[{"status":"public","date_updated":"2023-02-23T10:25:37Z","article_processing_charge":"No","type":"research_data_reference","month":"09","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis"},{"last_name":"Adlam","full_name":"Adlam, Ben","first_name":"Ben"},{"last_name":"Novak","full_name":"Novak, Martin","first_name":"Martin"}],"date_created":"2021-07-28T08:13:57Z","year":"2014","doi":"10.1371/journal.pcbi.1003818.s001","day":"11","related_material":{"record":[{"status":"public","id":"2039","relation":"used_in_publication"}]},"title":"Detailed proofs for “The time scale of evolutionary innovation”","date_published":"2014-09-11T00:00:00Z","oa_version":"Published Version","publisher":"Public Library of Science","department":[{"_id":"KrCh"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9739","citation":{"ama":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time scale of evolutionary innovation.” 2014. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>","apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., &#38; Novak, M. (2014). Detailed proofs for “The time scale of evolutionary innovation.” Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak. “Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014).","mla":"Chatterjee, Krishnendu, et al. <i>Detailed Proofs for “The Time Scale of Evolutionary Innovation.”</i> Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>.","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for ‘The time scale of evolutionary innovation.’” Public Library of Science, 2014.","ista":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for “The time scale of evolutionary innovation”, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>."}},{"publisher":"Dryad","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5061/dryad.vm0vc","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"SyCr"}],"date_published":"2014-11-13T00:00:00Z","citation":{"apa":"Konrad, M., Grasse, A. V., Tragust, S., &#38; Cremer, S. (2014). Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Dryad. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>.","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host.” Dryad, 2014.","mla":"Konrad, Matthias, et al. <i>Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014).","ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad, <a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>."},"abstract":[{"text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens.","lang":"eng"}],"_id":"9740","oa":1,"author":[{"id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","full_name":"Konrad, Matthias","last_name":"Konrad"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","first_name":"Anna V","last_name":"Grasse"},{"full_name":"Tragust, Simon","first_name":"Simon","last_name":"Tragust","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sylvia","full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"month":"11","type":"research_data_reference","status":"public","article_processing_charge":"No","date_updated":"2023-02-23T10:23:32Z","day":"13","doi":"10.5061/dryad.vm0vc","title":"Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1993"}]},"year":"2014","date_created":"2021-07-28T08:38:40Z"},{"_id":"9741","abstract":[{"text":"In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments.","lang":"eng"}],"citation":{"ista":"Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses, Dryad, <a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>.","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses.” Dryad, 2014.","mla":"Lagator, Mato, et al. <i>Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>.","short":"M. Lagator, N. Colegrave, P. Neve, (2014).","chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.85dn7\">https://doi.org/10.5061/dryad.85dn7</a>.","ama":"Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>","apa":"Lagator, M., Colegrave, N., &#38; Neve, P. (2014). Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Dryad. <a href=\"https://doi.org/10.5061/dryad.85dn7\">https://doi.org/10.5061/dryad.85dn7</a>"},"date_published":"2014-08-21T00:00:00Z","department":[{"_id":"CaGu"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"url":"https://doi.org/10.5061/dryad.85dn7","open_access":"1"}],"oa_version":"Published Version","publisher":"Dryad","date_created":"2021-07-28T08:48:06Z","year":"2014","related_material":{"record":[{"status":"public","id":"2036","relation":"used_in_publication"}]},"title":"Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","doi":"10.5061/dryad.85dn7","day":"21","date_updated":"2023-02-23T10:25:31Z","article_processing_charge":"No","status":"public","type":"research_data_reference","oa":1,"month":"08","author":[{"full_name":"Lagator, Mato","first_name":"Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Colegrave","first_name":"Nick","full_name":"Colegrave, Nick"},{"last_name":"Neve","first_name":"Paul","full_name":"Neve, Paul"}]},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"CaGu"}],"oa_version":"Published Version","publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.s42n1","open_access":"1"}],"date_published":"2014-04-17T00:00:00Z","citation":{"ama":"Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration in adaptation to sink environments. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>","apa":"Lagator, M., Morgan, A., Neve, P., &#38; Colegrave, N. (2014). Data from: Role of sex and migration in adaptation to sink environments. Dryad. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>","chicago":"Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from: Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>.","short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014).","mla":"Lagator, Mato, et al. <i>Data from: Role of Sex and Migration in Adaptation to Sink Environments</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>.","ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex and migration in adaptation to sink environments.” Dryad, 2014.","ista":"Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and migration in adaptation to sink environments, Dryad, <a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>."},"abstract":[{"lang":"eng","text":"Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment."}],"_id":"9747","month":"04","author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","full_name":"Lagator, Mato","first_name":"Mato"},{"last_name":"Morgan","full_name":"Morgan, Andrew","first_name":"Andrew"},{"last_name":"Neve","full_name":"Neve, Paul","first_name":"Paul"},{"first_name":"Nick","full_name":"Colegrave, Nick","last_name":"Colegrave"}],"oa":1,"type":"research_data_reference","article_processing_charge":"No","date_updated":"2023-02-23T10:27:31Z","status":"public","title":"Data from: Role of sex and migration in adaptation to sink environments","related_material":{"record":[{"status":"public","id":"2083","relation":"used_in_publication"}]},"doi":"10.5061/dryad.s42n1","day":"17","year":"2014","date_created":"2021-07-28T15:32:55Z"},{"citation":{"ista":"Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad, <a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>.","ieee":"K. Simmons <i>et al.