358326600063"]},"_id":"1734","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Computer Graphics Forum","article_processing_charge":"No","day":"01","main_file_link":[{"url":"https://graphics.ethz.ch/~mpapas/publications/fac_star.pdf"}],"publisher":"Wiley-Blackwell","title":"Recent advances in facial appearance capture","abstract":[{"text":"Facial appearance capture is now firmly established within academic research and used extensively across various application domains, perhaps most prominently in the entertainment industry through the design of virtual characters in video games and films. While significant progress has occurred over the last two decades, no single survey currently exists that discusses the similarities, differences, and practical considerations of the available appearance capture techniques as applied to human faces. A central difficulty of facial appearance capture is the way light interacts with skin-which has a complex multi-layered structure-and the interactions that occur below the skin surface can, by definition, only be observed indirectly. In this report, we distinguish between two broad strategies for dealing with this complexity. &quot;Image-based methods&quot; try to exhaustively capture the exact face appearance under different lighting and viewing conditions, and then render the face through weighted image combinations. &quot;Parametric methods&quot; instead fit the captured reflectance data to some parametric appearance model used during rendering, allowing for a more lightweight and flexible representation but at the cost of potentially increased rendering complexity or inexact reproduction. The goal of this report is to provide an overview that can guide practitioners and researchers in assessing the tradeoffs between current approaches and identifying directions for future advances in facial appearance capture.","lang":"eng"}],"quality_controlled":"1","status":"public","date_updated":"2025-09-23T10:32:38Z","doi":"10.1111/cgf.12594","language":[{"iso":"eng"}],"page":"709 - 733","oa_version":"None","publication_status":"published","isi":1,"department":[{"_id":"BeBi"}],"author":[{"last_name":"Klehm","full_name":"Klehm, Oliver","first_name":"Oliver"},{"last_name":"Rousselle","full_name":"Rousselle, Fabrice","first_name":"Fabrice"},{"full_name":"Papas, Marios","last_name":"Papas","first_name":"Marios"},{"last_name":"Bradley","full_name":"Bradley, Derek","first_name":"Derek"},{"last_name":"Hery","full_name":"Hery, Christophe","first_name":"Christophe"},{"orcid":"0000-0001-6511-9385","last_name":"Bickel","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jarosz","full_name":"Jarosz, Wojciech","first_name":"Wojciech"},{"first_name":"Thabo","last_name":"Beeler","full_name":"Beeler, Thabo"}],"volume":34,"month":"05","intvolume":"        34","scopus_import":"1","citation":{"short":"O. Klehm, F. Rousselle, M. Papas, D. Bradley, C. Hery, B. Bickel, W. Jarosz, T. Beeler, Computer Graphics Forum 34 (2015) 709–733.","apa":"Klehm, O., Rousselle, F., Papas, M., Bradley, D., Hery, C., Bickel, B., … Beeler, T. (2015). Recent advances in facial appearance capture. <i>Computer Graphics Forum</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/cgf.12594\">https://doi.org/10.1111/cgf.12594</a>","ama":"Klehm O, Rousselle F, Papas M, et al. Recent advances in facial appearance capture. <i>Computer Graphics Forum</i>. 2015;34(2):709-733. doi:<a href=\"https://doi.org/10.1111/cgf.12594\">10.1111/cgf.12594</a>","ista":"Klehm O, Rousselle F, Papas M, Bradley D, Hery C, Bickel B, Jarosz W, Beeler T. 2015. Recent advances in facial appearance capture. Computer Graphics Forum. 34(2), 709–733.","mla":"Klehm, Oliver, et al. “Recent Advances in Facial Appearance Capture.” <i>Computer Graphics Forum</i>, vol. 34, no. 2, Wiley-Blackwell, 2015, pp. 709–33, doi:<a href=\"https://doi.org/10.1111/cgf.12594\">10.1111/cgf.12594</a>.","chicago":"Klehm, Oliver, Fabrice Rousselle, Marios Papas, Derek Bradley, Christophe Hery, Bernd Bickel, Wojciech Jarosz, and Thabo Beeler. “Recent Advances in Facial Appearance Capture.” <i>Computer Graphics Forum</i>. Wiley-Blackwell, 2015. <a href=\"https://doi.org/10.1111/cgf.12594\">https://doi.org/10.1111/cgf.12594</a>.","ieee":"O. Klehm <i>et al.</i>, “Recent advances in facial appearance capture,” <i>Computer Graphics Forum</i>, vol. 34, no. 2. Wiley-Blackwell, pp. 709–733, 2015."