[{"department":[{"_id":"CampIT"}],"date_updated":"2022-06-07T09:12:32Z","type":"journal_article","article_type":"original","status":"public","_id":"1892","issue":"1794","volume":281,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211437/","open_access":"1"}],"month":"11","intvolume":" 281","abstract":[{"lang":"eng","text":"Behavioural variation among conspecifics is typically contingent on individual state or environmental conditions. Sex-specific genetic polymorphisms are enigmatic because they lack conditionality, and genes causing adaptive trait variation in one sex may reduce Darwinian fitness in the other. One way to avoid such genetic antagonism is to control sex-specific traits by inheritance via sex chromosomes. Here, controlled laboratory crossings suggest that in snail-brooding cichlid fish a single locus, two-allele polymorphism located on a sex-linked chromosome of heterogametic males generates an extreme reproductive dimorphism. Both natural and sexual selection are responsible for exceptionally large body size of bourgeois males, creating a niche for a miniature male phenotype to evolve. This extreme intrasexual dimorphism results from selection on opposite size thresholds caused by a single ecological factor, empty snail shells used as breeding substrate. Paternity analyses reveal that in the field parasitic dwarf males sire the majority of offspring in direct sperm competition with large nest owners exceeding their size more than 40 times. Apparently, use of empty snail shells as breeding substrate and single locus sex-linked inheritance of growth are the major ecological and genetic mechanisms responsible for the extreme intrasexual diversity observed in Lamprologus callipterus."}],"oa_version":"Submitted Version","pmid":1,"author":[{"full_name":"Ocana, Sabine","last_name":"Ocana","first_name":"Sabine"},{"first_name":"Patrick","id":"4709BCE6-F248-11E8-B48F-1D18A9856A87","full_name":"Meidl, Patrick","last_name":"Meidl"},{"first_name":"Danielle","full_name":"Bonfils, Danielle","last_name":"Bonfils"},{"first_name":"Michael","full_name":"Taborsky, Michael","last_name":"Taborsky"}],"publist_id":"5203","external_id":{"pmid":["25232141"]},"article_processing_charge":"No","title":"Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids","citation":{"mla":"Ocana, Sabine, et al. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794, 20140253, The Royal Society, 2014, doi:10.1098/rspb.2014.0253.","ieee":"S. Ocana, P. Meidl, D. Bonfils, and M. Taborsky, “Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794. The Royal Society, 2014.","short":"S. Ocana, P. Meidl, D. Bonfils, M. Taborsky, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014).","apa":"Ocana, S., Meidl, P., Bonfils, D., & Taborsky, M. (2014). Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2014.0253","ama":"Ocana S, Meidl P, Bonfils D, Taborsky M. Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. 2014;281(1794). doi:10.1098/rspb.2014.0253","chicago":"Ocana, Sabine, Patrick Meidl, Danielle Bonfils, and Michael Taborsky. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.” Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society, 2014. https://doi.org/10.1098/rspb.2014.0253.","ista":"Ocana S, Meidl P, Bonfils D, Taborsky M. 2014. Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. 281(1794), 20140253."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"20140253","date_published":"2014-11-07T00:00:00Z","doi":"10.1098/rspb.2014.0253","date_created":"2018-12-11T11:54:34Z","year":"2014","day":"07","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","publisher":"The Royal Society","quality_controlled":"1","oa":1,"acknowledgement":"This research was supported by grants of the Swiss National Science Foundation to M.T.\r\nWe thank Tetsu Sato for providing field samples, Olivier Goffinet for field assistance, Dolores Schütz for vital help in the field and with the manuscript, David Lank, Barbara Taborsky, Suzanne Alonzo and two anonymous referees for comments on earlier manuscript versions, and the Fisheries Department, Ministry of Agriculture and Livestock of Zambia, for permission and support."},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M, Cieplak M. 2014. Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. 82(5), 717–726.","chicago":"Chwastyk, Mateusz, Albert Galera Prat, Mateusz K Sikora, Àngel Gómez Sicilia, Mariano Carrión Vázquez, and Marek Cieplak. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell, 2014. https://doi.org/10.1002/prot.24436.","ama":"Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M, Cieplak M. Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. 2014;82(5):717-726. doi:10.1002/prot.24436","apa":"Chwastyk, M., Galera Prat, A., Sikora, M. K., Gómez Sicilia, À., Carrión Vázquez, M., & Cieplak, M. (2014). Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.24436","short":"M. Chwastyk, A. Galera Prat, M.K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez, M. Cieplak, Proteins: Structure, Function and Bioinformatics 82 (2014) 717–726.","ieee":"M. Chwastyk, A. Galera Prat, M. K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez, and M. Cieplak, “Theoretical tests of the mechanical protection strategy in protein nanomechanics,” Proteins: Structure, Function and Bioinformatics, vol. 82, no. 5. Wiley-Blackwell, pp. 717–726, 2014.","mla":"Chwastyk, Mateusz, et al. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” Proteins: Structure, Function and Bioinformatics, vol. 82, no. 5, Wiley-Blackwell, 2014, pp. 717–26, doi:10.1002/prot.24436."},"date_updated":"2021-01-12T06:53:52Z","title":"Theoretical tests of the mechanical protection strategy in protein nanomechanics","department":[{"_id":"CaHe"}],"publist_id":"5204","author":[{"full_name":"Chwastyk, Mateusz","last_name":"Chwastyk","first_name":"Mateusz"},{"first_name":"Albert","full_name":"Galera Prat, Albert","last_name":"Galera Prat"},{"last_name":"Sikora","full_name":"Sikora, Mateusz K","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Àngel","last_name":"Gómez Sicilia","full_name":"Gómez Sicilia, Àngel"},{"last_name":"Carrión Vázquez","full_name":"Carrión Vázquez, Mariano","first_name":"Mariano"},{"full_name":"Cieplak, Marek","last_name":"Cieplak","first_name":"Marek"}],"_id":"1891","status":"public","type":"journal_article","day":"01","publication":"Proteins: Structure, Function and Bioinformatics","language":[{"iso":"eng"}],"publication_status":"published","year":"2014","issue":"5","volume":82,"doi":"10.1002/prot.24436","date_published":"2014-05-01T00:00:00Z","date_created":"2018-12-11T11:54:34Z","page":"717 - 726","oa_version":"None","acknowledgement":"Grant Nr. 2011/01/N/ST3/02475","abstract":[{"text":"We provide theoretical tests of a novel experimental technique to determine mechanostability of proteins based on stretching a mechanically protected protein by single-molecule force spectroscopy. This technique involves stretching a homogeneous or heterogeneous chain of reference proteins (single-molecule markers) in which one of them acts as host to the guest protein under study. The guest protein is grafted into the host through genetic engineering. It is expected that unraveling of the host precedes the unraveling of the guest removing ambiguities in the reading of the force-extension patterns of the guest protein. We study examples of such systems within a coarse-grained structure-based model. We consider systems with various ratios of mechanostability for the host and guest molecules and compare them to experimental results involving cohesin I as the guest molecule. For a comparison, we also study the force-displacement patterns in proteins that are linked in a serial fashion. We find that the mechanostability of the guest is similar to that of the isolated or serially linked protein. We also demonstrate that the ideal configuration of this strategy would be one in which the host is much more mechanostable than the single-molecule markers. We finally show that it is troublesome to use the highly stable cystine knot proteins as a host to graft a guest in stretching studies because this would involve a cleaving procedure.","lang":"eng"}],"month":"05","intvolume":" 82","publisher":"Wiley-Blackwell","scopus_import":1},{"date_created":"2018-12-11T11:54:32Z","date_published":"2014-12-04T00:00:00Z","volume":124,"issue":"21","page":"1952 - 1952","publication":"Blood","language":[{"iso":"eng"}],"day":"04","publication_status":"published","year":"2014","intvolume":" 124","month":"12","main_file_link":[{"url":"http://www.bloodjournal.org/content/124/21/1952?sso-checked=true"}],"publisher":"American Society of Hematology","oa_version":"None","abstract":[{"text":"Unbiased high-throughput massively parallel sequencing methods have transformed the process of discovery of novel putative driver gene mutations in cancer. In chronic lymphocytic leukemia (CLL), these methods have yielded several unexpected findings, including the driver genes SF3B1, NOTCH1 and POT1. Recent analysis, utilizing down-sampling of existing datasets, has shown that the discovery process of putative drivers is far from complete across cancer. In CLL, while driver gene mutations affecting >10% of patients were efficiently discovered with previously published CLL cohorts of up to 160 samples subjected to whole exome sequencing (WES), this sample size has only 0.78 power to detect drivers affecting 5% of patients, and only 0.12 power for drivers affecting 2% of patients. These calculations emphasize the need to apply unbiased WES to larger patient cohorts.","lang":"eng"}],"department":[{"_id":"KrCh"}],"title":"Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples","publist_id":"5211","author":[{"first_name":"Dan","last_name":"Landau","full_name":"Landau, Dan"},{"first_name":"Chip","full_name":"Stewart, Chip","last_name":"Stewart"},{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Reiter","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353"},{"last_name":"Lawrence","full_name":"Lawrence, Michael","first_name":"Michael"},{"full_name":"Sougnez, Carrie","last_name":"Sougnez","first_name":"Carrie"},{"first_name":"Jennifer","full_name":"Brown, Jennifer","last_name":"Brown"},{"last_name":"Lopez Guillermo","full_name":"Lopez Guillermo, Armando","first_name":"Armando"},{"first_name":"Stacey","last_name":"Gabriel","full_name":"Gabriel, Stacey"},{"last_name":"Lander","full_name":"Lander, Eric","first_name":"Eric"},{"full_name":"Neuberg, Donna","last_name":"Neuberg","first_name":"Donna"},{"first_name":"Carlos","full_name":"López Otín, Carlos","last_name":"López Otín"},{"full_name":"Campo, Elias","last_name":"Campo","first_name":"Elias"},{"first_name":"Gad","full_name":"Getz, Gad","last_name":"Getz"},{"first_name":"Catherine","last_name":"Wu","full_name":"Wu, Catherine"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Landau, Dan, Chip Stewart, Johannes Reiter, Michael Lawrence, Carrie Sougnez, Jennifer Brown, Armando Lopez Guillermo, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” Blood. American Society of Hematology, 2014.","ista":"Landau D, Stewart C, Reiter J, Lawrence M, Sougnez C, Brown J, Lopez Guillermo A, Gabriel S, Lander E, Neuberg D, López Otín C, Campo E, Getz G, Wu C. 2014. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. 124(21), 1952–1952.","mla":"Landau, Dan, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” Blood, vol. 124, no. 21, American Society of Hematology, 2014, pp. 1952–1952.","ama":"Landau D, Stewart C, Reiter J, et al. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. 2014;124(21):1952-1952.","apa":"Landau, D., Stewart, C., Reiter, J., Lawrence, M., Sougnez, C., Brown, J., … Wu, C. (2014). Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. American Society of Hematology.","short":"D. Landau, C. Stewart, J. Reiter, M. Lawrence, C. Sougnez, J. Brown, A. Lopez Guillermo, S. Gabriel, E. Lander, D. Neuberg, C. López Otín, E. Campo, G. Getz, C. Wu, Blood 124 (2014) 1952–1952.","ieee":"D. Landau et al., “Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples,” Blood, vol. 124, no. 21. American Society of Hematology, pp. 1952–1952, 2014."},"date_updated":"2021-01-12T06:53:50Z","status":"public","type":"journal_article","_id":"1884"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bräunlich G, Hainzl C, Seiringer R. 2014. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. 26(7), 1450012.","chicago":"Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews in Mathematical Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X14500123.","ieee":"G. Bräunlich, C. Hainzl, and R. Seiringer, “Translation-invariant quasi-free states for fermionic systems and the BCS approximation,” Reviews in Mathematical Physics, vol. 26, no. 7. World Scientific Publishing, 2014.","short":"G. Bräunlich, C. Hainzl, R. Seiringer, Reviews in Mathematical Physics 26 (2014).","apa":"Bräunlich, G., Hainzl, C., & Seiringer, R. (2014). Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X14500123","ama":"Bräunlich G, Hainzl C, Seiringer R. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. 2014;26(7). doi:10.1142/S0129055X14500123","mla":"Bräunlich, Gerhard, et al. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews in Mathematical Physics, vol. 26, no. 7, 1450012, World Scientific Publishing, 2014, doi:10.1142/S0129055X14500123."},"title":"Translation-invariant quasi-free states for fermionic systems and the BCS approximation","external_id":{"arxiv":["1305.5135"]},"article_processing_charge":"No","publist_id":"5206","author":[{"last_name":"Bräunlich","full_name":"Bräunlich, Gerhard","first_name":"Gerhard"},{"first_name":"Christian","last_name":"Hainzl","full_name":"Hainzl, Christian"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"article_number":"1450012","publication":"Reviews in Mathematical Physics","day":"01","year":"2014","date_created":"2018-12-11T11:54:33Z","date_published":"2014-08-01T00:00:00Z","doi":"10.1142/S0129055X14500123","acknowledgement":"We would like to thank Max Lein and Andreas Deuchert for valuable suggestions and remarks. Partial financial support by the NSERC (R.S.) is gratefully acknowledged.","oa":1,"publisher":"World Scientific Publishing","quality_controlled":"1","date_updated":"2022-06-07T09:03:09Z","department":[{"_id":"RoSe"}],"_id":"1889","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","volume":26,"issue":"7","oa_version":"Submitted Version","abstract":[{"text":"We study translation-invariant quasi-free states for a system of fermions with two-particle interactions. The associated energy functional is similar to the BCS functional but also includes direct and exchange energies. We show that for suitable short-range interactions, these latter terms only lead to a renormalization of the chemical potential, with the usual properties of the BCS functional left unchanged. Our analysis thus represents a rigorous justification of part of the BCS approximation. We give bounds on the critical temperature below which the system displays superfluidity.","lang":"eng"}],"intvolume":" 26","month":"08","main_file_link":[{"url":"http://arxiv.org/abs/1305.5135","open_access":"1"}],"scopus_import":"1"},{"abstract":[{"lang":"eng","text":"Background: Bacterial Dsb enzymes are involved in the oxidative folding of many proteins, through the formation of disulfide bonds between their cysteine residues. The Dsb protein network has been well characterized in cells of the model microorganism Escherichia coli. To gain insight into the functioning of the Dsb system in epsilon-Proteobacteria, where it plays an important role in the colonization process, we studied two homologs of the main Escherichia coli Dsb oxidase (EcDsbA) that are present in the cells of the enteric pathogen Campylobacter jejuni, the most frequently reported bacterial cause of human enteritis in the world. Methods and Results: Phylogenetic analysis suggests the horizontal transfer of the epsilon-Proteobacterial DsbAs from a common ancestor to gamma-Proteobacteria, which then gave rise to the DsbL lineage. Phenotype and enzymatic assays suggest that the two C. jejuni DsbAs play different roles in bacterial cells and have divergent substrate spectra. CjDsbA1 is essential for the motility and autoagglutination phenotypes, while CjDsbA2 has no impact on those processes. CjDsbA1 plays a critical role in the oxidative folding that ensures the activity of alkaline phosphatase CjPhoX, whereas CjDsbA2 is crucial for the activity of arylsulfotransferase CjAstA, encoded within the dsbA2-dsbB-astA operon. Conclusions: Our results show that CjDsbA1 is the primary thiol-oxidoreductase affecting life processes associated with bacterial spread and host colonization, as well as ensuring the oxidative folding of particular protein substrates. In contrast, CjDsbA2 activity does not affect the same processes and so far its oxidative folding activity has been demonstrated for one substrate, arylsulfotransferase CjAstA. The results suggest the cooperation between CjDsbA2 and CjDsbB. In the case of the CjDsbA1, this cooperation is not exclusive and there is probably another protein to be identified in C. jejuni cells that acts to re-oxidize CjDsbA1. Altogether the data presented here constitute the considerable insight to the Epsilonproteobacterial Dsb systems, which have been poorly understood so far."}],"oa_version":"Published Version","scopus_import":1,"month":"09","intvolume":" 9","publication_status":"published","file":[{"file_id":"5205","checksum":"7d02c3da7f72b82bb5d7932d80c3251f","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2016-438-v1+1_journal.pone.0106247.pdf","date_created":"2018-12-12T10:16:19Z","file_size":4248801,"date_updated":"2020-07-14T12:45:20Z","creator":"system"}],"language":[{"iso":"eng"}],"volume":9,"issue":"9","_id":"1894","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"438","date_updated":"2021-01-12T06:53:54Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:20Z","department":[{"_id":"CaGu"}],"publisher":"Public Library of Science","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2014","day":"02","publication":"PLoS One","doi":"10.1371/journal.pone.0106247","date_published":"2014-09-02T00:00:00Z","date_created":"2018-12-11T11:54:35Z","article_number":"e106247","citation":{"mla":"Grabowska, Anna, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” PLoS One, vol. 9, no. 9, e106247, Public Library of Science, 2014, doi:10.1371/journal.pone.0106247.","short":"A. Grabowska, E. Wywiał, S. Dunin Horkawicz, A. Łasica, M. Wösten, A.A. Nagy-Staron, R. Godlewska, K. Bocian Ostrzycka, K. Pieńkowska, P. Łaniewski, J. Bujnicki, J. Van Putten, E. Jagusztyn Krynicka, PLoS One 9 (2014).","ieee":"A. Grabowska et al., “Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014.","apa":"Grabowska, A., Wywiał, E., Dunin Horkawicz, S., Łasica, A., Wösten, M., Nagy-Staron, A. A., … Jagusztyn Krynicka, E. (2014). Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0106247","ama":"Grabowska A, Wywiał E, Dunin Horkawicz S, et al. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0106247","chicago":"Grabowska, Anna, Ewa Wywiał, Stanislaw Dunin Horkawicz, Anna Łasica, Marc Wösten, Anna A Nagy-Staron, Renata Godlewska, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0106247.","ista":"Grabowska A, Wywiał E, Dunin Horkawicz S, Łasica A, Wösten M, Nagy-Staron AA, Godlewska R, Bocian Ostrzycka K, Pieńkowska K, Łaniewski P, Bujnicki J, Van Putten J, Jagusztyn Krynicka E. 2014. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. 9(9), e106247."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Grabowska","full_name":"Grabowska, Anna","first_name":"Anna"},{"first_name":"Ewa","full_name":"Wywiał, Ewa","last_name":"Wywiał"},{"first_name":"Stanislaw","last_name":"Dunin Horkawicz","full_name":"Dunin Horkawicz, Stanislaw"},{"full_name":"Łasica, Anna","last_name":"Łasica","first_name":"Anna"},{"first_name":"Marc","full_name":"Wösten, Marc","last_name":"Wösten"},{"last_name":"Nagy-Staron","full_name":"Nagy-Staron, Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A"},{"full_name":"Godlewska, Renata","last_name":"Godlewska","first_name":"Renata"},{"last_name":"Bocian Ostrzycka","full_name":"Bocian Ostrzycka, Katarzyna","first_name":"Katarzyna"},{"last_name":"Pieńkowska","full_name":"Pieńkowska, Katarzyna","first_name":"Katarzyna"},{"first_name":"Paweł","full_name":"Łaniewski, Paweł","last_name":"Łaniewski"},{"last_name":"Bujnicki","full_name":"Bujnicki, Janusz","first_name":"Janusz"},{"last_name":"Van Putten","full_name":"Van Putten, Jos","first_name":"Jos"},{"last_name":"Jagusztyn Krynicka","full_name":"Jagusztyn Krynicka, Elzbieta","first_name":"Elzbieta"}],"publist_id":"5201","title":"Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA"},{"department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:45:20Z","ddc":["570"],"date_updated":"2021-01-12T06:53:54Z","pubrep_id":"439","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1895","issue":"9","volume":9,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4724","checksum":"1f3be936be93114596d61ba44cacee69","file_size":6262085,"date_updated":"2020-07-14T12:45:20Z","creator":"system","file_name":"IST-2016-439-v1+1_journal.pone.0107099.pdf","date_created":"2018-12-12T10:09:01Z"}],"publication_status":"published","intvolume":" 9","month":"09","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Major histocompatibility complex class I (MHCI) molecules were recently identified as novel regulators of synaptic plasticity. These molecules are expressed in various brain areas, especially in regions undergoing activity-dependent synaptic plasticity, but their role in the nucleus accumbens (NAc) is unknown. In this study, we investigated the effects of genetic disruption of MHCI function, through deletion of β2-microblobulin, which causes lack of cell surface expression of MHCI. First, we confirmed that MHCI molecules are expressed in the NAc core in wild-type mice. Second, we performed electrophysiological recordings with NAc core slices from wild-type and β2-microglobulin knock-out mice lacking cell surface expression of MHCI. We found that low frequency stimulation induced long-term depression in wild-type but not knock-out mice, whereas high frequency stimulation induced long-term potentiation in both genotypes, with a larger magnitude in knock-out mice. Furthermore, we demonstrated that knock-out mice showed more persistent behavioral sensitization to cocaine, which is a NAc-related behavior. Using this model, we analyzed the density of total AMPA receptors and their subunits GluR1 and GluR2 in the NAc core, by SDS-digested freeze-fracture replica labeling. After repeated cocaine exposure, the density of GluR1 was increased, but there was no change in total AMPA receptors and GluR2 levels in wildtype mice. In contrast, following repeated cocaine exposure, increased densities of total AMPA receptors, GluR1 and GluR2 were observed in knock-out mice. These results indicate that functional deficiency of MHCI enhances synaptic potentiation, induced by electrical and pharmacological stimulation."}],"title":"Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice","publist_id":"5200","author":[{"full_name":"Edamura, Mitsuhiro","last_name":"Edamura","first_name":"Mitsuhiro"},{"first_name":"Gen","last_name":"Murakami","full_name":"Murakami, Gen"},{"full_name":"Meng, Hongrui","last_name":"Meng","first_name":"Hongrui"},{"last_name":"Itakura","full_name":"Itakura, Makoto","first_name":"Makoto"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"last_name":"Fukuda","full_name":"Fukuda, Atsuo","first_name":"Atsuo"},{"first_name":"Daiichiro","full_name":"Nakahara, Daiichiro","last_name":"Nakahara"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Edamura M, Murakami G, Meng H, Itakura M, Shigemoto R, Fukuda A, Nakahara D. 2014. Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. 9(9), e107099.","chicago":"Edamura, Mitsuhiro, Gen Murakami, Hongrui Meng, Makoto Itakura, Ryuichi Shigemoto, Atsuo Fukuda, and Daiichiro Nakahara. “Functional Deficiency of MHC Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0107099.","apa":"Edamura, M., Murakami, G., Meng, H., Itakura, M., Shigemoto, R., Fukuda, A., & Nakahara, D. (2014). Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0107099","ama":"Edamura M, Murakami G, Meng H, et al. Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0107099","short":"M. Edamura, G. Murakami, H. Meng, M. Itakura, R. Shigemoto, A. Fukuda, D. Nakahara, PLoS One 9 (2014).","ieee":"M. Edamura et al., “Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014.","mla":"Edamura, Mitsuhiro, et al. “Functional Deficiency of MHC Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS One, vol. 9, no. 9, e107099, Public Library of Science, 2014, doi:10.1371/journal.pone.0107099."},"article_number":"e107099","date_created":"2018-12-11T11:54:35Z","date_published":"2014-09-30T00:00:00Z","doi":"10.1371/journal.pone.0107099","publication":"PLoS One","day":"30","year":"2014","has_accepted_license":"1","oa":1,"publisher":"Public Library of Science","acknowledgement":"This work was supported in part by a Grant-in-Aid for Scientific Research on Innovative Areas (Comprehensive Brain Science Network) and (B) 17330153, from the Ministry of Education, Culture, Sports, Science and Technology of Japan."},{"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Phosphatidylinositol (PtdIns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, PtdIns3P and PtdIns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vacuolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with PtdIns3P, the presumable product of their activity. In SAC gain- and loss-of-function mutants, the levels of PtdIns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with PtdIns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants."}],"month":"02","intvolume":" 111","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932866/","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":111,"issue":"7","ec_funded":1,"_id":"1893","status":"public","type":"journal_article","date_updated":"2021-01-12T06:53:53Z","department":[{"_id":"JiFr"}],"acknowledgement":"This work was supported by grants from the Research Foundation-Flanders (Odysseus).","publisher":"National Academy of Sciences","oa":1,"day":"18","publication":"PNAS","year":"2014","doi":"10.1073/pnas.1324264111","date_published":"2014-02-18T00:00:00Z","date_created":"2018-12-11T11:54:34Z","page":"2818 - 2823","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Marhavá, Petra, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS, vol. 111, no. 7, National Academy of Sciences, 2014, pp. 2818–23, doi:10.1073/pnas.1324264111.","apa":"Marhavá, P., Hirsch, S., Feraru, E., Tejos, R., Van Wijk, R., Viaene, T., … Friml, J. (2014). SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1324264111","ama":"Marhavá P, Hirsch S, Feraru E, et al. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 2014;111(7):2818-2823. doi:10.1073/pnas.1324264111","ieee":"P. Marhavá et al., “SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis,” PNAS, vol. 111, no. 7. National Academy of Sciences, pp. 2818–2823, 2014.","short":"P. Marhavá, S. Hirsch, E. Feraru, R. Tejos, R. Van Wijk, T. Viaene, M. Heilmann, J. Lerche, R. De Rycke, M. Feraru, P. Grones, M. Van Montagu, I. Heilmann, T. Munnik, J. Friml, PNAS 111 (2014) 2818–2823.","chicago":"Marhavá, Petra, Sibylle Hirsch, Elena Feraru, Ricardo Tejos, Ringo Van Wijk, Tom Viaene, Mareike Heilmann, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1324264111.","ista":"Marhavá P, Hirsch S, Feraru E, Tejos R, Van Wijk R, Viaene T, Heilmann M, Lerche J, De Rycke R, Feraru M, Grones P, Van Montagu M, Heilmann I, Munnik T, Friml J. 2014. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 111(7), 2818–2823."},"title":"SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis","author":[{"last_name":"Nováková","full_name":"Nováková, Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra"},{"first_name":"Sibylle","full_name":"Hirsch, Sibylle","last_name":"Hirsch"},{"full_name":"Feraru, Elena","last_name":"Feraru","first_name":"Elena"},{"last_name":"Tejos","full_name":"Tejos, Ricardo","first_name":"Ricardo"},{"first_name":"Ringo","full_name":"Van Wijk, Ringo","last_name":"Van Wijk"},{"last_name":"Viaene","full_name":"Viaene, Tom","first_name":"Tom"},{"first_name":"Mareike","last_name":"Heilmann","full_name":"Heilmann, Mareike"},{"first_name":"Jennifer","last_name":"Lerche","full_name":"Lerche, Jennifer"},{"last_name":"De Rycke","full_name":"De Rycke, Riet","first_name":"Riet"},{"last_name":"Feraru","full_name":"Feraru, Mugurel","first_name":"Mugurel"},{"full_name":"Grones, Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"first_name":"Marc","last_name":"Van Montagu","full_name":"Van Montagu, Marc"},{"first_name":"Ingo","last_name":"Heilmann","full_name":"Heilmann, Ingo"},{"first_name":"Teun","last_name":"Munnik","full_name":"Munnik, Teun"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"publist_id":"5202"},{"scopus_import":"1","main_file_link":[{"url":"http://arxiv.org/abs/1402.0430","open_access":"1"}],"month":"03","intvolume":" 89","abstract":[{"lang":"eng","text":"Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings."}],"oa_version":"Submitted Version","issue":"3","volume":89,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1896","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"date_updated":"2022-08-01T10:50:10Z","publisher":"American Institute of Physics","oa":1,"acknowledgement":"The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.).","doi":"10.1103/PhysRevE.89.032701","date_published":"2014-03-04T00:00:00Z","date_created":"2018-12-11T11:54:35Z","year":"2014","day":"04","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","article_number":"032701","author":[{"first_name":"Richard","full_name":"Kollár, Richard","last_name":"Kollár"},{"last_name":"Bod'ová","full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171","first_name":"Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jozef","last_name":"Nosek","full_name":"Nosek, Jozef"},{"full_name":"Tomáška, Ľubomír","last_name":"Tomáška","first_name":"Ľubomír"}],"publist_id":"5198","article_processing_charge":"No","title":"Mathematical model of alternative mechanism of telomere length maintenance","citation":{"chicago":"Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.032701.","ista":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701.","mla":"Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701.","apa":"Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.032701","ama":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701","short":"R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","ieee":"R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"text":"GNOM is one of the most characterized membrane trafficking regulators in plants, with crucial roles in development. GNOM encodes an ARF-guanine nucleotide exchange factor (ARF-GEF) that activates small GTPases of the ARF (ADP ribosylation factor) class to mediate vesicle budding at endomembranes. The crucial role of GNOM in recycling of PIN auxin transporters and other proteins to the plasma membrane was identified in studies using the ARF-GEF inhibitor brefeldin A (BFA). GNOM, the most prominent regulator of recycling in plants, has been proposed to act and localize at so far elusive recycling endosomes. Here, we report the GNOM localization in context of its cellular function in Arabidopsis thaliana. State-of-the-art imaging, pharmacological interference, and ultrastructure analysis show that GNOM predominantly localizes to Golgi apparatus. Super-resolution confocal live imaging microscopy identified GNOM and its closest homolog GNOM-like 1 at distinct subdomains on Golgi cisternae. Short-term BFA treatment stabilizes GNOM at the Golgi apparatus, whereas prolonged exposures results in GNOM translocation to trans-Golgi network (TGN)/early endosomes (EEs). Malformed TGN/EE in gnom mutants suggests a role for GNOM in maintaining TGN/EE function. Our results redefine the subcellular action of GNOM and reevaluate the identity and function of recycling endosomes in plants.","lang":"eng"}],"acknowledgement":"This work was supported by the Odysseus Program of the Research Foundation-Flanders (J.F.).","oa_version":"Submitted Version","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145132/","open_access":"1"}],"publisher":"American Society of Plant Biologists","scopus_import":1,"intvolume":" 26","month":"07","publication_status":"published","year":"2014","publication":"Plant Cell","language":[{"iso":"eng"}],"day":"01","page":"3062 - 3076","date_created":"2018-12-11T11:54:36Z","date_published":"2014-07-01T00:00:00Z","volume":26,"issue":"7","doi":"10.1105/tpc.114.125880","_id":"1897","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:55Z","citation":{"apa":"Naramoto, S., Otegui, M., Kutsuna, N., De Rycke, R., Dainobu, T., Karampelias, M., … Friml, J. (2014). Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.125880","ama":"Naramoto S, Otegui M, Kutsuna N, et al. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 2014;26(7):3062-3076. doi:10.1105/tpc.114.125880","short":"S. Naramoto, M. Otegui, N. Kutsuna, R. De Rycke, T. Dainobu, M. Karampelias, M. Fujimoto, E. Feraru, D. Miki, H. Fukuda, A. Nakano, J. Friml, Plant Cell 26 (2014) 3062–3076.","ieee":"S. Naramoto et al., “Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis,” Plant Cell, vol. 26, no. 7. American Society of Plant Biologists, pp. 3062–3076, 2014.","mla":"Naramoto, Satoshi, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” Plant Cell, vol. 26, no. 7, American Society of Plant Biologists, 2014, pp. 3062–76, doi:10.1105/tpc.114.125880.","ista":"Naramoto S, Otegui M, Kutsuna N, De Rycke R, Dainobu T, Karampelias M, Fujimoto M, Feraru E, Miki D, Fukuda H, Nakano A, Friml J. 2014. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 26(7), 3062–3076.","chicago":"Naramoto, Satoshi, Marisa Otegui, Natsumaro Kutsuna, Riet De Rycke, Tomoko Dainobu, Michael Karampelias, Masaru Fujimoto, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2014. https://doi.org/10.1105/tpc.114.125880."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5199","author":[{"first_name":"Satoshi","full_name":"Naramoto, Satoshi","last_name":"Naramoto"},{"first_name":"Marisa","full_name":"Otegui, Marisa","last_name":"Otegui"},{"first_name":"Natsumaro","last_name":"Kutsuna","full_name":"Kutsuna, Natsumaro"},{"first_name":"Riet","full_name":"De Rycke, Riet","last_name":"De Rycke"},{"full_name":"Dainobu, Tomoko","last_name":"Dainobu","first_name":"Tomoko"},{"first_name":"Michael","full_name":"Karampelias, Michael","last_name":"Karampelias"},{"last_name":"Fujimoto","full_name":"Fujimoto, Masaru","first_name":"Masaru"},{"first_name":"Elena","last_name":"Feraru","full_name":"Feraru, Elena"},{"first_name":"Daisuke","last_name":"Miki","full_name":"Miki, Daisuke"},{"last_name":"Fukuda","full_name":"Fukuda, Hiroo","first_name":"Hiroo"},{"first_name":"Akihiko","full_name":"Nakano, Akihiko","last_name":"Nakano"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"title":"Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis","department":[{"_id":"JiFr"}]},{"language":[{"iso":"eng"}],"publication_status":"published","volume":16,"issue":"8","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Asymmetric cell divisions allow stem cells to balance proliferation and differentiation. During embryogenesis, murine epidermis expands rapidly from a single layer of unspecified basal layer progenitors to a stratified, differentiated epithelium. Morphogenesis involves perpendicular (asymmetric) divisions and the spindle orientation protein LGN, but little is known about how the apical localization of LGN is regulated. Here, we combine conventional genetics and lentiviral-mediated in vivo RNAi to explore the functions of the LGN-interacting proteins Par3, mInsc and Gα i3. Whereas loss of each gene alone leads to randomized division angles, combined loss of Gnai3 and mInsc causes a phenotype of mostly planar divisions, akin to loss of LGN. These findings lend experimental support for the hitherto untested model that Par3-mInsc and Gα i3 act cooperatively to polarize LGN and promote perpendicular divisions. Finally, we uncover a developmental switch between delamination-driven early stratification and spindle-orientation-dependent differentiation that occurs around E15, revealing a two-step mechanism underlying epidermal maturation."}],"intvolume":" 16","month":"07","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159251/","open_access":"1"}],"scopus_import":1,"date_updated":"2021-01-12T06:53:55Z","department":[{"_id":"SiHi"}],"_id":"1899","status":"public","article_type":"original","type":"journal_article","publication":"Nature Cell Biology","day":"13","year":"2014","date_created":"2018-12-11T11:54:36Z","date_published":"2014-07-13T00:00:00Z","doi":"10.1038/ncb3001","page":"758 - 769","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. 2014;16(8):758-769. doi:10.1038/ncb3001","apa":"Williams, S., Ratliff, L., Postiglione, M. P., Knoblich, J., & Fuchs, E. (2014). Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3001","short":"S. Williams, L. Ratliff, M.P. Postiglione, J. Knoblich, E. Fuchs, Nature Cell Biology 16 (2014) 758–769.","ieee":"S. Williams, L. Ratliff, M. P. Postiglione, J. Knoblich, and E. Fuchs, “Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN,” Nature Cell Biology, vol. 16, no. 8. Nature Publishing Group, pp. 758–769, 2014.","mla":"Williams, Scott, et al. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” Nature Cell Biology, vol. 16, no. 8, Nature Publishing Group, 2014, pp. 758–69, doi:10.1038/ncb3001.","ista":"Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. 2014. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. 16(8), 758–769.","chicago":"Williams, Scott, Lyndsay Ratliff, Maria P Postiglione, Juergen Knoblich, and Elaine Fuchs. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” Nature Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb3001."},"title":"Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN","article_processing_charge":"No","external_id":{"pmid":["25016959"]},"author":[{"first_name":"Scott","full_name":"Williams, Scott","last_name":"Williams"},{"full_name":"Ratliff, Lyndsay","last_name":"Ratliff","first_name":"Lyndsay"},{"id":"2C67902A-F248-11E8-B48F-1D18A9856A87","first_name":"Maria P","full_name":"Postiglione, Maria P","last_name":"Postiglione"},{"first_name":"Juergen","full_name":"Knoblich, Juergen","last_name":"Knoblich"},{"first_name":"Elaine","full_name":"Fuchs, Elaine","last_name":"Fuchs"}],"publist_id":"5196"},{"_id":"1898","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:55Z","citation":{"chicago":"Ritzau Jost, Andreas, Igor Delvendahl, Annika Rings, Niklas Byczkowicz, Harumi Harada, Ryuichi Shigemoto, Johannes Hirrlinger, Jens Eilers, and Stefan Hallermann. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.08.036.","ista":"Ritzau Jost A, Delvendahl I, Rings A, Byczkowicz N, Harada H, Shigemoto R, Hirrlinger J, Eilers J, Hallermann S. 2014. Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. 84(1), 152–163.","mla":"Ritzau Jost, Andreas, et al. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” Neuron, vol. 84, no. 1, Elsevier, 2014, pp. 152–63, doi:10.1016/j.neuron.2014.08.036.","ama":"Ritzau Jost A, Delvendahl I, Rings A, et al. Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. 2014;84(1):152-163. doi:10.1016/j.neuron.2014.08.036","apa":"Ritzau Jost, A., Delvendahl, I., Rings, A., Byczkowicz, N., Harada, H., Shigemoto, R., … Hallermann, S. (2014). Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.08.036","short":"A. Ritzau Jost, I. Delvendahl, A. Rings, N. Byczkowicz, H. Harada, R. Shigemoto, J. Hirrlinger, J. Eilers, S. Hallermann, Neuron 84 (2014) 152–163.","ieee":"A. Ritzau Jost et al., “Ultrafast action potentials mediate kilohertz signaling at a central synapse,” Neuron, vol. 84, no. 1. Elsevier, pp. 152–163, 2014."},"title":"Ultrafast action potentials mediate kilohertz signaling at a central synapse","department":[{"_id":"RySh"}],"publist_id":"5197","author":[{"first_name":"Andreas","last_name":"Ritzau Jost","full_name":"Ritzau Jost, Andreas"},{"full_name":"Delvendahl, Igor","last_name":"Delvendahl","first_name":"Igor"},{"last_name":"Rings","full_name":"Rings, Annika","first_name":"Annika"},{"last_name":"Byczkowicz","full_name":"Byczkowicz, Niklas","first_name":"Niklas"},{"orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi","last_name":"Harada","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Harumi"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"first_name":"Johannes","last_name":"Hirrlinger","full_name":"Hirrlinger, Johannes"},{"first_name":"Jens","last_name":"Eilers","full_name":"Eilers, Jens"},{"last_name":"Hallermann","full_name":"Hallermann, Stefan","first_name":"Stefan"}],"oa_version":"None","abstract":[{"text":"Fast synaptic transmission is important for rapid information processing. To explore the maximal rate of neuronal signaling and to analyze the presynaptic mechanisms, we focused on the input layer of the cerebellar cortex, where exceptionally high action potential (AP) frequencies have been reported invivo. With paired recordings between presynaptic cerebellar mossy fiber boutons and postsynaptic granule cells, we demonstrate reliable neurotransmission upto ~1 kHz. Presynaptic APs are ultrafast, with ~100μs half-duration. Both Kv1 and Kv3 potassium channels mediate the fast repolarization, rapidly inactivating sodium channels ensure metabolic efficiency, and little AP broadening occurs during bursts of up to 1.5 kHz. Presynaptic Cav2.1 (P/Q-type) calcium channels open efficiently during ultrafast APs. Furthermore, a subset of synaptic vesicles is tightly coupled to Ca2+ channels, and vesicles are rapidly recruited to the release site. These data reveal mechanisms of presynaptic AP generation and transmitter release underlying neuronal kHz signaling.","lang":"eng"}],"month":"10","intvolume":" 84","publisher":"Elsevier","quality_controlled":"1","scopus_import":1,"day":"01","language":[{"iso":"eng"}],"publication":"Neuron","year":"2014","publication_status":"published","doi":"10.1016/j.neuron.2014.08.036","date_published":"2014-10-01T00:00:00Z","issue":"1","volume":84,"date_created":"2018-12-11T11:54:36Z","page":"152 - 163"},{"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-573-v1+1_arikan-2014-pcvis-draft.pdf","date_created":"2018-12-12T10:17:41Z","creator":"system","file_size":13594598,"date_updated":"2020-07-14T12:45:20Z","file_id":"5297","checksum":"5bf58942d2eb20adf03c7f9ea2e68124","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"issue":"9","volume":20,"abstract":[{"text":"In this paper, we introduce a novel scene representation for the visualization of large-scale point clouds accompanied by a set of high-resolution photographs. Many real-world applications deal with very densely sampled point-cloud data, which are augmented with photographs that often reveal lighting variations and inaccuracies in registration. Consequently, the high-quality representation of the captured data, i.e., both point clouds and photographs together, is a challenging and time-consuming task. We propose a two-phase approach, in which the first (preprocessing) phase generates multiple overlapping surface patches and handles the problem of seamless texture generation locally for each patch. The second phase stitches these patches at render-time to produce a high-quality visualization of the data. As a result of the proposed localization of the global texturing problem, our algorithm is more than an order of magnitude faster than equivalent mesh-based texturing techniques. Furthermore, since our preprocessing phase requires only a minor fraction of the whole data set at once, we provide maximum flexibility when dealing with growing data sets.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"intvolume":" 20","month":"09","date_updated":"2021-01-12T06:53:59Z","ddc":["000"],"department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:45:20Z","_id":"1906","type":"journal_article","pubrep_id":"573","status":"public","year":"2014","has_accepted_license":"1","publication":"IEEE Transactions on Visualization and Computer Graphics","day":"09","page":"1280 - 1292","date_created":"2018-12-11T11:54:39Z","doi":"10.1109/TVCG.2014.2312011","date_published":"2014-09-09T00:00:00Z","acknowledgement":"This research was supported by the Austrian Research Promotion Agency (FFG) project REPLICATE (no. 835948), the EU FP7 project HARVEST4D (no. 323567).","oa":1,"publisher":"IEEE","citation":{"chicago":"Arikan, Murat, Reinhold Preiner, Claus Scheiblauer, Stefan Jeschke, and Michael Wimmer. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2014. https://doi.org/10.1109/TVCG.2014.2312011.","ista":"Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. 2014. Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. 20(9), 1280–1292.","mla":"Arikan, Murat, et al. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 9, IEEE, 2014, pp. 1280–92, doi:10.1109/TVCG.2014.2312011.","ama":"Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. 2014;20(9):1280-1292. doi:10.1109/TVCG.2014.2312011","apa":"Arikan, M., Preiner, R., Scheiblauer, C., Jeschke, S., & Wimmer, M. (2014). Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2014.2312011","ieee":"M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, and M. Wimmer, “Large-scale point-cloud visualization through localized textured surface reconstruction,” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 9. IEEE, pp. 1280–1292, 2014.","short":"M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, M. Wimmer, IEEE Transactions on Visualization and Computer Graphics 20 (2014) 1280–1292."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5189","author":[{"full_name":"Arikan, Murat","last_name":"Arikan","first_name":"Murat"},{"first_name":"Reinhold","last_name":"Preiner","full_name":"Preiner, Reinhold"},{"first_name":"Claus","last_name":"Scheiblauer","full_name":"Scheiblauer, Claus"},{"full_name":"Jeschke, Stefan","last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wimmer, Michael","last_name":"Wimmer","first_name":"Michael"}],"title":"Large-scale point-cloud visualization through localized textured surface reconstruction","project":[{"_id":"25357BD2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 24352-N23","name":"Deep Pictures: Creating Visual and Haptic Vector Images"}]},{"abstract":[{"lang":"eng","text":"The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution)."}],"pmid":1,"oa_version":"None","scopus_import":"1","month":"04","intvolume":" 27","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":27,"issue":"5","_id":"1905","type":"journal_article","article_type":"original","status":"public","date_updated":"2022-06-07T09:22:20Z","department":[{"_id":"SyCr"}],"acknowledgement":"This study was funded by grants from the National Science Foundation (NSF) to MT (IOS-1121832) and IS (DEB-0743406) and from the German Science Foundation (DFG; PL 470/1-2) and ‘LOEWE − Landesoffensive zur Entwicklung wissenschaftlich-ökonomischer Exzellenz’ of Hesse's Ministry of Higher Education, Research, and the Arts, to MP.","publisher":"Wiley","quality_controlled":"1","year":"2014","day":"12","publication":"Journal of Evolutionary Biology","page":"960 - 974","date_published":"2014-04-12T00:00:00Z","doi":"10.1111/jeb.12370","date_created":"2018-12-11T11:54:38Z","citation":{"chicago":"Tobler, Michael, Martin Plath, Rüdiger Riesch, Ingo Schlupp, Anna V Grasse, Gopi Munimanda, C Setzer, Dustin Penn, and Yoshan Moodley. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary Biology. Wiley, 2014. https://doi.org/10.1111/jeb.12370.","ista":"Tobler M, Plath M, Riesch R, Schlupp I, Grasse AV, Munimanda G, Setzer C, Penn D, Moodley Y. 2014. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. 27(5), 960–974.","mla":"Tobler, Michael, et al. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary Biology, vol. 27, no. 5, Wiley, 2014, pp. 960–74, doi:10.1111/jeb.12370.","apa":"Tobler, M., Plath, M., Riesch, R., Schlupp, I., Grasse, A. V., Munimanda, G., … Moodley, Y. (2014). Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.12370","ama":"Tobler M, Plath M, Riesch R, et al. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. 2014;27(5):960-974. doi:10.1111/jeb.12370","short":"M. Tobler, M. Plath, R. Riesch, I. Schlupp, A.V. Grasse, G. Munimanda, C. Setzer, D. Penn, Y. Moodley, Journal of Evolutionary Biology 27 (2014) 960–974.","ieee":"M. Tobler et al., “Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations,” Journal of Evolutionary Biology, vol. 27, no. 5. Wiley, pp. 960–974, 2014."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5190","author":[{"first_name":"Michael","full_name":"Tobler, Michael","last_name":"Tobler"},{"first_name":"Martin","full_name":"Plath, Martin","last_name":"Plath"},{"first_name":"Rüdiger","full_name":"Riesch, Rüdiger","last_name":"Riesch"},{"full_name":"Schlupp, Ingo","last_name":"Schlupp","first_name":"Ingo"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","last_name":"Grasse"},{"first_name":"Gopi","full_name":"Munimanda, Gopi","last_name":"Munimanda"},{"full_name":"Setzer, C","last_name":"Setzer","first_name":"C"},{"full_name":"Penn, Dustin","last_name":"Penn","first_name":"Dustin"},{"first_name":"Yoshan","full_name":"Moodley, Yoshan","last_name":"Moodley"}],"external_id":{"pmid":["24725091"]},"article_processing_charge":"No","title":"Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations"},{"quality_controlled":"1","publisher":"Oxford University Press","year":"2014","publication":"Molecular Biology and Evolution","day":"01","page":"232 - 238","date_created":"2018-12-11T11:54:37Z","date_published":"2014-01-01T00:00:00Z","doi":"10.1093/molbev/mst187","citation":{"ista":"Hall B, Acar H, Nandipati A, Barlow M. 2014. Growth rates made easy. Molecular Biology and Evolution. 31(1), 232–238.","chicago":"Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates Made Easy.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/mst187.","ama":"Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. Molecular Biology and Evolution. 2014;31(1):232-238. doi:10.1093/molbev/mst187","apa":"Hall, B., Acar, H., Nandipati, A., & Barlow, M. (2014). Growth rates made easy. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst187","ieee":"B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” Molecular Biology and Evolution, vol. 31, no. 1. Oxford University Press, pp. 232–238, 2014.","short":"B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution 31 (2014) 232–238.","mla":"Hall, Barry, et al. “Growth Rates Made Easy.” Molecular Biology and Evolution, vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:10.1093/molbev/mst187."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["24170494"]},"publist_id":"5193","author":[{"first_name":"Barry","last_name":"Hall","full_name":"Hall, Barry"},{"orcid":"0000-0003-1986-9753","full_name":"Acar, Hande","last_name":"Acar","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","first_name":"Hande"},{"full_name":"Nandipati, Anna","last_name":"Nandipati","first_name":"Anna"},{"first_name":"Miriam","full_name":"Barlow, Miriam","last_name":"Barlow"}],"title":"Growth rates made easy","abstract":[{"text":"In the 1960s-1980s, determination of bacterial growth rates was an important tool in microbial genetics, biochemistry, molecular biology, and microbial physiology. The exciting technical developments of the 1990s and the 2000s eclipsed that tool; as a result, many investigators today lack experience with growth rate measurements. Recently, investigators in a number of areas have started to use measurements of bacterial growth rates for a variety of purposes. Those measurements have been greatly facilitated by the availability of microwell plate readers that permit the simultaneous measurements on up to 384 different cultures. Only the exponential (logarithmic) portions of the resulting growth curves are useful for determining growth rates, and manual determination of that portion and calculation of growth rates can be tedious for high-throughput purposes. Here, we introduce the program GrowthRates that uses plate reader output files to automatically determine the exponential portion of the curve and to automatically calculate the growth rate, the maximum culture density, and the duration of the growth lag phase. GrowthRates is freely available for Macintosh, Windows, and Linux.We discuss the effects of culture volume, the classical bacterial growth curve, and the differences between determinations in rich media and minimal (mineral salts) media. This protocol covers calibration of the plate reader, growth of culture inocula for both rich and minimal media, and experimental setup. As a guide to reliability, we report typical day-to-day variation in growth rates and variation within experiments with respect to position of wells within the plates.","lang":"eng"}],"oa_version":"None","pmid":1,"scopus_import":"1","intvolume":" 31","month":"01","publication_status":"published","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"language":[{"iso":"eng"}],"volume":31,"issue":"1","_id":"1902","article_type":"original","type":"journal_article","status":"public","date_updated":"2022-06-07T11:08:13Z","department":[{"_id":"JoBo"}]},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Tian, Huiyu, Krzysztof T Wabnik, Tiantian Niu, Hongjiang Li, Qianqian Yu, Stephan Pollmann, Steffen Vanneste, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular Plant. Oxford University Press, 2014. https://doi.org/10.1093/mp/sst118.","ista":"Tian H, Wabnik KT, Niu T, Li H, Yu Q, Pollmann S, Vanneste S, Govaerts W, Rolčík J, Geisler M, Friml J, Ding Z. 2014. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. 7(2), 277–289.","mla":"Tian, Huiyu, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular Plant, vol. 7, no. 2, Oxford University Press, 2014, pp. 277–89, doi:10.1093/mp/sst118.","short":"H. Tian, K.T. Wabnik, T. Niu, H. Li, Q. Yu, S. Pollmann, S. Vanneste, W. Govaerts, J. Rolčík, M. Geisler, J. Friml, Z. Ding, Molecular Plant 7 (2014) 277–289.","ieee":"H. Tian et al., “WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis,” Molecular Plant, vol. 7, no. 2. Oxford University Press, pp. 277–289, 2014.","apa":"Tian, H., Wabnik, K. T., Niu, T., Li, H., Yu, Q., Pollmann, S., … Ding, Z. (2014). WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. Oxford University Press. https://doi.org/10.1093/mp/sst118","ama":"Tian H, Wabnik KT, Niu T, et al. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. 2014;7(2):277-289. doi:10.1093/mp/sst118"},"date_updated":"2021-01-12T06:53:57Z","department":[{"_id":"JiFr"}],"title":"WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis","publist_id":"5194","author":[{"last_name":"Tian","full_name":"Tian, Huiyu","first_name":"Huiyu"},{"first_name":"Krzysztof T","full_name":"Wabnik, Krzysztof T","last_name":"Wabnik"},{"full_name":"Niu, Tiantian","last_name":"Niu","first_name":"Tiantian"},{"first_name":"Hongjiang","full_name":"Li, Hongjiang","last_name":"Li"},{"full_name":"Yu, Qianqian","last_name":"Yu","first_name":"Qianqian"},{"first_name":"Stephan","full_name":"Pollmann, Stephan","last_name":"Pollmann"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"first_name":"Willy","last_name":"Govaerts","full_name":"Govaerts, Willy"},{"first_name":"Jakub","last_name":"Rolčík","full_name":"Rolčík, Jakub"},{"full_name":"Geisler, Markus","last_name":"Geisler","first_name":"Markus"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zhaojun","full_name":"Ding, Zhaojun","last_name":"Ding"}],"_id":"1901","status":"public","type":"journal_article","publication":"Molecular Plant","language":[{"iso":"eng"}],"day":"01","year":"2014","publication_status":"published","date_created":"2018-12-11T11:54:37Z","volume":7,"doi":"10.1093/mp/sst118","date_published":"2014-02-01T00:00:00Z","issue":"2","page":"277 - 289","acknowledgement":"This work was supported by funding from the projects CZ.1.07/2.3.00/20.0043 and CZ.1.05/1.1.00/02.0068 (to CEITEC, Central European Institute of Technology) and the Odysseus program of the Research Foundation-Flanders to J.F\r\n","oa_version":"None","abstract":[{"text":"In plants, the patterning of stem cell-enriched meristems requires a graded auxin response maximum that emerges from the concerted action of polar auxin transport, auxin biosynthesis, auxin metabolism, and cellular auxin response machinery. However, mechanisms underlying this auxin response maximum-mediated root stem cell maintenance are not fully understood. Here, we present unexpected evidence that WUSCHEL-RELATED HOMEOBOX 5 (WOX5) transcription factor modulates expression of auxin biosynthetic genes in the quiescent center (QC) of the root and thus provides a robust mechanism for the maintenance of auxin response maximum in the root tip. This WOX5 action is balanced through the activity of indole-3-acetic acid 17 (IAA17) auxin response repressor. Our combined genetic, cell biology, and computational modeling studies revealed a previously uncharacterized feedback loop linking WOX5-mediated auxin production to IAA17-dependent repression of auxin responses. This WOX5-IAA17 feedback circuit further assures the maintenance of auxin response maximum in the root tip and thereby contributes to the maintenance of distal stem cell (DSC) populations. Our experimental studies and in silico computer simulations both demonstrate that the WOX5-IAA17 feedback circuit is essential for the maintenance of auxin gradient in the root tip and the auxin-mediated root DSC differentiation.","lang":"eng"}],"intvolume":" 7","month":"02","scopus_import":1,"publisher":"Oxford University Press"},{"project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"title":"Strichartz inequality for orthonormal functions","author":[{"full_name":"Frank, Rupert","last_name":"Frank","first_name":"Rupert"},{"full_name":"Lewin, Mathieu","last_name":"Lewin","first_name":"Mathieu"},{"full_name":"Lieb, Élliott","last_name":"Lieb","first_name":"Élliott"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5191","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “Strichartz inequality for orthonormal functions,” Journal of the European Mathematical Society, vol. 16, no. 7. European Mathematical Society, pp. 1507–1526, 2014.","short":"R. Frank, M. Lewin, É. Lieb, R. Seiringer, Journal of the European Mathematical Society 16 (2014) 1507–1526.","apa":"Frank, R., Lewin, M., Lieb, É., & Seiringer, R. (2014). Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/467","ama":"Frank R, Lewin M, Lieb É, Seiringer R. Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. 2014;16(7):1507-1526. doi:10.4171/JEMS/467","mla":"Frank, Rupert, et al. “Strichartz Inequality for Orthonormal Functions.” Journal of the European Mathematical Society, vol. 16, no. 7, European Mathematical Society, 2014, pp. 1507–26, doi:10.4171/JEMS/467.","ista":"Frank R, Lewin M, Lieb É, Seiringer R. 2014. Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. 16(7), 1507–1526.","chicago":"Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “Strichartz Inequality for Orthonormal Functions.” Journal of the European Mathematical Society. European Mathematical Society, 2014. https://doi.org/10.4171/JEMS/467."},"oa":1,"publisher":"European Mathematical Society","quality_controlled":"1","date_created":"2018-12-11T11:54:38Z","doi":"10.4171/JEMS/467","date_published":"2014-08-23T00:00:00Z","page":"1507 - 1526","publication":"Journal of the European Mathematical Society","day":"23","year":"2014","status":"public","type":"journal_article","_id":"1904","department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T06:53:58Z","intvolume":" 16","month":"08","main_file_link":[{"url":"http://arxiv.org/abs/1306.1309","open_access":"1"}],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We prove a Strichartz inequality for a system of orthonormal functions, with an optimal behavior of the constant in the limit of a large number of functions. The estimate generalizes the usual Strichartz inequality, in the same fashion as the Lieb-Thirring inequality generalizes the Sobolev inequality. As an application, we consider the Schrödinger equation with a time-dependent potential and we show the existence of the wave operator in Schatten spaces."}],"volume":16,"issue":"7","language":[{"iso":"eng"}],"publication_status":"published"},{"_id":"1900","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Lateral Junction Dynamics Lead the Way Out.” Nature Cell Biology, vol. 16, no. 2, Nature Publishing Group, 2014, pp. 127–29, doi:10.1038/ncb2913.","short":"M. Behrndt, C.-P.J. Heisenberg, Nature Cell Biology 16 (2014) 127–129.","ieee":"M. Behrndt and C.-P. J. Heisenberg, “Lateral junction dynamics lead the way out,” Nature Cell Biology, vol. 16, no. 2. Nature Publishing Group, pp. 127–129, 2014.","ama":"Behrndt M, Heisenberg C-PJ. Lateral junction dynamics lead the way out. Nature Cell Biology. 2014;16(2):127-129. doi:10.1038/ncb2913","apa":"Behrndt, M., & Heisenberg, C.-P. J. (2014). Lateral junction dynamics lead the way out. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2913","chicago":"Behrndt, Martin, and Carl-Philipp J Heisenberg. “Lateral Junction Dynamics Lead the Way Out.” Nature Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb2913.","ista":"Behrndt M, Heisenberg C-PJ. 2014. Lateral junction dynamics lead the way out. Nature Cell Biology. 16(2), 127–129."},"date_updated":"2021-01-12T06:53:56Z","title":"Lateral junction dynamics lead the way out","department":[{"_id":"CaHe"}],"publist_id":"5195","author":[{"last_name":"Behrndt","full_name":"Behrndt, Martin","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"oa_version":"None","abstract":[{"lang":"eng","text":"Epithelial cell layers need to be tightly regulated to maintain their integrity and correct function. Cell integration into epithelial sheets is now shown to depend on the N-WASP-regulated stabilization of cortical F-actin, which generates distinct patterns of apical-lateral contractility at E-cadherin-based cell-cell junctions."}],"intvolume":" 16","month":"01","quality_controlled":"1","scopus_import":1,"publisher":"Nature Publishing Group","language":[{"iso":"eng"}],"publication":"Nature Cell Biology","day":"31","year":"2014","publication_status":"published","date_created":"2018-12-11T11:54:37Z","issue":"2","volume":16,"doi":"10.1038/ncb2913","date_published":"2014-01-31T00:00:00Z","page":"127 - 129"},{"citation":{"mla":"Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell, 2014, pp. 693–701, doi:10.1111/1365-2435.12207.","short":"T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.","ieee":"T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell, pp. 693–701, 2014.","ama":"Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701. doi:10.1111/1365-2435.12207","apa":"Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell. https://doi.org/10.1111/1365-2435.12207","chicago":"Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology. Wiley-Blackwell, 2014. https://doi.org/10.1111/1365-2435.12207.","ista":"Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 28(3), 693–701."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5186","author":[{"first_name":"Thomas","full_name":"Ezard, Thomas","last_name":"Ezard"},{"last_name":"Prizak","full_name":"Prizak, Roshan","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rebecca","last_name":"Hoyle","full_name":"Hoyle, Rebecca"}],"title":"The fitness costs of adaptation via phenotypic plasticity and maternal effects","acknowledgement":"Engineering and Physical Sciences Research Council. Grant Number: EP/H031928/1","publisher":"Wiley-Blackwell","oa":1,"has_accepted_license":"1","year":"2014","day":"01","publication":"Functional Ecology","page":"693 - 701","doi":"10.1111/1365-2435.12207","date_published":"2014-06-01T00:00:00Z","date_created":"2018-12-11T11:54:40Z","_id":"1909","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"419","date_updated":"2021-01-12T06:54:00Z","ddc":["570"],"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:20Z","abstract":[{"lang":"eng","text":"Summary: Phenotypes are often environmentally dependent, which requires organisms to track environmental change. The challenge for organisms is to construct phenotypes using the most accurate environmental cue. Here, we use a quantitative genetic model of adaptation by additive genetic variance, within- and transgenerational plasticity via linear reaction norms and indirect genetic effects respectively. We show how the relative influence on the eventual phenotype of these components depends on the predictability of environmental change (fast or slow, sinusoidal or stochastic) and the developmental lag τ between when the environment is perceived and when selection acts. We then decompose expected mean fitness into three components (variance load, adaptation and fluctuation load) to study the fitness costs of within- and transgenerational plasticity. A strongly negative maternal effect coefficient m minimizes the variance load, but a strongly positive m minimises the fluctuation load. The adaptation term is maximized closer to zero, with positive or negative m preferred under different environmental scenarios. Phenotypic plasticity is higher when τ is shorter and when the environment changes frequently between seasonal extremes. Expected mean population fitness is highest away from highest observed levels of phenotypic plasticity. Within- and transgenerational plasticity act in concert to deliver well-adapted phenotypes, which emphasizes the need to study both simultaneously when investigating phenotypic evolution."}],"oa_version":"Published Version","scopus_import":1,"month":"06","intvolume":" 28","publication_status":"published","file":[{"creator":"system","file_size":536154,"date_updated":"2020-07-14T12:45:20Z","file_name":"IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf","date_created":"2018-12-12T10:15:45Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"3cbe8623174709a8ceec2103246f8fe0","file_id":"5167"}],"language":[{"iso":"eng"}],"issue":"3","volume":28},{"author":[{"last_name":"Konradi","full_name":"Konradi, Sabine","first_name":"Sabine"},{"first_name":"Nighat","last_name":"Yasmin","full_name":"Yasmin, Nighat"},{"first_name":"Denise","full_name":"Haslwanter, Denise","last_name":"Haslwanter"},{"last_name":"Weber","full_name":"Weber, Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","first_name":"Michele"},{"first_name":"Bernd","full_name":"Gesslbauer, Bernd","last_name":"Gesslbauer"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Strobl, Herbert","last_name":"Strobl","first_name":"Herbert"}],"publist_id":"5185","title":"Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2","department":[{"_id":"MiSi"}],"citation":{"ista":"Konradi S, Yasmin N, Haslwanter D, Weber M, Gesslbauer B, Sixt MK, Strobl H. 2014. Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. 44(2), 553–560.","chicago":"Konradi, Sabine, Nighat Yasmin, Denise Haslwanter, Michele Weber, Bernd Gesslbauer, Michael K Sixt, and Herbert Strobl. “Langerhans Cell Maturation Is Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition ZEB1/2.” European Journal of Immunology. Wiley-Blackwell, 2014. https://doi.org/10.1002/eji.201343681.","ieee":"S. Konradi et al., “Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2,” European Journal of Immunology, vol. 44, no. 2. Wiley-Blackwell, pp. 553–560, 2014.","short":"S. Konradi, N. Yasmin, D. Haslwanter, M. Weber, B. Gesslbauer, M.K. Sixt, H. Strobl, European Journal of Immunology 44 (2014) 553–560.","apa":"Konradi, S., Yasmin, N., Haslwanter, D., Weber, M., Gesslbauer, B., Sixt, M. K., & Strobl, H. (2014). Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. Wiley-Blackwell. https://doi.org/10.1002/eji.201343681","ama":"Konradi S, Yasmin N, Haslwanter D, et al. Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. 2014;44(2):553-560. doi:10.1002/eji.201343681","mla":"Konradi, Sabine, et al. “Langerhans Cell Maturation Is Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition ZEB1/2.” European Journal of Immunology, vol. 44, no. 2, Wiley-Blackwell, 2014, pp. 553–60, doi:10.1002/eji.201343681."