</i>, “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.","short":"K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).","mla":"Simmons, Kristina, et al. <i>Data from: Transformation of Stimulus Correlations by the Retina</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>.","chicago":"Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation of Stimulus Correlations by the Retina.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>.","apa":"Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations by the retina. Dryad. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>","ama":"Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus correlations by the retina. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>"},"abstract":[{"text":"Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible.","lang":"eng"}],"_id":"9752","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"GaTk"}],"publisher":"Dryad","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.246qg"}],"date_published":"2014-11-07T00:00:00Z","related_material":{"record":[{"id":"2277","relation":"used_in_publication","status":"public"}]},"title":"Data from: Transformation of stimulus correlations by the retina","day":"07","doi":"10.5061/dryad.246qg","year":"2014","date_created":"2021-07-30T08:13:52Z","month":"11","oa":1,"author":[{"last_name":"Simmons","first_name":"Kristina","full_name":"Simmons, Kristina"},{"last_name":"Prentice","first_name":"Jason","full_name":"Prentice, Jason"},{"last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Homann","full_name":"Homann, Jan","first_name":"Jan"},{"full_name":"Yee, Heather","first_name":"Heather","last_name":"Yee"},{"last_name":"Palmer","first_name":"Stephanie","full_name":"Palmer, Stephanie"},{"first_name":"Philip","full_name":"Nelson, Philip","last_name":"Nelson"},{"last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay","first_name":"Vijay"}],"type":"research_data_reference","article_processing_charge":"No","date_updated":"2023-02-23T10:35:57Z","status":"public"},{"month":"10","oa":1,"author":[{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","full_name":"Tragust, Simon","first_name":"Simon","last_name":"Tragust"},{"last_name":"Ugelvig","first_name":"Line V","full_name":"Ugelvig, Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883"},{"full_name":"Chapuisat, Michel","first_name":"Michel","last_name":"Chapuisat"},{"full_name":"Heinze, Jürgen","first_name":"Jürgen","last_name":"Heinze"},{"first_name":"Sylvia","full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"type":"research_data_reference","status":"public","article_processing_charge":"No","date_updated":"2023-02-23T10:36:17Z","doi":"10.5061/dryad.nc0gc","day":"08","related_material":{"record":[{"relation":"used_in_publication","id":"2284","status":"public"}]},"title":"Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies","year":"2014","date_created":"2021-07-30T08:24:11Z","publisher":"Dryad","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5061/dryad.nc0gc","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"SyCr"}],"date_published":"2014-10-08T00:00:00Z","citation":{"chicago":"Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia Cremer. “Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.nc0gc\">https://doi.org/10.5061/dryad.nc0gc</a>.","apa":"Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., &#38; Cremer, S. (2014). Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. Dryad. <a href=\"https://doi.org/10.5061/dryad.nc0gc\">https://doi.org/10.5061/dryad.nc0gc</a>","ama":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>","ista":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2014. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies, Dryad, <a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>.","mla":"Tragust, Simon, et al. <i>Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>.","short":"S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, (2014).","ieee":"S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies.” Dryad, 2014."},"abstract":[{"text":"Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal - originally described for honeybees as “hygienic behaviour” – is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies.","lang":"eng"}],"_id":"9753"},{"article_processing_charge":"No","date_updated":"2023-02-23T10:27:38Z","status":"public","month":"08","author":[{"first_name":"Stephan","full_name":"Wolf, Stephan","last_name":"Wolf"},{"last_name":"Mcmahon","first_name":"Dino","full_name":"Mcmahon, Dino"},{"first_name":"Ka","full_name":"Lim, Ka","last_name":"Lim"},{"full_name":"Pull, Christopher","first_name":"Christopher","last_name":"Pull","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982"},{"last_name":"Clark","full_name":"Clark, Suzanne","first_name":"Suzanne"},{"first_name":"Robert","full_name":"Paxton, Robert","last_name":"Paxton"},{"full_name":"Osborne, Juliet","first_name":"Juliet","last_name":"Osborne"}],"type":"research_data_reference","year":"2014","date_created":"2021-08-11T14:17:53Z","related_material":{"record":[{"relation":"used_in_publication","id":"2086","status":"public"}]},"title":"Supporting information","day":"06","doi":"10.1371/journal.pone.0103989.s003","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"SyCr"}],"publisher":"Public Library of Science","oa_version":"Published Version","_id":"9888","citation":{"ista":"Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. Supporting information, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">10.1371/journal.pone.0103989.s003</a>.","ieee":"S. Wolf <i>et al.</i>, “Supporting information.” Public Library of Science, 2014.","short":"S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, (2014).","mla":"Wolf, Stephan, et al. <i>Supporting Information</i>. Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">10.1371/journal.pone.0103989.s003</a>.","chicago":"Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark, Robert Paxton, and Juliet Osborne. “Supporting Information.” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">https://doi.org/10.1371/journal.pone.0103989.s003</a>.","apa":"Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., &#38; Osborne, J. (2014). Supporting information. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">https://doi.org/10.1371/journal.pone.0103989.s003</a>","ama":"Wolf S, Mcmahon D, Lim K, et al. Supporting information. 2014. doi:<a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">10.1371/journal.pone.0103989.s003</a>"},"abstract":[{"text":"Detailed description of the experimental prodedures, data analyses and additional statistical analyses of the results.","lang":"eng"}]},{"issue":"6","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"title":"Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes","day":"03","doi":"10.1111/evo.12373","year":"2014","external_id":{"pmid":["24495000"]},"date_updated":"2023-02-23T14:13:27Z","intvolume":"        68","status":"public","citation":{"chicago":"Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” <i>Evolution</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/evo.12373\">https://doi.org/10.1111/evo.12373</a>.","ama":"Dhar R, Bergmiller T, Wagner A. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. <i>Evolution</i>. 2014;68(6):1775-1791. doi:<a href=\"https://doi.org/10.1111/evo.12373\">10.1111/evo.12373</a>","apa":"Dhar, R., Bergmiller, T., &#38; Wagner, A. (2014). Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.12373\">https://doi.org/10.1111/evo.12373</a>","ista":"Dhar R, Bergmiller T, Wagner A. 2014. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution. 68(6), 1775–1791.","mla":"Dhar, Riddhiman, et al. “Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” <i>Evolution</i>, vol. 68, no. 6, Wiley, 2014, pp. 1775–91, doi:<a href=\"https://doi.org/10.1111/evo.12373\">10.1111/evo.12373</a>.","short":"R. Dhar, T. Bergmiller, A. Wagner, Evolution 68 (2014) 1775–1791.","ieee":"R. Dhar, T. Bergmiller, and A. Wagner, “Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes,” <i>Evolution</i>, vol. 68, no. 6. Wiley, pp. 1775–1791, 2014."},"publication_status":"published","quality_controlled":"1","department":[{"_id":"CaGu"}],"oa_version":"None","article_type":"original","date_published":"2014-06-03T00:00:00Z","related_material":{"record":[{"status":"public","id":"9932","relation":"research_data"}]},"volume":68,"page":"1775-1791","date_created":"2021-08-17T09:03:09Z","type":"journal_article","language":[{"iso":"eng"}],"author":[{"full_name":"Dhar, Riddhiman","first_name":"Riddhiman","last_name":"Dhar"},{"full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wagner","first_name":"Andreas","full_name":"Wagner, Andreas"}],"month":"06","publication":"Evolution","article_processing_charge":"No","scopus_import":"1","abstract":[{"lang":"eng","text":"Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, subfunctionalization, and neofunctionalization. Little experimental data exist on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in Escherichia coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region."}],"pmid":1,"acknowledgement":"We thank the Functional Genomics Center Zurich for its service in generating sequencing data, M. Ackermann and E. Hayden for helpful discussions, A. de Visser for comments on earlier versions of this manuscript, and M. Moser for help with quantitative PCR. This work was supported by Swiss National Science Foundation (grant 315230–129708), as well as through the YeastX project of SystemsX.ch, and the University Priority Research Program in Systems Biology at the University of Zurich. RD acknowledges support from the Forschungskredit program of the University of Zurich. The authors declare no conflict of interest.","_id":"9931","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Wiley"},{"date_published":"2014-01-27T00:00:00Z","oa_version":"Published Version","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.jc402"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"CaGu"}],"_id":"9932","citation":{"ista":"Dhar R, Bergmiller T, Wagner A. 2014. Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes, Dryad, <a href=\"https://doi.org/10.5061/dryad.jc402\">10.5061/dryad.jc402</a>.","mla":"Dhar, Riddhiman, et al. <i>Data from: Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.jc402\">10.5061/dryad.jc402</a>.","short":"R. Dhar, T. Bergmiller, A. Wagner, (2014).","ieee":"R. Dhar, T. Bergmiller, and A. Wagner, “Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes.” Dryad, 2014.","chicago":"Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Data from: Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.jc402\">https://doi.org/10.5061/dryad.jc402</a>.","ama":"Dhar R, Bergmiller T, Wagner A. Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.jc402\">10.5061/dryad.jc402</a>","apa":"Dhar, R., Bergmiller, T., &#38; Wagner, A. (2014). Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Dryad. <a href=\"https://doi.org/10.5061/dryad.jc402\">https://doi.org/10.5061/dryad.jc402</a>"},"abstract":[{"text":"Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, sub-functionalization, and neo-functionalization. Little experimental data exists on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in E. coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region.","lang":"eng"}],"status":"public","article_processing_charge":"No","date_updated":"2023-02-23T14:13:24Z","author":[{"full_name":"Dhar, Riddhiman","first_name":"Riddhiman","last_name":"Dhar"},{"orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias"},{"first_name":"Andreas","full_name":"Wagner, Andreas","last_name":"Wagner"}],"month":"01","oa":1,"type":"research_data_reference","year":"2014","date_created":"2021-08-17T09:11:40Z","doi":"10.5061/dryad.jc402","day":"27","title":"Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes","related_material":{"record":[{"status":"public","id":"9931","relation":"used_in_publication"}]}},{"_id":"2443","acknowledgement":"The authors thank Dr Christian Luschnig (University of Natural Resources and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds and, last but not least, to Dr David Morris for critical reading of the manuscript. We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance. This work was supported by the Grant Agency of the Czech Republic (P305/11/0797 to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European Research Council starting independent research grant ERC-2011-StG-20101109-PSDP (to J.F.).","abstract":[{"text":"The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery.","lang":"eng"}],"publist_id":"4460","ec_funded":1,"publisher":"Wiley","project":[{"grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"main_file_link":[{"url":"https://doi.org/10.1111/nph.12437","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:57:41Z","page":"1034 - 1048","volume":200,"scopus_import":"1","article_processing_charge":"No","publication":"New Phytologist","language":[{"iso":"eng"}],"author":[{"last_name":"Simon","full_name":"Simon, Sibu","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741"},{"full_name":"Kubeš, Martin","first_name":"Martin","last_name":"Kubeš"},{"id":"3028BD74-F248-11E8-B48F-1D18A9856A87","last_name":"Baster","first_name":"Pawel","full_name":"Baster, Pawel"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"full_name":"Dobrev, Petre","first_name":"Petre","last_name":"Dobrev"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"}],"month":"12","type":"journal_article","quality_controlled":"1","citation":{"apa":"Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová, E. (2013). Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>","ama":"Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. 2013;200(4):1034-1048. doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>","chicago":"Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>.","ieee":"S. Simon <i>et al.</i>, “Defining the selectivity of processes along the auxin response chain: A study using auxin analogues,” <i>New Phytologist</i>, vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.","mla":"Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>, vol. 200, no. 4, Wiley, 2013, pp. 1034–48, doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>.","short":"S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek, E. Zažímalová, New Phytologist 200 (2013) 1034–1048.","ista":"Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová E. 2013. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 200(4), 1034–1048."},"publication_status":"published","date_published":"2013-12-01T00:00:00Z","article_type":"original","oa_version":"Published Version","department":[{"_id":"JiFr"}],"year":"2013","day":"01","doi":"10.1111/nph.12437","issue":"4","title":"Defining the selectivity of processes along the auxin response chain: A study using auxin analogues","status":"public","intvolume":"       200","date_updated":"2025-05-07T11:12:32Z","oa":1},{"title":"Faster algorithms for Markov decision processes with low treewidth","day":"01","doi":"10.1007/978-3-642-39799-8_36","year":"2013","oa":1,"external_id":{"arxiv":["1304.0084"]},"date_updated":"2020-08-11T10:09:47Z","status":"public","intvolume":"      8044","citation":{"chicago":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">https://doi.org/10.1007/978-3-642-39799-8_36</a>.","ama":"Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with low treewidth. 2013;8044:543-558. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">10.1007/978-3-642-39799-8_36</a>","apa":"Chatterjee, K., &#38; Ła̧Cki, J. (2013). Faster algorithms for Markov decision processes with low treewidth. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">https://doi.org/10.1007/978-3-642-39799-8_36</a>","ista":"Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes with low treewidth. 8044, 543–558.","short":"K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558.","mla":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. <i>Faster Algorithms for Markov Decision Processes with Low Treewidth</i>. Vol. 8044, Springer, 2013, pp. 543–58, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">10.1007/978-3-642-39799-8_36</a>.","ieee":"K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013."},"publication_status":"published","arxiv":1,"quality_controlled":"1","department":[{"_id":"KrCh"}],"oa_version":"Preprint","series_title":"Lecture Notes in Computer Science","date_published":"2013-07-01T00:00:00Z","volume":8044,"page":"543 - 558","date_created":"2018-12-11T11:57:42Z","month":"07","conference":{"end_date":"2013-07-19","start_date":"2013-07-13","location":"St. Petersburg, Russia","name":"CAV: Computer Aided Verification"},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Ła̧Cki","full_name":"Ła̧Cki, Jakub","first_name":"Jakub"}],"language":[{"iso":"eng"}],"type":"conference","scopus_import":1,"abstract":[{"text":"We consider two core algorithmic problems for probabilistic verification: the maximal end-component decomposition and the almost-sure reachability set computation for Markov decision processes (MDPs). For MDPs with treewidth k, we present two improved static algorithms for both the problems that run in time O(n·k 2.38·2k ) and O(m·logn· k), respectively, where n is the number of states and m is the number of edges, significantly improving the previous known O(n·k·√n· k) bound for low treewidth. We also present decremental algorithms for both problems for MDPs with constant treewidth that run in amortized logarithmic time, which is a huge improvement over the previously known algorithms that require amortized linear time.","lang":"eng"}],"_id":"2444","alternative_title":["LNCS"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.0084"}],"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"ec_funded":1,"publist_id":"4459"},{"page":"951 - 967","date_created":"2018-12-11T11:57:42Z","related_material":{"record":[{"relation":"dissertation_contains","id":"1130","status":"public"}]},"file_date_updated":"2020-07-14T12:45:40Z","ddc":["000","004"],"volume":8044,"scopus_import":1,"type":"conference","month":"07","language":[{"iso":"eng"}],"author":[{"last_name":"Cerny","full_name":"Cerny, Pavol","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","first_name":"Arjun","last_name":"Radhakrishna"},{"full_name":"Ryzhyk, Leonid","first_name":"Leonid","last_name":"Ryzhyk"},{"orcid":"0000-0003-4409-8487","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","last_name":"Tarrach","first_name":"Thorsten","full_name":"Tarrach, Thorsten"}],"conference":{"name":"CAV: Computer Aided Verification","location":"St. Petersburg, Russia","end_date":"2013-07-19","start_date":"2013-07-13"},"alternative_title":["LNCS"],"_id":"2445","abstract":[{"lang":"eng","text":"We develop program synthesis techniques that can help programmers fix concurrency-related bugs. We make two new contributions to synthesis for concurrency, the first improving the efficiency of the synthesized code, and the second improving the efficiency of the synthesis procedure itself. The first contribution is to have the synthesis procedure explore a variety of (sequential) semantics-preserving program transformations. Classically, only one such transformation has been considered, namely, the insertion of synchronization primitives (such as locks). Based on common manual bug-fixing techniques used by Linux device-driver developers, we explore additional, more efficient transformations, such as the reordering of independent instructions. The second contribution is to speed up the counterexample-guided removal of concurrency bugs within the synthesis procedure by considering partial-order traces (instead of linear traces) as counterexamples. A partial-order error trace represents a set of linear (interleaved) traces of a concurrent program all of which lead to the same error. By eliminating a partial-order error trace, we eliminate in a single iteration of the synthesis procedure all linearizations of the partial-order trace. We evaluated our techniques on several simplified examples of real concurrency bugs that occurred in Linux device drivers."}],"ec_funded":1,"publist_id":"4458","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"publisher":"Springer","year":"2013","has_accepted_license":"1","title":"Efficient synthesis for concurrency by semantics-preserving transformations","doi":"10.1007/978-3-642-39799-8_68","day":"01","date_updated":"2023-09-07T11:57:01Z","pubrep_id":"199","intvolume":"      8044","status":"public","oa":1,"quality_controlled":"1","publication_status":"published","citation":{"ama":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. Efficient synthesis for concurrency by semantics-preserving transformations. In: Vol 8044. Springer; 2013:951-967. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">10.1007/978-3-642-39799-8_68</a>","apa":"Cerny, P., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., &#38; Tarrach, T. (2013). Efficient synthesis for concurrency by semantics-preserving transformations (Vol. 8044, pp. 951–967). Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">https://doi.org/10.1007/978-3-642-39799-8_68</a>","chicago":"Cerny, Pavol, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, and Thorsten Tarrach. “Efficient Synthesis for Concurrency by Semantics-Preserving Transformations,” 8044:951–67. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">https://doi.org/10.1007/978-3-642-39799-8_68</a>.","mla":"Cerny, Pavol, et al. <i>Efficient Synthesis for Concurrency by Semantics-Preserving Transformations</i>. Vol. 8044, Springer, 2013, pp. 951–67, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">10.1007/978-3-642-39799-8_68</a>.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer, 2013, pp. 951–967.","ieee":"P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Efficient synthesis for concurrency by semantics-preserving transformations,” presented at the CAV: Computer Aided Verification, St. Petersburg, Russia, 2013, vol. 8044, pp. 951–967.","ista":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. 2013. Efficient synthesis for concurrency by semantics-preserving transformations. CAV: Computer Aided Verification, LNCS, vol. 8044, 951–967."},"date_published":"2013-07-01T00:00:00Z","department":[{"_id":"ToHe"}],"file":[{"content_type":"application/pdf","file_id":"5158","date_created":"2018-12-12T10:15:37Z","creator":"system","date_updated":"2020-07-14T12:45:40Z","file_name":"IST-2014-199-v1+1_cav2013-final.pdf","file_size":365548,"checksum":"70c70ca5487faba82262c63e1b678a27","access_level":"open_access","relation":"main_file"}],"oa_version":"Submitted Version"},{"volume":8044,"date_created":"2018-12-11T11:57:42Z","page":"559 - 575","type":"conference","month":"07","language":[{"iso":"eng"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Gaiser, Andreas","first_name":"Andreas","last_name":"Gaiser"},{"orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","full_name":"Kretinsky, Jan","first_name":"Jan"}],"conference":{"end_date":"2013-07-19","start_date":"2013-07-13","location":"St. Petersburg, Russia","name":"CAV: Computer Aided Verification"},"scopus_import":1,"abstract":[{"lang":"eng","text":"The model-checking problem for probabilistic systems crucially relies on the translation of LTL to deterministic Rabin automata (DRW). Our recent Safraless translation [KE12, GKE12] for the LTL(F,G) fragment produces smaller automata as compared to the traditional approach. In this work, instead of DRW we consider deterministic automata with acceptance condition given as disjunction of generalized Rabin pairs (DGRW). The Safraless translation of LTL(F,G) formulas to DGRW results in smaller automata as compared to DRW. We present algorithms for probabilistic model-checking as well as game solving for DGRW conditions. Our new algorithms lead to improvement both in terms of theoretical bounds as well as practical evaluation. We compare PRISM with and without our new translation, and show that the new translation leads to significant improvements."}],"alternative_title":["LNCS"],"_id":"2446","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.5281"}],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4457","ec_funded":1,"doi":"10.1007/978-3-642-39799-8_37","day":"01","title":"Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis","year":"2013","external_id":{"arxiv":["1304.5281"]},"oa":1,"intvolume":"      8044","status":"public","date_updated":"2020-08-11T10:09:47Z","publication_status":"published","citation":{"chicago":"Chatterjee, Krishnendu, Andreas Gaiser, and Jan Kretinsky. “Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">https://doi.org/10.1007/978-3-642-39799-8_37</a>.","ama":"Chatterjee K, Gaiser A, Kretinsky J. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 2013;8044:559-575. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">10.1007/978-3-642-39799-8_37</a>","apa":"Chatterjee, K., Gaiser, A., &#38; Kretinsky, J. (2013). Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">https://doi.org/10.1007/978-3-642-39799-8_37</a>","ista":"Chatterjee K, Gaiser A, Kretinsky J. 2013. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 8044, 559–575.","short":"K. Chatterjee, A. Gaiser, J. Kretinsky, 8044 (2013) 559–575.","mla":"Chatterjee, Krishnendu, et al. <i>Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis</i>. Vol. 8044, Springer, 2013, pp. 559–75, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">10.1007/978-3-642-39799-8_37</a>.","ieee":"K. Chatterjee, A. Gaiser, and J. Kretinsky, “Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis,” vol. 8044. Springer, pp. 559–575, 2013."},"quality_controlled":"1","arxiv":1,"series_title":"Lecture Notes in Computer Science","oa_version":"Preprint","department":[{"_id":"KrCh"}],"date_published":"2013-07-01T00:00:00Z"},{"conference":{"start_date":"2013-07-13","end_date":"2013-07-19","name":"CAV: Computer Aided Verification","location":"St. Petersburg, Russia"},"author":[{"last_name":"Piskac","full_name":"Piskac, Ruzica","first_name":"Ruzica"},{"last_name":"Wies","full_name":"Wies, Thomas","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zufferey, Damien","first_name":"Damien","last_name":"Zufferey","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"month":"07","type":"conference","scopus_import":1,"article_processing_charge":"No","volume":8044,"ddc":["000"],"file_date_updated":"2020-07-14T12:45:41Z","date_created":"2018-12-11T11:57:43Z","page":"773 - 789","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4456","abstract":[{"lang":"eng","text":"Separation logic (SL) has gained widespread popularity because of its ability to succinctly express complex invariants of a program’s heap configurations. Several specialized provers have been developed for decidable SL fragments. However, these provers cannot be easily extended or combined with solvers for other theories that are important in program verification, e.g., linear arithmetic. In this paper, we present a reduction of decidable SL fragments to a decidable first-order theory that fits well into the satisfiability modulo theories (SMT) framework. We show how to use this reduction to automate satisfiability, entailment, frame inference, and abduction problems for separation logic using SMT solvers. Our approach provides a simple method of integrating separation logic into existing verification tools that provide SMT backends, and an elegant way of combining SL fragments with other decidable first-order theories. We implemented this approach in a verification tool and applied it to heap-manipulating programs whose verification involves reasoning in theory combinations.\r\n"}],"_id":"2447","alternative_title":["LNCS"],"oa":1,"status":"public","intvolume":"      8044","date_updated":"2020-08-11T10:09:47Z","doi":"10.1007/978-3-642-39799-8_54","day":"01","has_accepted_license":"1","title":"Automating separation logic using SMT","year":"2013","oa_version":"Submitted Version","file":[{"creator":"dernst","file_id":"7859","content_type":"application/pdf","date_created":"2020-05-15T11:13:01Z","file_name":"2013_CAV_Piskac.pdf","access_level":"open_access","relation":"main_file","file_size":309182,"checksum":"2e866932ab688f47ecd504acb4d5c7d4","date_updated":"2020-07-14T12:45:41Z"}],"series_title":"Lecture Notes in Computer Science","department":[{"_id":"ToHe"}],"date_published":"2013-07-01T00:00:00Z","citation":{"ista":"Piskac R, Wies T, Zufferey D. 2013. Automating separation logic using SMT. 8044, 773–789.","ieee":"R. Piskac, T. Wies, and D. Zufferey, “Automating separation logic using SMT,” vol. 8044. Springer, pp. 773–789, 2013.","short":"R. Piskac, T. Wies, D. Zufferey, 8044 (2013) 773–789.","mla":"Piskac, Ruzica, et al. <i>Automating Separation Logic Using SMT</i>. Vol. 8044, Springer, 2013, pp. 773–89, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">10.1007/978-3-642-39799-8_54</a>.","chicago":"Piskac, Ruzica, Thomas Wies, and Damien Zufferey. “Automating Separation Logic Using SMT.