},"issue":"2"},{"pubrep_id":"607","oa_version":"Submitted Version","page":"473 - 480","language":[{"iso":"eng"}],"acknowledgement":"The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad","scopus_import":"1","ddc":["000"],"intvolume":"        34","month":"05","volume":34,"author":[{"first_name":"Ryoichi","full_name":"Ando, Ryoichi","last_name":"Ando"},{"last_name":"Thürey","full_name":"Thürey, Nils","first_name":"Nils"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"ChWo"}],"publication_status":"published","isi":1,"has_accepted_license":"1","issue":"2","citation":{"ama":"Ando R, Thürey N, Wojtan C. A dimension-reduced pressure solver for liquid simulations. <i>Computer Graphics Forum</i>. 2015;34(2):473-480. doi:<a href=\"https://doi.org/10.1111/cgf.12576\">10.1111/cgf.12576</a>","apa":"Ando, R., Thürey, N., &#38; Wojtan, C. (2015). A dimension-reduced pressure solver for liquid simulations. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.12576\">https://doi.org/10.1111/cgf.12576</a>","short":"R. Ando, N. Thürey, C. Wojtan, Computer Graphics Forum 34 (2015) 473–480.","ieee":"R. Ando, N. Thürey, and C. Wojtan, “A dimension-reduced pressure solver for liquid simulations,” <i>Computer Graphics Forum</i>, vol. 34, no. 2. Wiley, pp. 473–480, 2015.","chicago":"Ando, Ryoichi, Nils Thürey, and Chris Wojtan. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” <i>Computer Graphics Forum</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/cgf.12576\">https://doi.org/10.1111/cgf.12576</a>.","mla":"Ando, Ryoichi, et al. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” <i>Computer Graphics Forum</i>, vol. 34, no. 2, Wiley, 2015, pp. 473–80, doi:<a href=\"https://doi.org/10.1111/cgf.12576\">10.1111/cgf.12576</a>.","ista":"Ando R, Thürey N, Wojtan C. 2015. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 34(2), 473–480."},"external_id":{"isi":["000358326600045"]},"_id":"1735","date_published":"2015-05-01T00:00:00Z","date_created":"2018-12-11T11:53:44Z","file_date_updated":"2020-07-14T12:45:15Z","publist_id":"5389","year":"2015","day":"01","article_processing_charge":"No","publication":"Computer Graphics Forum","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","file":[{"file_size":6312352,"creator":"system","access_level":"open_access","date_created":"2018-12-12T10:16:30Z","relation":"main_file","file_name":"IST-2016-607-v1+1_coarsegrid.pdf","date_updated":"2020-07-14T12:45:15Z","content_type":"application/pdf","file_id":"5218","checksum":"590752bf977855b337a80f78a9bc2404"}],"title":"A dimension-reduced pressure solver for liquid simulations","quality_controlled":"1","abstract":[{"lang":"eng","text":"This work presents a method for efficiently simplifying the pressure projection step in a liquid simulation. We first devise a straightforward dimension reduction technique that dramatically reduces the cost of solving the pressure projection. Next, we introduce a novel change of basis that satisfies free-surface boundary conditions exactly, regardless of the accuracy of the pressure solve. When combined, these ideas greatly reduce the computational complexity of the pressure solve without compromising free surface boundary conditions at the highest level of detail. Our techniques are easy to parallelize, and they effectively eliminate the computational bottleneck for large liquid simulations."}],"publisher":"Wiley","status":"public","date_updated":"2025-09-22T14:29:19Z","doi":"10.1111/cgf.12576","oa":1},{"abstract":[{"lang":"eng","text":"Intellectual disability (ID) has an estimated prevalence of 2-3%. Due to its extreme heterogeneity, the genetic basis of ID remains elusive in many cases. Recently, whole exome sequencing (WES) studies revealed that a large proportion of sporadic cases are caused by de novo gene variants. To identify further genes involved in ID, we performed WES in 250 patients with unexplained ID and their unaffected parents and included exomes of 51 previously sequenced child-parents trios in the analysis. Exome analysis revealed de novo intragenic variants in SET domain-containing 5 (SETD5) in two patients. One patient carried a nonsense variant, and the other an 81 bp deletion located across a splice-donor site. Chromosomal microarray diagnostics further identified four de novo non-recurrent microdeletions encompassing SETD5. CRISPR/Cas9 mutation modelling of the two intragenic variants demonstrated nonsense-mediated decay of the resulting transcripts, pointing to a loss-of-function (LoF) and haploinsufficiency as the common disease-causing mechanism of intragenic SETD5 sequence variants and SETD5-containing microdeletions. In silico domain prediction of SETD5, a predicted SET domain-containing histone methyltransferase (HMT), substantiated the presence of a SET domain and identified a novel putative PHD domain, strengthening a functional link to well-known histone-modifying ID genes. All six patients presented with ID and certain facial dysmorphisms, suggesting that SETD5 sequence variants contribute substantially to the microdeletion 3p25.3 phenotype. The present report of two SETD5 LoF variants in 301 patients demonstrates a prevalence of 0.7% and thus SETD5 variants as a relatively frequent cause of ID."