[{"month":"11","department":[{"_id":"JoCs"}],"date_updated":"2023-02-23T10:24:07Z","title":"Transition probability between TF expression states when Dbx2 inhibits Nkx2.2","article_processing_charge":"No","year":"2014","author":[{"full_name":"Lovrics, Anna","last_name":"Lovrics","first_name":"Anna"},{"last_name":"Gao","full_name":"Gao, Yu","first_name":"Yu"},{"first_name":"Bianka","full_name":"Juhász, Bianka","last_name":"Juhász"},{"first_name":"István","last_name":"Bock","full_name":"Bock, István"},{"last_name":"Byrne","full_name":"Byrne, Helen M.","first_name":"Helen M."},{"first_name":"András","last_name":"Dinnyés","full_name":"Dinnyés, András"},{"id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztián","full_name":"Kovács, Krisztián","last_name":"Kovács"}],"date_published":"2014-11-14T00:00:00Z","oa_version":"Published Version","doi":"10.1371/journal.pone.0111430.s006","day":"14","date_created":"2021-07-26T14:35:00Z","publisher":"Public Library of Science","_id":"9722","status":"public","related_material":{"record":[{"id":"2004","status":"public","relation":"used_in_publication"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","citation":{"ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","mla":"Lovrics, Anna, et al. <i>Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2</i>. Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>.","ama":"Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. 2014. doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>","ieee":"A. Lovrics <i>et al.</i>, “Transition probability between TF expression states when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács, (2014).","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., &#38; Kovács, K. (2014). Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>"}},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2039"}]},"status":"public","citation":{"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>.","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>","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>.","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>.","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>","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014).","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for ‘The time scale of evolutionary innovation.’” Public Library of Science, 2014."},"type":"research_data_reference","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis"},{"first_name":"Ben","last_name":"Adlam","full_name":"Adlam, Ben"},{"first_name":"Martin","full_name":"Novak, Martin","last_name":"Novak"}],"date_published":"2014-09-11T00:00:00Z","year":"2014","article_processing_charge":"No","date_updated":"2023-02-23T10:25:37Z","title":"Detailed proofs for “The time scale of evolutionary innovation”","department":[{"_id":"KrCh"}],"month":"09","_id":"9739","publisher":"Public Library of Science","date_created":"2021-07-28T08:13:57Z","day":"11","doi":"10.1371/journal.pcbi.1003818.s001","oa_version":"Published Version"},{"oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"id":"1993","status":"public","relation":"used_in_publication"}]},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.vm0vc","open_access":"1"}],"abstract":[{"lang":"eng","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."}],"status":"public","type":"research_data_reference","citation":{"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.","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>","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>.","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>.","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>.","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>"},"year":"2014","article_processing_charge":"No","author":[{"full_name":"Konrad, Matthias","last_name":"Konrad","id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","last_name":"Grasse"},{"first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","full_name":"Tragust, Simon","last_name":"Tragust"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"date_published":"2014-11-13T00:00:00Z","department":[{"_id":"SyCr"}],"date_updated":"2023-02-23T10:23:32Z","title":"Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","month":"11","_id":"9740","publisher":"Dryad","day":"13","date_created":"2021-07-28T08:38:40Z","doi":"10.5061/dryad.vm0vc","oa_version":"Published Version"},{"month":"08","title":"Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","date_updated":"2023-02-23T10:25:31Z","department":[{"_id":"CaGu"}],"date_published":"2014-08-21T00:00:00Z","author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","last_name":"Lagator","full_name":"Lagator, Mato"},{"first_name":"Nick","full_name":"Colegrave, Nick","last_name":"Colegrave"},{"full_name":"Neve, Paul","last_name":"Neve","first_name":"Paul"}],"article_processing_charge":"No","year":"2014","oa_version":"Published Version","doi":"10.5061/dryad.85dn7","date_created":"2021-07-28T08:48:06Z","day":"21","_id":"9741","publisher":"Dryad","status":"public","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"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2036"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.85dn7"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"citation":{"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>","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>.","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>.","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>.","short":"M. Lagator, N. Colegrave, P. Neve, (2014).","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>","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."},"type":"research_data_reference"},{"citation":{"ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex and migration in adaptation to sink environments.” Dryad, 2014.","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>","short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, (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>.","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>.","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>.","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>"},"type":"research_data_reference","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."}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2083"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s42n1"}],"status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"doi":"10.5061/dryad.s42n1","oa_version":"Published Version","publisher":"Dryad","_id":"9747","date_created":"2021-07-28T15:32:55Z","day":"17","title":"Data from: Role of sex and migration in adaptation to sink environments","date_updated":"2023-02-23T10:27:31Z","department":[{"_id":"CaGu"}],"month":"04","author":[{"full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrew","last_name":"Morgan","full_name":"Morgan, Andrew"},{"first_name":"Paul","full_name":"Neve, Paul","last_name":"Neve"},{"last_name":"Colegrave","full_name":"Colegrave, Nick","first_name":"Nick"}],"date_published":"2014-04-17T00:00:00Z","article_processing_charge":"No","year":"2014"},{"oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","related_material":{"record":[{"id":"2277","status":"public","relation":"used_in_publication"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.246qg"}],"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"}],"citation":{"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>","short":"K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).","ieee":"K. Simmons <i>et al.