[{"acknowledgement":"This work has been supported by the National Research Network RiSE on Rigorous Systems Engineering\r\n(Austrian Science Fund (FWF): S11402-N23, S11403-N23, S11404-N23, S11411-N23), a Google\r\nPhD Fellowship, an Erwin Schrödinger Fellowship (Austrian Science Fund (FWF): J3696-N26), EPSRC\r\ngrants EP/H005633/1 and EP/K008528/1, the Vienna Science and Technology Fund (WWTF) trough\r\ngrant PROSEED, the European Research Council (ERC) under grant 267989 (QUAREM) and by the\r\nAustrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","year":"2016","has_accepted_license":"1","publication":"Leibniz International Proceedings in Informatics","day":"01","date_created":"2018-12-11T11:50:07Z","doi":"10.4230/LIPIcs.CONCUR.2016.6","date_published":"2016-08-01T00:00:00Z","article_number":"6","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"chicago":"Haas, Andreas, Thomas A Henzinger, Andreas Holzer, Christoph Kirsch, Michael Lippautz, Hannes Payer, Ali Sezgin, Ana Sokolova, and Helmut Veith. “Local Linearizability for Concurrent Container-Type Data Structures.” In Leibniz International Proceedings in Informatics, Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.6.","ista":"Haas A, Henzinger TA, Holzer A, Kirsch C, Lippautz M, Payer H, Sezgin A, Sokolova A, Veith H. 2016. Local linearizability for concurrent container-type data structures. Leibniz International Proceedings in Informatics. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 6.","mla":"Haas, Andreas, et al. “Local Linearizability for Concurrent Container-Type Data Structures.” Leibniz International Proceedings in Informatics, vol. 59, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.6.","apa":"Haas, A., Henzinger, T. A., Holzer, A., Kirsch, C., Lippautz, M., Payer, H., … Veith, H. (2016). Local linearizability for concurrent container-type data structures. In Leibniz International Proceedings in Informatics (Vol. 59). Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.6","ama":"Haas A, Henzinger TA, Holzer A, et al. Local linearizability for concurrent container-type data structures. In: Leibniz International Proceedings in Informatics. Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.6","short":"A. Haas, T.A. Henzinger, A. Holzer, C. Kirsch, M. Lippautz, H. Payer, A. Sezgin, A. Sokolova, H. Veith, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ieee":"A. Haas et al., “Local linearizability for concurrent container-type data structures,” in Leibniz International Proceedings in Informatics, Quebec City; Canada, 2016, vol. 59."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6280","author":[{"full_name":"Haas, Andreas","last_name":"Haas","first_name":"Andreas"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Holzer","full_name":"Holzer, Andreas","first_name":"Andreas"},{"first_name":"Christoph","full_name":"Kirsch, Christoph","last_name":"Kirsch"},{"first_name":"Michael","last_name":"Lippautz","full_name":"Lippautz, Michael"},{"full_name":"Payer, Hannes","last_name":"Payer","first_name":"Hannes"},{"id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali","last_name":"Sezgin","full_name":"Sezgin, Ali"},{"full_name":"Sokolova, Ana","last_name":"Sokolova","first_name":"Ana"},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"}],"title":"Local linearizability for concurrent container-type data structures","abstract":[{"text":" The semantics of concurrent data structures is usually given by a sequential specification and a consistency condition. Linearizability is the most popular consistency condition due to its simplicity and general applicability. Nevertheless, for applications that do not require all guarantees offered by linearizability, recent research has focused on improving performance and scalability of concurrent data structures by relaxing their semantics. In this paper, we present local linearizability, a relaxed consistency condition that is applicable to container-type concurrent data structures like pools, queues, and stacks. While linearizability requires that the effect of each operation is observed by all threads at the same time, local linearizability only requires that for each thread T, the effects of its local insertion operations and the effects of those removal operations that remove values inserted by T are observed by all threads at the same time. We investigate theoretical and practical properties of local linearizability and its relationship to many existing consistency conditions. We present a generic implementation method for locally linearizable data structures that uses existing linearizable data structures as building blocks. Our implementations show performance and scalability improvements over the original building blocks and outperform the fastest existing container-type implementations. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"scopus_import":1,"intvolume":" 59","month":"08","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"4795","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:10:10Z","file_name":"IST-2017-793-v1+1_LIPIcs-CONCUR-2016-6.pdf","date_updated":"2018-12-12T10:10:10Z","file_size":589747,"creator":"system"}],"ec_funded":1,"volume":59,"_id":"1095","conference":{"name":"CONCUR: Concurrency Theory","location":"Quebec City; Canada","end_date":"2016-08-26","start_date":"2016-08-23"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","pubrep_id":"793","status":"public","date_updated":"2021-01-12T06:48:14Z","ddc":["004"],"department":[{"_id":"ToHe"}],"file_date_updated":"2018-12-12T10:10:10Z"},{"has_accepted_license":"1","year":"2016","day":"01","doi":"10.1145/2980179.2982427","date_published":"2016-11-01T00:00:00Z","date_created":"2018-12-11T11:50:07Z","acknowledgement":"We thank Nobuyuki Umetani for his insightful suggestions in our discussions. We thank Alan Schultz and his colleagues at NRL for building the hexacopter and for the valuable discussions. We thank Randall Davis, Boris Katz, and Howard Shrobe at MIT for their advice. We are grateful to Nick Bandiera for preprocessing mechanical parts and providing 3D printing technical support; Charles Blouin from RCBenchmark for dynamometer hardware support; Brian Saavedra for the composition UI; Yingzhe Yuan for data acquisition and video recording in the experiments; Michael Foshey and David Kim for their comments on the draft of the paper. \r\n\r\n\r\nThis work was partially supported by Air Force Research Laboratory’s sponsorship of Julia: A Fresh Approach to Technical Computing and Data Processing (Sponsor Award ID FA8750-15-2- 0272, MIT Award ID 024831-00003), and NSF Expedition project (Sponsor Award ID CCF-1138967, MIT Award ID 020610-00002). The views expressed herein are not endorsed by the sponsors. This project has also received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 645599. ","publisher":"ACM","quality_controlled":"1","oa":1,"citation":{"chicago":"Du, Tao, Adriana Schulz, Bo Zhu, Bernd Bickel, and Wojciech Matusik. “Computational Multicopter Design,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2980179.2982427.","ista":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. 2016. Computational multicopter design. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 227.","mla":"Du, Tao, et al. Computational Multicopter Design. Vol. 35, no. 6, 227, ACM, 2016, doi:10.1145/2980179.2982427.","short":"T. Du, A. Schulz, B. Zhu, B. Bickel, W. Matusik, in:, ACM, 2016.","ieee":"T. Du, A. Schulz, B. Zhu, B. Bickel, and W. Matusik, “Computational multicopter design,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6.","ama":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. Computational multicopter design. In: Vol 35. ACM; 2016. doi:10.1145/2980179.2982427","apa":"Du, T., Schulz, A., Zhu, B., Bickel, B., & Matusik, W. (2016). Computational multicopter design (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. https://doi.org/10.1145/2980179.2982427"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Du","full_name":"Du, Tao","first_name":"Tao"},{"first_name":"Adriana","full_name":"Schulz, Adriana","last_name":"Schulz"},{"full_name":"Zhu, Bo","last_name":"Zhu","first_name":"Bo"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"}],"publist_id":"6278","title":"Computational multicopter design","article_number":"227","project":[{"_id":"25082902-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Soft-bodied intelligence for Manipulation","grant_number":"645599"}],"publication_status":"published","file":[{"file_id":"5298","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:17:42Z","file_name":"IST-2017-759-v1+1_copter.pdf","date_updated":"2018-12-12T10:17:42Z","file_size":33114420,"creator":"system"}],"language":[{"iso":"eng"}],"volume":35,"issue":"6","ec_funded":1,"abstract":[{"text":"We present an interactive system for computational design, optimization, and fabrication of multicopters. Our computational approach allows non-experts to design, explore, and evaluate a wide range of different multicopters. We provide users with an intuitive interface for assembling a multicopter from a collection of components (e.g., propellers, motors, and carbon fiber rods). Our algorithm interactively optimizes shape and controller parameters of the current design to ensure its proper operation. In addition, we allow incorporating a variety of other metrics (such as payload, battery usage, size, and cost) into the design process and exploring tradeoffs between them. We show the efficacy of our method and system by designing, optimizing, fabricating, and operating multicopters with complex geometries and propeller configurations. We also demonstrate the ability of our optimization algorithm to improve the multicopter performance under different metrics.","lang":"eng"}],"oa_version":"Submitted Version","alternative_title":["ACM Transactions on Graphics"],"scopus_import":1,"month":"11","intvolume":" 35","date_updated":"2021-01-12T06:48:15Z","ddc":["006"],"file_date_updated":"2018-12-12T10:17:42Z","department":[{"_id":"BeBi"}],"_id":"1097","type":"conference","conference":{"name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","location":"Macao, China","end_date":"2016-12-08","start_date":"2016-12-05"},"status":"public","pubrep_id":"759"},{"project":[{"call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"}],"author":[{"id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","first_name":"Anastasia","last_name":"Pentina","full_name":"Pentina, Anastasia"},{"first_name":"Ruth","full_name":"Urner, Ruth","last_name":"Urner"}],"publist_id":"6277","title":"Lifelong learning with weighted majority votes","citation":{"short":"A. Pentina, R. Urner, in:, Neural Information Processing Systems, 2016, pp. 3619–3627.","ieee":"A. Pentina and R. Urner, “Lifelong learning with weighted majority votes,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 3619–3627.","apa":"Pentina, A., & Urner, R. (2016). Lifelong learning with weighted majority votes (Vol. 29, pp. 3619–3627). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems.","ama":"Pentina A, Urner R. Lifelong learning with weighted majority votes. In: Vol 29. Neural Information Processing Systems; 2016:3619-3627.","mla":"Pentina, Anastasia, and Ruth Urner. Lifelong Learning with Weighted Majority Votes. Vol. 29, Neural Information Processing Systems, 2016, pp. 3619–27.","ista":"Pentina A, Urner R. 2016. Lifelong learning with weighted majority votes. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3619–3627.","chicago":"Pentina, Anastasia, and Ruth Urner. “Lifelong Learning with Weighted Majority Votes,” 29:3619–27. Neural Information Processing Systems, 2016."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Neural Information Processing Systems","quality_controlled":"1","acknowledgement":"This work was in parts funded by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 308036.\r\n\r\n","page":"3619-3627","date_created":"2018-12-11T11:50:08Z","date_published":"2016-12-01T00:00:00Z","year":"2016","has_accepted_license":"1","day":"01","conference":{"end_date":"2016-12-10","location":"Barcelona, Spain","start_date":"2016-12-05","name":"NIPS: Neural Information Processing Systems"},"type":"conference","pubrep_id":"775","status":"public","_id":"1098","file_date_updated":"2018-12-12T10:12:43Z","department":[{"_id":"ChLa"}],"date_updated":"2021-01-12T06:48:15Z","ddc":["006"],"scopus_import":1,"alternative_title":["Advances in Neural Information Processing Systems"],"intvolume":" 29","month":"12","abstract":[{"text":"Better understanding of the potential benefits of information transfer and representation learning is an important step towards the goal of building intelligent systems that are able to persist in the world and learn over time. In this work, we consider a setting where the learner encounters a stream of tasks but is able to retain only limited information from each encountered task, such as a learned predictor. In contrast to most previous works analyzing this scenario, we do not make any distributional assumptions on the task generating process. Instead, we formulate a complexity measure that captures the diversity of the observed tasks. We provide a lifelong learning algorithm with error guarantees for every observed task (rather than on average). We show sample complexity reductions in comparison to solving every task in isolation in terms of our task complexity measure. Further, our algorithmic framework can naturally be viewed as learning a representation from encountered tasks with a neural network.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"volume":29,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"4961","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-775-v1+1_main.pdf","date_created":"2018-12-12T10:12:42Z","file_size":237111,"date_updated":"2018-12-12T10:12:42Z","creator":"system"},{"date_updated":"2018-12-12T10:12:43Z","file_size":185818,"creator":"system","date_created":"2018-12-12T10:12:43Z","file_name":"IST-2017-775-v1+2_supplementary.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4962"}]},{"ddc":["000","005"],"date_updated":"2021-01-12T06:48:16Z","file_date_updated":"2018-12-12T10:12:01Z","department":[{"_id":"BeBi"}],"_id":"1099","pubrep_id":"760","status":"public","conference":{"end_date":"2016-12-08","location":"Macao, China","start_date":"2016-12-05","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia"},"type":"conference","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2018-12-12T10:12:01Z","file_size":11122029,"date_created":"2018-12-12T10:12:01Z","file_name":"IST-2017-760-v1+1_flexmolds.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4918"}],"publication_status":"published","ec_funded":1,"volume":35,"issue":"6","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We present FlexMolds, a novel computational approach to automatically design flexible, reusable molds that, once 3D printed, allow us to physically fabricate, by means of liquid casting, multiple copies of complex shapes with rich surface details and complex topology. The approach to design such flexible molds is based on a greedy bottom-up search of possible cuts over an object, evaluating for each possible cut the feasibility of the resulting mold. We use a dynamic simulation approach to evaluate candidate molds, providing a heuristic to generate forces that are able to open, detach, and remove a complex mold from the object it surrounds. We have tested the approach with a number of objects with nontrivial shapes and topologies."}],"intvolume":" 35","month":"11","scopus_import":1,"alternative_title":["ACM Transactions on Graphics"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Malomo, Luigi, et al. FlexMolds: Automatic Design of Flexible Shells for Molding. Vol. 35, no. 6, 223, ACM, 2016, doi:10.1145/2980179.2982397.","apa":"Malomo, L., Pietroni, N., Bickel, B., & Cignoni, P. (2016). FlexMolds: Automatic design of flexible shells for molding (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. https://doi.org/10.1145/2980179.2982397","ama":"Malomo L, Pietroni N, Bickel B, Cignoni P. FlexMolds: Automatic design of flexible shells for molding. In: Vol 35. ACM; 2016. doi:10.1145/2980179.2982397","ieee":"L. Malomo, N. Pietroni, B. Bickel, and P. Cignoni, “FlexMolds: Automatic design of flexible shells for molding,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6.","short":"L. Malomo, N. Pietroni, B. Bickel, P. Cignoni, in:, ACM, 2016.","chicago":"Malomo, Luigi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “FlexMolds: Automatic Design of Flexible Shells for Molding,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2980179.2982397.","ista":"Malomo L, Pietroni N, Bickel B, Cignoni P. 2016. FlexMolds: Automatic design of flexible shells for molding. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 223."},"title":"FlexMolds: Automatic design of flexible shells for molding","publist_id":"6276","author":[{"first_name":"Luigi","last_name":"Malomo","full_name":"Malomo, Luigi"},{"full_name":"Pietroni, Nico","last_name":"Pietroni","first_name":"Nico"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"first_name":"Paolo","full_name":"Cignoni, Paolo","last_name":"Cignoni"}],"article_number":"223","project":[{"call_identifier":"H2020","_id":"25082902-B435-11E9-9278-68D0E5697425","name":"Soft-bodied intelligence for Manipulation","grant_number":"645599"}],"day":"01","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:50:08Z","date_published":"2016-11-01T00:00:00Z","doi":"10.1145/2980179.2982397","acknowledgement":"The armadillo, bunny and dragon models are courtesy of the Stanford 3D Scanning Repository. The bimba, fertility and elephant models are courtesy of the AIM@SHAPE Shape Repository. \r\nThis project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement\r\nNo. 645599.","oa":1,"quality_controlled":"1","publisher":"ACM"},{"project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” In Proceedings of the British Machine Vision Conference 2016, 2016–September:92.1-92.12. BMVA Press, 2016. https://doi.org/10.5244/C.30.92.","ista":"Kolesnikov A, Lampert C. 2016. Improving weakly-supervised object localization by micro-annotation. Proceedings of the British Machine Vision Conference 2016. BMVC: British Machine Vision Conference vol. 2016–September, 92.1-92.12.","mla":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” Proceedings of the British Machine Vision Conference 2016, vol. 2016–September, BMVA Press, 2016, p. 92.1-92.12, doi:10.5244/C.30.92.","ieee":"A. Kolesnikov and C. Lampert, “Improving weakly-supervised object localization by micro-annotation,” in Proceedings of the British Machine Vision Conference 2016, York, United Kingdom, 2016, vol. 2016–September, p. 92.1-92.12.","short":"A. Kolesnikov, C. Lampert, in:, Proceedings of the British Machine Vision Conference 2016, BMVA Press, 2016, p. 92.1-92.12.","ama":"Kolesnikov A, Lampert C. Improving weakly-supervised object localization by micro-annotation. In: Proceedings of the British Machine Vision Conference 2016. Vol 2016-September. BMVA Press; 2016:92.1-92.12. doi:10.5244/C.30.92","apa":"Kolesnikov, A., & Lampert, C. (2016). Improving weakly-supervised object localization by micro-annotation. In Proceedings of the British Machine Vision Conference 2016 (Vol. 2016–September, p. 92.1-92.12). York, United Kingdom: BMVA Press. https://doi.org/10.5244/C.30.92"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","full_name":"Kolesnikov, Alexander"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"publist_id":"6273","title":"Improving weakly-supervised object localization by micro-annotation","acknowledgement":"This work was funded in parts by the European Research Council\r\nunder the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant\r\nagreement no 308036. We gratefully acknowledge the support of NVIDIA Corporation with\r\nthe donation of the GPUs used for this research.","publisher":"BMVA Press","quality_controlled":"1","oa":1,"year":"2016","day":"01","publication":"Proceedings of the British Machine Vision Conference 2016","page":"92.1-92.12","doi":"10.5244/C.30.92","date_published":"2016-09-01T00:00:00Z","date_created":"2018-12-11T11:50:09Z","_id":"1102","type":"conference","conference":{"name":"BMVC: British Machine Vision Conference","end_date":"2016-09-22","location":"York, United Kingdom","start_date":"2016-09-19"},"status":"public","date_updated":"2021-01-12T06:48:18Z","department":[{"_id":"ChLa"}],"abstract":[{"lang":"eng","text":"Weakly-supervised object localization methods tend to fail for object classes that consistently co-occur with the same background elements, e.g. trains on tracks. We propose a method to overcome these failures by adding a very small amount of model-specific additional annotation. The main idea is to cluster a deep network\\'s mid-level representations and assign object or distractor labels to each cluster. Experiments show substantially improved localization results on the challenging ILSVC2014 dataset for bounding box detection and the PASCAL VOC2012 dataset for semantic segmentation."}],"oa_version":"Published Version","scopus_import":1,"main_file_link":[{"url":"http://www.bmva.org/bmvc/2016/papers/paper092/paper092.pdf","open_access":"1"}],"month":"09","publication_status":"published","language":[{"iso":"eng"}],"volume":"2016-September","ec_funded":1},{"oa_version":"Preprint","acknowledgement":"This work was supported in part by DST-SERB, GoI under Project No. YSS/2014/000623 and 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).","abstract":[{"text":"We propose two parallel state-space-exploration algorithms for hybrid automaton (HA), with the goal of enhancing performance on multi-core shared-memory systems. The first uses the parallel, breadth-first-search algorithm (PBFS) of the SPIN model checker, when traversing the discrete modes of the HA, and enhances it with a parallel exploration of the continuous states within each mode. We show that this simple-minded extension of PBFS does not provide the desired load balancing in many HA benchmarks. The second algorithm is a task-parallel BFS algorithm (TP-BFS), which uses a cheap precomputation of the cost associated with the post operations (both continuous and discrete) in order to improve load balancing. We illustrate the TP-BFS and the cost precomputation of the post operators on a support-function-based algorithm for state-space exploration. The performance comparison of the two algorithms shows that, in general, TP-BFS provides a better utilization/load-balancing of the CPU. Both algorithms are implemented in the model checker XSpeed. Our experiments show a maximum speed-up of more than 2000 χ on a navigation benchmark, with respect to SpaceEx LGG scenario. In order to make the comparison fair, we employed an equal number of post operations in both tools. To the best of our knowledge, this paper represents the first attempt to provide parallel, reachability-analysis algorithms for HA.","lang":"eng"}],"month":"12","publisher":"IEEE","scopus_import":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.05473"}],"oa":1,"day":"27","language":[{"iso":"eng"}],"year":"2016","publication_status":"published","date_published":"2016-12-27T00:00:00Z","doi":"10.1109/MEMCOD.2016.7797741","ec_funded":1,"date_created":"2018-12-11T11:50:09Z","article_number":"7797741","_id":"1103","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"status":"public","type":"conference","conference":{"start_date":"2016-11-18","location":"Kanpur, India ","end_date":"2016-11-20","name":"MEMOCODE: International Conference on Formal Methods and Models for System Design"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:48:18Z","citation":{"ista":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. 2016. Parallel reachability analysis for hybrid systems. MEMOCODE: International Conference on Formal Methods and Models for System Design, 7797741.","chicago":"Gurung, Amit, Arup Deka, Ezio Bartocci, Sergiy Bogomolov, Radu Grosu, and Rajarshi Ray. “Parallel Reachability Analysis for Hybrid Systems.” IEEE, 2016. https://doi.org/10.1109/MEMCOD.2016.7797741.","ieee":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, and R. Ray, “Parallel reachability analysis for hybrid systems,” presented at the MEMOCODE: International Conference on Formal Methods and Models for System Design, Kanpur, India , 2016.","short":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, R. Ray, in:, IEEE, 2016.","apa":"Gurung, A., Deka, A., Bartocci, E., Bogomolov, S., Grosu, R., & Ray, R. (2016). Parallel reachability analysis for hybrid systems. Presented at the MEMOCODE: International Conference on Formal Methods and Models for System Design, Kanpur, India : IEEE. https://doi.org/10.1109/MEMCOD.2016.7797741","ama":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. Parallel reachability analysis for hybrid systems. In: IEEE; 2016. doi:10.1109/MEMCOD.2016.7797741","mla":"Gurung, Amit, et al. Parallel Reachability Analysis for Hybrid Systems. 7797741, IEEE, 2016, doi:10.1109/MEMCOD.2016.7797741."},"department":[{"_id":"ToHe"}],"title":"Parallel reachability analysis for hybrid systems","author":[{"last_name":"Gurung","full_name":"Gurung, Amit","first_name":"Amit"},{"first_name":"Arup","full_name":"Deka, Arup","last_name":"Deka"},{"first_name":"Ezio","full_name":"Bartocci, Ezio","last_name":"Bartocci"},{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","last_name":"Bogomolov","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy"},{"first_name":"Radu","full_name":"Grosu, Radu","last_name":"Grosu"},{"last_name":"Ray","full_name":"Ray, Rajarshi","first_name":"Rajarshi"}],"publist_id":"6272"},{"publisher":"Neural Information Processing Systems","quality_controlled":"1","acknowledgement":"We thank Jozsef Csicsvari for kindly sharing the CA1 data.\r\nThis work was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no. 291734.","page":"3610-3618","date_published":"2016-12-01T00:00:00Z","date_created":"2018-12-11T11:50:10Z","year":"2016","day":"01","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publist_id":"6265","author":[{"full_name":"Savin, Cristina","last_name":"Savin","id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"title":"Estimating nonlinear neural response functions using GP priors and Kronecker methods","citation":{"mla":"Savin, Cristina, and Gašper Tkačik. Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods. Vol. 29, Neural Information Processing Systems, 2016, pp. 3610–18.","ieee":"C. Savin and G. Tkačik, “Estimating nonlinear neural response functions using GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.","short":"C. Savin, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp. 3610–3618.","apa":"Savin, C., & Tkačik, G. (2016). Estimating nonlinear neural response functions using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information Processing Systems.","ama":"Savin C, Tkačik G. Estimating nonlinear neural response functions using GP priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems; 2016:3610-3618.","chicago":"Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information Processing Systems, 2016.","ista":"Savin C, Tkačik G. 2016. Estimating nonlinear neural response functions using GP priors and Kronecker methods. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3610–3618."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"alternative_title":["Advances in Neural Information Processing Systems"],"main_file_link":[{"url":"http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods"}],"month":"12","intvolume":" 29","abstract":[{"lang":"eng","text":"Jointly characterizing neural responses in terms of several external variables promises novel insights into circuit function, but remains computationally prohibitive in practice. Here we use gaussian process (GP) priors and exploit recent advances in fast GP inference and learning based on Kronecker methods, to efficiently estimate multidimensional nonlinear tuning functions. Our estimator require considerably less data than traditional methods and further provides principled uncertainty estimates. We apply these tools to hippocampal recordings during open field exploration and use them to characterize the joint dependence of CA1 responses on the position of the animal and several other variables, including the animal\\'s speed, direction of motion, and network oscillations.Our results provide an unprecedentedly detailed quantification of the tuning of hippocampal neurons. The model\\'s generality suggests that our approach can be used to estimate neural response properties in other brain regions."}],"oa_version":"None","volume":29,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"end_date":"2016-12-10","location":"Barcelona; Spain","start_date":"2016-12-05","name":"NIPS: Neural Information Processing Systems"},"status":"public","_id":"1105","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T06:48:19Z"},{"language":[{"iso":"eng"}],"day":"16","year":"2016","publication_status":"published","date_created":"2018-12-11T11:50:14Z","doi":"10.1364/CLEO_SI.2016.SF2G.3","related_material":{"link":[{"url":"http://ieeexplore.ieee.org/document/7788479/","relation":"other"}]},"date_published":"2016-12-16T00:00:00Z","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We present a coherent microwave to telecom signal converter based on the electro-optical effect using a crystalline WGM-resonator coupled to a 3D microwave cavity, achieving high photon conversion efficiency of 0.1% with MHz bandwidth."}],"month":"12","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1601.07261","open_access":"1"}],"publisher":"IEEE","scopus_import":"1","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D, Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. CLEO: Conference on Lasers and Electro Optics, 7788479.","chicago":"Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit Stiller, Georg Schunk, Dimitry Strekalov, et al. “Efficient Single Sideband Microwave to Optical Conversion Using a LiNbO₃ WGM-Resonator.” IEEE, 2016. https://doi.org/10.1364/CLEO_SI.2016.SF2G.3.","apa":"Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., … Schwefel, H. (2016). Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. Presented at the CLEO: Conference on Lasers and Electro Optics, San Jose, CA, USA: IEEE. https://doi.org/10.1364/CLEO_SI.2016.SF2G.3","ama":"Rueda A, Sedlmeir F, Collodo M, et al. Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. In: IEEE; 2016. doi:10.1364/CLEO_SI.2016.SF2G.3","ieee":"A. Rueda et al., “Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator,” presented at the CLEO: Conference on Lasers and Electro Optics, San Jose, CA, USA, 2016.","short":"A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov, C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, in:, IEEE, 2016.","mla":"Rueda, Alfredo, et al. Efficient Single Sideband Microwave to Optical Conversion Using a LiNbO₃ WGM-Resonator. 7788479, IEEE, 2016, doi:10.1364/CLEO_SI.2016.SF2G.3."},"date_updated":"2022-09-06T07:23:25Z","title":"Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator","department":[{"_id":"JoFi"}],"article_processing_charge":"No","author":[{"last_name":"Rueda","full_name":"Rueda, Alfredo","first_name":"Alfredo"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"last_name":"Collodo","full_name":"Collodo, Michele","first_name":"Michele"},{"last_name":"Vogl","full_name":"Vogl, Ulrich","first_name":"Ulrich"},{"full_name":"Stiller, Birgit","last_name":"Stiller","first_name":"Birgit"},{"last_name":"Schunk","full_name":"Schunk, Georg","first_name":"Georg"},{"last_name":"Strekalov","full_name":"Strekalov, Dimitry","first_name":"Dimitry"},{"full_name":"Marquardt, Christoph","last_name":"Marquardt","first_name":"Christoph"},{"last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"},{"first_name":"Oskar","full_name":"Painter, Oskar","last_name":"Painter"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"full_name":"Schwefel, Harald","last_name":"Schwefel","first_name":"Harald"}],"publist_id":"6251","article_number":"7788479","_id":"1115","status":"public","conference":{"name":"CLEO: Conference on Lasers and Electro Optics","start_date":"2016-06-05","end_date":"2016-06-10","location":"San Jose, CA, USA"},"type":"conference"},{"file_date_updated":"2018-12-12T10:09:31Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2021-01-12T06:48:33Z","pubrep_id":"644","status":"public","conference":{"name":"EMSOFT: Embedded Software ","end_date":"2016-10-07","location":"Pittsburgh, PA, USA","start_date":"2016-10-01"},"type":"conference","_id":"1135","ec_funded":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:09:31Z","file_name":"IST-2016-644-v1+1_emsoft-no-format.pdf","creator":"system","date_updated":"2018-12-12T10:09:31Z","file_size":279240,"file_id":"4755","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","month":"10","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Time-triggered (TT) switched networks are a deterministic communication infrastructure used by real-time distributed embedded systems. These networks rely on the notion of globally discretized time (i.e. time slots) and a static TT schedule that prescribes which message is sent through which link at every time slot, such that all messages reach their destination before a global timeout. These schedules are generated offline, assuming a static network with fault-free links, and entrusting all error-handling functions to the end user. Assuming the network is static is an over-optimistic view, and indeed links tend to fail in practice. We study synthesis of TT schedules on a network in which links fail over time and we assume the switches run a very simple error-recovery protocol once they detect a crashed link. We address the problem of finding a pk; qresistant schedule; namely, one that, assuming the switches run a fixed error-recovery protocol, guarantees that the number of messages that arrive at their destination by the timeout is at least no matter what sequence of at most k links fail. Thus, we maintain the simplicity of the switches while giving a guarantee on the number of messages that meet the timeout. We show how a pk; q-resistant schedule can be obtained using a CEGAR-like approach: find a schedule, decide whether it is pk; q-resistant, and if it is not, use the witnessing fault sequence to generate a constraint that is added to the program. The newly added constraint disallows the schedule to be regenerated in a future iteration while also eliminating several other schedules that are not pk; q-resistant. We illustrate the applicability of our approach using an SMT-based implementation. © 2016 ACM."}],"title":"Synthesizing time triggered schedules for switched networks with faulty links","publist_id":"6223","author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy"},{"first_name":"Shibashis","full_name":"Guha, Shibashis","last_name":"Guha"},{"last_name":"Rodríguez Navas","full_name":"Rodríguez Navas, Guillermo","first_name":"Guillermo"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Avni, Guy, Shibashis Guha, and Guillermo Rodríguez Navas. “Synthesizing Time Triggered Schedules for Switched Networks with Faulty Links.” In Proceedings of the 13th International Conference on Embedded Software . ACM, 2016. https://doi.org/10.1145/2968478.2968499.","ista":"Avni G, Guha S, Rodríguez Navas G. 2016. Synthesizing time triggered schedules for switched networks with faulty links. Proceedings of the 13th International Conference on Embedded Software . EMSOFT: Embedded Software , 26.","mla":"Avni, Guy, et al. “Synthesizing Time Triggered Schedules for Switched Networks with Faulty Links.” Proceedings of the 13th International Conference on Embedded Software , 26, ACM, 2016, doi:10.1145/2968478.2968499.","apa":"Avni, G., Guha, S., & Rodríguez Navas, G. (2016). Synthesizing time triggered schedules for switched networks with faulty links. In Proceedings of the 13th International Conference on Embedded Software . Pittsburgh, PA, USA: ACM. https://doi.org/10.1145/2968478.2968499","ama":"Avni G, Guha S, Rodríguez Navas G. Synthesizing time triggered schedules for switched networks with faulty links. In: Proceedings of the 13th International Conference on Embedded Software . ACM; 2016. doi:10.1145/2968478.2968499","ieee":"G. Avni, S. Guha, and G. Rodríguez Navas, “Synthesizing time triggered schedules for switched networks with faulty links,” in Proceedings of the 13th International Conference on Embedded Software , Pittsburgh, PA, USA, 2016.","short":"G. Avni, S. Guha, G. Rodríguez Navas, in:, Proceedings of the 13th International Conference on Embedded Software , ACM, 2016."