}],"title":"Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome","quality_controlled":"1","publisher":"Nature Publishing Group","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795044/","open_access":"1"}],"status":"public","doi":"10.1038/ejhg.2014.165","date_updated":"2025-09-23T09:30:27Z","oa":1,"pmid":1,"date_created":"2018-12-11T11:54:01Z","_id":"1789","external_id":{"isi":["000354474600013"],"pmid":["25138099"]},"date_published":"2015-06-15T00:00:00Z","publist_id":"5324","year":"2015","day":"15","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","publication":"European Journal of Human Genetics","citation":{"short":"A. Kuechler, A. Zink, T. Wieland, H. Lüdecke, K. Cremer, L. Salviati, P. Magini, K. Najafi, C. Zweier, J. Czeschik, S. Aretz, S. Endele, F. Tamburrino, C. Pinato, M. Clementi, J. Gundlach, C. Maylahn, L. Mazzanti, E. Wohlleber, T. Schwarzmayr, R. Kariminejad, A. Schlessinger, D. Wieczorek, T. Strom, G. Novarino, H. Engels, European Journal of Human Genetics 23 (2015) 753–760.","ama":"Kuechler A, Zink A, Wieland T, et al. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. <i>European Journal of Human Genetics</i>. 2015;23(6):753-760. doi:<a href=\"https://doi.org/10.1038/ejhg.2014.165\">10.1038/ejhg.2014.165</a>","apa":"Kuechler, A., Zink, A., Wieland, T., Lüdecke, H., Cremer, K., Salviati, L., … Engels, H. (2015). Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. <i>European Journal of Human Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ejhg.2014.165\">https://doi.org/10.1038/ejhg.2014.165</a>","ista":"Kuechler A, Zink A, Wieland T, Lüdecke H, Cremer K, Salviati L, Magini P, Najafi K, Zweier C, Czeschik J, Aretz S, Endele S, Tamburrino F, Pinato C, Clementi M, Gundlach J, Maylahn C, Mazzanti L, Wohlleber E, Schwarzmayr T, Kariminejad R, Schlessinger A, Wieczorek D, Strom T, Novarino G, Engels H. 2015. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 23(6), 753–760.","ieee":"A. Kuechler <i>et al.</i>, “Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome,” <i>European Journal of Human Genetics</i>, vol. 23, no. 6. Nature Publishing Group, pp. 753–760, 2015.","chicago":"Kuechler, Alma, Alexander Zink, Thomas Wieland, Hermann Lüdecke, Kirsten Cremer, Leonardo Salviati, Pamela Magini, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” <i>European Journal of Human Genetics</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ejhg.2014.165\">https://doi.org/10.1038/ejhg.2014.165</a>.","mla":"Kuechler, Alma, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” <i>European Journal of Human Genetics</i>, vol. 23, no. 6, Nature Publishing Group, 2015, pp. 753–60, doi:<a href=\"https://doi.org/10.1038/ejhg.2014.165\">10.1038/ejhg.2014.165</a>."},"issue":"6","language":[{"iso":"eng"}],"oa_version":"Submitted Version","page":"753 - 760","intvolume":"        23","department":[{"_id":"GaNo"}],"author":[{"last_name":"Kuechler","full_name":"Kuechler, Alma","first_name":"Alma"},{"full_name":"Zink, Alexander","last_name":"Zink","first_name":"Alexander"},{"last_name":"Wieland","full_name":"Wieland, Thomas","first_name":"Thomas"},{"full_name":"Lüdecke, Hermann","last_name":"Lüdecke","first_name":"Hermann"},{"first_name":"Kirsten","full_name":"Cremer, Kirsten","last_name":"Cremer"},{"last_name":"Salviati","full_name":"Salviati, Leonardo","first_name":"Leonardo"},{"first_name":"Pamela","last_name":"Magini","full_name":"Magini, Pamela"},{"full_name":"Najafi, Kimia","last_name":"Najafi","first_name":"Kimia"},{"first_name":"Christiane","full_name":"Zweier, Christiane","last_name":"Zweier"},{"full_name":"Czeschik, Johanna","last_name":"Czeschik","first_name":"Johanna"},{"first_name":"Stefan","full_name":"Aretz, Stefan","last_name":"Aretz"},{"last_name":"Endele","full_name":"Endele, Sabine","first_name":"Sabine"},{"first_name":"Federica","full_name":"Tamburrino, Federica","last