[{"oa_version":"Preprint","citation":{"ama":"Erdös L, Yau H. Gap universality of generalized Wigner and β ensembles. <i>Journal of the European Mathematical Society</i>. 2015;17(8):1927-2036. doi:<a href=\"https://doi.org/10.4171/JEMS/548\">10.4171/JEMS/548</a>","apa":"Erdös, L., &#38; Yau, H. (2015). Gap universality of generalized Wigner and β ensembles. <i>Journal of the European Mathematical Society</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/JEMS/548\">https://doi.org/10.4171/JEMS/548</a>","mla":"Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” <i>Journal of the European Mathematical Society</i>, vol. 17, no. 8, European Mathematical Society, 2015, pp. 1927–2036, doi:<a href=\"https://doi.org/10.4171/JEMS/548\">10.4171/JEMS/548</a>.","short":"L. Erdös, H. Yau, Journal of the European Mathematical Society 17 (2015) 1927–2036.","ieee":"L. Erdös and H. Yau, “Gap universality of generalized Wigner and β ensembles,” <i>Journal of the European Mathematical Society</i>, vol. 17, no. 8. European Mathematical Society, pp. 1927–2036, 2015.","ista":"Erdös L, Yau H. 2015. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 17(8), 1927–2036.","chicago":"Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” <i>Journal of the European Mathematical Society</i>. European Mathematical Society, 2015. <a href=\"https://doi.org/10.4171/JEMS/548\">https://doi.org/10.4171/JEMS/548</a>."},"date_created":"2018-12-11T11:52:26Z","issue":"8","scopus_import":1,"publication":"Journal of the European Mathematical Society","year":"2015","type":"journal_article","volume":17,"abstract":[{"lang":"eng","text":"We consider generalized Wigner ensembles and general β-ensembles with analytic potentials for any β ≥ 1. The recent universality results in particular assert that the local averages of consecutive eigenvalue gaps in the bulk of the spectrum are universal in the sense that they coincide with those of the corresponding Gaussian β-ensembles. In this article, we show that local averaging is not necessary for this result, i.e. we prove that the single gap distributions in the bulk are universal. In fact, with an additional step, our result can be extended to any C4(ℝ) potential."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","date_updated":"2021-01-12T06:51:15Z","author":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","last_name":"Erdös","orcid":"0000-0001-5366-9603"},{"full_name":"Yau, Horng","last_name":"Yau","first_name":"Horng"}],"month":"08","language":[{"iso":"eng"}],"publication_status":"published","status":"public","_id":"1508","date_published":"2015-08-01T00:00:00Z","doi":"10.4171/JEMS/548","publisher":"European Mathematical Society","publist_id":"5669","intvolume":"        17","department":[{"_id":"LaEr"}],"page":"1927 - 2036","title":"Gap universality of generalized Wigner and β ensembles","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1211.3786"}],"day":"01"},{"day":"01","oa":1,"date_published":"2015-10-01T00:00:00Z","doi":"10.12688/f1000research.7143.1","intvolume":"         4","status":"public","month":"10","pubrep_id":"497","quality_controlled":"1","license":"https://creativecommons.org/licenses/by/4.0/","acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG-20101109-PSDP to JF). JM internship was supported by the grant “Action Austria – Slovakia”.\r\nData associated with the article are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication). \r\n\r\nData availability: \r\nF1000Research: Dataset 1. Dataset 1, 10.5256/f1000research.7143.d104552\r\n\r\nF1000Research: Dataset 2. Dataset 2, 10.5256/f1000research.7143.d104553\r\n\r\nF1000Research: Dataset 3. Dataset 3, 10.5256/f1000research.7143.d104554","type":"journal_article","publication":"F1000 Research ","oa_version":"Published Version","citation":{"ieee":"J. Michalko, M. Lukacisinova, M. T. Bollenbach, and J. Friml, “Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene,” <i>F1000 Research </i>, vol. 4. F1000 Research, 2015.","short":"J. Michalko, M. Lukacisinova, M.T. Bollenbach, J. Friml, F1000 Research  4 (2015).","chicago":"Michalko, Jaroslav, Marta Lukacisinova, Mark Tobias Bollenbach, and Jiří Friml. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” <i>F1000 Research </i>. F1000 Research, 2015. <a href=\"https://doi.org/10.12688/f1000research.7143.1\">https://doi.org/10.12688/f1000research.7143.1</a>.","ista":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. 2015. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 4.","ama":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. <i>F1000 Research </i>. 2015;4. doi:<a href=\"https://doi.org/10.12688/f1000research.7143.1\">10.12688/f1000research.7143.1</a>","mla":"Michalko, Jaroslav, et al. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” <i>F1000 Research </i>, vol. 4, F1000 Research, 2015, doi:<a href=\"https://doi.org/10.12688/f1000research.7143.1\">10.12688/f1000research.7143.1</a>.","apa":"Michalko, J., Lukacisinova, M., Bollenbach, M. T., &#38; Friml, J. (2015). Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. <i>F1000 Research </i>. F1000 Research. <a href=\"https://doi.org/10.12688/f1000research.7143.1\">https://doi.org/10.12688/f1000research.7143.1</a>"},"date_created":"2018-12-11T11:52:26Z","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"title":"Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene","department":[{"_id":"JiFr"},{"_id":"ToBo"}],"publisher":"F1000 Research","publist_id":"5668","ec_funded":1,"_id":"1509","file_date_updated":"2020-07-14T12:44:59Z","publication_status":"published","ddc":["570"],"language":[{"iso":"eng"}],"author":[{"full_name":"Michalko, Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","last_name":"Michalko","first_name":"Jaroslav"},{"first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Dravecka, Marta","last_name":"Dravecka","orcid":"0000-0002-2519-8004"},{"first_name":"Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"},{"first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"article_processing_charge":"No","date_updated":"2025-05-07T11:12:30Z","file":[{"checksum":"8beae5cbe988e1060265ae7de2ee8306","date_updated":"2020-07-14T12:44:59Z","file_name":"IST-2016-497-v1+1_10.12688_f1000research.7143.1_20151102.pdf","relation":"main_file","file_id":"5198","creator":"system","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:16:12Z","file_size":4414248}],"abstract":[{"text":"The Auxin Binding Protein1 (ABP1) has been identified based on its ability to bind auxin with high affinity and studied for a long time as a prime candidate for the extracellular auxin receptor responsible for mediating in particular the fast non-transcriptional auxin responses. However, the contradiction between the embryo-lethal phenotypes of the originally described Arabidopsis T-DNA insertional knock-out alleles (abp1-1 and abp1-1s) and the wild type-like phenotypes of other recently described loss-of-function alleles (abp1-c1 and abp1-TD1) questions the biological importance of ABP1 and relevance of the previous genetic studies. Here we show that there is no hidden copy of the ABP1 gene in the Arabidopsis genome but the embryo-lethal phenotypes of abp1-1 and abp1-1s alleles are very similar to the knock-out phenotypes of the neighboring gene, BELAYA SMERT (BSM). Furthermore, the allelic complementation test between bsm and abp1 alleles shows that the embryo-lethality in the abp1-1 and abp1-1s alleles is caused by the off-target disruption of the BSM locus by the T-DNA insertions. This clarifies the controversy of different phenotypes among published abp1 knock-out alleles and asks for reflections on the developmental role of ABP1.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":4,"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","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)"},"scopus_import":"1","year":"2015"},{"has_accepted_license":"1","volume":34,"year":"2015","tmp":{"short":"CC BY (4.0)","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)"},"scopus_import":1,"author":[{"first_name":"Peter","last_name":"Franek","id":"473294AE-F248-11E8-B48F-1D18A9856A87","full_name":"Franek, Peter"},{"first_name":"Marek","last_name":"Krcál","id":"33E21118-F248-11E8-B48F-1D18A9856A87","full_name":"Krcál, Marek"}],"conference":{"location":"Eindhoven, Netherlands","name":"SoCG: Symposium on Computational Geometry","start_date":"2015-06-22","end_date":"2015-06-25"},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The concept of well group in a special but important case captures homological properties of the zero set of a continuous map f from K to R^n on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within L_infty distance r from f for a given r &gt; 0. The main drawback of the approach is that the computability of well groups was shown only when dim K = n or n = 1. Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of R^n by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and dim K &lt; 2n-2, our approximation of the (dim K-n)th well group is exact. For the second part, we find examples of maps f, f' from K to R^n with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status. "}],"date_updated":"2023-02-21T17:02:57Z","file":[{"file_size":623563,"date_created":"2018-12-12T10:13:19Z","content_type":"application/pdf","access_level":"open_access","creator":"system","file_id":"5001","relation":"main_file","file_name":"IST-2016-503-v1+1_32.pdf","date_updated":"2020-07-14T12:44:59Z","checksum":"49eb5021caafaabe5356c65b9c5f8c9c"}],"_id":"1510","ec_funded":1,"publist_id":"5667","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","file_date_updated":"2020-07-14T12:44:59Z","ddc":["510"],"page":"842 - 856","title":"On computability and triviality of well groups","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"department":[{"_id":"UlWa"},{"_id":"HeEd"}],"alternative_title":["LIPIcs"],"type":"conference","date_created":"2018-12-11T11:52:26Z","oa_version":"Published Version","citation":{"ama":"Franek P, Krcál M. On computability and triviality of well groups. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:842-856. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.842\">10.4230/LIPIcs.SOCG.2015.842</a>","apa":"Franek, P., &#38; Krcál, M. (2015). On computability and triviality of well groups (Vol. 34, pp. 842–856). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.842\">https://doi.org/10.4230/LIPIcs.SOCG.2015.842</a>","mla":"Franek, Peter, and Marek Krcál. <i>On Computability and Triviality of Well Groups</i>. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–56, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.842\">10.4230/LIPIcs.SOCG.2015.842</a>.","short":"P. Franek, M. Krcál, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–856.","ieee":"P. Franek and M. Krcál, “On computability and triviality of well groups,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 842–856.","ista":"Franek P, Krcál M. 2015. On computability and triviality of well groups. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 842–856.","chicago":"Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups,” 34:842–56. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.842\">https://doi.org/10.4230/LIPIcs.SOCG.2015.842</a>."},"month":"06","pubrep_id":"503","quality_controlled":"1","intvolume":"        34","doi":"10.4230/LIPIcs.SOCG.2015.842","date_published":"2015-06-11T00:00:00Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"1408"}]},"status":"public","oa":1,"day":"11"},{"file_date_updated":"2020-07-14T12:44:59Z","publication_status":"published","ddc":["510"],"ec_funded":1,"_id":"1511","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publist_id":"5666","alternative_title":["LIPIcs"],"department":[{"_id":"UlWa"}],"page":"476 - 490","title":"On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"scopus_import":1,"tmp":{"short":"CC BY (4.0)","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)"},"year":"2015","has_accepted_license":"1","volume":"34 ","abstract":[{"lang":"eng","text":"The fact that the complete graph K_5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph K_n embeds in a closed surface M if and only if (n-3)(n-4) is at most 6b_1(M), where b_1(M) is the first Z_2-Betti number of M. On the other hand, Van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of K_{n+1}) embeds in R^{2k} if and only if n is less or equal to 2k+2. Two decades ago, Kuhnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k-1)-connected 2k-manifold with kth Z_2-Betti number b_k only if the following generalized Heawood inequality holds: binom{n-k-1}{k+1} is at most binom{2k+1}{k+1} b_k. This is a common generalization of the case of graphs on surfaces as well as the Van Kampen--Flores theorem. In the spirit of Kuhnel's conjecture, we prove that if the k-skeleton of the n-simplex embeds in a 2k-manifold with kth Z_2-Betti number b_k, then n is at most 2b_k binom{2k+2}{k} + 2k + 5. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k-1)-connected. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T12:38:00Z","file":[{"date_created":"2018-12-12T10:11:18Z","file_size":636735,"relation":"main_file","file_id":"4871","creator":"system","content_type":"application/pdf","access_level":"open_access","checksum":"0945811875351796324189312ca29e9e","date_updated":"2020-07-14T12:44:59Z","file_name":"IST-2016-502-v1+1_42.pdf"}],"author":[{"last_name":"Goaoc","full_name":"Goaoc, Xavier","first_name":"Xavier"},{"first_name":"Isaac","full_name":"Mabillard, Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","last_name":"Mabillard"},{"first_name":"Pavel","last_name":"Paták","full_name":"Paták, Pavel"},{"orcid":"0000-0002-3975-1683","first_name":"Zuzana","last_name":"Patakova","id":"48B57058-F248-11E8-B48F-1D18A9856A87","full_name":"Patakova, Zuzana"},{"first_name":"Martin","full_name":"Tancer, Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","last_name":"Tancer","orcid":"0000-0002-1191-6714"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli"}],"conference":{"location":"Eindhoven, Netherlands","start_date":"2015-06-22","name":"SoCG: Symposium on Computational Geometry","end_date":"2015-06-25"},"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"later_version","id":"610","status":"public"}]},"status":"public","date_published":"2015-06-11T00:00:00Z","doi":"10.4230/LIPIcs.SOCG.2015.476","oa":1,"day":"11","citation":{"ama":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:476-490. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.476\">10.4230/LIPIcs.SOCG.2015.476</a>","mla":"Goaoc, Xavier, et al. <i>On Generalized Heawood Inequalities for Manifolds: A Van Kampen–Flores-Type Nonembeddability Result</i>. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–90, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.476\">10.4230/LIPIcs.SOCG.2015.476</a>.","apa":"Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., &#38; Wagner, U. (2015). On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result (Vol. 34, pp. 476–490). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.476\">https://doi.org/10.4230/LIPIcs.SOCG.2015.476</a>","ieee":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 476–490.","short":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–490.","ista":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2015. On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 476–490.","chicago":"Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A Van Kampen–Flores-Type Nonembeddability Result,” 34:476–90. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.476\">https://doi.org/10.4230/LIPIcs.SOCG.2015.476</a>."},"oa_version":"Published Version","date_created":"2018-12-11T11:52:27Z","type":"conference","acknowledgement":"The work by Z. P. was partially supported by the Charles University Grant SVV-2014-260103. The\r\nwork by Z. P. and M. T. was partially supported by the project CE-ITI (GACR P202/12/G061) of\r\nthe Czech Science Foundation and by the ERC Advanced Grant No. 267165. Part of the research\r\nwork of M. T. was conducted at IST Austria, supported by an IST Fellowship. The work by U.W.\r\nwas partially supported by the Swiss National Science Foundation (grants SNSF-200020-138230 and\r\nSNSF-PP00P2-138948).","quality_controlled":"1","month":"06","pubrep_id":"502"},{"scopus_import":"1","tmp":{"short":"CC BY (4.0)","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)"},"year":"2015","volume":34,"has_accepted_license":"1","article_processing_charge":"No","file":[{"checksum":"e6881df44d87fe0c2529c9f7b2724614","date_updated":"2020-07-14T12:45:00Z","file_name":"IST-2016-501-v1+1_46.pdf","date_created":"2018-12-12T10:10:09Z","file_size":633712,"relation":"main_file","file_id":"4794","creator":"system","content_type":"application/pdf","access_level":"open_access"}],"date_updated":"2024-02-28T12:59:37Z","abstract":[{"text":"We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b,d) such that the following holds. If F is a finite family of subsets of R^d such that the ith reduced Betti number (with Z_2 coefficients in singular homology) of the intersection of any proper subfamily G of F is at most b for every non-negative integer i less or equal to (d-1)/2, then F has Helly number at most h(b,d). These topological conditions are sharp: not controlling any of these first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map from C_*(K) to C_*(R^d). Both techniques are of independent interest.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"conference":{"start_date":"2015-06-22","name":"SoCG: Symposium on Computational Geometry","location":"Eindhoven, Netherlands","end_date":"2015-06-25"},"author":[{"first_name":"Xavier","last_name":"Goaoc","full_name":"Goaoc, Xavier"},{"first_name":"Pavel","last_name":"Paták","full_name":"Paták, Pavel"},{"last_name":"Patakova","full_name":"Patakova, Zuzana","first_name":"Zuzana","orcid":"0000-0002-3975-1683"},{"orcid":"0000-0002-1191-6714","first_name":"Martin","full_name":"Tancer, Martin","last_name":"Tancer"},{"full_name":"Wagner, Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568"}],"ddc":["510"],"publication_status":"published","file_date_updated":"2020-07-14T12:45:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publist_id":"5665","_id":"1512","alternative_title":["LIPIcs"],"department":[{"_id":"UlWa"}],"page":"507 - 521","title":"Bounding Helly numbers via Betti numbers","oa_version":"Submitted Version","citation":{"ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Bounding Helly numbers via Betti numbers,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 507–521.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–521.","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Bounding Helly Numbers via Betti Numbers,” 34:507–21. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.507\">https://doi.org/10.4230/LIPIcs.SOCG.2015.507</a>.","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2015. Bounding Helly numbers via Betti numbers. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 507–521.","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Bounding Helly numbers via Betti numbers. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:507-521. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.507\">10.4230/LIPIcs.SOCG.2015.507</a>","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., &#38; Wagner, U. (2015). Bounding Helly numbers via Betti numbers (Vol. 34, pp. 507–521). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.507\">https://doi.org/10.4230/LIPIcs.SOCG.2015.507</a>","mla":"Goaoc, Xavier, et al. <i>Bounding Helly Numbers via Betti Numbers</i>. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–21, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.507\">10.4230/LIPIcs.SOCG.2015.507</a>."},"date_created":"2018-12-11T11:52:27Z","type":"conference","quality_controlled":"1","acknowledgement":"PP, ZP and MT were partially supported by the Charles University Grant GAUK 421511. ZP was\r\npartially supported by the Charles University Grant SVV-2014-260103. ZP and MT were partially\r\nsupported by the ERC Advanced Grant No. 267165 and by the project CE-ITI (GACR P202/12/G061)\r\nof the Czech Science Foundation. UW was partially supported by the Swiss National Science Foundation\r\n(grants SNSF-200020-138230 and SNSF-PP00P2-138948). Part of this work was done when XG was affiliated with INRIA Nancy Grand-Est and when MT was affiliated with Institutionen för matematik, Kungliga Tekniska Högskolan, then IST Austria.","pubrep_id":"501","month":"01","status":"public","related_material":{"record":[{"id":"424","relation":"later_version","status":"public"}]},"date_published":"2015-01-01T00:00:00Z","doi":"10.4230/LIPIcs.SOCG.2015.507","intvolume":"        34","day":"01","oa":1},{"_id":"1513","ec_funded":1,"publist_id":"5664","publisher":"Oxford University Press","file_date_updated":"2020-07-14T12:45:00Z","publication_status":"published","ddc":["570"],"page":"3259 - 3268","title":"The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"department":[{"_id":"BeVi"}],"has_accepted_license":"1","volume":7,"year":"2015","tmp":{"short":"CC BY (4.0)","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)"},"scopus_import":1,"issue":"12","author":[{"first_name":"Arka","full_name":"Pal, Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306"}],"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order.\r\n\r\nIn this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order. "}],"date_updated":"2021-01-12T06:51:18Z","file":[{"file_size":858027,"date_created":"2018-12-12T10:17:29Z","file_id":"5284","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"system","checksum":"2b56b8c2e2a1d4cc3c9cb8daba26dd9b","file_name":"IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf","date_updated":"2020-07-14T12:45:00Z"}],"article_processing_charge":"No","intvolume":"         7","doi":"10.1093/gbe/evv215","date_published":"2015-12-01T00:00:00Z","status":"public","oa":1,"day":"01","type":"journal_article","date_created":"2018-12-11T11:52:27Z","oa_version":"Published Version","citation":{"mla":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” <i>Genome Biology and Evolution</i>, vol. 7, no. 12, Oxford University Press, 2015, pp. 3259–68, doi:<a href=\"https://doi.org/10.1093/gbe/evv215\">10.1093/gbe/evv215</a>.","apa":"Pal, A., &#38; Vicoso, B. (2015). The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evv215\">https://doi.org/10.1093/gbe/evv215</a>","ama":"Pal A, Vicoso B. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. <i>Genome Biology and Evolution</i>. 2015;7(12):3259-3268. doi:<a href=\"https://doi.org/10.1093/gbe/evv215\">10.1093/gbe/evv215</a>","chicago":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/gbe/evv215\">https://doi.org/10.1093/gbe/evv215</a>.","ista":"Pal A, Vicoso B. 2015. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. 7(12), 3259–3268.","ieee":"A. Pal and B. Vicoso, “The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression,” <i>Genome Biology and Evolution</i>, vol. 7, no. 12. Oxford University Press, pp. 3259–3268, 2015.","short":"A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268."},"publication":"Genome Biology and Evolution","month":"12","pubrep_id":"496","quality_controlled":"1"},{"oa_version":"Published Version","citation":{"ista":"Erbar M, Maas J, Renger M. 2015. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 20, 89.","chicago":"Erbar, Matthias, Jan Maas, and Michiel Renger. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics, 2015. <a href=\"https://doi.org/10.1214/ECP.v20-4315\">https://doi.org/10.1214/ECP.v20-4315</a>.","ieee":"M. Erbar, J. Maas, and M. Renger, “From large deviations to Wasserstein gradient flows in multiple dimensions,” <i>Electronic Communications in Probability</i>, vol. 20. Institute of Mathematical Statistics, 2015.","short":"M. Erbar, J. Maas, M. Renger, Electronic Communications in Probability 20 (2015).","apa":"Erbar, M., Maas, J., &#38; Renger, M. (2015). From large deviations to Wasserstein gradient flows in multiple dimensions. <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/ECP.v20-4315\">https://doi.org/10.1214/ECP.v20-4315</a>","mla":"Erbar, Matthias, et al. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” <i>Electronic Communications in Probability</i>, vol. 20, 89, Institute of Mathematical Statistics, 2015, doi:<a href=\"https://doi.org/10.1214/ECP.v20-4315\">10.1214/ECP.v20-4315</a>.","ama":"Erbar M, Maas J, Renger M. From large deviations to Wasserstein gradient flows in multiple dimensions. <i>Electronic Communications in Probability</i>. 2015;20. doi:<a href=\"https://doi.org/10.1214/ECP.v20-4315\">10.1214/ECP.v20-4315</a>"},"date_created":"2018-12-11T11:52:29Z","publication":"Electronic Communications in Probability","type":"journal_article","quality_controlled":"1","month":"11","pubrep_id":"494","status":"public","article_number":"89","doi":"10.1214/ECP.v20-4315","date_published":"2015-11-29T00:00:00Z","intvolume":"        20","oa":1,"day":"29","tmp":{"short":"CC BY (4.0)","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)"},"scopus_import":1,"year":"2015","has_accepted_license":"1","volume":20,"abstract":[{"lang":"eng","text":"We study the large deviation rate functional for the empirical distribution of independent Brownian particles with drift. In one dimension, it has been shown by Adams, Dirr, Peletier and Zimmer that this functional is asymptotically equivalent (in the sense of Γ-convergence) to the Jordan-Kinderlehrer-Otto functional arising in the Wasserstein gradient flow structure of the Fokker-Planck equation. In higher dimensions, part of this statement (the lower bound) has been recently proved by Duong, Laschos and Renger, but the upper bound remained open, since the proof of Duong et al relies on regularity properties of optimal transport maps that are restricted to one dimension. In this note we present a new proof of the upper bound, thereby generalising the result of Adams et al to arbitrary dimensions.\r\n"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"4828","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"system","file_size":230525,"date_created":"2018-12-12T10:10:39Z","checksum":"135741c17d3e1547ca696b6fbdcd559c","file_name":"IST-2016-494-v1+1_4315-23820-1-PB.pdf","date_updated":"2020-07-14T12:45:00Z"}],"date_updated":"2021-01-12T06:51:19Z","author":[{"last_name":"Erbar","full_name":"Erbar, Matthias","first_name":"Matthias"},{"full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan","orcid":"0000-0002-0845-1338"},{"first_name":"Michiel","full_name":"Renger, Michiel","last_name":"Renger"}],"language":[{"iso":"eng"}],"publication_status":"published","file_date_updated":"2020-07-14T12:45:00Z","ddc":["519"],"_id":"1517","publisher":"Institute of Mathematical Statistics","publist_id":"5660","department":[{"_id":"JaMa"}],"title":"From large deviations to Wasserstein gradient flows in multiple dimensions"},{"ddc":["570"],"file_date_updated":"2020-07-14T12:45:00Z","publication_status":"published","ec_funded":1,"_id":"1519","publisher":"Wiley","publist_id":"5656","department":[{"_id":"NiBa"}],"page":"1101 - 1112","title":"The interpretation of selection coefficients","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"issue":"5","scopus_import":1,"year":"2015","has_accepted_license":"1","volume":69,"abstract":[{"text":"Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under &quot;direct&quot; versus &quot;indirect&quot; selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2018-12-12T10:10:34Z","file_size":188872,"relation":"main_file","file_id":"4822","creator":"system","content_type":"application/pdf","access_level":"open_access","checksum":"fd8d23f476bc194419929b72ca265c02","date_updated":"2020-07-14T12:45:00Z","file_name":"IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf"},{"creator":"system","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"4823","date_created":"2018-12-12T10:10:35Z","file_size":577415,"date_updated":"2020-07-14T12:45:00Z","file_name":"IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf","checksum":"b774911e70044641d556e258efcb52ef"}],"date_updated":"2021-01-12T06:51:20Z","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Maria","last_name":"Servedio","full_name":"Servedio, Maria"}],"language":[{"iso":"eng"}],"status":"public","doi":"10.1111/evo.12641","date_published":"2015-03-19T00:00:00Z","intvolume":"        69","oa":1,"day":"19","citation":{"mla":"Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.” <i>Evolution</i>, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:<a href=\"https://doi.org/10.1111/evo.12641\">10.1111/evo.12641</a>.","apa":"Barton, N. H., &#38; Servedio, M. (2015). The interpretation of selection coefficients. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.12641\">https://doi.org/10.1111/evo.12641</a>","ama":"Barton NH, Servedio M. The interpretation of selection coefficients. <i>Evolution</i>. 2015;69(5):1101-1112. doi:<a href=\"https://doi.org/10.1111/evo.12641\">10.1111/evo.12641</a>","chicago":"Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection Coefficients.” <i>Evolution</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/evo.12641\">https://doi.org/10.1111/evo.12641</a>.","ista":"Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112.","short":"N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.","ieee":"N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” <i>Evolution</i>, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015."