[{"type":"journal_article","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-09-07T11:58:33Z","oa_version":"Preprint","oa":1,"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","first_name":"Martin"},{"last_name":"Daca","first_name":"Przemyslaw","full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"}],"citation":{"chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” <i>Formal Methods in System Design</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s10703-015-0235-2\">https://doi.org/10.1007/s10703-015-0235-2</a>.","ama":"Chatterjee K, Chmelik M, Daca P. CEGAR for compositional analysis of qualitative properties in Markov decision processes. <i>Formal Methods in System Design</i>. 2015;47(2):230-264. doi:<a href=\"https://doi.org/10.1007/s10703-015-0235-2\">10.1007/s10703-015-0235-2</a>","short":"K. Chatterjee, M. Chmelik, P. Daca, Formal Methods in System Design 47 (2015) 230–264.","ieee":"K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for compositional analysis of qualitative properties in Markov decision processes,” <i>Formal Methods in System Design</i>, vol. 47, no. 2. Springer, pp. 230–264, 2015.","mla":"Chatterjee, Krishnendu, et al. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” <i>Formal Methods in System Design</i>, vol. 47, no. 2, Springer, 2015, pp. 230–64, doi:<a href=\"https://doi.org/10.1007/s10703-015-0235-2\">10.1007/s10703-015-0235-2</a>.","apa":"Chatterjee, K., Chmelik, M., &#38; Daca, P. (2015). CEGAR for compositional analysis of qualitative properties in Markov decision processes. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-015-0235-2\">https://doi.org/10.1007/s10703-015-0235-2</a>","ista":"Chatterjee K, Chmelik M, Daca P. 2015. CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. 47(2), 230–264."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1501","scopus_import":1,"date_created":"2018-12-11T11:52:23Z","year":"2015","main_file_link":[{"url":"https://arxiv.org/abs/1405.0835","open_access":"1"}],"volume":47,"publication":"Formal Methods in System Design","title":"CEGAR for compositional analysis of qualitative properties in Markov decision processes","date_published":"2015-10-01T00:00:00Z","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"}],"quality_controlled":"1","month":"10","related_material":{"record":[{"status":"public","id":"1155","relation":"dissertation_contains"}]},"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No. P23499- N23, FWF NFN Grant No. S11407-N23, FWF Grant S11403-N23 (RiSE), and FWF Grant Z211-N23 (Wittgenstein Award), ERC Start Grant (279307: Graph Games), Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling).","publication_status":"published","ec_funded":1,"day":"01","status":"public","issue":"2","doi":"10.1007/s10703-015-0235-2","publist_id":"5677","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph algorithms with quadratic complexity to compute the simulation relation. We present an automated technique for assume-guarantee style reasoning for compositional analysis of two-player games by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We show a tight link between two-player games and MDPs, and as a consequence the results for games are lifted to MDPs with qualitative properties. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. "}],"intvolume":"        47","page":"230 - 264","language":[{"iso":"eng"}],"publisher":"Springer"},{"file_date_updated":"2020-07-14T12:44:59Z","scopus_import":1,"_id":"1502","oa_version":"Submitted Version","date_updated":"2023-09-07T11:58:33Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"file":[{"date_updated":"2020-07-14T12:44:59Z","content_type":"application/pdf","file_size":467561,"file_name":"IST-2016-625-v1+1_conf-cbse-BenesDHKN15.pdf","file_id":"5303","date_created":"2018-12-12T10:17:46Z","access_level":"open_access","creator":"system","checksum":"c6ce681035c163a158751f240cb7d389","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Beneš, N., Daca, P., Henzinger, T. A., Kretinsky, J., &#38; Nickovic, D. (2015). Complete composition operators for IOCO-testing theory (pp. 101–110). Presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada: ACM. <a href=\"https://doi.org/10.1145/2737166.2737175\">https://doi.org/10.1145/2737166.2737175</a>","mla":"Beneš, Nikola, et al. <i>Complete Composition Operators for IOCO-Testing Theory</i>. ACM, 2015, pp. 101–10, doi:<a href=\"https://doi.org/10.1145/2737166.2737175\">10.1145/2737166.2737175</a>.","ista":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. 2015. Complete composition operators for IOCO-testing theory. CBSE: Component-Based Software Engineering , Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering , , 101–110.","ieee":"N. Beneš, P. Daca, T. A. Henzinger, J. Kretinsky, and D. Nickovic, “Complete composition operators for IOCO-testing theory,” presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada, 2015, pp. 101–110.","chicago":"Beneš, Nikola, Przemyslaw Daca, Thomas A Henzinger, Jan Kretinsky, and Dejan Nickovic. “Complete Composition Operators for IOCO-Testing Theory,” 101–10. ACM, 2015. <a href=\"https://doi.org/10.1145/2737166.2737175\">https://doi.org/10.1145/2737166.2737175</a>.","short":"N. Beneš, P. Daca, T.A. Henzinger, J. Kretinsky, D. Nickovic, in:, ACM, 2015, pp. 101–110.","ama":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. Complete composition operators for IOCO-testing theory. In: ACM; 2015:101-110. doi:<a href=\"https://doi.org/10.1145/2737166.2737175\">10.1145/2737166.2737175</a>"},"has_accepted_license":"1","author":[{"first_name":"Nikola","full_name":"Beneš, Nikola","last_name":"Beneš"},{"first_name":"Przemyslaw","full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Kretinsky","orcid":"0000-0002-8122-2881","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan"}],"oa":1,"pubrep_id":"625","type":"conference","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"title":"Complete composition operators for IOCO-testing theory","date_published":"2015-05-01T00:00:00Z","quality_controlled":"1","conference":{"name":"CBSE: Component-Based Software Engineering ","start_date":"2015-05-04","location":"Montreal, QC, Canada","end_date":"2015-05-08"},"year":"2015","ddc":["000"],"date_created":"2018-12-11T11:52:24Z","publist_id":"5676","doi":"10.1145/2737166.2737175","abstract":[{"text":"We extend the theory of input-output conformance with operators for merge and quotient. The former is useful when testing against multiple requirements or views. The latter can be used to generate tests for patches of an already tested system. Both operators can combine systems with different action alphabets, which is usually the case when constructing complex systems and specifications from parts, for instance different views as well as newly defined functionality of a~previous version of the system.","lang":"eng"}],"status":"public","publication_identifier":{"isbn":["978-1-4503-3471-6"]},"publication_status":"published","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23(RiSE) and Z211-N23 (Wittgestein Award), by People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 291734, and by the ARTEMIS JU under grant agreement 295373 (nSafeCer).  