[{"publist_id":"5782","abstract":[{"lang":"eng","text":"We consider the problem of statistical computations with persistence diagrams, a summary representation of topological features in data. These diagrams encode persistent homology, a widely used invariant in topological data analysis. While several avenues towards a statistical treatment of the diagrams have been explored recently, we follow an alternative route that is motivated by the success of methods based on the embedding of probability measures into reproducing kernel Hilbert spaces. In fact, a positive definite kernel on persistence diagrams has recently been proposed, connecting persistent homology to popular kernel-based learning techniques such as support vector machines. However, important properties of that kernel enabling a principled use in the context of probability measure embeddings remain to be explored. Our contribution is to close this gap by proving universality of a variant of the original kernel, and to demonstrate its effective use in twosample hypothesis testing on synthetic as well as real-world data."}],"alternative_title":["Advances in Neural Information Processing Systems"],"type":"conference","oa_version":"Submitted Version","volume":28,"date_updated":"2021-01-12T06:50:38Z","date_created":"2018-12-11T11:51:56Z","author":[{"full_name":"Kwitt, Roland","last_name":"Kwitt","first_name":"Roland"},{"first_name":"Stefan","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan"},{"full_name":"Niethammer, Marc","last_name":"Niethammer","first_name":"Marc"},{"full_name":"Lin, Weili","first_name":"Weili","last_name":"Lin"},{"full_name":"Bauer, Ulrich","first_name":"Ulrich","last_name":"Bauer","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9683-0724"}],"publisher":"Neural Information Processing Systems","department":[{"_id":"HeEd"}],"intvolume":" 28","status":"public","publication_status":"published","title":"Statistical topological data analysis-A kernel perspective","_id":"1424","year":"2015","acknowledgement":"This work was partially supported by the Austrian Science FUnd, project no. KLI 00012.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","day":"01","language":[{"iso":"eng"}],"date_published":"2015-12-01T00:00:00Z","conference":{"name":"NIPS: Neural Information Processing Systems","start_date":"2015-12-07","location":"Montreal, Canada","end_date":"2015-12-12"},"page":"3070 - 3078","quality_controlled":"1","citation":{"mla":"Kwitt, Roland, et al. Statistical Topological Data Analysis-A Kernel Perspective. Vol. 28, Neural Information Processing Systems, 2015, pp. 3070–78.","short":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, U. Bauer, in:, Neural Information Processing Systems, 2015, pp. 3070–3078.","chicago":"Kwitt, Roland, Stefan Huber, Marc Niethammer, Weili Lin, and Ulrich Bauer. “Statistical Topological Data Analysis-A Kernel Perspective,” 28:3070–78. Neural Information Processing Systems, 2015.","ama":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. Statistical topological data analysis-A kernel perspective. In: Vol 28. Neural Information Processing Systems; 2015:3070-3078.","ista":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. 2015. Statistical topological data analysis-A kernel perspective. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 28, 3070–3078.","apa":"Kwitt, R., Huber, S., Niethammer, M., Lin, W., & Bauer, U. (2015). Statistical topological data analysis-A kernel perspective (Vol. 28, pp. 3070–3078). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.","ieee":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, and U. Bauer, “Statistical topological data analysis-A kernel perspective,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 28, pp. 3070–3078."},"oa":1,"main_file_link":[{"url":"https://papers.nips.cc/paper/5887-statistical-topological-data-analysis-a-kernel-perspective","open_access":"1"}]},{"publist_id":"5768","ec_funded":1,"abstract":[{"text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient.","lang":"eng"}],"type":"conference","author":[{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"full_name":"Heredia, Jorge","last_name":"Heredia","first_name":"Jorge"},{"full_name":"Trubenova, Barbora","last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","date_created":"2018-12-11T11:51:58Z","date_updated":"2021-01-12T06:50:41Z","_id":"1430","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"ACM","title":"First steps towards a runtime comparison of natural and artificial evolution","status":"public","publication_status":"published","day":"11","month":"07","scopus_import":1,"doi":"10.1145/2739480.2754758","date_published":"2015-07-11T00:00:00Z","conference":{"location":"Madrid, Spain","start_date":"2015-07-11","end_date":"2015-07-15","name":"GECCO: Genetic and evolutionary computation conference"},"language":[{"iso":"eng"}],"citation":{"ama":"Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462. doi:10.1145/2739480.2754758","ieee":"T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid, Spain, 2015, pp. 1455–1462.","apa":"Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp. 1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758","ista":"Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a runtime comparison of natural and artificial evolution. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462.","short":"T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–1462.","mla":"Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758.","chicago":"Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62. ACM, 2015. https://doi.org/10.1145/2739480.2754758."},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.06260"}],"publication":"Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation","page":"1455 - 1462","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"}],"quality_controlled":"1"},{"day":"04","month":"09","article_processing_charge":"No","conference":{"end_date":"2015-07-17","location":"Verona, Italy","start_date":"2015-07-13","name":"CSF: Computer Security Foundations"},"doi":"10.1109/CSF.2015.11","date_published":"2015-09-04T00:00:00Z","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://epubs.surrey.ac.uk/808055/"}],"citation":{"ama":"Ferrara A, Fuchsbauer G, Liu B, Warinschi B. Policy privacy in cryptographic access control. In: IEEE; 2015:46-60. doi:10.1109/CSF.2015.11","ista":"Ferrara A, Fuchsbauer G, Liu B, Warinschi B. 2015. Policy privacy in cryptographic access control. CSF: Computer Security Foundations, 46–60.","ieee":"A. Ferrara, G. Fuchsbauer, B. Liu, and B. Warinschi, “Policy privacy in cryptographic access control,” presented at the CSF: Computer Security Foundations, Verona, Italy, 2015, pp. 46–60.","apa":"Ferrara, A., Fuchsbauer, G., Liu, B., & Warinschi, B. (2015). Policy privacy in cryptographic access control (pp. 46–60). Presented at the CSF: Computer Security Foundations, Verona, Italy: IEEE. https://doi.org/10.1109/CSF.2015.11","mla":"Ferrara, Anna, et al. Policy Privacy in Cryptographic Access Control. IEEE, 2015, pp. 46–60, doi:10.1109/CSF.2015.11.","short":"A. Ferrara, G. Fuchsbauer, B. Liu, B. Warinschi, in:, IEEE, 2015, pp. 46–60.","chicago":"Ferrara, Anna, Georg Fuchsbauer, Bin Liu, and Bogdan Warinschi. “Policy Privacy in Cryptographic Access Control,” 46–60. IEEE, 2015. https://doi.org/10.1109/CSF.2015.11."},"oa":1,"quality_controlled":"1","page":"46-60","project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"}],"abstract":[{"lang":"eng","text":"Cryptographic access control offers selective access to encrypted data via a combination of key management and functionality-rich cryptographic schemes, such as attribute-based encryption. Using this approach, publicly available meta-data may inadvertently leak information on the access policy that is enforced by cryptography, which renders cryptographic access control unusable in settings where this information is highly sensitive. We begin to address this problem by presenting rigorous definitions for policy privacy in cryptographic access control. For concreteness we set our results in the model of Role-Based Access Control (RBAC), where we identify and formalize several different flavors of privacy, however, our framework should serve as inspiration for other models of access control. Based on our insights we propose a new system which significantly improves on the privacy properties of state-of-the-art constructions. Our design is based on a novel type of privacy-preserving attribute-based encryption, which we introduce and show how to instantiate. We present our results in the context of a cryptographic RBAC system by Ferrara et al. (CSF'13), which uses cryptography to control read access to files, while write access is still delegated to trusted monitors. We give an extension of the construction that permits cryptographic control over write access. Our construction assumes that key management uses out-of-band channels between the policy enforcer and the users but eliminates completely the need for monitoring read/write access to the data."}],"publist_id":"5722","ec_funded":1,"type":"conference","author":[{"first_name":"Anna","last_name":"Ferrara","full_name":"Ferrara, Anna"},{"full_name":"Fuchsbauer, Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Fuchsbauer"},{"last_name":"Liu","first_name":"Bin","full_name":"Liu, Bin"},{"full_name":"Warinschi, Bogdan","last_name":"Warinschi","first_name":"Bogdan"}],"date_created":"2018-12-11T11:52:14Z","date_updated":"2021-01-12T06:50:59Z","oa_version":"Submitted Version","year":"2015","_id":"1474","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Policy privacy in cryptographic access control","status":"public","department":[{"_id":"KrPi"}],"publisher":"IEEE"},{"month":"01","day":"01","citation":{"ista":"Hausel T, Rodríguez Villegas F. 2015. Cohomology of large semiprojective hyperkähler varieties. Asterisque. 2015(370), 113–156.","apa":"Hausel, T., & Rodríguez Villegas, F. (2015). Cohomology of large semiprojective hyperkähler varieties. Asterisque. Societe Mathematique de France.","ieee":"T. Hausel and F. Rodríguez Villegas, “Cohomology of large semiprojective hyperkähler varieties,” Asterisque, vol. 2015, no. 370. Societe Mathematique de France, pp. 113–156, 2015.","ama":"Hausel T, Rodríguez Villegas F. Cohomology of large semiprojective hyperkähler varieties. Asterisque. 2015;2015(370):113-156.","chicago":"Hausel, Tamás, and Fernando Rodríguez Villegas. “Cohomology of Large Semiprojective Hyperkähler Varieties.” Asterisque. Societe Mathematique de France, 2015.","mla":"Hausel, Tamás, and Fernando Rodríguez Villegas. “Cohomology of Large Semiprojective Hyperkähler Varieties.” Asterisque, vol. 2015, no. 370, Societe Mathematique de France, 2015, pp. 113–56.","short":"T. Hausel, F. Rodríguez Villegas, Asterisque 2015 (2015) 113–156."},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1309.4914"}],"publication":"Asterisque","page":"113 - 156","quality_controlled":0,"date_published":"2015-01-01T00:00:00Z","type":"review","issue":"370","publist_id":"5723","abstract":[{"lang":"eng","text":"In this paper we survey geometric and arithmetic techniques to study the cohomology of semiprojective hyperkähler manifolds including toric hyperkähler varieties, Nakajima quiver varieties and moduli spaces of Higgs bundles on Riemann surfaces. The resulting formulae for their Poincaré polynomials are combinatorial and representation theoretical in nature. In particular we will look at their Betti numbers and will establish some results and state some expectations on their asymptotic shape."}],"extern":1,"_id":"1473","year":"2015","intvolume":" 2015","publisher":"Societe Mathematique de France","status":"public","title":"Cohomology of large semiprojective hyperkähler varieties","publication_status":"published","author":[{"full_name":"Tamas Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","first_name":"Tamas"},{"full_name":"Rodríguez Villegas, Fernando","last_name":"Rodríguez Villegas","first_name":"Fernando"}],"volume":2015,"date_created":"2018-12-11T11:52:13Z","date_updated":"2021-01-12T06:50:59Z"},{"page":"4741 - 4748","citation":{"apa":"Reininghaus, J., Huber, S., Bauer, U., & Kwitt, R. (2015). A stable multi-scale kernel for topological machine learning (pp. 4741–4748). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7299106","ieee":"J. Reininghaus, S. Huber, U. Bauer, and R. Kwitt, “A stable multi-scale kernel for topological machine learning,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp. 4741–4748.","ista":"Reininghaus J, Huber S, Bauer U, Kwitt R. 2015. A stable multi-scale kernel for topological machine learning. CVPR: Computer Vision and Pattern Recognition, 4741–4748.","ama":"Reininghaus J, Huber S, Bauer U, Kwitt R. A stable multi-scale kernel for topological machine learning. In: IEEE; 2015:4741-4748. doi:10.1109/CVPR.2015.7299106","chicago":"Reininghaus, Jan, Stefan Huber, Ulrich Bauer, and Roland Kwitt. “A Stable Multi-Scale Kernel for Topological Machine Learning,” 4741–48. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7299106.","short":"J. Reininghaus, S. Huber, U. Bauer, R. Kwitt, in:, IEEE, 2015, pp. 4741–4748.","mla":"Reininghaus, Jan, et al. A Stable Multi-Scale Kernel for Topological Machine Learning. IEEE, 2015, pp. 4741–48, doi:10.1109/CVPR.2015.7299106."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1412.6821"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"CVPR: Computer Vision and Pattern Recognition","location":"Boston, MA, USA","start_date":"2015-06-07","end_date":"2015-06-12"},"date_published":"2015-10-14T00:00:00Z","doi":"10.1109/CVPR.2015.7299106","scopus_import":1,"month":"10","day":"14","publication_identifier":{"eisbn":["978-1-4673-6964-0 "]},"publication_status":"published","title":"A stable multi-scale kernel for topological machine learning","status":"public","publisher":"IEEE","department":[{"_id":"HeEd"}],"year":"2015","_id":"1483","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:03Z","date_created":"2018-12-11T11:52:17Z","oa_version":"Preprint","author":[{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"full_name":"Huber, Stefan","last_name":"Huber","first_name":"Stefan","orcid":"0000-0002-8871-5814","id":"4700A070-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bauer","first_name":"Ulrich","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich"},{"full_name":"Kwitt, Roland","last_name":"Kwitt","first_name":"Roland"}],"type":"conference","abstract":[{"lang":"eng","text":"Topological data analysis offers a rich source of valuable information to study vision problems. Yet, so far we lack a theoretically sound connection to popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In this work, we establish such a connection by designing a multi-scale kernel for persistence diagrams, a stable summary representation of topological features in data. We show that this kernel is positive definite and prove its stability with respect to the 1-Wasserstein distance. Experiments on two benchmark datasets for 3D shape classification/retrieval and texture recognition show considerable performance gains of the proposed method compared to an alternative approach that is based on the recently introduced persistence landscapes."}],"publist_id":"5709"},{"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. Nonetheless there is surprisingly little language and verification support to build distributed systems based on fault-tolerant algorithms. In this paper, we present some of the challenges that a designer has to overcome to implement a fault-tolerant distributed system. Then we review different models that have been proposed to reason about distributed algorithms and sketch how such a model can form the basis for a domain-specific programming language. Adopting a high-level programming model can simplify the programmer's life and make the code amenable to automated verification, while still compiling to efficiently executable code. We conclude by summarizing the current status of an ongoing language design and implementation project that is based on this idea.","lang":"eng"}],"_id":"1498","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The need for language support for fault-tolerant distributed systems","ddc":["005"],"status":"public","intvolume":" 32","pubrep_id":"499","oa_version":"Published Version","file":[{"file_size":489362,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-499-v1+1_9.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:58Z","date_created":"2018-12-12T10:14:02Z","checksum":"cf5e94baa89a2dc4c5de01abc676eda8","relation":"main_file","file_id":"5050"}],"scopus_import":1,"series_title":"Leibniz International Proceedings in Informatics","day":"01","has_accepted_license":"1","citation":{"short":"C. Dragoi, T.A. Henzinger, D. Zufferey, 32 (2015) 90–102.","mla":"Dragoi, Cezara, et al. The Need for Language Support for Fault-Tolerant Distributed Systems. Vol. 32, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:10.4230/LIPIcs.SNAPL.2015.90.","chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “The Need for Language Support for Fault-Tolerant Distributed Systems.” Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90.","ama":"Dragoi C, Henzinger TA, Zufferey D. The need for language support for fault-tolerant distributed systems. 2015;32:90-102. doi:10.4230/LIPIcs.SNAPL.2015.90","apa":"Dragoi, C., Henzinger, T. A., & Zufferey, D. (2015). The need for language support for fault-tolerant distributed systems. Presented at the SNAPL: Summit oN Advances in Programming Languages, Asilomar, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90","ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “The need for language support for fault-tolerant distributed systems,” vol. 32. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 90–102, 2015.","ista":"Dragoi C, Henzinger TA, Zufferey D. 2015. The need for language support for fault-tolerant distributed systems. 32, 90–102."},"page":"90 - 102","date_published":"2015-01-01T00:00:00Z","file_date_updated":"2020-07-14T12:44:58Z","ec_funded":1,"publist_id":"5681","year":"2015","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"}],"author":[{"full_name":"Dragoi, Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","last_name":"Dragoi","first_name":"Cezara"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"full_name":"Zufferey, Damien","last_name":"Zufferey","first_name":"Damien","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:52:22Z","date_updated":"2020-08-11T10:09:14Z","volume":32,"month":"01","publication_identifier":{"isbn":["978-3-939897-80-4 "]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"conference":{"end_date":"2015-05-06","start_date":"2015-05-03","location":"Asilomar, CA, United States","name":"SNAPL: Summit oN Advances in Programming Languages"},"doi":"10.4230/LIPIcs.SNAPL.2015.90","language":[{"iso":"eng"}]},{"_id":"1497","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 43","status":"public","title":"Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data","ddc":["570"],"oa_version":"Published Version","file":[{"file_id":"5768","relation":"main_file","date_created":"2018-12-20T14:18:57Z","date_updated":"2020-07-14T12:44:58Z","checksum":"385b83854fd0eb2e4f386867da2823e2","file_name":"2015_NucleicAcidsRes_Andergassen.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":6863297}],"type":"journal_article","issue":"21","abstract":[{"text":"Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide.","lang":"eng"}],"citation":{"chicago":"Andergassen, Daniel, Christoph Dotter, Tomasz Kulinski, Philipp Guenzl, Philipp Bammer, Denise Barlow, Florian Pauler, and Quanah Hudson. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv727.","mla":"Andergassen, Daniel, et al. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research, vol. 43, no. 21, e146, Oxford University Press, 2015, doi:10.1093/nar/gkv727.","short":"D. Andergassen, C. Dotter, T. Kulinski, P. Guenzl, P. Bammer, D. Barlow, F. Pauler, Q. Hudson, Nucleic Acids Research 43 (2015).","ista":"Andergassen D, Dotter C, Kulinski T, Guenzl P, Bammer P, Barlow D, Pauler F, Hudson Q. 2015. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 43(21), e146.","ieee":"D. Andergassen et al., “Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data,” Nucleic Acids Research, vol. 43, no. 21. Oxford University Press, 2015.","apa":"Andergassen, D., Dotter, C., Kulinski, T., Guenzl, P., Bammer, P., Barlow, D., … Hudson, Q. (2015). Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv727","ama":"Andergassen D, Dotter C, Kulinski T, et al. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 2015;43(21). doi:10.1093/nar/gkv727"},"publication":"Nucleic Acids Research","date_published":"2015-07-21T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"21","acknowledgement":"Austrian Science Fund [FWF P25185-B22, FWF F4302- B09, FWFW1207-B09]. Funding for open access charge: Austrian Science Fund.