},"date_updated":"2021-01-12T06:54:01Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1910","page":"553 - 560","date_published":"2014-02-01T00:00:00Z","volume":44,"issue":"2","doi":"10.1002/eji.201343681","date_created":"2018-12-11T11:54:40Z","publication_status":"published","year":"2014","day":"01","language":[{"iso":"eng"}],"publication":"European Journal of Immunology","scopus_import":1,"publisher":"Wiley-Blackwell","month":"02","intvolume":" 44","abstract":[{"text":"angerhans cells (LCs) are a unique subset of dendritic cells (DCs) that express epithelial adhesion molecules, allowing them to form contacts with epithelial cells and reside in epidermal/epithelial tissues. The dynamic regulation of epithelial adhesion plays a decisive role in the life cycle of LCs. It controls whether LCs remain immature and sessile within the epidermis or mature and egress to initiate immune responses. So far, the molecular machinery regulating epithelial adhesion molecules during LC maturation remains elusive. Here, we generated pure populations of immature human LCs in vitro to systematically probe for gene-expression changes during LC maturation. LCs down-regulate a set of epithelial genes including E-cadherin, while they upregulate the mesenchymal marker N-cadherin known to facilitate cell migration. In addition, N-cadherin is constitutively expressed by monocyte-derived DCs known to exhibit characteristics of both inflammatory-type and interstitial/dermal DCs. Moreover, the transcription factors ZEB1 and ZEB2 (ZEB is zinc-finger E-box-binding homeobox) are upregulated in migratory LCs. ZEB1 and ZEB2 have been shown to induce epithelial-to-mesenchymal transition (EMT) and invasive behavior in cancer cells undergoing metastasis. Our results provide the first hint that the molecular EMT machinery might facilitate LC mobilization. Moreover, our study suggests that N-cadherin plays a role during DC migration.","lang":"eng"}],"oa_version":"None","acknowledgement":"FWF. Grant Number: P22058-B20"},{"publisher":"IEEE","scopus_import":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2014/299","open_access":"1"}],"month":"01","abstract":[{"text":"Most cryptographic security proofs require showing that two systems are indistinguishable. A central tool in such proofs is that of a game, where winning the game means provoking a certain condition, and it is shown that the two systems considered cannot be distinguished unless this condition is provoked. Upper bounding the probability of winning such a game, i.e., provoking this condition, for an arbitrary strategy is usually hard, except in the special case where the best strategy for winning such a game is known to be non-adaptive. A sufficient criterion for ensuring the optimality of non-adaptive strategies is that of conditional equivalence to a system, a notion introduced in [1]. In this paper, we show that this criterion is not necessary to ensure the optimality of non-adaptive strategies by giving two results of independent interest: 1) the optimality of non-adaptive strategies is not preserved under parallel composition; 2) in contrast, conditional equivalence is preserved under parallel composition.","lang":"eng"}],"oa_version":"Submitted Version","doi":"10.1109/ISIT.2014.6875125","date_published":"2014-01-01T00:00:00Z","date_created":"2018-12-11T11:54:39Z","publication_status":"published","year":"2014","day":"01","publication":"IEEE International Symposium on Information Theory","language":[{"iso":"eng"}],"type":"conference","conference":{"name":"IEEE International Symposium on Information Theory Proceedings","start_date":"2014-06-29","end_date":"2014-07-04","location":"Honolulu, USA"},"status":"public","_id":"1907","article_number":"6875125","publist_id":"5188","author":[{"full_name":"Demay, Grégory","last_name":"Demay","first_name":"Grégory"},{"last_name":"Gazi","full_name":"Gazi, Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"full_name":"Maurer, Ueli","last_name":"Maurer","first_name":"Ueli"},{"first_name":"Björn","last_name":"Tackmann","full_name":"Tackmann, Björn"}],"department":[{"_id":"KrPi"}],"title":"Optimality of non-adaptive strategies: The case of parallel games","citation":{"ista":"Demay G, Gazi P, Maurer U, Tackmann B. 2014. Optimality of non-adaptive strategies: The case of parallel games. IEEE International Symposium on Information Theory. IEEE International Symposium on Information Theory Proceedings, 6875125.","chicago":"Demay, Grégory, Peter Gazi, Ueli Maurer, and Björn Tackmann. “Optimality of Non-Adaptive Strategies: The Case of Parallel Games.” In IEEE International Symposium on Information Theory. IEEE, 2014. https://doi.org/10.1109/ISIT.2014.6875125.","short":"G. Demay, P. Gazi, U. Maurer, B. Tackmann, in:, IEEE International Symposium on Information Theory, IEEE, 2014.","ieee":"G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Optimality of non-adaptive strategies: The case of parallel games,” in IEEE International Symposium on Information Theory, Honolulu, USA, 2014.","ama":"Demay G, Gazi P, Maurer U, Tackmann B. Optimality of non-adaptive strategies: The case of parallel games. In: IEEE International Symposium on Information Theory. IEEE; 2014. doi:10.1109/ISIT.2014.6875125","apa":"Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2014). Optimality of non-adaptive strategies: The case of parallel games. In IEEE International Symposium on Information Theory. Honolulu, USA: IEEE. https://doi.org/10.1109/ISIT.2014.6875125","mla":"Demay, Grégory, et al. “Optimality of Non-Adaptive Strategies: The Case of Parallel Games.” IEEE International Symposium on Information Theory, 6875125, IEEE, 2014, doi:10.1109/ISIT.2014.6875125."},"date_updated":"2021-01-12T06:53:59Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"title":"The rate of adaptation in large sexual populations with linear chromosomes","author":[{"full_name":"Weissman, Daniel","last_name":"Weissman","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"},{"first_name":"Oskar","last_name":"Hallatschek","full_name":"Hallatschek, Oskar"}],"publist_id":"5187","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Weissman D, Hallatschek O. 2014. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 196(4), 1167–1183.","chicago":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics. Genetics Society of America, 2014. https://doi.org/10.1534/genetics.113.160705.","apa":"Weissman, D., & Hallatschek, O. (2014). The rate of adaptation in large sexual populations with linear chromosomes. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.160705","ama":"Weissman D, Hallatschek O. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 2014;196(4):1167-1183. doi:10.1534/genetics.113.160705","ieee":"D. Weissman and O. Hallatschek, “The rate of adaptation in large sexual populations with linear chromosomes,” Genetics, vol. 196, no. 4. Genetics Society of America, pp. 1167–1183, 2014.","short":"D. Weissman, O. Hallatschek, Genetics 196 (2014) 1167–1183.","mla":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics, vol. 196, no. 4, Genetics Society of America, 2014, pp. 1167–83, doi:10.1534/genetics.113.160705."},"project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"doi":"10.1534/genetics.113.160705","date_published":"2014-04-01T00:00:00Z","date_created":"2018-12-11T11:54:39Z","page":"1167 - 1183","day":"01","publication":"Genetics","year":"2014","publisher":"Genetics Society of America","quality_controlled":"1","oa":1,"department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:53:59Z","status":"public","type":"journal_article","_id":"1908","volume":196,"issue":"4","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"04","intvolume":" 196","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1307.0737","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"text":"In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can bring together beneficial alleles from different backgrounds, but tightly linked alleles may still greatly interfere with each other. We show for well-mixed populations that when this interference is strong, the genome can be seen as consisting of many effectively asexual stretches linked together. The rate at which beneficial alleles fix is thus roughly proportional to the rate of recombination and depends only logarithmically on the mutation supply and the strength of selection. Our scaling arguments also allow us to predict, with reasonable accuracy, the fitness distribution of fixed mutations when the mutational effect sizes are broad. We focus on the regime in which crossovers occur more frequently than beneficial mutations, as is likely to be the case for many natural populations.","lang":"eng"}]},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:01Z","citation":{"mla":"Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.” Discrete & Computational Geometry, vol. 51, no. 1, Springer, 2014, pp. 207–20, doi:10.1007/s00454-013-9556-3.","apa":"Engström, A., & Noren, P. (2014). Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-013-9556-3","ama":"Engström A, Noren P. Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. 2014;51(1):207-220. doi:10.1007/s00454-013-9556-3","ieee":"A. Engström and P. Noren, “Tverberg’s Theorem and Graph Coloring,” Discrete & Computational Geometry, vol. 51, no. 1. Springer, pp. 207–220, 2014.","short":"A. Engström, P. Noren, Discrete & Computational Geometry 51 (2014) 207–220.","chicago":"Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-013-9556-3.","ista":"Engström A, Noren P. 2014. Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. 51(1), 207–220."},"title":"Tverberg's Theorem and Graph Coloring","department":[{"_id":"CaUh"}],"author":[{"last_name":"Engström","full_name":"Engström, Alexander","first_name":"Alexander"},{"last_name":"Noren","full_name":"Noren, Patrik","first_name":"Patrik","id":"46870C74-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5183","_id":"1911","status":"public","type":"journal_article","publication":"Discrete & Computational Geometry","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2014","date_created":"2018-12-11T11:54:40Z","doi":"10.1007/s00454-013-9556-3","date_published":"2014-01-01T00:00:00Z","volume":51,"issue":"1","page":"207 - 220","acknowledgement":"Patrik Norén gratefully acknowledges support from the Wallenberg foundation","oa_version":"None","abstract":[{"text":"The topological Tverberg theorem has been generalized in several directions by setting extra restrictions on the Tverberg partitions. Restricted Tverberg partitions, defined by the idea that certain points cannot be in the same part, are encoded with graphs. When two points are adjacent in the graph, they are not in the same part. If the restrictions are too harsh, then the topological Tverberg theorem fails. The colored Tverberg theorem corresponds to graphs constructed as disjoint unions of small complete graphs. Hell studied the case of paths and cycles. In graph theory these partitions are usually viewed as graph colorings. As explored by Aharoni, Haxell, Meshulam and others there are fundamental connections between several notions of graph colorings and topological combinatorics. For ordinary graph colorings it is enough to require that the number of colors q satisfy q>Δ, where Δ is the maximal degree of the graph. It was proven by the first author using equivariant topology that if q>Δ 2 then the topological Tverberg theorem still works. It is conjectured that q>KΔ is also enough for some constant K, and in this paper we prove a fixed-parameter version of that conjecture. The required topological connectivity results are proven with shellability, which also strengthens some previous partial results where the topological connectivity was proven with the nerve lemma.","lang":"eng"}],"intvolume":" 51","month":"01","publisher":"Springer","scopus_import":1},{"_id":"1916","article_type":"original","type":"journal_article","status":"public","date_updated":"2021-01-12T06:54:03Z","department":[{"_id":"GaNo"}],"abstract":[{"text":"Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases characterized by progressive age-dependent loss of corticospinal motor tract function. Although the genetic basis is partly understood, only a fraction of cases can receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome sequencing in combination with network analysis, we identified 18 previously unknown putative HSP genes and validated nearly all of these genes functionally or genetically. The pathways highlighted by these mutations link HSP to cellular transport, nucleotide metabolism, and synapse and axon development. Network analysis revealed a host of further candidate genes, of which three were mutated in our cohort. Our analysis links HSP to other neurodegenerative disorders and can facilitate gene discovery and mechanistic understanding of disease.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157572/","open_access":"1"}],"scopus_import":1,"intvolume":" 343","month":"01","publication_status":"published","language":[{"iso":"eng"}],"issue":"6170","volume":343,"citation":{"mla":"Novarino, Gaia, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders.” Science, vol. 343, no. 6170, American Association for the Advancement of Science, 2014, pp. 506–11, doi:10.1126/science.1247363.","short":"G. Novarino, A. Fenstermaker, M. Zaki, M. Hofree, J. Silhavy, A. Heiberg, M. Abdellateef, B. Rosti, E. Scott, L. Mansour, A. Masri, H. Kayserili, J. Al Aama, G. Abdel Salam, A. Karminejad, M. Kara, B. Kara, B. Bozorgmehri, T. Ben Omran, F. Mojahedi, I. Mahmoud, N. Bouslam, A. Bouhouche, A. Benomar, S. Hanein, L. Raymond, S. Forlani, M. Mascaro, L. Selim, N. Shehata, N. Al Allawi, P. Bindu, M. Azam, M. Günel, A. Caglayan, K. Bilgüvar, A. Tolun, M. Issa, J. Schroth, E. Spencer, R. Rosti, N. Akizu, K. Vaux, A. Johansen, A. Koh, H. Megahed, A. Dürr, A. Brice, G. Stévanin, S. Gabriel, T. Ideker, J. Gleeson, Science 343 (2014) 506–511.","ieee":"G. Novarino et al., “Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders,” Science, vol. 343, no. 6170. American Association for the Advancement of Science, pp. 506–511, 2014.","ama":"Novarino G, Fenstermaker A, Zaki M, et al. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 2014;343(6170):506-511. doi:10.1126/science.1247363","apa":"Novarino, G., Fenstermaker, A., Zaki, M., Hofree, M., Silhavy, J., Heiberg, A., … Gleeson, J. (2014). Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1247363","chicago":"Novarino, Gaia, Ali Fenstermaker, Maha Zaki, Matan Hofree, Jennifer Silhavy, Andrew Heiberg, Mostafa Abdellateef, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1247363.","ista":"Novarino G, Fenstermaker A, Zaki M, Hofree M, Silhavy J, Heiberg A, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al Aama J, Abdel Salam G, Karminejad A, Kara M, Kara B, Bozorgmehri B, Ben Omran T, Mojahedi F, Mahmoud I, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro M, Selim L, Shehata N, Al Allawi N, Bindu P, Azam M, Günel M, Caglayan A, Bilgüvar K, Tolun A, Issa M, Schroth J, Spencer E, Rosti R, Akizu N, Vaux K, Johansen A, Koh A, Megahed H, Dürr A, Brice A, Stévanin G, Gabriel S, Ideker T, Gleeson J. 2014. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 343(6170), 506–511."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["24482476"]},"author":[{"last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ali","last_name":"Fenstermaker","full_name":"Fenstermaker, Ali"},{"first_name":"Maha","full_name":"Zaki, Maha","last_name":"Zaki"},{"full_name":"Hofree, Matan","last_name":"Hofree","first_name":"Matan"},{"first_name":"Jennifer","full_name":"Silhavy, Jennifer","last_name":"Silhavy"},{"full_name":"Heiberg, Andrew","last_name":"Heiberg","first_name":"Andrew"},{"first_name":"Mostafa","last_name":"Abdellateef","full_name":"Abdellateef, Mostafa"},{"full_name":"Rosti, Başak","last_name":"Rosti","first_name":"Başak"},{"full_name":"Scott, Eric","last_name":"Scott","first_name":"Eric"},{"first_name":"Lobna","last_name":"Mansour","full_name":"Mansour, Lobna"},{"first_name":"Amira","full_name":"Masri, Amira","last_name":"Masri"},{"full_name":"Kayserili, Hülya","last_name":"Kayserili","first_name":"Hülya"},{"full_name":"Al Aama, Jumana","last_name":"Al Aama","first_name":"Jumana"},{"first_name":"Ghada","full_name":"Abdel Salam, Ghada","last_name":"Abdel Salam"},{"last_name":"Karminejad","full_name":"Karminejad, Ariana","first_name":"Ariana"},{"last_name":"Kara","full_name":"Kara, Majdi","first_name":"Majdi"},{"full_name":"Kara, Bülent","last_name":"Kara","first_name":"Bülent"},{"full_name":"Bozorgmehri, Bita","last_name":"Bozorgmehri","first_name":"Bita"},{"full_name":"Ben Omran, Tawfeg","last_name":"Ben Omran","first_name":"Tawfeg"},{"first_name":"Faezeh","full_name":"Mojahedi, Faezeh","last_name":"Mojahedi"},{"last_name":"Mahmoud","full_name":"Mahmoud, Iman","first_name":"Iman"},{"first_name":"Naïma","last_name":"Bouslam","full_name":"Bouslam, Naïma"},{"full_name":"Bouhouche, Ahmed","last_name":"Bouhouche","first_name":"Ahmed"},{"first_name":"Ali","last_name":"Benomar","full_name":"Benomar, Ali"},{"full_name":"Hanein, Sylvain","last_name":"Hanein","first_name":"Sylvain"},{"last_name":"Raymond","full_name":"Raymond, Laure","first_name":"Laure"},{"last_name":"Forlani","full_name":"Forlani, Sylvie","first_name":"Sylvie"},{"last_name":"Mascaro","full_name":"Mascaro, Massimo","first_name":"Massimo"},{"full_name":"Selim, Laila","last_name":"Selim","first_name":"Laila"},{"last_name":"Shehata","full_name":"Shehata, Nabil","first_name":"Nabil"},{"last_name":"Al Allawi","full_name":"Al Allawi, Nasir","first_name":"Nasir"},{"first_name":"Parayil","last_name":"Bindu","full_name":"Bindu, Parayil"},{"last_name":"Azam","full_name":"Azam, Matloob","first_name":"Matloob"},{"full_name":"Günel, Murat","last_name":"Günel","first_name":"Murat"},{"first_name":"Ahmet","last_name":"Caglayan","full_name":"Caglayan, Ahmet"},{"full_name":"Bilgüvar, Kaya","last_name":"Bilgüvar","first_name":"Kaya"},{"first_name":"Aslihan","last_name":"Tolun","full_name":"Tolun, Aslihan"},{"full_name":"Issa, Mahmoud","last_name":"Issa","first_name":"Mahmoud"},{"full_name":"Schroth, Jana","last_name":"Schroth","first_name":"Jana"},{"last_name":"Spencer","full_name":"Spencer, Emily","first_name":"Emily"},{"last_name":"Rosti","full_name":"Rosti, Rasim","first_name":"Rasim"},{"last_name":"Akizu","full_name":"Akizu, Naiara","first_name":"Naiara"},{"first_name":"Keith","full_name":"Vaux, Keith","last_name":"Vaux"},{"full_name":"Johansen, Anide","last_name":"Johansen","first_name":"Anide"},{"last_name":"Koh","full_name":"Koh, Alice","first_name":"Alice"},{"full_name":"Megahed, Hisham","last_name":"Megahed","first_name":"Hisham"},{"full_name":"Dürr, Alexandra","last_name":"Dürr","first_name":"Alexandra"},{"last_name":"Brice","full_name":"Brice, Alexis","first_name":"Alexis"},{"last_name":"Stévanin","full_name":"Stévanin, Giovanni","first_name":"Giovanni"},{"first_name":"Stacy","last_name":"Gabriel","full_name":"Gabriel, Stacy"},{"last_name":"Ideker","full_name":"Ideker, Trey","first_name":"Trey"},{"last_name":"Gleeson","full_name":"Gleeson, Joseph","first_name":"Joseph"}],"publist_id":"5178","title":"Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders","acknowledgement":"Supported by the Deutsche Forschungsgemeinschaft (G.N.)","oa":1,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","year":"2014","publication":"Science","day":"31","page":"506 - 511","date_created":"2018-12-11T11:54:42Z","doi":"10.1126/science.1247363","date_published":"2014-01-31T00:00:00Z"},{"department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:54:03Z","status":"public","article_type":"original","type":"journal_article","_id":"1917","issue":"6174","volume":343,"language":[{"iso":"eng"}],"publication_status":"published","month":"02","intvolume":" 343","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166562/","open_access":"1"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Auxin-binding protein 1 (ABP1) was discovered nearly 40 years ago and was shown to be essential for plant development and morphogenesis, but its mode of action remains unclear. Here, we report that the plasma membrane-localized transmembrane kinase (TMK) receptor-like kinases interact with ABP1 and transduce auxin signal to activate plasma membrane-associated ROPs [Rho-like guanosine triphosphatases (GTPase) from plants], leading to changes in the cytoskeleton and the shape of leaf pavement cells in Arabidopsis. The interaction between ABP1 and TMK at the cell surface is induced by auxin and requires ABP1 sensing of auxin. These findings show that TMK proteins and ABP1 form a cell surface auxin perception complex that activates ROP signaling pathways, regulating nontranscriptional cytoplasmic responses and associated fundamental processes.","lang":"eng"}],"title":"Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling","publist_id":"5177","author":[{"full_name":"Xu, Tongda","last_name":"Xu","first_name":"Tongda"},{"last_name":"Dai","full_name":"Dai, Ning","first_name":"Ning"},{"full_name":"Chen, Jisheng","last_name":"Chen","first_name":"Jisheng"},{"first_name":"Shingo","full_name":"Nagawa, Shingo","last_name":"Nagawa"},{"last_name":"Cao","full_name":"Cao, Min","first_name":"Min"},{"first_name":"Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li","orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang"},{"last_name":"Zhou","full_name":"Zhou, Zimin","first_name":"Zimin"},{"full_name":"Chen, Xu","last_name":"Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"last_name":"Rakusová","full_name":"Rakusová, Hana","first_name":"Hana"},{"full_name":"Wang, Wen","last_name":"Wang","first_name":"Wen"},{"first_name":"Alan","last_name":"Jones","full_name":"Jones, Alan"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sara","last_name":"Patterson","full_name":"Patterson, Sara"},{"first_name":"Anthony","last_name":"Bleecker","full_name":"Bleecker, Anthony"},{"last_name":"Yang","full_name":"Yang, Zhenbiao","first_name":"Zhenbiao"}],"article_processing_charge":"No","external_id":{"pmid":["24578577"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"T. Xu, N. Dai, J. Chen, S. Nagawa, M. Cao, H. Li, Z. Zhou, X. Chen, R. De Rycke, H. Rakusová, W. Wang, A. Jones, J. Friml, S. Patterson, A. Bleecker, Z. Yang, Science 343 (2014) 1025–1028.","ieee":"T. Xu et al., “Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling,” Science, vol. 343, no. 6174. American Association for the Advancement of Science, pp. 1025–1028, 2014.","apa":"Xu, T., Dai, N., Chen, J., Nagawa, S., Cao, M., Li, H., … Yang, Z. (2014). Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1245125","ama":"Xu T, Dai N, Chen J, et al. Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. 2014;343(6174):1025-1028. doi:10.1126/science.1245125","mla":"Xu, Tongda, et al. “Cell Surface ABP1-TMK Auxin Sensing Complex Activates ROP GTPase Signaling.” Science, vol. 343, no. 6174, American Association for the Advancement of Science, 2014, pp. 1025–28, doi:10.1126/science.1245125.","ista":"Xu T, Dai N, Chen J, Nagawa S, Cao M, Li H, Zhou Z, Chen X, De Rycke R, Rakusová H, Wang W, Jones A, Friml J, Patterson S, Bleecker A, Yang Z. 2014. Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. 343(6174), 1025–1028.","chicago":"Xu, Tongda, Ning Dai, Jisheng Chen, Shingo Nagawa, Min Cao, Hongjiang Li, Zimin Zhou, et al. “Cell Surface ABP1-TMK Auxin Sensing Complex Activates ROP GTPase Signaling.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1245125."},"date_published":"2014-02-28T00:00:00Z","doi":"10.1126/science.1245125","date_created":"2018-12-11T11:54:42Z","page":"1025 - 1028","day":"28","publication":"Science","year":"2014","publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"acknowledgement":"Supported by the intramural research program of the National Institute of Arthritis and Musculoskeletal and Skin Diseases and by its Laboratory Animal Care and Use Section and Flow Cytometry Group, Office of Science and Technology"},{"day":"07","language":[{"iso":"eng"}],"publication":"PNAS","publication_status":"published","year":"2014","date_published":"2014-01-07T00:00:00Z","volume":111,"issue":"1","doi":"10.1073/pnas.1315541111","date_created":"2018-12-11T11:54:43Z","page":"E188 - E193","oa_version":"Submitted Version","acknowledgement":"This work was supported by Solution-Oriented Research for Science and Technology from the Japan Science and Technology Agency; Ministry of Education, Culture, Sports, Science and Technology of Japan Grant 16300114 (to R.S.).","abstract":[{"text":"Cerebellar motor learning is suggested to be caused by long-term plasticity of excitatory parallel fiber-Purkinje cell (PF-PC) synapses associated with changes in the number of synaptic AMPA-type glutamate receptors (AMPARs). However, whether the AMPARs decrease or increase in individual PF-PC synapses occurs in physiological motor learning and accounts for memory that lasts over days remains elusive. We combined quantitative SDS-digested freeze-fracture replica labeling for AMPAR and physical dissector electron microscopy with a simple model of cerebellar motor learning, adaptation of horizontal optokinetic response (HOKR) in mouse. After 1-h training of HOKR, short-term adaptation (STA) was accompanied with transient decrease in AMPARs by 28% in target PF-PC synapses. STA was well correlated with AMPAR decrease in individual animals and both STA and AMPAR decrease recovered to basal levels within 24 h. Surprisingly, long-termadaptation (LTA) after five consecutive daily trainings of 1-h HOKR did not alter the number of AMPARs in PF-PC synapses but caused gradual and persistent synapse elimination by 45%, with corresponding PC spine loss by the fifth training day. Furthermore, recovery of LTA after 2 wk was well correlated with increase of PF-PC synapses to the control level. Our findings indicate that the AMPARs decrease in PF-PC synapses and the elimination of these synapses are in vivo engrams in short- and long-term motor learning, respectively, showing a unique type of synaptic plasticity that may contribute to memory consolidation.","lang":"eng"}],"month":"01","intvolume":" 111","publisher":"National Academy of Sciences","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890858/"}],"oa":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:05Z","citation":{"ista":"Wang W, Nakadate K, Masugi Tokita M, Shutoh F, Aziz W, Tarusawa E, Lörincz A, Molnár E, Kesaf S, Li Y, Fukazawa Y, Nagao S, Shigemoto R. 2014. Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. 111(1), E188–E193.","chicago":"Wang, Wen, Kazuhiko Nakadate, Miwako Masugi Tokita, Fumihiro Shutoh, Wajeeha Aziz, Etsuko Tarusawa, Andrea Lörincz, et al. “Distinct Cerebellar Engrams in Short-Term and Long-Term Motor Learning.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1315541111.","short":"W. Wang, K. Nakadate, M. Masugi Tokita, F. Shutoh, W. Aziz, E. Tarusawa, A. Lörincz, E. Molnár, S. Kesaf, Y. Li, Y. Fukazawa, S. Nagao, R. Shigemoto, PNAS 111 (2014) E188–E193.","ieee":"W. Wang et al., “Distinct cerebellar engrams in short-term and long-term motor learning,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. E188–E193, 2014.","apa":"Wang, W., Nakadate, K., Masugi Tokita, M., Shutoh, F., Aziz, W., Tarusawa, E., … Shigemoto, R. (2014). Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1315541111","ama":"Wang W, Nakadate K, Masugi Tokita M, et al. Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. 2014;111(1):E188-E193. doi:10.1073/pnas.1315541111","mla":"Wang, Wen, et al. “Distinct Cerebellar Engrams in Short-Term and Long-Term Motor Learning.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. E188–93, doi:10.1073/pnas.1315541111."},"title":"Distinct cerebellar engrams in short-term and long-term motor learning","department":[{"_id":"RySh"}],"author":[{"full_name":"Wang, Wen","last_name":"Wang","first_name":"Wen"},{"first_name":"Kazuhiko","full_name":"Nakadate, Kazuhiko","last_name":"Nakadate"},{"full_name":"Masugi Tokita, Miwako","last_name":"Masugi Tokita","first_name":"Miwako"},{"first_name":"Fumihiro","last_name":"Shutoh","full_name":"Shutoh, Fumihiro"},{"last_name":"Aziz","full_name":"Aziz, Wajeeha","first_name":"Wajeeha"},{"full_name":"Tarusawa, Etsuko","last_name":"Tarusawa","first_name":"Etsuko"},{"first_name":"Andrea","full_name":"Lörincz, Andrea","last_name":"Lörincz"},{"first_name":"Elek","full_name":"Molnár, Elek","last_name":"Molnár"},{"full_name":"Kesaf, Sebnem","last_name":"Kesaf","first_name":"Sebnem","id":"401AB46C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Li","full_name":"Li, Yunqing","first_name":"Yunqing"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"first_name":"Soichi","full_name":"Nagao, Soichi","last_name":"Nagao"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"publist_id":"5174","_id":"1920","status":"public","type":"journal_article"},{"date_updated":"2022-06-07T11:20:56Z","department":[{"_id":"JiFr"}],"_id":"1915","type":"journal_article","article_type":"original","status":"public","publication_identifier":{"eissn":["1470-8752"],"issn":["0300-5127"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"1","volume":42,"ec_funded":1,"abstract":[{"text":"ROPs (Rho of plants) belong to a large family of plant-specific Rho-like small GTPases that function as essential molecular switches to control diverse cellular processes including cytoskeleton organization, cell polarization, cytokinesis, cell differentiation and vesicle trafficking. Although the machineries of vesicle trafficking and cell polarity in plants have been individually well addressed, how ROPs co-ordinate those processes is still largely unclear. Recent progress has been made towards an understanding of the coordination of ROP signalling and trafficking of PIN (PINFORMED) transporters for the plant hormone auxin in both root and leaf pavement cells. PIN transporters constantly shuttle between the endosomal compartments and the polar plasma membrane domains, therefore the modulation of PIN-dependent auxin transport between cells is a main developmental output of ROP-regulated vesicle trafficking. The present review focuses on these cellular mechanisms, especially the integration of ROP-based vesicle trafficking and plant cell polarity.","lang":"eng"}],"oa_version":"None","pmid":1,"scopus_import":"1","month":"02","intvolume":" 42","citation":{"short":"X. Chen, J. Friml, Biochemical Society Transactions 42 (2014) 212–218.","ieee":"X. Chen and J. Friml, “Rho-GTPase-regulated vesicle trafficking in plant cell polarity,” Biochemical Society Transactions, vol. 42, no. 1. Portland Press, pp. 212–218, 2014.","apa":"Chen, X., & Friml, J. (2014). Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/BST20130269","ama":"Chen X, Friml J. Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. 2014;42(1):212-218. doi:10.1042/BST20130269","mla":"Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant Cell Polarity.” Biochemical Society Transactions, vol. 42, no. 1, Portland Press, 2014, pp. 212–18, doi:10.1042/BST20130269.","ista":"Chen X, Friml J. 2014. Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. 42(1), 212–218.","chicago":"Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant Cell Polarity.” Biochemical Society Transactions. Portland Press, 2014. https://doi.org/10.1042/BST20130269."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5179","author":[{"full_name":"Chen, Xu","last_name":"Chen","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"article_processing_charge":"No","external_id":{"pmid":["24450654"]},"title":"Rho-GTPase-regulated vesicle trafficking in plant cell polarity","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"year":"2014","day":"01","publication":"Biochemical Society Transactions","page":"212 - 218","doi":"10.1042/BST20130269","date_published":"2014-02-01T00:00:00Z","date_created":"2018-12-11T11:54:41Z","acknowledgement":"This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP], Central European Institute of Technology (CEITEC) [grant number CZ.1.05/1.1.00/02.0068], European Social Fund [grant number CZ.1.07/2.3.00/20.0043] and the Czec","publisher":"Portland Press","quality_controlled":"1"},{"type":"journal_article","status":"public","_id":"1919","publist_id":"5175","author":[{"first_name":"Wajeeha","last_name":"Aziz","full_name":"Aziz, Wajeeha"},{"full_name":"Wang, Wen","last_name":"Wang","first_name":"Wen"},{"full_name":"Kesaf, Sebnem","last_name":"Kesaf","id":"401AB46C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebnem"},{"first_name":"Alsayed","last_name":"Mohamed","full_name":"Mohamed, Alsayed"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"department":[{"_id":"RySh"}],"title":"Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning","date_updated":"2021-01-12T06:54:04Z","citation":{"ama":"Aziz W, Wang W, Kesaf S, Mohamed A, Fukazawa Y, Shigemoto R. Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. 2014;111(1):E194-E202. doi:10.1073/pnas.1303317110","apa":"Aziz, W., Wang, W., Kesaf, S., Mohamed, A., Fukazawa, Y., & Shigemoto, R. (2014). Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1303317110","short":"W. Aziz, W. Wang, S. Kesaf, A. Mohamed, Y. Fukazawa, R. Shigemoto, PNAS 111 (2014) E194–E202.","ieee":"W. Aziz, W. Wang, S. Kesaf, A. Mohamed, Y. Fukazawa, and R. Shigemoto, “Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. E194–E202, 2014.","mla":"Aziz, Wajeeha, et al. “Distinct Kinetics of Synaptic Structural Plasticity, Memory Formation, and Memory Decay in Massed and Spaced Learning.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. E194–202, doi:10.1073/pnas.1303317110.","ista":"Aziz W, Wang W, Kesaf S, Mohamed A, Fukazawa Y, Shigemoto R. 2014. Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. 111(1), E194–E202.","chicago":"Aziz, Wajeeha, Wen Wang, Sebnem Kesaf, Alsayed Mohamed, Yugo Fukazawa, and Ryuichi Shigemoto. “Distinct Kinetics of Synaptic Structural Plasticity, Memory Formation, and Memory Decay in Massed and Spaced Learning.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1303317110."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890840/","open_access":"1"}],"oa":1,"scopus_import":1,"publisher":"National Academy of Sciences","intvolume":" 111","month":"01","abstract":[{"text":"Long-lasting memories are formed when the stimulus is temporally distributed (spacing effect). However, the synaptic mechanisms underlying this robust phenomenon and the precise time course of the synaptic modifications that occur during learning remain unclear. Here we examined the adaptation of horizontal optokinetic response in mice that underwent 1 h of massed and spaced training at varying intervals. Despite similar acquisition by all training protocols, 1 h of spacing produced the highest memory retention at 24 h, which lasted for 1 mo. The distinct kinetics of memory are strongly correlated with the reduction of floccular parallel fiber-Purkinje cell synapses but not with AMPA receptor (AMPAR) number and synapse size. After the spaced training, we observed 25%, 23%, and 12% reduction in AMPAR density, synapse size, and synapse number, respectively. Four hours after the spaced training, half of the synapses and Purkinje cell spines had been eliminated, whereas AMPAR density and synapse size were recovered in remaining synapses. Surprisingly, massed training also produced long-term memory and halving of synapses; however, this occurred slowly over days, and the memory lasted for only 1 wk. This distinct kinetics of structural plasticity may serve as a basis for unique temporal profiles in the formation and decay of memory with or without intervals.","lang":"eng"}],"acknowledgement":"his work was supported by Solution Oriented Research for Science and Technology (R.S.), Core Research for Evolutional Science and Technology, Japan Science and Technology Agency (Y.F.), and Grants-in-Aid for Scientific Research on Priority Areas-Molecular Brain Sciences 16300114 (to R.S.) and 18022043 (to Y.F.).","oa_version":"Submitted Version","page":"E194 - E202","date_created":"2018-12-11T11:54:43Z","volume":111,"issue":"1","doi":"10.1073/pnas.1303317110","date_published":"2014-01-07T00:00:00Z","publication_status":"published","year":"2014","language":[{"iso":"eng"}],"publication":"PNAS","day":"07"},{"doi":"10.1142/S0129055X13500219","date_published":"2014-02-01T00:00:00Z","date_created":"2018-12-11T11:54:42Z","day":"01","publication":"Reviews in Mathematical Physics","year":"2014","quality_controlled":"1","publisher":"World Scientific Publishing","oa":1,"title":"Existence of ground states for negative ions at the binding threshold","publist_id":"5176","author":[{"full_name":"Bellazzini, Jacopo","last_name":"Bellazzini","first_name":"Jacopo"},{"first_name":"Rupert","full_name":"Frank, Rupert","last_name":"Frank"},{"full_name":"Lieb, Élliott","last_name":"Lieb","first_name":"Élliott"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Bellazzini, Jacopo, Rupert Frank, Élliott Lieb, and Robert Seiringer. “Existence of Ground States for Negative Ions at the Binding Threshold.” Reviews in Mathematical Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X13500219.","ista":"Bellazzini J, Frank R, Lieb É, Seiringer R. 2014. Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. 26(1), 1350021.","mla":"Bellazzini, Jacopo, et al. “Existence of Ground States for Negative Ions at the Binding Threshold.” Reviews in Mathematical Physics, vol. 26, no. 1, 1350021, World Scientific Publishing, 2014, doi:10.1142/S0129055X13500219.","apa":"Bellazzini, J., Frank, R., Lieb, É., & Seiringer, R. (2014). Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X13500219","ama":"Bellazzini J, Frank R, Lieb É, Seiringer R. Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. 2014;26(1). doi:10.1142/S0129055X13500219","short":"J. Bellazzini, R. Frank, É. Lieb, R. Seiringer, Reviews in Mathematical Physics 26 (2014).","ieee":"J. Bellazzini, R. Frank, É. Lieb, and R. Seiringer, “Existence of ground states for negative ions at the binding threshold,” Reviews in Mathematical Physics, vol. 26, no. 1. World Scientific Publishing, 2014."},"project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"article_number":"1350021","volume":26,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","month":"02","intvolume":" 26","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1301.5370"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"As the nuclear charge Z is continuously decreased an N-electron atom undergoes a binding-unbinding transition. We investigate whether the electrons remain bound and whether the radius of the system stays finite as the critical value Zc is approached. Existence of a ground state at Zc is shown under the condition Zc < N-K, where K is the maximal number of electrons that can be removed at Zc without changing the energy."}],"department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T06:54:04Z","status":"public","type":"journal_article","_id":"1918"},{"publication_status":"published","year":"2014","day":"06","publication":"Current Biology","language":[{"iso":"eng"}],"page":"R27 - R29","date_published":"2014-01-06T00:00:00Z","volume":24,"issue":"1","doi":"10.1016/j.cub.2013.11.019","date_created":"2018-12-11T11:54:41Z","abstract":[{"text":"Targeting membrane proteins for degradation requires the sequential action of ESCRT sub-complexes ESCRT-0 to ESCRT-III. Although this machinery is generally conserved among kingdoms, plants lack the essential ESCRT-0 components. A new report closes this gap by identifying a novel protein family that substitutes for ESCRT-0 function in plants.","lang":"eng"}],"oa_version":"None","scopus_import":1,"publisher":"Cell Press","quality_controlled":"1","month":"01","intvolume":" 24","date_updated":"2021-01-12T06:54:02Z","citation":{"ama":"Sauer M, Friml J. Plant biology: Gatekeepers of the road to protein perdition. Current Biology. 2014;24(1):R27-R29. doi:10.1016/j.cub.2013.11.019","apa":"Sauer, M., & Friml, J. (2014). Plant biology: Gatekeepers of the road to protein perdition. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.11.019","short":"M. Sauer, J. Friml, Current Biology 24 (2014) R27–R29.","ieee":"M. Sauer and J. Friml, “Plant biology: Gatekeepers of the road to protein perdition,” Current Biology, vol. 24, no. 1. Cell Press, pp. R27–R29, 2014.","mla":"Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to Protein Perdition.” Current Biology, vol. 24, no. 1, Cell Press, 2014, pp. R27–29, doi:10.1016/j.cub.2013.11.019.","ista":"Sauer M, Friml J. 2014. Plant biology: Gatekeepers of the road to protein perdition. Current Biology. 24(1), R27–R29.","chicago":"Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to Protein Perdition.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2013.11.019."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5180","author":[{"first_name":"Michael","full_name":"Sauer, Michael","last_name":"Sauer"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"title":"Plant biology: Gatekeepers of the road to protein perdition","department":[{"_id":"JiFr"}],"_id":"1914","type":"journal_article","status":"public"},{"ddc":["570"],"date_updated":"2021-01-12T06:54:07Z","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:45:21Z","_id":"1925","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"df4e03d225a19179e7790f6d87a12332","file_id":"7856","creator":"dernst","file_size":3804152,"date_updated":"2020-07-14T12:45:21Z","file_name":"2014_Nanotechnology_Lamprecht.pdf","date_created":"2020-05-15T09:21:19Z"}],"publication_status":"published","issue":"12","volume":25,"oa_version":"Submitted Version","abstract":[{"text":"In the past decade carbon nanotubes (CNTs) have been widely studied as a potential drug-delivery system, especially with functionality for cellular targeting. Yet, little is known about the actual process of docking to cell receptors and transport dynamics after internalization. Here we performed single-particle studies of folic acid (FA) mediated CNT binding to human carcinoma cells and their transport inside the cytosol. In particular, we employed molecular recognition force spectroscopy, an atomic force microscopy based method, to visualize and quantify docking of FA functionalized CNTs to FA binding receptors in terms of binding probability and binding force. We then traced individual fluorescently labeled, FA functionalized CNTs after specific uptake, and created a dynamic 'roadmap' that clearly showed trajectories of directed diffusion and areas of nanotube confinement in the cytosol. Our results demonstrate the potential of a single-molecule approach for investigation of drug-delivery vehicles and their targeting capacity.","lang":"eng"}],"intvolume":" 25","month":"03","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Lamprecht C, Plochberger B, Ruprecht V, Wieser S, Rankl C, Heister E, Unterauer B, Brameshuber M, Danzberger J, Lukanov P, Flahaut E, Schütz G, Hinterdorfer P, Ebner A. 2014. A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. 25(12), 125704.","chicago":"Lamprecht, Constanze, Birgit Plochberger, Verena Ruprecht, Stefan Wieser, Christian Rankl, Elena Heister, Barbara Unterauer, et al. “A Single-Molecule Approach to Explore Binding Uptake and Transport of Cancer Cell Targeting Nanotubes.” Nanotechnology. IOP Publishing, 2014. https://doi.org/10.1088/0957-4484/25/12/125704.","ieee":"C. Lamprecht et al., “A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes,” Nanotechnology, vol. 25, no. 12. IOP Publishing, 2014.","short":"C. Lamprecht, B. Plochberger, V. Ruprecht, S. Wieser, C. Rankl, E. Heister, B. Unterauer, M. Brameshuber, J. Danzberger, P. Lukanov, E. Flahaut, G. Schütz, P. Hinterdorfer, A. Ebner, Nanotechnology 25 (2014).","ama":"Lamprecht C, Plochberger B, Ruprecht V, et al. A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. 2014;25(12). doi:10.1088/0957-4484/25/12/125704","apa":"Lamprecht, C., Plochberger, B., Ruprecht, V., Wieser, S., Rankl, C., Heister, E., … Ebner, A. (2014). A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. IOP Publishing. https://doi.org/10.1088/0957-4484/25/12/125704","mla":"Lamprecht, Constanze, et al. “A Single-Molecule Approach to Explore Binding Uptake and Transport of Cancer Cell Targeting Nanotubes.” Nanotechnology, vol. 25, no. 12, 125704, IOP Publishing, 2014, doi:10.1088/0957-4484/25/12/125704."},"title":"A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes","article_processing_charge":"No","author":[{"last_name":"Lamprecht","full_name":"Lamprecht, Constanze","first_name":"Constanze"},{"first_name":"Birgit","full_name":"Plochberger, Birgit","last_name":"Plochberger"},{"first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633","last_name":"Ruprecht"},{"id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Wieser","full_name":"Wieser, Stefan","orcid":"0000-0002-2670-2217"},{"full_name":"Rankl, Christian","last_name":"Rankl","first_name":"Christian"},{"full_name":"Heister, Elena","last_name":"Heister","first_name":"Elena"},{"last_name":"Unterauer","full_name":"Unterauer, Barbara","first_name":"Barbara"},{"last_name":"Brameshuber","full_name":"Brameshuber, Mario","first_name":"Mario"},{"first_name":"Jürgen","last_name":"Danzberger","full_name":"Danzberger, Jürgen"},{"last_name":"Lukanov","full_name":"Lukanov, Petar","first_name":"Petar"},{"last_name":"Flahaut","full_name":"Flahaut, Emmanuel","first_name":"Emmanuel"},{"first_name":"Gerhard","full_name":"Schütz, Gerhard","last_name":"Schütz"},{"first_name":"Peter","full_name":"Hinterdorfer, Peter","last_name":"Hinterdorfer"},{"first_name":"Andreas","full_name":"Ebner, Andreas","last_name":"Ebner"}],"publist_id":"5169","article_number":"125704","publication":"Nanotechnology","day":"28","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:54:45Z","date_published":"2014-03-28T00:00:00Z","doi":"10.1088/0957-4484/25/12/125704","acknowledgement":"This work was supported by EC grant Marie Curie RTN-CT-2006-035616, CARBIO 'Carbon nanotubes for biomedical applications' and Austrian FFG grant mnt-era.net 823980, 'IntelliTip'.\r\n","oa":1,"publisher":"IOP Publishing"},{"oa":1,"publisher":"IOP Publishing Ltd.","quality_controlled":"1","year":"2014","has_accepted_license":"1","publication":"New Journal of Physics","day":"01","date_created":"2018-12-11T11:54:44Z","doi":"10.1088/1367-2630/16/6/065005","date_published":"2014-06-01T00:00:00Z","article_number":"065005","citation":{"apa":"Berthoumieux, H., Maître, J.-L., Heisenberg, C.-P. J., Paluch, E., Julicher, F., & Salbreux, G. (2014). Active elastic thin shell theory for cellular deformations. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/16/6/065005","ama":"Berthoumieux H, Maître J-L, Heisenberg C-PJ, Paluch E, Julicher F, Salbreux G. Active elastic thin shell theory for cellular deformations. New Journal of Physics. 2014;16. doi:10.1088/1367-2630/16/6/065005","short":"H. Berthoumieux, J.-L. Maître, C.-P.J. Heisenberg, E. Paluch, F. Julicher, G. Salbreux, New Journal of Physics 16 (2014).","ieee":"H. Berthoumieux, J.-L. Maître, C.-P. J. Heisenberg, E. Paluch, F. Julicher, and G. Salbreux, “Active elastic thin shell theory for cellular deformations,” New Journal of Physics, vol. 16. IOP Publishing Ltd., 2014.","mla":"Berthoumieux, Hélène, et al. “Active Elastic Thin Shell Theory for Cellular Deformations.” New Journal of Physics, vol. 16, 065005, IOP Publishing Ltd., 2014, doi:10.1088/1367-2630/16/6/065005.","ista":"Berthoumieux H, Maître J-L, Heisenberg C-PJ, Paluch E, Julicher F, Salbreux G. 2014. Active elastic thin shell theory for cellular deformations. New Journal of Physics. 16, 065005.","chicago":"Berthoumieux, Hélène, Jean-Léon Maître, Carl-Philipp J Heisenberg, Ewa Paluch, Frank Julicher, and Guillaume Salbreux. “Active Elastic Thin Shell Theory for Cellular Deformations.” New Journal of Physics. IOP Publishing Ltd., 2014. https://doi.org/10.1088/1367-2630/16/6/065005."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5171","author":[{"first_name":"Hélène","full_name":"Berthoumieux, Hélène","last_name":"Berthoumieux"},{"first_name":"Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","last_name":"Maître","orcid":"0000-0002-3688-1474","full_name":"Maître, Jean-Léon"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"},{"first_name":"Ewa","full_name":"Paluch, Ewa","last_name":"Paluch"},{"first_name":"Frank","full_name":"Julicher, Frank","last_name":"Julicher"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"}],"title":"Active elastic thin shell theory for cellular deformations","abstract":[{"text":"We derive the equations for a thin, axisymmetric elastic shell subjected to an internal active stress giving rise to active tension and moments within the shell. We discuss the stability of a cylindrical elastic shell and its response to a localized change in internal active stress. This description is relevant to describe the cellular actomyosin cortex, a thin shell at the cell surface behaving elastically at a short timescale and subjected to active internal forces arising from myosin molecular motor activity. We show that the recent observations of cell deformation following detachment of adherent cells (Maître J-L et al 2012 Science 338 253-6) are well accounted for by this mechanical description. The actin cortex elastic and bending moduli can be obtained from a quantitative analysis of cell shapes observed in these experiments. Our approach thus provides a non-invasive, imaging-based method for the extraction of cellular physical parameters.