Jan Křetínský has been partially supported by the Czech Science Foundation, grant No.  P202/12/G061.  Nikola Beneš has been supported by the\r\nMEYS project No. CZ.1.07/2.3.00/30.0009 Employment of Newly Graduated Doctors of Science for Scientific Excellence.","day":"01","ec_funded":1,"alternative_title":["Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering "],"related_material":{"record":[{"status":"public","id":"1155","relation":"dissertation_contains"}]},"month":"05","publisher":"ACM","language":[{"iso":"eng"}],"page":"101 - 110"},{"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Bao, Z., Pan, G., &#38; Zhou, W. (2015). Universality for the largest eigenvalue of sample covariance matrices with general population. <i>Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/14-AOS1281\">https://doi.org/10.1214/14-AOS1281</a>","mla":"Bao, Zhigang, et al. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” <i>Annals of Statistics</i>, vol. 43, no. 1, Institute of Mathematical Statistics, 2015, pp. 382–421, doi:<a href=\"https://doi.org/10.1214/14-AOS1281\">10.1214/14-AOS1281</a>.","ista":"Bao Z, Pan G, Zhou W. 2015. Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. 43(1), 382–421.","ieee":"Z. Bao, G. Pan, and W. Zhou, “Universality for the largest eigenvalue of sample covariance matrices with general population,” <i>Annals of Statistics</i>, vol. 43, no. 1. Institute of Mathematical Statistics, pp. 382–421, 2015.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” <i>Annals of Statistics</i>. Institute of Mathematical Statistics, 2015. <a href=\"https://doi.org/10.1214/14-AOS1281\">https://doi.org/10.1214/14-AOS1281</a>.","short":"Z. Bao, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 382–421.","ama":"Bao Z, Pan G, Zhou W. Universality for the largest eigenvalue of sample covariance matrices with general population. <i>Annals of Statistics</i>. 2015;43(1):382-421. doi:<a href=\"https://doi.org/10.1214/14-AOS1281\">10.1214/14-AOS1281</a>"},"author":[{"last_name":"Bao","first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475"},{"full_name":"Pan, Guangming","first_name":"Guangming","last_name":"Pan"},{"last_name":"Zhou","full_name":"Zhou, Wang","first_name":"Wang"}],"oa":1,"oa_version":"Preprint","publication_status":"published","acknowledgement":"B.Z. was supported  in  part  by  NSFC  Grant  11071213,  ZJNSF  Grant  R6090034  and  SRFDP  Grant 20100101110001. P.G. was supported in part by the Ministry of Education, Singapore, under Grant ARC 14/11. Z.W. was supported  in  part  by  the  Ministry  of  Education,  Singapore,  under  Grant  ARC  14/11,  and  by a Grant R-155-000-131-112 at the National University of Singapore\r\n","date_updated":"2021-01-12T06:51:14Z","department":[{"_id":"LaEr"}],"type":"journal_article","month":"02","doi":"10.1214/14-AOS1281","abstract":[{"lang":"eng","text":"This paper is aimed at deriving the universality of the largest eigenvalue of a class of high-dimensional real or complex sample covariance matrices of the form W N =Σ 1/2XX∗Σ 1/2 . Here, X = (xij )M,N is an M× N random matrix with independent entries xij , 1 ≤ i M,≤ 1 ≤ j ≤ N such that Exij = 0, E|xij |2 = 1/N . On dimensionality, we assume that M = M(N) and N/M → d ε (0, ∞) as N ∞→. For a class of general deterministic positive-definite M × M matrices Σ , under some additional assumptions on the distribution of xij 's, we show that the limiting behavior of the largest eigenvalue of W N is universal, via pursuing a Green function comparison strategy raised in [Probab. Theory Related Fields 154 (2012) 341-407, Adv. Math. 229 (2012) 1435-1515] by Erd″os, Yau and Yin for Wigner matrices and extended by Pillai and Yin [Ann. Appl. Probab. 24 (2014) 935-1001] to sample covariance matrices in the null case (&amp;Epsi = I ). Consequently, in the standard complex case (Ex2 ij = 0), combing this universality property and the results known for Gaussian matrices obtained by El Karoui in [Ann. Probab. 35 (2007) 663-714] (nonsingular case) and Onatski in [Ann. Appl. Probab. 18 (2008) 470-490] (singular case), we show that after an appropriate normalization the largest eigenvalue of W N converges weakly to the type 2 Tracy-Widom distribution TW2 . Moreover, in the real case, we show that whenΣ is spiked with a fixed number of subcritical spikes, the type 1 Tracy-Widom limit TW1 holds for the normalized largest eigenvalue of W N , which extends a result of Féral and Péché in [J. Math. Phys. 50 (2009) 073302] to the scenario of nondiagonal Σ and more generally distributed X . In summary, we establish the Tracy-Widom type universality for the largest eigenvalue of generally distributed sample covariance matrices under quite light assumptions on &amp;Sigma . Applications of these limiting results to statistical signal detection and structure recognition of separable covariance matrices are also discussed."}],"publist_id":"5672","issue":"1","status":"public","_id":"1505","publication":"Annals of Statistics","volume":43,"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1304.5690"}],"year":"2015","page":"382 - 421","intvolume":"        43","date_created":"2018-12-11T11:52:25Z","quality_controlled":"1","date_published":"2015-02-01T00:00:00Z","title":"Universality for the largest eigenvalue of sample covariance matrices with general population","publisher":"Institute of Mathematical Statistics"},{"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1208.5823"}],"year":"2015","publication":"Bernoulli","language":[{"iso":"eng"}],"volume":21,"date_created":"2018-12-11T11:52:25Z","intvolume":"        21","page":"1600 - 1628","title":"The logarithmic law of random determinant","date_published":"2015-08-01T00:00:00Z","quality_controlled":"1","publisher":"Bernoulli Society for Mathematical Statistics and Probability","oa_version":"Preprint","date_updated":"2021-01-12T06:51:14Z","publication_status":"published","department":[{"_id":"LaEr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"Z. Bao, G. Pan, and W. Zhou, “The logarithmic law of random determinant,” <i>Bernoulli</i>, vol. 21, no. 3. Bernoulli Society for Mathematical Statistics and Probability, pp. 1600–1628, 2015.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “The Logarithmic Law of Random Determinant.” <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability, 2015. <a href=\"https://doi.org/10.3150/14-BEJ615\">https://doi.org/10.3150/14-BEJ615</a>.","ama":"Bao Z, Pan G, Zhou W. The logarithmic law of random determinant. <i>Bernoulli</i>. 2015;21(3):1600-1628. doi:<a href=\"https://doi.org/10.3150/14-BEJ615\">10.3150/14-BEJ615</a>","short":"Z. Bao, G. Pan, W. Zhou, Bernoulli 21 (2015) 1600–1628.","mla":"Bao, Zhigang, et al. “The Logarithmic Law of Random Determinant.” <i>Bernoulli</i>, vol. 21, no. 3, Bernoulli Society for Mathematical Statistics and Probability, 2015, pp. 1600–28, doi:<a href=\"https://doi.org/10.3150/14-BEJ615\">10.3150/14-BEJ615</a>.","apa":"Bao, Z., Pan, G., &#38; Zhou, W. (2015). The logarithmic law of random determinant. <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability. <a href=\"https://doi.org/10.3150/14-BEJ615\">https://doi.org/10.3150/14-BEJ615</a>","ista":"Bao Z, Pan G, Zhou W. 2015. The logarithmic law of random determinant. Bernoulli. 