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">https://doi.org/10.1007/978-3-642-39799-8_54</a>.","ama":"Piskac R, Wies T, Zufferey D. Automating separation logic using SMT. 2013;8044:773-789. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">10.1007/978-3-642-39799-8_54</a>","apa":"Piskac, R., Wies, T., &#38; Zufferey, D. (2013). Automating separation logic using SMT. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">https://doi.org/10.1007/978-3-642-39799-8_54</a>"},"publication_status":"published","quality_controlled":"1"},{"quality_controlled":"1","publication_status":"published","citation":{"chicago":"Remy, Estelle, Pawel Baster, Jiří Friml, and Paula Duque. “ZIFL1.1 Transporter Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis, 2013. <a href=\"https://doi.org/10.4161/psb.25688\">https://doi.org/10.4161/psb.25688</a>.","ama":"Remy E, Baster P, Friml J, Duque P. ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. <i>Plant Signaling &#38; Behavior</i>. 2013;8(10). doi:<a href=\"https://doi.org/10.4161/psb.25688\">10.4161/psb.25688</a>","apa":"Remy, E., Baster, P., Friml, J., &#38; Duque, P. (2013). ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.4161/psb.25688\">https://doi.org/10.4161/psb.25688</a>","ista":"Remy E, Baster P, Friml J, Duque P. 2013. ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. Plant Signaling &#38; Behavior. 8(10), e25688.","ieee":"E. Remy, P. Baster, J. Friml, and P. Duque, “ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip,” <i>Plant Signaling &#38; Behavior</i>, vol. 8, no. 10. Taylor &#38; Francis, 2013.","mla":"Remy, Estelle, et al. “ZIFL1.1 Transporter Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” <i>Plant Signaling &#38; Behavior</i>, vol. 8, no. 10, e25688, Taylor &#38; Francis, 2013, doi:<a href=\"https://doi.org/10.4161/psb.25688\">10.4161/psb.25688</a>.","short":"E. Remy, P. Baster, J. Friml, P. Duque, Plant Signaling &#38; Behavior 8 (2013)."},"date_published":"2013-07-10T00:00:00Z","article_type":"original","department":[{"_id":"JiFr"}],"oa_version":"Submitted Version","year":"2013","title":"ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip","issue":"10","article_number":"e25688","day":"10","doi":"10.4161/psb.25688","date_updated":"2025-05-07T11:12:32Z","status":"public","intvolume":"         8","oa":1,"external_id":{"pmid":["23857365"]},"pmid":1,"_id":"2448","abstract":[{"lang":"eng","text":"Cell-to-cell directional flow of the phytohormone auxin is primarily established by polar localization of the PIN auxin transporters, a process tightly regulated at multiple levels by auxin itself. We recently reported that, in the context of strong auxin flows, activity of the vacuolar ZIFL1.1 transporter is required for fine-tuning of polar auxin transport rates in the Arabidopsis root. In particular, ZIFL1.1 function protects plasma-membrane stability of the PIN2 carrier in epidermal root tip cells under conditions normally triggering PIN2 degradation. Here, we show that ZIFL1.1 activity at the root tip also promotes PIN1 plasma-membrane abundance in central cylinder cells, thus supporting the notion that ZIFL1.1 acts as a general positive modulator of polar auxin transport in roots."}],"ec_funded":1,"publist_id":"4455","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Taylor & Francis","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091088/","open_access":"1"}],"date_created":"2018-12-11T11:57:43Z","volume":8,"article_processing_charge":"No","publication":"Plant Signaling & Behavior","scopus_import":"1","month":"07","language":[{"iso":"eng"}],"author":[{"last_name":"Remy","first_name":"Estelle","full_name":"Remy, Estelle"},{"first_name":"Pawel","full_name":"Baster, Pawel","last_name":"Baster","id":"3028BD74-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"last_name":"Duque","full_name":"Duque, Paula","first_name":"Paula"}],"type":"journal_article"},{"publist_id":"4454","date_published":"2013-11-01T00:00:00Z","publisher":"Cell Press","oa_version":"None","department":[{"_id":"JiFr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2449","quality_controlled":"1","abstract":[{"lang":"eng","text":"Intracellular protein routing is mediated by vesicular transport which is tightly regulated in eukaryotes. The protein and lipid homeostasis depends on coordinated delivery of de novo synthesized or recycled cargoes to the plasma membrane by exocytosis and their subsequent removal by rerouting them for recycling or degradation. Here, we report the characterization of protein affected trafficking 3 (pat3) mutant that we identified by an epifluorescence-based forward genetic screen for mutants defective in subcellular distribution of Arabidopsis auxin transporter PIN1–GFP. While pat3 displays largely normal plant morphology and development in nutrient-rich conditions, it shows strong ectopic intracellular accumulations of different plasma membrane cargoes in structures that resemble prevacuolar compartments (PVC) with an aberrant morphology. Genetic mapping revealed that pat3 is defective in vacuolar protein sorting 35A (VPS35A), a putative subunit of the retromer complex that mediates retrograde trafficking between the PVC and trans-Golgi network. Similarly, a mutant defective in another retromer subunit, vps29, shows comparable subcellular defects in PVC morphology and protein accumulation. Thus, our data provide evidence that the retromer components VPS35A and VPS29 are essential for normal PVC morphology and normal trafficking of plasma membrane proteins in plants. In addition, we show that, out of the three VPS35 retromer subunits present in Arabidopsis thaliana genome, the VPS35 homolog A plays a prevailing role in trafficking to the lytic vacuole, presenting another level of complexity in the retromer-dependent vacuolar sorting. "}],"citation":{"chicago":"Nodzyński, Tomasz, Murguel Feraru, Sibylle Hirsch, Riet De Rycke, Claudiu Nicuales, Jelle Van Leene, Geert De Jaeger, Steffen Vanneste, and Jiří Friml. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” <i>Molecular Plant</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1093/mp/sst044\">https://doi.org/10.1093/mp/sst044</a>.","ama":"Nodzyński T, Feraru M, Hirsch S, et al. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. <i>Molecular Plant</i>. 2013;6(6):1849-1862. doi:<a href=\"https://doi.org/10.1093/mp/sst044\">10.1093/mp/sst044</a>","apa":"Nodzyński, T., Feraru, M., Hirsch, S., De Rycke, R., Nicuales, C., Van Leene, J., … Friml, J. (2013). Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. <i>Molecular Plant</i>. Cell Press. <a href=\"https://doi.org/10.1093/mp/sst044\">https://doi.org/10.1093/mp/sst044</a>","ista":"Nodzyński T, Feraru M, Hirsch S, De Rycke R, Nicuales C, Van Leene J, De Jaeger G, Vanneste S, Friml J. 2013. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. 