_name":"Tamburrino"},{"last_name":"Pinato","full_name":"Pinato, Claudia","first_name":"Claudia"},{"last_name":"Clementi","full_name":"Clementi, Maurizio","first_name":"Maurizio"},{"full_name":"Gundlach, Jasmin","last_name":"Gundlach","first_name":"Jasmin"},{"first_name":"Carina","last_name":"Maylahn","full_name":"Maylahn, Carina"},{"last_name":"Mazzanti","full_name":"Mazzanti, Laura","first_name":"Laura"},{"first_name":"Eva","full_name":"Wohlleber, Eva","last_name":"Wohlleber"},{"first_name":"Thomas","full_name":"Schwarzmayr, Thomas","last_name":"Schwarzmayr"},{"full_name":"Kariminejad, Roxana","last_name":"Kariminejad","first_name":"Roxana"},{"full_name":"Schlessinger, Avner","last_name":"Schlessinger","first_name":"Avner"},{"full_name":"Wieczorek, Dagmar","last_name":"Wieczorek","first_name":"Dagmar"},{"last_name":"Strom","full_name":"Strom, Tim","first_name":"Tim"},{"full_name":"Novarino, Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hartmut","last_name":"Engels","full_name":"Engels, Hartmut"}],"isi":1,"publication_status":"published","volume":23,"month":"06"},{"issue":"6","corr_author":"1","article_number":"e0127657","citation":{"short":"O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (2015).","apa":"Symonova, O., Topp, C., &#38; Edelsbrunner, H. (2015). DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0127657\">https://doi.org/10.1371/journal.pone.0127657</a>","ama":"Symonova O, Topp C, Edelsbrunner H. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. <i>PLoS One</i>. 2015;10(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657\">10.1371/journal.pone.0127657</a>","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 10(6), e0127657.","mla":"Symonova, Olga, et al. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” <i>PLoS One</i>, vol. 10, no. 6, e0127657, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657\">10.1371/journal.pone.0127657</a>.","chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0127657\">https://doi.org/10.1371/journal.pone.0127657</a>.","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots,” <i>PLoS One</i>, vol. 10, no. 6. Public Library of Science, 2015."},"related_material":{"record":[{"status":"public","id":"9737","relation":"research_data"}]},"has_accepted_license":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"pubrep_id":"454","volume":10,"month":"06","isi":1,"publication_status":"published","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"author":[{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","full_name":"Symonova, Olga","last_name":"Symonova","orcid":"0000-0003-2012-9947"},{"full_name":"Topp, Christopher","last_name":"Topp","first_name":"Christopher"},{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"ddc":["000"],"intvolume":"        10","scopus_import":"1","file":[{"date_updated":"2020-07-14T12:45:16Z","file_id":"5150","checksum":"d20f26461ca575276ad3ed9ce4bfc787","content_type":"application/pdf","creator":"system","file_size":1850825,"access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:15:30Z","file_name":"IST-2016-454-v1+1_journal.pone.0127657.pdf"}],"publisher":"Public Library of Science","title":"DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots","quality_controlled":"1","abstract":[{"text":"We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth.","lang":"eng"}],"oa":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","date_updated":"2025-09-23T08:30:43Z","doi":"10.1371/journal.pone.0127657","file_date_updated":"2020-07-14T12:45:16Z","year":"2015","publist_id":"5318","date_published":"2015-06-01T00:00:00Z","external_id":{"isi":["000356630900069"]},"_id":"1793","date_created":"2018-12-11T11:54:02Z","publication":"PLoS One","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","article_processing_charge":"No","day":"01"},{"has_accepted_license":"1","citation":{"short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).","apa":"Altmeyer, S., Do, Y., &#38; Lai, Y. (2015). Transition to turbulence in Taylor-Couette ferrofluidic flow. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep10781\">https://doi.org/10.1038/srep10781</a>","ama":"Altmeyer S, Do Y, Lai Y. Transition to turbulence in Taylor-Couette ferrofluidic flow. <i>Scientific Reports</i>. 2015;5. doi:<a href=\"https://doi.org/10.1038/srep10781\">10.1038/srep10781</a>","ista":"Altmeyer S, Do Y, Lai Y. 2015. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 5, 10781.","mla":"Altmeyer, Sebastian, et al. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” <i>Scientific Reports</i>, vol. 5, 10781, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/srep10781\">10.1038/srep10781</a>.","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” <i>Scientific Reports</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/srep10781\">https://doi.org/10.1038/srep10781</a>.","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Transition to turbulence in Taylor-Couette ferrofluidic flow,” <i>Scientific Reports</i>, vol. 5. Nature Publishing Group, 2015."},"article_number":"10781","corr_author":"1","pubrep_id":"450","language":[{"iso":"eng"}],"oa_version":"Published Version","scopus_import":"1","ddc":["530"],"intvolume":"         5","author":[{"last_name":"Altmeyer","full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"},{"full_name":"Do, Younghae","last_name":"Do","first_name":"Younghae"},{"first_name":"Ying","full_name":"Lai, Ying","last_name":"Lai"}],"department":[{"_id":"BjHo"}],"publication_status":"published","isi":1,"volume":5,"month":"06","title":"Transition to turbulence in Taylor-Couette ferrofluidic flow","abstract":[{"lang":"eng","text":"It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field transverse to the symmetry axis of the system, turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed investigation of transitions in the flow structure, and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A finding is that, as the magnetic field is increased, onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence may be feasible by using ferrofluids. Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic flow system provides insights into the challenging problem of turbulence control."}],"quality_controlled":"1","publisher":"Nature Publishing Group","file":[{"checksum":"7716f582f8c9d82d8f2bf80bf896b440","content_type":"application/pdf","file_id":"5280","date_updated":"2020-07-14T12:45:16Z","file_name":"IST-2016-450-v1+1_srep10781.pdf","creator":"system","file_size":2449723,"access_level":"open_access","date_created":"2018-12-12T10:17:26Z","relation":"main_file"}],"date_updated":"2025-09-29T10:58:13Z","status":"public","doi":"10.1038/srep10781","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"date_created":"2018-12-11T11:54:06Z","_id":"1804","external_id":{"isi":["000356150200001"]},"date_published":"2015-06-12T00:00:00Z","publist_id":"5306","year":"2015","file_date_updated":"2020-07-14T12:45:16Z","day":"12","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","publication":"Scientific Reports"},{"oa":1,"article_type":"original","project":[{"name":"Topological Complex Systems","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"doi":"10.1016/j.comgeo.2014.08.010","date_updated":"2026-06-18T17:57:28Z","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.comgeo.2014.08.010"}],"publisher":"Elsevier","title":"Homological reconstruction and simplification in R3","abstract":[{"text":"We consider the problem of deciding whether the persistent homology group of a simplicial pair (K,L) can be realized as the homology H∗(X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in double-struck R3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on double-struck S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard.","lang":"eng"}],"quality_controlled":"1","publication":"Computational Geometry: Theory and Applications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","article_processing_charge":"No","day":"03","year":"2015","publist_id":"5305","date_published":"2015-06-03T00:00:00Z","external_id":{"isi":["000357353200006"]},"_id":"1805","date_created":"2018-12-11T11:54:06Z","OA_place":"publisher","issue":"8","OA_type":"free access","corr_author":"1","citation":{"mla":"Attali, Dominique, et al. “Homological Reconstruction and Simplification in R3.” <i>Computational Geometry: Theory and Applications</i>, vol. 48, no. 8, Elsevier, 2015, pp. 606–21, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">10.1016/j.comgeo.2014.08.010</a>.","ieee":"D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological reconstruction and simplification in R3,” <i>Computational Geometry: Theory and Applications</i>, vol. 48, no. 8. Elsevier, pp. 606–621, 2015.","chicago":"Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André Lieutier. “Homological Reconstruction and Simplification in R3.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">https://doi.org/10.1016/j.comgeo.2014.08.010</a>.","ista":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2015. Homological reconstruction and simplification in R3. Computational Geometry: Theory and Applications. 