21(3), 1600–1628."},"day":"01","author":[{"first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475","last_name":"Bao"},{"last_name":"Pan","first_name":"Guangming","full_name":"Pan, Guangming"},{"last_name":"Zhou","first_name":"Wang","full_name":"Zhou, Wang"}],"oa":1,"type":"journal_article","month":"08","issue":"3","doi":"10.3150/14-BEJ615","publist_id":"5671","abstract":[{"lang":"eng","text":"Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i, j = 1, . . . , n} is a collection of independent real random variables with means zero and variances one. Under the additional moment condition supn max1≤i,j ≤n Ea4ij &lt;∞, we prove Girko's logarithmic law of det An in the sense that as n→∞ log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1)."}],"status":"public","_id":"1506"},{"issue":"8","scopus_import":1,"doi":"10.4171/JEMS/548","publist_id":"5669","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."}],"_id":"1508","status":"public","department":[{"_id":"LaEr"}],"publication_status":"published","oa_version":"Preprint","date_updated":"2021-01-12T06:51:15Z","oa":1,"author":[{"last_name":"Erdös","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"last_name":"Yau","full_name":"Yau, Horng","first_name":"Horng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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>.","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>","short":"L. Erdös, H. Yau, Journal of the European Mathematical Society 17 (2015) 1927–2036.","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>.","ista":"Erdös L, Yau H. 2015. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 17(8), 1927–2036."},"day":"01","month":"08","type":"journal_article","date_published":"2015-08-01T00:00:00Z","title":"Gap universality of generalized Wigner and β ensembles","quality_controlled":"1","publisher":"European Mathematical Society","main_file_link":[{"url":"http://arxiv.org/abs/1211.3786","open_access":"1"}],"year":"2015","language":[{"iso":"eng"}],"volume":17,"publication":"Journal of the European Mathematical Society","date_created":"2018-12-11T11:52:26Z","intvolume":"        17","page":"1927 - 2036"},{"month":"10","publication_status":"published","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","day":"01","ec_funded":1,"status":"public","publist_id":"5668","doi":"10.12688/f1000research.7143.1","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"}],"intvolume":"         4","language":[{"iso":"eng"}],"publisher":"F1000 Research","pubrep_id":"497","type":"journal_article","date_updated":"2025-05-07T11:12:30Z","oa_version":"Published Version","department":[{"_id":"JiFr"},{"_id":"ToBo"}],"file":[{"access_level":"open_access","date_created":"2018-12-12T10:16:12Z","file_id":"5198","file_name":"IST-2016-497-v1+1_10.12688_f1000research.7143.1_20151102.pdf","file_size":4414248,"date_updated":"2020-07-14T12:44:59Z","content_type":"application/pdf","relation":"main_file","checksum":"8beae5cbe988e1060265ae7de2ee8306","creator":"system"}],"has_accepted_license":"1","citation":{"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.","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>","short":"J. Michalko, M. Lukacisinova, M.T. Bollenbach, J. Friml, F1000 Research  4 (2015).","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>","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>.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"last_name":"Michalko","first_name":"Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","full_name":"Michalko, Jaroslav"},{"last_name":"Dravecka","first_name":"Marta","full_name":"Dravecka, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004"},{"orcid":"0000-0003-4398-476X","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias","last_name":"Bollenbach"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"_id":"1509","file_date_updated":"2020-07-14T12:44:59Z","scopus_import":"1","ddc":["570"],"date_created":"2018-12-11T11:52:26Z","year":"2015","publication":"F1000 Research ","article_processing_charge":"No","volume":4,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"title":"Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene","date_published":"2015-10-01T00:00:00Z","quality_controlled":"1"},{"_id":"1510","scopus_import":1,"file_date_updated":"2020-07-14T12:44:59Z","type":"conference","pubrep_id":"503","oa":1,"author":[{"last_name":"Franek","id":"473294AE-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Franek, Peter"},{"last_name":"Krcál","first_name":"Marek","full_name":"Krcál, Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","citation":{"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>.","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>","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>.","short":"P. Franek, M. Krcál, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–856.","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>","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."},"department":[{"_id":"UlWa"},{"_id":"HeEd"}],"file":[{"creator":"system","checksum":"49eb5021caafaabe5356c65b9c5f8c9c","relation":"main_file","file_id":"5001","date_created":"2018-12-12T10:13:19Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:44:59Z","file_size":623563,"file_name":"IST-2016-503-v1+1_32.pdf"}],"date_updated":"2023-02-21T17:02:57Z","oa_version":"Published Version","conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2015-06-25","location":"Eindhoven, Netherlands","start_date":"2015-06-22"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","date_published":"2015-06-11T00:00:00Z","title":"On computability and triviality of well groups","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:52:26Z","ddc":["510"],"volume":34,"year":"2015","status":"public","doi":"10.4230/LIPIcs.SOCG.2015.842","abstract":[{"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. ","lang":"eng"}],"publist_id":"5667","related_material":{"record":[{"relation":"later_version","id":"1408","status":"public"}]},"month":"06","alternative_title":["LIPIcs"],"ec_funded":1,"day":"11","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","page":"842 - 856","intvolume":"        34","language":[{"iso":"eng"}]},{"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).","publication_status":"published","day":"11","ec_funded":1,"alternative_title":["LIPIcs"],"month":"06","related_material":{"record":[{"status":"public","id":"610","relation":"later_version"}]},"publist_id":"5666","doi":"10.4230/LIPIcs.SOCG.2015.476","abstract":[{"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.","lang":"eng"}],"status":"public","language":[{"iso":"eng"}],"page":"476 - 490","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa_version":"Published Version","date_updated":"2023-02-23T12:38:00Z","department":[{"_id":"UlWa"}],"file":[{"access_level":"open_access","date_created":"2018-12-12T10:11:18Z","file_id":"4871","file_name":"IST-2016-502-v1+1_42.pdf","file_size":636735,"date_updated":"2020-07-14T12:44:59Z","content_type":"application/pdf","relation":"main_file","checksum":"0945811875351796324189312ca29e9e","creator":"system"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","citation":{"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>.","short":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–490.","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>","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.","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>","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>.","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."