6(6), 1849–1862.","short":"T. Nodzyński, M. Feraru, S. Hirsch, R. De Rycke, C. Nicuales, J. Van Leene, G. De Jaeger, S. Vanneste, J. Friml, Molecular Plant 6 (2013) 1849–1862.","mla":"Nodzyński, Tomasz, et al. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” <i>Molecular Plant</i>, vol. 6, no. 6, Cell Press, 2013, pp. 1849–62, doi:<a href=\"https://doi.org/10.1093/mp/sst044\">10.1093/mp/sst044</a>.","ieee":"T. Nodzyński <i>et al.</i>, “Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis,” <i>Molecular Plant</i>, vol. 6, no. 6. Cell Press, pp. 1849–1862, 2013."},"publication_status":"published","scopus_import":1,"intvolume":"         6","status":"public","publication":"Molecular Plant","date_updated":"2021-01-12T06:57:33Z","type":"journal_article","author":[{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"full_name":"Feraru, Murguel","first_name":"Murguel","last_name":"Feraru"},{"last_name":"Hirsch","first_name":"Sibylle","full_name":"Hirsch, Sibylle"},{"last_name":"De Rycke","full_name":"De Rycke, Riet","first_name":"Riet"},{"last_name":"Nicuales","first_name":"Claudiu","full_name":"Nicuales, Claudiu"},{"last_name":"Van Leene","full_name":"Van Leene, Jelle","first_name":"Jelle"},{"last_name":"De Jaeger","full_name":"De Jaeger, Geert","first_name":"Geert"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"month":"11","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:57:44Z","year":"2013","page":"1849 - 1862","day":"01","doi":"10.1093/mp/sst044","title":"Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis","issue":"6","volume":6},{"has_accepted_license":"1","issue":"4","title":"Highly adaptive liquid simulations on tetrahedral meshes","article_number":"103","doi":"10.1145/2461912.2461982","day":"01","year":"2013","oa":1,"pubrep_id":"605","date_updated":"2024-11-19T11:56:45Z","status":"public","intvolume":"        32","publication_status":"published","quality_controlled":"1","department":[{"_id":"ChWo"}],"oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:45:41Z","access_level":"open_access","relation":"main_file","file_size":8601561,"checksum":"aeea6b0ff2b27c695aeb8408c7d2fc50","file_name":"IST-2016-605-v1+1_tetflip_fixed.pdf","date_created":"2018-12-12T10:17:25Z","file_id":"5279","content_type":"application/pdf","creator":"system"}],"date_published":"2013-07-01T00:00:00Z","volume":32,"ddc":["000"],"file_date_updated":"2020-07-14T12:45:41Z","date_created":"2018-12-11T11:57:50Z","month":"07","language":[{"iso":"eng"}],"author":[{"full_name":"Ando, Ryoichi","first_name":"Ryoichi","last_name":"Ando"},{"last_name":"Thuerey","first_name":"Nils","full_name":"Thuerey, Nils"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","full_name":"Wojtan, Christopher J","last_name":"Wojtan"}],"type":"journal_article","article_processing_charge":"No","publication":"ACM Transactions on Graphics","scopus_import":"1","abstract":[{"text":"We introduce a new method for efficiently simulating liquid with extreme amounts of spatial adaptivity. Our method combines several key components to drastically speed up the simulation of large-scale fluid phenomena: We leverage an alternative Eulerian tetrahedral mesh discretization to significantly reduce the complexity of the pressure solve while increasing the robustness with respect to element quality and removing the possibility of locking. Next, we enable subtle free-surface phenomena by deriving novel second-order boundary conditions consistent with our discretization. We couple this discretization with a spatially adaptive Fluid-Implicit Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations that can undergo sharp changes in spatial resolution while minimizing artifacts. Along the way, we provide a new method for generating a smooth and detailed surface from a set of particles with variable sizes. Finally, we explore several new sizing functions for determining spatially adaptive simulation resolutions, and we show how to couple them to our simulator. We combine each of these elements to produce a simulation algorithm that is capable of creating animations at high maximum resolutions while avoiding common pitfalls like inaccurate boundary conditions and inefficient computation.","lang":"eng"}],"_id":"2466","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","publist_id":"4436"},{"date_created":"2018-12-11T11:57:50Z","ddc":["000"],"volume":32,"file_date_updated":"2020-07-14T12:45:41Z","publication":"ACM Transactions on Graphics","scopus_import":1,"month":"07","author":[{"last_name":"Bernstein","full_name":"Bernstein, Gilbert","first_name":"Gilbert"},{"last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"type":"journal_article","_id":"2467","abstract":[{"text":"This paper presents a method for computing topology changes for triangle meshes in an interactive geometric modeling environment. Most triangle meshes in practice do not exhibit desirable geometric properties, so we develop a solution that is independent of standard assumptions and robust to geometric errors. Specifically, we provide the first method for topology change applicable to arbitrary non-solid, non-manifold, non-closed, self-intersecting surfaces. We prove that this new method for topology change produces the expected conventional results when applied to solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a backwards-compatibility property relative to prior work. Beyond solid surfaces, we present empirical evidence that our method remains tolerant to a variety of surface aberrations through the incorporation of a novel error correction scheme. Finally, we demonstrate how topology change applied to non-solid objects enables wholly new and useful behaviors.","lang":"eng"}],"publist_id":"4435","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","year":"2013","issue":"4","has_accepted_license":"1","title":"Putting holes in holey geometry: Topology change for arbitrary surfaces","article_number":"34","doi":"10.1145/2461912.2462027","day":"01","pubrep_id":"604","date_updated":"2023-02-23T10:44:16Z","status":"public","intvolume":"        32","oa":1,"quality_controlled":"1","publication_status":"published","citation":{"ama":"Bernstein G, Wojtan C. Putting holes in holey geometry: Topology change for arbitrary surfaces. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2462027\">10.1145/2461912.2462027</a>","apa":"Bernstein, G., &#38; Wojtan, C. (2013). Putting holes in holey geometry: Topology change for arbitrary surfaces. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2462027\">https://doi.org/10.1145/2461912.2462027</a>","chicago":"Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2462027\">https://doi.org/10.1145/2461912.2462027</a>.","mla":"Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, 34, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2462027\">10.1145/2461912.2462027</a>.","short":"G. Bernstein, C. Wojtan, ACM Transactions on Graphics 32 (2013).","ieee":"G. Bernstein and C. Wojtan, “Putting holes in holey geometry: Topology change for arbitrary surfaces,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","ista":"Bernstein G, Wojtan C. 2013. Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. 