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Supporting information text. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">10.1371/journal.pcbi.1004055.s001</a>","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., &#38; Alon, U. (2015). Supporting information text. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">https://doi.org/10.1371/journal.pcbi.1004055.s001</a>","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Supporting Information Text.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">https://doi.org/10.1371/journal.pcbi.1004055.s001</a>.","ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">10.1371/journal.pcbi.1004055.s001</a>.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015)."},"type":"research_data_reference","date_updated":"2023-02-23T10:16:13Z","author":[{"full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander","first_name":"Tamar"},{"full_name":"Mayo, Avraham E.","last_name":"Mayo","first_name":"Avraham E."},{"full_name":"Tlusty, Tsvi","last_name":"Tlusty","first_name":"Tsvi"},{"first_name":"Uri","last_name":"Alon","full_name":"Alon, Uri"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"23"},{"day":"21","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"citation":{"short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, (2015).","mla":"Wielgoss, Sébastien, et al. <i>Data from: Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Non-Mutator Bacteria</i>. Dryad, 2015, doi:<a href=\"https://doi.org/10.5061/dryad.cj910\">10.5061/dryad.cj910</a>.","apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &#38; Hall, A. R. (2015). Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria. Dryad. <a href=\"https://doi.org/10.5061/dryad.cj910\">https://doi.org/10.5061/dryad.cj910</a>","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria.” Dryad, 2015.","ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria. 2015. doi:<a href=\"https://doi.org/10.5061/dryad.cj910\">10.5061/dryad.cj910</a>","chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Data from: Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Non-Mutator Bacteria.” Dryad, 2015. <a href=\"https://doi.org/10.5061/dryad.cj910\">https://doi.org/10.5061/dryad.cj910</a>.","ista":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2015. Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria, Dryad, <a href=\"https://doi.org/10.5061/dryad.cj910\">10.5061/dryad.cj910</a>."},"type":"research_data_reference","date_updated":"2023-09-05T13:46:04Z","author":[{"first_name":"Sébastien","last_name":"Wielgoss","full_name":"Wielgoss, Sébastien"},{"first_name":"Tobias","last_name":"Bergmiller","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346"},{"full_name":"Bischofberger, Anna M.","last_name":"Bischofberger","first_name":"Anna M."},{"last_name":"Hall","first_name":"Alex R.","full_name":"Hall, Alex R."}],"doi":"10.5061/dryad.cj910","date_published":"2015-12-21T00:00:00Z","title":"Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria","status":"public","date_created":"2021-07-26T08:44:04Z","year":"2015","_id":"9719","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.cj910"}],"oa_version":"Published Version","article_processing_charge":"No","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"5749"}]},"publisher":"Dryad","department":[{"_id":"CaGu"}],"month":"12","abstract":[{"lang":"eng","text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance."}]},{"title":"Data from: Opposing effects of allogrooming on disease transmission in ant societies","status":"public","doi":"10.5061/dryad.dj2bf","date_published":"2015-12-29T00:00:00Z","author":[{"full_name":"Theis, Fabian","last_name":"Theis","first_name":"Fabian"},{"orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","full_name":"Ugelvig, Line V","last_name":"Ugelvig","first_name":"Line V"},{"full_name":"Marr, Carsten","last_name":"Marr","first_name":"Carsten"},{"first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"date_updated":"2023-02-23T10:16:22Z","type":"research_data_reference","citation":{"short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, (2015).","chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Dryad, 2015. <a href=\"https://doi.org/10.5061/dryad.dj2bf\">https://doi.org/10.5061/dryad.dj2bf</a>.","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Data from: Opposing effects of allogrooming on disease transmission in ant societies, Dryad, <a href=\"https://doi.org/10.5061/dryad.dj2bf\">10.5061/dryad.dj2bf</a>.","mla":"Theis, Fabian, et al. <i>Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies</i>. Dryad, 2015, doi:<a href=\"https://doi.org/10.5061/dryad.dj2bf\">10.5061/dryad.dj2bf</a>.","apa":"Theis, F., Ugelvig, L. V., Marr, C., &#38; Cremer, S. (2015). Data from: Opposing effects of allogrooming on disease transmission in ant societies. Dryad. <a href=\"https://doi.org/10.5061/dryad.dj2bf\">https://doi.org/10.5061/dryad.dj2bf</a>","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Data from: Opposing effects of allogrooming on disease transmission in ant societies.” Dryad, 2015.","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Data from: Opposing effects of allogrooming on disease transmission in ant societies. 2015. doi:<a href=\"https://doi.org/10.5061/dryad.dj2bf\">10.5061/dryad.dj2bf</a>"},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"day":"29","abstract":[{"text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems.","lang":"eng"}],"department":[{"_id":"SyCr"}],"related_material":{"record":[{"relation":"used_in_publication","id":"1830","status":"public"}]},"publisher":"Dryad","month":"12","oa_version":"Published Version","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5061/dryad.dj2bf","open_access":"1"}],"year":"2015","_id":"9721","date_created":"2021-07-26T09:38:36Z"},{"_id":"9737","year":"2015","date_created":"2021-07-28T06:20:13Z","article_processing_charge":"No","oa_version":"Published Version","month":"06","publisher":"Public Library of Science","related_material":{"record":[{"status":"public","id":"1793","relation":"used_in_publication"}]},"department":[{"_id":"MaJö"},{"_id":"HeEd"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"01","author":[{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","full_name":"Symonova, Olga","last_name":"Symonova","first_name":"Olga"},{"full_name":"Topp, Christopher","last_name":"Topp","first_name":"Christopher"},{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"type":"research_data_reference","citation":{"short":"O. Symonova, C. Topp, H. Edelsbrunner, (2015).","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. Root traits computed by DynamicRoots for the maize root shown in fig 2, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">10.1371/journal.pone.0127657.s001</a>.","chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">https://doi.org/10.1371/journal.pone.0127657.s001</a>.","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “Root traits computed by DynamicRoots for the maize root shown in fig 2.” Public Library of Science, 2015.","ama":"Symonova O, Topp C, Edelsbrunner H. Root traits computed by DynamicRoots for the maize root shown in fig 2. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">10.1371/journal.pone.0127657.s001</a>","apa":"Symonova, O., Topp, C., &#38; Edelsbrunner, H. (2015). Root traits computed by DynamicRoots for the maize root shown in fig 2. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">https://doi.org/10.1371/journal.pone.0127657.s001</a>","mla":"Symonova, Olga, et al. <i>Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">10.1371/journal.pone.0127657.s001</a>."},"date_updated":"2023-02-23T10:14:42Z","status":"public","title":"Root traits computed by DynamicRoots for the maize root shown in fig 2","date_published":"2015-06-01T00:00:00Z","doi":"10.1371/journal.pone.0127657.s001"},{"status":"public","title":"Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant","date_published":"2015-07-09T00:00:00Z","doi":"10.5061/dryad.7kc79","date_updated":"2023-02-23T10:30:52Z","citation":{"short":"C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, (2015).","chicago":"Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie Doums, and Sylvia Cremer. “Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant.” Dryad, 2015. <a href=\"https://doi.org/10.5061/dryad.7kc79\">https://doi.org/10.5061/dryad.7kc79</a>.","ista":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2015. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant, Dryad, <a href=\"https://doi.org/10.5061/dryad.7kc79\">10.5061/dryad.7kc79</a>.","mla":"Westhus, Claudia, et al. <i>Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant</i>. Dryad, 2015, doi:<a href=\"https://doi.org/10.5061/dryad.7kc79\">10.5061/dryad.7kc79</a>.","apa":"Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., &#38; Cremer, S. (2015). Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Dryad. <a href=\"https://doi.org/10.5061/dryad.7kc79\">https://doi.org/10.5061/dryad.7kc79</a>","ieee":"C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer, “Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant.” Dryad, 2015.","ama":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. 2015. doi:<a href=\"https://doi.org/10.5061/dryad.7kc79\">10.5061/dryad.7kc79</a>"},"author":[{"first_name":"Claudia","last_name":"Westhus","full_name":"Westhus, Claudia"},{"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":"Tourdot, Edouard","first_name":"Edouard","last_name":"Tourdot"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"},{"last_name":"Doums","first_name":"Claudie","full_name":"Doums, Claudie"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia"}],"type":"research_data_reference","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"09","abstract":[{"text":"Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects.","lang":"eng"}],"month":"07","publisher":"Dryad","related_material":{"record":[{"id":"2161","status":"public","relation":"used_in_publication"}]},"department":[{"_id":"SyCr"}],"article_processing_charge":"No","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5061/dryad.7kc79","open_access":"1"}],"_id":"9742","year":"2015","date_created":"2021-07-28T08:52:53Z"},{"type":"research_data_reference","author":[{"id":"424D78A0-F248-11E8-B48F-1D18A9856A87","full_name":"Chevereau, Guillaume","last_name":"Chevereau","first_name":"Guillaume"},{"last_name":"Lukacisinova","first_name":"Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta"},{"full_name":"Batur, Tugce","last_name":"Batur","first_name":"Tugce"},{"full_name":"Guvenek, Aysegul","first_name":"Aysegul","last_name":"Guvenek"},{"full_name":"Ayhan, Dilay Hazal","last_name":"Ayhan","first_name":"Dilay Hazal"},{"full_name":"Toprak, Erdal","last_name":"Toprak","first_name":"Erdal"},{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Mark Tobias"}],"date_updated":"2023-02-23T10:07:02Z","citation":{"short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","mla":"Chevereau, Guillaume, et al. <i>Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">10.1371/journal.pbio.1002299.s008</a>.","ieee":"G. Chevereau <i>et al.</i>, “Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs.” Public Library of Science, 2015.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., &#38; Bollenbach, M. T. (2015). Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">https://doi.org/10.1371/journal.pbio.1002299.s008</a>","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">10.1371/journal.pbio.1002299.s008</a>","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">https://doi.org/10.1371/journal.pbio.1002299.s008</a>.","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">10.1371/journal.pbio.1002299.s008</a>."},"day":"18","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2015-11-18T00:00:00Z","doi":"10.1371/journal.pbio.1002299.s008","status":"public","title":"Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs","date_created":"2021-08-03T07:05:16Z","_id":"9765","year":"2015","month":"11","related_material":{"record":[{"status":"public","id":"1619","relation":"used_in_publication"}]},"department":[{"_id":"ToBo"}],"publisher":"Public Library of Science","article_processing_charge":"No","oa_version":"Published Version"},{"date_updated":"2023-02-23T10:15:25Z","author":[{"last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"},{"first_name":"Sebastian","last_name":"Novak","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hager","first_name":"Reinmar","full_name":"Hager, Reinmar"}],"citation":{"short":"B. Trubenova, S. Novak, R. Hager, (2015).","ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>.","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">https://doi.org/10.1371/journal.pone.0126907.s003</a>.","ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015.","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Description of the agent based simulations. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">https://doi.org/10.1371/journal.pone.0126907.s003</a>","ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>","mla":"Trubenova, Barbora, et al. <i>Description of the Agent Based Simulations</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>."},"type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"18","title":"Description of the agent based simulations","status":"public","doi":"10.1371/journal.pone.0126907.s003","date_published":"2015-05-18T00:00:00Z","year":"2015","_id":"9772","date_created":"2021-08-05T12:55:20Z","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1809"}]},"month":"05","oa_version":"Published Version","article_processing_charge":"No"},{"doi":"10.1371/journal.pcbi.1004055.s002","date_published":"2015-03-23T00:00:00Z","status":"public","title":"Evolutionary simulation code","type":"research_data_reference","date_updated":"2023-02-23T10:16:13Z","citation":{"ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">10.1371/journal.pcbi.1004055.s002</a>.","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary Simulation Code.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">https://doi.org/10.1371/journal.pcbi.1004055.s002</a>.","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., &#38; Alon, U. (2015). Evolutionary simulation code. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">https://doi.org/10.1371/journal.pcbi.1004055.s002</a>","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015.","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">10.1371/journal.pcbi.1004055.s002</a>","mla":"Friedlander, Tamar, et al. <i>Evolutionary Simulation Code</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">10.1371/journal.pcbi.1004055.s002</a>.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015)."},"author":[{"full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar","last_name":"Friedlander"},{"first_name":"Avraham E.","last_name":"Mayo","full_name":"Mayo, Avraham E."},{"first_name":"Tsvi","last_name":"Tlusty","full_name":"Tlusty, Tsvi"},{"full_name":"Alon, Uri","last_name":"Alon","first_name":"Uri"}],"day":"23","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","related_material":{"record":[{"id":"1827","status":"public","relation":"used_in_publication"}]},"department":[{"_id":"GaTk"}],"month":"03","oa_version":"Published Version","article_processing_charge":"No","date_created":"2021-08-05T12:58:07Z","year":"2015","_id":"9773"},{"quality_controlled":0,"main_file_link":[{"url":"https://arxiv.org/abs/1403.4906","open_access":"1"}],"publication_status":"published","publisher":"Nature Publishing Group","month":"03","abstract":[{"lang":"eng","text":"The tunability of topological surface states and controllable opening of the Dirac gap are of fundamental and practical interest in the field of topological materials. In the newly discovered topological crystalline insulators (TCIs), theory predicts that the Dirac node is protected by a crystalline symmetry and that the surface state electrons can acquire a mass if this symmetry is broken. Recent studies have detected signatures of a spontaneously generated Dirac gap in TCIs; however, the mechanism of mass formation remains elusive. In this work, we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x Sn x Se for a wide range of alloy compositions spanning the topological and non-topological regimes. The STM topographies reveal a symmetry-breaking distortion on the surface, which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous to the long sought-after Higgs mechanism in particle physics. Interestingly, the measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude of the distortion remains nearly constant. Our data and calculations reveal that the penetration depth of Dirac surface states controls the magnitude of the Dirac mass. At the limit of the critical composition, the penetration depth is predicted to go to infinity, resulting in zero mass, consistent with our measurements. Finally, we discover the existence of surface states in the non-topological regime, which have the characteristics of gapped, double-branched Dirac fermions and could be exploited in realizing superconductivity in these materials."}],"date_created":"2018-12-11T11:49:31Z","acknowledgement":"We thank R. Buczko, C. Chamon, J. C. Seamus Davis, M. El-Batanouny, A. Mesaros, Y. Ran and A. Soumyanarayanan for useful conversations and G. McMahon for help with EDS measurements. V.M. gratefully acknowledges funding from the US Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880 for the support of I.Z., Y.O., W.Z. and D.W. for this project. 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. Y.O. was partly supported by JSPS KAKENHI Grant Numbers 26707016 and 00707656. 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 supercomputer time at the NERSC through DOE grant number DE-AC02-05CH11231. 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.","year":"2015","_id":"981","page":"318 - 324","issue":"3","intvolume":"        14","extern":1,"doi":"10.1038/nmat4215","date_published":"2015-03-01T00:00:00Z","status":"public","title":"Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators","day":"01","publist_id":"6419","publication":"Nature Materials","oa":1,"type":"journal_article","date_updated":"2021-01-12T08:22:24Z","author":[{"first_name":"Ilija","last_name":"Zeljkovic","full_name":"Zeljkovic, Ilija"},{"first_name":"Yoshinori","last_name":"Okada","full_name":"Okada, Yoshinori"},{"first_name":"Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Maksym Serbyn"},{"first_name":"Raman","last_name":"Sankar","full_name":"Sankar, Raman"},{"last_name":"Walkup","first_name":"Daniel","full_name":"Walkup, Daniel"},{"full_name":"Zhou, Wenwen","last_name":"Zhou","first_name":"Wenwen"},{"last_name":"Liu","first_name":"Junwei","full_name":"Liu, Junwei"},{"last_name":"Chang","first_name":"Guoqing","full_name":"Chang, Guoqing"},{"full_name":"Wang, Yungjui","first_name":"Yungjui","last_name":"Wang"},{"full_name":"Hasan, Md Z","first_name":"Md","last_name":"Hasan"},{"full_name":"Chou, Fangcheng","first_name":"Fangcheng","last_name":"Chou"},{"first_name":"Hsin","last_name":"Lin","full_name":"Lin, Hsin"},{"last_name":"Bansil","first_name":"Arun","full_name":"Bansil, Arun"},{"full_name":"Fu, Liang","first_name":"Liang","last_name":"Fu"},{"full_name":"Madhavan, Vidya","last_name":"Madhavan","first_name":"Vidya"}],"citation":{"short":"I. Zeljkovic, Y. Okada, M. Serbyn, R. Sankar, D. Walkup, W. Zhou, J. Liu, G. Chang, Y. Wang, M. Hasan, F. Chou, H. Lin, A. Bansil, L. Fu, V. Madhavan, Nature Materials 14 (2015) 318–324.","apa":"Zeljkovic, I., Okada, Y., Serbyn, M., Sankar, R., Walkup, D., Zhou, W., … Madhavan, V. (2015). Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. <i>Nature Materials</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nmat4215\">https://doi.org/10.1038/nmat4215</a>","ama":"Zeljkovic I, Okada Y, Serbyn M, et al. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. <i>Nature Materials</i>. 2015;14(3):318-324. doi:<a href=\"https://doi.org/10.1038/nmat4215\">10.1038/nmat4215</a>","ieee":"I. Zeljkovic <i>et al.</i>, “Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators,” <i>Nature Materials</i>, vol. 14, no. 3. Nature Publishing Group, pp. 318–324, 2015.","mla":"Zeljkovic, Ilija, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” <i>Nature Materials</i>, vol. 14, no. 3, Nature Publishing Group, 2015, pp. 318–24, doi:<a href=\"https://doi.org/10.1038/nmat4215\">10.1038/nmat4215</a>.","ista":"Zeljkovic I, Okada Y, Serbyn M, Sankar R, Walkup D, Zhou W, Liu J, Chang G, Wang Y, Hasan M, Chou F, Lin H, Bansil A, Fu L, Madhavan V. 2015. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 14(3), 318–324.","chicago":"Zeljkovic, Ilija, Yoshinori Okada, Maksym Serbyn, Raman Sankar, Daniel Walkup, Wenwen Zhou, Junwei Liu, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” <i>Nature Materials</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nmat4215\">https://doi.org/10.1038/nmat4215</a>."},"volume":14},{"publication":"Physical Review X","oa":1,"day":"01","publist_id":"6418","volume":5,"author":[{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Maksym Serbyn","orcid":"0000-0002-2399-5827"},{"full_name":"Papić, Zlatko","last_name":"Papić","first_name":"Zlatko"},{"full_name":"Abanin, Dmitry A","first_name":"Dmitry","last_name":"Abanin"}],"type":"journal_article","citation":{"short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review X 5 (2015).","mla":"Serbyn, Maksym, et al. “Criterion for Many-Body Localization-Delocalization Phase Transition.” <i>Physical Review X</i>, vol. 5, no. 4, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevX.5.041047\">10.1103/PhysRevX.5.041047</a>.","apa":"Serbyn, M., Papić, Z., &#38; Abanin, D. (2015). Criterion for many-body localization-delocalization phase transition. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.5.041047\">https://doi.org/10.1103/PhysRevX.5.041047</a>","ama":"Serbyn M, Papić Z, Abanin D. Criterion for many-body localization-delocalization phase transition. <i>Physical Review X</i>. 2015;5(4). doi:<a href=\"https://doi.org/10.1103/PhysRevX.5.041047\">10.1103/PhysRevX.5.041047</a>","ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Criterion for many-body localization-delocalization phase transition,” <i>Physical Review X</i>, vol. 5, no. 4. American Physical Society, 2015.","chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Criterion for Many-Body Localization-Delocalization Phase Transition.” <i>Physical Review X</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevX.5.041047\">https://doi.org/10.1103/PhysRevX.5.041047</a>.","ista":"Serbyn M, Papić Z, Abanin D. 2015. Criterion for many-body localization-delocalization phase transition. Physical Review X. 5(4)."},"date_updated":"2021-01-12T08:22:25Z","issue":"4","intvolume":"         5","extern":1,"status":"public","title":"Criterion for many-body localization-delocalization phase transition","doi":"10.1103/PhysRevX.5.041047","date_published":"2015-01-01T00:00:00Z","year":"2015","_id":"982","date_created":"2018-12-11T11:49:32Z","acknowledgement":"We acknowledge helpful discussions with Sid Parameswaran, Andrew Potter, Antonello Scardicchio, Romain Vasseur, and especially with Ehud Altman and David Huse. We would like to thank Miles Stoudenmire for the assistance with ITensor library. 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. This research was supported by Gordon and Betty Moore Foundation EPiQS Initiative through Grant No. GBMF4307 (M. S.), Sloan Foundation, NSERC, and Early Researcher Award of Ontario (D. A.). This work made use of the facilities of N8 HPC Centre of Excellence, provided and funded by the N8 consortium and EPSRC (Grant No. EP/K000225/1). The Centre is coordinated by the Universities of Leeds and Manchester.","quality_controlled":0,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.01635"}],"abstract":[{"text":"We propose a new approach to probing ergodicity and its breakdown in one-dimensional quantum manybody systems based on their response to a local perturbation. We study the distribution of matrix elements of a local operator between the system's eigenstates, finding a qualitatively different behavior in the manybody localized (MBL) and ergodic phases. To characterize how strongly a local perturbation modifies the eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the disorder-averaged ratio of a typical matrix element of a local operator V to energy level spacing δ this parameter is reminiscent of the Thouless conductance in the single-particle localization. We show that the parameter g(L) decreases with system size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate our approach by studying the many-body localization transition and resolving the many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using exact diagonalization and time-evolving block-decimation methods. Our criterion for the MBL transition gives insights into microscopic details of transition. Its direct physical consequences, in particular, logarithmically slow transport at the transition and extensive entanglement entropy of the eigenstates, are consistent with recent renormalization-group predictions.","lang":"eng"}],"publication_status":"published","publisher":"American Physical Society","month":"01"},{"publication_status":"published","abstract":[{"lang":"eng","text":"Quasiparticle excitations can compromise the performance of superconducting devices, causing high-frequency dissipation, decoherence in Josephson qubits, and braiding errors in proposed Majorana-based topological quantum computers. Quasiparticle dynamics have been studied in detail in metallic superconductors but remain relatively unexplored in semiconductor-superconductor structures, which are now being intensely pursued in the context of topological superconductivity. To this end, we use a system comprising a gate-confined semiconductor nanowire with an epitaxially grown superconductor layer, yielding an isolated, proximitized nanowire segment. We identify bound states in the semiconductor by means of bias spectroscopy, determine the characteristic temperatures and magnetic fields for quasiparticle excitations, and extract a parity lifetime (poisoning time) of the bound state in the semiconductor exceeding 10 ms."}],"quality_controlled":"1","oa_version":"Preprint","date_created":"2018-12-11T11:44:37Z","_id":"99","year":"2015","title":"Parity lifetime of bound states in a proximitized semiconductor nanowire","external_id":{"arxiv":["1501.05155"]},"issue":"12","citation":{"mla":"Higginbotham, Andrew P., et al. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” <i>Nature Physics</i>, vol. 11, no. 12, Nature Publishing Group, 2015, pp. 1017–21, doi:<a href=\"https://doi.org/10.1038/nphys3461\">10.1038/nphys3461</a>.","ieee":"A. P. Higginbotham <i>et al.</i>, “Parity lifetime of bound states in a proximitized semiconductor nanowire,” <i>Nature Physics</i>, vol. 11, no. 12. Nature Publishing Group, pp. 1017–1021, 2015.","apa":"Higginbotham, A. P., Albrecht, S. M., Kiršanskas, G., Chang, W., Kuemmeth, F., Krogstrup, P., … Marcus, C. (2015). Parity lifetime of bound states in a proximitized semiconductor nanowire. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nphys3461\">https://doi.org/10.1038/nphys3461</a>","ama":"Higginbotham AP, Albrecht SM, Kiršanskas G, et al. Parity lifetime of bound states in a proximitized semiconductor nanowire. <i>Nature Physics</i>. 2015;11(12):1017-1021. doi:<a href=\"https://doi.org/10.1038/nphys3461\">10.1038/nphys3461</a>","chicago":"Higginbotham, Andrew P, S M Albrecht, Gediminas Kiršanskas, W Chang, Ferdinand Kuemmeth, Peter Krogstrup, Thomas Jespersen, Jesper Nygård, Karsten Flensberg, and Charles Marcus. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” <i>Nature Physics</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nphys3461\">https://doi.org/10.1038/nphys3461</a>.","ista":"Higginbotham AP, Albrecht SM, Kiršanskas G, Chang W, Kuemmeth F, Krogstrup P, Jespersen T, Nygård J, Flensberg K, Marcus C. 2015. Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. 11(12), 1017–1021.","short":"A.P. Higginbotham, S.M. Albrecht, G. Kiršanskas, W. Chang, F. Kuemmeth, P. Krogstrup, T. Jespersen, J. Nygård, K. Flensberg, C. Marcus, Nature Physics 11 (2015) 1017–1021."