},"author":[{"last_name":"Goaoc","first_name":"Xavier","full_name":"Goaoc, Xavier"},{"id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac","first_name":"Isaac","last_name":"Mabillard"},{"last_name":"Paták","full_name":"Paták, Pavel","first_name":"Pavel"},{"last_name":"Patakova","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","full_name":"Patakova, Zuzana"},{"last_name":"Tancer","first_name":"Martin","full_name":"Tancer, Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1191-6714"},{"last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","first_name":"Uli","orcid":"0000-0002-1494-0568"}],"oa":1,"pubrep_id":"502","type":"conference","file_date_updated":"2020-07-14T12:44:59Z","scopus_import":1,"_id":"1511","year":"2015","volume":"34 ","ddc":["510"],"date_created":"2018-12-11T11:52:27Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"date_published":"2015-06-11T00:00:00Z","title":"On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2015-06-22","location":"Eindhoven, Netherlands","end_date":"2015-06-25"}},{"related_material":{"record":[{"relation":"later_version","id":"424","status":"public"}]},"month":"01","alternative_title":["LIPIcs"],"day":"01","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.","publication_status":"published","status":"public","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"}],"publist_id":"5665","doi":"10.4230/LIPIcs.SOCG.2015.507","page":"507 - 521","intvolume":"        34","language":[{"iso":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","type":"conference","pubrep_id":"501","has_accepted_license":"1","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.","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>","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.","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>.","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>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Goaoc, Xavier","first_name":"Xavier","last_name":"Goaoc"},{"last_name":"Paták","full_name":"Paták, Pavel","first_name":"Pavel"},{"last_name":"Patakova","first_name":"Zuzana","full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683"},{"first_name":"Martin","full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714","last_name":"Tancer"},{"last_name":"Wagner","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","full_name":"Wagner, Uli"}],"oa":1,"oa_version":"Submitted Version","date_updated":"2024-02-28T12:59:37Z","file":[{"file_size":633712,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:00Z","file_name":"IST-2016-501-v1+1_46.pdf","date_created":"2018-12-12T10:10:09Z","file_id":"4794","access_level":"open_access","creator":"system","relation":"main_file","checksum":"e6881df44d87fe0c2529c9f7b2724614"}],"department":[{"_id":"UlWa"}],"_id":"1512","file_date_updated":"2020-07-14T12:45:00Z","scopus_import":"1","ddc":["510"],"date_created":"2018-12-11T11:52:27Z","volume":34,"article_processing_charge":"No","year":"2015","conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2015-06-25","start_date":"2015-06-22","location":"Eindhoven, Netherlands"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","date_published":"2015-01-01T00:00:00Z","title":"Bounding Helly numbers via Betti numbers"},{"_id":"1513","scopus_import":1,"file_date_updated":"2020-07-14T12:45:00Z","type":"journal_article","pubrep_id":"496","author":[{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","first_name":"Arka","full_name":"Pal, Arka","last_name":"Pal"},{"last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"oa":1,"citation":{"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>.","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>","short":"A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 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.","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>","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."},"has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_id":"5284","date_created":"2018-12-12T10:17:29Z","file_name":"IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf","date_updated":"2020-07-14T12:45:00Z","content_type":"application/pdf","file_size":858027,"checksum":"2b56b8c2e2a1d4cc3c9cb8daba26dd9b","relation":"main_file","creator":"system"}],"department":[{"_id":"BeVi"}],"date_updated":"2021-01-12T06:51:18Z","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","date_published":"2015-12-01T00:00:00Z","title":"The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"date_created":"2018-12-11T11:52:27Z","ddc":["570"],"volume":7,"article_processing_charge":"No","publication":"Genome Biology and Evolution","year":"2015","status":"public","publist_id":"5664","abstract":[{"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. ","lang":"eng"}],"doi":"10.1093/gbe/evv215","issue":"12","month":"12","ec_funded":1,"day":"01","publication_status":"published","publisher":"Oxford University Press","page":"3259 - 3268","intvolume":"         7","language":[{"iso":"eng"}]},{"publication":"Electronic Communications in Probability","volume":20,"year":"2015","ddc":["519"],"date_created":"2018-12-11T11:52:29Z","quality_controlled":"1","date_published":"2015-11-29T00:00:00Z","title":"From large deviations to Wasserstein gradient flows in multiple dimensions","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"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>.","ista":"Erbar M, Maas J, Renger M. 2015. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 20, 89.","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.","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>.","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>","short":"M. Erbar, J. Maas, M. Renger, Electronic Communications in Probability 20 (2015)."