</i>, “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.","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>.","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>","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>.","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>."},"type":"research_data_reference","year":"2014","article_processing_charge":"No","date_published":"2014-11-07T00:00:00Z","author":[{"first_name":"Kristina","last_name":"Simmons","full_name":"Simmons, Kristina"},{"full_name":"Prentice, Jason","last_name":"Prentice","first_name":"Jason"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"first_name":"Jan","full_name":"Homann, Jan","last_name":"Homann"},{"full_name":"Yee, Heather","last_name":"Yee","first_name":"Heather"},{"full_name":"Palmer, Stephanie","last_name":"Palmer","first_name":"Stephanie"},{"full_name":"Nelson, Philip","last_name":"Nelson","first_name":"Philip"},{"last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay","first_name":"Vijay"}],"month":"11","department":[{"_id":"GaTk"}],"title":"Data from: Transformation of stimulus correlations by the retina","date_updated":"2023-02-23T10:35:57Z","day":"07","date_created":"2021-07-30T08:13:52Z","_id":"9752","publisher":"Dryad","oa_version":"Published Version","doi":"10.5061/dryad.246qg"},{"related_material":{"record":[{"id":"2284","status":"public","relation":"used_in_publication"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.nc0gc"}],"abstract":[{"lang":"eng","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."}],"status":"public","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","citation":{"short":"S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, (2014).","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>","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.","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>.","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>."},"department":[{"_id":"SyCr"}],"title":"Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies","date_updated":"2023-02-23T10:36:17Z","month":"10","year":"2014","article_processing_charge":"No","date_published":"2014-10-08T00:00:00Z","author":[{"last_name":"Tragust","full_name":"Tragust, Simon","first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ugelvig","full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V"},{"full_name":"Chapuisat, Michel","last_name":"Chapuisat","first_name":"Michel"},{"last_name":"Heinze","full_name":"Heinze, Jürgen","first_name":"Jürgen"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"doi":"10.5061/dryad.nc0gc","oa_version":"Published Version","publisher":"Dryad","_id":"9753","day":"08","date_created":"2021-07-30T08:24:11Z"},{"acknowledgement":"We thank E. Altman, Y. Bahri, I. Bloch, T. Giamarchi, D. Huse, V. Oganesyan, A. Pal, D. Pekker, and G. Refael for insightful discussions. The authors acknowledge support from the Harvard Quantum Optics Center, Harvard-MIT CUA, the DARPA OLE program, AFOSR Quantum Simulation MURI, ARO-MURI on Atomtronics, the ARO-MURI Quism program, the Austrian Science Fund (FWF) Project No. J 3361-N20, NSERC grant, and Sloan Research Fellowship. Simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University and the Research Computing Center at Harvard University. Research at Perimeter Institute was supported by the Government of Canada and by the Province of Ontario.\n\nM. S., M. K., and S. G. contributed equally to this work.","issue":"14","oa":1,"intvolume":"       113","quality_controlled":0,"status":"public","volume":113,"abstract":[{"text":"We propose a method for detecting many-body localization (MBL) in disordered spin systems. The method involves pulsed coherent spin manipulations that probe the dephasing of a given spin due to its entanglement with a set of distant spins. It allows one to distinguish the MBL phase from a noninteracting localized phase and a delocalized phase. In particular, we show that for a properly chosen pulse sequence the MBL phase exhibits a characteristic power-law decay reflecting its slow growth of entanglement. We find that this power-law decay is robust with respect to thermal and disorder averaging, provide numerical simulations supporting our results, and discuss possible experimental realizations in solid-state and cold-atom systems.","lang":"eng"}],"publication_status":"published","publist_id":"6421","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1403.0693"}],"citation":{"ieee":"M. Serbyn <i>et al.</i>, “Interferometric probes of many-body localization,” <i>Physical Review Letters</i>, vol. 113, no. 14. American Physical Society, 2014.","apa":"Serbyn, M., Knap, M., Gopalakrishnan, S., Papić, Z., Yao, N., Laumann, C., … Demler, E. (2014). Interferometric probes of many-body localization. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.113.147204\">https://doi.org/10.1103/PhysRevLett.113.147204</a>","short":"M. Serbyn, M. Knap, S. Gopalakrishnan, Z. Papić, N. Yao, C. Laumann, D. Abanin, M. Lukin, E. Demler, Physical Review Letters 113 (2014).","mla":"Serbyn, Maksym, et al. “Interferometric Probes of Many-Body Localization.” <i>Physical Review Letters</i>, vol. 113, no. 14, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.113.147204\">10.1103/PhysRevLett.113.147204</a>.","ista":"Serbyn M, Knap M, Gopalakrishnan S, Papić Z, Yao N, Laumann C, Abanin D, Lukin M, Demler E. 2014. Interferometric probes of many-body localization. Physical Review Letters. 113(14).","ama":"Serbyn M, Knap M, Gopalakrishnan S, et al. Interferometric probes of many-body localization. <i>Physical Review Letters</i>. 2014;113(14). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.113.147204\">10.1103/PhysRevLett.113.147204</a>","chicago":"Serbyn, Maksym, Michael Knap, Sarang Gopalakrishnan, Zlatko Papić, Norman Yao, Chris Laumann, Dmitry Abanin, Mikhail Lukin, and Eugene Demler. “Interferometric Probes of Many-Body Localization.” <i>Physical Review Letters</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevLett.113.147204\">https://doi.org/10.1103/PhysRevLett.113.147204</a>."