},"author":[{"first_name":"Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Albrecht, S M","first_name":"S M","last_name":"Albrecht"},{"first_name":"Gediminas","last_name":"Kiršanskas","full_name":"Kiršanskas, Gediminas"},{"last_name":"Chang","first_name":"W","full_name":"Chang, W"},{"first_name":"Ferdinand","last_name":"Kuemmeth","full_name":"Kuemmeth, Ferdinand"},{"full_name":"Krogstrup, Peter","first_name":"Peter","last_name":"Krogstrup"},{"full_name":"Jespersen, Thomas","last_name":"Jespersen","first_name":"Thomas"},{"last_name":"Nygård","first_name":"Jesper","full_name":"Nygård, Jesper"},{"full_name":"Flensberg, Karsten","last_name":"Flensberg","first_name":"Karsten"},{"full_name":"Marcus, Charles","first_name":"Charles","last_name":"Marcus"}],"date_updated":"2021-01-12T08:22:28Z","publist_id":"7955","day":"14","oa":1,"publication":"Nature Physics","month":"09","publisher":"Nature Publishing Group","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1501.05155"}],"arxiv":1,"page":"1017 - 1021","acknowledgement":"Research support by Microsoft Project Q, the Danish National Research Foundation, the Lundbeck Foundation, the Carlsberg Foundation, and the European Commission. A.P.H. acknowledges support from the US Department of Energy, C.M.M. acknowledges support from the Villum Foundation.","date_published":"2015-09-14T00:00:00Z","doi":"10.1038/nphys3461","status":"public","language":[{"iso":"eng"}],"extern":"1","intvolume":"        11","type":"journal_article","volume":11,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"intvolume":"       111","extern":"1","doi":"10.1073/pnas.1410159111","date_published":"2014-12-01T00:00:00Z","language":[{"iso":"eng"}],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","volume":111,"main_file_link":[{"url":"https://www.pnas.org/content/111/50/17869","open_access":"1"}],"publisher":"National Academy of Sciences","month":"12","acknowledgement":"We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs, for helpful discussions. A.Š. acknowledges support from the Human Frontier Science Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology and Biological Sciences Research Council. D.F. acknowledges European Research Council Advanced Grant 227758.","scopus_import":"1","arxiv":1,"page":"17869-17874","issue":"50","title":"Crucial role of nonspecific interactions in amyloid nucleation","external_id":{"pmid":["25453085"],"arxiv":["1412.0897"]},"day":"01","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication":"Proceedings of the National Academy of Sciences","oa":1,"citation":{"mla":"Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:<a href=\"https://doi.org/10.1073/pnas.1410159111\">10.1073/pnas.1410159111</a>.","apa":"Šarić, A., Chebaro, Y. C., Knowles, T. P. J., &#38; Frenkel, D. (2014). Crucial role of nonspecific interactions in amyloid nucleation. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1410159111\">https://doi.org/10.1073/pnas.1410159111</a>","ieee":"A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of nonspecific interactions in amyloid nucleation,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874, 2014.","ama":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions in amyloid nucleation. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(50):17869-17874. doi:<a href=\"https://doi.org/10.1073/pnas.1410159111\">10.1073/pnas.1410159111</a>","chicago":"Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1410159111\">https://doi.org/10.1073/pnas.1410159111</a>.","ista":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 111(50), 17869–17874.","short":"A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National Academy of Sciences 111 (2014) 17869–17874."},"date_updated":"2021-11-29T13:29:05Z","author":[{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Chebaro, Yassmine C.","last_name":"Chebaro","first_name":"Yassmine C."},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."},{"full_name":"Frenkel, Daan","last_name":"Frenkel","first_name":"Daan"}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"No","keyword":["multidisciplinary"],"publication_status":"published","article_type":"original","abstract":[{"lang":"eng","text":"Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical one-step nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory."}],"pmid":1,"date_created":"2021-11-29T13:09:53Z","year":"2014","_id":"10382"},{"scopus_import":"1","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1310.0826"}],"month":"05","publisher":"American Physical Society","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":89,"type":"journal_article","extern":"1","intvolume":"        89","status":"public","language":[{"iso":"eng"}],"date_published":"2014-05-06T00:00:00Z","doi":"10.1103/physreve.89.052303","_id":"10383","year":"2014","pmid":1,"date_created":"2021-11-29T13:10:33Z","article_processing_charge":"No","oa_version":"Preprint","quality_controlled":"1","abstract":[{"lang":"eng","text":"We use numerical simulations to compute the equation of state of a suspension of spherical self-propelled nanoparticles in two and three dimensions. We study in detail the effect of excluded volume interactions and confinement as a function of the system's temperature, concentration, and strength of the propulsion. We find a striking nonmonotonic dependence of the pressure on the temperature and provide simple scaling arguments to predict and explain the occurrence of such anomalous behavior. We explicitly show how our results have important implications for the effective forces on passive components suspended in a bath of active particles."}],"publication_status":"published","article_type":"original","oa":1,"publication_identifier":{"eissn":["1550-2376"],"issn":["1539-3755"]},"publication":"Physical Review E","day":"06","author":[{"last_name":"Mallory","first_name":"S. A.","full_name":"Mallory, S. A."},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"},{"first_name":"C.","last_name":"Valeriani","full_name":"Valeriani, C."},{"full_name":"Cacciuto, A.","first_name":"A.","last_name":"Cacciuto"}],"date_updated":"2021-11-29T13:29:01Z","citation":{"short":"S.A. Mallory, A. Šarić, C. Valeriani, A. Cacciuto, Physical Review E 89 (2014).","mla":"Mallory, S. A., et al. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” <i>Physical Review E</i>, vol. 89, no. 5, 052303, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.89.052303\">10.1103/physreve.89.052303</a>.","ieee":"S. A. Mallory, A. Šarić, C. Valeriani, and A. Cacciuto, “Anomalous thermomechanical properties of a self-propelled colloidal fluid,” <i>Physical Review E</i>, vol. 89, no. 5. American Physical Society, 2014.","apa":"Mallory, S. A., Šarić, A., Valeriani, C., &#38; Cacciuto, A. (2014). Anomalous thermomechanical properties of a self-propelled colloidal fluid. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.89.052303\">https://doi.org/10.1103/physreve.89.052303</a>","ama":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties of a self-propelled colloidal fluid. <i>Physical Review E</i>. 2014;89(5). doi:<a href=\"https://doi.org/10.1103/physreve.89.052303\">10.1103/physreve.89.052303</a>","chicago":"Mallory, S. A., Anđela Šarić, C. Valeriani, and A. Cacciuto. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.89.052303\">https://doi.org/10.1103/physreve.89.052303</a>.","ista":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. 2014. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 89(5), 052303."},"issue":"5","article_number":"052303","external_id":{"pmid":["25353796"],"arxiv":["1310.0826"]},"title":"Anomalous thermomechanical properties of a self-propelled colloidal fluid"},{"volume":15,"citation":{"ieee":"N. Jensen <i>et al.