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 16","month":"06","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:16:16Z","file_name":"IST-2016-429-v1+1_document.pdf","creator":"system","date_updated":"2020-07-14T12:45:21Z","file_size":941387,"file_id":"5202","checksum":"8dbe81ec656bf1264d8889bda9b2b985","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"volume":16,"_id":"1923","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"429","status":"public","date_updated":"2021-01-12T06:54:06Z","ddc":["570"],"department":[{"_id":"CaHe"}],"file_date_updated":"2020-07-14T12:45:21Z"},{"scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079372/","open_access":"1"}],"month":"05","intvolume":" 26","abstract":[{"lang":"eng","text":"Cell polarity manifested by asymmetric distribution of cargoes, such as receptors and transporters, within the plasma membrane (PM) is crucial for essential functions in multicellular organisms. In plants, cell polarity (re)establishment is intimately linked to patterning processes. Despite the importance of cell polarity, its underlying mechanisms are still largely unknown, including the definition and distinctiveness of the polar domains within the PM. Here, we show in Arabidopsis thaliana that the signaling membrane components, the phosphoinositides phosphatidylinositol 4-phosphate (PtdIns4P) and phosphatidylinositol 4, 5-bisphosphate [PtdIns(4, 5)P2] as well as PtdIns4P 5-kinases mediating their interconversion, are specifically enriched at apical and basal polar plasma membrane domains. The PtdIns4P 5-kinases PIP5K1 and PIP5K2 are redundantly required for polar localization of specifically apical and basal cargoes, such as PIN-FORMED transporters for the plant hormone auxin. As a consequence of the polarity defects, instructive auxin gradients as well as embryonic and postembryonic patterning are severely compromised. Furthermore, auxin itself regulates PIP5K transcription and PtdIns4P and PtdIns(4, 5)P2 levels, in particular their association with polar PM domains. Our results provide insight into the polar domain-delineating mechanisms in plant cells that depend on apical and basal distribution of membrane lipids and are essential for embryonic and postembryonic patterning."}],"oa_version":"Submitted Version","volume":26,"issue":"5","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1921","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:54:05Z","publisher":"American Society of Plant Biologists","oa":1,"acknowledgement":"This work was supported by grants from the Odysseus program of the Research Foundation-Flanders (to J.F.).","page":"2114 - 2128","doi":"10.1105/tpc.114.126185","date_published":"2014-05-01T00:00:00Z","date_created":"2018-12-11T11:54:43Z","year":"2014","day":"01","publication":"Plant Cell","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"author":[{"first_name":"Ricardo","last_name":"Tejos","full_name":"Tejos, Ricardo"},{"last_name":"Sauer","full_name":"Sauer, Michael","first_name":"Michael"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"first_name":"MiriamPalacios ","full_name":"Palacios-Gomez, MiriamPalacios ","last_name":"Palacios-Gomez"},{"first_name":"Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li","orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang"},{"full_name":"Heilmann, Mareike","last_name":"Heilmann","first_name":"Mareike"},{"last_name":"Van Wijk","full_name":"Van Wijk, Ringo","first_name":"Ringo"},{"full_name":"Vermeer, Joop","last_name":"Vermeer","first_name":"Joop"},{"first_name":"Ingo","full_name":"Heilmann, Ingo","last_name":"Heilmann"},{"first_name":"Teun","full_name":"Munnik, Teun","last_name":"Munnik"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"5173","title":"Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis","citation":{"chicago":"Tejos, Ricardo, Michael Sauer, Steffen Vanneste, MiriamPalacios Palacios-Gomez, Hongjiang Li, Mareike Heilmann, Ringo Van Wijk, et al. “Bipolar Plasma Membrane Distribution of Phosphoinositides and Their Requirement for Auxin-Mediated Cell Polarity and Patterning in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2014. https://doi.org/10.1105/tpc.114.126185.","ista":"Tejos R, Sauer M, Vanneste S, Palacios-Gomez M, Li H, Heilmann M, Van Wijk R, Vermeer J, Heilmann I, Munnik T, Friml J. 2014. Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis. Plant Cell. 26(5), 2114–2128.","mla":"Tejos, Ricardo, et al. “Bipolar Plasma Membrane Distribution of Phosphoinositides and Their Requirement for Auxin-Mediated Cell Polarity and Patterning in Arabidopsis.” Plant Cell, vol. 26, no. 5, American Society of Plant Biologists, 2014, pp. 2114–28, doi:10.1105/tpc.114.126185.","apa":"Tejos, R., Sauer, M., Vanneste, S., Palacios-Gomez, M., Li, H., Heilmann, M., … Friml, J. (2014). Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.126185","ama":"Tejos R, Sauer M, Vanneste S, et al. Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis. Plant Cell. 2014;26(5):2114-2128. doi:10.1105/tpc.114.126185","ieee":"R. Tejos et al., “Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis,” Plant Cell, vol. 26, no. 5. American Society of Plant Biologists, pp. 2114–2128, 2014.","short":"R. Tejos, M. Sauer, S. Vanneste, M. Palacios-Gomez, H. Li, M. Heilmann, R. Van Wijk, J. Vermeer, I. Heilmann, T. Munnik, J. Friml, Plant Cell 26 (2014) 2114–2128."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"lang":"eng","text":"Germination of Arabidopsis seeds in darkness induces apical hook development, based on a tightly regulated differential growth coordinated by a multiple hormone cross-talk. Here, we endeavoured to clarify the function of brassinosteroids (BRs) and cross-talk with ethylene in hook development. An automated infrared imaging system was developed to study the kinetics of hook development in etiolated Arabidopsis seedlings. To ascertain the photomorphogenic control of hook opening, the system was equipped with an automatic light dimmer. We demonstrate that ethylene and BRs are indispensable for hook formation and maintenance. Ethylene regulation of hook formation functions partly through BRs, with BR feedback inhibition of ethylene action. Conversely, BR-mediated extension of hook maintenance functions partly through ethylene. Furthermore, we revealed that a short light pulse is sufficient to induce rapid hook opening. Our dynamic infrared imaging system allows high-resolution, kinetic imaging of up to 112 seedlings in a single experimental run. At this high throughput, it is ideally suited to rapidly gain insight in pathway networks. We demonstrate that BRs and ethylene cooperatively regulate apical hook development in a phase-dependent manner. Furthermore, we show that light is a predominant regulator of hook opening, inhibiting ethylene- and BR-mediated postponement of hook opening."}],"oa_version":"None","acknowledgement":"Funded by Ghent University; Research Foundation Flanders Grant Number: G065613N European Research Council Grant Number: CZ.1.07/2.3.00/20.0043","publisher":"Wiley-Blackwell","scopus_import":1,"month":"06","intvolume":" 202","year":"2014","publication_status":"published","day":"01","publication":"New Phytologist","language":[{"iso":"eng"}],"page":"1398 - 1411","date_published":"2014-06-01T00:00:00Z","issue":"4","volume":202,"doi":"10.1111/nph.12751","ec_funded":1,"date_created":"2018-12-11T11:54:44Z","_id":"1922","type":"journal_article","status":"public","project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis"}],"citation":{"ista":"Smet D, Žádníková P, Vandenbussche F, Benková E, Van Der Straeten D. 2014. Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids. New Phytologist. 202(4), 1398–1411.","chicago":"Smet, Dajo, Petra Žádníková, Filip Vandenbussche, Eva Benková, and Dominique Van Der Straeten. “Dynamic Infrared Imaging Analysis of Apical Hook Development in Arabidopsis: The Case of Brassinosteroids.” New Phytologist. Wiley-Blackwell, 2014. https://doi.org/10.1111/nph.12751.","ieee":"D. Smet, P. Žádníková, F. Vandenbussche, E. Benková, and D. Van Der Straeten, “Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids,” New Phytologist, vol. 202, no. 4. Wiley-Blackwell, pp. 1398–1411, 2014.","short":"D. Smet, P. Žádníková, F. Vandenbussche, E. Benková, D. Van Der Straeten, New Phytologist 202 (2014) 1398–1411.","ama":"Smet D, Žádníková P, Vandenbussche F, Benková E, Van Der Straeten D. Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids. New Phytologist. 2014;202(4):1398-1411. doi:10.1111/nph.12751","apa":"Smet, D., Žádníková, P., Vandenbussche, F., Benková, E., & Van Der Straeten, D. (2014). Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.12751","mla":"Smet, Dajo, et al. “Dynamic Infrared Imaging Analysis of Apical Hook Development in Arabidopsis: The Case of Brassinosteroids.” New Phytologist, vol. 202, no. 4, Wiley-Blackwell, 2014, pp. 1398–411, doi:10.1111/nph.12751."},"date_updated":"2021-01-12T06:54:05Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5172","author":[{"first_name":"Dajo","last_name":"Smet","full_name":"Smet, Dajo"},{"last_name":"Žádníková","full_name":"Žádníková, Petra","first_name":"Petra"},{"full_name":"Vandenbussche, Filip","last_name":"Vandenbussche","first_name":"Filip"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"},{"last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique","first_name":"Dominique"}],"department":[{"_id":"EvBe"}],"title":"Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids"},{"doi":"10.1145/2591796.2591825","date_published":"2014-01-01T00:00:00Z","volume":8874,"date_created":"2018-12-11T11:54:45Z","page":"173 - 192","day":"01","year":"2014","publication_status":"published","month":"01","intvolume":" 8874","quality_controlled":0,"publisher":"Springer","oa":1,"main_file_link":[{"url":"http://eprint.iacr.org/2014/416","open_access":"1"}],"acknowledgement":"We are grateful to Mihir Bellare for his feedback on earlier versions of this paper. We are indebted to Vanishree Rao for her generous assistance in preparing this proceedings version.","abstract":[{"text":"Constrained pseudorandom functions have recently been introduced independently by Boneh and Waters (Asiacrypt’13), Kiayias et al. (CCS’13), and Boyle et al. (PKC’14). In a standard pseudorandom function (PRF) a key k is used to evaluate the PRF on all inputs in the domain. Constrained PRFs additionally offer the functionality to delegate “constrained” keys kS which allow to evaluate the PRF only on a subset S of the domain. The three above-mentioned papers all show that the classical GGM construction (J.ACM’86) of a PRF from a pseudorandom generator (PRG) directly yields a constrained PRF where one can compute constrained keys to evaluate the PRF on all inputs with a given prefix. This constrained PRF has already found many interesting applications. Unfortunately, the existing security proofs only show selective security (by a reduction to the security of the underlying PRG). To achieve full security, one has to use complexity leveraging, which loses an exponential factor 2N in security, where N is the input length. The first contribution of this paper is a new reduction that only loses a quasipolynomial factor qlog N, where q is the number of adversarial queries. For this we develop a new proof technique which constructs a distinguisher by interleaving simple guessing steps and hybrid arguments a small number of times. This approach might be of interest also in other contexts where currently the only technique to achieve full security is complexity leveraging. Our second contribution is concerned with another constrained PRF, due to Boneh and Waters, which allows for constrained keys for the more general class of bit-fixing functions. Their security proof also suffers from a 2N loss, which we show is inherent. We construct a meta-reduction which shows that any “simple” reduction of full security from a noninteractive hardness assumption must incur an exponential security loss.","lang":"eng"}],"title":"Adaptive security of constrained PRFs","publist_id":"5167","author":[{"full_name":"Georg Fuchsbauer","last_name":"Fuchsbauer","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg"},{"first_name":"Momchil","full_name":"Konstantinov, Momchil","last_name":"Konstantinov"},{"orcid":"0000-0002-9139-1654","full_name":"Krzysztof Pietrzak","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rao","full_name":"Rao, Vanishree","first_name":"Vanishree"}],"extern":1,"citation":{"mla":"Fuchsbauer, Georg, et al. Adaptive Security of Constrained PRFs. Vol. 8874, Springer, 2014, pp. 173–92, doi:10.1145/2591796.2591825.","ieee":"G. Fuchsbauer, M. Konstantinov, K. Z. Pietrzak, and V. Rao, “Adaptive security of constrained PRFs,” presented at the Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2014, vol. 8874, pp. 173–192.","short":"G. Fuchsbauer, M. Konstantinov, K.Z. Pietrzak, V. Rao, in:, Springer, 2014, pp. 173–192.","apa":"Fuchsbauer, G., Konstantinov, M., Pietrzak, K. Z., & Rao, V. (2014). Adaptive security of constrained PRFs (Vol. 8874, pp. 173–192). Presented at the Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer. https://doi.org/10.1145/2591796.2591825","ama":"Fuchsbauer G, Konstantinov M, Pietrzak KZ, Rao V. Adaptive security of constrained PRFs. In: Vol 8874. Springer; 2014:173-192. doi:10.1145/2591796.2591825","chicago":"Fuchsbauer, Georg, Momchil Konstantinov, Krzysztof Z Pietrzak, and Vanishree Rao. “Adaptive Security of Constrained PRFs,” 8874:173–92. Springer, 2014. https://doi.org/10.1145/2591796.2591825.","ista":"Fuchsbauer G, Konstantinov M, Pietrzak KZ, Rao V. 2014. Adaptive security of constrained PRFs. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) vol. 8874, 173–192."},"date_updated":"2021-01-12T06:54:08Z","status":"public","type":"conference","conference":{"name":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)"},"_id":"1927"},{"project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips","article_processing_charge":"No","external_id":{"arxiv":["1304.3862"]},"author":[{"orcid":"0000-0001-8255-3968","full_name":"Sadel, Christian","last_name":"Sadel","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"}],"publist_id":"5168","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"C. Sadel, Mathematical Physics, Analysis and Geometry 17 (2014) 409–440.","ieee":"C. Sadel, “Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips,” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4. Springer, pp. 409–440, 2014.","apa":"Sadel, C. (2014). Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-014-9163-4","ama":"Sadel C. Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips. Mathematical Physics, Analysis and Geometry. 2014;17(3-4):409-440. doi:10.1007/s11040-014-9163-4","mla":"Sadel, Christian. “Absolutely Continuous Spectrum for Random Schrödinger Operators on the Fibonacci and Similar Tree-Strips.” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4, Springer, 2014, pp. 409–40, doi:10.1007/s11040-014-9163-4.","ista":"Sadel C. 2014. Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips. Mathematical Physics, Analysis and Geometry. 17(3–4), 409–440.","chicago":"Sadel, Christian. “Absolutely Continuous Spectrum for Random Schrödinger Operators on the Fibonacci and Similar Tree-Strips.” Mathematical Physics, Analysis and Geometry. Springer, 2014. https://doi.org/10.1007/s11040-014-9163-4."},"oa":1,"quality_controlled":"1","publisher":"Springer","date_created":"2018-12-11T11:54:45Z","doi":"10.1007/s11040-014-9163-4","date_published":"2014-12-17T00:00:00Z","page":"409 - 440","publication":"Mathematical Physics, Analysis and Geometry","day":"17","year":"2014","status":"public","type":"journal_article","article_type":"original","_id":"1926","department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T06:54:07Z","intvolume":" 17","month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1304.3862"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"We consider cross products of finite graphs with a class of trees that have arbitrarily but finitely long line segments, such as the Fibonacci tree. Such cross products are called tree-strips. We prove that for small disorder random Schrödinger operators on such tree-strips have purely absolutely continuous spectrum in a certain set.","lang":"eng"}],"ec_funded":1,"volume":17,"issue":"3-4","language":[{"iso":"eng"}],"publication_status":"published"},{"abstract":[{"text":"Stomata are two-celled valves that control epidermal pores whose spacing optimizes shoot-atmosphere gas exchange. They develop from protodermal cells after unequal divisions followed by an equal division and differentiation. The concentration of the hormone auxin, a master plant developmental regulator, is tightly controlled in time and space, but its role, if any, in stomatal formation is obscure. Here dynamic changes of auxin activity during stomatal development are monitored using auxin input (DII-VENUS) and output (DR5:VENUS) markers by time-lapse imaging. A decrease in auxin levels in the smaller daughter cell after unequal division presages the acquisition of a guard mother cell fate whose equal division produces the two guard cells. Thus, stomatal patterning requires auxin pathway control of stem cell compartment size, as well as auxin depletion that triggers a developmental switch from unequal to equal division.","lang":"eng"}],"oa_version":"None","scopus_import":1,"quality_controlled":"1","publisher":"Nature Publishing Group","month":"01","intvolume":" 5","year":"2014","publication_status":"published","day":"27","publication":"Nature Communications","language":[{"iso":"eng"}],"doi":"10.1038/ncomms4090","date_published":"2014-01-27T00:00:00Z","volume":5,"date_created":"2018-12-11T11:54:44Z","_id":"1924","article_number":"3090","type":"journal_article","status":"public","date_updated":"2021-01-12T06:54:06Z","citation":{"ista":"Le J, Liu X, Yang K, Chen X, Zhu L, Wang H, Wang M, Vanneste S, Morita M, Tasaka M, Ding Z, Friml J, Beeckman T, Sack F. 2014. Auxin transport and activity regulate stomatal patterning and development. Nature Communications. 5, 3090.","chicago":"Le, Jie, Xuguang Liu, Kezhen Yang, Xiaolan Chen, Lingling Zhu, Hongzhe Wang, Ming Wang, et al. “Auxin Transport and Activity Regulate Stomatal Patterning and Development.” Nature Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms4090.","ieee":"J. Le et al., “Auxin transport and activity regulate stomatal patterning and development,” Nature Communications, vol. 5. Nature Publishing Group, 2014.","short":"J. Le, X. Liu, K. Yang, X. Chen, L. Zhu, H. Wang, M. Wang, S. Vanneste, M. Morita, M. Tasaka, Z. Ding, J. Friml, T. Beeckman, F. Sack, Nature Communications 5 (2014).","apa":"Le, J., Liu, X., Yang, K., Chen, X., Zhu, L., Wang, H., … Sack, F. (2014). Auxin transport and activity regulate stomatal patterning and development. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms4090","ama":"Le J, Liu X, Yang K, et al. Auxin transport and activity regulate stomatal patterning and development. Nature Communications. 2014;5. doi:10.1038/ncomms4090","mla":"Le, Jie, et al. “Auxin Transport and Activity Regulate Stomatal Patterning and Development.” Nature Communications, vol. 5, 3090, Nature Publishing Group, 2014, doi:10.1038/ncomms4090."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jie","last_name":"Le","full_name":"Le, Jie"},{"last_name":"Liu","full_name":"Liu, Xuguang","first_name":"Xuguang"},{"first_name":"Kezhen","full_name":"Yang, Kezhen","last_name":"Yang"},{"last_name":"Chen","full_name":"Chen, Xiaolan","first_name":"Xiaolan"},{"first_name":"Lingling","last_name":"Zhu","full_name":"Zhu, Lingling"},{"first_name":"Hongzhe","full_name":"Wang, Hongzhe","last_name":"Wang"},{"last_name":"Wang","full_name":"Wang, Ming","first_name":"Ming"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"first_name":"Miyo","full_name":"Morita, Miyo","last_name":"Morita"},{"full_name":"Tasaka, Masao","last_name":"Tasaka","first_name":"Masao"},{"first_name":"Zhaojun","last_name":"Ding","full_name":"Ding, Zhaojun"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"full_name":"Sack, Fred","last_name":"Sack","first_name":"Fred"}],"publist_id":"5170","department":[{"_id":"JiFr"}],"title":"Auxin transport and activity regulate stomatal patterning and development"},{"citation":{"apa":"Humplik, J., Hill, A., & Nowak, M. (2014). Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2014.06.039","ama":"Humplik J, Hill A, Nowak M. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 2014;360:149-162. doi:10.1016/j.jtbi.2014.06.039","short":"J. Humplik, A. Hill, M. Nowak, Journal of Theoretical Biology 360 (2014) 149–162.","ieee":"J. Humplik, A. Hill, and M. Nowak, “Evolutionary dynamics of infectious diseases in finite populations,” Journal of Theoretical Biology, vol. 360. Elsevier, pp. 149–162, 2014.","mla":"Humplik, Jan, et al. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology, vol. 360, Elsevier, 2014, pp. 149–62, doi:10.1016/j.jtbi.2014.06.039.","ista":"Humplik J, Hill A, Nowak M. 2014. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 360, 149–162.","chicago":"Humplik, Jan, Alison Hill, and Martin Nowak. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology. Elsevier, 2014. https://doi.org/10.1016/j.jtbi.2014.06.039."},"date_updated":"2021-01-12T06:54:08Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Humplik","full_name":"Humplik, Jan"},{"first_name":"Alison","last_name":"Hill","full_name":"Hill, Alison"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"publist_id":"5166","department":[{"_id":"GaTk"}],"title":"Evolutionary dynamics of infectious diseases in finite populations","_id":"1928","type":"journal_article","status":"public","year":"2014","publication_status":"published","language":[{"iso":"eng"}],"publication":"Journal of Theoretical Biology","day":"07","page":"149 - 162","date_created":"2018-12-11T11:54:46Z","date_published":"2014-11-07T00:00:00Z","volume":360,"doi":"10.1016/j.jtbi.2014.06.039","abstract":[{"text":"In infectious disease epidemiology the basic reproductive ratio, R0, is defined as the average number of new infections caused by a single infected individual in a fully susceptible population. Many models describing competition for hosts between non-interacting pathogen strains in an infinite population lead to the conclusion that selection favors invasion of new strains if and only if they have higher R0 values than the resident. Here we demonstrate that this picture fails in finite populations. Using a simple stochastic SIS model, we show that in general there is no analogous optimization principle. We find that successive invasions may in some cases lead to strains that infect a smaller fraction of the host population, and that mutually invasible pathogen strains exist. In the limit of weak selection we demonstrate that an optimization principle does exist, although it differs from R0 maximization. For strains with very large R0, we derive an expression for this local fitness function and use it to establish a lower bound for the error caused by neglecting stochastic effects. Furthermore, we apply this weak selection limit to investigate the selection dynamics in the presence of a trade-off between the virulence and the transmission rate of a pathogen.","lang":"eng"}],"acknowledgement":"J.H. received support from the Zdenek Bakala Foundation and the Mobility Fund of Charles University in Prague.","oa_version":"None","scopus_import":1,"publisher":"Elsevier","intvolume":" 360","month":"11"},{"title":"An algorithm for cartographic generalization that preserves global topology","author":[{"first_name":"V V","full_name":"Alexeev, V V","last_name":"Alexeev"},{"first_name":"V G","last_name":"Bogaevskaya","full_name":"Bogaevskaya, V G"},{"first_name":"M M","last_name":"Preobrazhenskaya","full_name":"Preobrazhenskaya, M M"},{"first_name":"A Y","full_name":"Ukhalov, A Y","last_name":"Ukhalov"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"full_name":"Yakimova, Olga","last_name":"Yakimova","first_name":"Olga"}],"publist_id":"5165","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Alexeev, V V, V G Bogaevskaya, M M Preobrazhenskaya, A Y Ukhalov, Herbert Edelsbrunner, and Olga Yakimova. “An Algorithm for Cartographic Generalization That Preserves Global Topology.” Journal of Mathematical Sciences. Springer, 2014. https://doi.org/10.1007/s10958-014-2165-8.","ista":"Alexeev VV, Bogaevskaya VG, Preobrazhenskaya MM, Ukhalov AY, Edelsbrunner H, Yakimova O. 2014. An algorithm for cartographic generalization that preserves global topology. Journal of Mathematical Sciences. 