},"has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Matthias","full_name":"Erbar, Matthias","last_name":"Erbar"},{"last_name":"Maas","full_name":"Maas, Jan","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338"},{"first_name":"Michiel","full_name":"Renger, Michiel","last_name":"Renger"}],"oa":1,"date_updated":"2021-01-12T06:51:19Z","oa_version":"Published Version","department":[{"_id":"JaMa"}],"file":[{"file_size":230525,"date_updated":"2020-07-14T12:45:00Z","content_type":"application/pdf","file_name":"IST-2016-494-v1+1_4315-23820-1-PB.pdf","date_created":"2018-12-12T10:10:39Z","file_id":"4828","access_level":"open_access","creator":"system","relation":"main_file","checksum":"135741c17d3e1547ca696b6fbdcd559c"}],"type":"journal_article","pubrep_id":"494","file_date_updated":"2020-07-14T12:45:00Z","scopus_import":1,"_id":"1517","language":[{"iso":"eng"}],"article_number":"89","intvolume":"        20","publisher":"Institute of Mathematical Statistics","day":"29","publication_status":"published","month":"11","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"}],"publist_id":"5660","doi":"10.1214/ECP.v20-4315","status":"public"},{"issue":"5","publist_id":"5656","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"}],"doi":"10.1111/evo.12641","status":"public","publication_status":"published","ec_funded":1,"day":"19","month":"03","publisher":"Wiley","language":[{"iso":"eng"}],"intvolume":"        69","page":"1101 - 1112","scopus_import":1,"file_date_updated":"2020-07-14T12:45:00Z","_id":"1519","department":[{"_id":"NiBa"}],"file":[{"file_name":"IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf","date_updated":"2020-07-14T12:45:00Z","content_type":"application/pdf","file_size":188872,"access_level":"open_access","file_id":"4822","date_created":"2018-12-12T10:10:34Z","checksum":"fd8d23f476bc194419929b72ca265c02","relation":"main_file","creator":"system"},{"creator":"system","checksum":"b774911e70044641d556e258efcb52ef","relation":"main_file","file_id":"4823","date_created":"2018-12-12T10:10:35Z","access_level":"open_access","date_updated":"2020-07-14T12:45:00Z","content_type":"application/pdf","file_size":577415,"file_name":"IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf"}],"date_updated":"2021-01-12T06:51:20Z","oa_version":"Submitted Version","author":[{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Servedio","full_name":"Servedio, Maria","first_name":"Maria"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","citation":{"ieee":"N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” <i>Evolution</i>, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.","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>.","short":"N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.","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>","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>","ista":"Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112."},"pubrep_id":"560","type":"journal_article","date_published":"2015-03-19T00:00:00Z","title":"The interpretation of selection coefficients","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","year":"2015","volume":69,"publication":"Evolution","date_created":"2018-12-11T11:52:29Z","ddc":["570"]},{"abstract":[{"text":"Creating mechanical automata that can walk in stable and pleasing manners is a challenging task that requires both skill and expertise. We propose to use computational design to offset the technical difficulties of this process. A simple drag-and-drop interface allows casual users to create personalized walking toys from a library of pre-defined template mechanisms. Provided with this input, our method leverages physical simulation and evolutionary optimization to refine the mechanical designs such that the resulting toys are able to walk. The optimization process is guided by an intuitive set of objectives that measure the quality of the walking motions. We demonstrate our approach on a set of simulated mechanical toys with different numbers of legs and various distinct gaits. Two fabricated prototypes showcase the feasibility of our designs.","lang":"eng"}],"publist_id":"5655","doi":"10.1145/2786784.2786803","scopus_import":1,"publication_identifier":{"isbn":["978-1-4503-3496-9"]},"status":"public","_id":"1520","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","citation":{"apa":"Bharaj, G., Coros, S., Thomaszewski, B., Tompkin, J., Bickel, B., &#38; Pfister, H. (2015). Computational design of walking automata (pp. 93–100). Presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2786784.2786803\">https://doi.org/10.1145/2786784.2786803</a>","mla":"Bharaj, Gaurav, et al. <i>Computational Design of Walking Automata</i>. ACM, 2015, pp. 93–100, doi:<a href=\"https://doi.org/10.1145/2786784.2786803\">10.1145/2786784.2786803</a>.","ista":"Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. 2015. Computational design of walking automata. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 93–100.","chicago":"Bharaj, Gaurav, Stelian Coros, Bernhard Thomaszewski, James Tompkin, Bernd Bickel, and Hanspeter Pfister. “Computational Design of Walking Automata,” 93–100. ACM, 2015. <a href=\"https://doi.org/10.1145/2786784.2786803\">https://doi.org/10.1145/2786784.2786803</a>.","ama":"Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. Computational design of walking automata. In: ACM; 2015:93-100. doi:<a href=\"https://doi.org/10.1145/2786784.2786803\">10.1145/2786784.2786803</a>","short":"G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, H. Pfister, in:, ACM, 2015, pp. 93–100.","ieee":"G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, and H. Pfister, “Computational design of walking automata,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles, CA, United States, 2015, pp. 93–100."},"author":[{"last_name":"Bharaj","full_name":"Bharaj, Gaurav","first_name":"Gaurav"},{"last_name":"Coros","full_name":"Coros, Stelian","first_name":"Stelian"},{"first_name":"Bernhard","full_name":"Thomaszewski, Bernhard","last_name":"Thomaszewski"},{"full_name":"Tompkin, James","first_name":"James","last_name":"Tompkin"},{"last_name":"Bickel","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"last_name":"Pfister","full_name":"Pfister, Hanspeter","first_name":"Hanspeter"}],"publication_status":"published","oa_version":"None","date_updated":"2021-01-12T06:51:21Z","department":[{"_id":"BeBi"}],"type":"conference","month":"08","quality_controlled":"1","title":"Computational design of walking automata","date_published":"2015-08-01T00:00:00Z","publisher":"ACM","conference":{"name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","location":"Los Angeles, CA, United States","start_date":"2015-08-07","end_date":"2015-08-09"},"language":[{"iso":"eng"}],"year":"2015","page":"93 - 100","date_created":"2018-12-11T11:52:30Z"},{"date_created":"2018-12-11T11:52:31Z","ddc":["020"],"volume":68,"article_processing_charge":"No","publication":"VÖB Mitteilungen","year":"2015","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","date_published":"2015-11-12T00:00:00Z","title":"Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA","type":"journal_article","pubrep_id":"720","author":[{"first_name":"Bruno","full_name":"Bauer, Bruno","last_name":"Bauer"},{"last_name":"Blechl","first_name":"Guido","full_name":"Blechl, Guido"},{"last_name":"Bock","first_name":"Christoph","full_name":"Bock, Christoph"},{"last_name":"Danowski","orcid":"0000-0002-6026-4409","first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","full_name":"Danowski, Patrick"},{"first_name":"Andreas","full_name":"Ferus, Andreas","last_name":"Ferus"},{"full_name":"Graschopf, Anton","first_name":"Anton","last_name":"Graschopf"},{"last_name":"König","full_name":"König, Thomas","first_name":"Thomas"},{"first_name":"Katja","full_name":"Mayer, Katja","last_name":"Mayer"},{"last_name":"Reckling","first_name":"Falk","full_name":"Reckling, Falk"},{"full_name":"Rieck, Katharina","first_name":"Katharina","last_name":"Rieck"},{"first_name":"Peter","full_name":"Seitz, Peter","last_name":"Seitz"},{"full_name":"Stöger, Herwig","first_name":"Herwig","last_name":"Stöger"},{"first_name":"Elvira","full_name":"Welzig, Elvira","last_name":"Welzig"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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>.","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.","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>","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."