},"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"article_number":"26","date_created":"2018-12-11T11:50:20Z","doi":"10.1145/2968478.2968499","date_published":"2016-10-01T00:00:00Z","publication":"Proceedings of the 13th International Conference on Embedded Software ","day":"01","year":"2016","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"ACM"},{"status":"public","type":"conference","conference":{"start_date":"2016-09-19","end_date":"2016-09-22","location":"Buenos Aires, Argentina ","name":"CCA: Control Applications "},"article_number":"7587948","_id":"1134","title":"Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP","department":[{"_id":"ToHe"}],"author":[{"first_name":"Parasara","full_name":"Duggirala, Parasara","last_name":"Duggirala"},{"first_name":"Chuchu","full_name":"Fan, Chuchu","last_name":"Fan"},{"first_name":"Matthew","full_name":"Potok, Matthew","last_name":"Potok"},{"first_name":"Bolun","last_name":"Qi","full_name":"Qi, Bolun"},{"last_name":"Mitra","full_name":"Mitra, Sayan","first_name":"Sayan"},{"first_name":"Mahesh","full_name":"Viswanathan, Mahesh","last_name":"Viswanathan"},{"full_name":"Bak, Stanley","last_name":"Bak","first_name":"Stanley"},{"first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","last_name":"Bogomolov"},{"full_name":"Johnson, Taylor","last_name":"Johnson","first_name":"Taylor"},{"first_name":"Luan","last_name":"Nguyen","full_name":"Nguyen, Luan"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","last_name":"Schilling"},{"full_name":"Sogokon, Andrew","last_name":"Sogokon","first_name":"Andrew"},{"first_name":"Hoang","full_name":"Tran, Hoang","last_name":"Tran"},{"last_name":"Xiang","full_name":"Xiang, Weiming","first_name":"Weiming"}],"publist_id":"6224","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Duggirala P, Fan C, Potok M, Qi B, Mitra S, Viswanathan M, Bak S, Bogomolov S, Johnson T, Nguyen L, Schilling C, Sogokon A, Tran H, Xiang W. 2016. Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP. 2016 IEEE Conference on Control Applications. CCA: Control Applications , 7587948.","chicago":"Duggirala, Parasara, Chuchu Fan, Matthew Potok, Bolun Qi, Sayan Mitra, Mahesh Viswanathan, Stanley Bak, et al. “Tutorial: Software Tools for Hybrid Systems Verification Transformation and Synthesis C2E2 HyST and TuLiP.” In 2016 IEEE Conference on Control Applications. IEEE, 2016. https://doi.org/10.1109/CCA.2016.7587948.","apa":"Duggirala, P., Fan, C., Potok, M., Qi, B., Mitra, S., Viswanathan, M., … Xiang, W. (2016). Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP. In 2016 IEEE Conference on Control Applications. Buenos Aires, Argentina : IEEE. https://doi.org/10.1109/CCA.2016.7587948","ama":"Duggirala P, Fan C, Potok M, et al. Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP. In: 2016 IEEE Conference on Control Applications. IEEE; 2016. doi:10.1109/CCA.2016.7587948","ieee":"P. Duggirala et al., “Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP,” in 2016 IEEE Conference on Control Applications, Buenos Aires, Argentina , 2016.","short":"P. Duggirala, C. Fan, M. Potok, B. Qi, S. Mitra, M. Viswanathan, S. Bak, S. Bogomolov, T. Johnson, L. Nguyen, C. Schilling, A. Sogokon, H. Tran, W. Xiang, in:, 2016 IEEE Conference on Control Applications, IEEE, 2016.","mla":"Duggirala, Parasara, et al. “Tutorial: Software Tools for Hybrid Systems Verification Transformation and Synthesis C2E2 HyST and TuLiP.” 2016 IEEE Conference on Control Applications, 7587948, IEEE, 2016, doi:10.1109/CCA.2016.7587948."},"date_updated":"2021-01-12T06:48:32Z","month":"10","publisher":"IEEE","scopus_import":1,"quality_controlled":"1","oa_version":"None","abstract":[{"text":"Hybrid systems have both continuous and discrete dynamics and are useful for modeling a variety of control systems, from air traffic control protocols to robotic maneuvers and beyond. Recently, numerous powerful and scalable tools for analyzing hybrid systems have emerged. Several of these tools implement automated formal methods for mathematically proving a system meets a specification. This tutorial session will present three recent hybrid systems tools: C2E2, HyST, and TuLiP. C2E2 is a simulated-based verification tool for hybrid systems, and uses validated numerical solvers and bloating of simulation traces to verify systems meet specifications. HyST is a hybrid systems model transformation and translation tool, and uses a canonical intermediate representation to support most of the recent verification tools, as well as automated sound abstractions that simplify verification of a given hybrid system. TuLiP is a controller synthesis tool for hybrid systems, where given a temporal logic specification to be satisfied for a system (plant) model, TuLiP will find a controller that meets a given specification. © 2016 IEEE.","lang":"eng"}],"date_published":"2016-10-10T00:00:00Z","doi":"10.1109/CCA.2016.7587948","date_created":"2018-12-11T11:50:20Z","day":"10","publication":"2016 IEEE Conference on Control Applications","language":[{"iso":"eng"}],"year":"2016","publication_status":"published"},{"month":"10","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01367181"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We propose an interactive sculpting system for seamlessly editing pre-computed animations of liquid, without the need for any resimulation. The input is a sequence of meshes without correspondences representing the liquid surface over time. Our method enables the efficient selection of consistent space-time parts of this animation, such as moving waves or droplets, which we call space-time features. Once selected, a feature can be copied, edited, or duplicated and then pasted back anywhere in space and time in the same or in another liquid animation sequence. Our method circumvents tedious user interactions by automatically computing the spatial and temporal ranges of the selected feature. We also provide space-time shape editing tools for non-uniform scaling, rotation, trajectory changes, and temporal editing to locally speed up or slow down motion. Using our tools, the user can edit and progressively refine any input simulation result, possibly using a library of precomputed space-time features extracted from other animations. In contrast to the trial-and-error loop usually required to edit animation results through the tuning of indirect simulation parameters, our method gives the user full control over the edited space-time behaviors. © 2016 Copyright held by the owner/author(s)."}],"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"conference","conference":{"name":"MIG: Motion in Games","start_date":"2016-10-10","location":"San Francisco, CA, USA","end_date":"2016-10-12"},"_id":"1136","department":[{"_id":"ChWo"}],"ddc":["004"],"date_updated":"2023-02-21T09:49:49Z","quality_controlled":"1","publisher":"ACM","oa":1,"acknowledgement":"This work was partly supported by the starting grant BigSplash, as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2014-StG 638176 , and ERC-2011-ADG 20110209).","date_published":"2016-10-10T00:00:00Z","doi":"10.1145/2994258.2994261","date_created":"2018-12-11T11:50:20Z","day":"10","publication":"Proceedings of the 9th International Conference on Motion in Games ","has_accepted_license":"1","year":"2016","project":[{"grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"2994261","title":"Space-time sculpting of liquid animation","author":[{"first_name":"Pierre","last_name":"Manteaux","full_name":"Manteaux, Pierre"},{"full_name":"Vimont, Ulysse","last_name":"Vimont","first_name":"Ulysse"},{"last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rohmer, Damien","last_name":"Rohmer","first_name":"Damien"},{"full_name":"Cani, Marie","last_name":"Cani","first_name":"Marie"}],"publist_id":"6222","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. Space-time sculpting of liquid animation. In: Proceedings of the 9th International Conference on Motion in Games . ACM; 2016. doi:10.1145/2994258.2994261","apa":"Manteaux, P., Vimont, U., Wojtan, C., Rohmer, D., & Cani, M. (2016). Space-time sculpting of liquid animation. In Proceedings of the 9th International Conference on Motion in Games . San Francisco, CA, USA: ACM. https://doi.org/10.1145/2994258.2994261","ieee":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, and M. Cani, “Space-time sculpting of liquid animation,” in Proceedings of the 9th International Conference on Motion in Games , San Francisco, CA, USA, 2016.","short":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, M. Cani, in:, Proceedings of the 9th International Conference on Motion in Games , ACM, 2016.","mla":"Manteaux, Pierre, et al. “Space-Time Sculpting of Liquid Animation.” Proceedings of the 9th International Conference on Motion in Games , 2994261, ACM, 2016, doi:10.1145/2994258.2994261.","ista":"Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. 2016. Space-time sculpting of liquid animation. Proceedings of the 9th International Conference on Motion in Games . MIG: Motion in Games, 2994261.","chicago":"Manteaux, Pierre, Ulysse Vimont, Chris Wojtan, Damien Rohmer, and Marie Cani. “Space-Time Sculpting of Liquid Animation.” In Proceedings of the 9th International Conference on Motion in Games . ACM, 2016. https://doi.org/10.1145/2994258.2994261."}},{"issue":"12","volume":17,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400263"}],"month":"12","intvolume":" 17","abstract":[{"text":"RASGRP1 is an important guanine nucleotide exchange factor and activator of the RAS-MAPK pathway following T cell antigen receptor (TCR) signaling. The consequences of RASGRP1 mutations in humans are unknown. In a patient with recurrent bacterial and viral infections, born to healthy consanguineous parents, we used homozygosity mapping and exome sequencing to identify a biallelic stop-gain variant in RASGRP1. This variant segregated perfectly with the disease and has not been reported in genetic databases. RASGRP1 deficiency was associated in T cells and B cells with decreased phosphorylation of the extracellular-signal-regulated serine kinase ERK, which was restored following expression of wild-type RASGRP1. RASGRP1 deficiency also resulted in defective proliferation, activation and motility of T cells and B cells. RASGRP1-deficient natural killer (NK) cells exhibited impaired cytotoxicity with defective granule convergence and actin accumulation. Interaction proteomics identified the dynein light chain DYNLL1 as interacting with RASGRP1, which links RASGRP1 to cytoskeletal dynamics. RASGRP1-deficient cells showed decreased activation of the GTPase RhoA. Treatment with lenalidomide increased RhoA activity and reversed the migration and activation defects of RASGRP1-deficient lymphocytes.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","department":[{"_id":"MiSi"}],"date_updated":"2021-01-12T06:48:33Z","article_type":"original","type":"journal_article","status":"public","_id":"1137","page":"1352 - 1360","doi":"10.1038/ni.3575","date_published":"2016-12-01T00:00:00Z","date_created":"2018-12-11T11:50:21Z","year":"2016","day":"01","publication":"Nature Immunology","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"publist_id":"6221","author":[{"last_name":"Salzer","full_name":"Salzer, Elisabeth","first_name":"Elisabeth"},{"last_name":"Çaǧdaş","full_name":"Çaǧdaş, Deniz","first_name":"Deniz"},{"first_name":"Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6625-3348","full_name":"Hons, Miroslav","last_name":"Hons"},{"first_name":"Emily","full_name":"Mace, Emily","last_name":"Mace"},{"first_name":"Wojciech","last_name":"Garncarz","full_name":"Garncarz, Wojciech"},{"first_name":"Oezlem","full_name":"Petronczki, Oezlem","last_name":"Petronczki"},{"first_name":"René","last_name":"Platzer","full_name":"Platzer, René"},{"first_name":"Laurène","full_name":"Pfajfer, Laurène","last_name":"Pfajfer"},{"full_name":"Bilic, Ivan","last_name":"Bilic","first_name":"Ivan"},{"full_name":"Ban, Sol","last_name":"Ban","first_name":"Sol"},{"first_name":"Katharina","full_name":"Willmann, Katharina","last_name":"Willmann"},{"first_name":"Malini","last_name":"Mukherjee","full_name":"Mukherjee, Malini"},{"first_name":"Verena","last_name":"Supper","full_name":"Supper, Verena"},{"last_name":"Hsu","full_name":"Hsu, Hsiangting","first_name":"Hsiangting"},{"last_name":"Banerjee","full_name":"Banerjee, Pinaki","first_name":"Pinaki"},{"last_name":"Sinha","full_name":"Sinha, Papiya","first_name":"Papiya"},{"last_name":"Mcclanahan","full_name":"Mcclanahan, Fabienne","first_name":"Fabienne"},{"last_name":"Zlabinger","full_name":"Zlabinger, Gerhard","first_name":"Gerhard"},{"last_name":"Pickl","full_name":"Pickl, Winfried","first_name":"Winfried"},{"first_name":"John","full_name":"Gribben, John","last_name":"Gribben"},{"first_name":"Hannes","full_name":"Stockinger, Hannes","last_name":"Stockinger"},{"last_name":"Bennett","full_name":"Bennett, Keiryn","first_name":"Keiryn"},{"full_name":"Huppa, Johannes","last_name":"Huppa","first_name":"Johannes"},{"last_name":"Dupré","full_name":"Dupré, Loï̈C","first_name":"Loï̈C"},{"full_name":"Sanal, Özden","last_name":"Sanal","first_name":"Özden"},{"full_name":"Jäger, Ulrich","last_name":"Jäger","first_name":"Ulrich"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tezcan","full_name":"Tezcan, Ilhan","first_name":"Ilhan"},{"first_name":"Jordan","last_name":"Orange","full_name":"Orange, Jordan"},{"first_name":"Kaan","last_name":"Boztug","full_name":"Boztug, Kaan"}],"article_processing_charge":"No","external_id":{"pmid":["27776107"]},"title":"RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics","citation":{"chicago":"Salzer, Elisabeth, Deniz Çaǧdaş, Miroslav Hons, Emily Mace, Wojciech Garncarz, Oezlem Petronczki, René Platzer, et al. “RASGRP1 Deficiency Causes Immunodeficiency with Impaired Cytoskeletal Dynamics.” Nature Immunology. Nature Publishing Group, 2016. https://doi.org/10.1038/ni.3575.","ista":"Salzer E, Çaǧdaş D, Hons M, Mace E, Garncarz W, Petronczki O, Platzer R, Pfajfer L, Bilic I, Ban S, Willmann K, Mukherjee M, Supper V, Hsu H, Banerjee P, Sinha P, Mcclanahan F, Zlabinger G, Pickl W, Gribben J, Stockinger H, Bennett K, Huppa J, Dupré L, Sanal Ö, Jäger U, Sixt MK, Tezcan I, Orange J, Boztug K. 2016. RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. Nature Immunology. 17(12), 1352–1360.","mla":"Salzer, Elisabeth, et al. “RASGRP1 Deficiency Causes Immunodeficiency with Impaired Cytoskeletal Dynamics.” Nature Immunology, vol. 17, no. 12, Nature Publishing Group, 2016, pp. 1352–60, doi:10.1038/ni.3575.","ama":"Salzer E, Çaǧdaş D, Hons M, et al. RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. Nature Immunology. 2016;17(12):1352-1360. doi:10.1038/ni.3575","apa":"Salzer, E., Çaǧdaş, D., Hons, M., Mace, E., Garncarz, W., Petronczki, O., … Boztug, K. (2016). RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/ni.3575","short":"E. Salzer, D. Çaǧdaş, M. Hons, E. Mace, W. Garncarz, O. Petronczki, R. Platzer, L. Pfajfer, I. Bilic, S. Ban, K. Willmann, M. Mukherjee, V. Supper, H. Hsu, P. Banerjee, P. Sinha, F. Mcclanahan, G. Zlabinger, W. Pickl, J. Gribben, H. Stockinger, K. Bennett, J. Huppa, L. Dupré, Ö. Sanal, U. Jäger, M.K. Sixt, I. Tezcan, J. Orange, K. Boztug, Nature Immunology 17 (2016) 1352–1360.","ieee":"E. Salzer et al., “RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics,” Nature Immunology, vol. 17, no. 12. Nature Publishing Group, pp. 1352–1360, 2016."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_updated":"2021-01-12T06:48:34Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"_id":"1138","type":"conference","conference":{"name":"LICS: Logic in Computer Science","start_date":"2016-07-05","end_date":"2016-07-08","location":"New York, NY, USA"},"status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"text":"Automata with monitor counters, where the transitions do not depend on counter values, and nested weighted automata are two expressive automata-theoretic frameworks for quantitative properties. For a well-studied and wide class of quantitative functions, we establish that automata with monitor counters and nested weighted automata are equivalent. We study for the first time such quantitative automata under probabilistic semantics. We show that several problems that are undecidable for the classical questions of emptiness and universality become decidable under the probabilistic semantics. We present a complete picture of decidability for such automata, and even an almost-complete picture of computational complexity, for the probabilistic questions we consider. © 2016 ACM.","lang":"eng"}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1604.06764","open_access":"1"}],"month":"07","citation":{"ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative automata under probabilistic semantics. Proceedings of the 31st Annual ACM/IEEE Symposium. LICS: Logic in Computer Science, 76–85.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Automata under Probabilistic Semantics.” In Proceedings of the 31st Annual ACM/IEEE Symposium, 76–85. IEEE, 2016. https://doi.org/10.1145/2933575.2933588.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Quantitative automata under probabilistic semantics. In Proceedings of the 31st Annual ACM/IEEE Symposium (pp. 76–85). New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2933588","ama":"Chatterjee K, Henzinger TA, Otop J. Quantitative automata under probabilistic semantics. In: Proceedings of the 31st Annual ACM/IEEE Symposium. IEEE; 2016:76-85. doi:10.1145/2933575.2933588","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative automata under probabilistic semantics,” in Proceedings of the 31st Annual ACM/IEEE Symposium, New York, NY, USA, 2016, pp. 76–85.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings of the 31st Annual ACM/IEEE Symposium, IEEE, 2016, pp. 76–85.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Automata under Probabilistic Semantics.” Proceedings of the 31st Annual ACM/IEEE Symposium, IEEE, 2016, pp. 76–85, doi:10.1145/2933575.2933588."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Otop","full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"publist_id":"6220","external_id":{"arxiv":["1604.06764"]},"title":"Quantitative automata under probabilistic semantics","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"year":"2016","day":"05","publication":"Proceedings of the 31st Annual ACM/IEEE Symposium","page":"76 - 85","date_published":"2016-07-05T00:00:00Z","doi":"10.1145/2933575.2933588","date_created":"2018-12-11T11:50:21Z","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), FWF Grant No P23499- N23, FWF NFN Grant No S114","quality_controlled":"1","publisher":"IEEE","oa":1},{"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["Proceedings Symposium on Logic in Computer Science"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.02670"}],"month":"07","abstract":[{"text":"Given a model of a system and an objective, the model-checking question asks whether the model satisfies the objective. We study polynomial-time problems in two classical models, graphs and Markov Decision Processes (MDPs), with respect to several fundamental -regular objectives, e.g., Rabin and Streett objectives. For many of these problems the best-known upper bounds are quadratic or cubic, yet no super-linear lower bounds are known. In this work our contributions are two-fold: First, we present several improved algorithms, and second, we present the first conditional super-linear lower bounds based on widely believed assumptions about the complexity of CNF-SAT and combinatorial Boolean matrix multiplication. A separation result for two models with respect to an objective means a conditional lower bound for one model that is strictly higher than the existing upper bound for the other model, and similarly for two objectives with respect to a model. Our results establish the following separation results: (1) A separation of models (graphs and MDPs) for disjunctive queries of reachability and Büchi objectives. (2) Two kinds of separations of objectives, both for graphs and MDPs, namely, (2a) the separation of dual objectives such as Streett/Rabin objectives, and (2b) the separation of conjunction and disjunction of multiple objectives of the same type such as safety, Büchi, and coBüchi. In summary, our results establish the first model and objective separation results for graphs and MDPs for various classical -regular objectives. Quite strikingly, we establish conditional lower bounds for the disjunction of objectives that are strictly higher than the existing upper bounds for the conjunction of the same objectives. © 2016 ACM.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"KrCh"}],"date_updated":"2022-09-09T11:46:17Z","type":"conference","conference":{"name":"LICS: Logic in Computer Science","end_date":"2016-07-08","location":"New York, NY, USA","start_date":"2016-07-05"},"status":"public","_id":"1140","page":"197 - 206","doi":"10.1145/2933575.2935304","date_published":"2016-07-05T00:00:00Z","date_created":"2018-12-11T11:50:22Z","year":"2016","day":"05","publication":"Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science","quality_controlled":"1","publisher":"IEEE","oa":1,"acknowledgement":"K. C., M. H., and W. D. are partially supported by the Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003.\r\nK. C. is partially supported by the Austrian Science Fund (FWF)\r\nNFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Start grant\r\n(279307: Graph Games). For W. D., M. H., and V. L. the research\r\nleading to these results has received funding from the European\r\nResearch Council under the European Union’s Seventh Framework\r\nProgramme (FP/2007-2013) / ERC Grant Agreement no. 340506.","publist_id":"6219","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Dvoák","full_name":"Dvoák, Wolfgang","first_name":"Wolfgang"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"}],"article_processing_charge":"No","external_id":{"arxiv":["1602.02670"]},"title":"Model and objective separation with conditional lower bounds: disjunction is harder than conjunction","citation":{"chicago":"Chatterjee, Krishnendu, Wolfgang Dvoák, Monika H Henzinger, and Veronika Loitzenbauer. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” In Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, 197–206. IEEE, 2016. https://doi.org/10.1145/2933575.2935304.","ista":"Chatterjee K, Dvoák W, Henzinger MH, Loitzenbauer V. 2016. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, Proceedings Symposium on Logic in Computer Science, , 197–206.","mla":"Chatterjee, Krishnendu, et al. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2016, pp. 197–206, doi:10.1145/2933575.2935304.","ama":"Chatterjee K, Dvoák W, Henzinger MH, Loitzenbauer V. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In: Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE; 2016:197-206. doi:10.1145/2933575.2935304","apa":"Chatterjee, K., Dvoák, W., Henzinger, M. H., & Loitzenbauer, V. (2016). Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 197–206). New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2935304","short":"K. Chatterjee, W. Dvoák, M.H. Henzinger, V. Loitzenbauer, in:, Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2016, pp. 197–206.","ieee":"K. Chatterjee, W. Dvoák, M. H. Henzinger, and V. Loitzenbauer, “Model and objective separation with conditional lower bounds: disjunction is harder than conjunction,” in Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, New York, NY, USA, 2016, pp. 197–206."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}]},{"department":[{"_id":"MiSi"},{"_id":"PeJo"}],"date_updated":"2021-01-12T06:48:36Z","status":"public","type":"journal_article","_id":"1142","issue":"12","volume":17,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 17","month":"12","main_file_link":[{"url":"https://ora.ox.ac.uk/objects/uuid:f53a464e-1e5b-4f08-a7d8-b6749b852b9d","open_access":"1"}],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Hemolysis drives susceptibility to bacterial infections and predicts poor outcome from sepsis. These detrimental effects are commonly considered to be a consequence of heme-iron serving as a nutrient for bacteria. We employed a Gram-negative sepsis model and found that elevated heme levels impaired the control of bacterial proliferation independently of heme-iron acquisition by pathogens. Heme strongly inhibited phagocytosis and the migration of human and mouse phagocytes by disrupting actin cytoskeletal dynamics via activation of the GTP-binding Rho family protein Cdc42 by the guanine nucleotide exchange factor DOCK8. A chemical screening approach revealed that quinine effectively prevented heme effects on the cytoskeleton, restored phagocytosis and improved survival in sepsis. These mechanistic insights provide potential therapeutic targets for patients with sepsis or hemolytic disorders."}],"title":"Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions","author":[{"first_name":"Rui","last_name":"Martins","full_name":"Martins, Rui"},{"first_name":"Julia","last_name":"Maier","full_name":"Maier, Julia"},{"last_name":"Gorki","full_name":"Gorki, Anna","first_name":"Anna"},{"last_name":"Huber","full_name":"Huber, Kilian","first_name":"Kilian"},{"first_name":"Omar","full_name":"Sharif, Omar","last_name":"Sharif"},{"first_name":"Philipp","full_name":"Starkl, Philipp","last_name":"Starkl"},{"first_name":"Simona","last_name":"Saluzzo","full_name":"Saluzzo, Simona"},{"full_name":"Quattrone, Federica","last_name":"Quattrone","first_name":"Federica"},{"first_name":"Riem","full_name":"Gawish, Riem","last_name":"Gawish"},{"first_name":"Karin","last_name":"Lakovits","full_name":"Lakovits, Karin"},{"first_name":"Michael","last_name":"Aichinger","full_name":"Aichinger, Michael"},{"first_name":"Branka","full_name":"Radic Sarikas, Branka","last_name":"Radic Sarikas"},{"first_name":"Charles","full_name":"Lardeau, Charles","last_name":"Lardeau"},{"last_name":"Hladik","full_name":"Hladik, Anastasiya","first_name":"Anastasiya"},{"first_name":"Ana","last_name":"Korosec","full_name":"Korosec, Ana"},{"first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","full_name":"Brown, Markus"},{"orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari","last_name":"Vaahtomeri","id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari"},{"last_name":"Duggan","full_name":"Duggan, Michelle","id":"2EDEA62C-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle"},{"last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho","first_name":"Dontscho"},{"full_name":"Esterbauer, Harald","last_name":"Esterbauer","first_name":"Harald"},{"first_name":"Jacques","full_name":"Colinge, Jacques","last_name":"Colinge"},{"last_name":"Eisenbarth","full_name":"Eisenbarth, Stephanie","first_name":"Stephanie"},{"first_name":"Thomas","full_name":"Decker, Thomas","last_name":"Decker"},{"last_name":"Bennett","full_name":"Bennett, Keiryn","first_name":"Keiryn"},{"full_name":"Kubicek, Stefan","last_name":"Kubicek","first_name":"Stefan"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"first_name":"Giulio","full_name":"Superti Furga, Giulio","last_name":"Superti Furga"},{"first_name":"Sylvia","last_name":"Knapp","full_name":"Knapp, Sylvia"}],"publist_id":"6216","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"R. Martins et al., “Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions,” Nature Immunology, vol. 17, no. 12. Nature Publishing Group, pp. 1361–1372, 2016.","short":"R. Martins, J. Maier, A. Gorki, K. Huber, O. Sharif, P. Starkl, S. Saluzzo, F. Quattrone, R. Gawish, K. Lakovits, M. Aichinger, B. Radic Sarikas, C. Lardeau, A. Hladik, A. Korosec, M. Brown, K. Vaahtomeri, M. Duggan, D. Kerjaschki, H. Esterbauer, J. Colinge, S. Eisenbarth, T. Decker, K. Bennett, S. Kubicek, M.K. Sixt, G. Superti Furga, S. Knapp, Nature Immunology 17 (2016) 1361–1372.","apa":"Martins, R., Maier, J., Gorki, A., Huber, K., Sharif, O., Starkl, P., … Knapp, S. (2016). Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/ni.3590","ama":"Martins R, Maier J, Gorki A, et al. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nature Immunology. 2016;17(12):1361-1372. doi:10.1038/ni.3590","mla":"Martins, Rui, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” Nature Immunology, vol. 17, no. 12, Nature Publishing Group, 2016, pp. 1361–72, doi:10.1038/ni.3590.","ista":"Martins R, Maier J, Gorki A, Huber K, Sharif O, Starkl P, Saluzzo S, Quattrone F, Gawish R, Lakovits K, Aichinger M, Radic Sarikas B, Lardeau C, Hladik A, Korosec A, Brown M, Vaahtomeri K, Duggan M, Kerjaschki D, Esterbauer H, Colinge J, Eisenbarth S, Decker T, Bennett K, Kubicek S, Sixt MK, Superti Furga G, Knapp S. 2016. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nature Immunology. 17(12), 1361–1372.","chicago":"Martins, Rui, Julia Maier, Anna Gorki, Kilian Huber, Omar Sharif, Philipp Starkl, Simona Saluzzo, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” Nature Immunology. Nature Publishing Group, 2016. https://doi.org/10.1038/ni.3590."},"date_created":"2018-12-11T11:50:22Z","doi":"10.1038/ni.3590","date_published":"2016-12-01T00:00:00Z","page":"1361 - 1372","publication":"Nature Immunology","day":"01","year":"2016","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","acknowledgement":"Y. Fukui (Medical Institute of Bioregulation, Kyushu University) and J. Stein (Theodor Kocher Institute, University of Bern) are acknowledged for providing the DOCK8 deficient bone marrow. and H. Häcker (St. Judes Children's Research Hospital) for providing the ERHBD-HoxB8-encoding retroviral construct. pSpCas9(BB)-2a-Puro (PX459) was a gift from F. Zhang (Massachusetts Institute of Technology) (Addgene plasmid # 48139) and pGRG36 was a gift from N. Craig (Johns Hopkins University School of Medicine) (Addgene plasmid # 16666). LifeAct-GFP-encoding retrovirus was kindly provided by A. Leithner (Institute of Science and Technology Austria). pSIM8 and TKC E. coli were gifts from D.L. Court (Center for Cancer Research, National Cancer Institute). We acknowledge M. Gröger and S. Rauscher for excellent technical support (Core imaging facility, Medical University of Vienna). We thank D.P. Barlow and L.R. Cheever for critical reading of the manuscript. This work was supported by the Austrian Academy of Sciences, the Science Fund of the Austrian National Bank (14107) and the Austrian Science Fund FWF (I1620-B22) in the Infect-ERA framework (to S.Knapp)."},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:48:35Z","citation":{"apa":"Łazarz, R., Idzik, M., Gądek, K., & Gajda-Zagorska, E. P. (2016). Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. Journal of Computational Science. Elsevier. https://doi.org/10.1016/j.jocs.2016.03.004","ama":"Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. Journal of Computational Science. 2016;17(1):249-260. doi:10.1016/j.jocs.2016.03.004","ieee":"R. Łazarz, M. Idzik, K. Gądek, and E. P. Gajda-Zagorska, “Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization,” Journal of Computational Science, vol. 17, no. 1. Elsevier, pp. 249–260, 2016.","short":"R. Łazarz, M. Idzik, K. Gądek, E.P. Gajda-Zagorska, Journal of Computational Science 17 (2016) 249–260.","mla":"Łazarz, Radosław, et al. “Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective Optimization.” Journal of Computational Science, vol. 17, no. 1, Elsevier, 2016, pp. 249–60, doi:10.1016/j.jocs.2016.03.004.","ista":"Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. 2016. Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. Journal of Computational Science. 17(1), 249–260.","chicago":"Łazarz, Radosław, Michał Idzik, Konrad Gądek, and Ewa P Gajda-Zagorska. “Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective Optimization.” Journal of Computational Science. Elsevier, 2016. https://doi.org/10.1016/j.jocs.2016.03.004."},"title":"Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization","department":[{"_id":"ChWo"}],"publist_id":"6217","author":[{"last_name":"Łazarz","full_name":"Łazarz, Radosław","first_name":"Radosław"},{"last_name":"Idzik","full_name":"Idzik, Michał","first_name":"Michał"},{"full_name":"Gądek, Konrad","last_name":"Gądek","first_name":"Konrad"},{"full_name":"Gajda-Zagorska, Ewa P","last_name":"Gajda-Zagorska","first_name":"Ewa P","id":"47794CF0-F248-11E8-B48F-1D18A9856A87"}],"_id":"1141","status":"public","type":"journal_article","publication":"Journal of Computational Science","language":[{"iso":"eng"}],"day":"01","year":"2016","publication_status":"published","date_created":"2018-12-11T11:50:22Z","volume":17,"date_published":"2016-11-01T00:00:00Z","doi":"10.1016/j.jocs.2016.03.004","issue":"1","page":"249 - 260","acknowledgement":"The work presented in this paper was partially supported by Polish National Science Centre grant nos. DEC-2012/05/N/ST6/03433 and DEC-2011/03/B/ST6/01393. Radosław Łazarz was supported by Polish National Science Centre grant no. DEC-2013/10/M/ST6/00531.","oa_version":"None","abstract":[{"lang":"eng","text":"In this paper we introduce the Multiobjective Optimization Hierarchic Genetic Strategy with maturing (MO-mHGS), a meta-algorithm that performs evolutionary optimization in a hierarchy of populations. The maturing mechanism improves growth and reduces redundancy. The performance of MO-mHGS with selected state-of-the-art multiobjective evolutionary algorithms as internal algorithms is analysed on benchmark problems and their modifications for which single fitness evaluation time depends on the solution accuracy. We compare the proposed algorithm with the Island Model Genetic Algorithm as well as with single-deme methods, and discuss the impact of internal algorithms on the MO-mHGS meta-algorithm. © 2016 Elsevier B.V."}],"intvolume":" 17","month":"11","publisher":"Elsevier","quality_controlled":"1","scopus_import":1},{"abstract":[{"text":"We study the ground state of a dilute Bose gas in a scaling limit where the Gross-Pitaevskii functional emerges. This is a repulsive nonlinear Schrödinger functional whose quartic term is proportional to the scattering length of the interparticle interaction potential. We propose a new derivation of this limit problem, with a method that bypasses some of the technical difficulties that previous derivations had to face. The new method is based on a combination of Dyson\\'s lemma, the quantum de Finetti theorem and a second moment estimate for ground states of the effective Dyson Hamiltonian. It applies equally well to the case where magnetic fields or rotation are present.","lang":"eng"}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1503.07061","open_access":"1"}],"month":"03","intvolume":" 9","publication_status":"published","language":[{"iso":"eng"}],"issue":"2","volume":9,"ec_funded":1,"_id":"1143","type":"journal_article","status":"public","date_updated":"2021-01-12T06:48:36Z","department":[{"_id":"RoSe"}],"publisher":"Mathematical Sciences Publishers","quality_controlled":"1","oa":1,"year":"2016","day":"24","publication":"Analysis and PDE","page":"459 - 485","date_published":"2016-03-24T00:00:00Z","doi":"10.2140/apde.2016.9.459","date_created":"2018-12-11T11:50:23Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"citation":{"mla":"Nam, Phan, et al. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” Analysis and PDE, vol. 9, no. 2, Mathematical Sciences Publishers, 2016, pp. 459–85, doi:10.2140/apde.2016.9.459.","ieee":"P. Nam, N. Rougerie, and R. Seiringer, “Ground states of large bosonic systems: The gross Pitaevskii limit revisited,” Analysis and PDE, vol. 9, no. 2. Mathematical Sciences Publishers, pp. 459–485, 2016.","short":"P. Nam, N. Rougerie, R. Seiringer, Analysis and PDE 9 (2016) 459–485.","apa":"Nam, P., Rougerie, N., & Seiringer, R. (2016). Ground states of large bosonic systems: The gross Pitaevskii limit revisited. Analysis and PDE. Mathematical Sciences Publishers. https://doi.org/10.2140/apde.2016.9.459","ama":"Nam P, Rougerie N, Seiringer R. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. Analysis and PDE. 2016;9(2):459-485. doi:10.2140/apde.2016.9.459","chicago":"Nam, Phan, Nicolas Rougerie, and Robert Seiringer. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” Analysis and PDE. Mathematical Sciences Publishers, 2016. https://doi.org/10.2140/apde.2016.9.459.","ista":"Nam P, Rougerie N, Seiringer R. 2016. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. Analysis and PDE. 9(2), 459–485."