\r\nWe thank Florian Breitwieser for advice during the early stages of this project. High-throughput sequencing was conducted by the Biomedical Sequencing Facility (BSF) at CeMM in Vienna.","year":"2015","department":[{"_id":"GaNo"}],"publisher":"Oxford University Press","publication_status":"published","author":[{"last_name":"Andergassen","first_name":"Daniel","full_name":"Andergassen, Daniel"},{"full_name":"Dotter, Christoph","first_name":"Christoph","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tomasz","last_name":"Kulinski","full_name":"Kulinski, Tomasz"},{"first_name":"Philipp","last_name":"Guenzl","full_name":"Guenzl, Philipp"},{"last_name":"Bammer","first_name":"Philipp","full_name":"Bammer, Philipp"},{"first_name":"Denise","last_name":"Barlow","full_name":"Barlow, Denise"},{"full_name":"Pauler, Florian","last_name":"Pauler","first_name":"Florian"},{"full_name":"Hudson, Quanah","first_name":"Quanah","last_name":"Hudson"}],"volume":43,"date_updated":"2021-01-12T06:51:09Z","date_created":"2018-12-11T11:52:22Z","article_number":"e146","publist_id":"5682","file_date_updated":"2020-07-14T12:44:58Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1093/nar/gkv727","language":[{"iso":"eng"}],"month":"07"},{"_id":"1499","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000","003"],"status":"public","title":"Polynomial time decidability of weighted synchronization under partial observability","intvolume":" 42","pubrep_id":"498","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":623563,"creator":"system","access_level":"open_access","file_name":"IST-2016-498-v1+1_32.pdf","checksum":"49eb5021caafaabe5356c65b9c5f8c9c","date_created":"2018-12-12T10:08:12Z","date_updated":"2020-07-14T12:44:58Z","relation":"main_file","file_id":"4672"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"We consider weighted automata with both positive and negative integer weights on edges and\r\nstudy the problem of synchronization using adaptive strategies that may only observe whether\r\nthe current weight-level is negative or nonnegative. We show that the synchronization problem is decidable in polynomial time for deterministic weighted automata."}],"citation":{"ama":"Kretinsky J, Larsen K, Laursen S, Srba J. Polynomial time decidability of weighted synchronization under partial observability. In: Vol 42. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:142-154. doi:10.4230/LIPIcs.CONCUR.2015.142","ieee":"J. Kretinsky, K. Larsen, S. Laursen, and J. Srba, “Polynomial time decidability of weighted synchronization under partial observability,” presented at the CONCUR: Concurrency Theory, Madrid, Spain, 2015, vol. 42, pp. 142–154.","apa":"Kretinsky, J., Larsen, K., Laursen, S., & Srba, J. (2015). Polynomial time decidability of weighted synchronization under partial observability (Vol. 42, pp. 142–154). Presented at the CONCUR: Concurrency Theory, Madrid, Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142","ista":"Kretinsky J, Larsen K, Laursen S, Srba J. 2015. Polynomial time decidability of weighted synchronization under partial observability. CONCUR: Concurrency Theory, LIPIcs, vol. 42, 142–154.","short":"J. Kretinsky, K. Larsen, S. Laursen, J. Srba, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–154.","mla":"Kretinsky, Jan, et al. Polynomial Time Decidability of Weighted Synchronization under Partial Observability. Vol. 42, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–54, doi:10.4230/LIPIcs.CONCUR.2015.142.","chicago":"Kretinsky, Jan, Kim Larsen, Simon Laursen, and Jiří Srba. “Polynomial Time Decidability of Weighted Synchronization under Partial Observability,” 42:142–54. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142."},"page":"142 - 154","date_published":"2015-01-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","year":"2015","acknowledgement":"The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement 601148 (CASSTING), EU FP7 FET project SENSATION, Sino-Danish Basic Research Center IDAE4CPS, the European Research Council (ERC) under grant agreement 267989 (QUAREM), the Austrian Science Fund (FWF) project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), the Czech Science Foundation under grant agreement P202/12/G061, and People Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734.","publication_status":"published","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","first_name":"Jan","full_name":"Kretinsky, Jan"},{"last_name":"Larsen","first_name":"Kim","full_name":"Larsen, Kim"},{"full_name":"Laursen, Simon","first_name":"Simon","last_name":"Laursen"},{"last_name":"Srba","first_name":"Jiří","full_name":"Srba, Jiří"}],"date_updated":"2021-01-12T06:51:10Z","date_created":"2018-12-11T11:52:22Z","volume":42,"file_date_updated":"2020-07-14T12:44:58Z","publist_id":"5680","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"conference":{"start_date":"2015-09-01","location":"Madrid, Spain","end_date":"2015-09-04","name":"CONCUR: Concurrency Theory"},"doi":"10.4230/LIPIcs.CONCUR.2015.142","language":[{"iso":"eng"}],"month":"01"},{"abstract":[{"text":"Motivated by biological questions, we study configurations of equal-sized disks in the Euclidean plane that neither pack nor cover. Measuring the quality by the probability that a random point lies in exactly one disk, we show that the regular hexagonal grid gives the maximum among lattice configurations. ","lang":"eng"}],"publist_id":"5684","ec_funded":1,"type":"conference","author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"full_name":"Iglesias Ham, Mabel","first_name":"Mabel","last_name":"Iglesias Ham","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kurlin, Vitaliy","first_name":"Vitaliy","last_name":"Kurlin"}],"date_created":"2018-12-11T11:52:21Z","date_updated":"2021-01-12T06:51:09Z","oa_version":"Submitted Version","volume":"2015-August","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1495","year":"2015","status":"public","title":"Relaxed disk packing","publication_status":"published","publisher":"Queen's University","department":[{"_id":"HeEd"}],"month":"08","day":"01","scopus_import":1,"conference":{"location":"Ontario, Canada","start_date":"2015-08-10","end_date":"2015-08-12","name":"CCCG: Canadian Conference on Computational Geometry"},"date_published":"2015-08-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Proceedings of the 27th Canadian Conference on Computational Geometry","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1505.03402","open_access":"1"}],"citation":{"apa":"Edelsbrunner, H., Iglesias Ham, M., & Kurlin, V. (2015). Relaxed disk packing. In Proceedings of the 27th Canadian Conference on Computational Geometry (Vol. 2015–August, pp. 128–135). Ontario, Canada: Queen’s University.","ieee":"H. Edelsbrunner, M. Iglesias Ham, and V. Kurlin, “Relaxed disk packing,” in Proceedings of the 27th Canadian Conference on Computational Geometry, Ontario, Canada, 2015, vol. 2015–August, pp. 128–135.","ista":"Edelsbrunner H, Iglesias Ham M, Kurlin V. 2015. Relaxed disk packing. Proceedings of the 27th Canadian Conference on Computational Geometry. CCCG: Canadian Conference on Computational Geometry vol. 2015–August, 128–135.","ama":"Edelsbrunner H, Iglesias Ham M, Kurlin V. Relaxed disk packing. In: Proceedings of the 27th Canadian Conference on Computational Geometry. Vol 2015-August. Queen’s University; 2015:128-135.","chicago":"Edelsbrunner, Herbert, Mabel Iglesias Ham, and Vitaliy Kurlin. “Relaxed Disk Packing.” In Proceedings of the 27th Canadian Conference on Computational Geometry, 2015–August:128–35. Queen’s University, 2015.","short":"H. Edelsbrunner, M. Iglesias Ham, V. Kurlin, in:, Proceedings of the 27th Canadian Conference on Computational Geometry, Queen’s University, 2015, pp. 128–135.","mla":"Edelsbrunner, Herbert, et al. “Relaxed Disk Packing.” Proceedings of the 27th Canadian Conference on Computational Geometry, vol. 2015–August, Queen’s University, 2015, pp. 128–35."},"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"}],"page":"128-135"},{"doi":"10.1214/15-AOS1353","date_published":"2015-12-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Annals of Statistics","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1312.5119","open_access":"1"}],"citation":{"ieee":"Z. Bao, L. Lin, G. Pan, and W. Zhou, “Spectral statistics of large dimensional spearman s rank correlation matrix and its application,” Annals of Statistics, vol. 43, no. 6. Institute of Mathematical Statistics, pp. 2588–2623, 2015.","apa":"Bao, Z., Lin, L., Pan, G., & Zhou, W. (2015). Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/15-AOS1353","ista":"Bao Z, Lin L, Pan G, Zhou W. 2015. Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. 43(6), 2588–2623.","ama":"Bao Z, Lin L, Pan G, Zhou W. Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. 2015;43(6):2588-2623. doi:10.1214/15-AOS1353","chicago":"Bao, Zhigang, Liang Lin, Guangming Pan, and Wang Zhou. “Spectral Statistics of Large Dimensional Spearman s Rank Correlation Matrix and Its Application.” Annals of Statistics. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/15-AOS1353.","short":"Z. Bao, L. Lin, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 2588–2623.","mla":"Bao, Zhigang, et al. “Spectral Statistics of Large Dimensional Spearman s Rank Correlation Matrix and Its Application.” Annals of Statistics, vol. 43, no. 6, Institute of Mathematical Statistics, 2015, pp. 2588–623, doi:10.1214/15-AOS1353."},"quality_controlled":"1","page":"2588 - 2623","month":"12","day":"01","author":[{"last_name":"Bao","first_name":"Zhigang","orcid":"0000-0003-3036-1475","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang"},{"full_name":"Lin, Liang","first_name":"Liang","last_name":"Lin"},{"full_name":"Pan, Guangming","first_name":"Guangming","last_name":"Pan"},{"first_name":"Wang","last_name":"Zhou","full_name":"Zhou, Wang"}],"date_created":"2018-12-11T11:52:24Z","date_updated":"2021-01-12T06:51:14Z","volume":43,"oa_version":"Published Version","_id":"1504","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","status":"public","title":"Spectral statistics of large dimensional spearman s rank correlation matrix and its application","publication_status":"published","publisher":"Institute of Mathematical Statistics","intvolume":" 43","abstract":[{"lang":"eng","text":"Let Q = (Q1, . . . , Qn) be a random vector drawn from the uniform distribution on the set of all n! permutations of {1, 2, . . . , n}. Let Z = (Z1, . . . , Zn), where Zj is the mean zero variance one random variable obtained by centralizing and normalizing Qj , j = 1, . . . , n. Assume that Xi , i = 1, . . . ,p are i.i.d. copies of 1/√ p Z and X = Xp,n is the p × n random matrix with Xi as its ith row. Then Sn = XX is called the p × n Spearman's rank correlation matrix which can be regarded as a high dimensional extension of the classical nonparametric statistic Spearman's rank correlation coefficient between two independent random variables. In this paper, we establish a CLT for the linear spectral statistics of this nonparametric random matrix model in the scenario of high dimension, namely, p = p(n) and p/n→c ∈ (0,∞) as n→∞.We propose a novel evaluation scheme to estimate the core quantity in Anderson and Zeitouni's cumulant method in [Ann. Statist. 36 (2008) 2553-2576] to bypass the so-called joint cumulant summability. In addition, we raise a two-step comparison approach to obtain the explicit formulae for the mean and covariance functions in the CLT. Relying on this CLT, we then construct a distribution-free statistic to test complete independence for components of random vectors. Owing to the nonparametric property, we can use this test on generally distributed random variables including the heavy-tailed ones."}],"issue":"6","publist_id":"5674","extern":"1","type":"journal_article"},{"date_created":"2018-12-11T11:52:23Z","date_updated":"2019-04-26T07:22:03Z","author":[{"full_name":"Nguyen, Luan V","first_name":"Luan","last_name":"Nguyen"},{"full_name":"Christian Schilling","last_name":"Schilling","first_name":"Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","first_name":"Sergiy","full_name":"Sergiy Bogomolov"},{"last_name":"Johnson","first_name":"Taylor","full_name":"Johnson, Taylor T"}],"publisher":"Springer","title":"Poster: HyRG: A random generation tool for affine hybrid automata","status":"public","publication_status":"published","_id":"1500","year":"2015","extern":1,"publist_id":"5678","abstract":[{"text":"In this poster, we present methods for randomly generating hybrid automata with affine differential equations, invariants, guards, and assignments. Selecting an arbitrary affine function from the set of all affine functions results in a low likelihood of generating hybrid automata with diverse and interesting behaviors, as there are an uncountable number of elements in the set of all affine functions. Instead, we partition the set of all affine functions into potentially interesting classes and randomly select elements from these classes. For example, we partition the set of all affine differential equations by using restrictions on eigenvalues such as those that yield stable, unstable, etc. equilibrium points. We partition the components describing discrete behavior (guards, assignments, and invariants) to allow either time-dependent or state-dependent switching, and in particular provide the ability to generate subclasses of piecewise-affine hybrid automata. Our preliminary experimental results with a prototype tool called HyRG (Hybrid Random Generator) illustrate the feasibility of this generation method to automatically create standard hybrid automaton examples like the bouncing ball and thermostat.","lang":"eng"}],"alternative_title":["18th ACM International Conference on Hybrid Systems: Computation and Control, HSCC 2015"],"type":"conference_poster","doi":"10.1145/2728606.2728650","date_published":"2015-04-14T00:00:00Z","page":"289 - 290","quality_controlled":0,"citation":{"ista":"Nguyen L, Schilling C, Bogomolov S, Johnson T. 2015. Poster: HyRG: A random generation tool for affine hybrid automata, Springer,p.","apa":"Nguyen, L., Schilling, C., Bogomolov, S., & Johnson, T. (2015). Poster: HyRG: A random generation tool for affine hybrid automata. HSCC: Hybrid Systems - Computation and Control (pp. 289–290). Springer. https://doi.org/10.1145/2728606.2728650","ieee":"L. Nguyen, C. Schilling, S. Bogomolov, and T. Johnson, Poster: HyRG: A random generation tool for affine hybrid automata. Springer, 2015, pp. 289–290.","ama":"Nguyen L, Schilling C, Bogomolov S, Johnson T. Poster: HyRG: A Random Generation Tool for Affine Hybrid Automata. Springer; 2015:289-290. doi:10.1145/2728606.2728650","chicago":"Nguyen, Luan, Christian Schilling, Sergiy Bogomolov, and Taylor Johnson. Poster: HyRG: A Random Generation Tool for Affine Hybrid Automata. HSCC: Hybrid Systems - Computation and Control. Springer, 2015. https://doi.org/10.1145/2728606.2728650.","mla":"Nguyen, Luan, et al. “Poster: HyRG: A Random Generation Tool for Affine Hybrid Automata.” HSCC: Hybrid Systems - Computation and Control, Springer, 2015, pp. 289–90, doi:10.1145/2728606.2728650.","short":"L. Nguyen, C. Schilling, S. Bogomolov, T. Johnson, Poster: HyRG: A Random Generation Tool for Affine Hybrid Automata, Springer, 2015."},"publication":"HSCC: Hybrid Systems - Computation and Control","month":"04","day":"14"},{"main_file_link":[{"url":"https://arxiv.org/abs/1307.8414","open_access":"1"}],"oa":1,"citation":{"ista":"Sadel C. 2015. A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. 35(5), 1582–1591.","ieee":"C. Sadel, “A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles,” Ergodic Theory and Dynamical Systems, vol. 35, no. 5. Cambridge University Press, pp. 1582–1591, 2015.","apa":"Sadel, C. (2015). A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/etds.2013.103","ama":"Sadel C. A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. 2015;35(5):1582-1591. doi:10.1017/etds.2013.103","chicago":"Sadel, Christian. “A Herman-Avila-Bochi Formula for Higher-Dimensional Pseudo-Unitary and Hermitian-Symplectic-Cocycles.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2015. https://doi.org/10.1017/etds.2013.103.","mla":"Sadel, Christian. “A Herman-Avila-Bochi Formula for Higher-Dimensional Pseudo-Unitary and Hermitian-Symplectic-Cocycles.” Ergodic Theory and Dynamical Systems, vol. 35, no. 5, Cambridge University Press, 2015, pp. 1582–91, doi:10.1017/etds.2013.103.","short":"C. Sadel, Ergodic Theory and Dynamical Systems 35 (2015) 1582–1591."},"publication":"Ergodic Theory and Dynamical Systems","page":"1582 - 1591","quality_controlled":"1","date_published":"2015-03-14T00:00:00Z","doi":"10.1017/etds.2013.103","language":[{"iso":"eng"}],"month":"03","day":"14","year":"2015","_id":"1503","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Cambridge University Press","intvolume":" 35","title":"A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles","status":"public","publication_status":"published","author":[{"last_name":"Sadel","first_name":"Christian","orcid":"0000-0001-8255-3968","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","full_name":"Sadel, Christian"}],"volume":35,"oa_version":"Preprint","date_created":"2018-12-11T11:52:24Z","date_updated":"2021-01-12T06:51:13Z","type":"journal_article","publist_id":"5675","issue":"5","abstract":[{"text":"A Herman-Avila-Bochi type formula is obtained for the average sum of the top d Lyapunov exponents over a one-parameter family of double-struck G-cocycles, where double-struck G is the group that leaves a certain, non-degenerate Hermitian form of signature (c, d) invariant. The generic example of such a group is the pseudo-unitary group U(c, d) or, in the case c = d, the Hermitian-symplectic group HSp(2d) which naturally appears for cocycles related to Schrödinger operators. In the case d = 1, the formula for HSp(2d) cocycles reduces to the Herman-Avila-Bochi formula for SL(2, ℝ) cocycles.","lang":"eng"}],"extern":"1"},{"ec_funded":1,"publist_id":"5667","file_date_updated":"2020-07-14T12:44:59Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"1408"}]},"author":[{"last_name":"Franek","first_name":"Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87","full_name":"Franek, Peter"},{"full_name":"Krcál, Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek","last_name":"Krcál"}],"volume":34,"date_updated":"2023-02-21T17:02:57Z","date_created":"2018-12-11T11:52:26Z","year":"2015","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"publication_status":"published","month":"06","doi":"10.4230/LIPIcs.SOCG.2015.842","conference":{"location":"Eindhoven, Netherlands","start_date":"2015-06-22","end_date":"2015-06-25","name":"SoCG: Symposium on Computational Geometry"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"The concept of well group in a special but important case captures homological properties of the zero set of a continuous map f from K to R^n on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within L_infty distance r from f for a given r > 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 < 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. "}],"type":"conference","alternative_title":["LIPIcs"],"pubrep_id":"503","file":[{"file_name":"IST-2016-503-v1+1_32.pdf","access_level":"open_access","file_size":623563,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5001","date_updated":"2020-07-14T12:44:59Z","date_created":"2018-12-12T10:13:19Z","checksum":"49eb5021caafaabe5356c65b9c5f8c9c"}],"oa_version":"Published Version","_id":"1510","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 34","title":"On computability and triviality of well groups","ddc":["510"],"status":"public","has_accepted_license":"1","day":"11","scopus_import":1,"date_published":"2015-06-11T00:00:00Z","citation":{"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.","apa":"Franek, P., & 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. https://doi.org/10.4230/LIPIcs.SOCG.2015.842","ista":"Franek P, Krcál M. 2015. On computability and triviality of well groups. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 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:10.4230/LIPIcs.SOCG.2015.842","chicago":"Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups,” 34:842–56. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.842.","short":"P. Franek, M. Krcál, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–856.","mla":"Franek, Peter, and Marek Krcál. On Computability and Triviality of Well Groups. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–56, doi:10.4230/LIPIcs.SOCG.2015.842."},"page":"842 - 856"},{"day":"01","month":"02","page":"382 - 421","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1304.5690"}],"citation":{"ama":"Bao Z, Pan G, Zhou W. Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. 2015;43(1):382-421. doi:10.1214/14-AOS1281","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,” Annals of Statistics, vol. 43, no. 1. Institute of Mathematical Statistics, pp. 382–421, 2015.","apa":"Bao, Z., Pan, G., & Zhou, W. (2015). Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/14-AOS1281","mla":"Bao, Zhigang, et al. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” Annals of Statistics, vol. 43, no. 1, Institute of Mathematical Statistics, 2015, pp. 382–421, doi:10.1214/14-AOS1281.","short":"Z. Bao, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 382–421.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” Annals of Statistics. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/14-AOS1281."},"oa":1,"publication":"Annals of Statistics","language":[{"iso":"eng"}],"doi":"10.1214/14-AOS1281","date_published":"2015-02-01T00:00:00Z","type":"journal_article","issue":"1","publist_id":"5672","abstract":[{"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 (&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 &Sigma . Applications of these limiting results to statistical signal detection and structure recognition of separable covariance matrices are also discussed.","lang":"eng"}],"department":[{"_id":"LaEr"}],"intvolume":" 43","publisher":"Institute of Mathematical Statistics","status":"public","publication_status":"published","title":"Universality for the largest eigenvalue of sample covariance matrices with general population","_id":"1505","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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","year":"2015","oa_version":"Preprint","volume":43,"date_created":"2018-12-11T11:52:25Z","date_updated":"2021-01-12T06:51:14Z","author":[{"full_name":"Bao, Zhigang","last_name":"Bao","first_name":"Zhigang","orcid":"0000-0003-3036-1475","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pan, Guangming","last_name":"Pan","first_name":"Guangming"},{"last_name":"Zhou","first_name":"Wang","full_name":"Zhou, Wang"}]},{"citation":{"ista":"Erdös L, Yau H. 2015. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 17(8), 1927–2036.","apa":"Erdös, L., & Yau, H. (2015). Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/548","ieee":"L. Erdös and H. Yau, “Gap universality of generalized Wigner and β ensembles,” Journal of the European Mathematical Society, vol. 17, no. 8. European Mathematical Society, pp. 1927–2036, 2015.","ama":"Erdös L, Yau H. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 2015;17(8):1927-2036. doi:10.4171/JEMS/548","chicago":"Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” Journal of the European Mathematical Society. European Mathematical Society, 2015. https://doi.org/10.4171/JEMS/548.","mla":"Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” Journal of the European Mathematical Society, vol. 17, no. 8, European Mathematical Society, 2015, pp. 1927–2036, doi:10.4171/JEMS/548.","short":"L. Erdös, H. Yau, Journal of the European Mathematical Society 17 (2015) 1927–2036."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1211.3786"}],"oa":1,"publication":"Journal of the European Mathematical Society","page":"1927 - 2036","quality_controlled":"1","doi":"10.4171/JEMS/548","date_published":"2015-08-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"month":"08","day":"01","_id":"1508","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 17","department":[{"_id":"LaEr"}],"publisher":"European Mathematical Society","status":"public","publication_status":"published","title":"Gap universality of generalized Wigner and β ensembles","author":[{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László"},{"full_name":"Yau, Horng","first_name":"Horng","last_name":"Yau"}],"volume":17,"oa_version":"Preprint","date_updated":"2021-01-12T06:51:15Z","date_created":"2018-12-11T11:52:26Z","type":"journal_article","issue":"8","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."}]},{"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 <∞, 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)."}],"publist_id":"5671","issue":"3","type":"journal_article","author":[{"orcid":"0000-0003-3036-1475","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao","first_name":"Zhigang","full_name":"Bao, Zhigang"},{"full_name":"Pan, Guangming","first_name":"Guangming","last_name":"Pan"},{"full_name":"Zhou, Wang","first_name":"Wang","last_name":"Zhou"}],"date_created":"2018-12-11T11:52:25Z","date_updated":"2021-01-12T06:51:14Z","volume":21,"oa_version":"Preprint","year":"2015","_id":"1506","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The logarithmic law of random determinant","status":"public","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Bernoulli Society for Mathematical Statistics and Probability","intvolume":" 21","month":"08","day":"01","date_published":"2015-08-01T00:00:00Z","doi":"10.3150/14-BEJ615","language":[{"iso":"eng"}],"publication":"Bernoulli","citation":{"mla":"Bao, Zhigang, et al. “The Logarithmic Law of Random Determinant.” Bernoulli, vol. 21, no. 3, Bernoulli Society for Mathematical Statistics and Probability, 2015, pp. 1600–28, doi:10.3150/14-BEJ615.","short":"Z. Bao, G. Pan, W. Zhou, Bernoulli 21 (2015) 1600–1628.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “The Logarithmic Law of Random Determinant.” Bernoulli. Bernoulli Society for Mathematical Statistics and Probability, 2015. https://doi.org/10.3150/14-BEJ615.","ama":"Bao Z, Pan G, Zhou W. The logarithmic law of random determinant. Bernoulli. 2015;21(3):1600-1628. doi:10.3150/14-BEJ615","ista":"Bao Z, Pan G, Zhou W. 2015. The logarithmic law of random determinant. Bernoulli. 21(3), 1600–1628.","ieee":"Z. Bao, G. Pan, and W. Zhou, “The logarithmic law of random determinant,” Bernoulli, vol. 21, no. 3. Bernoulli Society for Mathematical Statistics and Probability, pp. 1600–1628, 2015.","apa":"Bao, Z., Pan, G., & Zhou, W. (2015). The logarithmic law of random determinant. Bernoulli. Bernoulli Society for Mathematical Statistics and Probability. https://doi.org/10.3150/14-BEJ615"},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1208.5823"}],"quality_controlled":"1","page":"1600 - 1628"},{"month":"12","quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1093/gbe/evv215","file_date_updated":"2020-07-14T12:45:00Z","publist_id":"5664","ec_funded":1,"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"BeVi"}],"year":"2015","date_updated":"2021-01-12T06:51:18Z","date_created":"2018-12-11T11:52:27Z","volume":7,"author":[{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","first_name":"Arka","full_name":"Pal, Arka"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"scopus_import":1,"day":"01","article_processing_charge":"No","has_accepted_license":"1","page":"3259 - 3268","publication":"Genome Biology and Evolution","citation":{"ieee":"A. Pal and B. Vicoso, “The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression,” Genome Biology and Evolution, vol. 7, no. 12. Oxford University Press, pp. 3259–3268, 2015.","apa":"Pal, A., & Vicoso, B. (2015). The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evv215","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.","ama":"Pal A, Vicoso B. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. 2015;7(12):3259-3268. doi:10.1093/gbe/evv215","chicago":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/gbe/evv215.","short":"A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268.","mla":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution, vol. 7, no. 12, Oxford University Press, 2015, pp. 3259–68, doi:10.1093/gbe/evv215."},"date_published":"2015-12-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order.\r\n\r\nIn this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order. "}],"issue":"12","title":"The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression","status":"public","ddc":["570"],"intvolume":" 7","_id":"1513","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"5284","relation":"main_file","date_created":"2018-12-12T10:17:29Z","date_updated":"2020-07-14T12:45:00Z","checksum":"2b56b8c2e2a1d4cc3c9cb8daba26dd9b","file_name":"IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":858027}],"pubrep_id":"496"},{"intvolume":" 20","status":"public","ddc":["519"],"title":"From large deviations to Wasserstein gradient flows in multiple dimensions","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1517","oa_version":"Published Version","file":[{"file_name":"IST-2016-494-v1+1_4315-23820-1-PB.pdf","access_level":"open_access","content_type":"application/pdf","file_size":230525,"creator":"system","relation":"main_file","file_id":"4828","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:10:39Z","checksum":"135741c17d3e1547ca696b6fbdcd559c"}],"pubrep_id":"494","type":"journal_article","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"}],"citation":{"short":"M. Erbar, J. Maas, M. Renger, Electronic Communications in Probability 20 (2015).","mla":"Erbar, Matthias, et al. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” Electronic Communications in Probability, vol. 20, 89, Institute of Mathematical Statistics, 2015, doi:10.1214/ECP.v20-4315.","chicago":"Erbar, Matthias, Jan Maas, and Michiel Renger. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/ECP.v20-4315.","ama":"Erbar M, Maas J, Renger M. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 2015;20. doi:10.1214/ECP.v20-4315","ieee":"M. Erbar, J. Maas, and M. Renger, “From large deviations to Wasserstein gradient flows in multiple dimensions,” Electronic Communications in Probability, vol. 20. Institute of Mathematical Statistics, 2015.","apa":"Erbar, M., Maas, J., & Renger, M. (2015). From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/ECP.v20-4315","ista":"Erbar M, Maas J, Renger M. 2015. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 20, 89."},"publication":"Electronic Communications in Probability","date_published":"2015-11-29T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"29","department":[{"_id":"JaMa"}],"publisher":"Institute of Mathematical Statistics","publication_status":"published","year":"2015","volume":20,"date_updated":"2021-01-12T06:51:19Z","date_created":"2018-12-11T11:52:29Z","author":[{"full_name":"Erbar, Matthias","first_name":"Matthias","last_name":"Erbar"},{"full_name":"Maas, Jan","first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338"},{"first_name":"Michiel","last_name":"Renger","full_name":"Renger, Michiel"}],"article_number":"89","publist_id":"5660","file_date_updated":"2020-07-14T12:45:00Z","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1214/ECP.v20-4315","month":"11"},{"month":"01","day":"01","page":"157 - 167","quality_controlled":0,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"short":"M. Mansouri, Y. Kasugai, Y. Fukazawa, F. Bertaso, F. Raynaud, J. Perroy, L. Fagni, W. Kaufmann, M. Watanabe, R. Shigemoto, F. Ferraguti, European Journal of Neuroscience 41 (2015) 157–167.","mla":"Mansouri, Mahnaz, et al. “Distinct Subsynaptic Localization of Type 1 Metabotropic Glutamate Receptors at Glutamatergic and GABAergic Synapses in the Rodent Cerebellar Cortex.” European Journal of Neuroscience, vol. 41, no. 2, Wiley-Blackwell, 2015, pp. 157–67, doi:10.1111/ejn.12779.","chicago":"Mansouri, Mahnaz, Yu Kasugai, Yugo Fukazawa, Federica Bertaso, Fabrice Raynaud, Julie Perroy, Laurent Fagni, et al. “Distinct Subsynaptic Localization of Type 1 Metabotropic Glutamate Receptors at Glutamatergic and GABAergic Synapses in the Rodent Cerebellar Cortex.” European Journal of Neuroscience. Wiley-Blackwell, 2015. https://doi.org/10.1111/ejn.12779.","ama":"Mansouri M, Kasugai Y, Fukazawa Y, et al. Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex. European Journal of Neuroscience. 2015;41(2):157-167. doi:10.1111/ejn.12779","ieee":"M. Mansouri et al., “Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex,” European Journal of Neuroscience, vol. 41, no. 2. Wiley-Blackwell, pp. 157–167, 2015.","apa":"Mansouri, M., Kasugai, Y., Fukazawa, Y., Bertaso, F., Raynaud, F., Perroy, J., … Ferraguti, F. (2015). Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/ejn.12779","ista":"Mansouri M, Kasugai Y, Fukazawa Y, Bertaso F, Raynaud F, Perroy J, Fagni L, Kaufmann W, Watanabe M, Shigemoto R, Ferraguti F. 2015. Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex. European Journal of Neuroscience. 41(2), 157–167."},"publication":"European Journal of Neuroscience","date_published":"2015-01-01T00:00:00Z","doi":"10.1111/ejn.12779","type":"journal_article","extern":1,"publist_id":"5662","issue":"2","abstract":[{"lang":"eng","text":"Type 1 metabotropic glutamate (mGlu1) receptors play a pivotal role in different forms of synaptic plasticity in the cerebellar cortex, e.g. long-term depression at glutamatergic synapses and rebound potentiation at GABAergic synapses. These various forms of plasticity might depend on the subsynaptic arrangement of the receptor in Purkinje cells that can be regulated by protein-protein interactions. This study investigated, by means of the freeze-fracture replica immunogold labelling method, the subcellular localization of mGlu1 receptors in the rodent cerebellum and whether Homer proteins regulate their subsynaptic distribution. We observed a widespread extrasynaptic localization of mGlu1 receptors and confirmed their peri-synaptic enrichment at glutamatergic synapses. Conversely, we detected mGlu1 receptors within the main body of GABAergic synapses onto Purkinje cell dendrites. Although Homer proteins are known to interact with the mGlu1 receptor C-terminus, we could not detect Homer3, the most abundant Homer protein in the cerebellar cortex, at GABAergic synapses by pre-embedding and post-embedding immunoelectron microscopy. We then hypothesized a critical role for Homer proteins in the peri-junctional localization of mGlu1 receptors at glutamatergic synapses. To disrupt Homer-associated protein complexes, mice were tail-vein injected with the membrane-permeable dominant-negative TAT-Homer1a. Freeze-fracture replica immunogold labelling analysis showed no significant alteration in the mGlu1 receptor distribution pattern at parallel fibre-Purkinje cell synapses, suggesting that other scaffolding proteins are involved in the peri-synaptic confinement. The identification of interactors that regulate the subsynaptic localization of the mGlu1 receptor at neurochemically distinct synapses may offer new insight into its trafficking and intracellular signalling."}],"intvolume":" 41","publisher":"Wiley-Blackwell","status":"public","publication_status":"published","title":"Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) (project W012060-10 to F.F.), The Japan Society for the Promotion of Science (JSPS) (to R.S.) and Agence Nationale de la Recherche (ANR-11-BSV4-018-03, DELTAPLAN), Région Languedoc-Roussillon (Chercheur d’Avenir) (to J.P.). The authors thank S. Schönherr for excellent technical support and Dr Furuichi for kindly providing anti-Homer3 antibodies.","_id":"1515","year":"2015","volume":41,"date_created":"2018-12-11T11:52:28Z","date_updated":"2023-02-23T10:02:24Z","author":[{"last_name":"Mansouri","first_name":"Mahnaz","full_name":"Mansouri, Mahnaz"},{"last_name":"Kasugai","first_name":"Yu","full_name":"Kasugai, Yu"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"last_name":"Bertaso","first_name":"Federica","full_name":"Bertaso, Federica"},{"last_name":"Raynaud","first_name":"Fabrice","full_name":"Raynaud, Fabrice"},{"full_name":"Perroy, Julie","first_name":"Julie","last_name":"Perroy"},{"last_name":"Fagni","first_name":"Laurent","full_name":"Fagni, Laurent"},{"full_name":"Walter Kaufmann","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"last_name":"Watanabe","first_name":"Masahiko","full_name":"Watanabe, Masahiko"},{"full_name":"Ryuichi Shigemoto","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"full_name":"Ferraguti, Francesco","last_name":"Ferraguti","first_name":"Francesco"}]},{"doi":"10.1093/cercor/bhu231","date_published":"2015-10-10T00:00:00Z","page":"3699 - 3712","quality_controlled":0,"citation":{"chicago":"Gómez Gonzalo, Marta, Marta Navarrete, Gertrudis Perea, Ana Covelo, Mario Martín Fernández, Ryuichi Shigemoto, Rafael Luján, and Alfonso Araque. “Endocannabinoids Induce Lateral Long Term Potentiation of Transmitter Release by Stimulation of Gliotransmission.” Cerebral Cortex. Oxford University Press, 2015. https://doi.org/10.1093/cercor/bhu231.","mla":"Gómez Gonzalo, Marta, et al. “Endocannabinoids Induce Lateral Long Term Potentiation of Transmitter Release by Stimulation of Gliotransmission.” Cerebral Cortex, vol. 25, no. 10, Oxford University Press, 2015, pp. 3699–712, doi:10.1093/cercor/bhu231.","short":"M. Gómez Gonzalo, M. Navarrete, G. Perea, A. Covelo, M. Martín Fernández, R. Shigemoto, R. Luján, A. Araque, Cerebral Cortex 25 (2015) 3699–3712.","ista":"Gómez Gonzalo M, Navarrete M, Perea G, Covelo A, Martín Fernández M, Shigemoto R, Luján R, Araque A. 2015. Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission. Cerebral Cortex. 25(10), 3699–3712.","ieee":"M. Gómez Gonzalo et al., “Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission,” Cerebral Cortex, vol. 25, no. 10. Oxford University Press, pp. 3699–3712, 2015.","apa":"Gómez Gonzalo, M., Navarrete, M., Perea, G., Covelo, A., Martín Fernández, M., Shigemoto, R., … Araque, A. (2015). Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bhu231","ama":"Gómez Gonzalo M, Navarrete M, Perea G, et al. Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission. Cerebral Cortex. 2015;25(10):3699-3712. doi:10.1093/cercor/bhu231"},"publication":"Cerebral Cortex","month":"10","day":"10","volume":25,"date_created":"2018-12-11T11:52:27Z","date_updated":"2021-01-12T06:51:18Z","author":[{"full_name":"Gómez-Gonzalo, Marta","first_name":"Marta","last_name":"Gómez Gonzalo"},{"last_name":"Navarrete","first_name":"Marta","full_name":"Navarrete, Marta"},{"last_name":"Perea","first_name":"Gertrudis","full_name":"Perea, Gertrudis"},{"first_name":"Ana","last_name":"Covelo","full_name":"Covelo, Ana"},{"first_name":"Mario","last_name":"Martín Fernández","full_name":"Martín-Fernández, Mario"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Ryuichi Shigemoto"},{"full_name":"Luján, Rafael","first_name":"Rafael","last_name":"Luján"},{"last_name":"Araque","first_name":"Alfonso","full_name":"Araque, Alfonso"}],"intvolume":" 25","publisher":"Oxford University Press","status":"public","publication_status":"published","title":"Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission","_id":"1514","year":"2015","acknowledgement":"This work was supported by grants from Ministerio de Economia y Competitividad, Spain (MINECO; BFU2010-15832), European Union (HEALTH-F2-2007-202167), and Cajal Blue Brain to A.A. Grants from Spain (MINECO; BFU-2009-08404 and\nCSD2008-00005) to R.L. Grants from Spain (MINECO; Consolider, CSD2010-00045; Ramón y Cajal Program, RYC-2012-12014; and BFU2013-47265) to G.P. We thank Dr Atsu Aiba (Animal Resources, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo) for the donation of the mGluR1b rescue mice.","extern":1,"issue":"10","publist_id":"5663","abstract":[{"text":"Endocannabinoids (eCBs) play key roles in brain function, acting as modulatory signals in synaptic transmission and plasticity. They are recognized as retrograde messengers that mediate long-term synaptic depression (LTD), but their ability to induce long-term potentiation (LTP) is poorly known. We show that eCBs induce the long-term enhancement of transmitter release at single hippocampal synapses through stimulation of astrocytes when coincident with postsynaptic activity. This LTP requires the coordinated activity of the 3 elements of the tripartite synapse: 1) eCB-evoked astrocyte calcium signal that stimulates glutamate release; 2) postsynaptic nitric oxide production; and 3) activation of protein kinase C and presynaptic group I metabotropic glutamate receptors, whose location at presynaptic sites was confirmed by immunoelectron microscopy. Hence, while eCBs act as retrograde signals to depress homoneuronal synapses, they serve as lateral messengers to induce LTP in distant heteroneuronal synapses through stimulation of astrocytes. Therefore, eCBs can trigger LTP through stimulation of astrocyte-neuron signaling, revealing novel cellular mechanisms of eCB effects on synaptic plasticity.","lang":"eng"}],"type":"journal_article"},{"month":"03","doi":"10.1111/evo.12641","language":[{"iso":"eng"}],"oa":1,"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","ec_funded":1,"publist_id":"5656","file_date_updated":"2020-07-14T12:45:00Z","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"full_name":"Servedio, Maria","first_name":"Maria","last_name":"Servedio"}],"volume":69,"date_updated":"2021-01-12T06:51:20Z","date_created":"2018-12-11T11:52:29Z","year":"2015","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","has_accepted_license":"1","day":"19","scopus_import":1,"date_published":"2015-03-19T00:00:00Z","citation":{"chicago":"Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12641.","short":"N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.","mla":"Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:10.1111/evo.12641.","ieee":"N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” Evolution, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.","apa":"Barton, N. H., & Servedio, M. (2015). The interpretation of selection coefficients. Evolution. Wiley. https://doi.org/10.1111/evo.12641","ista":"Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112.","ama":"Barton NH, Servedio M. The interpretation of selection coefficients. Evolution. 