</i>, “Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang,” <i>ChemPhysChem</i>, vol. 15, no. 4. Wiley-Blackwell, pp. 756–762, 2014.","ama":"Jensen N, Danzl JG, Willig K, et al. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. <i>ChemPhysChem</i>. 2014;15(4):756-762. doi:<a href=\"https://doi.org/10.1002/cphc.201301034\">10.1002/cphc.201301034</a>","apa":"Jensen, N., Danzl, J. G., Willig, K., Lavoie Cardinal, F., Brakemann, T., Hell, S., &#38; Jakobs, S. (2014). Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. <i>ChemPhysChem</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cphc.201301034\">https://doi.org/10.1002/cphc.201301034</a>","mla":"Jensen, Nickels, et al. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” <i>ChemPhysChem</i>, vol. 15, no. 4, Wiley-Blackwell, 2014, pp. 756–62, doi:<a href=\"https://doi.org/10.1002/cphc.201301034\">10.1002/cphc.201301034</a>.","ista":"Jensen N, Danzl JG, Willig K, Lavoie Cardinal F, Brakemann T, Hell S, Jakobs S. 2014. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 15(4), 756–762.","chicago":"Jensen, Nickels, Johann G Danzl, Katrin Willig, Flavie Lavoie Cardinal, Tanja Brakemann, Stefan Hell, and Stefan Jakobs. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” <i>ChemPhysChem</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/cphc.201301034\">https://doi.org/10.1002/cphc.201301034</a>.","short":"N. Jensen, J.G. Danzl, K. Willig, F. Lavoie Cardinal, T. Brakemann, S. Hell, S. Jakobs, ChemPhysChem 15 (2014) 756–762."},"type":"journal_article","date_updated":"2021-01-12T06:47:58Z","author":[{"last_name":"Jensen","first_name":"Nickels","full_name":"Jensen, Nickels"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G"},{"first_name":"Katrin","last_name":"Willig","full_name":"Willig, Katrin"},{"last_name":"Lavoie Cardinal","first_name":"Flavie","full_name":"Lavoie Cardinal, Flavie"},{"last_name":"Brakemann","first_name":"Tanja","full_name":"Brakemann, Tanja"},{"last_name":"Hell","first_name":"Stefan","full_name":"Hell, Stefan"},{"full_name":"Jakobs, Stefan","first_name":"Stefan","last_name":"Jakobs"}],"publication":"ChemPhysChem","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6332","day":"17","title":"Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang","status":"public","language":[{"iso":"eng"}],"date_published":"2014-03-17T00:00:00Z","doi":"10.1002/cphc.201301034","extern":"1","intvolume":"        15","issue":"4","page":"756 - 762","_id":"1058","year":"2014","date_created":"2018-12-11T11:49:55Z","abstract":[{"text":"Diffraction-unlimited far-field super-resolution fluorescence (nanoscopy) methods typically rely on transiently transferring fluorophores between two states, whereby this transfer is usually laid out as a switch. However, depending on whether this is induced in a spatially controlled manner using a pattern of light (coordinate-targeted) or stochastically on a single-molecule basis, specific requirements on the fluorophores are imposed. Therefore, the fluorophores are usually utilized just for one class of methods only. In this study we demonstrate that the reversibly switchable fluorescent protein Dreiklang enables live-cell recordings in both spatially controlled and stochastic modes. We show that the Dreiklang chromophore entails three different light-induced switching mechanisms, namely a reversible photochemical one, off-switching by stimulated emission, and a reversible transfer to a long-lived dark state from the S1 state, all of which can be utilized to overcome the diffraction barrier. We also find that for the single-molecule- based stochastic GSDIM approach (ground-state depletion followed by individual molecule return), Dreiklang provides a larger number of on-off localization events as compared to its progenitor Citrine. Altogether, Dreiklang is a versatile probe for essentially all popular forms of live-cell fluorescence nanoscopy.","lang":"eng"}],"month":"03","publication_status":"published","publisher":"Wiley-Blackwell","article_processing_charge":"No","oa_version":"None"},{"external_id":{"arxiv":["1305.4519"]},"title":"Clustered planarity testing revisited","publication_identifier":{"issn":["0302-9743"]},"publication":"International Symposium on Graph Drawing","day":"01","citation":{"short":"R. Fulek, J. Kynčl, I. Malinović, D. Pálvölgyi, in:, International Symposium on Graph Drawing, Springer Nature, Cham, 2014, pp. 428–436.","ista":"Fulek R, Kynčl J, Malinović I, Pálvölgyi D. 2014. Clustered planarity testing revisited. International Symposium on Graph Drawing. , LNCS, vol. 8871, 428–436.","chicago":"Fulek, Radoslav, Jan Kynčl, Igor Malinović, and Dömötör Pálvölgyi. “Clustered Planarity Testing Revisited.” In <i>International Symposium on Graph Drawing</i>, 8871:428–36. Cham: Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">https://doi.org/10.1007/978-3-662-45803-7_36</a>.","apa":"Fulek, R., Kynčl, J., Malinović, I., &#38; Pálvölgyi, D. (2014). Clustered planarity testing revisited. In <i>International Symposium on Graph Drawing</i> (Vol. 8871, pp. 428–436). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">https://doi.org/10.1007/978-3-662-45803-7_36</a>","ieee":"R. Fulek, J. Kynčl, I. Malinović, and D. Pálvölgyi, “Clustered planarity testing revisited,” in <i>International Symposium on Graph Drawing</i>, 2014, vol. 8871, pp. 428–436.","ama":"Fulek R, Kynčl J, Malinović I, Pálvölgyi D. Clustered planarity testing revisited. In: <i>International Symposium on Graph Drawing</i>. Vol 8871. Cham: Springer Nature; 2014:428-436. doi:<a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">10.1007/978-3-662-45803-7_36</a>","mla":"Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” <i>International Symposium on Graph Drawing</i>, vol. 8871, Springer Nature, 2014, pp. 428–36, doi:<a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">10.1007/978-3-662-45803-7_36</a>."},"author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","last_name":"Fulek","first_name":"Radoslav"},{"last_name":"Kynčl","first_name":"Jan","full_name":"Kynčl, Jan"},{"full_name":"Malinović, Igor","last_name":"Malinović","first_name":"Igor"},{"full_name":"Pálvölgyi, Dömötör","last_name":"Pálvölgyi","first_name":"Dömötör"}],"date_updated":"2023-02-23T10:08:04Z","oa_version":"Preprint","article_processing_charge":"No","quality_controlled":"1","abstract":[{"lang":"eng","text":"The Hanani–Tutte theorem is a classical result proved for the first time in the 1930s that characterizes planar graphs as graphs that admit a drawing in the plane in which every pair of edges not sharing a vertex cross an even number of times. We generalize this classical result to clustered graphs with two disjoint clusters, and show that a straightforward extension of our result to flat clustered graphs with three or more disjoint clusters is not possible.\r\n\r\nWe also give a new and short proof for a related result by Di Battista and Frati based on the matroid intersection algorithm."