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Nam, Phan","last_name":"Nam","first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rougerie","full_name":"Rougerie, Nicolas","first_name":"Nicolas"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"publist_id":"6215","title":"Ground states of large bosonic systems: The gross Pitaevskii limit revisited"},{"ec_funded":1,"volume":9,"issue":"11","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5004","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf","date_created":"2018-12-12T10:13:22Z","creator":"system","file_size":5005876,"date_updated":"2018-12-12T10:13:22Z"}],"scopus_import":1,"intvolume":" 9","month":"11","abstract":[{"lang":"eng","text":"Auxin directs plant ontogenesis via differential accumulation within tissues depending largely on the activity of PIN proteins that mediate auxin efflux from cells and its directional cell-to-cell transport. Regardless of the developmental importance of PINs, the structure of these transporters is poorly characterized. Here, we present experimental data concerning protein topology of plasma membrane-localized PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters combined with immunolocalization techniques, we mapped the membrane topology of PINs and further cross-validated our results using available topology modeling software. We delineated the topology of PIN1 with two transmembrane (TM) bundles of five α-helices linked by a large intracellular loop and a C-terminus positioned outside the cytoplasm. Using constraints derived from our experimental data, we also provide an updated position of helical regions generating a verisimilitude model of PIN1. Since the canonical long PINs show a high degree of conservation in TM domains and auxin transport capacity has been demonstrated for Arabidopsis representatives of this group, this empirically enhanced topological model of PIN1 will be an important starting point for further studies on PIN structure–function relationships. In addition, we have established protocols that can be used to probe the topology of other plasma membrane proteins in plants. © 2016 The Authors"}],"oa_version":"Published Version","file_date_updated":"2018-12-12T10:13:22Z","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:48:37Z","ddc":["581"],"tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","pubrep_id":"746","status":"public","_id":"1145","page":"1504 - 1519","date_created":"2018-12-11T11:50:23Z","date_published":"2016-11-07T00:00:00Z","doi":"10.1016/j.molp.2016.08.010","year":"2016","has_accepted_license":"1","publication":"Molecular Plant","day":"07","oa":1,"publisher":"Cell Press","quality_controlled":"1","acknowledgement":"This research has been financially supported by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) (T.N., M.Z., M.P., J.H.), Czech Science Foundation (13-40637S [J.F., M.Z.], 13-39982S [J.H.]); Research Foundation Flanders (Grant number FWO09/PDO/196) (S.V.) and the European Research Council (project ERC-2011-StG-20101109-PSDP) (J.F.). We thank David G. Robinson and Ranjan Swarup for sharing published material; Maria Šimášková, Mamoona Khan, Eva Benková for technical assistance; and R. Tejos, J. Kleine-Vehn, and E. Feraru for helpful discussions.","publist_id":"6213","author":[{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"last_name":"Zwiewka","full_name":"Zwiewka, Marta","first_name":"Marta"},{"last_name":"Pernisová","full_name":"Pernisová, Markéta","first_name":"Markéta"},{"first_name":"Jan","full_name":"Hejátko, Jan","last_name":"Hejátko"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"title":"Enquiry into the topology of plasma membrane localized PIN auxin transport components","citation":{"mla":"Nodzyński, Tomasz, et al. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” Molecular Plant, vol. 9, no. 11, Cell Press, 2016, pp. 1504–19, doi:10.1016/j.molp.2016.08.010.","short":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, J. Friml, Molecular Plant 9 (2016) 1504–1519.","ieee":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, and J. Friml, “Enquiry into the topology of plasma membrane localized PIN auxin transport components,” Molecular Plant, vol. 9, no. 11. Cell Press, pp. 1504–1519, 2016.","apa":"Nodzyński, T., Vanneste, S., Zwiewka, M., Pernisová, M., Hejátko, J., & Friml, J. (2016). Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. Cell Press. https://doi.org/10.1016/j.molp.2016.08.010","ama":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. 2016;9(11):1504-1519. doi:10.1016/j.molp.2016.08.010","chicago":"Nodzyński, Tomasz, Steffen Vanneste, Marta Zwiewka, Markéta Pernisová, Jan Hejátko, and Jiří Friml. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” Molecular Plant. Cell Press, 2016. https://doi.org/10.1016/j.molp.2016.08.010.","ista":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. 2016. Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. 9(11), 1504–1519."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Balla, Jozef, et al. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” Scientific Reports, vol. 6, 35955, Nature Publishing Group, 2016, doi:10.1038/srep35955.","ieee":"J. Balla et al., “Auxin flow mediated competition between axillary buds to restore apical dominance,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","short":"J. Balla, Z. Medved’Ová, P. Kalousek, N. Matiješčuková, J. Friml, V. Reinöhl, S. Procházka, Scientific Reports 6 (2016).","apa":"Balla, J., Medved’Ová, Z., Kalousek, P., Matiješčuková, N., Friml, J., Reinöhl, V., & Procházka, S. (2016). Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep35955","ama":"Balla J, Medved’Ová Z, Kalousek P, et al. Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. 2016;6. doi:10.1038/srep35955","chicago":"Balla, Jozef, Zuzana Medved’Ová, Petr Kalousek, Natálie Matiješčuková, Jiří Friml, Vilém Reinöhl, and Stanislav Procházka. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep35955.","ista":"Balla J, Medved’Ová Z, Kalousek P, Matiješčuková N, Friml J, Reinöhl V, Procházka S. 2016. Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. 6, 35955."},"title":"Auxin flow mediated competition between axillary buds to restore apical dominance","publist_id":"6211","author":[{"first_name":"Jozef","last_name":"Balla","full_name":"Balla, Jozef"},{"full_name":"Medved'Ová, Zuzana","last_name":"Medved'Ová","first_name":"Zuzana"},{"first_name":"Petr","full_name":"Kalousek, Petr","last_name":"Kalousek"},{"full_name":"Matiješčuková, Natálie","last_name":"Matiješčuková","first_name":"Natálie"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Vilém","full_name":"Reinöhl, Vilém","last_name":"Reinöhl"},{"first_name":"Stanislav","full_name":"Procházka, Stanislav","last_name":"Procházka"}],"article_number":"35955","day":"08","publication":"Scientific Reports","has_accepted_license":"1","year":"2016","date_published":"2016-11-08T00:00:00Z","doi":"10.1038/srep35955","date_created":"2018-12-11T11:50:24Z","acknowledgement":"This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II., supported by the project “CEITEC–Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) and the Agronomy faculty grant from Mendel University “IGA AF MENDELU” (IP 14/2013).","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"ddc":["581"],"date_updated":"2021-01-12T06:48:38Z","department":[{"_id":"JiFr"}],"file_date_updated":"2018-12-12T10:09:28Z","_id":"1147","status":"public","pubrep_id":"745","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4752","creator":"system","date_updated":"2018-12-12T10:09:28Z","file_size":1587544,"date_created":"2018-12-12T10:09:28Z","file_name":"IST-2017-745-v1+1_srep35955.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":6,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Apical dominance is one of the fundamental developmental phenomena in plant biology, which determines the overall architecture of aerial plant parts. Here we show apex decapitation activated competition for dominance in adjacent upper and lower axillary buds. A two-nodal-bud pea (Pisum sativum L.) was used as a model system to monitor and assess auxin flow, auxin transport channels, and dormancy and initiation status of axillary buds. Auxin flow was manipulated by lateral stem wounds or chemically by auxin efflux inhibitors 2,3,5-triiodobenzoic acid (TIBA), 1-N-naphtylphtalamic acid (NPA), or protein synthesis inhibitor cycloheximide (CHX) treatments, which served to interfere with axillary bud competition. Redirecting auxin flow to different points influenced which bud formed the outgrowing and dominant shoot. The obtained results proved that competition between upper and lower axillary buds as secondary auxin sources is based on the same auxin canalization principle that operates between the shoot apex and axillary bud. © The Author(s) 2016."}],"month":"11","intvolume":" 6","scopus_import":1},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:48:38Z","citation":{"chicago":"Miyaji, Tomoyuki, Pawel Pilarczyk, Marcio Gameiro, Hiroshi Kokubu, and Konstantin Mischaikow. “A Study of Rigorous ODE Integrators for Multi Scale Set Oriented Computations.” Applied Numerical Mathematics. Elsevier, 2016. https://doi.org/10.1016/j.apnum.2016.04.005.","ista":"Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. 2016. A study of rigorous ODE integrators for multi scale set oriented computations. Applied Numerical Mathematics. 107, 34–47.","mla":"Miyaji, Tomoyuki, et al. “A Study of Rigorous ODE Integrators for Multi Scale Set Oriented Computations.” Applied Numerical Mathematics, vol. 107, Elsevier, 2016, pp. 34–47, doi:10.1016/j.apnum.2016.04.005.","apa":"Miyaji, T., Pilarczyk, P., Gameiro, M., Kokubu, H., & Mischaikow, K. (2016). A study of rigorous ODE integrators for multi scale set oriented computations. Applied Numerical Mathematics. Elsevier. https://doi.org/10.1016/j.apnum.2016.04.005","ama":"Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. A study of rigorous ODE integrators for multi scale set oriented computations. Applied Numerical Mathematics. 2016;107:34-47. doi:10.1016/j.apnum.2016.04.005","ieee":"T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, and K. Mischaikow, “A study of rigorous ODE integrators for multi scale set oriented computations,” Applied Numerical Mathematics, vol. 107. Elsevier, pp. 34–47, 2016.","short":"T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, K. Mischaikow, Applied Numerical Mathematics 107 (2016) 34–47."},"title":"A study of rigorous ODE integrators for multi scale set oriented computations","department":[{"_id":"HeEd"}],"publist_id":"6209","author":[{"first_name":"Tomoyuki","full_name":"Miyaji, Tomoyuki","last_name":"Miyaji"},{"id":"3768D56A-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","last_name":"Pilarczyk","full_name":"Pilarczyk, Pawel"},{"first_name":"Marcio","last_name":"Gameiro","full_name":"Gameiro, Marcio"},{"last_name":"Kokubu","full_name":"Kokubu, Hiroshi","first_name":"Hiroshi"},{"first_name":"Konstantin","full_name":"Mischaikow, Konstantin","last_name":"Mischaikow"}],"_id":"1149","status":"public","project":[{"call_identifier":"FP7","_id":"255F06BE-B435-11E9-9278-68D0E5697425","grant_number":"622033","name":"Persistent Homology - Images, Data and Maps"}],"type":"journal_article","day":"01","language":[{"iso":"eng"}],"publication":"Applied Numerical Mathematics","year":"2016","publication_status":"published","volume":107,"doi":"10.1016/j.apnum.2016.04.005","date_published":"2016-09-01T00:00:00Z","date_created":"2018-12-11T11:50:25Z","ec_funded":1,"page":"34 - 47","oa_version":"None","acknowledgement":"MG was partially supported by FAPESP grants 2013/07460-7 and 2010/00875-9, and by CNPq grants 305860/2013-5 and 306453/2009-6, Brazil. The work of HK was partially supported by Grant-in-Aid for Scientific Research (Nos.24654022, 25287029), Ministry of Education, Science, Technology, Culture and Sports, Japan. KM was supported by NSF grants NSF-DMS-0835621, 0915019, 1125174, 1248071, and contracts from AFOSR and DARPA. TM was supported by Grant-in-Aid for JSPS Fellows No. 245312. A part of the research of TM and HK was also supported by JST, CREST.\r\n\r\nResearch conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE – Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (Ref. FCT PTDC/MAT/098871/2008); from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. 622033; and from the same sources as HK.\r\n\r\nThe authors express their gratitude to the Department of Mathematics of Kyoto University for making their server available for conducting the computations described in the paper, and to the reviewers for helpful comments that contributed towards increasing the quality of the paper.","abstract":[{"text":"We study the usefulness of two most prominent publicly available rigorous ODE integrators: one provided by the CAPD group (capd.ii.uj.edu.pl), the other based on the COSY Infinity project (cosyinfinity.org). Both integrators are capable of handling entire sets of initial conditions and provide tight rigorous outer enclosures of the images under a time-T map. We conduct extensive benchmark computations using the well-known Lorenz system, and compare the computation time against the final accuracy achieved. We also discuss the effect of a few technical parameters, such as the order of the numerical integration method, the value of T, and the phase space resolution. We conclude that COSY may provide more precise results due to its ability of avoiding the variable dependency problem. However, the overall cost of computations conducted using CAPD is typically lower, especially when intervals of parameters are involved. Moreover, access to COSY is limited (registration required) and the rigorous ODE integrators are not publicly available, while CAPD is an open source free software project. Therefore, we recommend the latter integrator for this kind of computations. Nevertheless, proper choice of the various integration parameters turns out to be of even greater importance than the choice of the integrator itself. © 2016 IMACS. Published by Elsevier B.V. All rights reserved.","lang":"eng"}],"month":"09","intvolume":" 107","publisher":"Elsevier","quality_controlled":"1","scopus_import":1},{"volume":38,"issue":"5","date_published":"2016-09-12T00:00:00Z","doi":"10.1016/j.devcel.2016.08.017","date_created":"2018-12-11T11:50:25Z","page":"448 - 450","day":"12","language":[{"iso":"eng"}],"publication":"Developmental Cell","publication_status":"published","year":"2016","month":"09","intvolume":" 38","quality_controlled":"1","publisher":"Cell Press","scopus_import":1,"oa_version":"None","abstract":[{"text":"When neutrophils infiltrate a site of inflammation, they have to stop at the right place to exert their effector function. In this issue of Developmental Cell, Wang et al. (2016) show that neutrophils sense reactive oxygen species via the TRPM2 channel to arrest migration at their target site. © 2016 Elsevier Inc.","lang":"eng"}],"department":[{"_id":"MiSi"}],"title":"A Radical Break Restraining Neutrophil Migration","author":[{"first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"publist_id":"6208","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Renkawitz, Jörg, and Michael K Sixt. “A Radical Break Restraining Neutrophil Migration.” Developmental Cell. Cell Press, 2016. https://doi.org/10.1016/j.devcel.2016.08.017.","ista":"Renkawitz J, Sixt MK. 2016. A Radical Break Restraining Neutrophil Migration. Developmental Cell. 38(5), 448–450.","mla":"Renkawitz, Jörg, and Michael K. Sixt. “A Radical Break Restraining Neutrophil Migration.” Developmental Cell, vol. 38, no. 5, Cell Press, 2016, pp. 448–50, doi:10.1016/j.devcel.2016.08.017.","short":"J. Renkawitz, M.K. Sixt, Developmental Cell 38 (2016) 448–450.","ieee":"J. Renkawitz and M. K. Sixt, “A Radical Break Restraining Neutrophil Migration,” Developmental Cell, vol. 38, no. 5. Cell Press, pp. 448–450, 2016.","ama":"Renkawitz J, Sixt MK. A Radical Break Restraining Neutrophil Migration. Developmental Cell. 2016;38(5):448-450. doi:10.1016/j.devcel.2016.08.017","apa":"Renkawitz, J., & Sixt, M. K. (2016). A Radical Break Restraining Neutrophil Migration. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2016.08.017"},"date_updated":"2021-01-12T06:48:39Z","status":"public","type":"journal_article","_id":"1150"},{"page":"2286 - 2296","doi":"10.1101/gad.285361.116","date_published":"2016-10-15T00:00:00Z","date_created":"2018-12-11T11:50:25Z","has_accepted_license":"1","year":"2016","day":"15","publication":"Genes and Development","publisher":"Cold Spring Harbor Laboratory Press","quality_controlled":"1","oa":1,"acknowledgement":"We thank Norwich Research Park Bioimaging, Grant Calder, Roy\r\nDunford, Caroline Smith, Paul Thomas, and Mark Youles for\r\ntechnical support; Charlie Scutt, Alejandro Ferrando, and George\r\nLomonossoff for plasmids; Toshiro Ito for seeds; Brendan Davies\r\nand Barry Causier for the REGIA library; and Mark Buttner,\r\nSimona Masiero, Fabio Rossi, Doris Wagner, and Jun Xiao for\r\nhelp and material. We are also grateful to Stefano Bencivenga,\r\nMarie Brüser, Friederike Jantzen, Lukasz Langowski, Xinran Li,\r\nand Nicola Stacey for discussions and helpful comments on the\r\nmanuscript. This work was supported by grants BB/M004112/1\r\nand BB/I017232/1 (Crop Improvement Research Club) to L.Ø.\r\nfrom the Biotechnological and Biological Sciences Research\r\nCouncil, and Institute Strategic Programme grant (BB/J004553/\r\n1) to the John Innes Centre. S.S., J.D., and L.Ø conceived the ex-\r\nperiments. ","publist_id":"6207","author":[{"first_name":"Sara","last_name":"Simonini","full_name":"Simonini, Sara"},{"first_name":"Joyita","last_name":"Deb","full_name":"Deb, Joyita"},{"first_name":"Laila","last_name":"Moubayidin","full_name":"Moubayidin, Laila"},{"first_name":"Pauline","full_name":"Stephenson, Pauline","last_name":"Stephenson"},{"first_name":"Manoj","last_name":"Valluru","full_name":"Valluru, Manoj"},{"first_name":"Alejandra","last_name":"Freire Rios","full_name":"Freire Rios, Alejandra"},{"full_name":"Sorefan, Karim","last_name":"Sorefan","first_name":"Karim"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"last_name":"Östergaard","full_name":"Östergaard, Lars","first_name":"Lars"}],"external_id":{"pmid":["27898393"]},"title":"A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis","citation":{"ieee":"S. Simonini et al., “A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis,” Genes and Development, vol. 30, no. 20. Cold Spring Harbor Laboratory Press, pp. 2286–2296, 2016.","short":"S. Simonini, J. Deb, L. Moubayidin, P. Stephenson, M. Valluru, A. Freire Rios, K. Sorefan, D. Weijers, J. Friml, L. Östergaard, Genes and Development 30 (2016) 2286–2296.","ama":"Simonini S, Deb J, Moubayidin L, et al. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. 2016;30(20):2286-2296. doi:10.1101/gad.285361.116","apa":"Simonini, S., Deb, J., Moubayidin, L., Stephenson, P., Valluru, M., Freire Rios, A., … Östergaard, L. (2016). A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.285361.116","mla":"Simonini, Sara, et al. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” Genes and Development, vol. 30, no. 20, Cold Spring Harbor Laboratory Press, 2016, pp. 2286–96, doi:10.1101/gad.285361.116.","ista":"Simonini S, Deb J, Moubayidin L, Stephenson P, Valluru M, Freire Rios A, Sorefan K, Weijers D, Friml J, Östergaard L. 2016. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. 30(20), 2286–2296.","chicago":"Simonini, Sara, Joyita Deb, Laila Moubayidin, Pauline Stephenson, Manoj Valluru, Alejandra Freire Rios, Karim Sorefan, Dolf Weijers, Jiří Friml, and Lars Östergaard. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” Genes and Development. Cold Spring Harbor Laboratory Press, 2016. https://doi.org/10.1101/gad.285361.116."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"20","volume":30,"publication_status":"published","file":[{"date_created":"2019-01-25T09:32:55Z","file_name":"2016_GeneDev_Simonini.pdf","creator":"dernst","date_updated":"2019-01-25T09:32:55Z","file_size":1419263,"file_id":"5882","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"10","intvolume":" 30","abstract":[{"lang":"eng","text":"Tissue patterning in multicellular organisms is the output of precise spatio–temporal regulation of gene expression coupled with changes in hormone dynamics. In plants, the hormone auxin regulates growth and development at every stage of a plant’s life cycle. Auxin signaling occurs through binding of the auxin molecule to a TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional repressor proteins. These are subsequently ubiquitinated and degraded via the 26S proteasome, leading to derepression of auxin response factors (ARFs). How auxin is able to elicit such a diverse range of developmental responses through a single signaling module has not yet been resolved. Here we present an alternative auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through interactions with process-specific transcription factors. This noncanonical hormonesensing mechanism exhibits strong preference for the naturally occurring auxin indole 3-acetic acid (IAA) and is important for coordinating growth and patterning in diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence, ovule development, and primary branch formation. Disrupting this IAA-sensing ability induces morphological aberrations with consequences for plant fitness. Therefore, our findings introduce a novel transcription factor-based mechanism of hormone perception in plants. © 2016 Simonini et al."}],"pmid":1,"oa_version":"Published Version","file_date_updated":"2019-01-25T09:32:55Z","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:48:39Z","ddc":["570"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"1151"},{"oa":1,"publisher":"American Society of Plant Biologists","quality_controlled":"1","acknowledgement":"We thank Martine De Cock and Annick Bleys for help in preparing the manuscript, Daniel Van Damme for sharing material and stimulating discussion, and Rudiger Simon for support during revision of the manuscript.\r\nThis work was supported by grants from the European Research Council (StartingIndependentResearchGrantERC-2007-Stg-207362-HCPO)and the Czech Science Foundation (GACR CZ.1.07/2.3.00/20.0043) to E.B.\r\nand Natural Sciences and Engineering Research Council of Canada Discovery Grant 2014-05325 to P.P. K.W. acknowledges funding from a Human Frontier Science Program Long-Term Fellowship (LT-000209-2014).","date_created":"2018-12-11T11:50:26Z","date_published":"2016-10-01T00:00:00Z","doi":"10.1105/tpc.15.00569","page":"2464 - 2477","publication":"Plant Cell","day":"01","year":"2016","project":[{"grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"A model of differential growth guided apical hook formation in plants","publist_id":"6205","author":[{"full_name":"Žádníková, Petra","last_name":"Žádníková","first_name":"Petra"},{"first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","last_name":"Wabnik"},{"full_name":"Abuzeineh, Anas","last_name":"Abuzeineh","first_name":"Anas"},{"first_name":"Marçal","full_name":"Gallemí, Marçal","last_name":"Gallemí"},{"first_name":"Dominique","full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten"},{"full_name":"Smith, Richard","last_name":"Smith","first_name":"Richard"},{"first_name":"Dirk","full_name":"Inze, Dirk","last_name":"Inze"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Przemysław","full_name":"Prusinkiewicz, Przemysław","last_name":"Prusinkiewicz"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"P. Žádníková, K.T. Wabnik, A. Abuzeineh, M. Gallemí, D. Van Der Straeten, R. Smith, D. Inze, J. Friml, P. Prusinkiewicz, E. Benková, Plant Cell 28 (2016) 2464–2477.","ieee":"P. Žádníková et al., “A model of differential growth guided apical hook formation in plants,” Plant Cell, vol. 28, no. 10. American Society of Plant Biologists, pp. 2464–2477, 2016.","apa":"Žádníková, P., Wabnik, K. T., Abuzeineh, A., Gallemí, M., Van Der Straeten, D., Smith, R., … Benková, E. (2016). A model of differential growth guided apical hook formation in plants. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.15.00569","ama":"Žádníková P, Wabnik KT, Abuzeineh A, et al. A model of differential growth guided apical hook formation in plants. Plant Cell. 2016;28(10):2464-2477. doi:10.1105/tpc.15.00569","mla":"Žádníková, Petra, et al. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” Plant Cell, vol. 28, no. 10, American Society of Plant Biologists, 2016, pp. 2464–77, doi:10.1105/tpc.15.00569.","ista":"Žádníková P, Wabnik KT, Abuzeineh A, Gallemí M, Van Der Straeten D, Smith R, Inze D, Friml J, Prusinkiewicz P, Benková E. 2016. A model of differential growth guided apical hook formation in plants. Plant Cell. 28(10), 2464–2477.","chicago":"Žádníková, Petra, Krzysztof T Wabnik, Anas Abuzeineh, Marçal Gallemí, Dominique Van Der Straeten, Richard Smith, Dirk Inze, Jiří Friml, Przemysław Prusinkiewicz, and Eva Benková. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” Plant Cell. American Society of Plant Biologists, 2016. https://doi.org/10.1105/tpc.15.00569."},"intvolume":" 28","month":"10","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/","open_access":"1"}],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"Differential cell growth enables flexible organ bending in the presence of environmental signals such as light or gravity. A prominent example of the developmental processes based on differential cell growth is the formation of the apical hook that protects the fragile shoot apical meristem when it breaks through the soil during germination. Here, we combined in silico and in vivo approaches to identify a minimal mechanism producing auxin gradient-guided differential growth during the establishment of the apical hook in the model plant Arabidopsis thaliana. Computer simulation models based on experimental data demonstrate that asymmetric expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus convex (outer) side of the hook suffices to establish an auxin maximum in the epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism that translates this maximum into differential growth, and thus curvature, of the apical hook. Through a combination of experimental and in silico computational approaches, we have identified the individual contributions of differential cell elongation and proliferation to defining the apical hook and reveal the role of auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society of Plant Biologists. All rights reserved.","lang":"eng"}],"ec_funded":1,"issue":"10","volume":28,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"1153","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"date_updated":"2021-01-12T06:48:40Z"},{"month":"11","intvolume":" 6","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Cellular locomotion is a central hallmark of eukaryotic life. It is governed by cell-extrinsic molecular factors, which can either emerge in the soluble phase or as immobilized, often adhesive ligands. To encode for direction, every cue must be present as a spatial or temporal gradient. Here, we developed a microfluidic chamber that allows measurement of cell migration in combined response to surface immobilized and soluble molecular gradients. As a proof of principle we study the response of dendritic cells to their major guidance cues, chemokines. The majority of data on chemokine gradient sensing is based on in vitro studies employing soluble gradients. Despite evidence suggesting that in vivo chemokines are often immobilized to sugar residues, limited information is available how cells respond to immobilized chemokines. We tracked migration of dendritic cells towards immobilized gradients of the chemokine CCL21 and varying superimposed soluble gradients of CCL19. Differential migratory patterns illustrate the potential of our setup to quantitatively study the competitive response to both types of gradients. Beyond chemokines our approach is broadly applicable to alternative systems of chemo- and haptotaxis such as cells migrating along gradients of adhesion receptor ligands vs. any soluble cue. \r\n"}],"volume":6,"ec_funded":1,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4756","creator":"system","date_updated":"2018-12-12T10:09:32Z","file_size":2353456,"date_created":"2018-12-12T10:09:32Z","file_name":"IST-2017-744-v1+1_srep36440.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"744","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1154","file_date_updated":"2018-12-12T10:09:32Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"ToBo"}],"ddc":["579"],"date_updated":"2021-01-12T06:48:41Z","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the Swiss National Science Foundation (Ambizione fellowship; PZ00P3-154733 to M.M.), the Swiss Multiple Sclerosis Society (research support to M.M.), a fellowship from the Boehringer Ingelheim Fonds (BIF) to J.S., the European Research Council (grant ERC GA 281556) and a START award from the Austrian Science Foundation (FWF) to M.S. #BioimagingFacility","date_published":"2016-11-07T00:00:00Z","doi":"10.1038/srep36440","date_created":"2018-12-11T11:50:27Z","day":"07","publication":"Scientific Reports","has_accepted_license":"1","year":"2016","project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"},{"grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"article_number":"36440","title":"A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients","publist_id":"6204","author":[{"first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan","last_name":"Schwarz"},{"full_name":"Bierbaum, Veronika","last_name":"Bierbaum","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","first_name":"Veronika"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"first_name":"Tino","full_name":"Frank, Tino","last_name":"Frank"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"},{"first_name":"Savaş","full_name":"Tay, Savaş","last_name":"Tay"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8599-1226","full_name":"Mehling, Matthias","last_name":"Mehling","first_name":"Matthias","id":"3C23B994-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Schwarz, Jan, Veronika Bierbaum, Jack Merrin, Tino Frank, Robert Hauschild, Mark Tobias Bollenbach, Savaş Tay, Michael K Sixt, and Matthias Mehling. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep36440.","ista":"Schwarz J, Bierbaum V, Merrin J, Frank T, Hauschild R, Bollenbach MT, Tay S, Sixt MK, Mehling M. 2016. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. 6, 36440.","mla":"Schwarz, Jan, et al. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” Scientific Reports, vol. 6, 36440, Nature Publishing Group, 2016, doi:10.1038/srep36440.","apa":"Schwarz, J., Bierbaum, V., Merrin, J., Frank, T., Hauschild, R., Bollenbach, M. T., … Mehling, M. (2016). A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep36440","ama":"Schwarz J, Bierbaum V, Merrin J, et al. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. 2016;6. doi:10.1038/srep36440","short":"J. Schwarz, V. Bierbaum, J. Merrin, T. Frank, R. Hauschild, M.T. Bollenbach, S. Tay, M.K. Sixt, M. Mehling, Scientific Reports 6 (2016).","ieee":"J. Schwarz et al., “A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients,” Scientific Reports, vol. 6. Nature Publishing Group, 2016."}},{"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"title":"Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population","author":[{"full_name":"Lee, Ji","last_name":"Lee","first_name":"Ji"},{"last_name":"Schnelli","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin"}],"publist_id":"6201","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Lee J, Schnelli K. 2016. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. Annals of Applied Probability. 26(6), 3786–3839.","chicago":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” Annals of Applied Probability. Institute of Mathematical Statistics, 2016. https://doi.org/10.1214/16-AAP1193.","ama":"Lee J, Schnelli K. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. Annals of Applied Probability. 2016;26(6):3786-3839. doi:10.1214/16-AAP1193","apa":"Lee, J., & Schnelli, K. (2016). Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AAP1193","ieee":"J. Lee and K. Schnelli, “Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population,” Annals of Applied Probability, vol. 26, no. 6. Institute of Mathematical Statistics, pp. 3786–3839, 2016.","short":"J. Lee, K. Schnelli, Annals of Applied Probability 26 (2016) 3786–3839.","mla":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” Annals of Applied Probability, vol. 26, no. 6, Institute of Mathematical Statistics, 2016, pp. 3786–839, doi:10.1214/16-AAP1193."},"oa":1,"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","acknowledgement":"We thank Horng-Tzer Yau for numerous discussions and remarks. We are grateful to Ben Adlam, Jinho Baik, Zhigang Bao, Paul Bourgade, László Erd ̋os, Iain Johnstone and Antti Knowles for comments. We are also grate-\r\nful to the anonymous referee for carefully reading our manuscript and suggesting several improvements.","date_created":"2018-12-11T11:50:27Z","date_published":"2016-12-15T00:00:00Z","doi":"10.1214/16-AAP1193","page":"3786 - 3839","publication":"Annals of Applied Probability","day":"15","year":"2016","status":"public","type":"journal_article","_id":"1157","department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T06:48:43Z","intvolume":" 26","month":"12","main_file_link":[{"url":"https://arxiv.org/abs/1409.4979","open_access":"1"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"We consider sample covariance matrices of the form Q = ( σ1/2X)(σ1/2X)∗, where the sample X is an M ×N random matrix whose entries are real independent random variables with variance 1/N and whereσ is an M × M positive-definite deterministic matrix. We analyze the asymptotic fluctuations of the largest rescaled eigenvalue of Q when both M and N tend to infinity with N/M →d ϵ (0,∞). For a large class of populations σ in the sub-critical regime, we show that the distribution of the largest rescaled eigenvalue of Q is given by the type-1 Tracy-Widom distribution under the additional assumptions that (1) either the entries of X are i.i.d. Gaussians or (2) that σ is diagonal and that the entries of X have a sub-exponential decay.","lang":"eng"}],"ec_funded":1,"volume":26,"issue":"6","language":[{"iso":"eng"}],"publication_status":"published"},{"ddc":["003","518","570","621"],"date_updated":"2021-01-12T06:48:49Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:44:37Z","_id":"1170","pubrep_id":"811","status":"public","type":"journal_article","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"local","content_type":"application/pdf","file_id":"5095","checksum":"781bc3ffd30b2dd65b7727c5a285fc78","creator":"system","file_size":871964,"date_updated":"2020-07-14T12:44:37Z","file_name":"IST-2017-811-v1+1_modular_parameter_identification.pdf","date_created":"2018-12-12T10:14:41Z"}],"publication_status":"published","volume":38,"issue":"6","oa_version":"Submitted Version","abstract":[{"text":"The increasing complexity of dynamic models in systems and synthetic biology poses computational challenges especially for the identification of model parameters. While modularization of the corresponding optimization problems could help reduce the “curse of dimensionality,” abundant feedback and crosstalk mechanisms prohibit a simple decomposition of most biomolecular networks into subnetworks, or modules. Drawing on ideas from network modularization and multiple-shooting optimization, we present here a modular parameter identification approach that explicitly allows for such interdependencies. Interfaces between our modules are given by the experimentally measured molecular species. This definition allows deriving good (initial) estimates for the inter-module communication directly from the experimental data. Given these estimates, the states and parameter sensitivities of different modules can be integrated independently. To achieve consistency between modules, we iteratively adjust the estimates for inter-module communication while optimizing the parameters. After convergence to an optimal parameter set---but not during earlier iterations---the intermodule communication as well as the individual modules\\' state dynamics agree with the dynamics of the nonmodularized network. Our modular parameter identification approach allows for easy parallelization; it can reduce the computational complexity for larger networks and decrease the probability to converge to suboptimal local minima. We demonstrate the algorithm\\'s performance in parameter estimation for two biomolecular networks, a synthetic genetic oscillator and a mammalian signaling pathway.","lang":"eng"}],"intvolume":" 38","month":"11","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing, vol. 38, no. 6, Society for Industrial and Applied Mathematics , 2016, pp. B988–1008, doi:10.1137/15M103306X.","ama":"Lang M, Stelling J. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 2016;38(6):B988-B1008. doi:10.1137/15M103306X","apa":"Lang, M., & Stelling, J. (2016). Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/15M103306X","ieee":"M. Lang and J. Stelling, “Modular parameter identification of biomolecular networks,” SIAM Journal on Scientific Computing, vol. 38, no. 6. Society for Industrial and Applied Mathematics , pp. B988–B1008, 2016.","short":"M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.","chicago":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics , 2016. https://doi.org/10.1137/15M103306X.","ista":"Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008."},"title":"Modular parameter identification of biomolecular networks","author":[{"full_name":"Lang, Moritz","last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz"},{"first_name":"Jörg","last_name":"Stelling","full_name":"Stelling, Jörg"}],"publist_id":"6186","publication":"SIAM Journal on Scientific Computing","day":"15","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:50:31Z","date_published":"2016-11-15T00:00:00Z","doi":"10.1137/15M103306X","page":"B988 - B1008","publisher":"Society for Industrial and Applied Mathematics ","quality_controlled":"1"},{"type":"journal_article","status":"public","_id":"1171","author":[{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"publist_id":"6185","title":"Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al.","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T06:48:50Z","citation":{"ista":"Tkačik G. 2016. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al. Physics of Life Reviews. 17, 166–167.","chicago":"Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function" by O. C. Martin et Al.” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.005.","apa":"Tkačik, G. (2016). Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.005","ama":"Tkačik G. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al. Physics of Life Reviews. 2016;17:166-167. doi:10.1016/j.plrev.2016.06.005","short":"G. Tkačik, Physics of Life Reviews 17 (2016) 166–167.","ieee":"G. Tkačik, “Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al.,” Physics of Life Reviews, vol. 17. Elsevier, pp. 166–167, 2016.","mla":"Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function" by O. C. Martin et Al.” Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 166–67, doi:10.1016/j.plrev.2016.06.005."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"quality_controlled":"1","publisher":"Elsevier","intvolume":" 17","month":"07","oa_version":"None","page":"166 - 167","date_created":"2018-12-11T11:50:32Z","volume":17,"date_published":"2016-07-01T00:00:00Z","doi":"10.1016/j.plrev.2016.06.005","publication_status":"published","year":"2016","language":[{"iso":"eng"}],"publication":"Physics of Life Reviews","day":"01"},{"volume":6,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"cb378732da885ea4959ec5b845fb6e52","file_id":"4977","creator":"system","date_updated":"2020-07-14T12:44:37Z","file_size":760967,"date_created":"2018-12-12T10:12:56Z","file_name":"IST-2017-737-v1+1_srep38840.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"12","intvolume":" 6","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging."}],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:37Z","ddc":["576"],"date_updated":"2021-01-12T06:48:50Z","status":"public","pubrep_id":"737","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1172","date_published":"2016-12-19T00:00:00Z","doi":"10.1038/srep38840","date_created":"2018-12-11T11:50:32Z","day":"19","publication":"Scientific Reports","has_accepted_license":"1","year":"2016","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva"},{"first_name":"Mustansir","full_name":"Barma, Mustansir","last_name":"Barma"},{"first_name":"Madan","last_name":"Rao","full_name":"Rao, Madan"}],"publist_id":"6183","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","chicago":"Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38840.","ieee":"H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","ama":"Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 2016;6. doi:10.1038/srep38840","apa":"Sachdeva, H., Barma, M., & Rao, M. (2016). Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38840","mla":"Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific Reports, vol. 6, 38840, Nature Publishing Group, 2016, doi:10.1038/srep38840."},"article_number":"38840"},{"page":"1321 - 1362","doi":"10.1007/s00453-015-9997-6","issue":"4","volume":74,"date_published":"2016-04-01T00:00:00Z","date_created":"2018-12-11T11:50:33Z","year":"2016","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Algorithmica","quality_controlled":"1","publisher":"Springer","oa":1,"main_file_link":[{"url":"http://eprint.iacr.org/2013/651","open_access":"1"}],"month":"04","intvolume":" 74","abstract":[{"text":"Boldyreva, Palacio and Warinschi introduced a multiple forking game as an extension of general forking. The notion of (multiple) forking is a useful abstraction from the actual simulation of cryptographic scheme to the adversary in a security reduction, and is achieved through the intermediary of a so-called wrapper algorithm. Multiple forking has turned out to be a useful tool in the security argument of several cryptographic protocols. However, a reduction employing multiple forking incurs a significant degradation of (Formula presented.) , where (Formula presented.) denotes the upper bound on the underlying random oracle calls and (Formula presented.) , the number of forkings. In this work we take a closer look at the reasons for the degradation with a tighter security bound in mind. We nail down the exact set of conditions for success in the multiple forking game. A careful analysis of the cryptographic schemes and corresponding security reduction employing multiple forking leads to the formulation of ‘dependence’ and ‘independence’ conditions pertaining to the output of the wrapper in different rounds. Based on the (in)dependence conditions we propose a general framework of multiple forking and a General Multiple Forking Lemma. Leveraging (in)dependence to the full allows us to improve the degradation factor in the multiple forking game by a factor of (Formula presented.). By implication, the cost of a single forking involving two random oracles (augmented forking) matches that involving a single random oracle (elementary forking). Finally, we study the effect of these observations on the concrete security of existing schemes employing multiple forking. We conclude that by careful design of the protocol (and the wrapper in the security reduction) it is possible to harness our observations to the full extent.","lang":"eng"}],"oa_version":"Submitted Version","acknowledgement":"We are grateful to the anonymous reviewers for their insightful comments. The\r\ndetailed reports helped us a lot to address the technical mistakes as well as to improve the overall presentation of the paper.","author":[{"full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg","first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sanjit","full_name":"Chatterjee, Sanjit","last_name":"Chatterjee"}],"publist_id":"6177","title":"A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound","department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T06:48:52Z","citation":{"ieee":"C. Kamath Hosdurg and S. Chatterjee, “A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound,” Algorithmica, vol. 74, no. 4. Springer, pp. 1321–1362, 2016.","short":"C. Kamath Hosdurg, S. Chatterjee, Algorithmica 74 (2016) 1321–1362.","ama":"Kamath Hosdurg C, Chatterjee S. A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. Algorithmica. 2016;74(4):1321-1362. doi:10.1007/s00453-015-9997-6","apa":"Kamath Hosdurg, C., & Chatterjee, S. (2016). A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. Algorithmica. Springer. https://doi.org/10.1007/s00453-015-9997-6","mla":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” Algorithmica, vol. 74, no. 4, Springer, 2016, pp. 1321–62, doi:10.1007/s00453-015-9997-6.","ista":"Kamath Hosdurg C, Chatterjee S. 2016. A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. Algorithmica. 74(4), 1321–1362.","chicago":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” Algorithmica. Springer, 2016. https://doi.org/10.1007/s00453-015-9997-6."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1177"},{"page":"183 - 203","date_created":"2018-12-11T11:50:34Z","date_published":"2016-10-22T00:00:00Z","doi":"10.1007/978-3-662-53641-4_8","year":"2016","day":"22","oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"K. Pietrzak—Supported by the European Research Council consolidator grant (682815-TOCNeT).\r\nM. Skórski—Supported by the National Science Center, Poland (2015/17/N/ST6/03564).","author":[{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Maciej","full_name":"Maciej, Skorski","first_name":"Skorski"}],"publist_id":"6175","title":"Pseudoentropy: Lower-bounds for chain rules and transformations","citation":{"chicago":"Pietrzak, Krzysztof Z, and Skorski Maciej. “Pseudoentropy: Lower-Bounds for Chain Rules and Transformations,” 9985:183–203. Springer, 2016. https://doi.org/10.1007/978-3-662-53641-4_8.","ista":"Pietrzak KZ, Maciej S. 2016. Pseudoentropy: Lower-bounds for chain rules and transformations. TCC: Theory of Cryptography Conference, LNCS, vol. 9985, 183–203.","mla":"Pietrzak, Krzysztof Z., and Skorski Maciej. Pseudoentropy: Lower-Bounds for Chain Rules and Transformations. Vol. 9985, Springer, 2016, pp. 183–203, doi:10.1007/978-3-662-53641-4_8.","ieee":"K. Z. Pietrzak and S. Maciej, “Pseudoentropy: Lower-bounds for chain rules and transformations,” presented at the TCC: Theory of Cryptography Conference, Beijing, China, 2016, vol. 9985, pp. 183–203.","short":"K.Z. Pietrzak, S. Maciej, in:, Springer, 2016, pp. 183–203.","ama":"Pietrzak KZ, Maciej S. Pseudoentropy: Lower-bounds for chain rules and transformations. In: Vol 9985. Springer; 2016:183-203. doi:10.1007/978-3-662-53641-4_8","apa":"Pietrzak, K. Z., & Maciej, S. (2016). Pseudoentropy: Lower-bounds for chain rules and transformations (Vol. 9985, pp. 183–203). Presented at the TCC: Theory of Cryptography Conference, Beijing, China: Springer. https://doi.org/10.1007/978-3-662-53641-4_8"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"ec_funded":1,"volume":9985,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/159"}],"scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 9985","month":"10","abstract":[{"text":"Computational notions of entropy have recently found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The two main types of results which make computational notions so useful are (1) Chain rules, which quantify by how much the computational entropy of a variable decreases if conditioned on some other variable (2) Transformations, which quantify to which extend one type of entropy implies another.\r\n\r\nSuch chain rules and transformations typically lose a significant amount in quality of the entropy, and are the reason why applying these results one gets rather weak quantitative security bounds. In this paper we for the first time prove lower bounds in this context, showing that existing results for transformations are, unfortunately, basically optimal for non-adaptive black-box reductions (and it’s hard to imagine how non black-box reductions or adaptivity could be useful here.)\r\n\r\nA variable X has k bits of HILL entropy of quality (ϵ,s)\r\nif there exists a variable Y with k bits min-entropy which cannot be distinguished from X with advantage ϵ\r\n\r\nby distinguishing circuits of size s. A weaker notion is Metric entropy, where we switch quantifiers, and only require that for every distinguisher of size s, such a Y exists.\r\n\r\nWe first describe our result concerning transformations. By definition, HILL implies Metric without any loss in quality. Metric entropy often comes up in applications, but must be transformed to HILL for meaningful security guarantees. The best known result states that if a variable X has k bits of Metric entropy of quality (ϵ,s)\r\n, then it has k bits of HILL with quality (2ϵ,s⋅ϵ2). We show that this loss of a factor Ω(ϵ−2)\r\n\r\nin circuit size is necessary. In fact, we show the stronger result that this loss is already necessary when transforming so called deterministic real valued Metric entropy to randomised boolean Metric (both these variants of Metric entropy are implied by HILL without loss in quality).\r\n\r\nThe chain rule for HILL entropy states that if X has k bits of HILL entropy of quality (ϵ,s)\r\n, then for any variable Z of length m, X conditioned on Z has k−m bits of HILL entropy with quality (ϵ,s⋅ϵ2/2m). We show that a loss of Ω(2m/ϵ) in circuit size necessary here. Note that this still leaves a gap of ϵ between the known bound and our lower bound.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T06:48:53Z","conference":{"location":"Beijing, China","end_date":"2016-11-03","start_date":"2016-10-31","name":"TCC: Theory of Cryptography Conference"},"type":"conference","status":"public","_id":"1179"},{"scopus_import":1,"quality_controlled":"1","publisher":"Society for Neuroscience","intvolume":" 36","month":"11","abstract":[{"text":"This review accompanies a 2016 SFN mini-symposium presenting examples of current studies that address a central question: How do neural stem cells (NSCs) divide in different ways to produce heterogeneous daughter types at the right time and in proper numbers to build a cerebral cortex with the appropriate size and structure? We will focus on four aspects of corticogenesis: cytokinesis events that follow apical mitoses of NSCs; coordinating abscission with delamination from the apical membrane; timing of neurogenesis and its indirect regulation through emergence of intermediate progenitors; and capacity of single NSCs to generate the correct number and laminar fate of cortical neurons. Defects in these mechanisms can cause microcephaly and other brain malformations, and understanding them is critical to designing diagnostic tools and preventive and corrective therapies.","lang":"eng"}],"acknowledgement":"This work was supported by National Institutes of Health Grants R01NS089795 and R01NS098370 to H.T.G., R01NS076640 to N.D.D., and R01MH094589 and R01NS089777 to B.C., Academia Sinica AS-104-TPB09-2 to S.-J.C, European Union FP7-CIG618444 and Human Frontiers Science Program RGP0053 to S.H., and Fonds Léon Fredericq, from the Fondation Médicale Reine Elisabeth, and from the Fonation Simone et Pierre Clerdent to L.N. The authors apologize to colleagues whose work could not be cited due to space limitations.","oa_version":"None","page":"11394 - 11401","date_created":"2018-12-11T11:50:35Z","volume":36,"doi":"10.1523/JNEUROSCI.2359-16.2016","issue":"45","date_published":"2016-11-09T00:00:00Z","year":"2016","publication_status":"published","language":[{"iso":"eng"}],"publication":"Journal of Neuroscience","day":"09","type":"journal_article","status":"public","project":[{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425"}],"_id":"1181","publist_id":"6172","author":[{"full_name":"Dwyer, Noelle","last_name":"Dwyer","first_name":"Noelle"},{"first_name":"Bin","last_name":"Chen","full_name":"Chen, Bin"},{"first_name":"Shen","full_name":"Chou, Shen","last_name":"Chou"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"},{"first_name":"Laurent","last_name":"Nguyen","full_name":"Nguyen, Laurent"},{"full_name":"Ghashghaei, Troy","last_name":"Ghashghaei","first_name":"Troy"}],"department":[{"_id":"SiHi"}],"title":"Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity","date_updated":"2021-01-12T06:48:54Z","citation":{"ieee":"N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, and T. Ghashghaei, “Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity,” Journal of Neuroscience, vol. 36, no. 45. Society for Neuroscience, pp. 11394–11401, 2016.","short":"N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, T. Ghashghaei, Journal of Neuroscience 36 (2016) 11394–11401.","apa":"Dwyer, N., Chen, B., Chou, S., Hippenmeyer, S., Nguyen, L., & Ghashghaei, T. (2016). Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2359-16.2016","ama":"Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. Journal of Neuroscience. 2016;36(45):11394-11401. doi:10.1523/JNEUROSCI.2359-16.2016","mla":"Dwyer, Noelle, et al. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms Regulating Progenitor Behavior and Productivity.” Journal of Neuroscience, vol. 36, no. 45, Society for Neuroscience, 2016, pp. 11394–401, doi:10.1523/JNEUROSCI.2359-16.2016.","ista":"Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. 2016. Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. Journal of Neuroscience. 36(45), 11394–11401.","chicago":"Dwyer, Noelle, Bin Chen, Shen Chou, Simon Hippenmeyer, Laurent Nguyen, and Troy Ghashghaei. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms Regulating Progenitor Behavior and Productivity.” Journal of Neuroscience. Society for Neuroscience, 2016. https://doi.org/10.1523/JNEUROSCI.2359-16.2016."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"publication_status":"published","year":"2016","day":"01","language":[{"iso":"eng"}],"page":"172 - 179","date_published":"2016-01-01T00:00:00Z","volume":"2016-January","related_material":{"link":[{"url":"https://www.ijcai.org/proceedings/2016","relation":"table_of_contents"}]},"date_created":"2018-12-11T11:50:35Z","ec_funded":1,"abstract":[{"text":"Balanced knockout tournaments are ubiquitous in sports competitions and are also used in decisionmaking and elections. The traditional computational question, that asks to compute a draw (optimal draw) that maximizes the winning probability for a distinguished player, has received a lot of attention. Previous works consider the problem where the pairwise winning probabilities are known precisely, while we study how robust is the winning probability with respect to small errors in the pairwise winning probabilities. First, we present several illuminating examples to establish: (a) there exist deterministic tournaments (where the pairwise winning probabilities are 0 or 1) where one optimal draw is much more robust than the other; and (b) in general, there exist tournaments with slightly suboptimal draws that are more robust than all the optimal draws. The above examples motivate the study of the computational problem of robust draws that guarantee a specified winning probability. Second, we present a polynomial-time algorithm for approximating the robustness of a draw for sufficiently small errors in pairwise winning probabilities, and obtain that the stated computational problem is NP-complete. We also show that two natural cases of deterministic tournaments where the optimal draw could be computed in polynomial time also admit polynomial-time algorithms to compute robust optimal draws.","lang":"eng"}],"oa_version":"Preprint","publisher":"AAAI Press","quality_controlled":"1","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1604.05090v1","open_access":"1"}],"oa":1,"month":"01","date_updated":"2023-02-21T10:04:26Z","citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Josef Tkadlec. “Robust Draws in Balanced Knockout Tournaments,” 2016–January:172–79. AAAI Press, 2016.","ista":"Chatterjee K, Ibsen-Jensen R, Tkadlec J. 2016. Robust draws in balanced knockout tournaments. IJCAI: International Joint Conference on Artificial Intelligence vol. 2016–January, 172–179.","mla":"Chatterjee, Krishnendu, et al. Robust Draws in Balanced Knockout Tournaments. Vol. 2016–January, AAAI Press, 2016, pp. 172–79.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Tkadlec, J. (2016). Robust draws in balanced knockout tournaments (Vol. 2016–January, pp. 172–179). Presented at the IJCAI: International Joint Conference on Artificial Intelligence, New York, NY, USA: AAAI Press.","ama":"Chatterjee K, Ibsen-Jensen R, Tkadlec J. Robust draws in balanced knockout tournaments. In: Vol 2016-January. AAAI Press; 2016:172-179.","short":"K. Chatterjee, R. Ibsen-Jensen, J. Tkadlec, in:, AAAI Press, 2016, pp. 172–179.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and J. Tkadlec, “Robust draws in balanced knockout tournaments,” presented at the IJCAI: International Joint Conference on Artificial Intelligence, New York, NY, USA, 2016, vol. 2016–January, pp. 172–179."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6171","department":[{"_id":"KrCh"}],"title":"Robust draws in balanced knockout tournaments","_id":"1182","type":"conference","conference":{"start_date":"2016-07-09","location":"New York, NY, USA","end_date":"2016-07-15","name":"IJCAI: International Joint Conference on Artificial Intelligence"},"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"}],"status":"public"},{"publist_id":"6169","author":[{"full_name":"Metzler, Sina","last_name":"Metzler","first_name":"Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jürgen","full_name":"Heinze, Jürgen","last_name":"Heinze"},{"first_name":"Alexandra","full_name":"Schrempf, Alexandra","last_name":"Schrempf"}],"title":"Mating and longevity in ant males","citation":{"short":"S. Metzler, J. Heinze, A. Schrempf, Ecology and Evolution 6 (2016) 8903–8906.","ieee":"S. Metzler, J. Heinze, and A. Schrempf, “Mating and longevity in ant males,” Ecology and Evolution, vol. 6, no. 24. Wiley-Blackwell, pp. 8903–8906, 2016.","apa":"Metzler, S., Heinze, J., & Schrempf, A. (2016). Mating and longevity in ant males. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.2474","ama":"Metzler S, Heinze J, Schrempf A. Mating and longevity in ant males. Ecology and Evolution. 2016;6(24):8903-8906. doi:10.1002/ece3.2474","mla":"Metzler, Sina, et al. “Mating and Longevity in Ant Males.” Ecology and Evolution, vol. 6, no. 24, Wiley-Blackwell, 2016, pp. 8903–06, doi:10.1002/ece3.2474.","ista":"Metzler S, Heinze J, Schrempf A. 2016. Mating and longevity in ant males. Ecology and Evolution. 6(24), 8903–8906.","chicago":"Metzler, Sina, Jürgen Heinze, and Alexandra Schrempf. “Mating and Longevity in Ant Males.” Ecology and Evolution. Wiley-Blackwell, 2016. https://doi.org/10.1002/ece3.2474."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","acknowledgement":"German Science Foundation. Grant Number: SCHR 1135/2-1. We thank M. Adam for handling part of the setups and J. Zoellner for behavioral observations.","page":"8903 - 8906","date_created":"2018-12-11T11:50:36Z","date_published":"2016-12-01T00:00:00Z","doi":"10.1002/ece3.2474","year":"2016","has_accepted_license":"1","publication":"Ecology and Evolution","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"736","status":"public","_id":"1184","department":[{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:44:37Z","date_updated":"2021-01-12T06:48:55Z","ddc":["576","592"],"scopus_import":1,"intvolume":" 6","month":"12","abstract":[{"text":"Across multicellular organisms, the costs of reproduction and self-maintenance result in a life history trade-off between fecundity and longevity. Queens of perennial social Hymenoptera are both highly fertile and long-lived, and thus, this fundamental trade-off is lacking. Whether social insect males similarly evade the fecundity/longevity trade-off remains largely unstudied. Wingless males of the ant genus Cardiocondyla stay in their natal colonies throughout their relatively long lives and mate with multiple female sexuals. Here, we show that Cardiocondyla obscurior males that were allowed to mate with large numbers of female sexuals had a shortened life span compared to males that mated at a low frequency or virgin males. Although frequent mating negatively affects longevity, males clearly benefit from a “live fast, die young strategy” by inseminating as many female sexuals as possible at a cost to their own survival.","lang":"eng"}],"oa_version":"Published Version","issue":"24","volume":6,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2017-736-v1+1_Metzler_et_al-2016-Ecology_and_Evolution.pdf","date_created":"2018-12-12T10:14:12Z","file_size":328414,"date_updated":"2020-07-14T12:44:37Z","creator":"system","checksum":"789026eb9e1be2a0da08376f29f569cf","file_id":"5062","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}]},{"department":[{"_id":"EvBe"}],"title":"Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development","publist_id":"6168","author":[{"first_name":"Mara","last_name":"Cucinotta","full_name":"Cucinotta, Mara"},{"full_name":"Manrique, Silvia","last_name":"Manrique","first_name":"Silvia"},{"first_name":"Andrea","full_name":"Guazzotti, Andrea","last_name":"Guazzotti"},{"full_name":"Quadrelli, Nadia","last_name":"Quadrelli","first_name":"Nadia"},{"first_name":"Marta","last_name":"Mendes","full_name":"Mendes, Marta"},{"last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Colombo, Lucia","last_name":"Colombo","first_name":"Lucia"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Cucinotta, Mara, Silvia Manrique, Andrea Guazzotti, Nadia Quadrelli, Marta Mendes, Eva Benková, and Lucia Colombo. “Cytokinin Response Factors Integrate Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.143545.","ista":"Cucinotta M, Manrique S, Guazzotti A, Quadrelli N, Mendes M, Benková E, Colombo L. 2016. Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. Development. 143(23), 4419–4424.","mla":"Cucinotta, Mara, et al. “Cytokinin Response Factors Integrate Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” Development, vol. 143, no. 23, Company of Biologists, 2016, pp. 4419–24, doi:10.1242/dev.143545.","apa":"Cucinotta, M., Manrique, S., Guazzotti, A., Quadrelli, N., Mendes, M., Benková, E., & Colombo, L. (2016). Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. Development. Company of Biologists. https://doi.org/10.1242/dev.143545","ama":"Cucinotta M, Manrique S, Guazzotti A, et al. Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. Development. 2016;143(23):4419-4424. doi:10.1242/dev.143545","short":"M. Cucinotta, S. Manrique, A. Guazzotti, N. Quadrelli, M. Mendes, E. Benková, L. Colombo, Development 143 (2016) 4419–4424.","ieee":"M. Cucinotta et al., “Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development,” Development, vol. 143, no. 23. Company of Biologists, pp. 4419–4424, 2016."},"date_updated":"2021-01-12T06:48:56Z","status":"public","type":"journal_article","_id":"1185","date_published":"2016-12-01T00:00:00Z","doi":"10.1242/dev.143545","volume":143,"issue":"23","date_created":"2018-12-11T11:50:36Z","page":"4419 - 4424","day":"01","language":[{"iso":"eng"}],"publication":"Development","publication_status":"published","year":"2016","month":"12","intvolume":" 143","scopus_import":1,"publisher":"Company of Biologists","quality_controlled":"1","oa_version":"None","acknowledgement":"M.C. was funded by a PhD fellowship from the Università degli Studi di Milano-Bicocca and from Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR) [MIUR-PRIN 2012]. L.C. is also supported by MIUR [MIUR-PRIN 2012]. We would like to thank Andrew MacCabe and Edward Kiegle for editing the paper.","abstract":[{"lang":"eng","text":"The developmental programme of the pistil is under the control of both auxin and cytokinin. Crosstalk between these factors converges on regulation of the auxin carrier PIN-FORMED 1 (PIN1). Here, we show that in the triple transcription factor mutant cytokinin response factor 2 (crf2) crf3 crf6 both pistil length and ovule number were reduced. PIN1 expression was also lower in the triple mutant and the phenotypes could not be rescued by exogenous cytokinin application. pin1 complementation studies using genomic PIN1 constructs showed that the pistil phenotypes were only rescued when the PCRE1 domain, to which CRFs bind, was present. Without this domain, pin mutants resemble the crf2 crf3 crf6 triple mutant, indicating the pivotal role of CRFs in auxin-cytokinin crosstalk."}]},{"volume":6,"language":[{"iso":"eng"}],"file":[{"file_id":"4804","checksum":"e007d78b483bc59bf5ab98e9d42a6ec1","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:10:18Z","file_name":"IST-2017-735-v1+1_srep38094.pdf","date_updated":"2020-07-14T12:44:37Z","file_size":2716045,"creator":"system"}],"publication_status":"published","intvolume":" 6","month":"12","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"The human pathogen Streptococcus pneumoniae is decorated with a special class of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine (PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography, NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies, we provide structural information of choline-binding protein L (CbpL) and demonstrate its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated three-module protein composed of (i) an Excalibur Ca 2+ -binding domain -reported in this work for the very first time-, (ii) an unprecedented anchorage module showing alternate disposition of canonical and non-canonical choline-binding sites that allows vine-like binding of fully-PCho-substituted teichoic acids (with two choline moieties per unit), and (iii) a Ltp-Lipoprotein domain. Our structural and infection assays indicate an important role of the whole multimodular protein allowing both to locate CbpL at specific places on the cell wall and to interact with host components in order to facilitate pneumococcal lung infection and transmigration from nasopharynx to the lungs and blood. CbpL implication in both resistance against killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein as relevant among the pathogenic arsenal of the pneumococcus.","lang":"eng"}],"department":[{"_id":"LeSa"}],"file_date_updated":"2020-07-14T12:44:37Z","ddc":["576","610"],"date_updated":"2021-01-12T06:48:56Z","pubrep_id":"735","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1186","date_created":"2018-12-11T11:50:36Z","date_published":"2016-12-05T00:00:00Z","doi":"10.1038/srep38094","publication":"Scientific Reports","day":"05","year":"2016","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","acknowledgement":"We gratefully acknowledge Karsta Barnekow and Kristine Sievert-Giermann, for technical assistance and Lothar Petruschka for in silico analysis (all Dept. of Genetics, University of Greifswald). We are further grateful to the staff from SLS synchrotron beamline for help in data collection. This work was supported by grants from the Deutsche Forschungsgemeinschaft DFG GRK 1870 (to SH) and the Spanish Ministry of Economy and Competitiveness (BFU2014-59389-P to JAH, CTQ2014-52633-P to MB and SAF2012-39760-C02-02 to FG) and S2010/BMD-2457 (Community of Madrid to JAH and FG).","title":"Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis","author":[{"id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","first_name":"Javier","full_name":"Gutierrez-Fernandez, Javier","last_name":"Gutierrez-Fernandez"},{"full_name":"Saleh, Malek","last_name":"Saleh","first_name":"Malek"},{"first_name":"Martín","full_name":"Alcorlo, Martín","last_name":"Alcorlo"},{"first_name":"Alejandro","full_name":"Gómez Mejóa, Alejandro","last_name":"Gómez Mejóa"},{"full_name":"Pantoja Uceda, David","last_name":"Pantoja Uceda","first_name":"David"},{"full_name":"Treviño, Miguel","last_name":"Treviño","first_name":"Miguel"},{"full_name":"Vob, Franziska","last_name":"Vob","first_name":"Franziska"},{"first_name":"Mohammed","full_name":"Abdullah, Mohammed","last_name":"Abdullah"},{"first_name":"Sergio","last_name":"Galán Bartual","full_name":"Galán Bartual, Sergio"},{"last_name":"Seinen","full_name":"Seinen, Jolien","first_name":"Jolien"},{"first_name":"Pedro","last_name":"Sánchez Murcia","full_name":"Sánchez Murcia, Pedro"},{"full_name":"Gago, Federico","last_name":"Gago","first_name":"Federico"},{"first_name":"Marta","full_name":"Bruix, Marta","last_name":"Bruix"},{"first_name":"Sven","full_name":"Hammerschmidt, Sven","last_name":"Hammerschmidt"},{"last_name":"Hermoso","full_name":"Hermoso, Juan","first_name":"Juan"}],"publist_id":"6167","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Gutierrez-Fernandez J, Saleh M, Alcorlo M, et al. Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. Scientific Reports. 2016;6. doi:10.1038/srep38094","apa":"Gutierrez-Fernandez, J., Saleh, M., Alcorlo, M., Gómez Mejóa, A., Pantoja Uceda, D., Treviño, M., … Hermoso, J. (2016). Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38094","ieee":"J. Gutierrez-Fernandez et al., “Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","short":"J. Gutierrez-Fernandez, M. Saleh, M. Alcorlo, A. Gómez Mejóa, D. Pantoja Uceda, M. Treviño, F. Vob, M. Abdullah, S. Galán Bartual, J. Seinen, P. Sánchez Murcia, F. Gago, M. Bruix, S. Hammerschmidt, J. Hermoso, Scientific Reports 6 (2016).","mla":"Gutierrez-Fernandez, Javier, et al. “Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal Pathogenesis.” Scientific Reports, vol. 6, 38094, Nature Publishing Group, 2016, doi:10.1038/srep38094.","ista":"Gutierrez-Fernandez J, Saleh M, Alcorlo M, Gómez Mejóa A, Pantoja Uceda D, Treviño M, Vob F, Abdullah M, Galán Bartual S, Seinen J, Sánchez Murcia P, Gago F, Bruix M, Hammerschmidt S, Hermoso J. 2016. Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. Scientific Reports. 6, 38094.","chicago":"Gutierrez-Fernandez, Javier, Malek Saleh, Martín Alcorlo, Alejandro Gómez Mejóa, David Pantoja Uceda, Miguel Treviño, Franziska Vob, et al. “Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal Pathogenesis.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38094."},"article_number":"38094"},{"oa_version":"Preprint","abstract":[{"text":"We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation is solved for the steady state in the WKB\r\napproximation that maps it into the ground state of a quantum particle in an\r\nAiry potential plus a centrifugal term. We retrieve scaling laws for growth rate\r\nfluctuations and time response with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal populations can have a faster response\r\nto perturbations.","lang":"eng"}],"month":"12","intvolume":" 2016","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.09048"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"12","volume":2016,"ec_funded":1,"_id":"1188","status":"public","type":"journal_article","date_updated":"2021-01-12T06:48:57Z","department":[{"_id":"GaTk"}],"acknowledgement":"D De Martino is supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011. D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano and Vera Luz Masoero for useful discussions, also late at night.","quality_controlled":"1","publisher":"IOPscience","oa":1,"day":"30","publication":" Journal of Statistical Mechanics: Theory and Experiment","year":"2016","doi":"10.1088/1742-5468/aa4e8f","date_published":"2016-12-30T00:00:00Z","date_created":"2018-12-11T11:50:37Z","article_number":"123502","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism & Growth.” Journal of Statistical Mechanics: Theory and Experiment. IOPscience, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.","ista":"De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502.","mla":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism & Growth.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOPscience, 2016, doi:10.1088/1742-5468/aa4e8f.","apa":"De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa4e8f","ama":"De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f","short":"D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).","ieee":"D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12. IOPscience, 2016."},"title":"Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth","author":[{"last_name":"De Martino","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele"},{"last_name":"Masoero","full_name":"Masoero, Davide","first_name":"Davide"}],"publist_id":"6165"},{"has_accepted_license":"1","year":"2016","day":"03","publication":"Molecular Biology and Evolution","page":"174 - 184","doi":"10.1093/molbev/msw210","date_published":"2016-10-03T00:00:00Z","date_created":"2018-12-11T11:50:39Z","acknowledgement":"The authors thank all members of the Institute of Population\r\nGenetics for discussion and support on the project and par-\r\nticularly N. Barghi for helpful comments on earlier versions of\r\nthe manuscript. This work was supported by the European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”.","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"citation":{"ista":"Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 34(1), 174–184.","chicago":"Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msw210.","apa":"Franssen, S., Barton, N. H., & Schlötterer, C. (2016). Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msw210","ama":"Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 2016;34(1):174-184. doi:10.1093/molbev/msw210","ieee":"S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks selected during experimental evolution.,” Molecular Biology and Evolution, vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.","short":"S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution 34 (2016) 174–184.","mla":"Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution, vol. 34, no. 1, Oxford University Press, 2016, pp. 174–84, doi:10.1093/molbev/msw210."