},"has_accepted_license":"1","department":[{"_id":"E-Lib"}],"file":[{"creator":"system","checksum":"a495fe253bbc7615b1d60e9e85c94408","relation":"main_file","file_id":"5317","date_created":"2018-12-12T10:17:59Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:00Z","file_size":931707,"file_name":"IST-2016-720-v1+1_OANA_OA-Empfehlungen_12-11-2015.pdf"}],"oa_version":"Published Version","date_updated":"2021-01-12T06:51:22Z","_id":"1525","scopus_import":1,"file_date_updated":"2020-07-14T12:45:00Z","page":"580 - 607","article_type":"original","intvolume":"        68","language":[{"iso":"eng"}],"publisher":"Verein Österreichischer Bibliothekare","month":"11","day":"12","publication_status":"published","status":"public","doi":"10.5281/zenodo.33178","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."}],"publist_id":"5648","issue":"3"},{"year":"2015","publication":"Physical Biology","volume":12,"language":[{"iso":"eng"}],"article_number":"066003","intvolume":"        12","date_created":"2018-12-11T11:52:33Z","date_published":"2015-09-25T00:00:00Z","title":"Impact of the cell division cycle on gene circuits","quality_controlled":"1","publisher":"IOP Publishing Ltd.","date_updated":"2021-01-12T06:51:25Z","oa_version":"None","publication_status":"published","department":[{"_id":"MiSi"}],"citation":{"ama":"Bierbaum V, Klumpp S. Impact of the cell division cycle on gene circuits. <i>Physical Biology</i>. 2015;12(6). doi:<a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">10.1088/1478-3975/12/6/066003</a>","short":"V. Bierbaum, S. Klumpp, Physical Biology 12 (2015).","chicago":"Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” <i>Physical Biology</i>. IOP Publishing Ltd., 2015. <a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">https://doi.org/10.1088/1478-3975/12/6/066003</a>.","ieee":"V. Bierbaum and S. Klumpp, “Impact of the cell division cycle on gene circuits,” <i>Physical Biology</i>, vol. 12, no. 6. IOP Publishing Ltd., 2015.","ista":"Bierbaum V, Klumpp S. 2015. Impact of the cell division cycle on gene circuits. Physical Biology. 12(6), 066003.","apa":"Bierbaum, V., &#38; Klumpp, S. (2015). Impact of the cell division cycle on gene circuits. <i>Physical Biology</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">https://doi.org/10.1088/1478-3975/12/6/066003</a>","mla":"Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” <i>Physical Biology</i>, vol. 12, no. 6, 066003, IOP Publishing Ltd., 2015, doi:<a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">10.1088/1478-3975/12/6/066003</a>."},"day":"25","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3FD04378-F248-11E8-B48F-1D18A9856A87","first_name":"Veronika","full_name":"Bierbaum, Veronika","last_name":"Bierbaum"},{"full_name":"Klumpp, Stefan","first_name":"Stefan","last_name":"Klumpp"}],"type":"journal_article","month":"09","issue":"6","abstract":[{"text":"In growing cells, protein synthesis and cell growth are typically not synchronous, and, thus, protein concentrations vary over the cell division cycle. We have developed a theoretical description of genetic regulatory systems in bacteria that explicitly considers the cell division cycle to investigate its impact on gene expression. We calculate the cell-to-cell variations arising from cells being at different stages in the division cycle for unregulated genes and for basic regulatory mechanisms. These variations contribute to the extrinsic noise observed in single-cell experiments, and are most significant for proteins with short lifetimes. Negative autoregulation buffers against variation of protein concentration over the division cycle, but the effect is found to be relatively weak. Stronger buffering is achieved by an increased protein lifetime. Positive autoregulation can strongly amplify such variation if the parameters are set to values that lead to resonance-like behaviour. For cooperative positive autoregulation, the concentration variation over the division cycle diminishes the parameter region of bistability and modulates the switching times between the two stable states. The same effects are seen for a two-gene mutual-repression toggle switch. By contrast, an oscillatory circuit, the repressilator, is only weakly affected by the division cycle.","lang":"eng"}],"publist_id":"5641","doi":"10.1088/1478-3975/12/6/066003","scopus_import":1,"status":"public","_id":"1530"},{"scopus_import":"1","editor":[{"full_name":"Hotz, Ingrid","first_name":"Ingrid","last_name":"Hotz"},{"last_name":"Schultz","first_name":"Thomas","full_name":"Schultz, Thomas"}],"_id":"1531","author":[{"first_name":"Valentin","full_name":"Zobel, Valentin","last_name":"Zobel"},{"last_name":"Reininghaus","id":"4505473A-F248-11E8-B48F-1D18A9856A87","full_name":"Reininghaus, Jan","first_name":"Jan"},{"last_name":"Hotz","first_name":"Ingrid","full_name":"Hotz, Ingrid"}],"citation":{"ista":"Zobel V, Reininghaus J, Hotz I. 2015.Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Visualization and Processing of Higher Order Descriptors for Multi-Valued Data. Mathematics and Visualization, vol. 40, 257–267.","apa":"Zobel, V., Reininghaus, J., &#38; Hotz, I. (2015). Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In I. Hotz &#38; T. Schultz (Eds.), <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i> (1st ed., Vol. 40, pp. 257–267). Springer. <a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">https://doi.org/10.1007/978-3-319-15090-1_13</a>","mla":"Zobel, Valentin, et al. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>, edited by Ingrid Hotz and Thomas Schultz, 1st ed., vol. 40, Springer, 2015, pp. 257–67, doi:<a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">10.1007/978-3-319-15090-1_13</a>.","ieee":"V. Zobel, J. Reininghaus, and I. Hotz, “Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature,” in <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>, 1st ed., vol. 40, I. Hotz and T. Schultz, Eds. Springer, 2015, pp. 257–267.","ama":"Zobel V, Reininghaus J, Hotz I. Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Hotz I, Schultz T, eds. <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>. Vol 40. 1st ed. Springer; 2015:257-267. doi:<a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">10.1007/978-3-319-15090-1_13</a>","short":"V. Zobel, J. Reininghaus, I. Hotz, in:, I. Hotz, T. Schultz (Eds.), Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, 1st ed., Springer, 2015, pp. 257–267.","chicago":"Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” In <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>, edited by Ingrid Hotz and Thomas Schultz, 1st ed., 40:257–67. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">https://doi.org/10.1007/978-3-319-15090-1_13</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"oa_version":"None","date_updated":"2022-06-10T09:50:14Z","type":"book_chapter","quality_controlled":"1","title":"Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature","date_published":"2015-01-01T00:00:00Z","edition":"1","volume":40,"article_processing_charge":"No","publication":"Visualization and Processing of Higher Order Descriptors for Multi-Valued Data","year":"2015","date_created":"2018-12-11T11:52:33Z","publist_id":"5640","abstract":[{"text":"The Heat Kernel Signature (HKS) is a scalar quantity which is derived from the heat kernel of a given shape. Due to its robustness, isometry invariance, and multiscale nature, it has been successfully applied in many geometric applications. From a more general point of view, the HKS can be considered as a descriptor of the metric of a Riemannian manifold. Given a symmetric positive definite tensor field we may interpret it as the metric of some Riemannian manifold and thereby apply the HKS to visualize and analyze the given tensor data. In this paper, we propose a generalization of this approach that enables the treatment of indefinite tensor fields, like the stress tensor, by interpreting them as a generator of a positive definite tensor field. To investigate the usefulness of this approach we consider the stress tensor from the two-point-load model example and from a mechanical work piece.","lang":"eng"}],"doi":"10.1007/978-3-319-15090-1_13","publication_identifier":{"isbn":["978-3-319-15089-5"]},"status":"public","day":"01","publication_status":"published","month":"01","alternative_title":["Mathematics and Visualization"],"publisher":"Springer","language":[{"iso":"eng"}],"page":"257 - 267","intvolume":"        40"},{"publisher":"CSIRO","language":[{"iso":"eng"}],"article_type":"original","page":"239 - 251","intvolume":"        42","abstract":[{"lang":"eng","text":"Ammonium is the major nitrogen source in some plant ecosystems but is toxic at high concentrations, especially when available as the exclusive nitrogen source. Ammonium stress rapidly leads to various metabolic and hormonal imbalances that ultimately inhibit root and shoot growth in many plant species, including Arabidopsis thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with microarrays was used. Substantial transcriptional differences were most pronounced in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent with previous physiological analyses, major differences in the expression modules of photosynthesis-related genes, an altered mitochondrial metabolism, differential expression of the primary NH4+ assimilation, alteration of transporter gene expression and crucial changes in cell wall biosynthesis were found. A major difference in plant hormone responses, particularly of auxin but not cytokinin, was striking. The activity of the DR5::GUS reporter revealed a dramatically decreased auxin response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4 was partially rescued by exogenous auxin or in specific mutants in the auxin pathway. The data suggest that NH4+-induced nutritional and metabolic imbalances can be partially overcome by elevated auxin levels."}],"publist_id":"5639","doi":"10.1071/FP14171","issue":"3","publication_identifier":{"issn":["1445-4408"]},"pmid":1,"status":"public","day":"01","publication_status":"published","month":"03","quality_controlled":"1","title":"Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source","date_published":"2015-03-01T00:00:00Z","article_processing_charge":"No","volume":42,"publication":"Functional Plant Biology","year":"2015","date_created":"2018-12-11T11:52:34Z","scopus_import":"1","external_id":{"pmid":["32480670"]},"_id":"1532","author":[{"first_name":"Huaiyu","full_name":"Yang, Huaiyu","last_name":"Yang"},{"first_name":"Jenny","full_name":"Von Der Fecht Bartenbach, Jenny","last_name":"Von Der Fecht Bartenbach"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"last_name":"Lohmann","full_name":"Lohmann, Jan","first_name":"Jan"},{"full_name":"Neuhäuser, Benjamin","first_name":"Benjamin","last_name":"Neuhäuser"},{"full_name":"Ludewig, Uwe","first_name":"Uwe","last_name":"Ludewig"}],"citation":{"mla":"Yang, Huaiyu, et al. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” <i>Functional Plant Biology</i>, vol. 42, no. 3, CSIRO, 2015, pp. 239–51, doi:<a href=\"https://doi.org/10.1071/FP14171\">10.1071/FP14171</a>.","apa":"Yang, H., Von Der Fecht Bartenbach, J., Friml, J., Lohmann, J., Neuhäuser, B., &#38; Ludewig, U. (2015). Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. <i>Functional Plant Biology</i>. CSIRO. <a href=\"https://doi.org/10.1071/FP14171\">https://doi.org/10.1071/FP14171</a>","ista":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. 2015. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 42(3), 239–251.","chicago":"Yang, Huaiyu, Jenny Von Der Fecht Bartenbach, Jiří Friml, Jan Lohmann, Benjamin Neuhäuser, and Uwe Ludewig. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” <i>Functional Plant Biology</i>. CSIRO, 2015. <a href=\"https://doi.org/10.1071/FP14171\">https://doi.org/10.1071/FP14171</a>.","short":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, U. Ludewig, Functional Plant Biology 42 (2015) 239–251.","ama":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. <i>Functional Plant Biology</i>. 2015;42(3):239-251. doi:<a href=\"https://doi.org/10.1071/FP14171\">10.1071/FP14171</a>","ieee":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, and U. Ludewig, “Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source,” <i>Functional Plant Biology</i>, vol. 42, no. 3. CSIRO, pp. 239–251, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"oa_version":"None","date_updated":"2022-05-24T09:02:24Z","type":"journal_article"},{"year":"2015","publication":"IEEE Transactions on Circuits and Systems for Video Technology","language":[{"iso":"eng"}],"volume":25,"intvolume":"        25","date_created":"2018-12-11T11:52:34Z","page":"1295 - 1308","date_published":"2015-08-01T00:00:00Z","title":"Segmentation over detection via optimal sparse reconstructions","quality_controlled":"1","publisher":"IEEE","publication_status":"published","oa_version":"None","date_updated":"2021-01-12T06:51:26Z","department":[{"_id":"ChLa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","citation":{"ieee":"W. Xia, C. Domokos, J. Xiong, L. Cheong, and S. Yan, “Segmentation over detection via optimal sparse reconstructions,” <i>IEEE Transactions on Circuits and Systems for Video Technology</i>, vol. 25, no. 8. IEEE, pp. 1295–1308, 2015.","chicago":"Xia, Wei, Csaba Domokos, Junjun Xiong, Loongfah Cheong, and Shuicheng Yan. “Segmentation over Detection via Optimal Sparse Reconstructions.” <i>IEEE Transactions on Circuits and Systems for Video Technology</i>. IEEE, 2015. <a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">https://doi.org/10.1109/TCSVT.2014.2379972</a>.","ama":"Xia W, Domokos C, Xiong J, Cheong L, Yan S. Segmentation over detection via optimal sparse reconstructions. <i>IEEE Transactions on Circuits and Systems for Video Technology</i>. 