}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"1642","relation":"later_version"}]},"year":"2014","_id":"10793","date_created":"2022-02-25T10:32:14Z","intvolume":"      8871","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"status":"public","doi":"10.1007/978-3-662-45803-7_36","date_published":"2014-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":8871,"type":"conference","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","month":"01","scopus_import":"1","place":"Cham","page":"428-436","arxiv":1},{"abstract":[{"text":"Auxin is an important signaling compound in plants and vital for plant development and growth. The present book, Auxin and its Role in Plant Development, provides the reader with detailed and comprehensive insight into the functioning of the molecule on the whole and specifically in plant development. In the first part, the functioning, metabolism and signaling pathways of auxin in plants are explained, the second part depicts the specific role of auxin in plant development and the third part describes the interaction and functioning of the signaling compound  upon stimuli of the environment. Each chapter is written by international experts in the respective field and designed for scientists and researchers in plant biology, plant development and cell biology to summarize the recent progress in understanding the role of auxin and suggest future perspectives for auxin research.","lang":"eng"}],"publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Springer Nature","month":"04","editor":[{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková"}],"oa_version":"None","article_processing_charge":"No","quality_controlled":"1","page":"444","year":"2014","scopus_import":"1","_id":"10811","place":"Vienna","date_created":"2022-03-03T11:52:44Z","language":[{"iso":"eng"}],"status":"public","title":"Auxin and Its Role in Plant Development","doi":"10.1007/978-3-7091-1526-8","date_published":"2014-04-01T00:00:00Z","citation":{"ista":"Zažímalová E, Petrášek J, Benková E eds. 2014. Auxin and Its Role in Plant Development 1st ed., Vienna: Springer Nature, 444p.","chicago":"Zažímalová, Eva, Jan Petrášek, and Eva Benková, eds. <i>Auxin and Its Role in Plant Development</i>. 1st ed. Vienna: Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">https://doi.org/10.1007/978-3-7091-1526-8</a>.","ama":"Zažímalová E, Petrášek J, Benková E, eds. <i>Auxin and Its Role in Plant Development</i>. 1st ed. Vienna: Springer Nature; 2014. doi:<a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">10.1007/978-3-7091-1526-8</a>","ieee":"E. Zažímalová, J. Petrášek, and E. Benková, Eds., <i>Auxin and Its Role in Plant Development</i>, 1st ed. Vienna: Springer Nature, 2014.","apa":"Zažímalová, E., Petrášek, J., &#38; Benková, E. (Eds.). (2014). <i>Auxin and Its Role in Plant Development</i> (1st ed.). Vienna: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">https://doi.org/10.1007/978-3-7091-1526-8</a>","mla":"Zažímalová, Eva, et al., editors. <i>Auxin and Its Role in Plant Development</i>. 1st ed., Springer Nature, 2014, doi:<a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">10.1007/978-3-7091-1526-8</a>.","short":"E. Zažímalová, J. Petrášek, E. Benková, eds., Auxin and Its Role in Plant Development, 1st ed., Springer Nature, Vienna, 2014."},"date_updated":"2022-03-04T07:38:15Z","edition":"1","type":"book_editor","publication_identifier":{"isbn":["9783709115251"],"eisbn":["9783709115268"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01"},{"article_processing_charge":"No","keyword":["General Medicine"],"oa_version":"None","quality_controlled":"1","abstract":[{"lang":"eng","text":"We review recent progress towards a rigorous understanding of the excitation spectrum of bosonic quantum many-body systems. In particular, we explain how one can rigorously establish the predictions resulting from the Bogoliubov approximation in the mean field limit. The latter predicts that the spectrum is made up of elementary excitations, whose energy behaves linearly in the momentum for small momentum. This property is crucial for the superfluid behavior of the system. We also discuss a list of open problems in this field."}],"month":"03","publisher":"Springer Nature","department":[{"_id":"RoSe"}],"publication_status":"published","article_type":"original","_id":"10814","year":"2014","scopus_import":"1","date_created":"2022-03-04T07:54:39Z","page":"21-41","intvolume":"       116","title":"The excitation spectrum for Bose fluids with weak interactions","status":"public","language":[{"iso":"eng"}],"date_published":"2014-03-01T00:00:00Z","doi":"10.1365/s13291-014-0083-9","publication_identifier":{"issn":["0012-0456"],"eissn":["1869-7135"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Jahresbericht der Deutschen Mathematiker-Vereinigung","day":"01","volume":116,"citation":{"short":"R. Seiringer, Jahresbericht Der Deutschen Mathematiker-Vereinigung 116 (2014) 21–41.","ieee":"R. Seiringer, “The excitation spectrum for Bose fluids with weak interactions,” <i>Jahresbericht der Deutschen Mathematiker-Vereinigung</i>, vol. 116. Springer Nature, pp. 21–41, 2014.","ama":"Seiringer R. The excitation spectrum for Bose fluids with weak interactions. <i>Jahresbericht der Deutschen Mathematiker-Vereinigung</i>. 2014;116:21-41. doi:<a href=\"https://doi.org/10.1365/s13291-014-0083-9\">10.1365/s13291-014-0083-9</a>","apa":"Seiringer, R. (2014). The excitation spectrum for Bose fluids with weak interactions. <i>Jahresbericht Der Deutschen Mathematiker-Vereinigung</i>. Springer Nature. <a href=\"https://doi.org/10.1365/s13291-014-0083-9\">https://doi.org/10.1365/s13291-014-0083-9</a>","mla":"Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.” <i>Jahresbericht Der Deutschen Mathematiker-Vereinigung</i>, vol. 116, Springer Nature, 2014, pp. 21–41, doi:<a href=\"https://doi.org/10.1365/s13291-014-0083-9\">10.1365/s13291-014-0083-9</a>.","ista":"Seiringer R. 2014. The excitation spectrum for Bose fluids with weak interactions. Jahresbericht der Deutschen Mathematiker-Vereinigung. 116, 21–41.","chicago":"Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.” <i>Jahresbericht Der Deutschen Mathematiker-Vereinigung</i>. Springer Nature, 2014. <a href=\"https://doi.org/10.1365/s13291-014-0083-9\">https://doi.org/10.1365/s13291-014-0083-9</a>."},"type":"journal_article","author":[{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer"}],"date_updated":"2023-09-05T14:19:47Z"},{"acknowledgement":"The authors thank all the members of the Division of Morphogenesis, National Institute for Basic Biology, for their contributions to the research, their encouragement, and helpful discussions, particularly Dr M. Suzuki for his critical reading of the manuscript. We also thank the Model Animal Research and Spectrography and Bioimaging Facilities, NIBB Core Research Facilities, for technical support. M.H. was supported by a research fellowship from the Japan Society for the Promotion of Science (JSPS). Our work introduced in this review was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan, to N.U.","scopus_import":"1","page":"1-7","main_file_link":[{"url":"https://doi.org/10.1111/cga.12039","open_access":"1"}],"publisher":"Wiley","department":[{"_id":"CaHe"}],"month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":54,"intvolume":"        54","doi":"10.1111/cga.12039","date_published":"2014-02-01T00:00:00Z","language":[{"iso":"eng"}],"status":"public","pmid":1,"date_created":"2022-03-04T08:17:25Z","year":"2014","_id":"10815","quality_controlled":"1","oa_version":"None","keyword":["Developmental