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6155","author":[{"full_name":"Franssen, Susan","last_name":"Franssen","first_name":"Susan"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Christian","last_name":"Schlötterer","full_name":"Schlötterer, Christian"}],"title":"Reconstruction of haplotype-blocks selected during experimental evolution.","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"1e78d3aaffcb40dc8b02b7b4666019e0","file_id":"5223","creator":"system","file_size":295274,"date_updated":"2020-07-14T12:44:38Z","file_name":"IST-2017-770-v1+1_FranssenEtAl_nofigs-1.pdf","date_created":"2018-12-12T10:16:35Z"},{"checksum":"e13171843283774404c936c581b4543e","file_id":"5224","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:16:36Z","file_name":"IST-2017-770-v1+2_Fig1.pdf","date_updated":"2020-07-14T12:44:38Z","file_size":10902625,"creator":"system"},{"date_created":"2018-12-12T10:16:37Z","file_name":"IST-2017-770-v1+3_Fig2.pdf","date_updated":"2020-07-14T12:44:38Z","file_size":21437,"creator":"system","file_id":"5225","checksum":"63bc6e6e61f347594d8c00c37f874a0b","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"checksum":"da87cc7c78808837f22a3dae1c8397f9","file_id":"5226","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:16:38Z","file_name":"IST-2017-770-v1+4_Fig3.pdf","creator":"system","date_updated":"2020-07-14T12:44:38Z","file_size":1172194},{"file_size":50045,"date_updated":"2020-07-14T12:44:38Z","creator":"system","file_name":"IST-2017-770-v1+5_Fig4.pdf","date_created":"2018-12-12T10:16:38Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"e47b2a0c32142f423b3100150c0294f8","file_id":"5227"},{"date_created":"2018-12-12T10:16:39Z","file_name":"IST-2017-770-v1+6_Fig5.pdf","creator":"system","date_updated":"2020-07-14T12:44:38Z","file_size":50705,"file_id":"5228","checksum":"a5a7d6b32e7e17d35d337d7ec2a9f6c9","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":34,"issue":"1","ec_funded":1,"abstract":[{"text":"The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles. ","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"month":"10","intvolume":" 34","date_updated":"2021-01-12T06:49:00Z","ddc":["576"],"file_date_updated":"2020-07-14T12:44:38Z","department":[{"_id":"NiBa"}],"_id":"1195","type":"journal_article","status":"public","pubrep_id":"770"},{"_id":"1200","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"status":"public","pubrep_id":"798","date_updated":"2021-01-12T06:49:03Z","ddc":["530"],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:44:39Z","oa_version":"Submitted Version","scopus_import":1,"month":"12","intvolume":" 19","publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:44:39Z","file_size":171352,"date_created":"2018-12-12T10:11:02Z","file_name":"IST-2017-798-v1+1_comment_adami.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"95e6dc78278334b99dacbf8822509364","file_id":"4855"}],"language":[{"iso":"eng"}],"volume":19,"ec_funded":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"citation":{"mla":"Hilbe, Christian, and Arne Traulsen. “Only the Combination of Mathematics and Agent Based Simulations Can Leverage the Full Potential of Evolutionary Modeling: Comment on ‘Evolutionary Game Theory Using Agent-Based Methods’ by C. Adami, J. Schossau and A. Hintze.” Physics of Life Reviews, vol. 19, Elsevier, 2016, pp. 29–31, doi:10.1016/j.plrev.2016.10.004.","ieee":"C. Hilbe and A. Traulsen, “Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on ‘Evolutionary game theory using agent-based methods’ by C. Adami, J. Schossau and A. Hintze,” Physics of Life Reviews, vol. 19. Elsevier, pp. 29–31, 2016.","short":"C. Hilbe, A. Traulsen, Physics of Life Reviews 19 (2016) 29–31.","ama":"Hilbe C, Traulsen A. Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze. Physics of Life Reviews. 2016;19:29-31. doi:10.1016/j.plrev.2016.10.004","apa":"Hilbe, C., & Traulsen, A. (2016). Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.10.004","chicago":"Hilbe, Christian, and Arne Traulsen. “Only the Combination of Mathematics and Agent Based Simulations Can Leverage the Full Potential of Evolutionary Modeling: Comment on ‘Evolutionary Game Theory Using Agent-Based Methods’ by C. Adami, J. Schossau and A. Hintze.” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.10.004.","ista":"Hilbe C, Traulsen A. 2016. Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze. Physics of Life Reviews. 19, 29–31."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe"},{"first_name":"Arne","last_name":"Traulsen","full_name":"Traulsen, Arne"}],"publist_id":"6150","title":"Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze","acknowledgement":"C.H. acknowledges generous support from the ISTFELLOW program.","publisher":"Elsevier","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2016","day":"01","publication":"Physics of Life Reviews","page":"29 - 31","date_published":"2016-12-01T00:00:00Z","doi":"10.1016/j.plrev.2016.10.004","date_created":"2018-12-11T11:50:40Z"},{"abstract":[{"lang":"eng","text":"In this issue of Cell, Skau et al. show that the formin FMN2 organizes a perinuclear actin cytoskeleton that protects the nucleus and its genomic content of migrating cells squeezing through small spaces."}],"oa_version":"None","publisher":"Cell Press","quality_controlled":"1","scopus_import":1,"intvolume":" 167","month":"12","year":"2016","publication_status":"published","language":[{"iso":"eng"}],"publication":"Cell","day":"01","page":"1448 - 1449","date_created":"2018-12-11T11:50:41Z","doi":"10.1016/j.cell.2016.11.024","date_published":"2016-12-01T00:00:00Z","issue":"6","volume":167,"_id":"1201","type":"journal_article","status":"public","date_updated":"2021-01-12T06:49:03Z","citation":{"ama":"Renkawitz J, Sixt MK. 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Armitage and Jan N. Offenborn for helpful comments on the figures, and two anonymous reviewers for their helpful comments. The project was funded by the Deutsche Forschungsgemeinschaft (DFG, KU 1929/4-2) within the priority programme SPP 1399 “Host–Parasite Coevolution”.","author":[{"id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","last_name":"Milutinovic","full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758"},{"last_name":"Peuß","full_name":"Peuß, Robert","first_name":"Robert"},{"full_name":"Ferro, Kevin","last_name":"Ferro","first_name":"Kevin"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"}],"publist_id":"6147","title":"Immune priming in arthropods: an update focusing on the red flour beetle","citation":{"mla":"Milutinovic, Barbara, et al. “Immune Priming in Arthropods: An Update Focusing on the Red Flour Beetle.” Zoology , vol. 119, no. 4, Elsevier, 2016, pp. 254–61, doi:10.1016/j.zool.2016.03.006.","ama":"Milutinovic B, Peuß R, Ferro K, Kurtz J. Immune priming in arthropods: an update focusing on the red flour beetle. Zoology . 2016;119(4):254-261. doi:10.1016/j.zool.2016.03.006","apa":"Milutinovic, B., Peuß, R., Ferro, K., & Kurtz, J. (2016). Immune priming in arthropods: an update focusing on the red flour beetle. Zoology . Elsevier. https://doi.org/10.1016/j.zool.2016.03.006","short":"B. Milutinovic, R. Peuß, K. Ferro, J. Kurtz, Zoology 119 (2016) 254–261.","ieee":"B. Milutinovic, R. Peuß, K. Ferro, and J. Kurtz, “Immune priming in arthropods: an update focusing on the red flour beetle,” Zoology , vol. 119, no. 4. Elsevier, pp. 254–261, 2016.","chicago":"Milutinovic, Barbara, Robert Peuß, Kevin Ferro, and Joachim Kurtz. “Immune Priming in Arthropods: An Update Focusing on the Red Flour Beetle.” Zoology . Elsevier, 2016. https://doi.org/10.1016/j.zool.2016.03.006.","ista":"Milutinovic B, Peuß R, Ferro K, Kurtz J. 2016. Immune priming in arthropods: an update focusing on the red flour beetle. Zoology . 119(4), 254–261."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution"}]},{"publisher":"American Society for Microbiology","quality_controlled":"1","oa":1,"acknowledgement":"We are grateful to ABCs for providing strains and the Bacterial Meningitis Laboratory for technical support.","page":"3010 - 3017","doi":"10.1128/JCM.01511-16","date_published":"2016-12-01T00:00:00Z","date_created":"2018-12-11T11:50:41Z","year":"2016","day":"01","publication":"Journal of Clinical Microbiology","publist_id":"6146","author":[{"first_name":"Fang","full_name":"Hu, Fang","last_name":"Hu"},{"first_name":"Lavanya","last_name":"Rishishwar","full_name":"Rishishwar, Lavanya"},{"full_name":"Sivadas, Ambily","last_name":"Sivadas","first_name":"Ambily"},{"last_name":"Mitchell","full_name":"Mitchell, Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel"},{"full_name":"King, Jordan","last_name":"King","first_name":"Jordan"},{"last_name":"Murphy","full_name":"Murphy, Timothy","first_name":"Timothy"},{"first_name":"Janet","full_name":"Gilsdorf, Janet","last_name":"Gilsdorf"},{"first_name":"Leonard","full_name":"Mayer, Leonard","last_name":"Mayer"},{"first_name":"Xin","last_name":"Wang","full_name":"Wang, Xin"}],"title":"Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination","citation":{"chicago":"Hu, Fang, Lavanya Rishishwar, Ambily Sivadas, Gabriel Mitchell, Jordan King, Timothy Murphy, Janet Gilsdorf, Leonard Mayer, and Xin Wang. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” Journal of Clinical Microbiology. American Society for Microbiology, 2016. https://doi.org/10.1128/JCM.01511-16.","ista":"Hu F, Rishishwar L, Sivadas A, Mitchell G, King J, Murphy T, Gilsdorf J, Mayer L, Wang X. 2016. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 54(12), 3010–3017.","mla":"Hu, Fang, et al. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” Journal of Clinical Microbiology, vol. 54, no. 12, American Society for Microbiology, 2016, pp. 3010–17, doi:10.1128/JCM.01511-16.","ieee":"F. Hu et al., “Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination,” Journal of Clinical Microbiology, vol. 54, no. 12. American Society for Microbiology, pp. 3010–3017, 2016.","short":"F. Hu, L. Rishishwar, A. Sivadas, G. Mitchell, J. King, T. Murphy, J. Gilsdorf, L. Mayer, X. Wang, Journal of Clinical Microbiology 54 (2016) 3010–3017.","apa":"Hu, F., Rishishwar, L., Sivadas, A., Mitchell, G., King, J., Murphy, T., … Wang, X. (2016). Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. American Society for Microbiology. https://doi.org/10.1128/JCM.01511-16","ama":"Hu F, Rishishwar L, Sivadas A, et al. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 2016;54(12):3010-3017. doi:10.1128/JCM.01511-16"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121393/"}],"month":"12","intvolume":" 54","abstract":[{"text":"Haemophilus haemolyticus has been recently discovered to have the potential to cause invasive disease. It is closely related to nontypeable Haemophilus influenzae (NT H. influenzae). NT H. influenzae and H. haemolyticus are often misidentified because none of the existing tests targeting the known phenotypes of H. haemolyticus are able to specifically identify H. haemolyticus. Through comparative genomic analysis of H. haemolyticus and NT H. influenzae, we identified genes unique to H. haemolyticus that can be used as targets for the identification of H. haemolyticus. A real-time PCR targeting purT (encoding phosphoribosylglycinamide formyltransferase 2 in the purine synthesis pathway) was developed and evaluated. The lower limit of detection was 40 genomes/PCR; the sensitivity and specificity in detecting H. haemolyticus were 98.9% and 97%, respectively. To improve the discrimination of H. haemolyticus and NT H. influenzae, a testing scheme combining two targets (H. haemolyticus purT and H. influenzae hpd, encoding protein D lipoprotein) was also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification of H. haemolyticus and 92.8% sensitivity and 100% specificity for the identification of H. influenzae, respectively. The dual-target testing scheme can be used for the diagnosis and surveillance of infection and disease caused by H. haemolyticus and NT H. influenzae.","lang":"eng"}],"oa_version":"Submitted Version","issue":"12","volume":54,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1203","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T06:49:04Z"},{"scopus_import":1,"publisher":"Mathematical Association of America","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.00299"}],"oa":1,"month":"06","intvolume":" 123","abstract":[{"lang":"eng","text":"In science, as in life, "surprises" can be adequately appreciated only in the presence of a null model, what we expect a priori. In physics, theories sometimes express the values of dimensionless physical constants as combinations of mathematical constants like π or e. The inverse problem also arises, whereby the measured value of a physical constant admits a "surprisingly" simple approximation in terms of well-known mathematical constants. Can we estimate the probability for this to be a mere coincidence, rather than an inkling of some theory? We answer the question in the most naive form."}],"oa_version":"Preprint","page":"609 - 612","volume":123,"doi":"10.4169/amer.math.monthly.123.6.609","issue":"6","date_published":"2016-06-01T00:00:00Z","date_created":"2018-12-11T11:50:42Z","year":"2016","publication_status":"published","day":"01","publication":"American Mathematical Monthly","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1204","publist_id":"6143","author":[{"full_name":"Amir, Ariel","last_name":"Amir","first_name":"Ariel"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"first_name":"Tadashi","last_name":"Tokieda","full_name":"Tokieda, Tadashi"}],"department":[{"_id":"MiLe"}],"title":"Surprises in numerical expressions of physical constants","date_updated":"2021-01-12T06:49:04Z","citation":{"mla":"Amir, Ariel, et al. “Surprises in Numerical Expressions of Physical Constants.” American Mathematical Monthly, vol. 123, no. 6, Mathematical Association of America, 2016, pp. 609–12, doi:10.4169/amer.math.monthly.123.6.609.","short":"A. Amir, M. Lemeshko, T. Tokieda, American Mathematical Monthly 123 (2016) 609–612.","ieee":"A. Amir, M. Lemeshko, and T. Tokieda, “Surprises in numerical expressions of physical constants,” American Mathematical Monthly, vol. 123, no. 6. Mathematical Association of America, pp. 609–612, 2016.","ama":"Amir A, Lemeshko M, Tokieda T. Surprises in numerical expressions of physical constants. American Mathematical Monthly. 2016;123(6):609-612. doi:10.4169/amer.math.monthly.123.6.609","apa":"Amir, A., Lemeshko, M., & Tokieda, T. (2016). Surprises in numerical expressions of physical constants. American Mathematical Monthly. Mathematical Association of America. https://doi.org/10.4169/amer.math.monthly.123.6.609","chicago":"Amir, Ariel, Mikhail Lemeshko, and Tadashi Tokieda. “Surprises in Numerical Expressions of Physical Constants.” American Mathematical Monthly. Mathematical Association of America, 2016. https://doi.org/10.4169/amer.math.monthly.123.6.609.","ista":"Amir A, Lemeshko M, Tokieda T. 2016. Surprises in numerical expressions of physical constants. American Mathematical Monthly. 123(6), 609–612."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"_id":"1206","status":"public","type":"journal_article","date_updated":"2021-01-12T06:49:05Z","department":[{"_id":"JoFi"},{"_id":"MiLe"}],"oa_version":"Preprint","abstract":[{"text":"We study a polar molecule immersed in a superfluid environment, such as a helium nanodroplet or a Bose–Einstein condensate, in the presence of a strong electrostatic field. We show that coupling of the molecular pendular motion, induced by the field, to the fluctuating bath leads to formation of pendulons—spherical harmonic librators dressed by a field of many-particle excitations. We study the behavior of the pendulon in a broad range of molecule–bath and molecule–field interaction strengths, and reveal that its spectrum features a series of instabilities which are absent in the field-free case of the angulon quasiparticle. Furthermore, we show that an external field allows to fine-tune the positions of these instabilities in the molecular rotational spectrum. This opens the door to detailed experimental studies of redistribution of orbital angular momentum in many-particle systems. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim","lang":"eng"}],"intvolume":" 17","month":"09","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.08161"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":17,"issue":"22","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Redchenko, Elena, and Mikhail Lemeshko. “Libration of Strongly Oriented Polar Molecules inside a Superfluid.” ChemPhysChem. Wiley-Blackwell, 2016. https://doi.org/10.1002/cphc.201601042.","ista":"Redchenko E, Lemeshko M. 2016. Libration of strongly oriented polar molecules inside a superfluid. ChemPhysChem. 17(22), 3649–3654.","mla":"Redchenko, Elena, and Mikhail Lemeshko. “Libration of Strongly Oriented Polar Molecules inside a Superfluid.” ChemPhysChem, vol. 17, no. 22, Wiley-Blackwell, 2016, pp. 3649–54, doi:10.1002/cphc.201601042.","short":"E. Redchenko, M. Lemeshko, ChemPhysChem 17 (2016) 3649–3654.","ieee":"E. Redchenko and M. Lemeshko, “Libration of strongly oriented polar molecules inside a superfluid,” ChemPhysChem, vol. 17, no. 22. Wiley-Blackwell, pp. 3649–3654, 2016.","apa":"Redchenko, E., & Lemeshko, M. (2016). Libration of strongly oriented polar molecules inside a superfluid. ChemPhysChem. Wiley-Blackwell. https://doi.org/10.1002/cphc.201601042","ama":"Redchenko E, Lemeshko M. Libration of strongly oriented polar molecules inside a superfluid. ChemPhysChem. 2016;17(22):3649-3654. doi:10.1002/cphc.201601042"},"title":"Libration of strongly oriented polar molecules inside a superfluid","author":[{"full_name":"Redchenko, Elena","last_name":"Redchenko","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"}],"publist_id":"6140","oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","publication":"ChemPhysChem","day":"18","year":"2016","date_created":"2018-12-11T11:50:43Z","date_published":"2016-09-18T00:00:00Z","doi":"10.1002/cphc.201601042","page":"3649 - 3654"},{"_id":"1209","status":"public","type":"journal_article","date_updated":"2021-01-12T06:49:06Z","department":[{"_id":"LeSa"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"NADH-ubiquinone oxidoreductase (complex I) is the largest (∼1 MDa) and the least characterized complex of the mitochondrial electron transport chain. Because of the ease of sample availability, previous work has focused almost exclusively on bovine complex I. However, only medium resolution structural analyses of this complex have been reported. Working with other mammalian complex I homologues is a potential approach for overcoming these limitations. Due to the inherent difficulty of expressing large membrane protein complexes, screening of complex I homologues is limited to large mammals reared for human consumption. The high sequence identity among these available sources may preclude the benefits of screening. Here, we report the characterization of complex I purified from Ovis aries (ovine) heart mitochondria. All 44 unique subunits of the intact complex were identified by mass spectrometry. We identified differences in the subunit composition of subcomplexes of ovine complex I as compared with bovine, suggesting differential stability of inter-subunit interactions within the complex. Furthermore, the 42-kDa subunit, which is easily lost from the bovine enzyme, remains tightly bound to ovine complex I. Additionally, we developed a novel purification protocol for highly active and stable mitochondrial complex I using the branched-chain detergent lauryl maltose neopentyl glycol. Our data demonstrate that, although closely related, significant differences exist between the biochemical properties of complex I prepared from ovine and bovine mitochondria and that ovine complex I represents a suitable alternative target for further structural studies. "}],"month":"11","intvolume":" 291","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114416/"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"47","volume":291,"ec_funded":1,"project":[{"_id":"2593EBD6-B435-11E9-9278-68D0E5697425","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (FEBS)"},{"call_identifier":"H2020","_id":"2590DB08-B435-11E9-9278-68D0E5697425","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","grant_number":"701309"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Letts, James A., et al. “Purification of Ovine Respiratory Complex i Results in a Highly Active and Stable Preparation.” Journal of Biological Chemistry, vol. 291, no. 47, American Society for Biochemistry and Molecular Biology, 2016, pp. 24657–75, doi:10.1074/jbc.M116.735142.","ieee":"J. A. Letts, G. Degliesposti, K. Fiedorczuk, M. Skehel, and L. A. Sazanov, “Purification of ovine respiratory complex i results in a highly active and stable preparation,” Journal of Biological Chemistry, vol. 291, no. 47. American Society for Biochemistry and Molecular Biology, pp. 24657–24675, 2016.","short":"J.A. Letts, G. Degliesposti, K. Fiedorczuk, M. Skehel, L.A. Sazanov, Journal of Biological Chemistry 291 (2016) 24657–24675.","ama":"Letts JA, Degliesposti G, Fiedorczuk K, Skehel M, Sazanov LA. Purification of ovine respiratory complex i results in a highly active and stable preparation. Journal of Biological Chemistry. 2016;291(47):24657-24675. doi:10.1074/jbc.M116.735142","apa":"Letts, J. A., Degliesposti, G., Fiedorczuk, K., Skehel, M., & Sazanov, L. A. (2016). Purification of ovine respiratory complex i results in a highly active and stable preparation. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M116.735142","chicago":"Letts, James A, Gianluca Degliesposti, Karol Fiedorczuk, Mark Skehel, and Leonid A Sazanov. “Purification of Ovine Respiratory Complex i Results in a Highly Active and Stable Preparation.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2016. https://doi.org/10.1074/jbc.M116.735142.","ista":"Letts JA, Degliesposti G, Fiedorczuk K, Skehel M, Sazanov LA. 2016. Purification of ovine respiratory complex i results in a highly active and stable preparation. Journal of Biological Chemistry. 291(47), 24657–24675."},"title":"Purification of ovine respiratory complex i results in a highly active and stable preparation","author":[{"orcid":"0000-0002-9864-3586","full_name":"Letts, James A","last_name":"Letts","first_name":"James A","id":"322DA418-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gianluca","full_name":"Degliesposti, Gianluca","last_name":"Degliesposti"},{"first_name":"Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","full_name":"Fiedorczuk, Karol","last_name":"Fiedorczuk"},{"first_name":"Mark","full_name":"Skehel, Mark","last_name":"Skehel"},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989"}],"publist_id":"6139","acknowledgement":"J.A.S supported in part by a Medical Research D.G.Council UK Ph.D. fellowship.\r\nThis work was supported in part by European Union's 2020 Research and Innovation Program under Grant 701309. \r\n","quality_controlled":"1","publisher":"American Society for Biochemistry and Molecular Biology","oa":1,"day":"18","publication":"Journal of Biological Chemistry","year":"2016","date_published":"2016-11-18T00:00:00Z","doi":"10.1074/jbc.M116.735142","date_created":"2018-12-11T11:50:44Z","page":"24657 - 24675"},{"language":[{"iso":"eng"}],"publication":"Plant Hormones","day":"19","publication_status":"published","year":"2016","date_created":"2018-12-11T11:50:44Z","date_published":"2016-11-19T00:00:00Z","volume":1497,"doi":"10.1007/978-1-4939-6469-7_1","page":"1 - 8","acknowledgement":"We thank Herman \r\nHöfte \r\n, Todor Asenov, Robert Hauschield, and \r\nMarcal Gallemi for help with the establishment of the real-time \r\nimaging platform and technical support. This work was supported \r\nby the Czech Science Foundation (GA13-39982S) to Eva Benková. \r\nDominique Van Der Straeten acknowledges the Research \r\nFoundation Flanders for fi\r\n nancial support (G.0656.13N). Dajo \r\nSmet holds a PhD fellowship of the Research Foundation Flanders. ","oa_version":"None","abstract":[{"text":"Mechanisms for cell protection are essential for survival of multicellular organisms. In plants, the apical hook, which is transiently formed in darkness when the germinating seedling penetrates towards the soil surface, plays such protective role and shields the vitally important shoot apical meristem and cotyledons from damage. The apical hook is formed by bending of the upper hypocotyl soon after germination, and it is maintained in a closed stage while the hypocotyl continues to penetrate through the soil and rapidly opens when exposed to light in proximity of the soil surface. To uncover the complex molecular network orchestrating this spatiotemporally tightly coordinated process, monitoring of the apical hook development in real time is indispensable. Here we describe an imaging platform that enables high-resolution kinetic analysis of this dynamic developmental process. © Springer Science+Business Media New York 2017.","lang":"eng"}],"intvolume":" 1497","month":"11","publisher":"Humana Press","alternative_title":["Methods in Molecular Biology"],"scopus_import":1,"quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Zhu Q, Žádníková P, Smet D, Van Der Straeten D, Benková E. Real time analysis of the apical hook development. In: Plant Hormones. Vol 1497. Humana Press; 2016:1-8. doi:10.1007/978-1-4939-6469-7_1","apa":"Zhu, Q., Žádníková, P., Smet, D., Van Der Straeten, D., & Benková, E. (2016). Real time analysis of the apical hook development. In Plant Hormones (Vol. 1497, pp. 1–8). Humana Press. https://doi.org/10.1007/978-1-4939-6469-7_1","ieee":"Q. Zhu, P. Žádníková, D. Smet, D. Van Der Straeten, and E. Benková, “Real time analysis of the apical hook development,” in Plant Hormones, vol. 1497, Humana Press, 2016, pp. 1–8.","short":"Q. Zhu, P. Žádníková, D. Smet, D. Van Der Straeten, E. Benková, in:, Plant Hormones, Humana Press, 2016, pp. 1–8.","mla":"Zhu, Qiang, et al. “Real Time Analysis of the Apical Hook Development.” Plant Hormones, vol. 1497, Humana Press, 2016, pp. 1–8, doi:10.1007/978-1-4939-6469-7_1.","ista":"Zhu Q, Žádníková P, Smet D, Van Der Straeten D, Benková E. 2016.Real time analysis of the apical hook development. In: Plant Hormones. Methods in Molecular Biology, vol. 1497, 1–8.","chicago":"Zhu, Qiang, Petra Žádníková, Dajo Smet, Dominique Van Der Straeten, and Eva Benková. “Real Time Analysis of the Apical Hook Development.” In Plant Hormones, 1497:1–8. Humana Press, 2016. https://doi.org/10.1007/978-1-4939-6469-7_1."},"date_updated":"2021-01-12T06:49:07Z","department":[{"_id":"EvBe"}],"title":"Real time analysis of the apical hook development","author":[{"last_name":"Zhu","full_name":"Zhu, Qiang","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","first_name":"Qiang"},{"full_name":"Žádníková, Petra","last_name":"Žádníková","first_name":"Petra"},{"last_name":"Smet","full_name":"Smet, Dajo","first_name":"Dajo"},{"first_name":"Dominique","last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"}],"publist_id":"6135","_id":"1210","status":"public","type":"book_chapter"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Rakusová H, Abbas M, Han H, Song S, Robert H, Friml J. 2016. Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity. Current Biology. 26(22), 3026–3032.","chicago":"Rakusová, Hana, Mohamad Abbas, Huibin Han, Siyuan Song, Hélène Robert, and Jiří Friml. “Termination of Shoot Gravitropic Responses by Auxin Feedback on PIN3 Polarity.” Current Biology. Cell Press, 2016. https://doi.org/10.1016/j.cub.2016.08.067.","ieee":"H. Rakusová, M. Abbas, H. Han, S. Song, H. Robert, and J. Friml, “Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity,” Current Biology, vol. 26, no. 22. Cell Press, pp. 3026–3032, 2016.","short":"H. Rakusová, M. Abbas, H. Han, S. Song, H. Robert, J. Friml, Current Biology 26 (2016) 3026–3032.","apa":"Rakusová, H., Abbas, M., Han, H., Song, S., Robert, H., & Friml, J. (2016). Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2016.08.067","ama":"Rakusová H, Abbas M, Han H, Song S, Robert H, Friml J. Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity. Current Biology. 2016;26(22):3026-3032. doi:10.1016/j.cub.2016.08.067","mla":"Rakusová, Hana, et al. “Termination of Shoot Gravitropic Responses by Auxin Feedback on PIN3 Polarity.” Current Biology, vol. 26, no. 22, Cell Press, 2016, pp. 3026–32, doi:10.1016/j.cub.2016.08.067."},"title":"Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity","author":[{"first_name":"Hana","last_name":"Rakusová","full_name":"Rakusová, Hana"},{"first_name":"Mohamad","id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87","full_name":"Abbas, Mohamad","last_name":"Abbas"},{"first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","last_name":"Han"},{"full_name":"Song, Siyuan","last_name":"Song","first_name":"Siyuan"},{"full_name":"Robert, Hélène","last_name":"Robert","first_name":"Hélène"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6138","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"day":"21","publication":"Current Biology","has_accepted_license":"1","year":"2016","doi":"10.1016/j.cub.2016.08.067","date_published":"2016-11-21T00:00:00Z","date_created":"2018-12-11T11:50:44Z","page":"3026 - 3032","acknowledgement":"We thank Dr. Jie Li (Key Laboratory of Plant Molecular Physiology, Chinese Academy of Science, China) for the pPIN3::PIN3-GFP/DII::VENUS line and Martine De Cock for help in preparing the manuscript. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP), by the Czech Science Foundation GAČR (GA13-40637S) to J.F., and by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) to H.S.R. H.R. is indebted to the Agency for Innovation by Science and Technology (IWT) for a predoctoral fellowship.\r\n","publisher":"Cell Press","quality_controlled":"1","oa":1,"ddc":["581"],"date_updated":"2021-01-12T06:49:08Z","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:39Z","_id":"1212","status":"public","pubrep_id":"1008","type":"journal_article","file":[{"file_name":"IST-2018-1008-v1+1_Rakusova_CurrBiol_2016_proof.pdf","date_created":"2018-12-12T10:09:33Z","file_size":5391923,"date_updated":"2020-07-14T12:44:39Z","creator":"system","file_id":"4757","checksum":"79ed2498185a027cf51a8f88100379e6","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":26,"issue":"22","ec_funded":1,"oa_version":"Submitted Version","abstract":[{"text":"Plants adjust their growth according to gravity. Gravitropism involves gravity perception, signal transduction, and asymmetric growth response, with organ bending as a consequence [1]. Asymmetric growth results from the asymmetric distribution of the plant-specific signaling molecule auxin [2] that is generated by lateral transport, mediated in the hypocotyl predominantly by the auxin transporter PIN-FORMED3 (PIN3) [3–5]. Gravity stimulation polarizes PIN3 to the bottom sides of endodermal cells, correlating with increased auxin accumulation in adjacent tissues at the lower side of the stimulated organ, where auxin induces cell elongation and, hence, organ bending. A curvature response allows the hypocotyl to resume straight growth at a defined angle [6], implying that at some point auxin symmetry is restored to prevent overbending. Here, we present initial insights into cellular and molecular mechanisms that lead to the termination of the tropic response. We identified an auxin feedback on PIN3 polarization as underlying mechanism that restores symmetry of the PIN3-dependent auxin flow. Thus, two mechanistically distinct PIN3 polarization events redirect auxin fluxes at different time points of the gravity response: first, gravity-mediated redirection of PIN3-mediated auxin flow toward the lower hypocotyl side, where auxin gradually accumulates and promotes growth, and later PIN3 polarization to the opposite cell side, depleting this auxin maximum to end the bending. Accordingly, genetic or pharmacological interference with the late PIN3 polarization prevents termination of the response and leads to hypocotyl overbending. This observation reveals a role of auxin feedback on PIN polarity in the termination of the tropic response. © 2016 Elsevier Ltd","lang":"eng"}],"month":"11","intvolume":" 26","scopus_import":1},{"status":"public","conference":{"name":"IEEE RSJ International Conference on Intelligent Robots and Systems IROS ","start_date":"2016-09-09","location":"Daejeon, Korea","end_date":"2016-09-14"},"type":"conference","article_number":"7759138","_id":"1214","title":"Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"author":[{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","last_name":"Martius","full_name":"Martius, Georg S"},{"full_name":"Hostettler, Raphael","last_name":"Hostettler","first_name":"Raphael"},{"last_name":"Knoll","full_name":"Knoll, Alois","first_name":"Alois"},{"last_name":"Der","full_name":"Der, Ralf","first_name":"Ralf"}],"publist_id":"6121","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:49:08Z","citation":{"ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm,” presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea, 2016, vol. 2016–November.","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, IEEE, 2016.","apa":"Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm (Vol. 2016–November). Presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea: IEEE. https://doi.org/10.1109/IROS.2016.7759138","ama":"Martius GS, Hostettler R, Knoll A, Der R. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. In: Vol 2016-November. IEEE; 2016. doi:10.1109/IROS.2016.7759138","mla":"Martius, Georg S., et al. Compliant Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic Arm. Vol. 2016–November, 7759138, IEEE, 2016, doi:10.1109/IROS.2016.7759138.","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. IEEE RSJ International Conference on Intelligent Robots and Systems IROS vol. 2016–November, 7759138.","chicago":"Martius, Georg S, Raphael Hostettler, Alois Knoll, and Ralf Der. “Compliant Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic Arm,” Vol. 2016–November. IEEE, 2016. https://doi.org/10.1109/IROS.2016.7759138."},"month":"11","scopus_import":1,"publisher":"IEEE","quality_controlled":"1","acknowledgement":"RD thanks for the hospitality at the Max-Planck-Institute and for helpful discussions with Nihat Ay and Keyan Zahedi.","oa_version":"None","abstract":[{"text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. While very successful with classical robots, these methods run into severe difficulties when applied to soft robots, a new field of robotics with large interest for human-robot interaction. We claim that a novel controller paradigm opens new perspective for this field. This paper applies a recently developed neuro controller with differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently develops to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.","lang":"eng"}],"date_created":"2018-12-11T11:50:45Z","volume":"2016-November","doi":"10.1109/IROS.2016.7759138","date_published":"2016-11-28T00:00:00Z","language":[{"iso":"eng"}],"day":"28","year":"2016","publication_status":"published"},{"date_updated":"2021-01-12T06:49:09Z","citation":{"ista":"Kasten J, Reininghaus J, Hotz I, Hege H, Noack B, Daviller G, Morzyński M. 2016. Acceleration feature points of unsteady shear flows. Archives of Mechanics. 68(1), 55–80.","chicago":"Kasten, Jens, Jan Reininghaus, Ingrid Hotz, Hans Hege, Bernd Noack, Guillaume Daviller, and Marek Morzyński. “Acceleration Feature Points of Unsteady Shear Flows.” Archives of Mechanics. Polish Academy of Sciences Publishing House, 2016.","short":"J. Kasten, J. Reininghaus, I. Hotz, H. Hege, B. Noack, G. Daviller, M. Morzyński, Archives of Mechanics 68 (2016) 55–80.","ieee":"J. Kasten et al., “Acceleration feature points of unsteady shear flows,” Archives of Mechanics, vol. 68, no. 1. Polish Academy of Sciences Publishing House, pp. 55–80, 2016.","ama":"Kasten J, Reininghaus J, Hotz I, et al. Acceleration feature points of unsteady shear flows. Archives of Mechanics. 2016;68(1):55-80.","apa":"Kasten, J., Reininghaus, J., Hotz, I., Hege, H., Noack, B., Daviller, G., & Morzyński, M. (2016). Acceleration feature points of unsteady shear flows. Archives of Mechanics. Polish Academy of Sciences Publishing House.","mla":"Kasten, Jens, et al. “Acceleration Feature Points of Unsteady Shear Flows.” Archives of Mechanics, vol. 68, no. 1, Polish Academy of Sciences Publishing House, 2016, pp. 55–80."