2015;69(5):1101-1112. doi:10.1111/evo.12641"},"publication":"Evolution","page":"1101 - 1112","issue":"5","abstract":[{"lang":"eng","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 "direct" versus "indirect" 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."}],"type":"journal_article","pubrep_id":"560","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"4822","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:10:34Z","checksum":"fd8d23f476bc194419929b72ca265c02","file_name":"IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf","access_level":"open_access","file_size":188872,"content_type":"application/pdf","creator":"system"},{"file_id":"4823","relation":"main_file","date_created":"2018-12-12T10:10:35Z","date_updated":"2020-07-14T12:45:00Z","checksum":"b774911e70044641d556e258efcb52ef","file_name":"IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf","access_level":"open_access","creator":"system","file_size":577415,"content_type":"application/pdf"}],"_id":"1519","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 69","ddc":["570"],"status":"public","title":"The interpretation of selection coefficients"},{"scopus_import":1,"day":"12","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"580 - 607","publication":"VÖB Mitteilungen","citation":{"ama":"Bauer B, Blechl G, Bock C, et al. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 2015;68(3):580-607. doi:10.5281/zenodo.33178","ieee":"B. Bauer et al., “Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA,” VÖB Mitteilungen, vol. 68, no. 3. Verein Österreichischer Bibliothekare, pp. 580–607, 2015.","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. VÖB Mitteilungen. Verein Österreichischer Bibliothekare. https://doi.org/10.5281/zenodo.33178","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.","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.","mla":"Bauer, Bruno, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” VÖB Mitteilungen, vol. 68, no. 3, Verein Österreichischer Bibliothekare, 2015, pp. 580–607, doi:10.5281/zenodo.33178.","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.” VÖB Mitteilungen. Verein Österreichischer Bibliothekare, 2015. https://doi.org/10.5281/zenodo.33178."},"date_published":"2015-11-12T00:00:00Z","type":"journal_article","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."}],"issue":"3","ddc":["020"],"status":"public","title":"Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA","intvolume":" 68","_id":"1525","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"system","file_size":931707,"content_type":"application/pdf","file_name":"IST-2016-720-v1+1_OANA_OA-Empfehlungen_12-11-2015.pdf","access_level":"open_access","date_created":"2018-12-12T10:17:59Z","date_updated":"2020-07-14T12:45:00Z","checksum":"a495fe253bbc7615b1d60e9e85c94408","file_id":"5317","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"720","month":"11","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.5281/zenodo.33178","file_date_updated":"2020-07-14T12:45:00Z","publist_id":"5648","publication_status":"published","publisher":"Verein Österreichischer Bibliothekare","department":[{"_id":"E-Lib"}],"year":"2015","date_created":"2018-12-11T11:52:31Z","date_updated":"2021-01-12T06:51:22Z","volume":68,"author":[{"full_name":"Bauer, Bruno","first_name":"Bruno","last_name":"Bauer"},{"last_name":"Blechl","first_name":"Guido","full_name":"Blechl, Guido"},{"last_name":"Bock","first_name":"Christoph","full_name":"Bock, Christoph"},{"full_name":"Danowski, Patrick","last_name":"Danowski","first_name":"Patrick","orcid":"0000-0002-6026-4409","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","last_name":"Ferus","full_name":"Ferus, Andreas"},{"first_name":"Anton","last_name":"Graschopf","full_name":"Graschopf, Anton"},{"last_name":"König","first_name":"Thomas","full_name":"König, Thomas"},{"first_name":"Katja","last_name":"Mayer","full_name":"Mayer, Katja"},{"first_name":"Falk","last_name":"Reckling","full_name":"Reckling, Falk"},{"first_name":"Katharina","last_name":"Rieck","full_name":"Rieck, Katharina"},{"full_name":"Seitz, Peter","last_name":"Seitz","first_name":"Peter"},{"full_name":"Stöger, Herwig","first_name":"Herwig","last_name":"Stöger"},{"full_name":"Welzig, Elvira","last_name":"Welzig","first_name":"Elvira"}]},{"publisher":"ACM","department":[{"_id":"BeBi"}],"title":"Computational design of walking automata","status":"public","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1520","year":"2015","oa_version":"None","date_updated":"2021-01-12T06:51:21Z","date_created":"2018-12-11T11:52:30Z","author":[{"first_name":"Gaurav","last_name":"Bharaj","full_name":"Bharaj, Gaurav"},{"first_name":"Stelian","last_name":"Coros","full_name":"Coros, Stelian"},{"first_name":"Bernhard","last_name":"Thomaszewski","full_name":"Thomaszewski, Bernhard"},{"full_name":"Tompkin, James","last_name":"Tompkin","first_name":"James"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"},{"full_name":"Pfister, Hanspeter","first_name":"Hanspeter","last_name":"Pfister"}],"type":"conference","publist_id":"5655","abstract":[{"lang":"eng","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."}],"page":"93 - 100","quality_controlled":"1","citation":{"ama":"Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. Computational design of walking automata. In: ACM; 2015:93-100. doi:10.1145/2786784.2786803","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.","apa":"Bharaj, G., Coros, S., Thomaszewski, B., Tompkin, J., Bickel, B., & 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. https://doi.org/10.1145/2786784.2786803","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.","short":"G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, H. Pfister, in:, ACM, 2015, pp. 93–100.","mla":"Bharaj, Gaurav, et al. Computational Design of Walking Automata. ACM, 2015, pp. 93–100, doi:10.1145/2786784.2786803.","chicago":"Bharaj, Gaurav, Stelian Coros, Bernhard Thomaszewski, James Tompkin, Bernd Bickel, and Hanspeter Pfister. “Computational Design of Walking Automata,” 93–100. ACM, 2015. https://doi.org/10.1145/2786784.2786803."},"language":[{"iso":"eng"}],"doi":"10.1145/2786784.2786803","date_published":"2015-08-01T00:00:00Z","conference":{"location":"Los Angeles, CA, United States","start_date":"2015-08-07","end_date":"2015-08-09","name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation"},"scopus_import":1,"publication_identifier":{"isbn":["978-1-4503-3496-9"]},"month":"08","day":"01"},{"oa_version":"None","status":"public","title":"Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source","intvolume":" 42","_id":"1532","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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."}],"issue":"3","type":"journal_article","date_published":"2015-03-01T00:00:00Z","article_type":"original","page":"239 - 251","publication":"Functional Plant Biology","citation":{"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. Functional Plant Biology. 2015;42(3):239-251. doi:10.1071/FP14171","apa":"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. CSIRO. https://doi.org/10.1071/FP14171","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,” Functional Plant Biology, vol. 42, no. 3. CSIRO, pp. 239–251, 2015.","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.","short":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, U. Ludewig, Functional Plant Biology 42 (2015) 239–251.","mla":"Yang, Huaiyu, et al. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional Plant Biology, vol. 42, no. 3, CSIRO, 2015, pp. 239–51, doi:10.1071/FP14171.","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.” Functional Plant Biology. CSIRO, 2015. https://doi.org/10.1071/FP14171."},"day":"01","article_processing_charge":"No","scopus_import":"1","date_updated":"2022-05-24T09:02:24Z","date_created":"2018-12-11T11:52:34Z","volume":42,"author":[{"full_name":"Yang, Huaiyu","first_name":"Huaiyu","last_name":"Yang"},{"full_name":"Von Der Fecht Bartenbach, Jenny","last_name":"Von Der Fecht Bartenbach","first_name":"Jenny"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"first_name":"Jan","last_name":"Lohmann","full_name":"Lohmann, Jan"},{"full_name":"Neuhäuser, Benjamin","last_name":"Neuhäuser","first_name":"Benjamin"},{"full_name":"Ludewig, Uwe","last_name":"Ludewig","first_name":"Uwe"}],"publication_status":"published","publisher":"CSIRO","department":[{"_id":"JiFr"}],"year":"2015","pmid":1,"publist_id":"5639","language":[{"iso":"eng"}],"doi":"10.1071/FP14171","quality_controlled":"1","external_id":{"pmid":["32480670"]},"month":"03","publication_identifier":{"issn":["1445-4408"]}},{"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-15090-1_13","month":"01","publication_identifier":{"isbn":["978-3-319-15089-5"]},"publication_status":"published","department":[{"_id":"HeEd"}],"editor":[{"full_name":"Hotz, Ingrid","first_name":"Ingrid","last_name":"Hotz"},{"full_name":"Schultz, Thomas","first_name":"Thomas","last_name":"Schultz"}],"publisher":"Springer","year":"2015","date_created":"2018-12-11T11:52:33Z","date_updated":"2022-06-10T09:50:14Z","volume":40,"author":[{"first_name":"Valentin","last_name":"Zobel","full_name":"Zobel, Valentin"},{"full_name":"Reininghaus, Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus","first_name":"Jan"},{"last_name":"Hotz","first_name":"Ingrid","full_name":"Hotz, Ingrid"}],"edition":"1","publist_id":"5640","page":"257 - 267","publication":"Visualization and Processing of Higher Order Descriptors for Multi-Valued Data","citation":{"chicago":"Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” In Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, edited by Ingrid Hotz and Thomas Schultz, 1st ed., 40:257–67. Springer, 2015. https://doi.org/10.1007/978-3-319-15090-1_13.","mla":"Zobel, Valentin, et al. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, edited by Ingrid Hotz and Thomas Schultz, 1st ed., vol. 40, Springer, 2015, pp. 257–67, doi:10.1007/978-3-319-15090-1_13.","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.","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., & Hotz, I. (2015). Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In I. Hotz & T. Schultz (Eds.), Visualization and Processing of Higher Order Descriptors for Multi-Valued Data (1st ed., Vol. 40, pp. 257–267). Springer. https://doi.org/10.1007/978-3-319-15090-1_13","ieee":"V. Zobel, J. Reininghaus, and I. Hotz, “Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature,” in Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, 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. Visualization and Processing of Higher Order Descriptors for Multi-Valued Data. Vol 40. 1st ed. Springer; 2015:257-267. doi:10.1007/978-3-319-15090-1_13"},"date_published":"2015-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","title":"Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature","status":"public","intvolume":" 40","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1531","oa_version":"None","alternative_title":["Mathematics and Visualization"],"type":"book_chapter","abstract":[{"lang":"eng","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."}]},{"scopus_import":1,"day":"25","month":"09","citation":{"chicago":"Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” Physical Biology. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1478-3975/12/6/066003.","mla":"Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” Physical Biology, vol. 12, no. 6, 066003, IOP Publishing Ltd., 2015, doi:10.1088/1478-3975/12/6/066003.","short":"V. Bierbaum, S. Klumpp, Physical Biology 12 (2015).","ista":"Bierbaum V, Klumpp S. 2015. Impact of the cell division cycle on gene circuits. Physical Biology. 12(6), 066003.","apa":"Bierbaum, V., & Klumpp, S. (2015). Impact of the cell division cycle on gene circuits. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/12/6/066003","ieee":"V. Bierbaum and S. Klumpp, “Impact of the cell division cycle on gene circuits,” Physical Biology, vol. 12, no. 6. IOP Publishing Ltd., 2015.","ama":"Bierbaum V, Klumpp S. Impact of the cell division cycle on gene circuits. Physical Biology. 2015;12(6). doi:10.1088/1478-3975/12/6/066003"},"publication":"Physical Biology","quality_controlled":"1","date_published":"2015-09-25T00:00:00Z","doi":"10.1088/1478-3975/12/6/066003","language":[{"iso":"eng"}],"type":"journal_article","article_number":"066003","publist_id":"5641","issue":"6","abstract":[{"lang":"eng","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1530","year":"2015","publisher":"IOP Publishing Ltd.","intvolume":" 12","department":[{"_id":"MiSi"}],"title":"Impact of the cell division cycle on gene circuits","status":"public","publication_status":"published","author":[{"full_name":"Bierbaum, Veronika","last_name":"Bierbaum","first_name":"Veronika","id":"3FD04378-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Klumpp","first_name":"Stefan","full_name":"Klumpp, Stefan"}],"oa_version":"None","volume":12,"date_created":"2018-12-11T11:52:33Z","date_updated":"2021-01-12T06:51:25Z"},{"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2016-593-v1+1_Minimal_moment_equations.pdf","creator":"system","file_size":605355,"content_type":"application/pdf","file_id":"4641","relation":"main_file","checksum":"838657118ae286463a2b7737319f35ce","date_created":"2018-12-12T10:07:43Z","date_updated":"2020-07-14T12:45:01Z"}],"pubrep_id":"593","intvolume":" 143","status":"public","ddc":["000"],"title":"Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1539","issue":"24","abstract":[{"text":"Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space. ","lang":"eng"}],"type":"journal_article","date_published":"2015-12-22T00:00:00Z","citation":{"mla":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics, vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi:10.1063/1.4937937.","short":"J. Ruess, Journal of Chemical Physics 143 (2015).","chicago":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4937937.","ama":"Ruess J. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 2015;143(24). doi:10.1063/1.4937937","ista":"Ruess J. 2015. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 143(24), 244103.","apa":"Ruess, J. (2015). Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/1.4937937","ieee":"J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space,” Journal of Chemical Physics, vol. 143, no. 24. American Institute of Physics, 2015."},"publication":"Journal of Chemical Physics","has_accepted_license":"1","day":"22","scopus_import":1,"volume":143,"date_updated":"2021-01-12T06:51:28Z","date_created":"2018-12-11T11:52:36Z","author":[{"id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282","first_name":"Jakob","last_name":"Ruess","full_name":"Ruess, Jakob"}],"publisher":"American Institute of Physics","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"publication_status":"published","year":"2015","ec_funded":1,"publist_id":"5632","file_date_updated":"2020-07-14T12:45:01Z","article_number":"244103","language":[{"iso":"eng"}],"doi":"10.1063/1.4937937","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"month":"12"},{"intvolume":" 6","title":"Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1534","oa_version":"Published Version","file":[{"file_name":"IST-2016-485-v1+1_ncomms9822.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1852268,"creator":"system","relation":"main_file","file_id":"5259","date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-12T10:17:07Z","checksum":"3c06735fc7cd7e482ca830cbd26001bf"}],"pubrep_id":"485","type":"journal_article","abstract":[{"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.","lang":"eng"}],"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. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9822","ieee":"H. Wang et al., “Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","ama":"Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 2015;6. doi:10.1038/ncomms9822","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.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9822.","mla":"Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications, vol. 6, 8822, Nature Publishing Group, 2015, doi:10.1038/ncomms9822.","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)."},"publication":"Nature Communications","date_published":"2015-11-18T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"18","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","publication_status":"published","year":"2015","volume":6,"date_created":"2018-12-11T11:52:34Z","date_updated":"2021-01-12T06:51:26Z","author":[{"first_name":"Hongzhe","last_name":"Wang","full_name":"Wang, Hongzhe"},{"full_name":"Yang, Kezhen","last_name":"Yang","first_name":"Kezhen"},{"first_name":"Junjie","last_name":"Zou","full_name":"Zou, Junjie"},{"full_name":"Zhu, Lingling","first_name":"Lingling","last_name":"Zhu"},{"last_name":"Xie","first_name":"Zidian","full_name":"Xie, Zidian"},{"last_name":"Morita","first_name":"Miyoterao","full_name":"Morita, Miyoterao"},{"full_name":"Tasaka, Masao","last_name":"Tasaka","first_name":"Masao"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grotewold, Erich","last_name":"Grotewold","first_name":"Erich"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"full_name":"Sack, Fred","first_name":"Fred","last_name":"Sack"},{"last_name":"Le","first_name":"Jie","full_name":"Le, Jie"}],"article_number":"8822","ec_funded":1,"publist_id":"5637","file_date_updated":"2020-07-14T12:45:01Z","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1038/ncomms9822","month":"11"},{"publist_id":"5633","ec_funded":1,"date_updated":"2021-01-12T06:51:27Z","date_created":"2018-12-11T11:52:36Z","volume":112,"author":[{"orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","first_name":"Jakob","full_name":"Ruess, Jakob"},{"full_name":"Parise, Francesca","last_name":"Parise","first_name":"Francesca"},{"last_name":"Milias Argeitis","first_name":"Andreas","full_name":"Milias Argeitis, Andreas"},{"full_name":"Khammash, Mustafa","last_name":"Khammash","first_name":"Mustafa"},{"full_name":"Lygeros, John","first_name":"John","last_name":"Lygeros"}],"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"year":"2015","acknowledgement":"J.R., F.P., and J.L. acknowledge support from the European Commission under the Network of Excellence HYCON2 (highly-complex and networked control systems) and SystemsX.ch under the SignalX Project. J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme FP7/2007-2013 under REA (Research Executive Agency) Grant 291734. M.K. acknowledges support from Human Frontier Science Program Grant RP0061/2011 (www.hfsp.org). ","pmid":1,"month":"06","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1423947112","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"oa":1,"external_id":{"pmid":["26085136"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/","open_access":"1"}],"abstract":[{"text":"Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time.","lang":"eng"}],"issue":"26","type":"journal_article","oa_version":"Submitted Version","status":"public","title":"Iterative experiment design guides the characterization of a light-inducible gene expression circuit","intvolume":" 112","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1538","day":"30","scopus_import":1,"date_published":"2015-06-30T00:00:00Z","page":"8148 - 8153","publication":"PNAS","citation":{"mla":"Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS, vol. 112, no. 26, National Academy of Sciences, 2015, pp. 8148–53, doi:10.1073/pnas.1423947112.","short":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153.","chicago":"Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash, and John Lygeros. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1423947112.","ama":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 2015;112(26):8148-8153. doi:10.1073/pnas.1423947112","ista":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 112(26), 8148–8153.","apa":"Ruess, J., Parise, F., Milias Argeitis, A., Khammash, M., & Lygeros, J. (2015). Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1423947112","ieee":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative experiment design guides the characterization of a light-inducible gene expression circuit,” PNAS, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153, 2015."}},{"external_id":{"pmid":["25966692"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/"}],"oa":1,"quality_controlled":"1","doi":"10.2174/1874467208666150507105443","language":[{"iso":"eng"}],"month":"10","year":"2015","acknowledgement":"This work was supported by the Italian MIUR (PRIN 2010/2011 project 2010JFYFY2) and the University of Torino.","pmid":1,"publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Bentham Science Publishers","author":[{"full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","first_name":"David H"},{"full_name":"Marcantoni, Andrea","first_name":"Andrea","last_name":"Marcantoni"},{"full_name":"Carbone, Emilio","last_name":"Carbone","first_name":"Emilio"}],"date_created":"2018-12-11T11:52:35Z","date_updated":"2021-01-12T06:51:26Z","volume":8,"publist_id":"5636","publication":"Current Molecular Pharmacology","citation":{"mla":"Vandael, David H., et al. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” Current Molecular Pharmacology, vol. 8, no. 2, Bentham Science Publishers, 2015, pp. 149–61, doi:10.2174/1874467208666150507105443.","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.” Current Molecular Pharmacology. Bentham Science Publishers, 2015. https://doi.org/10.2174/1874467208666150507105443.","ama":"Vandael DH, Marcantoni A, Carbone E. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 2015;8(2):149-161. doi:10.2174/1874467208666150507105443","ista":"Vandael DH, Marcantoni A, Carbone E. 2015. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 8(2), 149–161.","ieee":"D. H. Vandael, A. Marcantoni, and E. Carbone, “Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells,” Current Molecular Pharmacology, vol. 8, no. 2. Bentham Science Publishers, pp. 149–161, 2015.","apa":"Vandael, D. H., Marcantoni, A., & Carbone, E. (2015). Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. Bentham Science Publishers. https://doi.org/10.2174/1874467208666150507105443"},"article_type":"original","page":"149 - 161","date_published":"2015-10-01T00:00:00Z","scopus_import":1,"day":"01","article_processing_charge":"No","_id":"1535","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells","status":"public","intvolume":" 8","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Neuronal and neuroendocrine L-type calcium channels (Cav1.2, Cav1.3) open readily at relatively low membrane potentials and allow Ca2+ to enter the cells near resting potentials. In this way, Cav1.2 and Cav1.3 shape the action potential waveform, contribute to gene expression, synaptic plasticity, neuronal differentiation, hormone secretion and pacemaker activity. In the chromaffin cells (CCs) of the adrenal medulla, Cav1.3 is highly expressed and is shown to support most of the pacemaking current that sustains action potential (AP) firings and part of the catecholamine secretion. Cav1.3 forms Ca2+-nanodomains with the fast inactivating BK channels and drives the resting SK currents. These latter set the inter-spike interval duration between consecutive spikes during spontaneous firing and the rate of spike adaptation during sustained depolarizations. Cav1.3 plays also a primary role in the switch from “tonic” to “burst” firing that occurs in mouse CCs when either the availability of voltage-gated Na channels (Nav) is reduced or the β2 subunit featuring the fast inactivating BK channels is deleted. Here, we discuss the functional role of these “neuronlike” firing modes in CCs and how Cav1.3 contributes to them. The open issue is to understand how these novel firing patterns are adapted to regulate the quantity of circulating catecholamines during resting condition or in response to acute and chronic stress."}],"issue":"2"},{"issue":"5","publist_id":"5635","abstract":[{"lang":"eng","text":"Strigolactones, first discovered as germination stimulants for parasitic weeds [1], are carotenoid-derived phytohormones that play major roles in inhibiting lateral bud outgrowth and promoting plant-mycorrhizal symbiosis [2-4]. Furthermore, strigolactones are involved in the regulation of lateral and adventitious root development, root cell division [5, 6], secondary growth [7], and leaf senescence [8]. Recently, we discovered the strigolactone transporter Petunia axillaris PLEIOTROPIC DRUG RESISTANCE 1 (PaPDR1), which is required for efficient mycorrhizal colonization and inhibition of lateral bud outgrowth [9]. However, how strigolactones are transported through the plant remained unknown. Here we show that PaPDR1 exhibits a cell-type-specific asymmetric localization in different root tissues. In root tips, PaPDR1 is co-expressed with the strigolactone biosynthetic gene DAD1 (CCD8), and it is localized at the apical membrane of root hypodermal cells, presumably mediating the shootward transport of strigolactone. Above the root tip, in the hypodermal passage cells that form gates for the entry of mycorrhizal fungi, PaPDR1 is present in the outer-lateral membrane, compatible with its postulated function as strigolactone exporter from root to soil. Transport studies are in line with our localization studies since (1) a papdr1 mutant displays impaired transport of strigolactones out of the root tip to the shoot as well as into the rhizosphere and (2) DAD1 expression and PIN1/PIN2 levels change in plants deregulated for PDR1 expression, suggestive of variations in endogenous strigolactone contents. In conclusion, our results indicate that the polar localizations of PaPDR1 mediate directional shootward strigolactone transport as well as localized exudation into the soil."}],"type":"journal_article","author":[{"full_name":"Sasse, Joëlle","last_name":"Sasse","first_name":"Joëlle"},{"full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","first_name":"Sibu"},{"full_name":"Gübeli, Christian","last_name":"Gübeli","first_name":"Christian"},{"last_name":"Liu","first_name":"Guowei","full_name":"Liu, Guowei"},{"last_name":"Cheng","first_name":"Xi","full_name":"Cheng, Xi"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Harro","last_name":"Bouwmeester","full_name":"Bouwmeester, Harro"},{"full_name":"Martinoia, Enrico","last_name":"Martinoia","first_name":"Enrico"},{"full_name":"Borghi, Lorenzo","last_name":"Borghi","first_name":"Lorenzo"}],"oa_version":"None","volume":25,"date_updated":"2021-01-12T06:51:27Z","date_created":"2018-12-11T11:52:35Z","_id":"1536","acknowledgement":"This work was funded by a grant of the Swiss National Foundation to E.M.\r\nWe thank Dr. José María Mateos (University of Zurich) for providing us with the vibratome, Prof. Dolf Weijers (Wageningen University, the Netherlands) for shipping us his set of ligation-independent cloning vectors, Prof. Bruno Humbel (University of Lausanne) for suggestions on GFP-PDR1 detection, and Dr. Undine Krügel (University of Zurich) and Prof. Michal Jasinski (Polish Academy of Science) for hints on protein quantification.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","publisher":"Cell Press","intvolume":" 25","department":[{"_id":"JiFr"}],"publication_status":"published","title":"Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport","status":"public","month":"02","day":"12","scopus_import":1,"date_published":"2015-02-12T00:00:00Z","doi":"10.1016/j.cub.2015.01.015","language":[{"iso":"eng"}],"citation":{"ama":"Sasse J, Simon S, Gübeli C, et al. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 2015;25(5):647-655. doi:10.1016/j.cub.2015.01.015","ista":"Sasse J, Simon S, Gübeli C, Liu G, Cheng X, Friml J, Bouwmeester H, Martinoia E, Borghi L. 2015. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 25(5), 647–655.","ieee":"J. Sasse et al., “Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport,” Current Biology, vol. 25, no. 5. Cell Press, pp. 647–655, 2015.","apa":"Sasse, J., Simon, S., Gübeli, C., Liu, G., Cheng, X., Friml, J., … Borghi, L. (2015). Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2015.01.015","mla":"Sasse, Joëlle, et al. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” Current Biology, vol. 25, no. 5, Cell Press, 2015, pp. 647–55, doi:10.1016/j.cub.2015.01.015.","short":"J. Sasse, S. Simon, C. Gübeli, G. Liu, X. Cheng, J. Friml, H. Bouwmeester, E. Martinoia, L. Borghi, Current Biology 25 (2015) 647–655.","chicago":"Sasse, Joëlle, Sibu Simon, Christian Gübeli, Guowei Liu, Xi Cheng, Jiří Friml, Harro Bouwmeester, Enrico Martinoia, and Lorenzo Borghi. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” Current Biology. Cell Press, 2015. https://doi.org/10.1016/j.cub.2015.01.015."},"publication":"Current Biology","page":"647 - 655","quality_controlled":"1"},{"page":"1295 - 1308","quality_controlled":"1","citation":{"ama":"Xia W, Domokos C, Xiong J, Cheong L, Yan S. Segmentation over detection via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for Video Technology. 2015;25(8):1295-1308. doi:10.1109/TCSVT.2014.2379972","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.","apa":"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. IEEE. https://doi.org/10.1109/TCSVT.2014.2379972","ieee":"W. Xia, C. Domokos, J. Xiong, L. Cheong, and S. Yan, “Segmentation over detection via optimal sparse reconstructions,” IEEE Transactions on Circuits and Systems for Video Technology, vol. 25, no. 8. IEEE, pp. 1295–1308, 2015.","mla":"Xia, Wei, et al. “Segmentation over Detection via Optimal Sparse Reconstructions.” IEEE Transactions on Circuits and Systems for Video Technology, vol. 25, no. 8, IEEE, 2015, pp. 1295–308, doi:10.1109/TCSVT.2014.2379972.","short":"W. Xia, C. Domokos, J. Xiong, L. Cheong, S. Yan, IEEE Transactions on Circuits and Systems for Video Technology 25 (2015) 1295–1308.","chicago":"Xia, Wei, Csaba Domokos, Junjun Xiong, Loongfah Cheong, and Shuicheng Yan. “Segmentation over Detection via Optimal Sparse Reconstructions.” IEEE Transactions on Circuits and Systems for Video Technology. IEEE, 2015. https://doi.org/10.1109/TCSVT.2014.2379972."},"publication":"IEEE Transactions on Circuits and Systems for Video Technology","language":[{"iso":"eng"}],"date_published":"2015-08-01T00:00:00Z","doi":"10.1109/TCSVT.2014.2379972","scopus_import":1,"day":"01","month":"08","department":[{"_id":"ChLa"}],"intvolume":" 25","publisher":"IEEE","title":"Segmentation over detection via optimal sparse reconstructions","publication_status":"published","status":"public","year":"2015","_id":"1533","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":25,"date_updated":"2021-01-12T06:51:26Z","date_created":"2018-12-11T11:52:34Z","author":[{"full_name":"Xia, Wei","first_name":"Wei","last_name":"Xia"},{"id":"492DACF8-F248-11E8-B48F-1D18A9856A87","first_name":"Csaba","last_name":"Domokos","full_name":"Domokos, Csaba"},{"full_name":"Xiong, Junjun","last_name":"Xiong","first_name":"Junjun"},{"full_name":"Cheong, Loongfah","first_name":"Loongfah","last_name":"Cheong"},{"full_name":"Yan, Shuicheng","first_name":"Shuicheng","last_name":"Yan"}],"type":"journal_article","issue":"8","publist_id":"5638","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."}]},{"project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.jtbi.2015.07.011","month":"10","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Elsevier","publication_status":"published","year":"2015","volume":383,"date_created":"2018-12-11T11:52:37Z","date_updated":"2021-01-12T06:51:29Z","author":[{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"},{"first_name":"Golnaz","last_name":"Badkobeh","full_name":"Badkobeh, Golnaz"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"last_name":"Çörüş","first_name":"Doğan","full_name":"Çörüş, Doğan"},{"full_name":"Dang, Duccuong","first_name":"Duccuong","last_name":"Dang"},{"full_name":"Friedrich, Tobias","last_name":"Friedrich","first_name":"Tobias"},{"first_name":"Per","last_name":"Lehre","full_name":"Lehre, Per"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"full_name":"Sutton, Andrew","first_name":"Andrew","last_name":"Sutton"},{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","first_name":"Barbora"}],"publist_id":"5629","ec_funded":1,"file_date_updated":"2020-07-14T12:45:01Z","page":"28 - 43","citation":{"ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011","ista":"Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 383, 28–43.","ieee":"T. Paixao et al., “Toward a unifying framework for evolutionary processes,” Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.","apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011","mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011.","short":"T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383 (2015) 28–43.","chicago":"Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011."},"publication":" Journal of Theoretical Biology","date_published":"2015-10-21T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"21","intvolume":" 383","title":"Toward a unifying framework for evolutionary processes","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1542","file":[{"creator":"system","file_size":595307,"content_type":"application/pdf","file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","access_level":"open_access","date_created":"2018-12-12T10:16:53Z","date_updated":"2020-07-14T12:45:01Z","checksum":"33b60ecfea60764756a9ee9df5eb65ca","file_id":"5244","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"483","type":"journal_article","abstract":[{"lang":"eng","text":"The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. "}]},{"type":"journal_article","issue":"1","abstract":[{"text":"Synaptic efficacy and precision are influenced by the coupling of voltage-gated Ca2+ channels (VGCCs) to vesicles. But because the topography of VGCCs and their proximity to vesicles is unknown, a quantitative understanding of the determinants of vesicular release at nanometer scale is lacking. To investigate this, we combined freeze-fracture replica immunogold labeling of Cav2.1 channels, local [Ca2+] imaging, and patch pipette perfusion of EGTA at the calyx of Held. Between postnatal day 7 and 21, VGCCs formed variable sized clusters and vesicular release became less sensitive to EGTA, whereas fixed Ca2+ buffer properties remained constant. Experimentally constrained reaction-diffusion simulations suggest that Ca2+ sensors for vesicular release are located at the perimeter of VGCC clusters (<30nm) and predict that VGCC number per cluster determines vesicular release probability without altering release time course. This "perimeter release model" provides a unifying framework accounting for developmental changes in both synaptic efficacy and time course.","lang":"eng"}],"intvolume":" 85","title":"Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development","status":"public","ddc":["570"],"_id":"1546","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":3080111,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-482-v1+1_1-s2.0-S0896627314010472-main.pdf","checksum":"725f4d5be2dbb44b283ce722645ef37d","date_created":"2018-12-12T10:15:47Z","date_updated":"2020-07-14T12:45:01Z","relation":"main_file","file_id":"5170"}],"oa_version":"Published Version","pubrep_id":"482","scopus_import":1,"has_accepted_license":"1","day":"07","page":"145 - 158","citation":{"chicago":"Nakamura, Yukihiro, Harumi Harada, Naomi Kamasawa, Ko Matsui, Jason Rothman, Ryuichi Shigemoto, R Angus Silver, David Digregorio, and Tomoyuki Takahashi. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2014.11.019.","short":"Y. Nakamura, H. Harada, N. Kamasawa, K. Matsui, J. Rothman, R. Shigemoto, R.A. Silver, D. Digregorio, T. Takahashi, Neuron 85 (2015) 145–158.","mla":"Nakamura, Yukihiro, et al. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” Neuron, vol. 85, no. 1, Elsevier, 2015, pp. 145–58, doi:10.1016/j.neuron.2014.11.019.","ieee":"Y. Nakamura et al., “Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development,” Neuron, vol. 85, no. 1. Elsevier, pp. 145–158, 2015.","apa":"Nakamura, Y., Harada, H., Kamasawa, N., Matsui, K., Rothman, J., Shigemoto, R., … Takahashi, T. (2015). Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.11.019","ista":"Nakamura Y, Harada H, Kamasawa N, Matsui K, Rothman J, Shigemoto R, Silver RA, Digregorio D, Takahashi T. 2015. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 85(1), 145–158.","ama":"Nakamura Y, Harada H, Kamasawa N, et al. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 2015;85(1):145-158. doi:10.1016/j.neuron.2014.11.019"},"publication":"Neuron","date_published":"2015-01-07T00:00:00Z","publist_id":"5625","file_date_updated":"2020-07-14T12:45:01Z","publisher":"Elsevier","department":[{"_id":"RySh"}],"publication_status":"published","year":"2015","acknowledgement":"This work was supported by the Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency to T.T. and R.S.; by the funding provided by Okinawa Institute of Science and Technology (OIST) to T.T. and Y.N.; by JSPS Core-to-Core Program, A. Advanced Networks to T.T.; by the Grant-in-Aid for Young Scientists from the Japanese Ministry of Education, Culture, Sports, Science and Technology (#23700474) to Y.N.; by the Centre National de la Recherche Scientifique through the Actions Thematiques et Initatives sur Programme, Fondation Fyssen, Fondation pour la Recherche Medicale, Federation pour la Recherche sur le Cerveau, Agence Nationale de la Recherche (ANR-2007-Neuro-008-01 and ANR-2010-BLAN-1411-01) to D.D. and Y.N.; and by the European Commission Coordination Action ENINET (LSHM-CT-2005-19063) to D.D. and R.A.S. R.A.S. and J.S.R. were funded by Wellcome Trust Senior (064413) and Principal (095667) Research Fellowship and an ERC advance grant (294667) to RAS.","volume":85,"date_created":"2018-12-11T11:52:39Z","date_updated":"2021-01-12T06:51:31Z","author":[{"full_name":"Nakamura, Yukihiro","last_name":"Nakamura","first_name":"Yukihiro"},{"first_name":"Harumi","last_name":"Harada","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi"},{"full_name":"Kamasawa, Naomi","first_name":"Naomi","last_name":"Kamasawa"},{"full_name":"Matsui, Ko","last_name":"Matsui","first_name":"Ko"},{"last_name":"Rothman","first_name":"Jason","full_name":"Rothman, Jason"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"full_name":"Silver, R Angus","first_name":"R Angus","last_name":"Silver"},{"first_name":"David","last_name":"Digregorio","full_name":"Digregorio, David"},{"full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki","last_name":"Takahashi"}],"month":"01","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2014.11.019"},{"abstract":[{"text":"We present XSpeed a parallel state-space exploration algorithm for continuous systems with linear dynamics and nondeterministic inputs. The motivation of having parallel algorithms is to exploit the computational power of multi-core processors to speed-up performance. The parallelization is achieved on two fronts. First, we propose a parallel implementation of the support function algorithm by sampling functions in parallel. Second, we propose a parallel state-space exploration by slicing the time horizon and computing the reachable states in the time slices in parallel. The second method can be however applied only to a class of linear systems with invertible dynamics and fixed input. A GP-GPU implementation is also presented following a lazy evaluation strategy on support functions. The parallel algorithms are implemented in the tool XSpeed. We evaluated the performance on two benchmarks including an 28 dimension Helicopter model. Comparison with the sequential counterpart shows a maximum speed-up of almost 7× on a 6 core, 12 thread Intel Xeon CPU E5-2420 processor. Our GP-GPU implementation shows a maximum speed-up of 12× over the sequential implementation and 53× over SpaceEx (LGG scenario), the state of the art tool for reachability analysis of linear hybrid systems. Experiments illustrate that our parallel algorithm with time slicing not only speeds-up performance but also improves precision.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"None","_id":"1541","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"XSpeed: Accelerating reachability analysis on multi-core processors","intvolume":" 9434","day":"28","scopus_import":1,"series_title":"Lecture Notes in Computer Science","date_published":"2015-11-28T00:00:00Z","citation":{"short":"R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, R. Grosu, 9434 (2015) 3–18.","mla":"Ray, Rajarshi, et al. XSpeed: Accelerating Reachability Analysis on Multi-Core Processors. Vol. 9434, Springer, 2015, pp. 3–18, doi:10.1007/978-3-319-26287-1_1.","chicago":"Ray, Rajarshi, Amit Gurung, Binayak Das, Ezio Bartocci, Sergiy Bogomolov, and Radu Grosu. “XSpeed: Accelerating Reachability Analysis on Multi-Core Processors.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_1.","ama":"Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. XSpeed: Accelerating reachability analysis on multi-core processors. 2015;9434:3-18. doi:10.1007/978-3-319-26287-1_1","apa":"Ray, R., Gurung, A., Das, B., Bartocci, E., Bogomolov, S., & Grosu, R. (2015). XSpeed: Accelerating reachability analysis on multi-core processors. Presented at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_1","ieee":"R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, and R. Grosu, “XSpeed: Accelerating reachability analysis on multi-core processors,” vol. 9434. Springer, pp. 3–18, 2015.","ista":"Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. 2015. XSpeed: Accelerating reachability analysis on multi-core processors. 9434, 3–18."