Biology","Embryology","General Medicine","Pediatrics","Perinatology","and Child Health"],"article_processing_charge":"No","publication_status":"published","article_type":"original","abstract":[{"text":"In the last several decades, developmental biology has clarified the molecular mechanisms of embryogenesis and organogenesis. In particular, it has demonstrated that the “tool-kit genes” essential for regulating developmental processes are not only highly conserved among species, but are also used as systems at various times and places in an organism to control distinct developmental events. Therefore, mutations in many of these tool-kit genes may cause congenital diseases involving morphological abnormalities. This link between genes and abnormal morphological phenotypes underscores the importance of understanding how cells behave and contribute to morphogenesis as a result of gene function. Recent improvements in live imaging and in quantitative analyses of cellular dynamics will advance our understanding of the cellular pathogenesis of congenital diseases associated with aberrant morphologies. In these studies, it is critical to select an appropriate model organism for the particular phenomenon of interest.","lang":"eng"}],"day":"01","publication_identifier":{"issn":["0914-3505"]},"publication":"Congenital Anomalies","oa":1,"citation":{"ista":"Hashimoto M, Morita H, Ueno N. 2014. Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. 54(1), 1–7.","chicago":"Hashimoto, Masakazu, Hitoshi Morita, and Naoto Ueno. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” <i>Congenital Anomalies</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/cga.12039\">https://doi.org/10.1111/cga.12039</a>.","ama":"Hashimoto M, Morita H, Ueno N. Molecular and cellular mechanisms of development underlying congenital diseases. <i>Congenital Anomalies</i>. 2014;54(1):1-7. doi:<a href=\"https://doi.org/10.1111/cga.12039\">10.1111/cga.12039</a>","apa":"Hashimoto, M., Morita, H., &#38; Ueno, N. (2014). Molecular and cellular mechanisms of development underlying congenital diseases. <i>Congenital Anomalies</i>. Wiley. <a href=\"https://doi.org/10.1111/cga.12039\">https://doi.org/10.1111/cga.12039</a>","ieee":"M. Hashimoto, H. Morita, and N. Ueno, “Molecular and cellular mechanisms of development underlying congenital diseases,” <i>Congenital Anomalies</i>, vol. 54, no. 1. Wiley, pp. 1–7, 2014.","mla":"Hashimoto, Masakazu, et al. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” <i>Congenital Anomalies</i>, vol. 54, no. 1, Wiley, 2014, pp. 1–7, doi:<a href=\"https://doi.org/10.1111/cga.12039\">10.1111/cga.12039</a>.","short":"M. Hashimoto, H. Morita, N. Ueno, Congenital Anomalies 54 (2014) 1–7."},"author":[{"first_name":"Masakazu","last_name":"Hashimoto","full_name":"Hashimoto, Masakazu"},{"last_name":"Morita","first_name":"Hitoshi","full_name":"Morita, Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Naoto","last_name":"Ueno","full_name":"Ueno, Naoto"}],"date_updated":"2022-03-04T08:26:05Z","issue":"1","external_id":{"pmid":["24666178"]},"title":"Molecular and cellular mechanisms of development underlying congenital diseases"},{"doi":"10.1007/978-3-319-04099-8_9","date_published":"2014-03-19T00:00:00Z","language":[{"iso":"eng"}],"status":"public","type":"book_chapter","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"month":"03","editor":[{"last_name":"Bremer","first_name":"Peer-Timo","full_name":"Bremer, Peer-Timo"},{"first_name":"Ingrid","last_name":"Hotz","full_name":"Hotz, Ingrid"},{"first_name":"Valerio","last_name":"Pascucci","full_name":"Pascucci, Valerio"},{"full_name":"Peikert, Ronald","last_name":"Peikert","first_name":"Ronald"}],"page":"135-150","place":"Cham","acknowledgement":"This research is supported and funded by the Digiteo unTopoVis project, the TOPOSYS project FP7-ICT-318493-STREP, and MPC-VCC.","scopus_import":"1","project":[{"name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"318493"}],"title":"Notes on the simplification of the Morse-Smale complex","date_updated":"2023-09-05T15:33:45Z","author":[{"first_name":"David","last_name":"Günther","full_name":"Günther, David"},{"last_name":"Reininghaus","first_name":"Jan","full_name":"Reininghaus, Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hans-Peter","last_name":"Seidel","full_name":"Seidel, Hans-Peter"},{"last_name":"Weinkauf","first_name":"Tino","full_name":"Weinkauf, Tino"}],"citation":{"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.","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>.","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>.","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.","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>"},"day":"19","publication_identifier":{"issn":["1612-3786"],"eissn":["2197-666X"],"isbn":["9783319040981"],"eisbn":["9783319040998"]},"publication":"Topological Methods in Data Analysis and Visualization III.","publication_status":"published","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"}],"quality_controlled":"1","oa_version":"None","article_processing_charge":"No","ec_funded":1,"date_created":"2022-03-04T08:33:57Z","series_title":"Mathematics and Visualization","year":"2014","_id":"10817"},{"day":"30","oa":1,"publication":"Verification, Model Checking, and Abstract Interpretation","publication_identifier":{"isbn":["9783642540127"],"eissn":["1611-3349"],"eisbn":["9783642540134"],"issn":["0302-9743"]},"citation":{"short":"B. Aminof, S. Jacobs, A. Khalimov, S. Rubin, in:, Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 262–281.","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>","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>","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>."},"author":[{"id":"4A55BD00-F248-11E8-B48F-1D18A9856A87","full_name":"Aminof, Benjamin","first_name":"Benjamin","last_name":"Aminof"},{"full_name":"Jacobs, Swen","last_name":"Jacobs","first_name":"Swen"},{"last_name":"Khalimov","first_name":"Ayrat","full_name":"Khalimov, Ayrat"},{"last_name":"Rubin","first_name":"Sasha","full_name":"Rubin, Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2022-05-17T08:36:01Z","external_id":{"arxiv":["1311.4425"]},"title":"Parameterized model checking of token-passing systems","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"ec_funded":1,"date_created":"2022-03-18T13:01:22Z","_id":"10884","year":"2014","quality_controlled":"1","article_processing_charge":"No","oa_version":"Preprint","publication_status":"published","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","volume":8318,"intvolume":"      8318","alternative_title":["LNCS"],"date_published":"2014-01-30T00:00:00Z","doi":"10.1007/978-3-642-54013-4_15","status":"public","language":[{"iso":"eng"}],"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.","scopus_import":"1","arxiv":1,"conference":{"start_date":"2014-01-19","location":"San Diego, CA, United States","name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation","end_date":"2014-01-21"},"page":"262-281","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1311.4425"}],"month":"01","department":[{"_id":"KrCh"}],"publisher":"Springer Nature"}]