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6118","author":[{"last_name":"Kasten","full_name":"Kasten, Jens","first_name":"Jens"},{"last_name":"Reininghaus","full_name":"Reininghaus, Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"last_name":"Hotz","full_name":"Hotz, Ingrid","first_name":"Ingrid"},{"first_name":"Hans","last_name":"Hege","full_name":"Hege, Hans"},{"last_name":"Noack","full_name":"Noack, Bernd","first_name":"Bernd"},{"first_name":"Guillaume","last_name":"Daviller","full_name":"Daviller, Guillaume"},{"first_name":"Marek","full_name":"Morzyński, Marek","last_name":"Morzyński"}],"title":"Acceleration feature points of unsteady shear flows","department":[{"_id":"HeEd"}],"_id":"1216","type":"journal_article","status":"public","year":"2016","publication_status":"published","day":"01","publication":"Archives of Mechanics","language":[{"iso":"eng"}],"page":"55 - 80","volume":68,"issue":"1","date_published":"2016-01-01T00:00:00Z","date_created":"2018-12-11T11:50:46Z","abstract":[{"lang":"eng","text":"A framework fo r extracting features in 2D transient flows, based on the acceleration field to ensure Galilean invariance is proposed in this paper. The minima of the acceleration magnitude (a superset of acceleration zeros) are extracted and discriminated into vortices and saddle points, based on the spectral properties of the velocity Jacobian. The extraction of topological features is performed with purely combinatorial algorithms from discrete computational topology. The feature points are prioritized with persistence, as a physically meaningful importance measure. These feature points are tracked in time with a robust algorithm for tracking features. Thus, a space-time hierarchy of the minima is built and vortex merging events are detected. We apply the acceleration feature extraction strategy to three two-dimensional shear flows: (1) an incompressible periodic cylinder wake, (2) an incompressible planar mixing layer and (3) a weakly compressible planar jet. The vortex-like acceleration feature points are shown to be well aligned with acceleration zeros, maxima of the vorticity magnitude, minima of the pressure field and minima of λ2."}],"oa_version":"Published Version","acknowledgement":"The authors acknowledge funding of the German Re-\r\nsearch Foundation (DFG) via the Collaborative Re-\r\nsearch Center (SFB 557) \\Control of Complex Turbu-\r\nlent Shear Flows\" and the Emmy Noether Program.\r\nFurther funding was provided by the Zuse Institute\r\nBerlin (ZIB), the DFG-CNRS research group \\Noise\r\nGeneration in Turbulent Flows\" (2003{2010), the Chaire\r\nd'Excellence 'Closed-loop control of turbulent shear ows\r\nusing reduced-order models' (TUCOROM) of the French\r\nAgence Nationale de la Recherche (ANR), and the Eu-\r\nropean Social Fund (ESF App. No. 100098251). We\r\nthank the Ambrosys Ltd. Society for Complex Sys-\r\ntems Management and the Bernd R. Noack Cybernet-\r\nics Foundation for additional support. A part of this\r\nwork was performed using HPC resources from GENCI-[CCRT/CINES/IDRIS] supported by the Grant 2011-\r\n[x2011020912","quality_controlled":"1","publisher":"Polish Academy of Sciences Publishing House","scopus_import":1,"oa":1,"main_file_link":[{"url":"http://am.ippt.pan.pl/am/article/viewFile/v68p55/pdf","open_access":"1"}],"month":"01","intvolume":" 68"},{"author":[{"full_name":"Sreeramkumar, Vinatha","last_name":"Sreeramkumar","first_name":"Vinatha"},{"id":"4167FE56-F248-11E8-B48F-1D18A9856A87","first_name":"Miroslav","last_name":"Hons","full_name":"Hons, Miroslav","orcid":"0000-0002-6625-3348"},{"last_name":"Punzón","full_name":"Punzón, Carmen","first_name":"Carmen"},{"full_name":"Stein, Jens","last_name":"Stein","first_name":"Jens"},{"last_name":"Sancho","full_name":"Sancho, David","first_name":"David"},{"first_name":"Manuel","last_name":"Fresno Forcelledo","full_name":"Fresno Forcelledo, Manuel"},{"first_name":"Natalia","last_name":"Cuesta","full_name":"Cuesta, Natalia"}],"publist_id":"6116","department":[{"_id":"MiSi"}],"title":"Efficient T-cell priming and activation requires signaling through prostaglandin E2 (EP) receptors","date_updated":"2021-01-12T06:49:09Z","citation":{"chicago":"Sreeramkumar, Vinatha, Miroslav Hons, Carmen Punzón, Jens Stein, David Sancho, Manuel Fresno Forcelledo, and Natalia Cuesta. “Efficient T-Cell Priming and Activation Requires Signaling through Prostaglandin E2 (EP) Receptors.” Immunology and Cell Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/icb.2015.62.","ista":"Sreeramkumar V, Hons M, Punzón C, Stein J, Sancho D, Fresno Forcelledo M, Cuesta N. 2016. Efficient T-cell priming and activation requires signaling through prostaglandin E2 (EP) receptors. Immunology and Cell Biology. 94(1), 39–51.","mla":"Sreeramkumar, Vinatha, et al. “Efficient T-Cell Priming and Activation Requires Signaling through Prostaglandin E2 (EP) Receptors.” Immunology and Cell Biology, vol. 94, no. 1, Nature Publishing Group, 2016, pp. 39–51, doi:10.1038/icb.2015.62.","ieee":"V. Sreeramkumar et al., “Efficient T-cell priming and activation requires signaling through prostaglandin E2 (EP) receptors,” Immunology and Cell Biology, vol. 94, no. 1. Nature Publishing Group, pp. 39–51, 2016.","short":"V. Sreeramkumar, M. Hons, C. Punzón, J. Stein, D. Sancho, M. Fresno Forcelledo, N. Cuesta, Immunology and Cell Biology 94 (2016) 39–51.","ama":"Sreeramkumar V, Hons M, Punzón C, et al. Efficient T-cell priming and activation requires signaling through prostaglandin E2 (EP) receptors. Immunology and Cell Biology. 2016;94(1):39-51. doi:10.1038/icb.2015.62","apa":"Sreeramkumar, V., Hons, M., Punzón, C., Stein, J., Sancho, D., Fresno Forcelledo, M., & Cuesta, N. (2016). Efficient T-cell priming and activation requires signaling through prostaglandin E2 (EP) receptors. Immunology and Cell Biology. Nature Publishing Group. https://doi.org/10.1038/icb.2015.62"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1217","page":"39 - 51","date_created":"2018-12-11T11:50:46Z","date_published":"2016-01-01T00:00:00Z","doi":"10.1038/icb.2015.62","volume":94,"issue":"1","publication_status":"published","year":"2016","language":[{"iso":"eng"}],"publication":"Immunology and Cell Biology","day":"01","quality_controlled":"1","publisher":"Nature Publishing Group","scopus_import":1,"intvolume":" 94","month":"01","abstract":[{"lang":"eng","text":"Understanding the regulation of T-cell responses during inflammation and auto-immunity is fundamental for designing efficient therapeutic strategies against immune diseases. In this regard, prostaglandin E 2 (PGE 2) is mostly considered a myeloid-derived immunosuppressive molecule. We describe for the first time that T cells secrete PGE 2 during T-cell receptor stimulation. In addition, we show that autocrine PGE 2 signaling through EP receptors is essential for optimal CD4 + T-cell activation in vitro and in vivo, and for T helper 1 (Th1) and regulatory T cell differentiation. PGE 2 was found to provide additive co-stimulatory signaling through AKT activation. Intravital multiphoton microscopy showed that triggering EP receptors in T cells is also essential for the stability of T cell-dendritic cell (DC) interactions and Th-cell accumulation in draining lymph nodes (LNs) during inflammation. We further demonstrated that blocking EP receptors in T cells during the initial phase of collagen-induced arthritis in mice resulted in a reduction of clinical arthritis. This could be attributable to defective T-cell activation, accompanied by a decline in activated and interferon-γ-producing CD4 + Th1 cells in draining LNs. In conclusion, we prove that T lymphocytes secret picomolar concentrations of PGE 2, which in turn provide additive co-stimulatory signaling, enabling T cells to attain a favorable activation threshold. PGE 2 signaling in T cells is also required for maintaining long and stable interactions with DCs within LNs. Blockade of EP receptors in vivo impairs T-cell activation and development of T cell-mediated inflammatory responses. This may have implications in various pathophysiological settings."}],"acknowledgement":"This manuscript has been supported by grants SAF2007-61716 and S-SAL-0159/2006 awarded by the Spanish Ministry of Science and Education and the Community of Madrid to Dr M Fresno.","oa_version":"None"},{"publication":"Applied and Environmental Microbiology","day":"01","year":"2016","date_created":"2018-12-11T11:50:46Z","doi":"10.1128/AEM.00256-16","date_published":"2016-07-01T00:00:00Z","page":"4180 - 4189","acknowledgement":"Dutch Ministry of Economic Affairs, Agriculture, and Innovation through the program BioSolar CellsS. Andreas Angermayr,Pascal van Alphen, Klaas J. Hellingwerf\r\nWe thank Naira Quintana (presently at Rousselot, Belgium) for the ini-\r\ntiative at the 10th Cyanobacterial Molecular Biology Workshop\r\n(CMBW), June 2010, Lake Arrowhead, Los Angeles, CA, USA, to start the\r\ncollaborative endeavor reported here. We thank Timo Maarleveld from\r\nCWI/VU (Amsterdam) for a custom-made Python script handling the output from the NMR analysis and for evaluating and visualizing the\r\nseparate metabolites for their evaluation. We thank Rob Verpoorte from\r\nLeiden University (metabolome analysis) and Hans Aerts from the AMC\r\n(proteome analysis) for lab space and equipment. We thank Robert Leh-\r\nmann (Humboldt University Berlin) and Ilka Axmann (University of\r\nDüsseldorf) for sharing the R-code for the LOS transformation of the\r\ntranscript data. We thank Hans C. P. Matthijs from IBED for inspiring\r\ndialogues and insightful thoughts on continuous culturing of cyanobac-\r\nteria. We thank Sandra Waaijenborg for performing the transcript nor-\r\nmalization and Johan Westerhuis from BDA, Jeroen van der Steen and\r\nFilipe Branco dos Santos from MMP, and Lucas Stal from IBED/NIOZ for\r\nhelpful discussions. We thank Milou Schuurmans from MMP for help\r\nwith sampling and glycogen determination. We thank the members of the\r\nRNA Biology & Applied Bioinformatics group at SILS, in particular Selina\r\nvan Leeuwen, Elisa Hoekstra, and Martijs Jonker, for the microarray anal-\r\nysis. We thank the reviewers of this work for their insightful comments\r\nwhich improved the quality of the manuscript. This work, including the efforts of S. Andreas Angermayr, Pascal van\r\nAlphen, and Klaas J. Hellingwerf, was funded by Dutch Ministry of Eco-\r\nnomic Affairs, Agriculture, and Innovation through the program BioSolar\r\nCells.","oa":1,"quality_controlled":"1","publisher":"American Society for Microbiology","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Angermayr, Andreas, et al. “Culturing Synechocystis Sp. Strain Pcc 6803 with N2 and CO2 in a Diel Regime Reveals Multiphase Glycogen Dynamics with Low Maintenance Costs.” Applied and Environmental Microbiology, vol. 82, no. 14, American Society for Microbiology, 2016, pp. 4180–89, doi:10.1128/AEM.00256-16.","ama":"Angermayr A, Van Alphen P, Hasdemir D, et al. Culturing synechocystis sp. Strain pcc 6803 with N2 and CO2 in a diel regime reveals multiphase glycogen dynamics with low maintenance costs. Applied and Environmental Microbiology. 2016;82(14):4180-4189. doi:10.1128/AEM.00256-16","apa":"Angermayr, A., Van Alphen, P., Hasdemir, D., Kramer, G., Iqbal, M., Van Grondelle, W., … Hellingwerf, K. (2016). Culturing synechocystis sp. Strain pcc 6803 with N2 and CO2 in a diel regime reveals multiphase glycogen dynamics with low maintenance costs. Applied and Environmental Microbiology. American Society for Microbiology. https://doi.org/10.1128/AEM.00256-16","ieee":"A. Angermayr et al., “Culturing synechocystis sp. Strain pcc 6803 with N2 and CO2 in a diel regime reveals multiphase glycogen dynamics with low maintenance costs,” Applied and Environmental Microbiology, vol. 82, no. 14. American Society for Microbiology, pp. 4180–4189, 2016.","short":"A. Angermayr, P. Van Alphen, D. Hasdemir, G. Kramer, M. Iqbal, W. Van Grondelle, H. Hoefsloot, Y. Choi, K. Hellingwerf, Applied and Environmental Microbiology 82 (2016) 4180–4189.","chicago":"Angermayr, Andreas, Pascal Van Alphen, Dicle Hasdemir, Gertjan Kramer, Muzamal Iqbal, Wilmar Van Grondelle, Huub Hoefsloot, Younghae Choi, and Klaas Hellingwerf. “Culturing Synechocystis Sp. Strain Pcc 6803 with N2 and CO2 in a Diel Regime Reveals Multiphase Glycogen Dynamics with Low Maintenance Costs.” Applied and Environmental Microbiology. American Society for Microbiology, 2016. https://doi.org/10.1128/AEM.00256-16.","ista":"Angermayr A, Van Alphen P, Hasdemir D, Kramer G, Iqbal M, Van Grondelle W, Hoefsloot H, Choi Y, Hellingwerf K. 2016. Culturing synechocystis sp. Strain pcc 6803 with N2 and CO2 in a diel regime reveals multiphase glycogen dynamics with low maintenance costs. Applied and Environmental Microbiology. 82(14), 4180–4189."},"title":"Culturing synechocystis sp. Strain pcc 6803 with N2 and CO2 in a diel regime reveals multiphase glycogen dynamics with low maintenance costs","author":[{"first_name":"Andreas","id":"4677C796-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8619-2223","full_name":"Angermayr, Andreas","last_name":"Angermayr"},{"first_name":"Pascal","full_name":"Van Alphen, Pascal","last_name":"Van Alphen"},{"full_name":"Hasdemir, Dicle","last_name":"Hasdemir","first_name":"Dicle"},{"last_name":"Kramer","full_name":"Kramer, Gertjan","first_name":"Gertjan"},{"first_name":"Muzamal","full_name":"Iqbal, Muzamal","last_name":"Iqbal"},{"first_name":"Wilmar","full_name":"Van Grondelle, Wilmar","last_name":"Van Grondelle"},{"first_name":"Huub","last_name":"Hoefsloot","full_name":"Hoefsloot, Huub"},{"last_name":"Choi","full_name":"Choi, Younghae","first_name":"Younghae"},{"full_name":"Hellingwerf, Klaas","last_name":"Hellingwerf","first_name":"Klaas"}],"publist_id":"6117","language":[{"iso":"eng"}],"publication_status":"published","issue":"14","volume":82,"oa_version":"Submitted Version","abstract":[{"text":"Investigating the physiology of cyanobacteria cultured under a diel light regime is relevant for a better understanding of the resulting growth characteristics and for specific biotechnological applications that are foreseen for these photosynthetic organisms. Here, we present the results of a multiomics study of the model cyanobacterium Synechocystis sp. strain PCC 6803, cultured in a lab-scale photobioreactor in physiological conditions relevant for large-scale culturing. The culture was sparged withN2 andCO2, leading to an anoxic environment during the dark period. Growth followed the availability of light. Metabolite analysis performed with 1Hnuclear magnetic resonance analysis showed that amino acids involved in nitrogen and sulfur assimilation showed elevated levels in the light. Most protein levels, analyzed through mass spectrometry, remained rather stable. However, several high-light-response proteins and stress-response proteins showed distinct changes at the onset of the light period. Microarray-based transcript analysis found common patterns of~56% of the transcriptome following the diel regime. These oscillating transcripts could be grouped coarsely into genes that were upregulated and downregulated in the dark period. The accumulated glycogen was degraded in the anaerobic environment in the dark. A small part was degraded gradually, reflecting basic maintenance requirements of the cells in darkness. Surprisingly, the largest part was degraded rapidly in a short time span at the end of the dark period. This degradation could allow rapid formation of metabolic intermediates at the end of the dark period, preparing the cells for the resumption of growth at the start of the light period.","lang":"eng"}],"intvolume":" 82","month":"07","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959195/","open_access":"1"}],"scopus_import":1,"date_updated":"2021-01-12T06:49:10Z","department":[{"_id":"ToBo"}],"_id":"1218","status":"public","type":"journal_article"},{"date_updated":"2021-01-12T06:49:10Z","department":[{"_id":"LaEr"}],"_id":"1219","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":44,"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider N×N random matrices of the form H = W + V where W is a real symmetric or complex Hermitian Wigner matrix and V is a random or deterministic, real, diagonal matrix whose entries are independent of W. We assume subexponential decay for the matrix entries of W, and we choose V so that the eigenvalues ofW and V are typically of the same order. For a large class of diagonal matrices V , we show that the local statistics in the bulk of the spectrum are universal in the limit of large N."}],"month":"01","intvolume":" 44","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1405.6634","open_access":"1"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"J. Lee, K. Schnelli, B. Stetler, and H. Yau, “Bulk universality for deformed wigner matrices,” Annals of Probability, vol. 44, no. 3. Institute of Mathematical Statistics, pp. 2349–2425, 2016.","short":"J. Lee, K. Schnelli, B. Stetler, H. Yau, Annals of Probability 44 (2016) 2349–2425.","apa":"Lee, J., Schnelli, K., Stetler, B., & Yau, H. (2016). Bulk universality for deformed wigner matrices. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/15-AOP1023","ama":"Lee J, Schnelli K, Stetler B, Yau H. Bulk universality for deformed wigner matrices. Annals of Probability. 2016;44(3):2349-2425. doi:10.1214/15-AOP1023","mla":"Lee, Jioon, et al. “Bulk Universality for Deformed Wigner Matrices.” Annals of Probability, vol. 44, no. 3, Institute of Mathematical Statistics, 2016, pp. 2349–425, doi:10.1214/15-AOP1023.","ista":"Lee J, Schnelli K, Stetler B, Yau H. 2016. Bulk universality for deformed wigner matrices. Annals of Probability. 44(3), 2349–2425.","chicago":"Lee, Jioon, Kevin Schnelli, Ben Stetler, and Horngtzer Yau. “Bulk Universality for Deformed Wigner Matrices.” Annals of Probability. Institute of Mathematical Statistics, 2016. https://doi.org/10.1214/15-AOP1023."},"title":"Bulk universality for deformed wigner matrices","publist_id":"6115","author":[{"full_name":"Lee, Jioon","last_name":"Lee","first_name":"Jioon"},{"first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","last_name":"Schnelli"},{"last_name":"Stetler","full_name":"Stetler, Ben","first_name":"Ben"},{"full_name":"Yau, Horngtzer","last_name":"Yau","first_name":"Horngtzer"}],"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"day":"01","publication":"Annals of Probability","year":"2016","date_published":"2016-01-01T00:00:00Z","doi":"10.1214/15-AOP1023","date_created":"2018-12-11T11:50:47Z","page":"2349 - 2425","acknowledgement":"J.C. was supported in part by National Research Foundation of Korea Grant 2011-0013474 and TJ Park Junior Faculty Fellowship.\r\nK.S. was supported by ERC Advanced Grant RANMAT, No. 338804, and the \"Fund for Math.\"\r\nB.S. was supported by NSF GRFP Fellowship DGE-1144152.\r\nH.Y. was supported in part by NSF Grant DMS-13-07444 and Simons investigator fellowship. We thank Paul Bourgade, László Erd ̋os and Antti Knowles for helpful comments. We are grateful to the Taida Institute for Mathematical\r\nSciences and National Taiwan Universality for their hospitality during part of this\r\nresearch. We thank Thomas Spencer and the Institute for Advanced Study for their\r\nhospitality during the academic year 2013–2014. ","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","oa":1},{"oa_version":"Preprint","abstract":[{"text":"Theoretical and numerical aspects of aerodynamic efficiency of propulsion systems coupled to the boundary layer of a fuselage are studied. We discuss the effects of local flow fields, which are affected both by conservative flow acceleration as well as total pressure losses, on the efficiency of boundary layer immersed propulsion devices. We introduce the concept of a boundary layer retardation turbine that helps reduce skin friction over the fuselage. We numerically investigate efficiency gains offered by boundary layer and wake interacting devices. We discuss the results in terms of a total energy consumption framework and show that efficiency gains of any device depend on all the other elements of the propulsion system.","lang":"eng"}],"month":"06","publisher":"AIAA","scopus_import":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://ntrs.nasa.gov/search.jsp?R=20160010167&hterms=Fuselage+boundary+layer+ingestion+propulsion+applied+thin+haul+commuter+aircraft+optimal+efficiency&qs=N%3D0%26Ntk%3DAll%26Ntt%3DFuselage%2520boundary%2520layer%2520ingestion%2520propulsion%2520applied%2520to%2520a%2520thin%2520haul%2520commuter%2520aircraft%2520for%2520optimal%2520efficiency%26Ntx%3Dmode%2520matchallpartial%26Nm%3D123%7CCollection%7CNASA%2520STI%7C%7C17%7CCollection%7CNACA","open_access":"1"}],"day":"01","language":[{"iso":"eng"}],"publication_status":"published","year":"2016","doi":"10.2514/6.2016-3764","date_published":"2016-06-01T00:00:00Z","date_created":"2018-12-11T11:50:47Z","page":"1 - 19","_id":"1220","status":"public","type":"conference","conference":{"end_date":"2016-06-17","location":"Washington, D.C., USA","start_date":"2016-06-13","name":"AIAA: Aviation Technology, Integration, and Operations Conference"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Mikić G, Stoll A, Bevirt J, Grah R, Moore M. Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency. In: AIAA; 2016:1-19. doi:10.2514/6.2016-3764","apa":"Mikić, G., Stoll, A., Bevirt, J., Grah, R., & Moore, M. (2016). Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency (pp. 1–19). Presented at the AIAA: Aviation Technology, Integration, and Operations Conference, Washington, D.C., USA: AIAA. https://doi.org/10.2514/6.2016-3764","ieee":"G. Mikić, A. Stoll, J. Bevirt, R. Grah, and M. Moore, “Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency,” presented at the AIAA: Aviation Technology, Integration, and Operations Conference, Washington, D.C., USA, 2016, pp. 1–19.","short":"G. Mikić, A. Stoll, J. Bevirt, R. Grah, M. Moore, in:, AIAA, 2016, pp. 1–19.","mla":"Mikić, Gregor, et al. Fuselage Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for Optimal Efficiency. AIAA, 2016, pp. 1–19, doi:10.2514/6.2016-3764.","ista":"Mikić G, Stoll A, Bevirt J, Grah R, Moore M. 2016. Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency. AIAA: Aviation Technology, Integration, and Operations Conference, 1–19.","chicago":"Mikić, Gregor, Alex Stoll, Joe Bevirt, Rok Grah, and Mark Moore. “Fuselage Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for Optimal Efficiency,” 1–19. AIAA, 2016. https://doi.org/10.2514/6.2016-3764."},"date_updated":"2023-02-21T10:17:50Z","title":"Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"author":[{"first_name":"Gregor","last_name":"Mikić","full_name":"Mikić, Gregor"},{"first_name":"Alex","last_name":"Stoll","full_name":"Stoll, Alex"},{"first_name":"Joe","full_name":"Bevirt, Joe","last_name":"Bevirt"},{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah"},{"full_name":"Moore, Mark","last_name":"Moore","first_name":"Mark"}],"publist_id":"6114"},{"volume":5,"ec_funded":1,"publication_status":"published","file":[{"creator":"system","file_size":2990459,"date_updated":"2020-07-14T12:44:39Z","file_name":"IST-2016-711-v1+1_770cf1e0-612f-4e85-a500-54b6349fbbab_7654_-_jaroslav_michalko.pdf","date_created":"2018-12-12T10:15:33Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5154","checksum":"c9e50bb6096a7ba4a832969935820f19"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 5","abstract":[{"lang":"eng","text":"The Auxin Binding Protein 1 (ABP1) is one of the most studied proteins in plants. Since decades ago, it has been the prime receptor candidate for the plant hormone auxin with a plethora of described functions in auxin signaling and development. The developmental importance of ABP1 has recently been questioned by identification of Arabidopsis thaliana abp1 knock-out alleles that show no obvious phenotypes under normal growth conditions. In this study, we examined the contradiction between the normal growth and development of the abp1 knock-outs and the strong morphological defects observed in three different ethanol-inducible abp1 knock-down mutants ( abp1-AS, SS12K, SS12S). By analyzing segregating populations of abp1 knock-out vs. abp1 knock-down crosses we show that the strong morphological defects that were believed to be the result of conditional down-regulation of ABP1 can be reproduced also in the absence of the functional ABP1 protein. This data suggests that the phenotypes in abp1 knock-down lines are due to the off-target effects and asks for further reflections on the biological function of ABP1 or alternative explanations for the missing phenotypic defects in the abp1 loss-of-function alleles."}],"oa_version":"Published Version","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:39Z","date_updated":"2022-03-24T09:12:49Z","ddc":["581"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"711","_id":"1221","date_published":"2016-01-20T00:00:00Z","doi":"10.12688/f1000research.7654.1","date_created":"2018-12-11T11:50:47Z","has_accepted_license":"1","year":"2016","day":"20","publication":"F1000 Research ","publisher":"F1000 Research","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG-20101109-PSDP to JF). JM internship was supported by the grant “Action Austria – Slovakia”. MG was supported by the scholarship \"Stipendien der Stipendienstiftung der Republik Österreich\". Work by EH and CPR were supported by ANR blanc ANR-14-CE11-0018. We would like to thank Mark Estelle and Yunde Zhao for provid\r\n-\r\ning \r\nabp1-c1\r\n, \r\nabp1-TD1 \r\nand \r\nabp1-WTc1 \r\nseeds. We thank Emeline \r\nHuault for technical assistance.","author":[{"first_name":"Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","last_name":"Michalko","full_name":"Michalko, Jaroslav"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783"},{"first_name":"Catherine","full_name":"Perrot Rechenmann, Catherine","last_name":"Perrot Rechenmann"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"publist_id":"6113","article_processing_charge":"No","title":"Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein","citation":{"ista":"Michalko J, Glanc M, Perrot Rechenmann C, Friml J. 2016. Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein. F1000 Research . 5, 86.","chicago":"Michalko, Jaroslav, Matous Glanc, Catherine Perrot Rechenmann, and Jiří Friml. “Strong Morphological Defects in Conditional Arabidopsis Abp1 Knock-down Mutants Generated in Absence of Functional ABP1 Protein.” F1000 Research . F1000 Research, 2016. https://doi.org/10.12688/f1000research.7654.1.","short":"J. Michalko, M. Glanc, C. Perrot Rechenmann, J. Friml, F1000 Research 5 (2016).","ieee":"J. Michalko, M. Glanc, C. Perrot Rechenmann, and J. Friml, “Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein,” F1000 Research , vol. 5. F1000 Research, 2016.","apa":"Michalko, J., Glanc, M., Perrot Rechenmann, C., & Friml, J. (2016). Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein. F1000 Research . F1000 Research. https://doi.org/10.12688/f1000research.7654.1","ama":"Michalko J, Glanc M, Perrot Rechenmann C, Friml J. Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein. F1000 Research . 2016;5. doi:10.12688/f1000research.7654.1","mla":"Michalko, Jaroslav, et al. “Strong Morphological Defects in Conditional Arabidopsis Abp1 Knock-down Mutants Generated in Absence of Functional ABP1 Protein.” F1000 Research , vol. 5, 86, F1000 Research, 2016, doi:10.12688/f1000research.7654.1."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"article_number":"86"},{"acknowledgement":"We wish to thank Alexey Tarasov, Vladislav Volkov and Brittany Fasy for some useful comments and remarks, and especially Thom Sulanke for modifying surftri to suit our purposes. Oleg R. Musin was partially supported by the NSF Grant DMS-1400876 and by the RFBR Grant 15-01-99563. Anton V. Nikitenko was supported by the Chebyshev Laboratory (Department of Mathematics and Mechanics, St. Petersburg State University) under RF Government Grant 11.G34.31.0026.","oa":1,"publisher":"Springer","quality_controlled":"1","year":"2016","publication":"Discrete & Computational Geometry","day":"01","page":"1 - 20","date_created":"2018-12-11T11:50:48Z","date_published":"2016-01-01T00:00:00Z","doi":"10.1007/s00454-015-9742-6","citation":{"ieee":"O. Musin and A. Nikitenko, “Optimal packings of congruent circles on a square flat torus,” Discrete & Computational Geometry, vol. 55, no. 1. Springer, pp. 1–20, 2016.","short":"O. Musin, A. Nikitenko, Discrete & Computational Geometry 55 (2016) 1–20.","ama":"Musin O, Nikitenko A. Optimal packings of congruent circles on a square flat torus. Discrete & Computational Geometry. 2016;55(1):1-20. doi:10.1007/s00454-015-9742-6","apa":"Musin, O., & Nikitenko, A. (2016). Optimal packings of congruent circles on a square flat torus. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-015-9742-6","mla":"Musin, Oleg, and Anton Nikitenko. “Optimal Packings of Congruent Circles on a Square Flat Torus.” Discrete & Computational Geometry, vol. 55, no. 1, Springer, 2016, pp. 1–20, doi:10.1007/s00454-015-9742-6.","ista":"Musin O, Nikitenko A. 2016. Optimal packings of congruent circles on a square flat torus. Discrete & Computational Geometry. 55(1), 1–20.","chicago":"Musin, Oleg, and Anton Nikitenko. “Optimal Packings of Congruent Circles on a Square Flat Torus.” Discrete & Computational Geometry. Springer, 2016. https://doi.org/10.1007/s00454-015-9742-6."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6111","author":[{"full_name":"Musin, Oleg","last_name":"Musin","first_name":"Oleg"},{"full_name":"Nikitenko, Anton","last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","first_name":"Anton"}],"title":"Optimal packings of congruent circles on a square flat torus","abstract":[{"text":"We consider packings of congruent circles on a square flat torus, i.e., periodic (w.r.t. a square lattice) planar circle packings, with the maximal circle radius. This problem is interesting due to a practical reason—the problem of “super resolution of images.” We have found optimal arrangements for N=6, 7 and 8 circles. Surprisingly, for the case N=7 there are three different optimal arrangements. Our proof is based on a computer enumeration of toroidal irreducible contact graphs.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1212.0649","open_access":"1"}],"scopus_import":1,"intvolume":" 55","month":"01","publication_status":"published","language":[{"iso":"eng"}],"issue":"1","volume":55,"_id":"1222","type":"journal_article","status":"public","date_updated":"2021-01-12T06:49:11Z","department":[{"_id":"HeEd"}]},{"citation":{"chicago":"Froese, Richard, Darrick Lee, Christian Sadel, Wolfgang Spitzer, and Günter Stolz. “Localization for Transversally Periodic Random Potentials on Binary Trees.” Journal of Spectral Theory. European Mathematical Society, 2016. https://doi.org/10.4171/JST/132.","ista":"Froese R, Lee D, Sadel C, Spitzer W, Stolz G. 2016. Localization for transversally periodic random potentials on binary trees. Journal of Spectral Theory. 6(3), 557–600.","mla":"Froese, Richard, et al. “Localization for Transversally Periodic Random Potentials on Binary Trees.” Journal of Spectral Theory, vol. 6, no. 3, European Mathematical Society, 2016, pp. 557–600, doi:10.4171/JST/132.","ama":"Froese R, Lee D, Sadel C, Spitzer W, Stolz G. Localization for transversally periodic random potentials on binary trees. Journal of Spectral Theory. 2016;6(3):557-600. doi:10.4171/JST/132","apa":"Froese, R., Lee, D., Sadel, C., Spitzer, W., & Stolz, G. (2016). Localization for transversally periodic random potentials on binary trees. Journal of Spectral Theory. European Mathematical Society. https://doi.org/10.4171/JST/132","ieee":"R. Froese, D. Lee, C. Sadel, W. Spitzer, and G. Stolz, “Localization for transversally periodic random potentials on binary trees,” Journal of Spectral Theory, vol. 6, no. 3. European Mathematical Society, pp. 557–600, 2016.","short":"R. Froese, D. Lee, C. Sadel, W. Spitzer, G. Stolz, Journal of Spectral Theory 6 (2016) 557–600."},"date_updated":"2021-01-12T06:49:12Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6112","author":[{"full_name":"Froese, Richard","last_name":"Froese","first_name":"Richard"},{"first_name":"Darrick","full_name":"Lee, Darrick","last_name":"Lee"},{"first_name":"Christian","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","last_name":"Sadel","full_name":"Sadel, Christian","orcid":"0000-0001-8255-3968"},{"full_name":"Spitzer, Wolfgang","last_name":"Spitzer","first_name":"Wolfgang"},{"full_name":"Stolz, Günter","last_name":"Stolz","first_name":"Günter"}],"title":"Localization for transversally periodic random potentials on binary trees","department":[{"_id":"LaEr"}],"_id":"1223","type":"journal_article","status":"public","year":"2016","publication_status":"published","publication":"Journal of Spectral Theory","language":[{"iso":"eng"}],"day":"01","page":"557 - 600","date_created":"2018-12-11T11:50:48Z","doi":"10.4171/JST/132","date_published":"2016-01-01T00:00:00Z","issue":"3","volume":6,"abstract":[{"lang":"eng","text":"We consider a random Schrödinger operator on the binary tree with a random potential which is the sum of a random radially symmetric potential, Qr, and a random transversally periodic potential, κQt, with coupling constant κ. Using a new one-dimensional dynamical systems approach combined with Jensen's inequality in hyperbolic space (our key estimate) we obtain a fractional moment estimate proving localization for small and large κ. Together with a previous result we therefore obtain a model with two Anderson transitions, from localization to delocalization and back to localization, when increasing κ. As a by-product we also have a partially new proof of one-dimensional Anderson localization at any disorder."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1408.3961","open_access":"1"}],"oa":1,"quality_controlled":"1","scopus_import":1,"publisher":"European Mathematical Society","intvolume":" 6","month":"01"},{"department":[{"_id":"NiBa"}],"title":"The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant","publist_id":"6110","author":[{"first_name":"Zachary","last_name":"Teitel","full_name":"Teitel, Zachary"},{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field"},{"first_name":"Spencer","full_name":"Barrett, Spencer","last_name":"Barrett"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Teitel, Z., Pickup, M., Field, D., & Barrett, S. (2016). The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. Plant Biology. Wiley-Blackwell. https://doi.org/10.1111/plb.12336","ama":"Teitel Z, Pickup M, Field D, Barrett S. The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. Plant Biology. 2016;18(1):98-103. doi:10.1111/plb.12336","short":"Z. Teitel, M. Pickup, D. Field, S. Barrett, Plant Biology 18 (2016) 98–103.","ieee":"Z. Teitel, M. Pickup, D. Field, and S. Barrett, “The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant,” Plant Biology, vol. 18, no. 1. Wiley-Blackwell, pp. 98–103, 2016.","mla":"Teitel, Zachary, et al. “The Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” Plant Biology, vol. 18, no. 1, Wiley-Blackwell, 2016, pp. 98–103, doi:10.1111/plb.12336.","ista":"Teitel Z, Pickup M, Field D, Barrett S. 2016. The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. Plant Biology. 18(1), 98–103.","chicago":"Teitel, Zachary, Melinda Pickup, David Field, and Spencer Barrett. “The Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” Plant Biology. Wiley-Blackwell, 2016. https://doi.org/10.1111/plb.12336."