},"type":"journal_article","extern":1,"date_published":"2014-10-03T00:00:00Z","author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Maksym Serbyn","orcid":"0000-0002-2399-5827","last_name":"Serbyn"},{"last_name":"Knap","full_name":"Knap, Michael J","first_name":"Michael"},{"first_name":"Sarang","full_name":"Gopalakrishnan, Sarang","last_name":"Gopalakrishnan"},{"first_name":"Zlatko","full_name":"Papić, Zlatko","last_name":"Papić"},{"last_name":"Yao","full_name":"Yao, Norman Y","first_name":"Norman"},{"first_name":"Chris","full_name":"Laumann, Chris R","last_name":"Laumann"},{"full_name":"Abanin, Dmitry A","last_name":"Abanin","first_name":"Dmitry"},{"last_name":"Lukin","full_name":"Lukin, Mikhail D","first_name":"Mikhail"},{"full_name":"Demler, Eugene A","last_name":"Demler","first_name":"Eugene"}],"year":"2014","month":"10","title":"Interferometric probes of many-body localization","date_updated":"2021-01-12T08:22:22Z","date_created":"2018-12-11T11:49:30Z","day":"03","publisher":"American Physical Society","_id":"977","publication":"Physical Review Letters","doi":"10.1103/PhysRevLett.113.147204"},{"publication":"Nature Physics","doi":"10.1038/nphys3012","page":"572 - 577","publisher":"Nature Publishing Group","_id":"978","day":"01","date_created":"2018-12-11T11:49:30Z","date_updated":"2021-01-12T08:22:23Z","title":"Mapping the unconventional orbital texture in topological crystalline insulators","month":"08","year":"2014","author":[{"first_name":"Ilija","last_name":"Zeljkovic","full_name":"Zeljkovic, Ilija"},{"last_name":"Okada","full_name":"Okada, Yoshinori","first_name":"Yoshinori"},{"first_name":"Chengyi","last_name":"Huang","full_name":"Huang, Chengyi"},{"last_name":"Sankar","full_name":"Sankar, Raman","first_name":"Raman"},{"last_name":"Walkup","full_name":"Walkup, Daniel","first_name":"Daniel"},{"full_name":"Zhou, Wenwen","last_name":"Zhou","first_name":"Wenwen"},{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Maksym Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fangcheng","last_name":"Chou","full_name":"Chou, Fangcheng"},{"last_name":"Tsai","full_name":"Tsai, Wei-Feng","first_name":"Wei"},{"last_name":"Lin","full_name":"Lin, Hsin","first_name":"Hsin"},{"last_name":"Bansil","full_name":"Bansil, Arun","first_name":"Arun"},{"last_name":"Fu","full_name":"Fu, Liang","first_name":"Liang"},{"first_name":"Md","last_name":"Hasan","full_name":"Hasan, Md Z"},{"full_name":"Madhavan, Vidya","last_name":"Madhavan","first_name":"Vidya"}],"date_published":"2014-08-01T00:00:00Z","extern":1,"type":"journal_article","citation":{"mla":"Zeljkovic, Ilija, et al. “Mapping the Unconventional Orbital Texture in Topological Crystalline Insulators.” <i>Nature Physics</i>, vol. 10, no. 8, Nature Publishing Group, 2014, pp. 572–77, doi:<a href=\"https://doi.org/10.1038/nphys3012\">10.1038/nphys3012</a>.","ista":"Zeljkovic I, Okada Y, Huang C, Sankar R, Walkup D, Zhou W, Serbyn M, Chou F, Tsai W, Lin H, Bansil A, Fu L, Hasan M, Madhavan V. 2014. Mapping the unconventional orbital texture in topological crystalline insulators. Nature Physics. 10(8), 572–577.","chicago":"Zeljkovic, Ilija, Yoshinori Okada, Chengyi Huang, Raman Sankar, Daniel Walkup, Wenwen Zhou, Maksym Serbyn, et al. “Mapping the Unconventional Orbital Texture in Topological Crystalline Insulators.” <i>Nature Physics</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nphys3012\">https://doi.org/10.1038/nphys3012</a>.","ama":"Zeljkovic I, Okada Y, Huang C, et al. Mapping the unconventional orbital texture in topological crystalline insulators. <i>Nature Physics</i>. 2014;10(8):572-577. doi:<a href=\"https://doi.org/10.1038/nphys3012\">10.1038/nphys3012</a>","ieee":"I. Zeljkovic <i>et al.</i>, “Mapping the unconventional orbital texture in topological crystalline insulators,” <i>Nature Physics</i>, vol. 10, no. 8. Nature Publishing Group, pp. 572–577, 2014.","apa":"Zeljkovic, I., Okada, Y., Huang, C., Sankar, R., Walkup, D., Zhou, W., … Madhavan, V. (2014). Mapping the unconventional orbital texture in topological crystalline insulators. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nphys3012\">https://doi.org/10.1038/nphys3012</a>","short":"I. Zeljkovic, Y. Okada, C. Huang, R. Sankar, D. Walkup, W. Zhou, M. Serbyn, F. Chou, W. Tsai, H. Lin, A. Bansil, L. Fu, M. Hasan, V. Madhavan, Nature Physics 10 (2014) 572–577."},"main_file_link":[{"url":"https://arxiv.org/abs/1312.0164","open_access":"1"}],"publist_id":"6423","abstract":[{"lang":"eng","text":"The newly discovered topological crystalline insulators feature a complex band structure involving multiple Dirac cones, and are potentially highly tunable by external electric field, temperature or strain. Theoretically, it has been predicted that the various Dirac cones, which are offset in energy and momentum, might harbour vastly different orbital character. However, their orbital texture, which is of immense importance in determining a variety of a materialâ €™ s properties remains elusive. Here, we unveil the orbital texture of Pb 1â ̂'x Sn x Se, a prototypical topological crystalline insulator. By using Fourier-transform scanning tunnelling spectroscopy we measure the interference patterns produced by the scattering of surface-state electrons. We discover that the intensity and energy dependences of the Fourier transforms show distinct characteristics, which can be directly attributed to orbital effects. Our experiments reveal a complex band topology involving two Lifshitz transitions and establish the orbital nature of the Dirac bands, which could provide an alternative pathway towards future quantum applications."}],"publication_status":"published","volume":10,"status":"public","quality_controlled":0,"intvolume":"        10","oa":1,"issue":"8","acknowledgement":"V.M. gratefully acknowledges funding from the US Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880 for the primary support of I.Z. and Y.O. (experiments, data analysis and writing the paper) and NSF-ECCS-1232105 for the partial support of W.Z. and D.W. (data acquisition). Work at Massachusetts Institute of Technology is supported by US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526 (L.F.), and NSF DMR 1104498 (M.S.). H.L. acknowledges the Singapore National Research Foundation for support under NRF Award No. NRF-NRFF2013-03. The work at Northeastern University is supported by the US Department of Energy grant number DE-FG02-07ER46352, and benefited from Northeastern University’s Advanced Scientific Computation Center (ASCC), theory support at the Advanced Light Source, Berkeley and the allocation of time at the NERSC supercomputing centre through DOE grant number DE-AC02-05CH11231. W-F.T. and C-Y.H. were supported by the NSC in Taiwan under Grant No. 102-2112-M-110-009. W-F.T. also thanks C. Fang for useful discussions. Work at Princeton University is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004."},{"month":"07","title":"Symmetry breaking and Landau quantization in topological crystalline insulators","date_updated":"2021-01-12T08:22:23Z","date_published":"2014-07-03T00:00:00Z","author":[{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Maksym Serbyn","orcid":"0000-0002-2399-5827"},{"first_name":"Liang","last_name":"Fu","full_name":"Fu, Liang"}],"year":"2014","doi":"10.1103/PhysRevB.90.035402","publication":"Physical Review B - Condensed Matter and Materials Physics","date_created":"2018-12-11T11:49:31Z","day":"03","_id":"979","publisher":"American Physical Society","status":"public","abstract":[{"lang":"eng","text":"In the recently discovered topological crystalline insulators SnTe and Pb1-xSnx(Te, Se), crystal symmetry and electronic topology intertwine to create topological surface states with many interesting features including Lifshitz transition, Van-Hove singularity, and fermion mass generation. These surface states are protected by mirror symmetry with respect to the (110) plane. In this work we present a comprehensive study of the effects of different mirror-symmetry-breaking perturbations on the (001) surface band structure. Pristine (001) surface states have four branches of Dirac fermions at low energy. We show that ferroelectric-type structural distortion generates a mass and gaps out some or all of these Dirac points, while strain shifts Dirac points in the Brillouin zone. An in-plane magnetic field leaves the surface state gapless, but introduces asymmetry between Dirac points. Finally, an out-of-plane magnetic field leads to discrete Landau levels. We show that the Landau level spectrum has an unusual pattern of degeneracy and interesting features due to the unique underlying band structure. This suggests that Landau level spectroscopy can detect and distinguish between different mechanisms of symmetry breaking in topological crystalline insulators."