48(8), 606–621.","apa":"Attali, D., Bauer, U., Devillers, O., Glisse, M., &#38; Lieutier, A. (2015). Homological reconstruction and simplification in R3. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">https://doi.org/10.1016/j.comgeo.2014.08.010</a>","ama":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction and simplification in R3. <i>Computational Geometry: Theory and Applications</i>. 2015;48(8):606-621. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">10.1016/j.comgeo.2014.08.010</a>","short":"D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, Computational Geometry: Theory and Applications 48 (2015) 606–621."},"ec_funded":1,"related_material":{"record":[{"id":"2812","status":"public","relation":"earlier_version"}]},"volume":48,"month":"06","publication_status":"published","isi":1,"author":[{"first_name":"Dominique","full_name":"Attali, Dominique","last_name":"Attali"},{"orcid":"0000-0002-9683-0724","last_name":"Bauer","full_name":"Bauer, Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"},{"full_name":"Devillers, Olivier","last_name":"Devillers","first_name":"Olivier"},{"first_name":"Marc","last_name":"Glisse","full_name":"Glisse, Marc"},{"full_name":"Lieutier, André","last_name":"Lieutier","first_name":"André"}],"department":[{"_id":"HeEd"}],"ddc":["500"],"intvolume":"        48","scopus_import":"1","page":"606 - 621","oa_version":"Published Version","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"We study a double Cahn-Hilliard type functional related to the Gross-Pitaevskii energy of two-components Bose-Einstein condensates. In the case of large but same order intercomponent and intracomponent coupling strengths, we prove Γ-convergence to a perimeter minimisation functional with an inhomogeneous surface tension. We study the asymptotic behavior of the surface tension as the ratio between the intercomponent and intracomponent coupling strengths becomes very small or very large and obtain good agreement with the physical literature. We obtain as a consequence, symmetry breaking of the minimisers for the harmonic potential."}],"quality_controlled":"1","title":"Sharp interface limit for two components Bose-Einstein condensates","publisher":"EDP Sciences","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1401.1727"}],"arxiv":1,"status":"public","doi":"10.1051/cocv/2014040","date_updated":"2025-09-23T10:45:09Z","oa":1,"date_created":"2018-12-11T11:54:07Z","_id":"1807","external_id":{"isi":["000356012000001"],"arxiv":["1401.1727"]},"date_published":"2015-05-01T00:00:00Z","publist_id":"5303","year":"2015","day":"01","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","publication":"ESAIM - Control, Optimisation and Calculus of Variations","citation":{"ieee":"M. Goldman and J. Royo-Letelier, “Sharp interface limit for two components Bose-Einstein condensates,” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>, vol. 21, no. 3. EDP Sciences, pp. 603–624, 2015.","chicago":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. EDP Sciences, 2015. <a href=\"https://doi.org/10.1051/cocv/2014040\">https://doi.org/10.1051/cocv/2014040</a>.","mla":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>, vol. 21, no. 3, EDP Sciences, 2015, pp. 603–24, doi:<a href=\"https://doi.org/10.1051/cocv/2014040\">10.1051/cocv/2014040</a>.","ista":"Goldman M, Royo-Letelier J. 2015. Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. 21(3), 603–624.","ama":"Goldman M, Royo-Letelier J. Sharp interface limit for two components Bose-Einstein condensates. <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. 2015;21(3):603-624. doi:<a href=\"https://doi.org/10.1051/cocv/2014040\">10.1051/cocv/2014040</a>","apa":"Goldman, M., &#38; Royo-Letelier, J. (2015). Sharp interface limit for two components Bose-Einstein condensates. <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/cocv/2014040\">https://doi.org/10.1051/cocv/2014040</a>","short":"M. Goldman, J. Royo-Letelier, ESAIM - Control, Optimisation and Calculus of Variations 21 (2015) 603–624."