32(4), 34."},"date_published":"2013-07-01T00:00:00Z","department":[{"_id":"ChWo"}],"file":[{"file_name":"IST-2016-604-v1+1_toptop2013.pdf","relation":"main_file","access_level":"open_access","checksum":"9c8425d62246996ca632c5a01870515b","file_size":3514674,"date_updated":"2020-07-14T12:45:41Z","creator":"system","file_id":"4768","content_type":"application/pdf","date_created":"2018-12-12T10:09:43Z"}],"oa_version":"Submitted Version"},{"publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4434","abstract":[{"lang":"eng","text":"Our work concerns the combination of an Eulerian liquid simulation with a high-resolution surface tracker (e.g. the level set method or a Lagrangian triangle mesh). The naive application of a high-resolution surface tracker to a low-resolution velocity field can produce many visually disturbing physical and topological artifacts that limit their use in practice. We address these problems by defining an error function which compares the current state of the surface tracker to the set of physically valid surface states. By reducing this error with a gradient descent technique, we introduce a novel physics-based surface fairing method. Similarly, by treating this error function as a potential energy, we derive a new surface correction force that mimics the vortex sheet equations. We demonstrate our results with both level set and mesh-based surface trackers."}],"_id":"2468","author":[{"id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4417-3224","full_name":"Bojsen-Hansen, Morten","first_name":"Morten","last_name":"Bojsen-Hansen"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","full_name":"Wojtan, Christopher J","first_name":"Christopher J"}],"language":[{"iso":"eng"}],"month":"07","type":"journal_article","scopus_import":1,"publication":"ACM Transactions on Graphics","ddc":["000"],"volume":32,"file_date_updated":"2020-07-14T12:45:41Z","date_created":"2018-12-11T11:57:50Z","file":[{"creator":"system","content_type":"application/pdf","file_id":"4761","date_created":"2018-12-12T10:09:37Z","file_name":"IST-2016-603-v1+1_liquidError_web.pdf","file_size":5813685,"checksum":"53d905e0180e23ef3e813b969ffed4e1","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:45:41Z"}],"oa_version":"Submitted Version","department":[{"_id":"ChWo"}],"date_published":"2013-07-01T00:00:00Z","publication_status":"published","citation":{"apa":"Bojsen-Hansen, M., &#38; Wojtan, C. (2013). Liquid surface tracking with error compensation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461991\">https://doi.org/10.1145/2461912.2461991</a>","ama":"Bojsen-Hansen M, Wojtan C. Liquid surface tracking with error compensation. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461991\">10.1145/2461912.2461991</a>","chicago":"Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461991\">https://doi.org/10.1145/2461912.2461991</a>.","short":"M. Bojsen-Hansen, C. Wojtan, ACM Transactions on Graphics 32 (2013).","mla":"Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, 68, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461991\">10.1145/2461912.2461991</a>.","ieee":"M. Bojsen-Hansen and C. Wojtan, “Liquid surface tracking with error compensation,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","ista":"Bojsen-Hansen M, Wojtan C. 2013. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 32(4), 68."},"quality_controlled":"1","oa":1,"status":"public","intvolume":"        32","pubrep_id":"603","date_updated":"2023-02-23T10:44:18Z","article_number":"68","doi":"10.1145/2461912.2461991","day":"01","title":"Liquid surface tracking with error compensation","issue":"4","has_accepted_license":"1","year":"2013"},{"quality_controlled":"1","citation":{"ama":"Maître J-L, Heisenberg C-PJ. Three functions of cadherins in cell adhesion. <i>Current Biology</i>. 2013;23(14):R626-R633. doi:<a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">10.1016/j.cub.2013.06.019</a>","apa":"Maître, J.-L., &#38; Heisenberg, C.-P. J. (2013). Three functions of cadherins in cell adhesion. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">https://doi.org/10.1016/j.cub.2013.06.019</a>","chicago":"Maître, Jean-Léon, and Carl-Philipp J Heisenberg. “Three Functions of Cadherins in Cell Adhesion.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">https://doi.org/10.1016/j.cub.2013.06.019</a>.","ieee":"J.-L. Maître and C.-P. J. Heisenberg, “Three functions of cadherins in cell adhesion,” <i>Current Biology</i>, vol. 23, no. 14. Cell Press, pp. R626–R633, 2013.","mla":"Maître, Jean-Léon, and Carl-Philipp J. Heisenberg. “Three Functions of Cadherins in Cell Adhesion.” <i>Current Biology</i>, vol. 23, no. 14, Cell Press, 2013, pp. R626–33, doi:<a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">10.1016/j.cub.2013.06.019</a>.","short":"J.-L. Maître, C.-P.J. Heisenberg, Current Biology 23 (2013) R626–R633.","ista":"Maître J-L, Heisenberg C-PJ. 2013. Three functions of cadherins in cell adhesion. Current Biology. 23(14), R626–R633."},"publication_status":"published","date_published":"2013-07-22T00:00:00Z","oa_version":"Published Version","file":[{"date_created":"2019-01-24T15:40:22Z","content_type":"application/pdf","file_id":"5881","creator":"dernst","date_updated":"2020-07-14T12:45:41Z","file_size":247320,"checksum":"6a424b2f007b41d4955a9135793b2162","access_level":"open_access","relation":"main_file","file_name":"2013_CurrentBiology_Maitre.pdf"}],"department":[{"_id":"CaHe"}],"year":"2013","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1016/j.cub.2013.06.019","day":"22","issue":"14","has_accepted_license":"1","title":"Three functions of cadherins in cell adhesion","status":"public","intvolume":"        23","date_updated":"2021-01-12T06:57:40Z","external_id":{"pmid":["23885883"]},"oa":1,"_id":"2469","pmid":1,"abstract":[{"text":"Cadherins are transmembrane proteins that mediate cell–cell adhesion in animals. By regulating contact formation and stability, cadherins play a crucial role in tissue morphogenesis and homeostasis. Here, we review the three major  unctions of cadherins in cell–cell contact formation and stability. Two of those functions lead to a decrease in interfacial ension at the forming cell–cell contact, thereby promoting contact expansion — first, by providing adhesion tension that lowers interfacial tension at the cell–cell contact, and second, by signaling to the actomyosin cytoskeleton in order to reduce cortex tension and thus interfacial tension at the contact. The third function of cadherins in cell–cell contact formation is to stabilize the contact by resisting mechanical forces that pull on the contact.","lang":"eng"}],"publist_id":"4433","publisher":"Cell Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:57:51Z","page":"R626 - R633","volume":23,"ddc":["570"],"file_date_updated":"2020-07-14T12:45:41Z","scopus_import":1,"publication":"Current Biology","month":"07","language":[{"iso":"eng"}],"author":[{"id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3688-1474","last_name":"Maître","full_name":"Maître, Jean-Léon","first_name":"Jean-Léon"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"type":"journal_article"}]