},"date_updated":"2021-01-12T06:49:12Z","status":"public","type":"journal_article","_id":"1224","date_created":"2018-12-11T11:50:48Z","issue":"1","date_published":"2016-01-01T00:00:00Z","doi":"10.1111/plb.12336","volume":18,"page":"98 - 103","language":[{"iso":"eng"}],"publication":"Plant Biology","day":"01","year":"2016","publication_status":"published","intvolume":" 18","month":"01","publisher":"Wiley-Blackwell","quality_controlled":"1","scopus_import":1,"oa_version":"None","abstract":[{"text":"Sexual dimorphism in resource allocation is expected to change during the life cycle of dioecious plants because of temporal differences between the sexes in reproductive investment. Given the potential for sex-specific differences in reproductive costs, resource availability may contribute to variation in reproductive allocation in females and males. Here, we used Rumex hastatulus, a dioecious, wind-pollinated annual plant, to investigate whether sexual dimorphism varies with life-history stage and nutrient availability, and determine whether allocation patterns differ depending on reproductive commitment. To examine if the costs of reproduction varied between the sexes, reproduction was either allowed or prevented through bud removal, and biomass allocation was measured at maturity. In a second experiment to assess variation in sexual dimorphism across the life cycle, and whether this varied with resource availability, plants were grown in high and low nutrients and allocation to roots, aboveground vegetative growth and reproduction were measured at three developmental stages. Males prevented from reproducing compensated with increased above- and belowground allocation to a much larger degree than females, suggesting that male reproductive costs reduce vegetative growth. The proportional allocation to roots, reproductive structures and aboveground vegetative growth varied between the sexes and among life-cycle stages, but not with nutrient treatment. Females allocated proportionally more resources to roots than males at peak flowering, but this pattern was reversed at reproductive maturity under low-nutrient conditions. Our study illustrates the importance of temporal dynamics in sex-specific resource allocation and provides support for high male reproductive costs in wind-pollinated plants.","lang":"eng"}]},{"department":[{"_id":"LeSa"}],"date_updated":"2021-01-12T06:49:13Z","status":"public","type":"journal_article","article_type":"original","_id":"1226","issue":"7625","volume":538,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 538","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5164932/","open_access":"1"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) contributes to cellular energy production by transferring electrons from NADH to ubiquinone coupled to proton translocation across the membrane. It is the largest protein assembly of the respiratory chain with a total mass of 970 kilodaltons. Here we present a nearly complete atomic structure of ovine (Ovis aries) mitochondrial complex I at 3.9 Å resolution, solved by cryo-electron microscopy with cross-linking and mass-spectrometry mapping experiments. All 14 conserved core subunits and 31 mitochondria-specific supernumerary subunits are resolved within the L-shaped molecule. The hydrophilic matrix arm comprises flavin mononucleotide and 8 iron-sulfur clusters involved in electron transfer, and the membrane arm contains 78 transmembrane helices, mostly contributed by antiporter-like subunits involved in proton translocation. Supernumerary subunits form an interlinked, stabilizing shell around the conserved core. Tightly bound lipids (including cardiolipins) further stabilize interactions between the hydrophobic subunits. Subunits with possible regulatory roles contain additional cofactors, NADPH and two phosphopantetheine molecules, which are shown to be involved in inter-subunit interactions. We observe two different conformations of the complex, which may be related to the conformationally driven coupling mechanism and to the active-deactive transition of the enzyme. Our structure provides insight into the mechanism, assembly, maturation and dysfunction of mitochondrial complex I, and allows detailed molecular analysis of disease-causing mutations.","lang":"eng"}],"title":"Atomic structure of the entire mammalian mitochondrial complex i","author":[{"last_name":"Fiedorczuk","full_name":"Fiedorczuk, Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","first_name":"Karol"},{"first_name":"James A","id":"322DA418-F248-11E8-B48F-1D18A9856A87","last_name":"Letts","orcid":"0000-0002-9864-3586","full_name":"Letts, James A"},{"first_name":"Gianluca","last_name":"Degliesposti","full_name":"Degliesposti, Gianluca"},{"id":"3FDF9472-F248-11E8-B48F-1D18A9856A87","first_name":"Karol","last_name":"Kaszuba","full_name":"Kaszuba, Karol"},{"first_name":"Mark","last_name":"Skehel","full_name":"Skehel, Mark"},{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"}],"publist_id":"6108","external_id":{"pmid":["27595392"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Fiedorczuk, Karol, et al. “Atomic Structure of the Entire Mammalian Mitochondrial Complex I.” Nature, vol. 538, no. 7625, Nature Publishing Group, 2016, pp. 406–10, doi:10.1038/nature19794.","apa":"Fiedorczuk, K., Letts, J. A., Degliesposti, G., Kaszuba, K., Skehel, M., & Sazanov, L. A. (2016). Atomic structure of the entire mammalian mitochondrial complex i. Nature. Nature Publishing Group. https://doi.org/10.1038/nature19794","ama":"Fiedorczuk K, Letts JA, Degliesposti G, Kaszuba K, Skehel M, Sazanov LA. Atomic structure of the entire mammalian mitochondrial complex i. Nature. 2016;538(7625):406-410. doi:10.1038/nature19794","ieee":"K. Fiedorczuk, J. A. Letts, G. Degliesposti, K. Kaszuba, M. Skehel, and L. A. Sazanov, “Atomic structure of the entire mammalian mitochondrial complex i,” Nature, vol. 538, no. 7625. Nature Publishing Group, pp. 406–410, 2016.","short":"K. Fiedorczuk, J.A. Letts, G. Degliesposti, K. Kaszuba, M. Skehel, L.A. Sazanov, Nature 538 (2016) 406–410.","chicago":"Fiedorczuk, Karol, James A Letts, Gianluca Degliesposti, Karol Kaszuba, Mark Skehel, and Leonid A Sazanov. “Atomic Structure of the Entire Mammalian Mitochondrial Complex I.” Nature. Nature Publishing Group, 2016. https://doi.org/10.1038/nature19794.","ista":"Fiedorczuk K, Letts JA, Degliesposti G, Kaszuba K, Skehel M, Sazanov LA. 2016. Atomic structure of the entire mammalian mitochondrial complex i. Nature. 538(7625), 406–410."},"project":[{"name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (FEBS)","_id":"2593EBD6-B435-11E9-9278-68D0E5697425"},{"_id":"2590DB08-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","grant_number":"701309"}],"doi":"10.1038/nature19794","date_published":"2016-10-20T00:00:00Z","date_created":"2018-12-11T11:50:49Z","page":"406 - 410","day":"20","publication":"Nature","year":"2016","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1},{"month":"09","intvolume":" 9957","scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"text":"Many biological systems can be modeled as multiaffine hybrid systems. Due to the nonlinearity of multiaffine systems, it is difficult to verify their properties of interest directly. A common strategy to tackle this problem is to construct and analyze a discrete overapproximation of the original system. However, the conservativeness of a discrete abstraction significantly determines the level of confidence we can have in the properties of the original system. In this paper, in order to reduce the conservativeness of a discrete abstraction, we propose a new method based on a sufficient and necessary decision condition for computing discrete transitions between states in the abstract system. We assume the state space partition of a multiaffine system to be based on a set of multivariate polynomials. Hence, a rectangular partition defined in terms of polynomials of the form (xi − c) is just a simple case of multivariate polynomial partition, and the new decision condition applies naturally. We analyze and demonstrate the improvement of our method over the existing methods using some examples.","lang":"eng"}],"volume":9957,"file":[{"file_name":"IST-2017-781-v1+1_main.pdf","date_created":"2018-12-12T10:10:49Z","file_size":683955,"date_updated":"2020-07-14T12:44:39Z","creator":"system","file_id":"4840","checksum":"994e164b558c47bacf8dc066dd27c8fc","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"781","type":"conference","conference":{"name":"HSB: Hybrid Systems Biology","start_date":"2016-10-20","end_date":"2016-10-21","location":"Grenoble, France"},"_id":"1227","file_date_updated":"2020-07-14T12:44:39Z","department":[{"_id":"ToHe"}],"ddc":["005"],"date_updated":"2021-01-12T06:49:13Z","quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","date_published":"2016-09-25T00:00:00Z","doi":"10.1007/978-3-319-47151-8_9","date_created":"2018-12-11T11:50:49Z","page":"128 - 144","day":"25","has_accepted_license":"1","year":"2016","project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"title":"Discrete abstraction of multiaffine systems","publist_id":"6107","author":[{"id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui","last_name":"Kong","orcid":"0000-0002-3066-6941","full_name":"Kong, Hui"},{"first_name":"Ezio","full_name":"Bartocci, Ezio","last_name":"Bartocci"},{"orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy"},{"last_name":"Grosu","full_name":"Grosu, Radu","first_name":"Radu"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Jiang, Yu","last_name":"Jiang","first_name":"Yu"},{"last_name":"Schilling","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Kong H, Bartocci E, Bogomolov S, et al. Discrete abstraction of multiaffine systems. In: Vol 9957. Springer; 2016:128-144. doi:10.1007/978-3-319-47151-8_9","apa":"Kong, H., Bartocci, E., Bogomolov, S., Grosu, R., Henzinger, T. A., Jiang, Y., & Schilling, C. (2016). Discrete abstraction of multiaffine systems (Vol. 9957, pp. 128–144). Presented at the HSB: Hybrid Systems Biology, Grenoble, France: Springer. https://doi.org/10.1007/978-3-319-47151-8_9","short":"H. Kong, E. Bartocci, S. Bogomolov, R. Grosu, T.A. Henzinger, Y. Jiang, C. Schilling, in:, Springer, 2016, pp. 128–144.","ieee":"H. Kong et al., “Discrete abstraction of multiaffine systems,” presented at the HSB: Hybrid Systems Biology, Grenoble, France, 2016, vol. 9957, pp. 128–144.","mla":"Kong, Hui, et al. Discrete Abstraction of Multiaffine Systems. Vol. 9957, Springer, 2016, pp. 128–44, doi:10.1007/978-3-319-47151-8_9.","ista":"Kong H, Bartocci E, Bogomolov S, Grosu R, Henzinger TA, Jiang Y, Schilling C. 2016. Discrete abstraction of multiaffine systems. HSB: Hybrid Systems Biology, LNCS, vol. 9957, 128–144.","chicago":"Kong, Hui, Ezio Bartocci, Sergiy Bogomolov, Radu Grosu, Thomas A Henzinger, Yu Jiang, and Christian Schilling. “Discrete Abstraction of Multiaffine Systems,” 9957:128–44. Springer, 2016. https://doi.org/10.1007/978-3-319-47151-8_9."}},{"scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/100"}],"month":"04","intvolume":" 9666","abstract":[{"text":"We study the time-and memory-complexities of the problem of computing labels of (multiple) randomly selected challenge-nodes in a directed acyclic graph. The w-bit label of a node is the hash of the labels of its parents, and the hash function is modeled as a random oracle. Specific instances of this problem underlie both proofs of space [Dziembowski et al. CRYPTO’15] as well as popular memory-hard functions like scrypt. As our main tool, we introduce the new notion of a probabilistic parallel entangled pebbling game, a new type of combinatorial pebbling game on a graph, which is closely related to the labeling game on the same graph. As a first application of our framework, we prove that for scrypt, when the underlying hash function is invoked n times, the cumulative memory complexity (CMC) (a notion recently introduced by Alwen and Serbinenko (STOC’15) to capture amortized memory-hardness for parallel adversaries) is at least Ω(w · (n/ log(n))2). This bound holds for adversaries that can store many natural functions of the labels (e.g., linear combinations), but still not arbitrary functions thereof. We then introduce and study a combinatorial quantity, and show how a sufficiently small upper bound on it (which we conjecture) extends our CMC bound for scrypt to hold against arbitrary adversaries. We also show that such an upper bound solves the main open problem for proofs-of-space protocols: namely, establishing that the time complexity of computing the label of a random node in a graph on n nodes (given an initial kw-bit state) reduces tightly to the time complexity for black pebbling on the same graph (given an initial k-node pebbling).","lang":"eng"}],"oa_version":"Submitted Version","volume":9666,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"start_date":"2016-05-08","end_date":"2016-05-12","location":"Vienna, Austria","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"status":"public","_id":"1231","department":[{"_id":"KrPi"},{"_id":"VlKo"}],"date_updated":"2021-01-12T06:49:15Z","quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"Joël Alwen, Chethan Kamath, and Krzysztof Pietrzak’s research is partially supported by an ERC starting grant (259668-PSPC). Vladimir Kolmogorov is partially supported by an ERC consolidator grant (616160-DOICV). Binyi Chen was partially supported by NSF grants CNS-1423566 and CNS-1514526, and a gift from the Gareatis Foundation. Stefano Tessaro was partially supported by NSF grants CNS-1423566, CNS-1528178, a Hellman Fellowship, and the Glen and Susanne Culler Chair.\r\n\r\nThis work was done in part while the authors were visiting the Simons Institute for the Theory of Computing, supported by the Simons Foundation and by the DIMACS/Simons Collaboration in Cryptography through NSF grant CNS-1523467.","page":"358 - 387","doi":"10.1007/978-3-662-49896-5_13","date_published":"2016-04-28T00:00:00Z","date_created":"2018-12-11T11:50:51Z","year":"2016","day":"28","project":[{"name":"Provable Security for Physical Cryptography","grant_number":"259668","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425"},{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"publist_id":"6103","author":[{"last_name":"Alwen","full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F"},{"last_name":"Chen","full_name":"Chen, Binyi","first_name":"Binyi"},{"last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan"},{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"first_name":"Stefano","last_name":"Tessaro","full_name":"Tessaro, Stefano"}],"title":"On the complexity of scrypt and proofs of space in the parallel random oracle model","citation":{"chicago":"Alwen, Joel F, Binyi Chen, Chethan Kamath Hosdurg, Vladimir Kolmogorov, Krzysztof Z Pietrzak, and Stefano Tessaro. “On the Complexity of Scrypt and Proofs of Space in the Parallel Random Oracle Model,” 9666:358–87. Springer, 2016. https://doi.org/10.1007/978-3-662-49896-5_13.","ista":"Alwen JF, Chen B, Kamath Hosdurg C, Kolmogorov V, Pietrzak KZ, Tessaro S. 2016. On the complexity of scrypt and proofs of space in the parallel random oracle model. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 9666, 358–387.","mla":"Alwen, Joel F., et al. On the Complexity of Scrypt and Proofs of Space in the Parallel Random Oracle Model. Vol. 9666, Springer, 2016, pp. 358–87, doi:10.1007/978-3-662-49896-5_13.","ama":"Alwen JF, Chen B, Kamath Hosdurg C, Kolmogorov V, Pietrzak KZ, Tessaro S. On the complexity of scrypt and proofs of space in the parallel random oracle model. In: Vol 9666. Springer; 2016:358-387. doi:10.1007/978-3-662-49896-5_13","apa":"Alwen, J. F., Chen, B., Kamath Hosdurg, C., Kolmogorov, V., Pietrzak, K. Z., & Tessaro, S. (2016). On the complexity of scrypt and proofs of space in the parallel random oracle model (Vol. 9666, pp. 358–387). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-662-49896-5_13","short":"J.F. Alwen, B. Chen, C. Kamath Hosdurg, V. Kolmogorov, K.Z. Pietrzak, S. Tessaro, in:, Springer, 2016, pp. 358–387.","ieee":"J. F. Alwen, B. Chen, C. Kamath Hosdurg, V. Kolmogorov, K. Z. Pietrzak, and S. Tessaro, “On the complexity of scrypt and proofs of space in the parallel random oracle model,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria, 2016, vol. 9666, pp. 358–387."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","status":"public","project":[{"_id":"2593EBD6-B435-11E9-9278-68D0E5697425","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (FEBS)"}],"_id":"1232","publist_id":"6102","author":[{"orcid":"0000-0002-9864-3586","full_name":"Letts, James A","last_name":"Letts","first_name":"James A","id":"322DA418-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fiedorczuk","full_name":"Fiedorczuk, Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","first_name":"Karol"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"title":"The architecture of respiratory supercomplexes","department":[{"_id":"LeSa"}],"citation":{"chicago":"Letts, James A, Karol Fiedorczuk, and Leonid A Sazanov. “The Architecture of Respiratory Supercomplexes.” Nature. Nature Publishing Group, 2016. https://doi.org/10.1038/nature19774.","ista":"Letts JA, Fiedorczuk K, Sazanov LA. 2016. The architecture of respiratory supercomplexes. Nature. 537(7622), 644–648.","mla":"Letts, James A., et al. “The Architecture of Respiratory Supercomplexes.” Nature, vol. 537, no. 7622, Nature Publishing Group, 2016, pp. 644–48, doi:10.1038/nature19774.","apa":"Letts, J. A., Fiedorczuk, K., & Sazanov, L. A. (2016). The architecture of respiratory supercomplexes. Nature. Nature Publishing Group. https://doi.org/10.1038/nature19774","ama":"Letts JA, Fiedorczuk K, Sazanov LA. The architecture of respiratory supercomplexes. Nature. 2016;537(7622):644-648. doi:10.1038/nature19774","short":"J.A. Letts, K. Fiedorczuk, L.A. Sazanov, Nature 537 (2016) 644–648.","ieee":"J. A. Letts, K. Fiedorczuk, and L. A. Sazanov, “The architecture of respiratory supercomplexes,” Nature, vol. 537, no. 7622. Nature Publishing Group, pp. 644–648, 2016."},"date_updated":"2021-01-12T06:49:16Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Nature Publishing Group","scopus_import":1,"month":"09","intvolume":" 537","abstract":[{"text":"Mitochondrial electron transport chain complexes are organized into supercomplexes responsible for carrying out cellular respiration. Here we present three architectures of mammalian (ovine) supercomplexes determined by cryo-electron microscopy. We identify two distinct arrangements of supercomplex CICIII 2 CIV (the respirasome) - a major 'tight' form and a minor 'loose' form (resolved at the resolution of 5.8 Å and 6.7 Å, respectively), which may represent different stages in supercomplex assembly or disassembly. We have also determined an architecture of supercomplex CICIII 2 at 7.8 Å resolution. All observed density can be attributed to the known 80 subunits of the individual complexes, including 132 transmembrane helices. The individual complexes form tight interactions that vary between the architectures, with complex IV subunit COX7a switching contact from complex III to complex I. The arrangement of active sites within the supercomplex may help control reactive oxygen species production. To our knowledge, these are the first complete architectures of the dominant, physiologically relevant state of the electron transport chain.","lang":"eng"}],"oa_version":"None","acknowledgement":"We thank the MRC LMB Cambridge for the use of the Titan Krios microscope. Data processing was performed using the IST high-performance computer cluster. J.A.L. holds a long-term fellowship from FEBS. K.F. is partially funded by a MRC UK PhD fellowship.","page":"644 - 648","issue":"7622","doi":"10.1038/nature19774","volume":537,"date_published":"2016-09-29T00:00:00Z","date_created":"2018-12-11T11:50:51Z","year":"2016","publication_status":"published","day":"29","publication":"Nature","language":[{"iso":"eng"}]},{"day":"01","year":"2016","date_created":"2018-12-11T11:50:51Z","doi":"10.1007/978-3-662-49096-9_12","date_published":"2016-01-01T00:00:00Z","page":"282 - 305","acknowledgement":"G. Fuchsbauer and K. Pietrzak are supported by the European Research Council, ERC Starting Grant (259668-PSPC). F. Heuer is funded by a Sofja Kovalevskaja Award of the Alexander von Humboldt Foundation and DFG SPP 1736, Algorithms for BIG DATA. E. Kiltz is supported by a Sofja Kovalevskaja Award of the Alexander von Humboldt Foundation, the German Israel Foundation, and ERC Project ERCC (FP7/615074).","oa":1,"quality_controlled":"1","publisher":"Springer","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Fuchsbauer, Georg, Felix Heuer, Eike Kiltz, and Krzysztof Z Pietrzak. “Standard Security Does Imply Security against Selective Opening for Markov Distributions,” 9562:282–305. Springer, 2016. https://doi.org/10.1007/978-3-662-49096-9_12.","ista":"Fuchsbauer G, Heuer F, Kiltz E, Pietrzak KZ. 2016. Standard security does imply security against selective opening for markov distributions. TCC: Theory of Cryptography Conference, LNCS, vol. 9562, 282–305.","mla":"Fuchsbauer, Georg, et al. Standard Security Does Imply Security against Selective Opening for Markov Distributions. Vol. 9562, Springer, 2016, pp. 282–305, doi:10.1007/978-3-662-49096-9_12.","ama":"Fuchsbauer G, Heuer F, Kiltz E, Pietrzak KZ. Standard security does imply security against selective opening for markov distributions. In: Vol 9562. Springer; 2016:282-305. doi:10.1007/978-3-662-49096-9_12","apa":"Fuchsbauer, G., Heuer, F., Kiltz, E., & Pietrzak, K. Z. (2016). Standard security does imply security against selective opening for markov distributions (Vol. 9562, pp. 282–305). Presented at the TCC: Theory of Cryptography Conference, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-662-49096-9_12","ieee":"G. Fuchsbauer, F. Heuer, E. Kiltz, and K. Z. Pietrzak, “Standard security does imply security against selective opening for markov distributions,” presented at the TCC: Theory of Cryptography Conference, Tel Aviv, Israel, 2016, vol. 9562, pp. 282–305.","short":"G. Fuchsbauer, F. Heuer, E. Kiltz, K.Z. Pietrzak, in:, Springer, 2016, pp. 282–305."},"title":"Standard security does imply security against selective opening for markov distributions","publist_id":"6100","author":[{"last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Felix","last_name":"Heuer","full_name":"Heuer, Felix"},{"first_name":"Eike","last_name":"Kiltz","full_name":"Kiltz, Eike"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"project":[{"call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","grant_number":"259668"}],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":9562,"oa_version":"Submitted Version","abstract":[{"text":"About three decades ago it was realized that implementing private channels between parties which can be adaptively corrupted requires an encryption scheme that is secure against selective opening attacks. Whether standard (IND-CPA) security implies security against selective opening attacks has been a major open question since. The only known reduction from selective opening to IND-CPA security loses an exponential factor. A polynomial reduction is only known for the very special case where the distribution considered in the selective opening security experiment is a product distribution, i.e., the messages are sampled independently from each other. In this paper we give a reduction whose loss is quantified via the dependence graph (where message dependencies correspond to edges) of the underlying message distribution. In particular, for some concrete distributions including Markov distributions, our reduction is polynomial.","lang":"eng"}],"intvolume":" 9562","month":"01","main_file_link":[{"url":"https://eprint.iacr.org/2015/853","open_access":"1"}],"scopus_import":1,"alternative_title":["LNCS"],"date_updated":"2021-01-12T06:49:16Z","department":[{"_id":"KrPi"}],"_id":"1233","status":"public","conference":{"start_date":"2016-01-10","end_date":"2016-01-13","location":"Tel Aviv, Israel","name":"TCC: Theory of Cryptography Conference"},"type":"conference"},{"article_number":"1262","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"von Wangenheim D, Rosero A, Komis G, et al. Endosomal interactions during root hair growth. Frontiers in Plant Science. 2016;6(JAN2016). doi:10.3389/fpls.2015.01262","apa":"von Wangenheim, D., Rosero, A., Komis, G., Šamajová, O., Ovečka, M., Voigt, B., & Šamaj, J. (2016). Endosomal interactions during root hair growth. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2015.01262","ieee":"D. von Wangenheim et al., “Endosomal interactions during root hair growth,” Frontiers in Plant Science, vol. 6, no. JAN2016. Frontiers Research Foundation, 2016.","short":"D. von Wangenheim, A. Rosero, G. Komis, O. Šamajová, M. Ovečka, B. Voigt, J. Šamaj, Frontiers in Plant Science 6 (2016).","mla":"von Wangenheim, Daniel, et al. “Endosomal Interactions during Root Hair Growth.” Frontiers in Plant Science, vol. 6, no. JAN2016, 1262, Frontiers Research Foundation, 2016, doi:10.3389/fpls.2015.01262.","ista":"von Wangenheim D, Rosero A, Komis G, Šamajová O, Ovečka M, Voigt B, Šamaj J. 2016. Endosomal interactions during root hair growth. Frontiers in Plant Science. 6(JAN2016), 1262.","chicago":"Wangenheim, Daniel von, Amparo Rosero, George Komis, Olga Šamajová, Miroslav Ovečka, Boris Voigt, and Jozef Šamaj. “Endosomal Interactions during Root Hair Growth.” Frontiers in Plant Science. Frontiers Research Foundation, 2016. https://doi.org/10.3389/fpls.2015.01262."},"title":"Endosomal interactions during root hair growth","publist_id":"6094","author":[{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Von Wangenheim","full_name":"Von Wangenheim, Daniel","orcid":"0000-0002-6862-1247"},{"first_name":"Amparo","full_name":"Rosero, Amparo","last_name":"Rosero"},{"first_name":"George","full_name":"Komis, George","last_name":"Komis"},{"first_name":"Olga","last_name":"Šamajová","full_name":"Šamajová, Olga"},{"last_name":"Ovečka","full_name":"Ovečka, Miroslav","first_name":"Miroslav"},{"first_name":"Boris","last_name":"Voigt","full_name":"Voigt, Boris"},{"first_name":"Jozef","last_name":"Šamaj","full_name":"Šamaj, Jozef"}],"acknowledgement":"This work was supported by National Program for Sustainability I (grant no. LO1204) provided by the Czech Ministry of Education and by Institutional Fund of Palacký University Olomouc (GK and OŠ).\r\nWe thank Sabine Fischer for help with the statistics.","publisher":"Frontiers Research Foundation","quality_controlled":"1","oa":1,"day":"29","publication":"Frontiers in Plant Science","has_accepted_license":"1","year":"2016","date_published":"2016-01-29T00:00:00Z","doi":"10.3389/fpls.2015.01262","date_created":"2018-12-11T11:50:53Z","_id":"1238","status":"public","pubrep_id":"710","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["581"],"date_updated":"2021-01-12T06:49:18Z","file_date_updated":"2020-07-14T12:44:41Z","department":[{"_id":"JiFr"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The dynamic localization of endosomal compartments labeled with targeted fluorescent protein tags is routinely followed by time lapse fluorescence microscopy approaches and single particle tracking algorithms. In this way trajectories of individual endosomes can be mapped and linked to physiological processes as cell growth. However, other aspects of dynamic behavior including endosomal interactions are difficult to follow in this manner. Therefore, we characterized the localization and dynamic properties of early and late endosomes throughout the entire course of root hair formation by means of spinning disc time lapse imaging and post-acquisition automated multitracking and quantitative analysis. Our results show differential motile behavior of early and late endosomes and interactions of late endosomes that may be specified to particular root hair domains. Detailed data analysis revealed a particular transient interaction between late endosomes—termed herein as dancing-endosomes—which is not concluding to vesicular fusion. Endosomes preferentially located in the root hair tip interacted as dancing-endosomes and traveled short distances during this interaction. Finally, sizes of early and late endosomes were addressed by means of super-resolution structured illumination microscopy (SIM) to corroborate measurements on the spinning disc. This is a first study providing quantitative microscopic data on dynamic spatio-temporal interactions of endosomes during root hair tip growth."}],"month":"01","intvolume":" 6","scopus_import":1,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4760","checksum":"3127eab844d53564bf47e2b6b42f1ca0","creator":"system","date_updated":"2020-07-14T12:44:41Z","file_size":1640550,"date_created":"2018-12-12T10:09:36Z","file_name":"IST-2016-710-v1+1_fpls-06-01262.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":6,"issue":"JAN2016"},{"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":9667,"abstract":[{"lang":"eng","text":"Bitmap images of arbitrary dimension may be formally perceived as unions of m-dimensional boxes aligned with respect to a rectangular grid in ℝm. Cohomology and homology groups are well known topological invariants of such sets. Cohomological operations, such as the cup product, provide higher-order algebraic topological invariants, especially important for digital images of dimension higher than 3. If such an operation is determined at the level of simplicial chains [see e.g. González-Díaz, Real, Homology, Homotopy Appl, 2003, 83-93], then it is effectively computable. However, decomposing a cubical complex into a simplicial one deleteriously affects the efficiency of such an approach. In order to avoid this overhead, a direct cubical approach was applied in [Pilarczyk, Real, Adv. Comput. Math., 2015, 253-275] for the cup product in cohomology, and implemented in the ChainCon software package [http://www.pawelpilarczyk.com/chaincon/]. We establish a formula for the Steenrod square operations [see Steenrod, Annals of Mathematics. Second Series, 1947, 290-320] directly at the level of cubical chains, and we prove the correctness of this formula. An implementation of this formula is programmed in C++ within the ChainCon software framework. We provide a few examples and discuss the effectiveness of this approach. One specific application follows from the fact that Steenrod squares yield tests for the topological extension problem: Can a given map A → Sd to a sphere Sd be extended to a given super-complex X of A? In particular, the ROB-SAT problem, which is to decide for a given function f: X → ℝm and a value r > 0 whether every g: X → ℝm with ∥g - f ∥∞ ≤ r has a root, reduces to the extension problem."}],"oa_version":"None","scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 9667","month":"06","date_updated":"2021-01-12T06:49:18Z","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"_id":"1237","conference":{"name":"CTIC: Computational Topology in Image Context","start_date":"2016-06-15","location":"Marseille, France","end_date":"2016-06-17"},"type":"conference","status":"public","year":"2016","day":"02","page":"140 - 151","date_created":"2018-12-11T11:50:52Z","date_published":"2016-06-02T00:00:00Z","doi":"10.1007/978-3-319-39441-1_13","acknowledgement":"The research conducted by both authors has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreements no. 291734 (for M. K.) and no. 622033 (for P. P.).","quality_controlled":"1","publisher":"Springer","citation":{"ieee":"M. Krcál and P. Pilarczyk, “Computation of cubical Steenrod squares,” presented at the CTIC: Computational Topology in Image Context, Marseille, France, 2016, vol. 9667, pp. 140–151.","short":"M. Krcál, P. Pilarczyk, in:, Springer, 2016, pp. 140–151.","ama":"Krcál M, Pilarczyk P. Computation of cubical Steenrod squares. In: Vol 9667. Springer; 2016:140-151. doi:10.1007/978-3-319-39441-1_13","apa":"Krcál, M., & Pilarczyk, P. (2016). Computation of cubical Steenrod squares (Vol. 9667, pp. 140–151). Presented at the CTIC: Computational Topology in Image Context, Marseille, France: Springer. https://doi.org/10.1007/978-3-319-39441-1_13","mla":"Krcál, Marek, and Pawel Pilarczyk. Computation of Cubical Steenrod Squares. Vol. 9667, Springer, 2016, pp. 140–51, doi:10.1007/978-3-319-39441-1_13.","ista":"Krcál M, Pilarczyk P. 2016. Computation of cubical Steenrod squares. CTIC: Computational Topology in Image Context, LNCS, vol. 9667, 140–151.","chicago":"Krcál, Marek, and Pawel Pilarczyk. “Computation of Cubical Steenrod Squares,” 9667:140–51. Springer, 2016. https://doi.org/10.1007/978-3-319-39441-1_13."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6096","author":[{"first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","last_name":"Krcál","full_name":"Krcál, Marek"},{"first_name":"Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk"}],"title":"Computation of cubical Steenrod squares","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"call_identifier":"FP7","_id":"255F06BE-B435-11E9-9278-68D0E5697425","grant_number":"622033","name":"Persistent Homology - Images, Data and Maps"}]},{"file_date_updated":"2020-07-14T12:44:41Z","department":[{"_id":"GaNo"}],"date_updated":"2021-01-12T06:49:20Z","ddc":["576"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"709","_id":"1240","volume":17,"issue":"1","publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4789","checksum":"a268beee1a690801c83ec6729f9ebc5b","file_size":2914601,"date_updated":"2020-07-14T12:44:41Z","creator":"system","file_name":"IST-2016-709-v1+1_s13059-016-0873-8.pdf","date_created":"2018-12-12T10:10:05Z"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"01","intvolume":" 17","abstract":[{"lang":"eng","text":"Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ultimately be more numerous than protein-coding genes in the human genome. Despite large numbers of reported lncRNAs, reference annotations are likely incomplete due to their lower and tighter tissue-specific expression compared to mRNAs. An unexplored factor potentially confounding lncRNA identification is inter-individual expression variability. Here, we characterize lncRNA natural expression variability in human primary granulocytes. Results: We annotate granulocyte lncRNAs and mRNAs in RNA-seq data from 10 healthy individuals, identifying multiple lncRNAs absent from reference annotations, and use this to investigate three known features (higher tissue-specificity, lower expression, and reduced splicing efficiency) of lncRNAs relative to mRNAs. Expression variability was examined in seven individuals sampled three times at 1- or more than 1-month intervals. We show that lncRNAs display significantly more inter-individual expression variability compared to mRNAs. We confirm this finding in two independent human datasets by analyzing multiple tissues from the GTEx project and lymphoblastoid cell lines from the GEUVADIS project. Using the latter dataset we also show that including more human donors into the transcriptome annotation pipeline allows identification of an increasing number of lncRNAs, but minimally affects mRNA gene number. Conclusions: A comprehensive annotation of lncRNAs is known to require an approach that is sensitive to low and tight tissue-specific expression. Here we show that increased inter-individual expression variability is an additional general lncRNA feature to consider when creating a comprehensive annotation of human lncRNAs or proposing their use as prognostic or disease markers."}],"oa_version":"Published Version","author":[{"first_name":"Aleksandra","full_name":"Kornienko, Aleksandra","last_name":"Kornienko"},{"full_name":"Dotter, Christoph","last_name":"Dotter","first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Philipp","last_name":"Guenzl","full_name":"Guenzl, Philipp"},{"first_name":"Heinz","last_name":"Gisslinger","full_name":"Gisslinger, Heinz"},{"full_name":"Gisslinger, Bettina","last_name":"Gisslinger","first_name":"Bettina"},{"first_name":"Ciara","full_name":"Cleary, Ciara","last_name":"Cleary"},{"first_name":"Robert","full_name":"Kralovics, Robert","last_name":"Kralovics"},{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","last_name":"Pauler"},{"last_name":"Barlow","full_name":"Barlow, Denise","first_name":"Denise"}],"publist_id":"6093","title":"Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans","citation":{"chicago":"Kornienko, Aleksandra, Christoph Dotter, Philipp Guenzl, Heinz Gisslinger, Bettina Gisslinger, Ciara Cleary, Robert Kralovics, Florian Pauler, and Denise Barlow. “Long Non-Coding RNAs Display Higher Natural Expression Variation than Protein-Coding Genes in Healthy Humans.” Genome Biology. BioMed Central, 2016. https://doi.org/10.1186/s13059-016-0873-8.","ista":"Kornienko A, Dotter C, Guenzl P, Gisslinger H, Gisslinger B, Cleary C, Kralovics R, Pauler F, Barlow D. 2016. Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. Genome Biology. 17(1), 14.","mla":"Kornienko, Aleksandra, et al. “Long Non-Coding RNAs Display Higher Natural Expression Variation than Protein-Coding Genes in Healthy Humans.” Genome Biology, vol. 17, no. 1, 14, BioMed Central, 2016, doi:10.1186/s13059-016-0873-8.","ama":"Kornienko A, Dotter C, Guenzl P, et al. Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. Genome Biology. 2016;17(1). doi:10.1186/s13059-016-0873-8","apa":"Kornienko, A., Dotter, C., Guenzl, P., Gisslinger, H., Gisslinger, B., Cleary, C., … Barlow, D. (2016). Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-016-0873-8","short":"A. Kornienko, C. Dotter, P. Guenzl, H. Gisslinger, B. Gisslinger, C. Cleary, R. Kralovics, F. Pauler, D. Barlow, Genome Biology 17 (2016).","ieee":"A. Kornienko et al., “Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans,” Genome Biology, vol. 17, no. 1. BioMed Central, 2016."