}],"volume":90,"publication_status":"published","publist_id":"6422","main_file_link":[{"url":"https://arxiv.org/abs/1403.8153","open_access":"1"}],"acknowledgement":"We thank V. Madhavan and Y. Okada for related collaborations, and P. A. Lee for discussions. M.S. was supported by P. A. Lee via Grant No. NSF DMR 1104498. L.F. is supported by the DOE Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under award DE-SC0010526.","issue":"3","intvolume":"        90","oa":1,"quality_controlled":0,"citation":{"chicago":"Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization in Topological Crystalline Insulators.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevB.90.035402\">https://doi.org/10.1103/PhysRevB.90.035402</a>.","ama":"Serbyn M, Fu L. Symmetry breaking and Landau quantization in topological crystalline insulators. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2014;90(3). doi:<a href=\"https://doi.org/10.1103/PhysRevB.90.035402\">10.1103/PhysRevB.90.035402</a>","mla":"Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization in Topological Crystalline Insulators.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 90, no. 3, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevB.90.035402\">10.1103/PhysRevB.90.035402</a>.","ista":"Serbyn M, Fu L. 2014. Symmetry breaking and Landau quantization in topological crystalline insulators. Physical Review B - Condensed Matter and Materials Physics. 90(3).","apa":"Serbyn, M., &#38; Fu, L. (2014). Symmetry breaking and Landau quantization in topological crystalline insulators. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.90.035402\">https://doi.org/10.1103/PhysRevB.90.035402</a>","short":"M. Serbyn, L. Fu, Physical Review B - Condensed Matter and Materials Physics 90 (2014).","ieee":"M. Serbyn and L. Fu, “Symmetry breaking and Landau quantization in topological crystalline insulators,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 90, no. 3. American Physical Society, 2014."},"type":"journal_article","extern":1},{"extern":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1403.2093"}],"volume":14,"oa":1,"intvolume":"        14","issue":"6","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Funding from the Department of Energy, Office of Science & SCGF, the EC FP7-ICT project SiSPIN no. 323841, and the Danish National Research Foundation is acknowledged.","publication":"Nano Letters","page":"3582 - 3586","_id":"98","external_id":{"arxiv":["1403.2093"]},"date_created":"2018-12-11T11:44:37Z","date_updated":"2021-01-12T08:22:24Z","title":"Hole spin coherence in a Ge/Si heterostructure nanowire","month":"05","date_published":"2014-05-05T00:00:00Z","citation":{"mla":"Higginbotham, Andrew P., et al. “Hole Spin Coherence in a Ge/Si Heterostructure Nanowire.” <i>Nano Letters</i>, vol. 14, no. 6, American Chemical Society, 2014, pp. 3582–86, doi:<a href=\"https://doi.org/10.1021/nl501242b\">10.1021/nl501242b</a>.","ista":"Higginbotham AP, Larsen T, Yao J, Yan H, Lieber C, Marcus C, Kuemmeth F. 2014. Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. 14(6), 3582–3586.","chicago":"Higginbotham, Andrew P, Thorvald Larsen, Jun Yao, Hao Yan, Charles Lieber, Charles Marcus, and Ferdinand Kuemmeth. “Hole Spin Coherence in a Ge/Si Heterostructure Nanowire.” <i>Nano Letters</i>. American Chemical Society, 2014. <a href=\"https://doi.org/10.1021/nl501242b\">https://doi.org/10.1021/nl501242b</a>.","ama":"Higginbotham AP, Larsen T, Yao J, et al. Hole spin coherence in a Ge/Si heterostructure nanowire. <i>Nano Letters</i>. 2014;14(6):3582-3586. doi:<a href=\"https://doi.org/10.1021/nl501242b\">10.1021/nl501242b</a>","ieee":"A. P. Higginbotham <i>et al.</i>, “Hole spin coherence in a Ge/Si heterostructure nanowire,” <i>Nano Letters</i>, vol. 14, no. 6. American Chemical Society, pp. 3582–3586, 2014.","short":"A.P. Higginbotham, T. Larsen, J. Yao, H. Yan, C. Lieber, C. Marcus, F. Kuemmeth, Nano Letters 14 (2014) 3582–3586.","apa":"Higginbotham, A. P., Larsen, T., Yao, J., Yan, H., Lieber, C., Marcus, C., &#38; Kuemmeth, F. (2014). Hole spin coherence in a Ge/Si heterostructure nanowire. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/nl501242b\">https://doi.org/10.1021/nl501242b</a>"},"type":"journal_article","publist_id":"7956","abstract":[{"text":"Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si nanowire double quantum dot using a fast pulsed-gate method and dispersive readout. An inhomogeneous dephasing time T2* ∼ 0.18 μs exceeds corresponding measurements in III-V semiconductors by more than an order of magnitude, as expected for predominately nuclear-spin-free materials. Dephasing is observed to be exponential in time, indicating the presence of a broadband noise source, rather than Gaussian, previously seen in systems with nuclear-spin-dominated dephasing.","lang":"eng"}],"publication_status":"published","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1021/nl501242b","oa_version":"Preprint","arxiv":1,"publisher":"American Chemical Society","day":"05","year":"2014","author":[{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham"},{"full_name":"Larsen, Thorvald","last_name":"Larsen","first_name":"Thorvald"},{"last_name":"Yao","full_name":"Yao, Jun","first_name":"Jun"},{"last_name":"Yan","full_name":"Yan, Hao","first_name":"Hao"},{"last_name":"Lieber","full_name":"Lieber, Charles","first_name":"Charles"},{"first_name":"Charles","full_name":"Marcus, Charles","last_name":"Marcus"},{"last_name":"Kuemmeth","full_name":"Kuemmeth, Ferdinand","first_name":"Ferdinand"}]},{"month":"11","date_updated":"2021-01-12T08:22:24Z","title":"Quantum quenches in the many-body localized phase","year":"2014","author":[{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Maksym Serbyn","orcid":"0000-0002-2399-5827","last_name":"Serbyn"},{"first_name":"Zlatko","last_name":"Papić","full_name":"Papić, Zlatko"},{"last_name":"Abanin","full_name":"Abanin, Dmitry A","first_name":"Dmitry"}],"date_published":"2014-11-06T00:00:00Z","doi":"10.1103/PhysRevB.90.174302","publication":"Physical Review B - Condensed Matter and Materials Physics","day":"06","date_created":"2018-12-11T11:49:31Z","publisher":"American Physical Society","_id":"980","status":"public","publist_id":"6420","main_file_link":[{"url":"https://arxiv.org/abs/1408.4105","open_access":"1"}],"publication_status":"published","volume":90,"abstract":[{"lang":"eng","text":"Many-body localized (MBL) systems are characterized