},"corr_author":"1","issue":"3","language":[{"iso":"eng"}],"oa_version":"Preprint","page":"603 - 624","scopus_import":"1","intvolume":"        21","department":[{"_id":"RoSe"}],"author":[{"last_name":"Goldman","full_name":"Goldman, Michael","first_name":"Michael"},{"id":"4D3BED28-F248-11E8-B48F-1D18A9856A87","first_name":"Jimena","full_name":"Royo-Letelier, Jimena","last_name":"Royo-Letelier"}],"isi":1,"publication_status":"published","month":"05","volume":21},{"status":"public","date_updated":"2025-09-23T09:11:51Z","doi":"10.1145/2745799","publisher":"ACM","quality_controlled":"1","title":"Guest editors' introduction to special issue on computational methods in systems biology","article_number":"7","citation":{"ista":"Gupta A, Henzinger TA. 2015. Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. 25(2), 7.","ieee":"A. Gupta and T. A. Henzinger, “Guest editors’ introduction to special issue on computational methods in systems biology,” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2. ACM, 2015.","chicago":"Gupta, Ashutosh, and Thomas A Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2745799\">https://doi.org/10.1145/2745799</a>.","mla":"Gupta, Ashutosh, and Thomas A. Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2, 7, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2745799\">10.1145/2745799</a>.","short":"A. Gupta, T.A. Henzinger, ACM Transactions on Modeling and Computer Simulation 25 (2015).","ama":"Gupta A, Henzinger TA. Guest editors’ introduction to special issue on computational methods in systems biology. <i>ACM Transactions on Modeling and Computer Simulation</i>. 2015;25(2). doi:<a href=\"https://doi.org/10.1145/2745799\">10.1145/2745799</a>","apa":"Gupta, A., &#38; Henzinger, T. A. (2015). Guest editors’ introduction to special issue on computational methods in systems biology. <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM. <a href=\"https://doi.org/10.1145/2745799\">https://doi.org/10.1145/2745799</a>"},"issue":"2","intvolume":"        25","article_processing_charge":"No","scopus_import":"1","day":"01","isi":1,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","department":[{"_id":"ToHe"}],"author":[{"last_name":"Gupta","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"month":"05","publication":"ACM Transactions on Modeling and Computer Simulation","volume":25,"date_created":"2018-12-11T11:54:07Z","date_published":"2015-05-01T00:00:00Z","_id":"1808","external_id":{"isi":["000354789200001"]},"year":"2015","publist_id":"5302","language":[{"iso":"eng"}],"oa_version":"None"},{"article_processing_charge":"No","day":"18","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","publication":"PLoS One","date_created":"2018-12-11T11:54:07Z","date_published":"2015-05-18T00:00:00Z","_id":"1809","external_id":{"isi":["000354917300064"]},"year":"2015","publist_id":"5299","file_date_updated":"2020-07-14T12:45:17Z","status":"public","date_updated":"2025-09-23T09:21:54Z","doi":"10.1371/journal.pone.0126907","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publisher":"Public Library of Science","title":"Indirect genetic effects and the dynamics of social interactions","quality_controlled":"1","abstract":[{"lang":"eng","text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations."}],"file":[{"checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","content_type":"application/pdf","file_id":"4730","date_updated":"2020-07-14T12:45:17Z","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf","date_created":"2018-12-12T10:09:07Z","relation":"main_file","access_level":"open_access","file_size":2748982,"creator":"system"}],"ddc":["570","576"],"intvolume":"        10","scopus_import":"1","publication_status":"published","isi":1,"department":[{"_id":"NiBa"}],"author":[{"orcid":"0000-0002-6873-2967","last_name":"Trubenova","full_name":"Trubenova, Barbora","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2519-824X","last_name":"Novak","full_name":"Novak, Sebastian","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Reinmar","last_name":"Hager","full_name":"Hager, Reinmar"}],"month":"05","volume":10,"pubrep_id":"453","language":[{"iso":"eng"}],"oa_version":"Published Version","has_accepted_license":"1","related_material":{"record":[{"id":"9715","status":"public","relation":"research_data"},{"id":"9772","status":"public","relation":"research_data"}]},"corr_author":"1","citation":{"chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>.","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” <i>PLoS One</i>, vol. 10, no. 5. Public Library of Science, 2015.","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>, vol. 10, no. 5, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>.","ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. 2015;10(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015)."},"issue":"5"}]