},"oa_version":"Submitted Version","date_created":"2018-12-11T11:52:29Z","publication":"Evolution","type":"journal_article","quality_controlled":"1","pubrep_id":"560","month":"03"},{"intvolume":"        68","doi":"10.5281/zenodo.33178","date_published":"2015-11-12T00:00:00Z","status":"public","day":"12","oa":1,"type":"journal_article","publication":"VÖB Mitteilungen","date_created":"2018-12-11T11:52:31Z","citation":{"ama":"Bauer B, Blechl G, Bock C, et al. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. <i>VÖB Mitteilungen</i>. 2015;68(3):580-607. doi:<a href=\"https://doi.org/10.5281/zenodo.33178\">10.5281/zenodo.33178</a>","mla":"Bauer, Bruno, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” <i>VÖB Mitteilungen</i>, vol. 68, no. 3, Verein Österreichischer Bibliothekare, 2015, pp. 580–607, doi:<a href=\"https://doi.org/10.5281/zenodo.33178\">10.5281/zenodo.33178</a>.","apa":"Bauer, B., Blechl, G., Bock, C., Danowski, P., Ferus, A., Graschopf, A., … Welzig, E. (2015). Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. <i>VÖB Mitteilungen</i>. Verein Österreichischer Bibliothekare. <a href=\"https://doi.org/10.5281/zenodo.33178\">https://doi.org/10.5281/zenodo.33178</a>","ieee":"B. Bauer <i>et al.</i>, “Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA,” <i>VÖB Mitteilungen</i>, vol. 68, no. 3. Verein Österreichischer Bibliothekare, pp. 580–607, 2015.","short":"B. Bauer, G. Blechl, C. Bock, P. Danowski, A. Ferus, A. Graschopf, T. König, K. Mayer, F. Reckling, K. Rieck, P. Seitz, H. Stöger, E. Welzig, VÖB Mitteilungen 68 (2015) 580–607.","ista":"Bauer B, Blechl G, Bock C, Danowski P, Ferus A, Graschopf A, König T, Mayer K, Reckling F, Rieck K, Seitz P, Stöger H, Welzig E. 2015. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 68(3), 580–607.","chicago":"Bauer, Bruno, Guido Blechl, Christoph Bock, Patrick Danowski, Andreas Ferus, Anton Graschopf, Thomas König, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” <i>VÖB Mitteilungen</i>. Verein Österreichischer Bibliothekare, 2015. <a href=\"https://doi.org/10.5281/zenodo.33178\">https://doi.org/10.5281/zenodo.33178</a>."},"oa_version":"Published Version","pubrep_id":"720","month":"11","quality_controlled":"1","publist_id":"5648","article_type":"original","publisher":"Verein Österreichischer Bibliothekare","_id":"1525","file_date_updated":"2020-07-14T12:45:00Z","ddc":["020"],"publication_status":"published","page":"580 - 607","title":"Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA","department":[{"_id":"E-Lib"}],"volume":68,"has_accepted_license":"1","year":"2015","tmp":{"short":"CC BY (4.0)","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)"},"issue":"3","scopus_import":1,"language":[{"iso":"eng"}],"author":[{"first_name":"Bruno","last_name":"Bauer","full_name":"Bauer, Bruno"},{"last_name":"Blechl","full_name":"Blechl, Guido","first_name":"Guido"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","last_name":"Danowski","full_name":"Danowski, Patrick","first_name":"Patrick","orcid":"0000-0002-6026-4409"},{"first_name":"Andreas","last_name":"Ferus","full_name":"Ferus, Andreas"},{"last_name":"Graschopf","full_name":"Graschopf, Anton","first_name":"Anton"},{"last_name":"König","full_name":"König, Thomas","first_name":"Thomas"},{"first_name":"Katja","last_name":"Mayer","full_name":"Mayer, Katja"},{"last_name":"Reckling","full_name":"Reckling, Falk","first_name":"Falk"},{"last_name":"Rieck","full_name":"Rieck, Katharina","first_name":"Katharina"},{"first_name":"Peter","full_name":"Seitz, Peter","last_name":"Seitz"},{"full_name":"Stöger, Herwig","last_name":"Stöger","first_name":"Herwig"},{"first_name":"Elvira","full_name":"Welzig, Elvira","last_name":"Welzig"}],"date_updated":"2021-01-12T06:51:22Z","file":[{"date_updated":"2020-07-14T12:45:00Z","file_name":"IST-2016-720-v1+1_OANA_OA-Empfehlungen_12-11-2015.pdf","checksum":"a495fe253bbc7615b1d60e9e85c94408","creator":"system","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5317","date_created":"2018-12-12T10:17:59Z","file_size":931707}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Based on 16 recommendations, efforts should be made to achieve the following goal: By 2025, all scholarly publication activity in Austria should be Open Access. In other words, the final versions of all scholarly publications resulting from the support of public resources must be freely accessible on the Internet without delay (Gold Open Access). The resources required to meet this obligation shall be provided to the authors, or the cost of the publication venues shall be borne directly by the research organisations."}]},{"type":"journal_article","publication":"Nature Communications","citation":{"mla":"Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” <i>Nature Communications</i>, vol. 6, 8822, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms9822\">10.1038/ncomms9822</a>.","apa":"Wang, H., Yang, K., Zou, J., Zhu, L., Xie, Z., Morita, M., … Le, J. (2015). Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms9822\">https://doi.org/10.1038/ncomms9822</a>","ama":"Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms9822\">10.1038/ncomms9822</a>","ista":"Wang H, Yang K, Zou J, Zhu L, Xie Z, Morita M, Tasaka M, Friml J, Grotewold E, Beeckman T, Vanneste S, Sack F, Le J. 2015. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 6, 8822.","chicago":"Wang, Hongzhe, Kezhen Yang, Junjie Zou, Lingling Zhu, Zidian Xie, Miyoterao Morita, Masao Tasaka, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” <i>Nature Communications</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ncomms9822\">https://doi.org/10.1038/ncomms9822</a>.","short":"H. Wang, K. Yang, J. Zou, L. Zhu, Z. Xie, M. Morita, M. Tasaka, J. Friml, E. Grotewold, T. Beeckman, S. Vanneste, F. Sack, J. Le, Nature Communications 6 (2015).","ieee":"H. Wang <i>et al.</i>, “Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism,” <i>Nature Communications</i>, vol. 6. Nature Publishing Group, 2015."},"oa_version":"Published Version","date_created":"2018-12-11T11:52:34Z","pubrep_id":"485","month":"11","quality_controlled":"1","date_published":"2015-11-18T00:00:00Z","doi":"10.1038/ncomms9822","intvolume":"         6","article_number":"8822","status":"public","day":"18","oa":1,"volume":6,"has_accepted_license":"1","scopus_import":1,"tmp":{"short":"CC BY (4.0)","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)"},"year":"2015","language":[{"iso":"eng"}],"author":[{"full_name":"Wang, Hongzhe","last_name":"Wang","first_name":"Hongzhe"},{"first_name":"Kezhen","last_name":"Yang","full_name":"Yang, Kezhen"},{"last_name":"Zou","full_name":"Zou, Junjie","first_name":"Junjie"},{"last_name":"Zhu","full_name":"Zhu, Lingling","first_name":"Lingling"},{"last_name":"Xie","full_name":"Xie, Zidian","first_name":"Zidian"},{"first_name":"Miyoterao","full_name":"Morita, Miyoterao","last_name":"Morita"},{"first_name":"Masao","last_name":"Tasaka","full_name":"Tasaka, Masao"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"Erich","full_name":"Grotewold, Erich","last_name":"Grotewold"},{"last_name":"Beeckman","full_name":"Beeckman, Tom","first_name":"Tom"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"first_name":"Fred","full_name":"Sack, Fred","last_name":"Sack"},{"last_name":"Le","full_name":"Le, Jie","first_name":"Jie"}],"date_updated":"2021-01-12T06:51:26Z","file":[{"access_level":"open_access","content_type":"application/pdf","creator":"system","file_id":"5259","relation":"main_file","file_size":1852268,"date_created":"2018-12-12T10:17:07Z","file_name":"IST-2016-485-v1+1_ncomms9822.pdf","date_updated":"2020-07-14T12:45:01Z","checksum":"3c06735fc7cd7e482ca830cbd26001bf"}],"abstract":[{"lang":"eng","text":"PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Publishing Group","publist_id":"5637","ec_funded":1,"_id":"1534","file_date_updated":"2020-07-14T12:45:01Z","ddc":["570"],"publication_status":"published","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"title":"Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism","department":[{"_id":"JiFr"}]},{"status":"public","date_published":"2015-10-01T00:00:00Z","doi":"10.2174/1874467208666150507105443","intvolume":"         8","oa":1,"external_id":{"pmid":["25966692"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/"}],"day":"01","citation":{"apa":"Vandael, D. H., Marcantoni, A., &#38; Carbone, E. (2015). Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. <i>Current Molecular Pharmacology</i>. Bentham Science Publishers. <a href=\"https://doi.org/10.2174/1874467208666150507105443\">https://doi.org/10.2174/1874467208666150507105443</a>","mla":"Vandael, David H., et al. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” <i>Current Molecular Pharmacology</i>, vol. 8, no. 2, Bentham Science Publishers, 2015, pp. 149–61, doi:<a href=\"https://doi.org/10.2174/1874467208666150507105443\">10.2174/1874467208666150507105443</a>.","ama":"Vandael DH, Marcantoni A, Carbone E. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. <i>Current Molecular Pharmacology</i>. 2015;8(2):149-161. doi:<a href=\"https://doi.org/10.2174/1874467208666150507105443\">10.2174/1874467208666150507105443</a>","chicago":"Vandael, David H, Andrea Marcantoni, and Emilio Carbone. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” <i>Current Molecular Pharmacology</i>. Bentham Science Publishers, 2015. <a href=\"https://doi.org/10.2174/1874467208666150507105443\">https://doi.org/10.2174/1874467208666150507105443</a>.","ista":"Vandael DH, Marcantoni A, Carbone E. 2015. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 8(2), 149–161.","ieee":"D. H. Vandael, A. Marcantoni, and E. Carbone, “Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells,” <i>Current Molecular Pharmacology</i>, vol. 8, no. 2. Bentham Science Publishers, pp. 149–161, 2015.","short":"D.H. Vandael, A. Marcantoni, E. Carbone, Current Molecular Pharmacology 8 (2015) 149–161."