},"page":"3 - 18","ec_funded":1,"publist_id":"5630","author":[{"full_name":"Ray, Rajarshi","last_name":"Ray","first_name":"Rajarshi"},{"full_name":"Gurung, Amit","first_name":"Amit","last_name":"Gurung"},{"full_name":"Das, Binayak","first_name":"Binayak","last_name":"Das"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"last_name":"Bogomolov","first_name":"Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","full_name":"Bogomolov, Sergiy"},{"full_name":"Grosu, Radu","first_name":"Radu","last_name":"Grosu"}],"date_created":"2018-12-11T11:52:37Z","date_updated":"2020-08-11T10:09:17Z","volume":9434,"year":"2015","acknowledgement":"This work was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","month":"11","conference":{"end_date":"2015-11-19","location":"Haifa, Israel","start_date":"2015-11-17","name":"HVC: Haifa Verification Conference"},"doi":"10.1007/978-3-319-26287-1_1","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}]},{"_id":"1543","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","intvolume":" 169","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"status":"public","publication_status":"published","title":"A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants","author":[{"first_name":"Yadira","last_name":"Olvera Carrillo","full_name":"Olvera Carrillo, Yadira"},{"first_name":"Michiel","last_name":"Van Bel","full_name":"Van Bel, Michiel"},{"first_name":"Tom","last_name":"Van Hautegem","full_name":"Van Hautegem, Tom"},{"full_name":"Fendrych, Matyas","last_name":"Fendrych","first_name":"Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Huysmans, Marlies","first_name":"Marlies","last_name":"Huysmans"},{"full_name":"Šimášková, Mária","last_name":"Šimášková","first_name":"Mária"},{"full_name":"Van Durme, Matthias","first_name":"Matthias","last_name":"Van Durme"},{"first_name":"Pierre","last_name":"Buscaill","full_name":"Buscaill, Pierre"},{"last_name":"Rivas","first_name":"Susana","full_name":"Rivas, Susana"},{"full_name":"Coll, Núria","first_name":"Núria","last_name":"Coll"},{"last_name":"Coppens","first_name":"Frederik","full_name":"Coppens, Frederik"},{"first_name":"Steven","last_name":"Maere","full_name":"Maere, Steven"},{"full_name":"Nowack, Moritz","last_name":"Nowack","first_name":"Moritz"}],"oa_version":"None","volume":169,"date_updated":"2021-01-12T06:51:30Z","date_created":"2018-12-11T11:52:38Z","type":"journal_article","issue":"4","publist_id":"5628","abstract":[{"text":"A plethora of diverse programmed cell death (PCD) processes has been described in living organisms. In animals and plants, different forms of PCD play crucial roles in development, immunity, and responses to the environment. While the molecular control of some animal PCD forms such as apoptosis is known in great detail, we still know comparatively little about the regulation of the diverse types of plant PCD. In part, this deficiency in molecular understanding is caused by the lack of reliable reporters to detect PCD processes. Here, we addressed this issue by using a combination of bioinformatics approaches to identify commonly regulated genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana). Our results indicate that the transcriptional signatures of developmentally controlled cell death are largely distinct from the ones associated with environmentally induced cell death. Moreover, different cases of developmental PCD share a set of cell death-associated genes. Most of these genes are evolutionary conserved within the green plant lineage, arguing for an evolutionary conserved core machinery of developmental PCD. Based on this information, we established an array of specific promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators represent a powerful resource that can be used in addition to established morphological and biochemical methods to detect and analyze PCD processes in vivo and in planta.","lang":"eng"}],"citation":{"chicago":"Olvera Carrillo, Yadira, Michiel Van Bel, Tom Van Hautegem, Matyas Fendrych, Marlies Huysmans, Mária Šimášková, Matthias Van Durme, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” Plant Physiology. American Society of Plant Biologists, 2015. https://doi.org/10.1104/pp.15.00769.","short":"Y. Olvera Carrillo, M. Van Bel, T. Van Hautegem, M. Fendrych, M. Huysmans, M. Šimášková, M. Van Durme, P. Buscaill, S. Rivas, N. Coll, F. Coppens, S. Maere, M. Nowack, Plant Physiology 169 (2015) 2684–2699.","mla":"Olvera Carrillo, Yadira, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” Plant Physiology, vol. 169, no. 4, American Society of Plant Biologists, 2015, pp. 2684–99, doi:10.1104/pp.15.00769.","ieee":"Y. Olvera Carrillo et al., “A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants,” Plant Physiology, vol. 169, no. 4. American Society of Plant Biologists, pp. 2684–2699, 2015.","apa":"Olvera Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans, M., Šimášková, M., … Nowack, M. (2015). A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.15.00769","ista":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, Fendrych M, Huysmans M, Šimášková M, Van Durme M, Buscaill P, Rivas S, Coll N, Coppens F, Maere S, Nowack M. 2015. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 169(4), 2684–2699.","ama":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, et al. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 2015;169(4):2684-2699. doi:10.1104/pp.15.00769"},"publication":"Plant Physiology","page":"2684 - 2699","doi":"10.1104/pp.15.00769","date_published":"2015-12-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"12"},{"month":"04","quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/","open_access":"1"}],"external_id":{"pmid":["25997350"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/bs.mcb.2015.01.007","publist_id":"5627","publisher":"Academic Press","department":[{"_id":"MaLo"}],"publication_status":"published","pmid":1,"year":"2015","volume":128,"date_updated":"2021-01-12T06:51:30Z","date_created":"2018-12-11T11:52:38Z","author":[{"full_name":"Nguyen, Phuong","last_name":"Nguyen","first_name":"Phuong"},{"last_name":"Field","first_name":"Christine","full_name":"Field, Christine"},{"first_name":"Aaron","last_name":"Groen","full_name":"Groen, Aaron"},{"first_name":"Timothy","last_name":"Mitchison","full_name":"Mitchison, Timothy"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"}],"scopus_import":1,"day":"08","page":"223 - 241","citation":{"short":"P. Nguyen, C. Field, A. Groen, T. Mitchison, M. Loose, in:, Building a Cell from Its Components Parts, Academic Press, 2015, pp. 223–241.","mla":"Nguyen, Phuong, et al. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” Building a Cell from Its Components Parts, vol. 128, Academic Press, 2015, pp. 223–41, doi:10.1016/bs.mcb.2015.01.007.","chicago":"Nguyen, Phuong, Christine Field, Aaron Groen, Timothy Mitchison, and Martin Loose. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” In Building a Cell from Its Components Parts, 128:223–41. Academic Press, 2015. https://doi.org/10.1016/bs.mcb.2015.01.007.","ama":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from Its Components Parts. Vol 128. Academic Press; 2015:223-241. doi:10.1016/bs.mcb.2015.01.007","ieee":"P. Nguyen, C. Field, A. Groen, T. Mitchison, and M. Loose, “Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins,” in Building a Cell from its Components Parts, vol. 128, Academic Press, 2015, pp. 223–241.","apa":"Nguyen, P., Field, C., Groen, A., Mitchison, T., & Loose, M. (2015). Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In Building a Cell from its Components Parts (Vol. 128, pp. 223–241). Academic Press. https://doi.org/10.1016/bs.mcb.2015.01.007","ista":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. 2015.Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from its Components Parts. vol. 128, 223–241."},"publication":"Building a Cell from its Components Parts","date_published":"2015-04-08T00:00:00Z","type":"book_chapter","abstract":[{"lang":"eng","text":"Cell division in prokaryotes and eukaryotes is commonly initiated by the well-controlled binding of proteins to the cytoplasmic side of the cell membrane. However, a precise characterization of the spatiotemporal dynamics of membrane-bound proteins is often difficult to achieve in vivo. Here, we present protocols for the use of supported lipid bilayers to rebuild the cytokinetic machineries of cells with greatly different dimensions: the bacterium Escherichia coli and eggs of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence microscopy, these experimental setups allow for precise quantitative analyses of membrane-bound proteins. The protocols described to obtain glass-supported membranes from bacterial and vertebrate lipids can be used as starting points for other reconstitution experiments. We believe that similar biochemical assays will be instrumental to study the biochemistry and biophysics underlying a variety of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility."}],"intvolume":" 128","status":"public","title":"Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins","_id":"1544","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version"},{"date_updated":"2021-01-12T06:51:29Z","date_created":"2018-12-11T11:52:36Z","oa_version":"None","volume":66,"author":[{"full_name":"Robert, Hélène","first_name":"Hélène","last_name":"Robert"},{"full_name":"Crhák Khaitová, Lucie","last_name":"Crhák Khaitová","first_name":"Lucie"},{"full_name":"Mroue, Souad","first_name":"Souad","last_name":"Mroue"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"}],"status":"public","title":"The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"EvBe"}],"intvolume":" 66","_id":"1540","acknowledgement":"The work was supported by grants from: the Employment of Best Young Scientists for International Cooperation Empowerment/OPVKII programme (CZ.1.07/2.3.00/30.0037) to HSR and LCK; the Czech Science Foundation (GA13-39982S) to EB, LCK and SM; and the SoMoPro II programme (3SGA5602), cofinanced by the South-Moravian Region and the EU (FP7/2007–2013 People Programme), to HSR.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","abstract":[{"lang":"eng","text":"Plant sexual reproduction involves highly structured and specialized organs: stamens (male) and gynoecia (female, containing ovules). These organs synchronously develop within protective flower buds, until anthesis, via tightly coordinated mechanisms that are essential for effective fertilization and production of viable seeds. The phytohormone auxin is one of the key endogenous signalling molecules controlling initiation and development of these, and other, plant organs. In particular, its uneven distribution, resulting from tightly controlled production, metabolism and directional transport, is an important morphogenic factor. In this review we discuss how developmentally controlled and localized auxin biosynthesis and transport contribute to the coordinated development of plants' reproductive organs, and their fertilized derivatives (embryos) via the regulation of auxin levels and distribution within and around them. Current understanding of the links between de novo local auxin biosynthesis, auxin transport and/or signalling is presented to highlight the importance of the non-cell autonomous action of auxin production on development and morphogenesis of reproductive organs and embryos. An overview of transcription factor families, which spatiotemporally define local auxin production by controlling key auxin biosynthetic enzymes, is also presented."}],"publist_id":"5631","issue":"16","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1093/jxb/erv256","date_published":"2015-05-05T00:00:00Z","quality_controlled":"1","page":"5029 - 5042","publication":"Journal of Experimental Botany","citation":{"ama":"Robert H, Crhák Khaitová L, Mroue S, Benková E. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. 2015;66(16):5029-5042. doi:10.1093/jxb/erv256","apa":"Robert, H., Crhák Khaitová, L., Mroue, S., & Benková, E. (2015). The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv256","ieee":"H. Robert, L. Crhák Khaitová, S. Mroue, and E. Benková, “The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis,” Journal of Experimental Botany, vol. 66, no. 16. Oxford University Press, pp. 5029–5042, 2015.","ista":"Robert H, Crhák Khaitová L, Mroue S, Benková E. 2015. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. 66(16), 5029–5042.","short":"H. Robert, L. Crhák Khaitová, S. Mroue, E. Benková, Journal of Experimental Botany 66 (2015) 5029–5042.","mla":"Robert, Hélène, et al. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” Journal of Experimental Botany, vol. 66, no. 16, Oxford University Press, 2015, pp. 5029–42, doi:10.1093/jxb/erv256.","chicago":"Robert, Hélène, Lucie Crhák Khaitová, Souad Mroue, and Eva Benková. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv256."},"day":"05","month":"05","scopus_import":1},{"scopus_import":1,"has_accepted_license":"1","day":"04","page":"1 - 30","citation":{"chicago":"El Masri, Leila, Antoine Branca, Anna Sheppard, Andrei Papkou, David Laehnemann, Patrick Guenther, Swantje Prahl, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002169.","short":"L. El Masri, A. Branca, A. Sheppard, A. Papkou, D. Laehnemann, P. Guenther, S. Prahl, M. Saebelfeld, J. Hollensteiner, H. Liesegang, E. Brzuszkiewicz, R. Daniel, N. Michiels, R. Schulte, J. Kurtz, P. Rosenstiel, A. Telschow, E. Bornberg Bauer, H. Schulenburg, PLoS Biology 13 (2015) 1–30.","mla":"El Masri, Leila, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS Biology, vol. 13, no. 6, Public Library of Science, 2015, pp. 1–30, doi:10.1371/journal.pbio.1002169.","apa":"El Masri, L., Branca, A., Sheppard, A., Papkou, A., Laehnemann, D., Guenther, P., … Schulenburg, H. (2015). Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002169","ieee":"L. El Masri et al., “Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes,” PLoS Biology, vol. 13, no. 6. Public Library of Science, pp. 1–30, 2015.","ista":"El Masri L, Branca A, Sheppard A, Papkou A, Laehnemann D, Guenther P, Prahl S, Saebelfeld M, Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels N, Schulte R, Kurtz J, Rosenstiel P, Telschow A, Bornberg Bauer E, Schulenburg H. 2015. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. 13(6), 1–30.","ama":"El Masri L, Branca A, Sheppard A, et al. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. 2015;13(6):1-30. doi:10.1371/journal.pbio.1002169"},"publication":"PLoS Biology","date_published":"2015-06-04T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Reciprocal coevolution between host and pathogen is widely seen as a major driver of evolution and biological innovation. Yet, to date, the underlying genetic mechanisms and associated trait functions that are unique to rapid coevolutionary change are generally unknown. We here combined experimental evolution of the bacterial biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans with large-scale phenotyping, whole genome analysis, and functional genetics to demonstrate the selective benefit of pathogen virulence and the underlying toxin genes during the adaptation process. We show that: (i) high virulence was specifically favoured during pathogen–host coevolution rather than pathogen one-sided adaptation to a nonchanging host or to an environment without host; (ii) the pathogen genotype BT-679 with known nematocidal toxin genes and high virulence specifically swept to fixation in all of the independent replicate populations under coevolution but only some under one-sided adaptation; (iii) high virulence in the BT-679-dominated populations correlated with elevated copy numbers of the plasmid containing the nematocidal toxin genes; (iv) loss of virulence in a toxin-plasmid lacking BT-679 isolate was reconstituted by genetic reintroduction or external addition of the toxins.We conclude that sustained coevolution is distinct from unidirectional selection in shaping the pathogen's genome and life history characteristics. To our knowledge, this study is the first to characterize the pathogen genes involved in coevolutionary adaptation in an animal host–pathogen interaction system."}],"intvolume":" 13","status":"public","title":"Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes","ddc":["570"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1551","file":[{"file_size":3468956,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-481-v1+1_journal.pbio.1002169.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:14:13Z","checksum":"30dee7a2c11ed09f2f5634655c0146f8","relation":"main_file","file_id":"5063"}],"oa_version":"Published Version","pubrep_id":"481","month":"06","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.1002169","ec_funded":1,"publist_id":"5620","file_date_updated":"2020-07-14T12:45:02Z","publisher":"Public Library of Science","department":[{"_id":"SyCr"}],"publication_status":"published","year":"2015","acknowledgement":"We are very grateful for funding from the German Science Foundation (DFG) to HS (SCHU 1415/8, SCHU 1415/9), PR (RO 2994/3), EBB (BO 2544/7), HL (LI 1690/2), AT (TE 976/2), RDS (SCHU 2522/1), JK (KU 1929/4); from the Kiel Excellence Cluster Inflammation at Interfaces to HS and PR; and from the ISTFELLOW program (Co-fund Marie Curie Actions of the European Commission) to LM.","volume":13,"date_created":"2018-12-11T11:52:40Z","date_updated":"2021-01-12T06:51:33Z","author":[{"full_name":"El Masri, Leila","last_name":"El Masri","first_name":"Leila","id":"349A6E66-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Antoine","last_name":"Branca","full_name":"Branca, Antoine"},{"full_name":"Sheppard, Anna","first_name":"Anna","last_name":"Sheppard"},{"last_name":"Papkou","first_name":"Andrei","full_name":"Papkou, Andrei"},{"first_name":"David","last_name":"Laehnemann","full_name":"Laehnemann, David"},{"full_name":"Guenther, Patrick","first_name":"Patrick","last_name":"Guenther"},{"first_name":"Swantje","last_name":"Prahl","full_name":"Prahl, Swantje"},{"full_name":"Saebelfeld, Manja","last_name":"Saebelfeld","first_name":"Manja"},{"full_name":"Hollensteiner, Jacqueline","last_name":"Hollensteiner","first_name":"Jacqueline"},{"first_name":"Heiko","last_name":"Liesegang","full_name":"Liesegang, Heiko"},{"first_name":"Elzbieta","last_name":"Brzuszkiewicz","full_name":"Brzuszkiewicz, Elzbieta"},{"last_name":"Daniel","first_name":"Rolf","full_name":"Daniel, Rolf"},{"full_name":"Michiels, Nico","first_name":"Nico","last_name":"Michiels"},{"first_name":"Rebecca","last_name":"Schulte","full_name":"Schulte, Rebecca"},{"last_name":"Kurtz","first_name":"Joachim","full_name":"Kurtz, Joachim"},{"first_name":"Philip","last_name":"Rosenstiel","full_name":"Rosenstiel, Philip"},{"full_name":"Telschow, Arndt","first_name":"Arndt","last_name":"Telschow"},{"full_name":"Bornberg Bauer, Erich","first_name":"Erich","last_name":"Bornberg Bauer"},{"full_name":"Schulenburg, Hinrich","first_name":"Hinrich","last_name":"Schulenburg"}]},{"citation":{"short":"C. Mckenzie, I. Sanchez-Romero, H.L. Janovjak, in:, Novel Chemical Tools to Study Ion Channel Biology, Springer, 2015, pp. 101–117.","mla":"Mckenzie, Catherine, et al. “Flipping the Photoswitch: Ion Channels under Light Control.” Novel Chemical Tools to Study Ion Channel Biology, vol. 869, Springer, 2015, pp. 101–17, doi:10.1007/978-1-4939-2845-3_6.","chicago":"Mckenzie, Catherine, Inmaculada Sanchez-Romero, and Harald L Janovjak. “Flipping the Photoswitch: Ion Channels under Light Control.” In Novel Chemical Tools to Study Ion Channel Biology, 869:101–17. Advances in Experimental Medicine and Biology. Springer, 2015. https://doi.org/10.1007/978-1-4939-2845-3_6.","ama":"Mckenzie C, Sanchez-Romero I, Janovjak HL. Flipping the photoswitch: Ion channels under light control. In: Novel Chemical Tools to Study Ion Channel Biology. Vol 869. Advances in Experimental Medicine and Biology. Springer; 2015:101-117. doi:10.1007/978-1-4939-2845-3_6","ieee":"C. Mckenzie, I. Sanchez-Romero, and H. L. Janovjak, “Flipping the photoswitch: Ion channels under light control,” in Novel chemical tools to study ion channel biology, vol. 869, Springer, 2015, pp. 101–117.","apa":"Mckenzie, C., Sanchez-Romero, I., & Janovjak, H. L. (2015). Flipping the photoswitch: Ion channels under light control. In Novel chemical tools to study ion channel biology (Vol. 869, pp. 101–117). Springer. https://doi.org/10.1007/978-1-4939-2845-3_6","ista":"Mckenzie C, Sanchez-Romero I, Janovjak HL. 2015.Flipping the photoswitch: Ion channels under light control. In: Novel chemical tools to study ion channel biology. vol. 869, 101–117."},"publication":"Novel chemical tools to study ion channel biology","page":"101 - 117","date_published":"2015-09-18T00:00:00Z","scopus_import":1,"series_title":"Advances in Experimental Medicine and Biology","has_accepted_license":"1","day":"18","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1549","intvolume":" 869","ddc":["571","576"],"title":"Flipping the photoswitch: Ion channels under light control","status":"public","pubrep_id":"839","oa_version":"Submitted Version","file":[{"file_name":"IST-2017-839-v1+1_mckenzie.