by the absence of transport and thermalization and, therefore, cannot be described by conventional statistical mechanics. In this paper, using analytic arguments and numerical simulations, we study the behavior of local observables in an isolated MBL system following a quantum quench. For the case of a global quench, we find that the local observables reach stationary, highly nonthermal values at long times as a result of slow dephasing characteristic of the MBL phase. These stationary values retain the local memory of the initial state due to the existence of local integrals of motion in the MBL phase. The temporal fluctuations around stationary values exhibit universal power-law decay in time, with an exponent set by the localization length and the diagonal entropy of the initial state. Such a power-law decay holds for any local observable and is related to the logarithmic in time growth of entanglement in the MBL phase. This behavior distinguishes the MBL phase from both the Anderson insulator (where no stationary state is reached) and from the ergodic phase (where relaxation is expected to be exponential). For the case of a local quench, we also find a power-law approach of local observables to their stationary values when the system is prepared in a mixed state. Quench protocols considered in this paper can be naturally implemented in systems of ultracold atoms in disordered optical lattices, and the behavior of local observables provides a direct experimental signature of many-body localization."}],"intvolume":"        90","oa":1,"issue":"17","acknowledgement":"Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. We acknowledge support by NSERC Discovery Grant (D.A.).","quality_controlled":0,"extern":1,"type":"journal_article","citation":{"short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 90 (2014).","apa":"Serbyn, M., Papić, Z., &#38; Abanin, D. (2014). Quantum quenches in the many-body localized phase. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.90.174302\">https://doi.org/10.1103/PhysRevB.90.174302</a>","ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Quantum quenches in the many-body localized phase,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 90, no. 17. American Physical Society, 2014.","ama":"Serbyn M, Papić Z, Abanin D. Quantum quenches in the many-body localized phase. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2014;90(17). doi:<a href=\"https://doi.org/10.1103/PhysRevB.90.174302\">10.1103/PhysRevB.90.174302</a>","chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Quantum Quenches in the Many-Body Localized Phase.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevB.90.174302\">https://doi.org/10.1103/PhysRevB.90.174302</a>.","mla":"Serbyn, Maksym, et al. “Quantum Quenches in the Many-Body Localized Phase.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 90, no. 17, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevB.90.174302\">10.1103/PhysRevB.90.174302</a>.","ista":"Serbyn M, Papić Z, Abanin D. 2014. Quantum quenches in the many-body localized phase. Physical Review B - Condensed Matter and Materials Physics. 90(17)."}},{"author":[{"first_name":"Stephan","full_name":"Wolf, Stephan","last_name":"Wolf"},{"first_name":"Dino","full_name":"Mcmahon, Dino","last_name":"Mcmahon"},{"first_name":"Ka","last_name":"Lim","full_name":"Lim, Ka"},{"first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull","orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher"},{"full_name":"Clark, Suzanne","last_name":"Clark","first_name":"Suzanne"},{"full_name":"Paxton, Robert","last_name":"Paxton","first_name":"Robert"},{"full_name":"Osborne, Juliet","last_name":"Osborne","first_name":"Juliet"}],"year":"2014","article_processing_charge":"No","title":"Supporting information","date_updated":"2023-02-23T10:27:38Z","department":[{"_id":"SyCr"}],"month":"08","_id":"9888","publisher":"Public Library of Science","date_created":"2021-08-11T14:17:53Z","day":"06","doi":"10.1371/journal.pone.0103989.s003","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"Detailed description of the experimental prodedures, data analyses and additional statistical analyses of the results."}],"related_material":{"record":[{"id":"2086","relation":"used_in_publication","status":"public"}]},"status":"public","type":"research_data_reference","citation":{"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>.","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>.","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>","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>.","ieee":"S. Wolf <i>et al.</i>, “Supporting information.” Public Library of Science, 2014.","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>","short":"S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, (2014)."}},{"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, 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.","lang":"eng"}],"publication_status":"published","language":[{"iso":"eng"}],"status":"public","pmid":1,"quality_controlled":"1","citation":{"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.","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>","short":"R. Dhar, T. Bergmiller, A. Wagner, Evolution 68 (2014) 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>.","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.","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>","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>."},"type":"journal_article","article_type":"original","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"department":[{"_id":"CaGu"}],"author":[{"first_name":"Riddhiman","full_name":"Dhar, Riddhiman","last_name":"Dhar"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller"},{"full_name":"Wagner, Andreas","last_name":"Wagner","first_name":"Andreas"}],"year":"2014","doi":"10.1111/evo.12373","oa_version":"None","publisher":"Wiley","day":"03","volume":68,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9932"}]},"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.","issue":"6","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","intvolume":"        68","scopus_import":"1","date_updated":"2023-02-23T14:13:27Z","title":"Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes","month":"06","date_published":"2014-06-03T00:00:00Z","article_processing_charge":"No","publication":"Evolution","page":"1775-1791","_id":"9931","date_created":"2021-08-17T09:03:09Z","external_id":{"pmid":["24495000"]}},{"_id":"9932","publisher":"Dryad","day":"27","date_created":"2021-08-17T09:11:40Z","doi":"10.5061/dryad.jc402","oa_version":"Published Version","article_processing_charge":"No","year":"2014","date_published":"2014-01-27T00:00:00Z","author":[{"last_name":"Dhar","full_name":"Dhar, Riddhiman","first_name":"Riddhiman"},{"last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","full_name":"Wagner, Andreas","last_name":"Wagner"}],"department":[{"_id":"CaGu"}],"date_updated":"2023-02-23T14:13:24Z","title":"Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes","month":"01","citation":{"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.","short":"R. Dhar, T. Bergmiller, A. Wagner, (2014).","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>","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>.","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>.","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>","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>."