},"oa_version":"Submitted Version","date_created":"2018-12-11T11:52:35Z","publication":"Current Molecular Pharmacology","type":"journal_article","acknowledgement":"This work was supported by the Italian MIUR (PRIN 2010/2011 project 2010JFYFY2) and the University of Torino.","quality_controlled":"1","month":"10","publication_status":"published","_id":"1535","publisher":"Bentham Science Publishers","publist_id":"5636","article_type":"original","department":[{"_id":"PeJo"}],"title":"Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells","page":"149 - 161","issue":"2","scopus_import":1,"year":"2015","volume":8,"abstract":[{"lang":"eng","text":"Neuronal and neuroendocrine L-type calcium channels (Cav1.2, Cav1.3) open readily at relatively low membrane potentials and allow Ca2+ to enter the cells near resting potentials. In this way, Cav1.2 and Cav1.3 shape the action potential waveform, contribute to gene expression, synaptic plasticity, neuronal differentiation, hormone secretion and pacemaker activity. In the chromaffin cells (CCs) of the adrenal medulla, Cav1.3 is highly expressed and is shown to support most of the pacemaking current that sustains action potential (AP) firings and part of the catecholamine secretion. Cav1.3 forms Ca2+-nanodomains with the fast inactivating BK channels and drives the resting SK currents. These latter set the inter-spike interval duration between consecutive spikes during spontaneous firing and the rate of spike adaptation during sustained depolarizations. Cav1.3 plays also a primary role in the switch from “tonic” to “burst” firing that occurs in mouse CCs when either the availability of voltage-gated Na channels (Nav) is reduced or the β2 subunit featuring the fast inactivating BK channels is deleted. Here, we discuss the functional role of these “neuronlike” firing modes in CCs and how Cav1.3 contributes to them. The open issue is to understand how these novel firing patterns are adapted to regulate the quantity of circulating catecholamines during resting condition or in response to acute and chronic stress."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2021-01-12T06:51:26Z","author":[{"orcid":"0000-0001-7577-1676","last_name":"Vandael","full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H"},{"first_name":"Andrea","last_name":"Marcantoni","full_name":"Marcantoni, Andrea"},{"first_name":"Emilio","last_name":"Carbone","full_name":"Carbone, Emilio"}],"pmid":1,"language":[{"iso":"eng"}]},{"title":"Cortical contractility triggers a stochastic switch to fast amoeboid cell motility","page":"673 - 685","project":[{"grant_number":"T 560-B17","_id":"2529486C-B435-11E9-9278-68D0E5697425","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","call_identifier":"FWF"},{"grant_number":"I 812-B12","call_identifier":"FWF","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","_id":"2527D5CC-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"CaHe"},{"_id":"MiSi"}],"_id":"1537","publist_id":"5634","publisher":"Cell Press","ddc":["570"],"publication_status":"published","file_date_updated":"2020-07-14T12:45:01Z","author":[{"orcid":"0000-0003-4088-8633","first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","full_name":"Ruprecht, Verena","last_name":"Ruprecht"},{"last_name":"Wieser","full_name":"Wieser, Stefan","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","orcid":"0000-0002-2670-2217"},{"last_name":"Callan Jones","full_name":"Callan Jones, Andrew","first_name":"Andrew"},{"id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","last_name":"Smutny","full_name":"Smutny, Michael","first_name":"Michael","orcid":"0000-0002-5920-9090"},{"first_name":"Hitoshi","full_name":"Morita, Hitoshi","last_name":"Morita","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Keisuke","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","full_name":"Sako, Keisuke","last_name":"Sako","orcid":"0000-0002-6453-8075"},{"orcid":"0000-0003-2676-3367","first_name":"Vanessa","full_name":"Barone, Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ritsch Marte","full_name":"Ritsch Marte, Monika","first_name":"Monika"},{"first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179"},{"first_name":"Raphaël","full_name":"Voituriez, Raphaël","last_name":"Voituriez"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"3D amoeboid cell migration is central to many developmental and disease-related processes such as cancer metastasis. Here, we identify a unique prototypic amoeboid cell migration mode in early zebrafish embryos, termed stable-bleb migration. Stable-bleb cells display an invariant polarized balloon-like shape with exceptional migration speed and persistence. Progenitor cells can be reversibly transformed into stable-bleb cells irrespective of their primary fate and motile characteristics by increasing myosin II activity through biochemical or mechanical stimuli. Using a combination of theory and experiments, we show that, in stable-bleb cells, cortical contractility fluctuations trigger a stochastic switch into amoeboid motility, and a positive feedback between cortical flows and gradients in contractility maintains stable-bleb cell polarization. We further show that rearward cortical flows drive stable-bleb cell migration in various adhesive and non-adhesive environments, unraveling a highly versatile amoeboid migration phenotype."}],"date_updated":"2023-09-07T12:05:08Z","file":[{"file_id":"5003","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"system","file_size":4362653,"date_created":"2018-12-12T10:13:21Z","checksum":"228d3edf40627d897b3875088a0ac51f","file_name":"IST-2016-484-v1+1_1-s2.0-S0092867415000094-main.pdf","date_updated":"2020-07-14T12:45:01Z"}],"has_accepted_license":"1","volume":160,"acknowledged_ssus":[{"_id":"SSU"}],"year":"2015","tmp":{"short":"CC BY (4.0)","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)"},"issue":"4","scopus_import":1,"oa":1,"day":"12","intvolume":"       160","date_published":"2015-02-12T00:00:00Z","doi":"10.1016/j.cell.2015.01.008","related_material":{"record":[{"id":"961","relation":"dissertation_contains","status":"public"}]},"status":"public","month":"02","pubrep_id":"484","acknowledgement":"We would like to thank R. Hausschild and E. Papusheva for technical assistance and the service facilities at the IST Austria for continuous support. The caRhoA plasmid was a kind gift of T. Kudoh and A. Takesono. We thank M. Piel and E. Paluch for exchanging unpublished data. ","quality_controlled":"1","type":"journal_article","date_created":"2018-12-11T11:52:35Z","citation":{"short":"V. Ruprecht, S. Wieser, A. Callan Jones, M. Smutny, H. Morita, K. Sako, V. Barone, M. Ritsch Marte, M.K. Sixt, R. Voituriez, C.-P.J. Heisenberg, Cell 160 (2015) 673–685.","ieee":"V. Ruprecht <i>et al.</i>, “Cortical contractility triggers a stochastic switch to fast amoeboid cell motility,” <i>Cell</i>, vol. 160, no. 4. Cell Press, pp. 673–685, 2015.","chicago":"Ruprecht, Verena, Stefan Wieser, Andrew Callan Jones, Michael Smutny, Hitoshi Morita, Keisuke Sako, Vanessa Barone, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” <i>Cell</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">https://doi.org/10.1016/j.cell.2015.01.008</a>.","ista":"Ruprecht V, Wieser S, Callan Jones A, Smutny M, Morita H, Sako K, Barone V, Ritsch Marte M, Sixt MK, Voituriez R, Heisenberg C-PJ. 2015. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 160(4), 673–685.","ama":"Ruprecht V, Wieser S, Callan Jones A, et al. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. <i>Cell</i>. 2015;160(4):673-685. doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">10.1016/j.cell.2015.01.008</a>","apa":"Ruprecht, V., Wieser, S., Callan Jones, A., Smutny, M., Morita, H., Sako, K., … Heisenberg, C.-P. J. (2015). Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">https://doi.org/10.1016/j.cell.2015.01.008</a>","mla":"Ruprecht, Verena, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” <i>Cell</i>, vol. 160, no. 4, Cell Press, 2015, pp. 673–85, doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">10.1016/j.cell.2015.01.008</a>."},"oa_version":"Published Version","publication":"Cell"},{"status":"public","date_published":"2015-06-30T00:00:00Z","doi":"10.1073/pnas.1423947112","intvolume":"       112","oa":1,"external_id":{"pmid":["26085136"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/","open_access":"1"}],"day":"30","oa_version":"Submitted Version","citation":{"ieee":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative experiment design guides the characterization of a light-inducible gene expression circuit,” <i>PNAS</i>, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153, 2015.","short":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153.","ista":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 112(26), 8148–8153.","chicago":"Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash, and John Lygeros. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1423947112\">https://doi.org/10.1073/pnas.1423947112</a>.","ama":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. <i>PNAS</i>. 2015;112(26):8148-8153. doi:<a href=\"https://doi.org/10.1073/pnas.1423947112\">10.1073/pnas.1423947112</a>","mla":"Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” <i>PNAS</i>, vol. 112, no. 26, National Academy of Sciences, 2015, pp. 8148–53, doi:<a href=\"https://doi.org/10.1073/pnas.1423947112\">10.1073/pnas.1423947112</a>.","apa":"Ruess, J., Parise, F., Milias Argeitis, A., Khammash, M., &#38; Lygeros, J. (2015). Iterative experiment design guides the characterization of a light-inducible gene expression circuit. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1423947112\">https://doi.org/10.1073/pnas.1423947112</a>"},"date_created":"2018-12-11T11:52:36Z","publication":"PNAS","type":"journal_article","acknowledgement":"J.R., F.P., and J.L. acknowledge support from the European Commission under the Network of Excellence HYCON2 (highly-complex and networked control systems) and SystemsX.ch under the SignalX Project. J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme FP7/2007-2013 under REA (Research Executive Agency) Grant 291734. M.K. acknowledges support from Human Frontier Science Program Grant RP0061/2011 (www.hfsp.org). ","quality_controlled":"1","month":"06","publication_status":"published","ec_funded":1,"_id":"1538","publisher":"National Academy of Sciences","publist_id":"5633","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"title":"Iterative experiment design guides the characterization of a light-inducible gene expression circuit","page":"8148 - 8153","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"scopus_import":1,"issue":"26","year":"2015","volume":112,"abstract":[{"lang":"eng","text":"Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:27Z","author":[{"orcid":"0000-0003-1615-3282","last_name":"Ruess","full_name":"Ruess, Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob"},{"first_name":"Francesca","full_name":"Parise, Francesca","last_name":"Parise"},{"full_name":"Milias Argeitis, Andreas","last_name":"Milias Argeitis","first_name":"Andreas"},{"full_name":"Khammash, Mustafa","last_name":"Khammash","first_name":"Mustafa"},{"first_name":"John","last_name":"Lygeros","full_name":"Lygeros, John"}],"pmid":1,"language":[{"iso":"eng"}]},{"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211"},{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"title":"Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space","publication_status":"published","file_date_updated":"2020-07-14T12:45:01Z","ddc":["000"],"publist_id":"5632","publisher":"American Institute of Physics","_id":"1539","ec_funded":1,"date_updated":"2021-01-12T06:51:28Z","file":[{"file_size":605355,"date_created":"2018-12-12T10:07:43Z","file_id":"4641","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"system","checksum":"838657118ae286463a2b7737319f35ce","file_name":"IST-2016-593-v1+1_Minimal_moment_equations.pdf","date_updated":"2020-07-14T12:45:01Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space. ","lang":"eng"}],"language":[{"iso":"eng"}],"author":[{"orcid":"0000-0003-1615-3282","first_name":"Jakob","last_name":"Ruess","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob"}],"year":"2015","scopus_import":1,"issue":"24","volume":143,"has_accepted_license":"1","day":"22","oa":1,"status":"public","intvolume":"       143","date_published":"2015-12-22T00:00:00Z","doi":"10.1063/1.4937937","article_number":"244103","quality_controlled":"1","month":"12","pubrep_id":"593","publication":"Journal of Chemical Physics","date_created":"2018-12-11T11:52:36Z","citation":{"ama":"Ruess J. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. <i>Journal of Chemical Physics</i>. 2015;143(24). doi:<a href=\"https://doi.org/10.1063/1.4937937\">10.1063/1.4937937</a>","mla":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” <i>Journal of Chemical Physics</i>, vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi:<a href=\"https://doi.org/10.1063/1.4937937\">10.1063/1.4937937</a>.","apa":"Ruess, J. (2015). Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. <i>Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4937937\">https://doi.org/10.1063/1.4937937</a>","short":"J. Ruess, Journal of Chemical Physics 143 (2015).","ieee":"J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space,” <i>Journal of Chemical Physics</i>, vol. 143, no. 24. American Institute of Physics, 2015.","chicago":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” <i>Journal of Chemical Physics</i>. American Institute of Physics, 2015. <a href=\"https://doi.org/10.1063/1.4937937\">https://doi.org/10.1063/1.4937937</a>.","ista":"Ruess J. 2015. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 143(24), 244103."},"oa_version":"Published Version","type":"journal_article"},{"status":"public","intvolume":"       383","doi":"10.1016/j.jtbi.2015.07.011","date_published":"2015-10-21T00:00:00Z","oa":1,"day":"21","date_created":"2018-12-11T11:52:37Z","citation":{"ieee":"T. Paixao <i>et al.</i>, “Toward a unifying framework for evolutionary processes,” <i> Journal of Theoretical Biology</i>, vol. 383. Elsevier, pp. 28–43, 2015.","short":"T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova,  Journal of Theoretical Biology 383 (2015) 28–43.","chicago":"Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” <i> Journal of Theoretical Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>.","ista":"Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes.  Journal of Theoretical Biology. 383, 28–43.","ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. <i> Journal of Theoretical Biology</i>. 2015;383:28-43. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>","apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. <i> Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>","mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” <i> Journal of Theoretical Biology</i>, vol. 383, Elsevier, 2015, pp. 28–43, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>."},"oa_version":"Published Version","publication":" Journal of Theoretical Biology","type":"journal_article","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","quality_controlled":"1","month":"10","pubrep_id":"483","ddc":["570"],"publication_status":"published","file_date_updated":"2020-07-14T12:45:01Z","_id":"1542","ec_funded":1,"publist_id":"5629","publisher":"Elsevier","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"title":"Toward a unifying framework for evolutionary processes","page":"28 - 43","project":[{"grant_number":"618091","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"year":"2015","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"scopus_import":1,"has_accepted_license":"1","volume":383,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. ","lang":"eng"}],"file":[{"checksum":"33b60ecfea60764756a9ee9df5eb65ca","file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","date_updated":"2020-07-14T12:45:01Z","file_size":595307,"date_created":"2018-12-12T10:16:53Z","file_id":"5244","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"system"}],"date_updated":"2021-01-12T06:51:29Z","author":[{"first_name":"Tiago","full_name":"Paixao, Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953"},{"first_name":"Golnaz","last_name":"Badkobeh","full_name":"Badkobeh, Golnaz"},{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Doğan","full_name":"Çörüş, Doğan","last_name":"Çörüş"},{"full_name":"Dang, Duccuong","last_name":"Dang","first_name":"Duccuong"},{"first_name":"Tobias","full_name":"Friedrich, Tobias","last_name":"Friedrich"},{"first_name":"Per","last_name":"Lehre","full_name":"Lehre, Per"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"first_name":"Andrew","last_name":"Sutton","full_name":"Sutton, Andrew"},{"orcid":"0000-0002-6873-2967","first_name":"Barbora","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova"}],"language":[{"iso":"eng"}]},{"oa":1,"external_id":{"pmid":["25997350"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/","open_access":"1"}],"day":"08","doi":"10.1016/bs.mcb.2015.01.007","date_published":"2015-04-08T00:00:00Z","intvolume":"       128","status":"public","month":"04","quality_controlled":"1","type":"book_chapter","citation":{"ieee":"P. Nguyen, C. Field, A. Groen, T. Mitchison, and M. Loose, “Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins,” in <i>Building a Cell from its Components Parts</i>, vol. 128, Academic Press, 2015, pp. 223–241.","short":"P. Nguyen, C. Field, A. Groen, T. Mitchison, M. Loose, in:, Building a Cell from Its Components Parts, Academic Press, 2015, pp. 223–241.","ista":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. 2015.Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from its Components Parts. vol. 128, 223–241.","chicago":"Nguyen, Phuong, Christine Field, Aaron Groen, Timothy Mitchison, and Martin Loose. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” In <i>Building a Cell from Its Components Parts</i>, 128:223–41. Academic Press, 2015. <a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">https://doi.org/10.1016/bs.mcb.2015.01.007</a>.","ama":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: <i>Building a Cell from Its Components Parts</i>. Vol 128. Academic Press; 2015:223-241. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">10.1016/bs.mcb.2015.01.007</a>","mla":"Nguyen, Phuong, et al. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” <i>Building a Cell from Its Components Parts</i>, vol. 128, Academic Press, 2015, pp. 223–41, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">10.1016/bs.mcb.2015.01.007</a>.","apa":"Nguyen, P., Field, C., Groen, A., Mitchison, T., &#38; Loose, M. (2015). Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In <i>Building a Cell from its Components Parts</i> (Vol. 128, pp. 223–241). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">https://doi.org/10.1016/bs.mcb.2015.01.007</a>"},"oa_version":"Submitted Version","date_created":"2018-12-11T11:52:38Z","publication":"Building a Cell from its Components Parts","title":"Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins","page":"223 - 241","department":[{"_id":"MaLo"}],"_id":"1544","publisher":"Academic Press","publist_id":"5627","publication_status":"published","author":[{"last_name":"Nguyen","full_name":"Nguyen, Phuong","first_name":"Phuong"},{"first_name":"Christine","full_name":"Field, Christine","last_name":"Field"},{"first_name":"Aaron","full_name":"Groen, Aaron","last_name":"Groen"},{"first_name":"Timothy","full_name":"Mitchison, Timothy","last_name":"Mitchison"},{"first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724"}],"pmid":1,"language":[{"iso":"eng"}],"abstract":[{"text":"Cell division in prokaryotes and eukaryotes is commonly initiated by the well-controlled binding of proteins to the cytoplasmic side of the cell membrane. However, a precise characterization of the spatiotemporal dynamics of membrane-bound proteins is often difficult to achieve in vivo. Here, we present protocols for the use of supported lipid bilayers to rebuild the cytokinetic machineries of cells with greatly different dimensions: the bacterium Escherichia coli and eggs of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence microscopy, these experimental setups allow for precise quantitative analyses of membrane-bound proteins. The protocols described to obtain glass-supported membranes from bacterial and vertebrate lipids can be used as starting points for other reconstitution experiments. We believe that similar biochemical assays will be instrumental to study the biochemistry and biophysics underlying a variety of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:30Z","volume":128,"scopus_import":1,"year":"2015"},{"oa":1,"day":"07","status":"public","intvolume":"        85","doi":"10.1016/j.neuron.2014.11.019","date_published":"2015-01-07T00:00:00Z","acknowledgement":"This work was supported by the Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency to T.T. and R.S.; by the funding provided by Okinawa Institute of Science and Technology (OIST) to T.T. and Y.N.; by JSPS Core-to-Core Program, A. Advanced Networks to T.T.; by the Grant-in-Aid for Young Scientists from the Japanese Ministry of Education, Culture, Sports, Science and Technology (#23700474) to Y.N.; by the Centre National de la Recherche Scientifique through the Actions Thematiques et Initatives sur Programme, Fondation Fyssen, Fondation pour la Recherche Medicale, Federation pour la Recherche sur le Cerveau, Agence Nationale de la Recherche (ANR-2007-Neuro-008-01 and ANR-2010-BLAN-1411-01) to D.D. and Y.N.; and by the European Commission Coordination Action ENINET (LSHM-CT-2005-19063) to D.D. and R.A.S. R.A.S. and J.S.R. were funded by Wellcome Trust Senior (064413) and Principal (095667) Research Fellowship and an ERC advance grant (294667) to RAS.","quality_controlled":"1","month":"01","pubrep_id":"482","date_created":"2018-12-11T11:52:39Z","citation":{"ama":"Nakamura Y, Harada H, Kamasawa N, et al. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. <i>Neuron</i>. 2015;85(1):145-158. doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">10.1016/j.neuron.2014.11.019</a>","apa":"Nakamura, Y., Harada, H., Kamasawa, N., Matsui, K., Rothman, J., Shigemoto, R., … Takahashi, T. (2015). Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">https://doi.org/10.1016/j.neuron.2014.11.019</a>","mla":"Nakamura, Yukihiro, et al. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” <i>Neuron</i>, vol. 85, no. 1, Elsevier, 2015, pp. 145–58, doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">10.1016/j.neuron.2014.11.019</a>.","ieee":"Y. Nakamura <i>et al.</i>, “Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development,” <i>Neuron</i>, vol. 85, no. 1. Elsevier, pp. 145–158, 2015.","short":"Y. Nakamura, H. Harada, N. Kamasawa, K. Matsui, J. Rothman, R. Shigemoto, R.A. Silver, D. Digregorio, T. Takahashi, Neuron 85 (2015) 145–158.","ista":"Nakamura Y, Harada H, Kamasawa N, Matsui K, Rothman J, Shigemoto R, Silver RA, Digregorio D, Takahashi T. 2015. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 85(1), 145–158.","chicago":"Nakamura, Yukihiro, Harumi Harada, Naomi Kamasawa, Ko Matsui, Jason Rothman, Ryuichi Shigemoto, R Angus Silver, David Digregorio, and Tomoyuki Takahashi. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” <i>Neuron</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">https://doi.org/10.1016/j.neuron.2014.11.019</a>."},"oa_version":"Published Version","publication":"Neuron","type":"journal_article","department":[{"_id":"RySh"}],"page":"145 - 158","title":"Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development","ddc":["570"],"file_date_updated":"2020-07-14T12:45:01Z","publication_status":"published","_id":"1546","publist_id":"5625","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Synaptic efficacy and precision are influenced by the coupling of voltage-gated Ca2+ channels (VGCCs) to vesicles. But because the topography of VGCCs and their proximity to vesicles is unknown, a quantitative understanding of the determinants of vesicular release at nanometer scale is lacking. To investigate this, we combined freeze-fracture replica immunogold labeling of Cav2.1 channels, local [Ca2+] imaging, and patch pipette perfusion of EGTA at the calyx of Held. Between postnatal day 7 and 21, VGCCs formed variable sized clusters and vesicular release became less sensitive to EGTA, whereas fixed Ca2+ buffer properties remained constant. Experimentally constrained reaction-diffusion simulations suggest that Ca2+ sensors for vesicular release are located at the perimeter of VGCC clusters (&lt;30nm) and predict that VGCC number per cluster determines vesicular release probability without altering release time course. This &quot;perimeter release model&quot; provides a unifying framework accounting for developmental changes in both synaptic efficacy and time course."}],"file":[{"date_created":"2018-12-12T10:15:47Z","file_size":3080111,"relation":"main_file","file_id":"5170","creator":"system","content_type":"application/pdf","access_level":"open_access","checksum":"725f4d5be2dbb44b283ce722645ef37d","date_updated":"2020-07-14T12:45:01Z","file_name":"IST-2016-482-v1+1_1-s2.0-S0896627314010472-main.pdf"}],"date_updated":"2021-01-12T06:51:31Z","author":[{"first_name":"Yukihiro","last_name":"Nakamura","full_name":"Nakamura, Yukihiro"},{"orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","full_name":"Harada, Harumi","first_name":"Harumi"},{"last_name":"Kamasawa","full_name":"Kamasawa, Naomi","first_name":"Naomi"},{"last_name":"Matsui","full_name":"Matsui, Ko","first_name":"Ko"},{"first_name":"Jason","full_name":"Rothman, Jason","last_name":"Rothman"},{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"first_name":"R Angus","last_name":"Silver","full_name":"Silver, R Angus"},{"full_name":"Digregorio, David","last_name":"Digregorio","first_name":"David"},{"last_name":"Takahashi","full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki"}],"language":[{"iso":"eng"}],"year":"2015","tmp":{"short":"CC BY (4.0)","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)"},"issue":"1","scopus_import":1,"has_accepted_license":"1","volume":85},{"date_created":"2018-12-11T11:52:39Z","oa_version":"Preprint","citation":{"ama":"Mohammadi F, Moradi S. Resolution of unmixed bipartite graphs. <i>Bulletin of the Korean Mathematical Society</i>. 2015;52(3):977-986. doi:<a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">10.4134/BKMS.2015.52.3.977</a>","apa":"Mohammadi, F., &#38; Moradi, S. (2015). Resolution of unmixed bipartite graphs. <i>Bulletin of the Korean Mathematical Society</i>. Korean Mathematical Society. <a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">https://doi.org/10.4134/BKMS.2015.52.3.977</a>","mla":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” <i>Bulletin of the Korean Mathematical Society</i>, vol. 52, no. 3, Korean Mathematical Society, 2015, pp. 977–86, doi:<a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">10.4134/BKMS.2015.52.3.977</a>.","short":"F. Mohammadi, S. Moradi, Bulletin of the Korean Mathematical Society 52 (2015) 977–986.","ieee":"F. Mohammadi and S. Moradi, “Resolution of unmixed bipartite graphs,” <i>Bulletin of the Korean Mathematical Society</i>, vol. 52, no. 3. Korean Mathematical Society, pp. 977–986, 2015.","ista":"Mohammadi F, Moradi S. 2015. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 52(3), 977–986.","chicago":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” <i>Bulletin of the Korean Mathematical Society</i>. Korean Mathematical Society, 2015. <a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">https://doi.org/10.4134/BKMS.2015.52.3.977</a>."},"publication":"Bulletin of the Korean Mathematical Society","type":"journal_article","quality_controlled":"1","month":"05","status":"public","intvolume":"        52","doi":"10.4134/BKMS.2015.52.3.977","date_published":"2015-05-31T00:00:00Z","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/0901.3015","open_access":"1"}],"day":"31","year":"2015","issue":"3","scopus_import":1,"volume":52,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Let G be a graph on the vertex set V(G) = {x1,…,xn} with the edge set E(G), and let R = K[x1,…, xn] be the polynomial ring over a field K. Two monomial ideals are associated to G, the edge ideal I(G) generated by all monomials xixj with {xi,xj} ∈ E(G), and the vertex cover ideal IG generated by monomials ∏xi∈Cxi for all minimal vertex covers C of G. A minimal vertex cover of G is a subset C ⊂ V(G) such that each edge has at least one vertex in C and no proper subset of C has the same property. Indeed, the vertex cover ideal of G is the Alexander dual of the edge ideal of G. In this paper, for an unmixed bipartite graph G we consider the lattice of vertex covers LG and we explicitly describe the minimal free resolution of the ideal associated to LG which is exactly the vertex cover ideal of G. Then we compute depth, projective dimension, regularity and extremal Betti numbers of R/I(G) in terms of the associated lattice.","lang":"eng"}],"date_updated":"2021-01-12T06:51:31Z","author":[{"full_name":"Mohammadi, Fatemeh","last_name":"Mohammadi","id":"2C29581E-F248-11E8-B48F-1D18A9856A87","first_name":"Fatemeh"},{"first_name":"Somayeh","full_name":"Moradi, Somayeh","last_name":"Moradi"}],"publication_identifier":{"eissn":["2234-3016"]},"language":[{"iso":"eng"}],"publication_status":"published","_id":"1547","publist_id":"5624","publisher":"Korean