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1919655,"file_id":"4854","relation":"main_file","date_created":"2018-12-12T10:11:02Z","date_updated":"2020-07-14T12:45:01Z","checksum":"bd1bfdf2423a0c3b6e7cabfa8b44bc0f"}],"type":"book_chapter","abstract":[{"text":"Nature has incorporated small photochromic molecules, colloquially termed 'photoswitches', in photoreceptor proteins to sense optical cues in photo-taxis and vision. While Nature's ability to employ light-responsive functionalities has long been recognized, it was not until recently that scientists designed, synthesized and applied synthetic photochromes to manipulate many of which open rapidly and locally in their native cell types, biological processes with the temporal and spatial resolution of light. Ion channels in particular have come to the forefront of proteins that can be put under the designer control of synthetic photochromes. Photochromic ion channel controllers are comprised of three classes, photochromic soluble ligands (PCLs), photochromic tethered ligands (PTLs) and photochromic crosslinkers (PXs), and in each class ion channel functionality is controlled through reversible changes in photochrome structure. By acting as light-dependent ion channel agonists, antagonist or modulators, photochromic controllers effectively converted a wide range of ion channels, including voltage-gated ion channels, 'leak channels', tri-, tetra- and pentameric ligand-gated ion channels, and temperaturesensitive ion channels, into man-made photoreceptors. Control by photochromes can be reversible, unlike in the case of 'caged' compounds, and non-invasive with high spatial precision, unlike pharmacology and electrical manipulation. Here, we introduce design principles of emerging photochromic molecules that act on ion channels and discuss the impact that these molecules are beginning to have on ion channel biophysics and neuronal physiology.","lang":"eng"}],"oa":1,"quality_controlled":"1","doi":"10.1007/978-1-4939-2845-3_6","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-4939-2844-6"]},"month":"09","year":"2015","publisher":"Springer","department":[{"_id":"HaJa"}],"publication_status":"published","author":[{"full_name":"Mckenzie, Catherine","first_name":"Catherine","last_name":"Mckenzie","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Inmaculada","last_name":"Sanchez Romero","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","full_name":"Sanchez Romero, Inmaculada"},{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"}],"volume":869,"date_updated":"2021-01-12T06:51:32Z","date_created":"2018-12-11T11:52:39Z","publist_id":"5622","file_date_updated":"2020-07-14T12:45:01Z"},{"day":"01","scopus_import":1,"date_published":"2015-12-01T00:00:00Z","citation":{"mla":"Milutinovic, Barbara, et al. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” Applied and Environmental Microbiology, vol. 81, no. 23, American Society for Microbiology, 2015, pp. 8135–44, doi:10.1128/AEM.02051-15.","short":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, J. Kurtz, Applied and Environmental Microbiology 81 (2015) 8135–8144.","chicago":"Milutinovic, Barbara, Christina Höfling, Momir Futo, Jörn Scharsack, and Joachim Kurtz. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” Applied and Environmental Microbiology. American Society for Microbiology, 2015. https://doi.org/10.1128/AEM.02051-15.","ama":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 2015;81(23):8135-8144. doi:10.1128/AEM.02051-15","ista":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. 2015. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 81(23), 8135–8144.","apa":"Milutinovic, B., Höfling, C., Futo, M., Scharsack, J., & Kurtz, J. (2015). Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. American Society for Microbiology. https://doi.org/10.1128/AEM.02051-15","ieee":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, and J. Kurtz, “Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination,” Applied and Environmental Microbiology, vol. 81, no. 23. American Society for Microbiology, pp. 8135–8144, 2015."},"publication":"Applied and Environmental Microbiology","page":"8135 - 8144","issue":"23","abstract":[{"text":"Reproduction within a host and transmission to the next host are crucial for the virulence and fitness of pathogens. Nevertheless, basic knowledge about such parameters is often missing from the literature, even for well-studied bacteria, such as Bacillus thuringiensis, an endospore-forming insect pathogen, which infects its hosts via the oral route. To characterize bacterial replication success, we made use of an experimental oral infection system for the red flour beetle Tribolium castaneum and developed a flow cytometric assay for the quantification of both spore ingestion by the individual beetle larvae and the resulting spore load after bacterial replication and resporulation within cadavers. On average, spore numbers increased 460-fold, showing that Bacillus thuringiensis grows and replicates successfully in insect cadavers. By inoculating cadaver-derived spores and spores from bacterial stock cultures into nutrient medium, we next investigated outgrowth characteristics of vegetative cells and found that cadaver- derived bacteria showed reduced growth compared to bacteria from the stock cultures. Interestingly, this reduced growth was a consequence of inhibited spore germination, probably originating from the host and resulting in reduced host mortality in subsequent infections by cadaver-derived spores. Nevertheless, we further showed that Bacillus thuringiensis transmission was possible via larval cannibalism when no other food was offered. These results contribute to our understanding of the ecology of Bacillus thuringiensis as an insect pathogen.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","_id":"1548","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 81","status":"public","title":"Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination","month":"12","doi":"10.1128/AEM.02051-15","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651099/"}],"external_id":{"pmid":["26386058"]},"oa":1,"quality_controlled":"1","publist_id":"5623","author":[{"full_name":"Milutinovic, Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8214-4758","first_name":"Barbara","last_name":"Milutinovic"},{"full_name":"Höfling, Christina","first_name":"Christina","last_name":"Höfling"},{"last_name":"Futo","first_name":"Momir","full_name":"Futo, Momir"},{"first_name":"Jörn","last_name":"Scharsack","full_name":"Scharsack, Jörn"},{"first_name":"Joachim","last_name":"Kurtz","full_name":"Kurtz, Joachim"}],"volume":81,"date_created":"2018-12-11T11:52:39Z","date_updated":"2021-01-12T06:51:31Z","pmid":1,"year":"2015","department":[{"_id":"SyCr"}],"publisher":"American Society for Microbiology","publication_status":"published"},{"month":"04","day":"09","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2015-04-09T00:00:00Z","doi":"10.1016/j.cell.2015.01.056","project":[{"name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","call_identifier":"FWF","_id":"2529486C-B435-11E9-9278-68D0E5697425","grant_number":"T 560-B17"},{"call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"_id":"25ABD200-B435-11E9-9278-68D0E5697425","grant_number":"RGP0058/2011","name":"Cell migration in complex environments: from in vivo experiments to theoretical models"}],"page":"374 - 386","quality_controlled":"1","citation":{"mla":"Maiuri, Paolo, et al. “Actin Flows Mediate a Universal Coupling between Cell Speed and Cell Persistence.” Cell, vol. 161, no. 2, Cell Press, 2015, pp. 374–86, doi:10.1016/j.cell.2015.01.056.","short":"P. Maiuri, J. Rupprecht, S. Wieser, V. Ruprecht, O. Bénichou, N. Carpi, M. Coppey, S. De Beco, N. Gov, C.-P.J. Heisenberg, C. Lage Crespo, F. Lautenschlaeger, M. Le Berre, A. Lennon Duménil, M. Raab, H. Thiam, M. Piel, M.K. Sixt, R. Voituriez, Cell 161 (2015) 374–386.","chicago":"Maiuri, Paolo, Jean Rupprecht, Stefan Wieser, Verena Ruprecht, Olivier Bénichou, Nicolas Carpi, Mathieu Coppey, et al. “Actin Flows Mediate a Universal Coupling between Cell Speed and Cell Persistence.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.01.056.","ama":"Maiuri P, Rupprecht J, Wieser S, et al. Actin flows mediate a universal coupling between cell speed and cell persistence. Cell. 2015;161(2):374-386. doi:10.1016/j.cell.2015.01.056","ista":"Maiuri P, Rupprecht J, Wieser S, Ruprecht V, Bénichou O, Carpi N, Coppey M, De Beco S, Gov N, Heisenberg C-PJ, Lage Crespo C, Lautenschlaeger F, Le Berre M, Lennon Duménil A, Raab M, Thiam H, Piel M, Sixt MK, Voituriez R. 2015. Actin flows mediate a universal coupling between cell speed and cell persistence. Cell. 161(2), 374–386.","ieee":"P. Maiuri et al., “Actin flows mediate a universal coupling between cell speed and cell persistence,” Cell, vol. 161, no. 2. Cell Press, pp. 374–386, 2015.","apa":"Maiuri, P., Rupprecht, J., Wieser, S., Ruprecht, V., Bénichou, O., Carpi, N., … Voituriez, R. (2015). Actin flows mediate a universal coupling between cell speed and cell persistence. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.01.056"},"publication":"Cell","issue":"2","publist_id":"5618","ec_funded":1,"abstract":[{"text":"Cell movement has essential functions in development, immunity, and cancer. Various cell migration patterns have been reported, but no general rule has emerged so far. Here, we show on the basis of experimental data in vitro and in vivo that cell persistence, which quantifies the straightness of trajectories, is robustly coupled to cell migration speed. We suggest that this universal coupling constitutes a generic law of cell migration, which originates in the advection of polarity cues by an actin cytoskeleton undergoing flows at the cellular scale. Our analysis relies on a theoretical model that we validate by measuring the persistence of cells upon modulation of actin flow speeds and upon optogenetic manipulation of the binding of an actin regulator to actin filaments. Beyond the quantitative prediction of the coupling, the model yields a generic phase diagram of cellular trajectories, which recapitulates the full range of observed migration patterns.","lang":"eng"}],"type":"journal_article","volume":161,"oa_version":"None","date_updated":"2021-01-12T06:51:33Z","date_created":"2018-12-11T11:52:41Z","author":[{"last_name":"Maiuri","first_name":"Paolo","full_name":"Maiuri, Paolo"},{"first_name":"Jean","last_name":"Rupprecht","full_name":"Rupprecht, Jean"},{"full_name":"Wieser, Stefan","first_name":"Stefan","last_name":"Wieser","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2670-2217"},{"orcid":"0000-0003-4088-8633","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht","first_name":"Verena","full_name":"Ruprecht, Verena"},{"last_name":"Bénichou","first_name":"Olivier","full_name":"Bénichou, Olivier"},{"full_name":"Carpi, Nicolas","first_name":"Nicolas","last_name":"Carpi"},{"first_name":"Mathieu","last_name":"Coppey","full_name":"Coppey, Mathieu"},{"first_name":"Simon","last_name":"De Beco","full_name":"De Beco, Simon"},{"full_name":"Gov, Nir","first_name":"Nir","last_name":"Gov"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"full_name":"Lage Crespo, Carolina","first_name":"Carolina","last_name":"Lage Crespo"},{"full_name":"Lautenschlaeger, Franziska","last_name":"Lautenschlaeger","first_name":"Franziska"},{"first_name":"Maël","last_name":"Le Berre","full_name":"Le Berre, Maël"},{"full_name":"Lennon Duménil, Ana","first_name":"Ana","last_name":"Lennon Duménil"},{"last_name":"Raab","first_name":"Matthew","full_name":"Raab, Matthew"},{"full_name":"Thiam, Hawa","last_name":"Thiam","first_name":"Hawa"},{"full_name":"Piel, Matthieu","first_name":"Matthieu","last_name":"Piel"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"full_name":"Voituriez, Raphaël","last_name":"Voituriez","first_name":"Raphaël"}],"publisher":"Cell Press","department":[{"_id":"MiSi"},{"_id":"CaHe"}],"intvolume":" 161","publication_status":"published","status":"public","title":"Actin flows mediate a universal coupling between cell speed and cell persistence","_id":"1553","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries","status":"public","intvolume":" 87","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1550","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"The medial ganglionic eminence (MGE) gives rise to the majority of mouse forebrain interneurons. Here, we examine the lineage relationship among MGE-derived interneurons using a replication-defective retroviral library containing a highly diverse set of DNA barcodes. Recovering the barcodes from the mature progeny of infected progenitor cells enabled us to unambiguously determine their respective lineal relationship. We found that clonal dispersion occurs across large areas of the brain and is not restricted by anatomical divisions. As such, sibling interneurons can populate the cortex, hippocampus striatum, and globus pallidus. The majority of interneurons appeared to be generated from asymmetric divisions of MGE progenitor cells, followed by symmetric divisions within the subventricular zone. Altogether, our findings uncover that lineage relationships do not appear to determine interneuron allocation to particular regions. As such, it is likely that clonally related interneurons have considerable flexibility as to the particular forebrain circuits to which they can contribute."}],"issue":"5","page":"989 - 998","publication":"Neuron","citation":{"ama":"Mayer C, Jaglin X, Cobbs L, et al. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. 2015;87(5):989-998. doi:10.1016/j.neuron.2015.07.011","ieee":"C. Mayer et al., “Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries,” Neuron, vol. 87, no. 5. Elsevier, pp. 989–998, 2015.","apa":"Mayer, C., Jaglin, X., Cobbs, L., Bandler, R., Streicher, C., Cepko, C., … Fishell, G. (2015). Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.07.011","ista":"Mayer C, Jaglin X, Cobbs L, Bandler R, Streicher C, Cepko C, Hippenmeyer S, Fishell G. 2015. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. 87(5), 989–998.","short":"C. Mayer, X. Jaglin, L. Cobbs, R. Bandler, C. Streicher, C. Cepko, S. Hippenmeyer, G. Fishell, Neuron 87 (2015) 989–998.","mla":"Mayer, Christian, et al. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” Neuron, vol. 87, no. 5, Elsevier, 2015, pp. 989–98, doi:10.1016/j.neuron.2015.07.011.","chicago":"Mayer, Christian, Xavier Jaglin, Lucy Cobbs, Rachel Bandler, Carmen Streicher, Constance Cepko, Simon Hippenmeyer, and Gord Fishell. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.07.011."},"date_published":"2015-09-02T00:00:00Z","scopus_import":1,"day":"02","publication_status":"published","publisher":"Elsevier","department":[{"_id":"SiHi"}],"year":"2015","acknowledgement":"Research in the G.F. laboratory is supported by NIH (NS 081297, MH095147, and P01NS074972) and the Simons Foundation. Research in the S.H. laboratory is supported by the European Union (FP7-CIG618444). C.M. is supported by EMBO ALTF (1295-2012). X.H.J. is supported by EMBO (ALTF 303-2010) and HFSP (LT000078/2011-L).\r\n\r\n","pmid":1,"date_updated":"2021-01-12T06:51:32Z","date_created":"2018-12-11T11:52:40Z","volume":87,"author":[{"first_name":"Christian","last_name":"Mayer","full_name":"Mayer, Christian"},{"full_name":"Jaglin, Xavier","last_name":"Jaglin","first_name":"Xavier"},{"full_name":"Cobbs, Lucy","last_name":"Cobbs","first_name":"Lucy"},{"last_name":"Bandler","first_name":"Rachel","full_name":"Bandler, Rachel"},{"full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen"},{"full_name":"Cepko, Constance","last_name":"Cepko","first_name":"Constance"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"full_name":"Fishell, Gord","last_name":"Fishell","first_name":"Gord"}],"publist_id":"5621","quality_controlled":"1","external_id":{"pmid":["26299473"]},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560602/","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2015.07.011","month":"09"},{"publication_identifier":{"eissn":["2234-3016"]},"month":"05","quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/0901.3015","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.4134/BKMS.2015.52.3.977","publist_id":"5624","department":[{"_id":"CaUh"}],"publisher":"Korean Mathematical Society","publication_status":"published","year":"2015","volume":52,"date_updated":"2021-01-12T06:51:31Z","date_created":"2018-12-11T11:52:39Z","author":[{"first_name":"Fatemeh","last_name":"Mohammadi","id":"2C29581E-F248-11E8-B48F-1D18A9856A87","full_name":"Mohammadi, Fatemeh"},{"full_name":"Moradi, Somayeh","last_name":"Moradi","first_name":"Somayeh"}],"scopus_import":1,"day":"31","page":"977 - 986","citation":{"ista":"Mohammadi F, Moradi S. 2015. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 52(3), 977–986.","apa":"Mohammadi, F., & Moradi, S. (2015). Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. Korean Mathematical Society. https://doi.org/10.4134/BKMS.2015.52.3.977","ieee":"F. Mohammadi and S. Moradi, “Resolution of unmixed bipartite graphs,” Bulletin of the Korean Mathematical Society, vol. 52, no. 3. Korean Mathematical Society, pp. 977–986, 2015.","ama":"Mohammadi F, Moradi S. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 2015;52(3):977-986. doi:10.4134/BKMS.2015.52.3.977","chicago":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” Bulletin of the Korean Mathematical Society. Korean Mathematical Society, 2015. https://doi.org/10.4134/BKMS.2015.52.3.977.","mla":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” Bulletin of the Korean Mathematical Society, vol. 52, no. 3, Korean Mathematical Society, 2015, pp. 977–86, doi:10.4134/BKMS.2015.52.3.977.","short":"F. Mohammadi, S. Moradi, Bulletin of the Korean Mathematical Society 52 (2015) 977–986."},"publication":"Bulletin of the Korean Mathematical Society","date_published":"2015-05-31T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"text":"Let G be a graph on the vertex set V(G) = {x1,…,xn} with the edge set E(G), and let R = K[x1,…, xn] be the polynomial ring over a field K. Two monomial ideals are associated to G, the edge ideal I(G) generated by all monomials xixj with {xi,xj} ∈ E(G), and the vertex cover ideal IG generated by monomials ∏xi∈Cxi for all minimal vertex covers C of G. A minimal vertex cover of G is a subset C ⊂ V(G) such that each edge has at least one vertex in C and no proper subset of C has the same property. Indeed, the vertex cover ideal of G is the Alexander dual of the edge ideal of G. In this paper, for an unmixed bipartite graph G we consider the lattice of vertex covers LG and we explicitly describe the minimal free resolution of the ideal associated to LG which is exactly the vertex cover ideal of G. Then we compute depth, projective dimension, regularity and extremal Betti numbers of R/I(G) in terms of the associated lattice.","lang":"eng"}],"intvolume":" 52","title":"Resolution of unmixed bipartite graphs","status":"public","_id":"1547","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"},{"department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","publication_status":"published","year":"2015","volume":66,"date_created":"2018-12-11T11:52:42Z","date_updated":"2021-01-12T06:51:35Z","author":[{"last_name":"Jia","first_name":"Yuebin","full_name":"Jia, Yuebin"},{"last_name":"Tian","first_name":"Huiyu","full_name":"Tian, Huiyu"},{"full_name":"Li, Hongjiang","orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Hongjiang"},{"full_name":"Yu, Qianqian","first_name":"Qianqian","last_name":"Yu"},{"last_name":"Wang","first_name":"Lei","full_name":"Wang, Lei"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"},{"full_name":"Ding, Zhaojun","first_name":"Zhaojun","last_name":"Ding"}],"publist_id":"5615","file_date_updated":"2020-07-14T12:45:02Z","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/jxb/erv230","month":"08","intvolume":" 66","ddc":["570"],"title":"The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1556","file":[{"access_level":"open_access","file_name":"IST-2016-480-v1+1_J._Exp._Bot.-2015-Jia-4631-42.pdf","creator":"system","content_type":"application/pdf","file_size":7753043,"file_id":"5051","relation":"main_file","checksum":"257919be0ce3d306185d3891ad7acf39","date_created":"2018-12-12T10:14:02Z","date_updated":"2020-07-14T12:45:02Z"}],"oa_version":"Published Version","pubrep_id":"480","type":"journal_article","issue":"15","abstract":[{"text":"The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily conserved histone acetyltransferase complex, has been shown to participate in leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana. Here, its role in root development was explored. Compared to the wild type, the elp2 mutant exhibited an accelerated differentiation of its root stem cells and cell division was more active in its quiescent centre (QC). The key transcription factors responsible for maintaining root stem cell and QC identity, such as AP2 transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5 transcription factor WOX5, were all strongly down-regulated in the mutant. On the other hand, expression of the G2/M transition activator CYCB1 was substantially induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased protein levels and PIN1 also displayed mild polarity alterations in elp2, which resulted in a reduced auxin content in the root tip. Either the acetylation or methylation level of each of these genes differed between the mutant and the wild type, suggesting that the ELP2 regulation of root development involves the epigenetic modification of a range of transcription factors and other developmental regulators.","lang":"eng"}],"page":"4631 - 4642","citation":{"mla":"Jia, Yuebin, et al. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany, vol. 66, no. 15, Oxford University Press, 2015, pp. 4631–42, doi:10.1093/jxb/erv230.","short":"Y. Jia, H. Tian, H. Li, Q. Yu, L. Wang, J. Friml, Z. Ding, Journal of Experimental Botany 66 (2015) 4631–4642.","chicago":"Jia, Yuebin, Huiyu Tian, Hongjiang Li, Qianqian Yu, Lei Wang, Jiří Friml, and Zhaojun Ding. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv230.","ama":"Jia Y, Tian H, Li H, et al. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 2015;66(15):4631-4642. doi:10.1093/jxb/erv230","ista":"Jia Y, Tian H, Li H, Yu Q, Wang L, Friml J, Ding Z. 2015. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 66(15), 4631–4642.","apa":"Jia, Y., Tian, H., Li, H., Yu, Q., Wang, L., Friml, J., & Ding, Z. (2015). The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv230","ieee":"Y. Jia et al., “The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development,” Journal of Experimental Botany, vol. 66, no. 15. Oxford University Press, pp. 4631–4642, 2015."},"publication":"Journal of Experimental Botany","date_published":"2015-08-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01"},{"publication_identifier":{"eissn":["1536-0040"]},"month":"01","project":[{"call_identifier":"FP7","name":"Persistent Homology - Images, Data and Maps","grant_number":"622033","_id":"255F06BE-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://discovery.ucl.ac.uk/1473750/1/99393.pdf"}],"language":[{"iso":"eng"}],"doi":"10.1137/140993934","publist_id":"5616","ec_funded":1,"department":[{"_id":"HeEd"}],"publisher":"Society for Industrial and Applied Mathematics ","publication_status":"published","year":"2015","acknowledgement":"Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria (pawel.pilarczyk@ist.ac.at). This author’s work was partially supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 622033, by Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC), by the Portuguese national funds through Funda ̧caoparaaCiˆencia e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008), and by European Research Council through StG 259559 in the framework of the EPIDELAY project.","volume":14,"date_updated":"2021-01-12T06:51:34Z","date_created":"2018-12-11T11:52:42Z","author":[{"last_name":"Knipl","first_name":"Diána","full_name":"Knipl, Diána"},{"full_name":"Pilarczyk, Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","last_name":"Pilarczyk","first_name":"Pawel"},{"full_name":"Röst, Gergely","first_name":"Gergely","last_name":"Röst"}],"scopus_import":1,"article_processing_charge":"No","day":"01","page":"980 - 1017","article_type":"original","citation":{"mla":"Knipl, Diána, et al. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” SIAM Journal on Applied Dynamical Systems, vol. 14, no. 2, Society for Industrial and Applied Mathematics , 2015, pp. 980–1017, doi:10.1137/140993934.","short":"D. Knipl, P. Pilarczyk, G. Röst, SIAM Journal on Applied Dynamical Systems 14 (2015) 980–1017.","chicago":"Knipl, Diána, Pawel Pilarczyk, and Gergely Röst. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” SIAM Journal on Applied Dynamical Systems. Society for Industrial and Applied Mathematics , 2015. https://doi.org/10.1137/140993934.","ama":"Knipl D, Pilarczyk P, Röst G. Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. 2015;14(2):980-1017. doi:10.1137/140993934","ista":"Knipl D, Pilarczyk P, Röst G. 2015. Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. 14(2), 980–1017.","ieee":"D. Knipl, P. Pilarczyk, and G. Röst, “Rich bifurcation structure in a two patch vaccination model,” SIAM Journal on Applied Dynamical Systems, vol. 14, no. 2. Society for Industrial and Applied Mathematics , pp. 980–1017, 2015.","apa":"Knipl, D., Pilarczyk, P., & Röst, G. (2015). Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/140993934"},"publication":"SIAM Journal on Applied Dynamical Systems","date_published":"2015-01-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"We show that incorporating spatial dispersal of individuals into a simple vaccination epidemic model may give rise to a model that exhibits rich dynamical behavior. Using an SIVS (susceptible-infected-vaccinated-susceptible) model as a basis, we describe the spread of an infectious disease in a population split into two regions. In each subpopulation, both forward and backward bifurcations can occur. This implies that for disconnected regions the two-patch system may admit several steady states. We consider traveling between the regions and investigate the impact of spatial dispersal of individuals on the model dynamics. We establish conditions for the existence of multiple nontrivial steady states in the system, and we study the structure of the equilibria. The mathematical analysis reveals an unusually rich dynamical behavior, not normally found in the simple epidemic models. In addition to the disease-free equilibrium, eight endemic equilibria emerge from backward transcritical and saddle-node bifurcation points, forming an interesting bifurcation diagram. Stability of steady states, their bifurcations, and the global dynamics are investigated with analytical tools, numerical simulations, and rigorous set-oriented numerical computations."}],"intvolume":" 14","status":"public","title":"Rich bifurcation structure in a two patch vaccination model","ddc":["510"],"_id":"1555","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version"},{"type":"journal_article","abstract":[{"lang":"eng","text":"CyclophilinAis a conserved peptidyl-prolyl cis-trans isomerase (PPIase) best known as the cellular receptor of the immunosuppressant cyclosporine A. Despite significant effort, evidence of developmental functions of cyclophilin A in non-plant systems has remained obscure. Mutations in a tomato (Solanum lycopersicum) cyclophilin A ortholog, DIAGEOTROPICA (DGT), have been shown to abolish the organogenesis of lateral roots; however, a mechanistic explanation of the phenotype is lacking. Here, we show that the dgt mutant lacks auxin maxima relevant to priming and specification of lateral root founder cells. DGT is expressed in shoot and root, and localizes to both the nucleus and cytoplasm during lateral root organogenesis. Mutation of ENTIRE/ IAA9, a member of the auxin-responsive Aux/IAA protein family of transcriptional repressors, partially restores the inability of dgt to initiate lateral root primordia but not the primordia outgrowth. By comparison, grafting of a wild-type scion restores the process of lateral root formation, consistent with participation of a mobile signal. Antibodies do not detect movement of the DGT protein into the dgt rootstock; however, experiments with radiolabeled auxin and an auxin-specific microelectrode demonstrate abnormal auxin fluxes. Functional studies of DGT in heterologous yeast and tobacco-leaf auxin-transport systems demonstrate that DGT negatively regulates PIN-FORMED (PIN) auxin efflux transporters by affecting their plasma membrane localization. Studies in tomato support complex effects of the dgt mutation on PIN expression level, expression domain and plasma membrane localization. Our data demonstrate that DGT regulates auxin transport in lateral root formation."}],"publist_id":"5613","issue":"4","title":"The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation","status":"public","publication_status":"published","intvolume":" 142","department":[{"_id":"JiFr"}],"publisher":"Company of Biologists","_id":"1558","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","date_created":"2018-12-11T11:52:42Z","date_updated":"2021-01-12T06:51:35Z","volume":142,"oa_version":"None","author":[{"full_name":"Ivanchenko, Maria","last_name":"Ivanchenko","first_name":"Maria"},{"first_name":"Jinsheng","last_name":"Zhu","full_name":"Zhu, Jinsheng"},{"first_name":"Bangjun","last_name":"Wang","full_name":"Wang, Bangjun"},{"id":"298814E2-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Medvecka","full_name":"Medvecka, Eva"},{"first_name":"Yunlong","last_name":"Du","full_name":"Du, Yunlong"},{"full_name":"Azzarello, Elisa","last_name":"Azzarello","first_name":"Elisa"},{"full_name":"Mancuso, Stefano","last_name":"Mancuso","first_name":"Stefano"},{"full_name":"Megraw, Molly","first_name":"Molly","last_name":"Megraw"},{"full_name":"Filichkin, Sergei","last_name":"Filichkin","first_name":"Sergei"},{"full_name":"Dubrovsky, Joseph","first_name":"Joseph","last_name":"Dubrovsky"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"last_name":"Geisler","first_name":"Markus","full_name":"Geisler, Markus"}],"scopus_import":1,"day":"15","month":"02","quality_controlled":"1","page":"712 - 721","publication":"Development","citation":{"chicago":"Ivanchenko, Maria, Jinsheng Zhu, Bangjun Wang, Eva Medvecka, Yunlong Du, Elisa Azzarello, Stefano Mancuso, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” Development. Company of Biologists, 2015. https://doi.org/10.1242/dev.113225.","mla":"Ivanchenko, Maria, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” Development, vol. 142, no. 4, Company of Biologists, 2015, pp. 712–21, doi:10.1242/dev.113225.","short":"M. Ivanchenko, J. Zhu, B. Wang, E. Medvecka, Y. Du, E. Azzarello, S. Mancuso, M. Megraw, S. Filichkin, J. Dubrovsky, J. Friml, M. Geisler, Development 142 (2015) 712–721.","ista":"Ivanchenko M, Zhu J, Wang B, Medvecka E, Du Y, Azzarello E, Mancuso S, Megraw M, Filichkin S, Dubrovsky J, Friml J, Geisler M. 2015. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 142(4), 712–721.","apa":"Ivanchenko, M., Zhu, J., Wang, B., Medvecka, E., Du, Y., Azzarello, E., … Geisler, M. (2015). The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. Company of Biologists. https://doi.org/10.1242/dev.113225","ieee":"M. Ivanchenko et al., “The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation,” Development, vol. 142, no. 4. Company of Biologists, pp. 712–721, 2015.","ama":"Ivanchenko M, Zhu J, Wang B, et al. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 2015;142(4):712-721. doi:10.1242/dev.113225"},"language":[{"iso":"eng"}],"date_published":"2015-02-15T00:00:00Z","doi":"10.1242/dev.113225"},{"scopus_import":1,"day":"01","month":"09","publication":"Journal of Comparative Neurology","citation":{"chicago":"Javdani, Fariba, Krisztina Holló, Krisztina Hegedűs, Gréta Kis, Zoltán Hegyi, Klaudia Dócs, Yu Kasugai, Yugo Fukazawa, Ryuichi Shigemoto, and Miklós Antal. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” Journal of Comparative Neurology. Wiley-Blackwell, 2015. https://doi.org/10.1002/cne.23774.","short":"F. Javdani, K. Holló, K. Hegedűs, G. Kis, Z. Hegyi, K. Dócs, Y. Kasugai, Y. Fukazawa, R. Shigemoto, M. Antal, Journal of Comparative Neurology 523 (2015) 1967–1983.","mla":"Javdani, Fariba, et al. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” Journal of Comparative Neurology, vol. 523, no. 13, Wiley-Blackwell, 2015, pp. 1967–83, doi:10.1002/cne.23774.","ieee":"F. Javdani et al., “Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats,” Journal of Comparative Neurology, vol. 523, no. 13. Wiley-Blackwell, pp. 1967–1983, 2015.","apa":"Javdani, F., Holló, K., Hegedűs, K., Kis, G., Hegyi, Z., Dócs, K., … Antal, M. (2015). Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. Wiley-Blackwell. https://doi.org/10.1002/cne.23774","ista":"Javdani F, Holló K, Hegedűs K, Kis G, Hegyi Z, Dócs K, Kasugai Y, Fukazawa Y, Shigemoto R, Antal M. 2015. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. 523(13), 1967–1983.","ama":"Javdani F, Holló K, Hegedűs K, et al. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. 2015;523(13):1967-1983. doi:10.1002/cne.23774"},"quality_controlled":"1","page":"1967 - 1983","date_published":"2015-09-01T00:00:00Z","doi":"10.1002/cne.23774","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"γ-Aminobutyric acid (GABA)- and glycine-mediated hyperpolarizing inhibition is associated with a chloride influx that depends on the inwardly directed chloride electrochemical gradient. In neurons, the extrusion of chloride from the cytosol primarily depends on the expression of an isoform of potassium-chloride cotransporters (KCC2s). KCC2 is crucial in the regulation of the inhibitory tone of neural circuits, including pain processing neural assemblies. Thus we investigated the cellular distribution of KCC2 in neurons underlying pain processing in the superficial spinal dorsal horn of rats by using high-resolution immunocytochemical methods. We demonstrated that perikarya and dendrites widely expressed KCC2, but axon terminals proved to be negative for KCC2. In single ultrathin sections, silver deposits labeling KCC2 molecules showed different densities on the surface of dendritic profiles, some of which were negative for KCC2. In freeze fracture replicas and tissue sections double stained for the β3-subunit of GABAA receptors and KCC2, GABAA receptors were revealed on dendritic segments with high and also with low KCC2 densities. By measuring the distances between spots immunoreactive for gephyrin (a scaffolding protein of GABAA and glycine receptors) and KCC2 on the surface of neurokinin 1 (NK1) receptor-immunoreactive dendrites, we found that gephyrin-immunoreactive spots were located at various distances from KCC2 cotransporters; 5.7 % of them were recovered in the middle of 4-10-μm-long dendritic segments that were free of KCC2 immunostaining. The variable local densities of KCC2 may result in variable postsynaptic potentials evoked by the activation of GABAA and glycine receptors along the dendrites of spinal neurons.","lang":"eng"}],"issue":"13","publist_id":"5614","_id":"1557","year":"2015","acknowledgement":"Funded by:\r\nHungarian Academy of Sciences. Grant Number: MTA-TKI 242\r\nHungarian Brain Research Program. Grant Number: KTIA_NAP_13-1-2013-0001\r\nSolution Oriented Research for Science and Technology from the Japan Science and Technology Agency Japanese Ministry of Education, Culture, Sports, Science and Technology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats","intvolume":" 523","publisher":"Wiley-Blackwell","department":[{"_id":"RySh"}],"author":[{"first_name":"Fariba","last_name":"Javdani","full_name":"Javdani, Fariba"},{"first_name":"Krisztina","last_name":"Holló","full_name":"Holló, Krisztina"},{"full_name":"Hegedűs, Krisztina","first_name":"Krisztina","last_name":"Hegedűs"},{"last_name":"Kis","first_name":"Gréta","full_name":"Kis, Gréta"},{"full_name":"Hegyi, Zoltán","last_name":"Hegyi","first_name":"Zoltán"},{"full_name":"Dócs, Klaudia","last_name":"Dócs","first_name":"Klaudia"},{"first_name":"Yu","last_name":"Kasugai","full_name":"Kasugai, Yu"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"full_name":"Antal, Miklós","first_name":"Miklós","last_name":"Antal"}],"date_created":"2018-12-11T11:52:42Z","date_updated":"2021-01-12T06:51:35Z","oa_version":"None","volume":523},{"publist_id":"5612","author":[{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"date_created":"2018-12-11T11:52:43Z","date_updated":"2021-01-12T06:51:36Z","volume":112,"year":"2015","pmid":1,"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","month":"12","doi":"10.1073/pnas.1511366112","language":[{"iso":"eng"}],"external_id":{"pmid":["26644569"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697423/","open_access":"1"}],"oa":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant)will take over a resident population?We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP)."}],"issue":"51","type":"journal_article","oa_version":"Submitted Version","_id":"1559","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Computational complexity of ecological and evolutionary spatial dynamics","intvolume":" 112","day":"22","scopus_import":1,"date_published":"2015-12-22T00:00:00Z","publication":"PNAS","citation":{"ista":"Ibsen-Jensen R, Chatterjee K, Nowak M. 2015. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 112(51), 15636–15641.","ieee":"R. Ibsen-Jensen, K. Chatterjee, and M. Nowak, “Computational complexity of ecological and evolutionary spatial dynamics,” PNAS, vol. 112, no. 51. National Academy of Sciences, pp. 15636–15641, 2015.","apa":"Ibsen-Jensen, R., Chatterjee, K., & Nowak, M. (2015). Computational complexity of ecological and evolutionary spatial dynamics. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1511366112","ama":"Ibsen-Jensen R, Chatterjee K, Nowak M. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 2015;112(51):15636-15641. doi:10.1073/pnas.1511366112","chicago":"Ibsen-Jensen, Rasmus, Krishnendu Chatterjee, and Martin Nowak. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511366112.","mla":"Ibsen-Jensen, Rasmus, et al. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS, vol. 112, no. 51, National Academy of Sciences, 2015, pp. 15636–41, doi:10.1073/pnas.1511366112.","short":"R. Ibsen-Jensen, K. Chatterjee, M. Nowak, PNAS 112 (2015) 15636–15641."},"page":"15636 - 15641"},{"author":[{"full_name":"Heger, Klaus","first_name":"Klaus","last_name":"Heger"},{"full_name":"Kober, Maike","first_name":"Maike","last_name":"Kober"},{"full_name":"Rieß, David","last_name":"Rieß","first_name":"David"},{"first_name":"Christoph","last_name":"Drees","full_name":"Drees, Christoph"},{"full_name":"De Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","last_name":"De Vries"},{"first_name":"Arianna","last_name":"Bertossi","full_name":"Bertossi, Arianna"},{"last_name":"Roers","first_name":"Axel","full_name":"Roers, Axel"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"last_name":"Schmidt Supprian","first_name":"Marc","full_name":"Schmidt Supprian, Marc"}],"date_created":"2018-12-11T11:52:44Z","date_updated":"2021-01-12T06:51:36Z","oa_version":"None","volume":45,"_id":"1561","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors","intvolume":" 45","publisher":"Wiley","department":[{"_id":"MiSi"}],"abstract":[{"lang":"eng","text":"Replication-deficient recombinant adenoviruses are potent vectors for the efficient transient expression of exogenous genes in resting immune cells. However, most leukocytes are refractory to efficient adenoviral transduction as they lack expression of the coxsackie/adenovirus receptor (CAR). To circumvent this obstacle, we generated the R26/CAG-CARΔ1StopF (where R26 is ROSA26 and CAG is CMV early enhancer/chicken β actin promoter) knock-in mouse line. This strain allows monitoring of in situ Cre recombinase activity through expression of CARΔ1. Simultaneously, CARΔ1 expression permits selective and highly efficient adenoviral transduction of immune cell populations, such as mast cells or T cells, directly ex vivo in bulk cultures without prior cell purification or activation. Furthermore, we show that CARΔ1 expression dramatically improves adenoviral infection of in vitro differentiated conventional and plasmacytoid dendritic cells (DCs), basophils, mast cells, as well as Hoxb8-immortalized hematopoietic progenitor cells. This novel dual function mouse strain will hence be a valuable tool to rapidly dissect the function of specific genes in leukocyte physiology."}],"issue":"6","publist_id":"5610","type":"journal_article","date_published":"2015-06-01T00:00:00Z","doi":"10.1002/eji.201545457","language":[{"iso":"eng"}],"publication":"European Journal of Immunology","citation":{"short":"K. Heger, M. Kober, D. Rieß, C. Drees, I. de Vries, A. Bertossi, A. Roers, M.K. Sixt, M. Schmidt Supprian, European Journal of Immunology 45 (2015) 1614–1620.","mla":"Heger, Klaus, et al. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.” European Journal of Immunology, vol. 45, no. 6, Wiley, 2015, pp. 1614–20, doi:10.1002/eji.201545457.","chicago":"Heger, Klaus, Maike Kober, David Rieß, Christoph Drees, Ingrid de Vries, Arianna Bertossi, Axel Roers, Michael K Sixt, and Marc Schmidt Supprian. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.” European Journal of Immunology. Wiley, 2015. https://doi.org/10.1002/eji.201545457.","ama":"Heger K, Kober M, Rieß D, et al. A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. 2015;45(6):1614-1620. doi:10.1002/eji.201545457","ieee":"K. Heger et al., “A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors,” European Journal of Immunology, vol. 45, no. 6. Wiley, pp. 1614–1620, 2015.","apa":"Heger, K., Kober, M., Rieß, D., Drees, C., de Vries, I., Bertossi, A., … Schmidt Supprian, M. (2015). A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. Wiley. https://doi.org/10.1002/eji.201545457","ista":"Heger K, Kober M, Rieß D, Drees C, de Vries I, Bertossi A, Roers A, Sixt MK, Schmidt Supprian M. 2015. A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. 45(6), 1614–1620."},"quality_controlled":"1","page":"1614 - 1620","month":"06","day":"01","scopus_import":1}]