203(6), 754–760.","mla":"Alexeev, V. V., et al. “An Algorithm for Cartographic Generalization That Preserves Global Topology.” Journal of Mathematical Sciences, vol. 203, no. 6, Springer, 2014, pp. 754–60, doi:10.1007/s10958-014-2165-8.","short":"V.V. Alexeev, V.G. Bogaevskaya, M.M. Preobrazhenskaya, A.Y. Ukhalov, H. Edelsbrunner, O. Yakimova, Journal of Mathematical Sciences 203 (2014) 754–760.","ieee":"V. V. Alexeev, V. G. Bogaevskaya, M. M. Preobrazhenskaya, A. Y. Ukhalov, H. Edelsbrunner, and O. Yakimova, “An algorithm for cartographic generalization that preserves global topology,” Journal of Mathematical Sciences, vol. 203, no. 6. Springer, pp. 754–760, 2014.","apa":"Alexeev, V. V., Bogaevskaya, V. G., Preobrazhenskaya, M. M., Ukhalov, A. Y., Edelsbrunner, H., & Yakimova, O. (2014). An algorithm for cartographic generalization that preserves global topology. Journal of Mathematical Sciences. Springer. https://doi.org/10.1007/s10958-014-2165-8","ama":"Alexeev VV, Bogaevskaya VG, Preobrazhenskaya MM, Ukhalov AY, Edelsbrunner H, Yakimova O. An algorithm for cartographic generalization that preserves global topology. Journal of Mathematical Sciences. 2014;203(6):754-760. doi:10.1007/s10958-014-2165-8"},"date_published":"2014-11-16T00:00:00Z","doi":"10.1007/s10958-014-2165-8","date_created":"2018-12-11T11:54:46Z","page":"754 - 760","day":"16","publication":"Journal of Mathematical Sciences","year":"2014","publisher":"Springer","quality_controlled":"1","acknowledgement":"We would like to offer our special thanks to students of the Department of Mathematics of Demidov Yaroslavl State University A. A. Gorokhov and V. N. Knyazev for participation in developing the program and assistance in preparation of test data. This work was supported by grant 11.G34.31.0053 from the government of the Russian Federation.","department":[{"_id":"HeEd"}],"date_updated":"2022-05-24T10:39:06Z","status":"public","type":"journal_article","article_type":"original","_id":"1929","volume":203,"issue":"6","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1573-8795"],"issn":["1072-3374"]},"publication_status":"published","month":"11","intvolume":" 203","scopus_import":"1","oa_version":"None","abstract":[{"text":"We propose an algorithm for the generalization of cartographic objects that can be used to represent maps on different scales.","lang":"eng"}]},{"oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"2014 by the authors. This paper may be reproduced, in its entirety, for non-commercial purposes.\r\n\r\nThe research leading to these results has received funding from the European Research\r\nCouncil under the European Union’s Seventh Framework Programme ERC Starting Grant CoMBoS (Grant Agreement No. 239694; A.G. and R.S.), the U.S. National Science Foundation (Grant PHY 0965859; E.H.L.), the Simons Foundation (Grant # 230207; E.H.L) and the NSERC (R.S.). The work is part of a project started in collaboration with Joel Lebowitz, whom we thank for many useful discussions and for his constant encouragement.","date_created":"2018-12-11T11:54:48Z","doi":"10.1007/s00220-014-1923-2","date_published":"2014-10-01T00:00:00Z","page":"333 - 350","publication":"Communications in Mathematical Physics","day":"01","year":"2014","has_accepted_license":"1","title":"Formation of stripes and slabs near the ferromagnetic transition","article_processing_charge":"No","external_id":{"arxiv":["1304.6344"]},"author":[{"first_name":"Alessandro","full_name":"Giuliani, Alessandro","last_name":"Giuliani"},{"full_name":"Lieb, Élliott","last_name":"Lieb","first_name":"Élliott"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"publist_id":"5159","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Giuliani, Alessandro, Élliott Lieb, and Robert Seiringer. “Formation of Stripes and Slabs near the Ferromagnetic Transition.” Communications in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s00220-014-1923-2.","ista":"Giuliani A, Lieb É, Seiringer R. 2014. Formation of stripes and slabs near the ferromagnetic transition. Communications in Mathematical Physics. 331, 333–350.","mla":"Giuliani, Alessandro, et al. “Formation of Stripes and Slabs near the Ferromagnetic Transition.” Communications in Mathematical Physics, vol. 331, Springer, 2014, pp. 333–50, doi:10.1007/s00220-014-1923-2.","ama":"Giuliani A, Lieb É, Seiringer R. Formation of stripes and slabs near the ferromagnetic transition. Communications in Mathematical Physics. 2014;331:333-350. doi:10.1007/s00220-014-1923-2","apa":"Giuliani, A., Lieb, É., & Seiringer, R. (2014). Formation of stripes and slabs near the ferromagnetic transition. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-014-1923-2","ieee":"A. Giuliani, É. Lieb, and R. Seiringer, “Formation of stripes and slabs near the ferromagnetic transition,” Communications in Mathematical Physics, vol. 331. Springer, pp. 333–350, 2014.","short":"A. Giuliani, É. Lieb, R. Seiringer, Communications in Mathematical Physics 331 (2014) 333–350."},"intvolume":" 331","month":"10","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We consider Ising models in d = 2 and d = 3 dimensions with nearest neighbor ferromagnetic and long-range antiferromagnetic interactions, the latter decaying as (distance)-p, p > 2d, at large distances. If the strength J of the ferromagnetic interaction is larger than a critical value J c, then the ground state is homogeneous. It has been conjectured that when J is smaller than but close to J c, the ground state is periodic and striped, with stripes of constant width h = h(J), and h → ∞ as J → Jc -. (In d = 3 stripes mean slabs, not columns.) Here we rigorously prove that, if we normalize the energy in such a way that the energy of the homogeneous state is zero, then the ratio e 0(J)/e S(J) tends to 1 as J → Jc -, with e S(J) being the energy per site of the optimal periodic striped/slabbed state and e 0(J) the actual ground state energy per site of the system. Our proof comes with explicit bounds on the difference e 0(J)-e S(J) at small but positive J c-J, and also shows that in this parameter range the ground state is striped/slabbed in a certain sense: namely, if one looks at a randomly chosen window, of suitable size ℓ (very large compared to the optimal stripe size h(J)), one finds a striped/slabbed state with high probability.","lang":"eng"}],"volume":331,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"c8423271cd1e1ba9e44c47af75efe7b6","file_id":"11409","creator":"dernst","file_size":334064,"date_updated":"2022-05-24T08:30:40Z","file_name":"2014_CommMathPhysics_Giuliani.pdf","date_created":"2022-05-24T08:30:40Z"}],"publication_status":"published","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"status":"public","article_type":"original","type":"journal_article","_id":"1935","department":[{"_id":"RoSe"}],"file_date_updated":"2022-05-24T08:30:40Z","ddc":["510"],"date_updated":"2022-05-24T08:32:50Z"},{"status":"public","type":"journal_article","_id":"1936","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:54:11Z","month":"02","intvolume":" 25","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014306/"}],"oa_version":"Submitted Version","abstract":[{"text":"The social intelligence hypothesis states that the need to cope with complexities of social life has driven the evolution of advanced cognitive abilities. It is usually invoked in the context of challenges arising from complex intragroup structures, hierarchies, and alliances. However, a fundamental aspect of group living remains largely unexplored as a driving force in cognitive evolution: the competition between individuals searching for resources (producers) and conspecifics that parasitize their findings (scroungers). In populations of social foragers, abilities that enable scroungers to steal by outsmarting producers, and those allowing producers to prevent theft by outsmarting scroungers, are likely to be beneficial and may fuel a cognitive arms race. Using analytical theory and agent-based simulations, we present a general model for such a race that is driven by the producer-scrounger game and show that the race's plausibility is dramatically affected by the nature of the evolving abilities. If scrounging and scrounging avoidance rely on separate, strategy-specific cognitive abilities, arms races are short-lived and have a limited effect on cognition. However, general cognitive abilities that facilitate both scrounging and scrounging avoidance undergo stable, long-lasting arms races. Thus, ubiquitous foraging interactions may lead to the evolution of general cognitive abilities in social animals, without the requirement of complex intragroup structures.","lang":"eng"}],"volume":25,"issue":"3","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"title":"An arms race between producers and scroungers can drive the evolution of social cognition","publist_id":"5157","author":[{"first_name":"Michal","last_name":"Arbilly","full_name":"Arbilly, Michal"},{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"Weissman, Daniel","last_name":"Weissman"},{"full_name":"Feldman, Marcus","last_name":"Feldman","first_name":"Marcus"},{"first_name":"Uri","full_name":"Grodzinski, Uri","last_name":"Grodzinski"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Arbilly, Michal, et al. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” Behavioral Ecology, vol. 25, no. 3, Oxford University Press, 2014, pp. 487–95, doi:10.1093/beheco/aru002.","short":"M. Arbilly, D. Weissman, M. Feldman, U. Grodzinski, Behavioral Ecology 25 (2014) 487–495.","ieee":"M. Arbilly, D. Weissman, M. Feldman, and U. Grodzinski, “An arms race between producers and scroungers can drive the evolution of social cognition,” Behavioral Ecology, vol. 25, no. 3. Oxford University Press, pp. 487–495, 2014.","apa":"Arbilly, M., Weissman, D., Feldman, M., & Grodzinski, U. (2014). An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. Oxford University Press. https://doi.org/10.1093/beheco/aru002","ama":"Arbilly M, Weissman D, Feldman M, Grodzinski U. An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. 2014;25(3):487-495. doi:10.1093/beheco/aru002","chicago":"Arbilly, Michal, Daniel Weissman, Marcus Feldman, and Uri Grodzinski. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” Behavioral Ecology. Oxford University Press, 2014. https://doi.org/10.1093/beheco/aru002.","ista":"Arbilly M, Weissman D, Feldman M, Grodzinski U. 2014. An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. 25(3), 487–495."},"quality_controlled":"1","publisher":"Oxford University Press","oa":1,"doi":"10.1093/beheco/aru002","date_published":"2014-02-13T00:00:00Z","date_created":"2018-12-11T11:54:48Z","page":"487 - 495","day":"13","publication":"Behavioral Ecology","year":"2014"},{"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"title":"Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis","publist_id":"5160","author":[{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Marhavy","full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741"},{"full_name":"Duclercq, Jérôme","last_name":"Duclercq","first_name":"Jérôme"},{"full_name":"Weller, Benjamin","last_name":"Weller","first_name":"Benjamin"},{"first_name":"Elena","full_name":"Feraru, Elena","last_name":"Feraru"},{"first_name":"Agnieszka","last_name":"Bielach","full_name":"Bielach, Agnieszka"},{"last_name":"Offringa","full_name":"Offringa, Remko","first_name":"Remko"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"Claus","last_name":"Schwechheimer","full_name":"Schwechheimer, Claus"},{"first_name":"Angus","last_name":"Murphy","full_name":"Murphy, Angus"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"short":"P. Marhavý, J. Duclercq, B. Weller, E. Feraru, A. Bielach, R. Offringa, J. Friml, C. Schwechheimer, A. Murphy, E. Benková, Current Biology 24 (2014) 1031–1037.","ieee":"P. Marhavý et al., “Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis,” Current Biology, vol. 24, no. 9. Cell Press, pp. 1031–1037, 2014.","ama":"Marhavý P, Duclercq J, Weller B, et al. Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. Current Biology. 2014;24(9):1031-1037. doi:10.1016/j.cub.2014.04.002","apa":"Marhavý, P., Duclercq, J., Weller, B., Feraru, E., Bielach, A., Offringa, R., … Benková, E. (2014). Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.04.002","mla":"Marhavý, Peter, et al. “Cytokinin Controls Polarity of PIN1-Dependent Auxin Transport during Lateral Root Organogenesis.” Current Biology, vol. 24, no. 9, Cell Press, 2014, pp. 1031–37, doi:10.1016/j.cub.2014.04.002.","ista":"Marhavý P, Duclercq J, Weller B, Feraru E, Bielach A, Offringa R, Friml J, Schwechheimer C, Murphy A, Benková E. 2014. Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. Current Biology. 24(9), 1031–1037.","chicago":"Marhavý, Peter, Jérôme Duclercq, Benjamin Weller, Elena Feraru, Agnieszka Bielach, Remko Offringa, Jiří Friml, Claus Schwechheimer, Angus Murphy, and Eva Benková. “Cytokinin Controls Polarity of PIN1-Dependent Auxin Transport during Lateral Root Organogenesis.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.04.002."},"date_updated":"2021-01-12T06:54:10Z","project":[{"grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"status":"public","type":"journal_article","_id":"1934","volume":24,"issue":"9","doi":"10.1016/j.cub.2014.04.002","date_published":"2014-05-05T00:00:00Z","ec_funded":1,"date_created":"2018-12-11T11:54:48Z","page":"1031 - 1037","day":"05","language":[{"iso":"eng"}],"publication":"Current Biology","publication_status":"published","year":"2014","month":"05","intvolume":" 24","publisher":"Cell Press","scopus_import":1,"quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"The plant hormones auxin and cytokinin mutually coordinate their activities to control various aspects of development [1-9], and their crosstalk occurs at multiple levels [10, 11]. Cytokinin-mediated modulation of auxin transport provides an efficient means to regulate auxin distribution in plant organs. Here, we demonstrate that cytokinin does not merely control the overall auxin flow capacity, but might also act as a polarizing cue and control the auxin stream directionality during plant organogenesis. Cytokinin enhances the PIN-FORMED1 (PIN1) auxin transporter depletion at specific polar domains, thus rearranging the cellular PIN polarities and directly regulating the auxin flow direction. This selective cytokinin sensitivity correlates with the PIN protein phosphorylation degree. PIN1 phosphomimicking mutations, as well as enhanced phosphorylation in plants with modulated activities of PIN-specific kinases and phosphatases, desensitize PIN1 to cytokinin. Our results reveal conceptually novel, cytokinin-driven polarization mechanism that operates in developmental processes involving rapid auxin stream redirection, such as lateral root organogenesis, in which a gradual PIN polarity switch defines the growth axis of the newly formed organ."}]},{"publication_status":"published","language":[{"iso":"eng"}],"volume":68,"issue":"12","ec_funded":1,"abstract":[{"text":"The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce "irreducibly complex" adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1310.6077","open_access":"1"}],"month":"12","intvolume":" 68","date_updated":"2021-01-12T06:54:10Z","department":[{"_id":"NiBa"}],"_id":"1932","type":"journal_article","status":"public","year":"2014","day":"01","publication":"Evolution","page":"3357 - 3367","doi":"10.1111/evo.12517","date_published":"2014-12-01T00:00:00Z","date_created":"2018-12-11T11:54:47Z","acknowledgement":"Funded by National Institutes of Health. Grant Numbers: R01GM076041, R01GM104040 \r\n\r\nSimons Foundation\r\n\r\n","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"citation":{"chicago":"Trotter, Meredith, Daniel Weissman, Grant Peterson, Kayla Peck, and Joanna Masel. “Cryptic Genetic Variation Can Make "Irreducible Complexity" a Common Mode of Adaptation in Sexual Populations.” Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1111/evo.12517.","ista":"Trotter M, Weissman D, Peterson G, Peck K, Masel J. 2014. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. 68(12), 3357–3367.","mla":"Trotter, Meredith, et al. “Cryptic Genetic Variation Can Make "Irreducible Complexity" a Common Mode of Adaptation in Sexual Populations.” Evolution, vol. 68, no. 12, Wiley-Blackwell, 2014, pp. 3357–67, doi:10.1111/evo.12517.","apa":"Trotter, M., Weissman, D., Peterson, G., Peck, K., & Masel, J. (2014). Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.12517","ama":"Trotter M, Weissman D, Peterson G, Peck K, Masel J. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations. Evolution. 2014;68(12):3357-3367. doi:10.1111/evo.12517","ieee":"M. Trotter, D. Weissman, G. Peterson, K. Peck, and J. Masel, “Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations,” Evolution, vol. 68, no. 12. Wiley-Blackwell, pp. 3357–3367, 2014.","short":"M. Trotter, D. Weissman, G. Peterson, K. Peck, J. Masel, Evolution 68 (2014) 3357–3367."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5162","author":[{"last_name":"Trotter","full_name":"Trotter, Meredith","first_name":"Meredith"},{"full_name":"Weissman, Daniel","last_name":"Weissman","first_name":"Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Peterson","full_name":"Peterson, Grant","first_name":"Grant"},{"last_name":"Peck","full_name":"Peck, Kayla","first_name":"Kayla"},{"full_name":"Masel, Joanna","last_name":"Masel","first_name":"Joanna"}],"title":"Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}]},{"_id":"1930","type":"journal_article","status":"public","citation":{"ista":"Günther D, Jacobson A, Reininghaus J, Seidel H, Sorkine Hornung O, Weinkauf T. 2014. Fast and memory-efficient topological denoising of 2D and 3D scalar fields. IEEE Transactions on Visualization and Computer Graphics. 20(12), 2585–2594.","chicago":"Günther, David, Alec Jacobson, Jan Reininghaus, Hans Seidel, Olga Sorkine Hornung, and Tino Weinkauf. “Fast and Memory-Efficient Topological Denoising of 2D and 3D Scalar Fields.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2014. https://doi.org/10.1109/TVCG.2014.2346432.","ama":"Günther D, Jacobson A, Reininghaus J, Seidel H, Sorkine Hornung O, Weinkauf T. Fast and memory-efficient topological denoising of 2D and 3D scalar fields. IEEE Transactions on Visualization and Computer Graphics. 2014;20(12):2585-2594. doi:10.1109/TVCG.2014.2346432","apa":"Günther, D., Jacobson, A., Reininghaus, J., Seidel, H., Sorkine Hornung, O., & Weinkauf, T. (2014). Fast and memory-efficient topological denoising of 2D and 3D scalar fields. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2014.2346432","ieee":"D. Günther, A. Jacobson, J. Reininghaus, H. Seidel, O. Sorkine Hornung, and T. Weinkauf, “Fast and memory-efficient topological denoising of 2D and 3D scalar fields,” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 12. IEEE, pp. 2585–2594, 2014.","short":"D. Günther, A. Jacobson, J. Reininghaus, H. Seidel, O. Sorkine Hornung, T. Weinkauf, IEEE Transactions on Visualization and Computer Graphics 20 (2014) 2585–2594.","mla":"Günther, David, et al. “Fast and Memory-Efficient Topological Denoising of 2D and 3D Scalar Fields.” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 12, IEEE, 2014, pp. 2585–94, doi:10.1109/TVCG.2014.2346432."},"date_updated":"2021-01-12T06:54:09Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5164","author":[{"last_name":"Günther","full_name":"Günther, David","first_name":"David"},{"first_name":"Alec","full_name":"Jacobson, Alec","last_name":"Jacobson"},{"first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"last_name":"Seidel","full_name":"Seidel, Hans","first_name":"Hans"},{"last_name":"Sorkine Hornung","full_name":"Sorkine Hornung, Olga","first_name":"Olga"},{"last_name":"Weinkauf","full_name":"Weinkauf, Tino","first_name":"Tino"}],"title":"Fast and memory-efficient topological denoising of 2D and 3D scalar fields","department":[{"_id":"HeEd"}],"abstract":[{"text":"(Figure Presented) Data acquisition, numerical inaccuracies, and sampling often introduce noise in measurements and simulations. Removing this noise is often necessary for efficient analysis and visualization of this data, yet many denoising techniques change the minima and maxima of a scalar field. For example, the extrema can appear or disappear, spatially move, and change their value. This can lead to wrong interpretations of the data, e.g., when the maximum temperature over an area is falsely reported being a few degrees cooler because the denoising method is unaware of these features. Recently, a topological denoising technique based on a global energy optimization was proposed, which allows the topology-controlled denoising of 2D scalar fields. While this method preserves the minima and maxima, it is constrained by the size of the data. We extend this work to large 2D data and medium-sized 3D data by introducing a novel domain decomposition approach. It allows processing small patches of the domain independently while still avoiding the introduction of new critical points. Furthermore, we propose an iterative refinement of the solution, which decreases the optimization energy compared to the previous approach and therefore gives smoother results that are closer to the input. We illustrate our technique on synthetic and real-world 2D and 3D data sets that highlight potential applications.","lang":"eng"}],"acknowledgement":"RTRA Digiteoproject; ERC grant; SNF award; Intel Doctoral Fellowship; MPC-VCC","oa_version":"None","quality_controlled":"1","publisher":"IEEE","scopus_import":1,"intvolume":" 20","month":"12","publication_status":"published","year":"2014","publication":"IEEE Transactions on Visualization and Computer Graphics","language":[{"iso":"eng"}],"day":"31","page":"2585 - 2594","date_created":"2018-12-11T11:54:46Z","issue":"12","doi":"10.1109/TVCG.2014.2346432","date_published":"2014-12-31T00:00:00Z","volume":20},{"publist_id":"5161","author":[{"full_name":"Hatakeyama, Jun","last_name":"Hatakeyama","first_name":"Jun"},{"first_name":"Yoshio","full_name":"Wakamatsu, Yoshio","last_name":"Wakamatsu"},{"first_name":"Akira","last_name":"Nagafuchi","full_name":"Nagafuchi, Akira"},{"last_name":"Kageyama","full_name":"Kageyama, Ryoichiro","first_name":"Ryoichiro"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"first_name":"Kenji","last_name":"Shimamura","full_name":"Shimamura, Kenji"}],"department":[{"_id":"RySh"}],"title":"Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates","date_updated":"2021-01-12T06:54:10Z","citation":{"mla":"Hatakeyama, Jun, et al. “Cadherin-Based Adhesions in the Apical Endfoot Are Required for Active Notch Signaling to Control Neurogenesis in Vertebrates.” Development, vol. 141, no. 8, Company of Biologists, 2014, pp. 1671–82, doi:10.1242/dev.102988.","ama":"Hatakeyama J, Wakamatsu Y, Nagafuchi A, Kageyama R, Shigemoto R, Shimamura K. Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates. Development. 2014;141(8):1671-1682. doi:10.1242/dev.102988","apa":"Hatakeyama, J., Wakamatsu, Y., Nagafuchi, A., Kageyama, R., Shigemoto, R., & Shimamura, K. (2014). Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates. Development. Company of Biologists. https://doi.org/10.1242/dev.102988","ieee":"J. Hatakeyama, Y. Wakamatsu, A. Nagafuchi, R. Kageyama, R. Shigemoto, and K. Shimamura, “Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates,” Development, vol. 141, no. 8. Company of Biologists, pp. 1671–1682, 2014.","short":"J. Hatakeyama, Y. Wakamatsu, A. Nagafuchi, R. Kageyama, R. Shigemoto, K. Shimamura, Development 141 (2014) 1671–1682.","chicago":"Hatakeyama, Jun, Yoshio Wakamatsu, Akira Nagafuchi, Ryoichiro Kageyama, Ryuichi Shigemoto, and Kenji Shimamura. “Cadherin-Based Adhesions in the Apical Endfoot Are Required for Active Notch Signaling to Control Neurogenesis in Vertebrates.” Development. Company of Biologists, 2014. https://doi.org/10.1242/dev.102988.","ista":"Hatakeyama J, Wakamatsu Y, Nagafuchi A, Kageyama R, Shigemoto R, Shimamura K. 2014. Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates. Development. 141(8), 1671–1682."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1933","page":"1671 - 1682","date_created":"2018-12-11T11:54:47Z","doi":"10.1242/dev.102988","date_published":"2014-04-01T00:00:00Z","volume":141,"issue":"8","publication_status":"published","year":"2014","publication":"Development","language":[{"iso":"eng"}],"day":"01","quality_controlled":"1","publisher":"Company of Biologists","scopus_import":1,"intvolume":" 141","month":"04","abstract":[{"lang":"eng","text":"The development of the vertebrate brain requires an exquisite balance between proliferation and differentiation of neural progenitors. Notch signaling plays a pivotal role in regulating this balance, yet the interaction between signaling and receiving cells remains poorly understood. We have found that numerous nascent neurons and/or intermediate neurogenic progenitors expressing the ligand of Notch retain apical endfeet transiently at the ventricular lumen that form adherens junctions (AJs) with the endfeet of progenitors. Forced detachment of the apical endfeet of those differentiating cells by disrupting AJs resulted in precocious neurogenesis that was preceded by the downregulation of Notch signaling. Both Notch1 and its ligand Dll1 are distributed around AJs in the apical endfeet, and these proteins physically interact with ZO-1, a constituent of the AJ. Furthermore, live imaging of a fluorescently tagged Notch1 demonstrated its trafficking from the apical endfoot to the nucleus upon cleavage. Our results identified the apical endfoot as the central site of active Notch signaling to securely prohibit inappropriate differentiation of neural progenitors."}],"oa_version":"None"},{"article_number":"57","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Savin, C., & Triesch, J. (2014). Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2014.00057","ama":"Savin C, Triesch J. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 2014;8(MAY). doi:10.3389/fncom.2014.00057","short":"C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014).","ieee":"C. Savin and J. Triesch, “Emergence of task-dependent representations in working memory circuits,” Frontiers in Computational Neuroscience, vol. 8, no. MAY. Frontiers Research Foundation, 2014.","mla":"Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience, vol. 8, no. MAY, 57, Frontiers Research Foundation, 2014, doi:10.3389/fncom.2014.00057.","ista":"Savin C, Triesch J. 2014. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 8(MAY), 57.","chicago":"Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2014. https://doi.org/10.3389/fncom.2014.00057."},"title":"Emergence of task-dependent representations in working memory circuits","author":[{"full_name":"Savin, Cristina","last_name":"Savin","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Triesch, Jochen","last_name":"Triesch","first_name":"Jochen"}],"publist_id":"5163","acknowledgement":"Supported in part by EC MEXT project PLICON and the LOEWE-Program “Neuronal Coordination Research Focus Frankfurt” (NeFF). Jochen Triesch was supported by the Quandt foundation.","oa":1,"publisher":"Frontiers Research Foundation","quality_controlled":"1","publication":"Frontiers in Computational Neuroscience","day":"28","year":"2014","date_created":"2018-12-11T11:54:46Z","doi":"10.3389/fncom.2014.00057","date_published":"2014-05-28T00:00:00Z","_id":"1931","status":"public","type":"journal_article","date_updated":"2021-01-12T06:54:09Z","department":[{"_id":"GaTk"}],"oa_version":"Submitted Version","abstract":[{"text":"A wealth of experimental evidence suggests that working memory circuits preferentially represent information that is behaviorally relevant. Still, we are missing a mechanistic account of how these representations come about. Here we provide a simple explanation for a range of experimental findings, in light of prefrontal circuits adapting to task constraints by reward-dependent learning. In particular, we model a neural network shaped by reward-modulated spike-timing dependent plasticity (r-STDP) and homeostatic plasticity (intrinsic excitability and synaptic scaling). We show that the experimentally-observed neural representations naturally emerge in an initially unstructured circuit as it learns to solve several working memory tasks. These results point to a critical, and previously unappreciated, role for reward-dependent learning in shaping prefrontal cortex activity.","lang":"eng"}],"intvolume":" 8","month":"05","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035833/","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","volume":8,"issue":"MAY"},{"department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T06:54:12Z","status":"public","type":"journal_article","_id":"1937","volume":332,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","month":"11","intvolume":" 332","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1306.5728","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We prove the edge universality of the beta ensembles for any β ≥ 1, provided that the limiting spectrum is supported on a single interval, and the external potential is C4 and regular. We also prove that the edge universality holds for generalized Wigner matrices for all symmetry classes. Moreover, our results allow us to extend bulk universality for beta ensembles from analytic potentials to potentials in class C4."}],"title":"Edge universality of beta ensembles","author":[{"full_name":"Bourgade, Paul","last_name":"Bourgade","first_name":"Paul"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"first_name":"Horngtzer","full_name":"Yau, Horngtzer","last_name":"Yau"}],"publist_id":"5158","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Bourgade, Paul, László Erdös, and Horngtzer Yau. “Edge Universality of Beta Ensembles.” Communications in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s00220-014-2120-z.","ista":"Bourgade P, Erdös L, Yau H. 2014. Edge universality of beta ensembles. Communications in Mathematical Physics. 332(1), 261–353.","mla":"Bourgade, Paul, et al. “Edge Universality of Beta Ensembles.” Communications in Mathematical Physics, vol. 332, no. 1, Springer, 2014, pp. 261–353, doi:10.1007/s00220-014-2120-z.","ieee":"P. Bourgade, L. Erdös, and H. Yau, “Edge universality of beta ensembles,” Communications in Mathematical Physics, vol. 332, no. 1. Springer, pp. 261–353, 2014.","short":"P. Bourgade, L. Erdös, H. Yau, Communications in Mathematical Physics 332 (2014) 261–353.","apa":"Bourgade, P., Erdös, L., & Yau, H. (2014). Edge universality of beta ensembles. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-014-2120-z","ama":"Bourgade P, Erdös L, Yau H. Edge universality of beta ensembles. Communications in Mathematical Physics. 2014;332(1):261-353. doi:10.1007/s00220-014-2120-z"},"project":[{"name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen","grant_number":"SFB-TR3-TP10B","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/s00220-014-2120-z","date_published":"2014-11-01T00:00:00Z","date_created":"2018-12-11T11:54:48Z","page":"261 - 353","day":"01","publication":"Communications in Mathematical Physics","year":"2014","quality_controlled":"1","publisher":"Springer","oa":1},{"extern":1,"date_updated":"2019-04-26T07:22:06Z","citation":{"chicago":"Garvin, Michael, Joseph Bielawski, Leonid A Sazanov, and Anthony Gharrett. “Review and Meta-Analysis of Natural Selection in Mitochondrial Complex I in Metazoans.” Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell, 2014. https://doi.org/10.1111/jzs.12079.","ista":"Garvin M, Bielawski J, Sazanov LA, Gharrett A. 2014. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. Journal of Zoological Systematics and Evolutionary Research. 53(1), 1–17.","mla":"Garvin, Michael, et al. “Review and Meta-Analysis of Natural Selection in Mitochondrial Complex I in Metazoans.” Journal of Zoological Systematics and Evolutionary Research, vol. 53, no. 1, Wiley-Blackwell, 2014, pp. 1–17, doi:10.1111/jzs.12079.","ieee":"M. Garvin, J. Bielawski, L. A. Sazanov, and A. Gharrett, “Review and meta-analysis of natural selection in mitochondrial complex I in metazoans,” Journal of Zoological Systematics and Evolutionary Research, vol. 53, no. 1. Wiley-Blackwell, pp. 1–17, 2014.","short":"M. Garvin, J. Bielawski, L.A. Sazanov, A. Gharrett, Journal of Zoological Systematics and Evolutionary Research 53 (2014) 1–17.","ama":"Garvin M, Bielawski J, Sazanov LA, Gharrett A. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. Journal of Zoological Systematics and Evolutionary Research. 2014;53(1):1-17. doi:10.1111/jzs.12079","apa":"Garvin, M., Bielawski, J., Sazanov, L. A., & Gharrett, A. (2014). Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell. https://doi.org/10.1111/jzs.12079"},"title":"Review and meta-analysis of natural selection in mitochondrial complex I in metazoans","publist_id":"5102","author":[{"full_name":"Garvin, Michael R","last_name":"Garvin","first_name":"Michael"},{"first_name":"Joseph","full_name":"Bielawski, Joseph P","last_name":"Bielawski"},{"last_name":"Sazanov","full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"},{"last_name":"Gharrett","full_name":"Gharrett, Anthony J","first_name":"Anthony"}],"_id":"1981","status":"public","type":"review","day":"01","publication":"Journal of Zoological Systematics and Evolutionary Research","publication_status":"published","year":"2014","issue":"1","doi":"10.1111/jzs.12079","volume":53,"date_published":"2014-02-01T00:00:00Z","date_created":"2018-12-11T11:55:02Z","page":"1 - 17","acknowledgement":"Funded by University of Alaska Center for Global Change Student Research Cooperative Institute for Alaska Research and the Rasmuson Foundation","abstract":[{"lang":"eng","text":"Variation in mitochondrial DNA is often assumed to be neutral and is used to construct the genealogical relationships among populations and species. However, if extant variation is the result of episodes of positive selection, these genealogies may be incorrect, although this information itself may provide biologically and evolutionary meaningful information. In fact, positive Darwinian selection has been detected in the mitochondrial-encoded subunits that comprise complex I from diverse taxa with seemingly dissimilar bioenergetic life histories, but the functional implications of the selected sites are unknown. Complex I produces roughly 40% of the proton flux that is used to synthesize ATP from ADP, and a functional model based on the high-resolution structure of complex I described a unique biomechanical apparatus for proton translocation. We reported positive selection at sites in this apparatus during the evolution of Pacific salmon, and it appeared this was also the case in published reports from other taxa, but a comparison among studies was difficult because different statistical tests were used to detect selection and oftentimes, specific sites were not reported. Here we review the literature of positive selection in mitochondrial genomes, the statistical tests used to detect selection, and the structural and functional models that are currently available to study the physiological implications of selection. We then search for signatures of positive selection among the coding mitochondrial genomes of 237 species with a common set of tests and verify that the ND5 subunit of complex I is a repeated target of positive Darwinian selection in diverse taxa. We propose a novel hypothesis to explain the results based on their bioenergetic life histories and provide a guide for laboratory and field studies to test this hypothesis."}],"month":"02","intvolume":" 53","quality_controlled":0,"publisher":"Wiley-Blackwell"},{"status":"public","type":"journal_article","_id":"1980","title":"Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation","publist_id":"5103","author":[{"full_name":"Heikal, Adam ","last_name":"Heikal","first_name":"Adam"},{"full_name":"Nakatani, Yoshio","last_name":"Nakatani","first_name":"Yoshio"},{"first_name":"Elyse","last_name":"Dunn","full_name":"Dunn, Elyse A"},{"first_name":"Marion","last_name":"Weimar","full_name":"Weimar, Marion R"},{"last_name":"Day","full_name":"Day, Catherine","first_name":"Catherine"},{"first_name":"Edward","full_name":"Baker, Edward N","last_name":"Baker"},{"first_name":"Shaun","last_name":"Lott","full_name":"Lott, Shaun J"},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Leonid Sazanov","last_name":"Sazanov"},{"last_name":"Cook","full_name":"Cook, Gregory","first_name":"Gregory"}],"extern":1,"citation":{"chicago":"Heikal, Adam, Yoshio Nakatani, Elyse Dunn, Marion Weimar, Catherine Day, Edward Baker, Shaun Lott, Leonid A Sazanov, and Gregory Cook. “Structure of the Bacterial Type II NADH Dehydrogenase: A Monotopic Membrane Protein with an Essential Role in Energy Generation.” Molecular Microbiology. Wiley-Blackwell, 2014. https://doi.org/10.1111/mmi.12507.","ista":"Heikal A, Nakatani Y, Dunn E, Weimar M, Day C, Baker E, Lott S, Sazanov LA, Cook G. 2014. Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation. Molecular Microbiology. 91(5), 950–964.","mla":"Heikal, Adam, et al. “Structure of the Bacterial Type II NADH Dehydrogenase: A Monotopic Membrane Protein with an Essential Role in Energy Generation.” Molecular Microbiology, vol. 91, no. 5, Wiley-Blackwell, 2014, pp. 950–64, doi:10.1111/mmi.12507.","ama":"Heikal A, Nakatani Y, Dunn E, et al. Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation. Molecular Microbiology. 2014;91(5):950-964. doi:10.1111/mmi.12507","apa":"Heikal, A., Nakatani, Y., Dunn, E., Weimar, M., Day, C., Baker, E., … Cook, G. (2014). Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation. Molecular Microbiology. Wiley-Blackwell. https://doi.org/10.1111/mmi.12507","short":"A. Heikal, Y. Nakatani, E. Dunn, M. Weimar, C. Day, E. Baker, S. Lott, L.A. Sazanov, G. Cook, Molecular Microbiology 91 (2014) 950–964.","ieee":"A. Heikal et al., “Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation,” Molecular Microbiology, vol. 91, no. 5. Wiley-Blackwell, pp. 950–964, 2014."},"date_updated":"2021-01-12T06:54:29Z","intvolume":" 91","month":"03","quality_controlled":0,"publisher":"Wiley-Blackwell","acknowledgement":"Funded by Health Research Council of New Zealand Royal Society of New Zealand University of Otago New Zealand Synchrotron Group","abstract":[{"lang":"eng","text":"Non-proton pumping type II NADH dehydrogenase (NDH-2) plays a central role in the respiratory metabolism of bacteria, and in the mitochondria of fungi, plants and protists. The lack of NDH-2 in mammalian mitochondria and its essentiality in important bacterial pathogens suggests these enzymes may represent a potential new drug target to combat microbial pathogens. Here, we report the first crystal structure of a bacterial NDH-2 enzyme at 2.5Å resolution from Caldalkalibacillus thermarum. The NDH-2 structure reveals a homodimeric organization that has a unique dimer interface. NDH-2 is localized to the cytoplasmic membrane by two separated C-terminal membrane-anchoring regions that are essential for membrane localization and FAD binding, but not NDH-2 dimerization. Comparison of bacterial NDH-2 with the yeast NADH dehydrogenase (Ndi1) structure revealed non-overlapping binding sites for quinone and NADH in the bacterial enzyme. The bacterial NDH-2 structure establishes a framework for the structure-based design of small-molecule inhibitors."}],"date_created":"2018-12-11T11:55:01Z","doi":"10.1111/mmi.12507","volume":91,"date_published":"2014-03-01T00:00:00Z","issue":"5","page":"950 - 964","publication":"Molecular Microbiology","day":"01","publication_status":"published","year":"2014"},{"extern":1,"citation":{"chicago":"Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer and Proton Translocation in Respiratory Complex I.” Journal of Bioenergetics and Biomembranes. Springer, 2014. https://doi.org/10.1007/s10863-014-9554-z.","ista":"Sazanov LA. 2014. The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes. 46(4), 247–253.","mla":"Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer and Proton Translocation in Respiratory Complex I.” Journal of Bioenergetics and Biomembranes, vol. 46, no. 4, Springer, 2014, pp. 247–53, doi:10.1007/s10863-014-9554-z.","short":"L.A. Sazanov, Journal of Bioenergetics and Biomembranes 46 (2014) 247–253.","ieee":"L. A. Sazanov, “The mechanism of coupling between electron transfer and proton translocation in respiratory complex I,” Journal of Bioenergetics and Biomembranes, vol. 46, no. 4. Springer, pp. 247–253, 2014.","apa":"Sazanov, L. A. (2014). The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes. Springer. https://doi.org/10.1007/s10863-014-9554-z","ama":"Sazanov LA. The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes. 2014;46(4):247-253. doi:10.1007/s10863-014-9554-z"},"date_updated":"2021-01-12T06:54:28Z","title":"The mechanism of coupling between electron transfer and proton translocation in respiratory complex I","publist_id":"5104","author":[{"full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"_id":"1979","status":"public","type":"journal_article","publication":"Journal of Bioenergetics and Biomembranes","day":"01","year":"2014","publication_status":"published","date_created":"2018-12-11T11:55:01Z","issue":"4","volume":46,"doi":"10.1007/s10863-014-9554-z","date_published":"2014-08-01T00:00:00Z","page":"247 - 253","abstract":[{"lang":"eng","text":"NADH-ubiquinone oxidoreductase (complex I) is the first and largest enzyme in the respiratory chain of mitochondria and many bacteria. It couples the transfer of two electrons between NADH and ubiquinone to the translocation of four protons across the membrane. Complex I is an L-shaped assembly formed by the hydrophilic (peripheral) arm, containing all the redox centres performing electron transfer and the membrane arm, containing proton-translocating machinery. Mitochondrial complex I consists of 44 subunits of about 1 MDa in total, whilst the prokaryotic enzyme is simpler and generally consists of 14 conserved “core” subunits. Recently we have determined the first atomic structure of the entire complex I, using the enzyme from Thermus thermophilus (536 kDa, 16 subunits, 9 Fe-S clusters, 64 TM helices). Structure suggests a unique coupling mechanism, with redox energy of electron transfer driving proton translocation via long-range (up to ~200 Å) conformational changes. It resembles a steam engine, with coupling elements (akin to coupling rods) linking parts of this molecular machine."}],"intvolume":" 46","month":"08","publisher":"Springer","quality_controlled":0},{"page":"244 - 247","date_created":"2018-12-11T11:55:04Z","issue":"6206","date_published":"2014-10-10T00:00:00Z","volume":346,"doi":"10.1126/science.1256773","year":"2014","publication_status":"published","publication":"Science","day":"10","publisher":"American Association for the Advancement of Science","quality_controlled":0,"intvolume":" 346","month":"10","abstract":[{"text":"During animal cell division, the cleavage furrow is positioned by microtubules that signal to the actin cortex at the cell midplane. We developed a cell-free system to recapitulate cytokinesis signaling using cytoplasmic extract from Xenopus eggs. Microtubules grew out as asters from artificial centrosomes and met to organize antiparallel overlap zones. These zones blocked the interpenetration of neighboring asters and recruited cytokinesis midzone proteins, including the chromosomal passenger complex (CPC) and centralspindlin. The CPC was transported to overlap zones, which required two motor proteins, Kif4A and a Kif20A paralog. Using supported lipid bilayers to mimic the plasma membrane, we observed the recruitment of cleavage furrow markers, including an active RhoA reporter, at microtubule overlaps. This system opens further approaches to understanding the biophysics of cytokinesis signaling.","lang":"eng"}],"acknowledgement":"This work was supported by NIH grant GM39565 (T.J.M.); MBL fellowships from the Evans Foundation, MBL Associates, and the Colwin Fund (T.J.M. and C.M.F.); HFSP fellowship LT000466/2012-L (M.L.); and NIH grant GM103785 (M.W.). ","author":[{"last_name":"Nguyen","full_name":"Nguyen, Phuong A","first_name":"Phuong"},{"last_name":"Groen","full_name":"Groen, Aaron C","first_name":"Aaron"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Martin Loose","last_name":"Loose"},{"last_name":"Ishihara","full_name":"Ishihara, Keisuke ","first_name":"Keisuke"},{"full_name":"Wühr, Martin ","last_name":"Wühr","first_name":"Martin"},{"last_name":"Field","full_name":"Field, Christine M","first_name":"Christine"},{"first_name":"Timothy","last_name":"Mitchison","full_name":"Mitchison, Timothy J"}],"publist_id":"5093","title":"Spatial organization of cytokinesis signaling reconstituted in a cell-free system","citation":{"short":"P. Nguyen, A. Groen, M. Loose, K. Ishihara, M. Wühr, C. Field, T. Mitchison, Science 346 (2014) 244–247.","ieee":"P. Nguyen et al., “Spatial organization of cytokinesis signaling reconstituted in a cell-free system,” Science, vol. 346, no. 6206. American Association for the Advancement of Science, pp. 244–247, 2014.","apa":"Nguyen, P., Groen, A., Loose, M., Ishihara, K., Wühr, M., Field, C., & Mitchison, T. (2014). Spatial organization of cytokinesis signaling reconstituted in a cell-free system. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1256773","ama":"Nguyen P, Groen A, Loose M, et al. Spatial organization of cytokinesis signaling reconstituted in a cell-free system. Science. 2014;346(6206):244-247. doi:10.1126/science.1256773","mla":"Nguyen, Phuong, et al. “Spatial Organization of Cytokinesis Signaling Reconstituted in a Cell-Free System.” Science, vol. 346, no. 6206, American Association for the Advancement of Science, 2014, pp. 244–47, doi:10.1126/science.1256773.","ista":"Nguyen P, Groen A, Loose M, Ishihara K, Wühr M, Field C, Mitchison T. 2014. Spatial organization of cytokinesis signaling reconstituted in a cell-free system. Science. 346(6206), 244–247.","chicago":"Nguyen, Phuong, Aaron Groen, Martin Loose, Keisuke Ishihara, Martin Wühr, Christine Field, and Timothy Mitchison. “Spatial Organization of Cytokinesis Signaling Reconstituted in a Cell-Free System.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1256773."},"date_updated":"2021-01-12T06:54:32Z","extern":1,"type":"journal_article","status":"public","_id":"1989"}]