2015;25(8):1295-1308. doi:<a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">10.1109/TCSVT.2014.2379972</a>","short":"W. Xia, C. Domokos, J. Xiong, L. Cheong, S. Yan, IEEE Transactions on Circuits and Systems for Video Technology 25 (2015) 1295–1308.","mla":"Xia, Wei, et al. “Segmentation over Detection via Optimal Sparse Reconstructions.” <i>IEEE Transactions on Circuits and Systems for Video Technology</i>, vol. 25, no. 8, IEEE, 2015, pp. 1295–308, doi:<a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">10.1109/TCSVT.2014.2379972</a>.","apa":"Xia, W., Domokos, C., Xiong, J., Cheong, L., &#38; Yan, S. (2015). Segmentation over detection via optimal sparse reconstructions. <i>IEEE Transactions on Circuits and Systems for Video Technology</i>. IEEE. <a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">https://doi.org/10.1109/TCSVT.2014.2379972</a>","ista":"Xia W, Domokos C, Xiong J, Cheong L, Yan S. 2015. Segmentation over detection via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for Video Technology. 25(8), 1295–1308."},"author":[{"last_name":"Xia","first_name":"Wei","full_name":"Xia, Wei"},{"last_name":"Domokos","id":"492DACF8-F248-11E8-B48F-1D18A9856A87","first_name":"Csaba","full_name":"Domokos, Csaba"},{"last_name":"Xiong","first_name":"Junjun","full_name":"Xiong, Junjun"},{"full_name":"Cheong, Loongfah","first_name":"Loongfah","last_name":"Cheong"},{"full_name":"Yan, Shuicheng","first_name":"Shuicheng","last_name":"Yan"}],"type":"journal_article","month":"08","issue":"8","publist_id":"5638","doi":"10.1109/TCSVT.2014.2379972","abstract":[{"lang":"eng","text":"This paper addresses the problem of semantic segmentation, where the possible class labels are from a predefined set. We exploit top-down guidance, i.e., the coarse localization of the objects and their class labels provided by object detectors. For each detected bounding box, figure-ground segmentation is performed and the final result is achieved by merging the figure-ground segmentations. The main idea of the proposed approach, which is presented in our preliminary work, is to reformulate the figure-ground segmentation problem as sparse reconstruction pursuing the object mask in a nonparametric manner. The latent segmentation mask should be coherent subject to sparse error caused by intra-category diversity; thus, the object mask is inferred by making use of sparse representations over the training set. To handle local spatial deformations, local patch-level masks are also considered and inferred by sparse representations over the spatially nearby patches. The sparse reconstruction coefficients and the latent mask are alternately optimized by applying the Lasso algorithm and the accelerated proximal gradient method. The proposed formulation results in a convex optimization problem; thus, the global optimal solution is achieved. In this paper, we provide theoretical analysis of the convergence and optimality. We also give an extended numerical analysis of the proposed algorithm and a comprehensive comparison with the related semantic segmentation methods on the challenging PASCAL visual object class object segmentation datasets and the Weizmann horse dataset. The experimental results demonstrate that the proposed algorithm achieves a competitive performance when compared with the state of the arts."}],"scopus_import":1,"status":"public","_id":"1533"},{"status":"public","publist_id":"5637","doi":"10.1038/ncomms9822","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."}],"month":"11","ec_funded":1,"day":"18","publication_status":"published","publisher":"Nature Publishing Group","intvolume":"         6","article_number":"8822","language":[{"iso":"eng"}],"_id":"1534","scopus_import":1,"file_date_updated":"2020-07-14T12:45:01Z","type":"journal_article","pubrep_id":"485","author":[{"first_name":"Hongzhe","full_name":"Wang, Hongzhe","last_name":"Wang"},{"last_name":"Yang","first_name":"Kezhen","full_name":"Yang, Kezhen"},{"full_name":"Zou, Junjie","first_name":"Junjie","last_name":"Zou"},{"first_name":"Lingling","full_name":"Zhu, Lingling","last_name":"Zhu"},{"first_name":"Zidian","full_name":"Xie, Zidian","last_name":"Xie"},{"first_name":"Miyoterao","full_name":"Morita, Miyoterao","last_name":"Morita"},{"first_name":"Masao","full_name":"Tasaka, Masao","last_name":"Tasaka"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml"},{"last_name":"Grotewold","full_name":"Grotewold, Erich","first_name":"Erich"},{"last_name":"Beeckman","first_name":"Tom","full_name":"Beeckman, Tom"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"first_name":"Fred","full_name":"Sack, Fred","last_name":"Sack"},{"last_name":"Le","full_name":"Le, Jie","first_name":"Jie"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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>","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>.","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).","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>","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>.","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."},"has_accepted_license":"1","file":[{"creator":"system","relation":"main_file","checksum":"3c06735fc7cd7e482ca830cbd26001bf","file_size":1852268,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:01Z","file_name":"IST-2016-485-v1+1_ncomms9822.pdf","date_created":"2018-12-12T10:17:07Z","file_id":"5259","access_level":"open_access"}],"department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:51:26Z","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","title":"Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism","date_published":"2015-11-18T00:00:00Z","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"date_created":"2018-12-11T11:52:34Z","ddc":["570"],"volume":6,"publication":"Nature Communications","year":"2015"},{"quality_controlled":"1","date_published":"2015-10-01T00:00:00Z","title":"Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells","article_processing_charge":"No","volume":8,"publication":"Current Molecular Pharmacology","year":"2015","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/","open_access":"1"}],"date_created":"2018-12-11T11:52:35Z","scopus_import":1,"external_id":{"pmid":["25966692"]},"_id":"1535","author":[{"orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H","first_name":"David H","last_name":"Vandael"},{"full_name":"Marcantoni, Andrea","first_name":"Andrea","last_name":"Marcantoni"},{"first_name":"Emilio","full_name":"Carbone, Emilio","last_name":"Carbone"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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>.","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>","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.","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>","short":"D.H. Vandael, A. Marcantoni, E. Carbone, Current Molecular Pharmacology 8 (2015) 149–161.","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>."},"department":[{"_id":"PeJo"}],"date_updated":"2021-01-12T06:51:26Z","oa_version":"Submitted Version","type":"journal_article","publisher":"Bentham Science Publishers","language":[{"iso":"eng"}],"article_type":"original","page":"149 - 161","intvolume":"         8","publist_id":"5636","abstract":[{"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.","lang":"eng"}],"doi":"10.2174/1874467208666150507105443","issue":"2","status":"public","pmid":1,"day":"01","publication_status":"published","acknowledgement":"This work was supported by the Italian MIUR (PRIN 2010/2011 project 2010JFYFY2) and the University of Torino.","month":"10"}]