},"type":"research_data_reference","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"url":"https://doi.org/10.5061/dryad.jc402","open_access":"1"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"9931"}]},"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, 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."}],"status":"public"},{"scopus_import":"1","acknowledgement":"This research is supported and funded by the Digiteo unTopoVis project, the TOPOSYS project FP7-ICT-318493-STREP, and MPC-VCC.","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","place":"Cham","date_created":"2022-03-04T08:33:57Z","_id":"10817","project":[{"call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems"}],"page":"135-150","publication":"Topological Methods in Data Analysis and Visualization III.","ec_funded":1,"date_published":"2014-03-19T00:00:00Z","article_processing_charge":"No","month":"03","title":"Notes on the simplification of the Morse-Smale complex","date_updated":"2023-09-05T15:33:45Z","type":"book_chapter","citation":{"chicago":"Günther, David, Jan Reininghaus, Hans-Peter Seidel, and Tino Weinkauf. “Notes on the Simplification of the Morse-Smale Complex.” In <i>Topological Methods in Data Analysis and Visualization III.</i>, edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 135–50. Mathematics and Visualization. Cham: Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-319-04099-8_9\">https://doi.org/10.1007/978-3-319-04099-8_9</a>.","ama":"Günther D, Reininghaus J, Seidel H-P, Weinkauf T. Notes on the simplification of the Morse-Smale complex. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. <i>Topological Methods in Data Analysis and Visualization III.</i> Mathematics and Visualization. Cham: Springer Nature; 2014:135-150. doi:<a href=\"https://doi.org/10.1007/978-3-319-04099-8_9\">10.1007/978-3-319-04099-8_9</a>","ista":"Günther D, Reininghaus J, Seidel H-P, Weinkauf T. 2014.Notes on the simplification of the Morse-Smale complex. In: Topological Methods in Data Analysis and Visualization III. , 135–150.","mla":"Günther, David, et al. “Notes on the Simplification of the Morse-Smale Complex.” <i>Topological Methods in Data Analysis and Visualization III.</i>, edited by Peer-Timo Bremer et al., Springer Nature, 2014, pp. 135–50, doi:<a href=\"https://doi.org/10.1007/978-3-319-04099-8_9\">10.1007/978-3-319-04099-8_9</a>.","short":"D. Günther, J. Reininghaus, H.-P. Seidel, T. Weinkauf, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III., Springer Nature, Cham, 2014, pp. 135–150.","apa":"Günther, D., Reininghaus, J., Seidel, H.-P., &#38; Weinkauf, T. (2014). Notes on the simplification of the Morse-Smale complex. In P.-T. Bremer, I. Hotz, V. Pascucci, &#38; R. Peikert (Eds.), <i>Topological Methods in Data Analysis and Visualization III.</i> (pp. 135–150). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-04099-8_9\">https://doi.org/10.1007/978-3-319-04099-8_9</a>","ieee":"D. Günther, J. Reininghaus, H.-P. Seidel, and T. Weinkauf, “Notes on the simplification of the Morse-Smale complex,” in <i>Topological Methods in Data Analysis and Visualization III.</i>, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Cham: Springer Nature, 2014, pp. 135–150."},"quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","abstract":[{"text":"The Morse-Smale complex can be either explicitly or implicitly represented. Depending on the type of representation, the simplification of the Morse-Smale complex works differently. In the explicit representation, the Morse-Smale complex is directly simplified by explicitly reconnecting the critical points during the simplification. In the implicit representation, on the other hand, the Morse-Smale complex is given by a combinatorial gradient field. In this setting, the simplification changes the combinatorial flow, which yields an indirect simplification of the Morse-Smale complex. The topological complexity of the Morse-Smale complex is reduced in both representations. However, the simplifications generally yield different results. In this chapter, we emphasize properties of the two representations that cause these differences. We also provide a complexity analysis of the two schemes with respect to running time and memory consumption.","lang":"eng"}],"publication_status":"published","day":"19","publisher":"Springer Nature","series_title":"Mathematics and Visualization","oa_version":"None","doi":"10.1007/978-3-319-04099-8_9","editor":[{"first_name":"Peer-Timo","last_name":"Bremer","full_name":"Bremer, Peer-Timo"},{"full_name":"Hotz, Ingrid","last_name":"Hotz","first_name":"Ingrid"},{"first_name":"Valerio","last_name":"Pascucci","full_name":"Pascucci, Valerio"},{"first_name":"Ronald","full_name":"Peikert, Ronald","last_name":"Peikert"}],"author":[{"first_name":"David","last_name":"Günther","full_name":"Günther, David"},{"first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"full_name":"Seidel, Hans-Peter","last_name":"Seidel","first_name":"Hans-Peter"},{"full_name":"Weinkauf, Tino","last_name":"Weinkauf","first_name":"Tino"}],"year":"2014","department":[{"_id":"HeEd"}],"publication_identifier":{"eissn":["2197-666X"],"issn":["1612-3786"],"eisbn":["9783319040998"],"isbn":["9783319040981"]}},{"type":"conference","citation":{"ieee":"B. Aminof, S. Jacobs, A. Khalimov, and S. Rubin, “Parameterized model checking of token-passing systems,” in <i>Verification, Model Checking, and Abstract Interpretation</i>, San Diego, CA, United States, 2014, vol. 8318, pp. 262–281.","apa":"Aminof, B., Jacobs, S., Khalimov, A., &#38; Rubin, S. (2014). Parameterized model checking of token-passing systems. In <i>Verification, Model Checking, and Abstract Interpretation</i> (Vol. 8318, pp. 262–281). San Diego, CA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-54013-4_15\">https://doi.org/10.1007/978-3-642-54013-4_15</a>","short":"B. Aminof, S. Jacobs, A. Khalimov, S. Rubin, in:, Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 262–281.","mla":"Aminof, Benjamin, et al. “Parameterized Model Checking of Token-Passing Systems.” <i>Verification, Model Checking, and Abstract Interpretation</i>, vol. 8318, Springer Nature, 2014, pp. 262–81, doi:<a href=\"https://doi.org/10.1007/978-3-642-54013-4_15\">10.1007/978-3-642-54013-4_15</a>.","ista":"Aminof B, Jacobs S, Khalimov A, Rubin S. 2014. Parameterized model checking of token-passing systems. Verification, Model Checking, and Abstract Interpretation. VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318, 262–281.","chicago":"Aminof, Benjamin, Swen Jacobs, Ayrat Khalimov, and Sasha Rubin. “Parameterized Model Checking of Token-Passing Systems.” In <i>Verification, Model Checking, and Abstract Interpretation</i>, 8318:262–81. Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54013-4_15\">https://doi.org/10.1007/978-3-642-54013-4_15</a>.","ama":"Aminof B, Jacobs S, Khalimov A, Rubin S. Parameterized model checking of token-passing systems. In: <i>Verification, Model Checking, and Abstract Interpretation</i>. Vol 8318. Springer Nature; 2014:262-281. doi:<a href=\"https://doi.org/10.1007/978-3-642-54013-4_15\">10.1007/978-3-642-54013-4_15</a>"},"quality_controlled":"1","abstract":[{"lang":"eng","text":"We revisit the parameterized model checking problem for token-passing systems and specifications in indexed CTL  ∗ \\X. Emerson and Namjoshi (1995, 2003) have shown that parameterized model checking of indexed CTL  ∗ \\X in uni-directional token rings can be reduced to checking rings up to some cutoff size. Clarke et al. (2004) have shown a similar result for general topologies and indexed LTL \\X, provided processes cannot choose the directions for sending or receiving the token.\r\nWe unify and substantially extend these results by systematically exploring fragments of indexed CTL  ∗ \\X with respect to general topologies. For each fragment we establish whether a cutoff exists, and for some concrete topologies, such as rings, cliques and stars, we infer small cutoffs. Finally, we show that the problem becomes undecidable, and thus no cutoffs exist, if processes are allowed to choose the directions in which they send or from which they receive the token."}],"publication_status":"published","language":[{"iso":"eng"}],"status":"public","publisher":"Springer Nature","day":"30","doi":"10.1007/978-3-642-54013-4_15","oa_version":"Preprint","arxiv":1,"author":[{"full_name":"Aminof, Benjamin","last_name":"Aminof","id":"4A55BD00-F248-11E8-B48F-1D18A9856A87","first_name":"Benjamin"},{"full_name":"Jacobs, Swen","last_name":"Jacobs","first_name":"Swen"},{"full_name":"Khalimov, Ayrat","last_name":"Khalimov","first_name":"Ayrat"},{"full_name":"Rubin, Sasha","last_name":"Rubin","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha"}],"conference":{"name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation","end_date":"2014-01-21","start_date":"2014-01-19","location":"San Diego, CA, United States"},"year":"2014","publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783642540134"],"issn":["0302-9743"],"isbn":["9783642540127"]},"department":[{"_id":"KrCh"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by the Austrian Science Fund through grant P23499-N23\r\nand through the RiSE network (S11403, S11405, S11406, S11407-N23); ERC Starting Grant (279307: Graph Games); Vienna Science and Technology Fund (WWTF)\r\ngrants PROSEED, ICT12-059, and VRG11-005.","intvolume":"      8318","oa":1,"volume":8318,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1311.4425"}],"_id":"10884","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"}],"date_created":"2022-03-18T13:01:22Z","external_id":{"arxiv":["1311.4425"]},"publication":"Verification, Model Checking, and Abstract Interpretation","page":"262-281","date_published":"2014-01-30T00:00:00Z","article_processing_charge":"No","ec_funded":1,"title":"Parameterized model checking of token-passing systems","date_updated":"2022-05-17T08:36:01Z","month":"01"},{"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":" Supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No\r\nS11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","intvolume":"      8318","volume":8318,"alternative_title":["LNCS"],"related_material":{"record":[{"status":"public","relation":"later_version","id":"681"}]},"date_created":"2022-03-18T13:03:15Z","external_id":{"arxiv":["1311.3238"]},"project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"_id":"10885","page":"78-97","publication":"VMCAI 2014: Verification, Model Checking, and Abstract Interpretation","ec_funded":1,"date_published":"2014-01-30T00:00:00Z","article_processing_charge":"No","month":"01","title":"Doomsday equilibria for omega-regular games","date_updated":"2023-02-23T12:52:24Z","citation":{"apa":"Chatterjee, K., Doyen, L., Filiot, E., &#38; Raskin, J.-F. (2014). Doomsday equilibria for omega-regular games. In <i>VMCAI 2014: Verification, Model Checking, and Abstract Interpretation</i> (Vol. 8318, pp. 78–97). San Diego, CA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-54013-4_5\">https://doi.org/10.1007/978-3-642-54013-4_5</a>","short":"K. Chatterjee, L. Doyen, E. Filiot, J.-F. Raskin, in:, VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 78–97.","ieee":"K. Chatterjee, L. Doyen, E. Filiot, and J.-F. Raskin, “Doomsday equilibria for omega-regular games,” in <i>VMCAI 2014: Verification, Model Checking, and Abstract Interpretation</i>, San Diego, CA, United States, 2014, vol. 8318, pp. 78–97.","ama":"Chatterjee K, Doyen L, Filiot E, Raskin J-F. Doomsday equilibria for omega-regular games. In: <i>VMCAI 2014: Verification, Model Checking, and Abstract Interpretation</i>. Vol 8318. Springer Nature; 2014:78-97. doi:<a href=\"https://doi.org/10.1007/978-3-642-54013-4_5\">10.1007/978-3-642-54013-4_5</a>","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean-François Raskin. “Doomsday Equilibria for Omega-Regular Games.” In <i>VMCAI 2014: Verification, Model Checking, and Abstract Interpretation</i>, 8318:78–97. Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54013-4_5\">https://doi.org/10.1007/978-3-642-54013-4_5</a>.","mla":"Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.” <i>VMCAI 2014: Verification, Model Checking, and Abstract Interpretation</i>, vol. 8318, Springer Nature, 2014, pp. 78–97, doi:<a href=\"https://doi.org/10.1007/978-3-642-54013-4_5\">10.1007/978-3-642-54013-4_5</a>.","ista":"Chatterjee K, Doyen L, Filiot E, Raskin J-F. 2014. Doomsday equilibria for omega-regular games. VMCAI 2014: Verification, Model Checking, and Abstract Interpretation. VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318, 78–97."},"type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","abstract":[{"text":"Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information games.\r\nIn this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile such that all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players objective, then the objective of every player is violated.\r\nWe present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games.We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games.","lang":"eng"}],"publication_status":"published","day":"30","publisher":"Springer Nature","oa_version":"Preprint","arxiv":1,"doi":"10.1007/978-3-642-54013-4_5","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"first_name":"Emmanuel","last_name":"Filiot","full_name":"Filiot, Emmanuel"},{"full_name":"Raskin, Jean-François","last_name":"Raskin","first_name":"Jean-François"}],"conference":{"name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation","start_date":"2014-01-19","location":"San Diego, CA, United States","end_date":"2014-01-21"},"year":"2014","publication_identifier":{"isbn":["9783642540127"],"eisbn":["9783642540134"],"issn":["0302-9743"],"eissn":["1611-3349"]},"department":[{"_id":"KrCh"}]},{"_id":"10886","publisher":"Springer","day":"19","date_created":"2022-03-18T13:05:39Z","doi":"10.1007/978-3-319-04099-8_16","publication":"Topological Methods in Data Analysis and Visualization III ","page":"249-262","oa_version":"None","year":"2014","article_processing_charge":"No","author":[{"full_name":"Zobel, Valentin","last_name":"Zobel","first_name":"Valentin"},{"first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"first_name":"Ingrid","full_name":"Hotz, Ingrid","last_name":"Hotz"}],"date_published":"2014-03-19T00:00:00Z","publication_identifier":{"isbn":["9783319040981"],"eissn":["2197-666X"],"issn":["1612-3786"],"eisbn":["9783319040998"]},"department":[{"_id":"HeEd"}],"title":"Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature","date_updated":"2023-09-05T14:13:16Z","month":"03","type":"conference","scopus_import":"1","citation":{"short":"V. Zobel, J. Reininghaus, I. Hotz, in:, Topological Methods in Data Analysis and Visualization III , Springer, 2014, pp. 249–262.","apa":"Zobel, V., Reininghaus, J., &#38; Hotz, I. (2014). Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. In <i>Topological Methods in Data Analysis and Visualization III </i> (pp. 249–262). Springer. <a href=\"https://doi.org/10.1007/978-3-319-04099-8_16\">https://doi.org/10.1007/978-3-319-04099-8_16</a>","ieee":"V. Zobel, J. Reininghaus, and I. Hotz, “Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature,” in <i>Topological Methods in Data Analysis and Visualization III </i>, 2014, pp. 249–262.","ama":"Zobel V, Reininghaus J, Hotz I. Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. In: <i>Topological Methods in Data Analysis and Visualization III </i>. Springer; 2014:249-262. doi:<a href=\"https://doi.org/10.1007/978-3-319-04099-8_16\">10.1007/978-3-319-04099-8_16</a>","chicago":"Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualization of Two-Dimensional Symmetric Positive Definite Tensor Fields Using the Heat Kernel Signature.” In <i>Topological Methods in Data Analysis and Visualization III </i>, 249–62. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-04099-8_16\">https://doi.org/10.1007/978-3-319-04099-8_16</a>.","mla":"Zobel, Valentin, et al. “Visualization of Two-Dimensional Symmetric Positive Definite Tensor Fields Using the Heat Kernel Signature.” <i>Topological Methods in Data Analysis and Visualization III </i>, Springer, 2014, pp. 249–62, doi:<a href=\"https://doi.org/10.1007/978-3-319-04099-8_16\">10.1007/978-3-319-04099-8_16</a>.","ista":"Zobel V, Reininghaus J, Hotz I. 2014. Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. Topological Methods in Data Analysis and Visualization III . , Mathematics and Visualization, , 249–262."},"quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"This research is partially supported by the TOPOSYS project FP7-ICT-318493-STREP.","abstract":[{"text":"We propose a method for visualizing two-dimensional symmetric positive definite tensor fields using the Heat Kernel Signature (HKS). The HKS is derived from the heat kernel and was originally introduced as an isometry invariant shape signature. Each positive definite tensor field defines a Riemannian manifold by considering the tensor field as a Riemannian metric. On this Riemmanian manifold we can apply the definition of the HKS. The resulting scalar quantity is used for the visualization of tensor fields. The HKS is closely related to the Gaussian curvature of the Riemannian manifold and the time parameter of the heat kernel allows a multiscale analysis in a natural way. In this way, the HKS represents field related scale space properties, enabling a level of detail analysis of tensor fields. This makes the HKS an interesting new scalar quantity for tensor fields, which differs significantly from usual tensor invariants like the trace or the determinant. A method for visualization and a numerical realization of the HKS for tensor fields is proposed in this chapter. To validate the approach we apply it to some illustrating simple examples as isolated critical points and to a medical diffusion tensor data set.","lang":"eng"}],"publication_status":"published","alternative_title":["Mathematics and Visualization"],"status":"public","language":[{"iso":"eng"}]},{"conference":{"name":"ISAAC: International Symposium on Algorithms and Computation","end_date":"2014-12-17","location":"Jeonju, Korea","start_date":"2014-12-15"},"year":"2014","author":[{"first_name":"Therese","full_name":"Biedl, Therese","last_name":"Biedl"},{"id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Huber","orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan"},{"first_name":"Peter","full_name":"Palfrader, Peter","last_name":"Palfrader"}],"publication_identifier":{"isbn":["9783319130743"],"issn":["0302-9743"],"eisbn":["9783319130750"],"eissn":["1611-3349"]},"department":[{"_id":"HeEd"}],"publisher":"Springer Nature","day":"08","doi":"10.1007/978-3-319-13075-0_10","oa_version":"None","quality_controlled":"1","abstract":[{"lang":"eng","text":"In this paper, we introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist.\r\nUsing our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings."}],"publication_status":"published","status":"public","language":[{"iso":"eng"}],"citation":{"mla":"Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.” <i>25th International Symposium, ISAAC 2014</i>, vol. 8889, Springer Nature, 2014, pp. 117–27, doi:<a href=\"https://doi.org/10.1007/978-3-319-13075-0_10\">10.1007/978-3-319-13075-0_10</a>.","ista":"Biedl T, Huber S, Palfrader P. 2014. Planar matchings for weighted straight skeletons. 25th International Symposium, ISAAC 2014. ISAAC: International Symposium on Algorithms and Computation, LNCS, vol. 8889, 117–127.","chicago":"Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for Weighted Straight Skeletons.” In <i>25th International Symposium, ISAAC 2014</i>, 8889:117–27. Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-319-13075-0_10\">https://doi.org/10.1007/978-3-319-13075-0_10</a>.","ama":"Biedl T, Huber S, Palfrader P. Planar matchings for weighted straight skeletons. In: <i>25th International Symposium, ISAAC 2014</i>. Vol 8889. Springer Nature; 2014:117-127. doi:<a href=\"https://doi.org/10.1007/978-3-319-13075-0_10\">10.1007/978-3-319-13075-0_10</a>","ieee":"T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight skeletons,” in <i>25th International Symposium, ISAAC 2014</i>, Jeonju, Korea, 2014, vol. 8889, pp. 117–127.","short":"T. Biedl, S. Huber, P. Palfrader, in:, 25th International Symposium, ISAAC 2014, Springer Nature, 2014, pp. 117–127.","apa":"Biedl, T., Huber, S., &#38; Palfrader, P. (2014). Planar matchings for weighted straight skeletons. In <i>25th International Symposium, ISAAC 2014</i> (Vol. 8889, pp. 117–127). Jeonju, Korea: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-13075-0_10\">https://doi.org/10.1007/978-3-319-13075-0_10</a>"},"type":"conference","article_processing_charge":"No","date_published":"2014-11-08T00:00:00Z","date_updated":"2023-02-23T12:20:55Z","title":"Planar matchings for weighted straight skeletons","month":"11","_id":"10892","date_created":"2022-03-21T07:09:03Z","publication":"25th International Symposium, ISAAC 2014","page":"117-127","intvolume":"      8889","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"T. Biedl was supported by NSERC and the Ross and Muriel Cheriton Fellowship. P. Palfrader was supported by Austrian Science Fund (FWF): P25816-N15.","related_material":{"record":[{"id":"481","relation":"later_version","status":"public"}]},"alternative_title":["LNCS"],"volume":8889,"scopus_import":"1"}]