Mathematical Society","department":[{"_id":"CaUh"}],"page":"977 - 986","title":"Resolution of unmixed bipartite graphs"},{"date_updated":"2021-01-12T06:51:31Z","abstract":[{"text":"Reproduction within a host and transmission to the next host are crucial for the virulence and fitness of pathogens. Nevertheless, basic knowledge about such parameters is often missing from the literature, even for well-studied bacteria, such as Bacillus thuringiensis, an endospore-forming insect pathogen, which infects its hosts via the oral route. To characterize bacterial replication success, we made use of an experimental oral infection system for the red flour beetle Tribolium castaneum and developed a flow cytometric assay for the quantification of both spore ingestion by the individual beetle larvae and the resulting spore load after bacterial replication and resporulation within cadavers. On average, spore numbers increased 460-fold, showing that Bacillus thuringiensis grows and replicates successfully in insect cadavers. By inoculating cadaver-derived spores and spores from bacterial stock cultures into nutrient medium, we next investigated outgrowth characteristics of vegetative cells and found that cadaver- derived bacteria showed reduced growth compared to bacteria from the stock cultures. Interestingly, this reduced growth was a consequence of inhibited spore germination, probably originating from the host and resulting in reduced host mortality in subsequent infections by cadaver-derived spores. Nevertheless, we further showed that Bacillus thuringiensis transmission was possible via larval cannibalism when no other food was offered. These results contribute to our understanding of the ecology of Bacillus thuringiensis as an insect pathogen.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"language":[{"iso":"eng"}],"author":[{"first_name":"Barbara","last_name":"Milutinovic","full_name":"Milutinovic, Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8214-4758"},{"full_name":"Höfling, Christina","last_name":"Höfling","first_name":"Christina"},{"last_name":"Futo","full_name":"Futo, Momir","first_name":"Momir"},{"full_name":"Scharsack, Jörn","last_name":"Scharsack","first_name":"Jörn"},{"last_name":"Kurtz","full_name":"Kurtz, Joachim","first_name":"Joachim"}],"issue":"23","scopus_import":1,"year":"2015","volume":81,"department":[{"_id":"SyCr"}],"page":"8135 - 8144","title":"Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination","publication_status":"published","publisher":"American Society for Microbiology","publist_id":"5623","_id":"1548","quality_controlled":"1","month":"12","publication":"Applied and Environmental Microbiology","citation":{"short":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, J. Kurtz, Applied and Environmental Microbiology 81 (2015) 8135–8144.","ieee":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, and J. Kurtz, “Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination,” <i>Applied and Environmental Microbiology</i>, vol. 81, no. 23. American Society for Microbiology, pp. 8135–8144, 2015.","ista":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. 2015. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 81(23), 8135–8144.","chicago":"Milutinovic, Barbara, Christina Höfling, Momir Futo, Jörn Scharsack, and Joachim Kurtz. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” <i>Applied and Environmental Microbiology</i>. American Society for Microbiology, 2015. <a href=\"https://doi.org/10.1128/AEM.02051-15\">https://doi.org/10.1128/AEM.02051-15</a>.","ama":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. <i>Applied and Environmental Microbiology</i>. 2015;81(23):8135-8144. doi:<a href=\"https://doi.org/10.1128/AEM.02051-15\">10.1128/AEM.02051-15</a>","mla":"Milutinovic, Barbara, et al. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” <i>Applied and Environmental Microbiology</i>, vol. 81, no. 23, American Society for Microbiology, 2015, pp. 8135–44, doi:<a href=\"https://doi.org/10.1128/AEM.02051-15\">10.1128/AEM.02051-15</a>.","apa":"Milutinovic, B., Höfling, C., Futo, M., Scharsack, J., &#38; Kurtz, J. (2015). Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. <i>Applied and Environmental Microbiology</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/AEM.02051-15\">https://doi.org/10.1128/AEM.02051-15</a>"},"oa_version":"Submitted Version","date_created":"2018-12-11T11:52:39Z","type":"journal_article","external_id":{"pmid":["26386058"]},"day":"01","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651099/","open_access":"1"}],"oa":1,"status":"public","date_published":"2015-12-01T00:00:00Z","doi":"10.1128/AEM.02051-15","intvolume":"        81"},{"day":"18","oa":1,"status":"public","date_published":"2015-09-18T00:00:00Z","doi":"10.1007/978-1-4939-2845-3_6","intvolume":"       869","quality_controlled":"1","pubrep_id":"839","month":"09","publication":"Novel chemical tools to study ion channel biology","citation":{"mla":"Mckenzie, Catherine, et al. “Flipping the Photoswitch: Ion Channels under Light Control.” <i>Novel Chemical Tools to Study Ion Channel Biology</i>, vol. 869, Springer, 2015, pp. 101–17, doi:<a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">10.1007/978-1-4939-2845-3_6</a>.","apa":"Mckenzie, C., Sanchez-Romero, I., &#38; Janovjak, H. L. (2015). Flipping the photoswitch: Ion channels under light control. In <i>Novel chemical tools to study ion channel biology</i> (Vol. 869, pp. 101–117). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">https://doi.org/10.1007/978-1-4939-2845-3_6</a>","ama":"Mckenzie C, Sanchez-Romero I, Janovjak HL. Flipping the photoswitch: Ion channels under light control. In: <i>Novel Chemical Tools to Study Ion Channel Biology</i>. Vol 869. Advances in Experimental Medicine and Biology. Springer; 2015:101-117. doi:<a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">10.1007/978-1-4939-2845-3_6</a>","ista":"Mckenzie C, Sanchez-Romero I, Janovjak HL. 2015.Flipping the photoswitch: Ion channels under light control. In: Novel chemical tools to study ion channel biology. vol. 869, 101–117.","chicago":"Mckenzie, Catherine, Inmaculada Sanchez-Romero, and Harald L Janovjak. “Flipping the Photoswitch: Ion Channels under Light Control.” In <i>Novel Chemical Tools to Study Ion Channel Biology</i>, 869:101–17. Advances in Experimental Medicine and Biology. Springer, 2015. <a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">https://doi.org/10.1007/978-1-4939-2845-3_6</a>.","short":"C. Mckenzie, I. Sanchez-Romero, H.L. Janovjak, in:, Novel Chemical Tools to Study Ion Channel Biology, Springer, 2015, pp. 101–117.","ieee":"C. Mckenzie, I. Sanchez-Romero, and H. L. Janovjak, “Flipping the photoswitch: Ion channels under light control,” in <i>Novel chemical tools to study ion channel biology</i>, vol. 869, Springer, 2015, pp. 101–117."},"oa_version":"Submitted Version","date_created":"2018-12-11T11:52:39Z","type":"book_chapter","department":[{"_id":"HaJa"}],"title":"Flipping the photoswitch: Ion channels under light control","page":"101 - 117","ddc":["571","576"],"file_date_updated":"2020-07-14T12:45:01Z","publication_status":"published","series_title":"Advances in Experimental Medicine and Biology","publisher":"Springer","publist_id":"5622","_id":"1549","file":[{"file_name":"IST-2017-839-v1+1_mckenzie.pdf","date_updated":"2020-07-14T12:45:01Z","checksum":"bd1bfdf2423a0c3b6e7cabfa8b44bc0f","access_level":"open_access","content_type":"application/pdf","creator":"system","file_id":"4854","relation":"main_file","file_size":1919655,"date_created":"2018-12-12T10:11:02Z"}],"date_updated":"2021-01-12T06:51:32Z","abstract":[{"text":"Nature has incorporated small photochromic molecules, colloquially termed 'photoswitches', in photoreceptor proteins to sense optical cues in photo-taxis and vision. While Nature's ability to employ light-responsive functionalities has long been recognized, it was not until recently that scientists designed, synthesized and applied synthetic photochromes to manipulate many of which open rapidly and locally in their native cell types, biological processes with the temporal and spatial resolution of light. Ion channels in particular have come to the forefront of proteins that can be put under the designer control of synthetic photochromes. Photochromic ion channel controllers are comprised of three classes, photochromic soluble ligands (PCLs), photochromic tethered ligands (PTLs) and photochromic crosslinkers (PXs), and in each class ion channel functionality is controlled through reversible changes in photochrome structure. By acting as light-dependent ion channel agonists, antagonist or modulators, photochromic controllers effectively converted a wide range of ion channels, including voltage-gated ion channels, 'leak channels', tri-, tetra- and pentameric ligand-gated ion channels, and temperaturesensitive ion channels, into man-made photoreceptors. Control by photochromes can be reversible, unlike in the case of 'caged' compounds, and non-invasive with high spatial precision, unlike pharmacology and electrical manipulation. Here, we introduce design principles of emerging photochromic molecules that act on ion channels and discuss the impact that these molecules are beginning to have on ion channel biophysics and neuronal physiology.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-4939-2844-6"]},"author":[{"first_name":"Catherine","last_name":"Mckenzie","full_name":"Mckenzie, Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Inmaculada","last_name":"Sanchez Romero","full_name":"Sanchez Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"}],"scopus_import":1,"year":"2015","volume":869,"has_accepted_license":"1"}]