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"14","doi":"10.1186/s13059-016-0873-8","date_published":"2016-01-29T00:00:00Z","date_created":"2018-12-11T11:50:53Z","has_accepted_license":"1","year":"2016","day":"29","publication":"Genome Biology","quality_controlled":"1","publisher":"BioMed Central","oa":1,"acknowledgement":"This study was partly funded by the Austrian Science Fund (FWF F43-B09, FWF W1207-B09). PMG is a recipient of a DOC Fellowship of the Austrian Academy of Sciences.\r\nWe thank Ruth Klement, Tomasz Kulinski, Elisangela Valente, Elisabeth Salzer,\r\nand Roland Jäger for technical/bioinformatic assistance and advice, the CeMM\r\nIT department and José Manuel Molero for help and advice on software usage,\r\nthe Biomedical Sequencing Facility (http://biomedical-sequencing.at/) for\r\nsequencing and advice, Jacques Colinge, Daniel Andergassen, and Tomasz\r\nKulinski for discussions, Quanah Hudson and Jörg Menche for reading and\r\ncommenting on the manuscript."},{"project":[{"name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","grant_number":"T 560-B17","call_identifier":"FWF","_id":"2529486C-B435-11E9-9278-68D0E5697425"}],"status":"public","type":"journal_article","article_number":"028102","_id":"1239","title":"Cortical flow-driven shapes of nonadherent cells","department":[{"_id":"CaHe"}],"publist_id":"6095","author":[{"full_name":"Callan Jones, Andrew","last_name":"Callan Jones","first_name":"Andrew"},{"id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","first_name":"Verena","last_name":"Ruprecht","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena"},{"last_name":"Wieser","orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan","first_name":"Stefan","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"first_name":"Raphaël","last_name":"Voituriez","full_name":"Voituriez, Raphaël"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:49:19Z","citation":{"ieee":"A. Callan Jones, V. Ruprecht, S. Wieser, C.-P. J. Heisenberg, and R. Voituriez, “Cortical flow-driven shapes of nonadherent cells,” Physical Review Letters, vol. 116, no. 2. American Physical Society, 2016.","short":"A. Callan Jones, V. Ruprecht, S. Wieser, C.-P.J. Heisenberg, R. Voituriez, Physical Review Letters 116 (2016).","ama":"Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. Cortical flow-driven shapes of nonadherent cells. Physical Review Letters. 2016;116(2). doi:10.1103/PhysRevLett.116.028102","apa":"Callan Jones, A., Ruprecht, V., Wieser, S., Heisenberg, C.-P. J., & Voituriez, R. (2016). Cortical flow-driven shapes of nonadherent cells. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.116.028102","mla":"Callan Jones, Andrew, et al. “Cortical Flow-Driven Shapes of Nonadherent Cells.” Physical Review Letters, vol. 116, no. 2, 028102, American Physical Society, 2016, doi:10.1103/PhysRevLett.116.028102.","ista":"Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. 2016. Cortical flow-driven shapes of nonadherent cells. Physical Review Letters. 116(2), 028102.","chicago":"Callan Jones, Andrew, Verena Ruprecht, Stefan Wieser, Carl-Philipp J Heisenberg, and Raphaël Voituriez. “Cortical Flow-Driven Shapes of Nonadherent Cells.” Physical Review Letters. American Physical Society, 2016. https://doi.org/10.1103/PhysRevLett.116.028102."},"intvolume":" 116","month":"01","quality_controlled":"1","scopus_import":1,"publisher":"American Physical Society","acknowledgement":"V. R. acknowledges support by the Austrian Science Fund (FWF): (Grant No. T560-B17).","oa_version":"None","abstract":[{"lang":"eng","text":"Nonadherent polarized cells have been observed to have a pearlike, elongated shape. Using a minimal model that describes the cell cortex as a thin layer of contractile active gel, we show that the anisotropy of active stresses, controlled by cortical viscosity and filament ordering, can account for this morphology. The predicted shapes can be determined from the flow pattern only; they prove to be independent of the mechanism at the origin of the cortical flow, and are only weakly sensitive to the cytoplasmic rheology. In the case of actin flows resulting from a contractile instability, we propose a phase diagram of three-dimensional cell shapes that encompasses nonpolarized spherical, elongated, as well as oblate shapes, all of which have been observed in experiment."}],"date_created":"2018-12-11T11:50:53Z","volume":116,"doi":"10.1103/PhysRevLett.116.028102","date_published":"2016-01-15T00:00:00Z","issue":"2","publication":"Physical Review Letters","language":[{"iso":"eng"}],"day":"15","year":"2016","publication_status":"published"},{"publication_status":"published","language":[{"iso":"eng"}],"volume":93,"issue":"2","abstract":[{"lang":"eng","text":"A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule acts as an independent sensor of the input concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.02562"}],"scopus_import":1,"intvolume":" 93","month":"02","date_updated":"2021-01-12T06:49:20Z","department":[{"_id":"GaTk"}],"_id":"1242","type":"journal_article","status":"public","year":"2016","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","day":"04","date_created":"2018-12-11T11:50:54Z","date_published":"2016-02-04T00:00:00Z","doi":"10.1103/PhysRevE.93.022404","acknowledgement":"We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions. This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370 from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W. acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561. G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S.","oa":1,"publisher":"American Institute of Physics","quality_controlled":"1","citation":{"ista":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404.","chicago":"Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2016. https://doi.org/10.1103/PhysRevE.93.022404.","ieee":"T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic range of transcription factor action by translational regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2. American Institute of Physics, 2016.","short":"T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (2016).","apa":"Sokolowski, T. R., Walczak, A., Bialek, W., & Tkačik, G. (2016). Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.93.022404","ama":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2016;93(2). doi:10.1103/PhysRevE.93.022404","mla":"Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2, 022404, American Institute of Physics, 2016, doi:10.1103/PhysRevE.93.022404."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6088","author":[{"last_name":"Sokolowski","full_name":"Sokolowski, Thomas R","orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R"},{"full_name":"Walczak, Aleksandra","last_name":"Walczak","first_name":"Aleksandra"},{"first_name":"William","full_name":"Bialek, William","last_name":"Bialek"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"title":"Extending the dynamic range of transcription factor action by translational regulation","article_number":"022404","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}]},{"issue":"2","volume":202,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://biorxiv.org/content/early/2015/07/06/022020.abstract"}],"month":"02","intvolume":" 202","abstract":[{"text":"How likely is it that a population escapes extinction through adaptive evolution? The answer to this question is of great relevance in conservation biology, where we aim at species’ rescue and the maintenance of biodiversity, and in agriculture and medicine, where we seek to hamper the emergence of pesticide or drug resistance. By reshuffling the genome, recombination has two antagonistic effects on the probability of evolutionary rescue: It generates and it breaks up favorable gene combinations. Which of the two effects prevails depends on the fitness effects of mutations and on the impact of stochasticity on the allele frequencies. In this article, we analyze a mathematical model for rescue after a sudden environmental change when adaptation is contingent on mutations at two loci. The analysis reveals a complex nonlinear dependence of population survival on recombination. We moreover find that, counterintuitively, a fast eradication of the wild type can promote rescue in the presence of recombination. The model also shows that two-step rescue is not unlikely to happen and can even be more likely than single-step rescue (where adaptation relies on a single mutation), depending on the circumstances.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"NiBa"}],"date_updated":"2023-02-21T10:24:19Z","type":"journal_article","status":"public","_id":"1241","page":"721 - 732","doi":"10.1534/genetics.115.180299","date_published":"2016-02-01T00:00:00Z","date_created":"2018-12-11T11:50:54Z","year":"2016","day":"01","publication":"Genetics","publisher":"Genetics Society of America","quality_controlled":"1","oa":1,"acknowledgement":"This work was made possible by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria) and European Research Council grant 250152 (to Nick Barton).","publist_id":"6091","author":[{"full_name":"Uecker, Hildegard","orcid":"0000-0001-9435-2813","last_name":"Uecker","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","first_name":"Hildegard"},{"first_name":"Joachim","full_name":"Hermisson, Joachim","last_name":"Hermisson"}],"title":"The role of recombination in evolutionary rescue","citation":{"chicago":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.180299.","ista":"Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 721–732.","mla":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016, pp. 721–32, doi:10.1534/genetics.115.180299.","ama":"Uecker H, Hermisson J. The role of recombination in evolutionary rescue. Genetics. 2016;202(2):721-732. doi:10.1534/genetics.115.180299","apa":"Uecker, H., & Hermisson, J. (2016). The role of recombination in evolutionary rescue. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.180299","short":"H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.","ieee":"H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,” Genetics, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"_id":"25B67606-B435-11E9-9278-68D0E5697425","name":"L'OREAL Fellowship"}]},{"acknowledgement":"This work was supported by the Ghent University Special Research Fund (M.K.), the European Research Council (Project ERC-2011-StG-20101109-PSDP) (to J.F.), and the Körber European Science Foun-\r\ndation (J.F.). S.D.G. is indebted to the Agency for Science and Technology for\r\na predoctoral fellowship.","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","publication":"PNAS","day":"08","year":"2016","date_created":"2018-12-11T11:50:56Z","date_published":"2016-03-08T00:00:00Z","doi":"10.1073/pnas.1501343112","page":"2768 - 2773","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Karampelias, Michael, Pia Neyt, Steven De Groeve, Stijn Aesaert, Griet Coussens, Jakub Rolčík, Leonardo Bruno, et al. “ROTUNDA3 Function in Plant Development by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1501343112.","ista":"Karampelias M, Neyt P, De Groeve S, Aesaert S, Coussens G, Rolčík J, Bruno L, De Winne N, Van Minnebruggen A, Van Montagu M, Ponce M, Micol J, Friml J, De Jaeger G, Van Lijsebettens M. 2016. ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. 113(10), 2768–2773.","mla":"Karampelias, Michael, et al. “ROTUNDA3 Function in Plant Development by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” PNAS, vol. 113, no. 10, National Academy of Sciences, 2016, pp. 2768–73, doi:10.1073/pnas.1501343112.","ama":"Karampelias M, Neyt P, De Groeve S, et al. ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. 2016;113(10):2768-2773. doi:10.1073/pnas.1501343112","apa":"Karampelias, M., Neyt, P., De Groeve, S., Aesaert, S., Coussens, G., Rolčík, J., … Van Lijsebettens, M. (2016). ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1501343112","ieee":"M. Karampelias et al., “ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling,” PNAS, vol. 113, no. 10. National Academy of Sciences, pp. 2768–2773, 2016.","short":"M. Karampelias, P. Neyt, S. De Groeve, S. Aesaert, G. Coussens, J. Rolčík, L. Bruno, N. De Winne, A. Van Minnebruggen, M. Van Montagu, M. Ponce, J. Micol, J. Friml, G. De Jaeger, M. Van Lijsebettens, PNAS 113 (2016) 2768–2773."},"title":"ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling","publist_id":"6081","author":[{"full_name":"Karampelias, Michael","last_name":"Karampelias","first_name":"Michael"},{"first_name":"Pia","last_name":"Neyt","full_name":"Neyt, Pia"},{"full_name":"De Groeve, Steven","last_name":"De Groeve","first_name":"Steven"},{"first_name":"Stijn","full_name":"Aesaert, Stijn","last_name":"Aesaert"},{"full_name":"Coussens, Griet","last_name":"Coussens","first_name":"Griet"},{"last_name":"Rolčík","full_name":"Rolčík, Jakub","first_name":"Jakub"},{"last_name":"Bruno","full_name":"Bruno, Leonardo","first_name":"Leonardo"},{"full_name":"De Winne, Nancy","last_name":"De Winne","first_name":"Nancy"},{"first_name":"Annemie","last_name":"Van Minnebruggen","full_name":"Van Minnebruggen, Annemie"},{"last_name":"Van Montagu","full_name":"Van Montagu, Marc","first_name":"Marc"},{"first_name":"Maria","last_name":"Ponce","full_name":"Ponce, Maria"},{"full_name":"Micol, José","last_name":"Micol","first_name":"José"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Geert","full_name":"De Jaeger, Geert","last_name":"De Jaeger"},{"first_name":"Mieke","last_name":"Van Lijsebettens","full_name":"Van Lijsebettens, Mieke"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The shaping of organs in plants depends on the intercellular flow of the phytohormone auxin, of which the directional signaling is determined by the polar subcellular localization of PIN-FORMED (PIN) auxin transport proteins. Phosphorylation dynamics of PIN proteins are affected by the protein phosphatase 2A (PP2A) and the PINOID kinase, which act antagonistically to mediate their apical-basal polar delivery. Here, we identified the ROTUNDA3 (RON3) protein as a regulator of the PP2A phosphatase activity in Arabidopsis thaliana. The RON3 gene was map-based cloned starting from the ron3-1 leaf mutant and found to be a unique, plant-specific gene coding for a protein with high and dispersed proline content. The ron3-1 and ron3-2 mutant phenotypes [i.e., reduced apical dominance, primary root length, lateral root emergence, and growth; increased ectopic stages II, IV, and V lateral root primordia; decreased auxin maxima in indole-3-acetic acid (IAA)-treated root apical meristems; hypergravitropic root growth and response; increased IAA levels in shoot apices; and reduced auxin accumulation in root meristems] support a role for RON3 in auxin biology. The affinity-purified PP2A complex with RON3 as bait suggested that RON3 might act in PIN transporter trafficking. Indeed, pharmacological interference with vesicle trafficking processes revealed that single ron3-2 and double ron3-2 rcn1 mutants have altered PIN polarity and endocytosis in specific cells. Our data indicate that RON3 contributes to auxin-mediated development by playing a role in PIN recycling and polarity establishment through regulation of the PP2A complex activity."}],"intvolume":" 113","month":"03","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791031/","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":113,"issue":"10","_id":"1247","status":"public","type":"journal_article","date_updated":"2021-01-12T06:49:22Z","department":[{"_id":"JiFr"}]},{"article_number":"22665","citation":{"ieee":"I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, and L. Kuipers, “Imaging of electric and magnetic fields near plasmonic nanowires,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","short":"I. Kabakova, A. De Hoogh, R. Van Der Wel, M. Wulf, B. Le Feber, L. Kuipers, Scientific Reports 6 (2016).","apa":"Kabakova, I., De Hoogh, A., Van Der Wel, R., Wulf, M., Le Feber, B., & Kuipers, L. (2016). Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep22665","ama":"Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports. 2016;6. doi:10.1038/srep22665","mla":"Kabakova, Irina, et al. “Imaging of Electric and Magnetic Fields near Plasmonic Nanowires.” Scientific Reports, vol. 6, 22665, Nature Publishing Group, 2016, doi:10.1038/srep22665.","ista":"Kabakova I, De Hoogh A, Van Der Wel R, Wulf M, Le Feber B, Kuipers L. 2016. Imaging of electric and magnetic fields near plasmonic nanowires. Scientific Reports. 6, 22665.","chicago":"Kabakova, Irina, Anouk De Hoogh, Ruben Van Der Wel, Matthias Wulf, Boris Le Feber, and Laurens Kuipers. “Imaging of Electric and Magnetic Fields near Plasmonic Nanowires.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep22665."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6082","author":[{"full_name":"Kabakova, Irina","last_name":"Kabakova","first_name":"Irina"},{"first_name":"Anouk","full_name":"De Hoogh, Anouk","last_name":"De Hoogh"},{"last_name":"Van Der Wel","full_name":"Van Der Wel, Ruben","first_name":"Ruben"},{"orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","last_name":"Wulf","first_name":"Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Boris","full_name":"Le Feber, Boris","last_name":"Le Feber"},{"first_name":"Laurens","last_name":"Kuipers","full_name":"Kuipers, Laurens"}],"title":"Imaging of electric and magnetic fields near plasmonic nanowires","acknowledgement":"This work is supported part of the research program of the Netherlands Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization for Scientific Research (NWO), and part of this work has been funded by the project ‘SPANGL4Q’, which acknowledges the financial support of the Future and Emerging Technologies (FET) program within the Seventh Framework Programme for Research of the European Commission, under FETOpen grant number: FP7-284743. L.K. acknowledges funding from ERC Advanced, Investigator Grant (no. 240438-CONSTANS).","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","year":"2016","has_accepted_license":"1","publication":"Scientific Reports","day":"07","date_created":"2018-12-11T11:50:55Z","doi":"10.1038/srep22665","date_published":"2016-03-07T00:00:00Z","_id":"1246","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"707","status":"public","date_updated":"2021-01-12T06:49:22Z","ddc":["539"],"department":[{"_id":"JoFi"}],"file_date_updated":"2020-07-14T12:44:41Z","abstract":[{"text":"Near-field imaging is a powerful tool to investigate the complex structure of light at the nanoscale. Recent advances in near-field imaging have indicated the possibility for the complete reconstruction of both electric and magnetic components of the evanescent field. Here we study the electro-magnetic field structure of surface plasmon polariton waves propagating along subwavelength gold nanowires by performing phase- and polarization-resolved near-field microscopy in collection mode. By applying the optical reciprocity theorem, we describe the signal collected by the probe as an overlap integral of the nanowire's evanescent field and the probe's response function. As a result, we find that the probe's sensitivity to the magnetic field is approximately equal to its sensitivity to the electric field. Through rigorous modeling of the nanowire mode as well as the aperture probe response function, we obtain a good agreement between experimentally measured signals and a numerical model. Our findings provide a better understanding of aperture-based near-field imaging of the nanoscopic plasmonic and photonic structures and are helpful for the interpretation of future near-field experiments.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 6","month":"03","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":1425165,"date_updated":"2020-07-14T12:44:41Z","creator":"system","file_name":"IST-2016-707-v1+1_srep22665.pdf","date_created":"2018-12-12T10:14:11Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"ca76236cb1aae22cb90c65313e2c5e98","file_id":"5061"}],"volume":6},{"status":"public","conference":{"start_date":"2016-02-26","end_date":"2016-03-02","location":"San Francisco, CA, USA","name":"CSCW: Computer Supported Cooperative Work and Social Computing"},"type":"conference","_id":"1245","department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T06:49:22Z","intvolume":" 26","month":"02","scopus_import":1,"oa_version":"None","abstract":[{"lang":"eng","text":"To facilitate collaboration in massive online classrooms, instructors must make many decisions. For instance, the following parameters need to be decided when designing a peer-feedback system where students review each others' essays: the number of students each student must provide feedback to, an algorithm to map feedback providers to receivers, constraints that ensure students do not become free-riders (receiving feedback but not providing it), the best times to receive feedback to improve learning etc. While instructors can answer these questions by running experiments or invoking past experience, game-theoretic models with data from online learning platforms can identify better initial designs for further improvements. As an example, we explore the design space of a peer feedback system by modeling it using game theory. Our simulations show that incentivizing students to provide feedback requires the value obtained from receiving a feedback to exceed the cost of providing it by a large factor (greater than 7). Furthermore, hiding feedback from low-effort students incentivizes them to provide more feedback."}],"ec_funded":1,"volume":26,"issue":"Februar-2016","language":[{"iso":"eng"}],"publication_status":"published","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"title":"Game-theoretic models identify useful principles for peer collaboration in online learning platforms","author":[{"first_name":"Vineet","last_name":"Pandey","full_name":"Pandey, Vineet"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"publist_id":"6083","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"V. Pandey, K. Chatterjee, in:, Proceedings of the ACM Conference on Computer Supported Cooperative Work, ACM, 2016, pp. 365–368.","ieee":"V. Pandey and K. Chatterjee, “Game-theoretic models identify useful principles for peer collaboration in online learning platforms,” in Proceedings of the ACM Conference on Computer Supported Cooperative Work, San Francisco, CA, USA, 2016, vol. 26, no. Februar-2016, pp. 365–368.","ama":"Pandey V, Chatterjee K. Game-theoretic models identify useful principles for peer collaboration in online learning platforms. In: Proceedings of the ACM Conference on Computer Supported Cooperative Work. Vol 26. ACM; 2016:365-368. doi:10.1145/2818052.2869122","apa":"Pandey, V., & Chatterjee, K. (2016). Game-theoretic models identify useful principles for peer collaboration in online learning platforms. In Proceedings of the ACM Conference on Computer Supported Cooperative Work (Vol. 26, pp. 365–368). San Francisco, CA, USA: ACM. https://doi.org/10.1145/2818052.2869122","mla":"Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify Useful Principles for Peer Collaboration in Online Learning Platforms.” Proceedings of the ACM Conference on Computer Supported Cooperative Work, vol. 26, no. Februar-2016, ACM, 2016, pp. 365–68, doi:10.1145/2818052.2869122.","ista":"Pandey V, Chatterjee K. 2016. Game-theoretic models identify useful principles for peer collaboration in online learning platforms. Proceedings of the ACM Conference on Computer Supported Cooperative Work. CSCW: Computer Supported Cooperative Work and Social Computing vol. 26, 365–368.","chicago":"Pandey, Vineet, and Krishnendu Chatterjee. “Game-Theoretic Models Identify Useful Principles for Peer Collaboration in Online Learning Platforms.” In Proceedings of the ACM Conference on Computer Supported Cooperative Work, 26:365–68. ACM, 2016. https://doi.org/10.1145/2818052.2869122."},"quality_controlled":"1","publisher":"ACM","acknowledgement":"ERC Start Grant Graph Games 279307 supported this research. ","date_created":"2018-12-11T11:50:55Z","doi":"10.1145/2818052.2869122","date_published":"2016-02-27T00:00:00Z","page":"365 - 368","publication":"Proceedings of the ACM Conference on Computer Supported Cooperative Work","day":"27","year":"2016"},{"acknowledgement":"We thank Sophie Martin, Ken Sawin, Stephen Huisman,\r\nand Damian Brunner for strains; Julianne\r\nTeapal, Marcel Janson, Sergio Rincon,\r\nand Phong Tran for technical assistance; Andrew Mugler and Bela Mulder for\r\ndiscussions; and Sander Tans, Phong Tran,\r\nand Anne Paoletti for critical reading\r\nof the manuscript. This work is part of the research program of the\r\n“\r\nStichting\r\nvoor Fundamenteel Onderzoek de Materie,\r\n”\r\nwhich is financially supported by\r\nthe\r\n“\r\nNederlandse organisatie voor Wete\r\nnschappelijk Onderzoek (NWO).\r\n”","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","publication":"PNAS","day":"16","year":"2016","date_created":"2018-12-11T11:50:55Z","date_published":"2016-02-16T00:00:00Z","doi":"10.1073/pnas.1419248113","page":"1811 - 1816","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom, PNAS 113 (2016) 1811–1816.","ieee":"P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom, “Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells,” PNAS, vol. 113, no. 7. National Academy of Sciences, pp. 1811–1816, 2016.","apa":"Recouvreux, P., Sokolowski, T. R., Grammoustianou, A., Tenwolde, P., & Dogterom, M. (2016). Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1419248113","ama":"Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. 2016;113(7):1811-1816. doi:10.1073/pnas.1419248113","mla":"Recouvreux, Pierre, et al. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS, vol. 113, no. 7, National Academy of Sciences, 2016, pp. 1811–16, doi:10.1073/pnas.1419248113.","ista":"Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. 113(7), 1811–1816.","chicago":"Recouvreux, Pierre, Thomas R Sokolowski, Aristea Grammoustianou, Pieter Tenwolde, and Marileen Dogterom. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1419248113."},"title":"Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells","author":[{"last_name":"Recouvreux","full_name":"Recouvreux, Pierre","first_name":"Pierre"},{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R","orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R","last_name":"Sokolowski"},{"full_name":"Grammoustianou, Aristea","last_name":"Grammoustianou","first_name":"Aristea"},{"last_name":"Tenwolde","full_name":"Tenwolde, Pieter","first_name":"Pieter"},{"first_name":"Marileen","last_name":"Dogterom","full_name":"Dogterom, Marileen"}],"publist_id":"6085","oa_version":"Submitted Version","abstract":[{"text":"Cell polarity refers to a functional spatial organization of proteins that is crucial for the control of essential cellular processes such as growth and division. To establish polarity, cells rely on elaborate regulation networks that control the distribution of proteins at the cell membrane. In fission yeast cells, a microtubule-dependent network has been identified that polarizes the distribution of signaling proteins that restricts growth to cell ends and targets the cytokinetic machinery to the middle of the cell. Although many molecular components have been shown to play a role in this network, it remains unknown which molecular functionalities are minimally required to establish a polarized protein distribution in this system. Here we show that a membrane-binding protein fragment, which distributes homogeneously in wild-type fission yeast cells, can be made to concentrate at cell ends by attaching it to a cytoplasmic microtubule end-binding protein. This concentration results in a polarized pattern of chimera proteins with a spatial extension that is very reminiscent of natural polarity patterns in fission yeast. However, chimera levels fluctuate in response to microtubule dynamics, and disruption of microtubules leads to disappearance of the pattern. Numerical simulations confirm that the combined functionality of membrane anchoring and microtubule tip affinity is in principle sufficient to create polarized patterns. Our chimera protein may thus represent a simple molecular functionality that is able to polarize the membrane, onto which additional layers of molecular complexity may be built to provide the temporal robustness that is typical of natural polarity patterns.","lang":"eng"}],"intvolume":" 113","month":"02","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","volume":113,"issue":"7","_id":"1244","status":"public","type":"journal_article","date_updated":"2021-01-12T06:49:21Z","department":[{"_id":"GaTk"}]},{"volume":7,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 7","month":"03","main_file_link":[{"url":"https://arxiv.org/abs/1412.8752","open_access":"1"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been possible to measure, directly, the flow of information in biological networks, or more generally where information-theoretic ideas have been used to guide the analysis of experiments. Systems of interest range from single molecules (the sequence diversity in families of proteins) to groups of organisms (the distribution of velocities in flocks of birds), and all scales in between. Many of these analyses are motivated by the idea that biological systems may have evolved to optimize the gathering and representation of information, and we review the experimental evidence for this optimization, again across a wide range of scales.","lang":"eng"}],"department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T06:49:23Z","status":"public","type":"journal_article","_id":"1248","date_created":"2018-12-11T11:50:56Z","doi":"10.1146/annurev-conmatphys-031214-014803","date_published":"2016-03-10T00:00:00Z","page":"89 - 117","publication":"Annual Review of Condensed Matter Physics","day":"10","year":"2016","oa":1,"quality_controlled":"1","publisher":"Annual Reviews","acknowledgement":"Our work was supported in part by the US\r\nNational Science Foundation (PHY–1305525 and CCF–\r\n0939370), by the Austrian Science Foundation (FWF\r\nP25651), by the Human Frontiers Science Program, and\r\nby the Simons and Swartz Foundations.","title":"Information processing in living systems","publist_id":"6080","author":[{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bialek","full_name":"Bialek, William","first_name":"William"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Tkačik, G., & Bialek, W. (2016). Information processing in living systems. Annual Review of Condensed Matter Physics. Annual Reviews. https://doi.org/10.1146/annurev-conmatphys-031214-014803","ama":"Tkačik G, Bialek W. Information processing in living systems. Annual Review of Condensed Matter Physics. 2016;7:89-117. doi:10.1146/annurev-conmatphys-031214-014803","ieee":"G. Tkačik and W. Bialek, “Information processing in living systems,” Annual Review of Condensed Matter Physics, vol. 7. Annual Reviews, pp. 89–117, 2016.","short":"G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117.","mla":"Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” Annual Review of Condensed Matter Physics, vol. 7, Annual Reviews, 2016, pp. 89–117, doi:10.1146/annurev-conmatphys-031214-014803.","ista":"Tkačik G, Bialek W. 2016. Information processing in living systems. Annual Review of Condensed Matter Physics. 7, 89–117.","chicago":"Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” Annual Review of Condensed Matter Physics. Annual Reviews, 2016. https://doi.org/10.1146/annurev-conmatphys-031214-014803."},"project":[{"name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}]},{"volume":110,"issue":"6","file":[{"file_size":1965645,"date_updated":"2020-07-14T12:44:41Z","creator":"system","file_name":"IST-2016-706-v1+1_1-s2.0-S0006349516001582-main.pdf","date_created":"2018-12-12T10:10:54Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"c408cf2e25a25c8d711cffea524bda55","file_id":"4845"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"03","intvolume":" 110","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Actin and myosin assemble into a thin layer of a highly dynamic network underneath the membrane of eukaryotic cells. This network generates the forces that drive cell- and tissue-scale morphogenetic processes. The effective material properties of this active network determine large-scale deformations and other morphogenetic events. For example, the characteristic time of stress relaxation (the Maxwell time τM) in the actomyosin sets the timescale of large-scale deformation of the cortex. Similarly, the characteristic length of stress propagation (the hydrodynamic length λ) sets the length scale of slow deformations, and a large hydrodynamic length is a prerequisite for long-ranged cortical flows. Here we introduce a method to determine physical parameters of the actomyosin cortical layer in vivo directly from laser ablation experiments. For this we investigate the cortical response to laser ablation in the one-cell-stage Caenorhabditis elegans embryo and in the gastrulating zebrafish embryo. These responses can be interpreted using a coarse-grained physical description of the cortex in terms of a two-dimensional thin film of an active viscoelastic gel. To determine the Maxwell time τM, the hydrodynamic length λ, the ratio of active stress ζΔμ, and per-area friction γ, we evaluated the response to laser ablation in two different ways: by quantifying flow and density fields as a function of space and time, and by determining the time evolution of the shape of the ablated region. Importantly, both methods provide best-fit physical parameters that are in close agreement with each other and that are similar to previous estimates in the two systems. Our method provides an accurate and robust means for measuring physical parameters of the actomyosin cortical layer. It can be useful for investigations of actomyosin mechanics at the cellular-scale, but also for providing insights into the active mechanics processes that govern tissue-scale morphogenesis."}],"file_date_updated":"2020-07-14T12:44:41Z","department":[{"_id":"CaHe"}],"ddc":["572","576"],"date_updated":"2021-01-12T06:49:23Z","status":"public","pubrep_id":"706","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"_id":"1249","date_published":"2016-03-29T00:00:00Z","doi":"10.1016/j.bpj.2016.02.013","date_created":"2018-12-11T11:50:56Z","page":"1421 - 1429","day":"29","publication":"Biophysical Journal","has_accepted_license":"1","year":"2016","publisher":"Biophysical Society","quality_controlled":"1","oa":1,"acknowledgement":"S.W.G. acknowledges support by grant no. 281903 from the European Research Council and by grant No. GR-7271/2-1 from the Deutsche Forschungsgemeinschaft. S.W.G. and C.-P.H. acknowledge support through a grant from the Fonds zur Förderung der Wissenschaftlichen Forschung and the Deutsche Forschungsgemeinschaft (No. I930-B20). We are grateful to Daniel Dickinson for providing the LP133 C. elegans strain. We thank G. Salbreux, V. K. Krishnamurthy, and J. S. Bois for fruitful discussions.","title":"Determining physical properties of the cell cortex","author":[{"last_name":"Saha","full_name":"Saha, Arnab","first_name":"Arnab"},{"full_name":"Nishikawa, Masatoshi","last_name":"Nishikawa","first_name":"Masatoshi"},{"last_name":"Behrndt","full_name":"Behrndt, Martin","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"},{"first_name":"Frank","full_name":"Julicher, Frank","last_name":"Julicher"},{"first_name":"Stephan","full_name":"Grill, Stephan","last_name":"Grill"}],"publist_id":"6079","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Saha, Arnab, et al. “Determining Physical Properties of the Cell Cortex.” Biophysical Journal, vol. 110, no. 6, Biophysical Society, 2016, pp. 1421–29, doi:10.1016/j.bpj.2016.02.013.","ama":"Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. Determining physical properties of the cell cortex. Biophysical Journal. 2016;110(6):1421-1429. doi:10.1016/j.bpj.2016.02.013","apa":"Saha, A., Nishikawa, M., Behrndt, M., Heisenberg, C.-P. J., Julicher, F., & Grill, S. (2016). Determining physical properties of the cell cortex. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2016.02.013","short":"A. Saha, M. Nishikawa, M. Behrndt, C.-P.J. Heisenberg, F. Julicher, S. Grill, Biophysical Journal 110 (2016) 1421–1429.","ieee":"A. Saha, M. Nishikawa, M. Behrndt, C.-P. J. Heisenberg, F. Julicher, and S. Grill, “Determining physical properties of the cell cortex,” Biophysical Journal, vol. 110, no. 6. Biophysical Society, pp. 1421–1429, 2016.","chicago":"Saha, Arnab, Masatoshi Nishikawa, Martin Behrndt, Carl-Philipp J Heisenberg, Frank Julicher, and Stephan Grill. “Determining Physical Properties of the Cell Cortex.” Biophysical Journal. Biophysical Society, 2016. https://doi.org/10.1016/j.bpj.2016.02.013.","ista":"Saha A, Nishikawa M, Behrndt M, Heisenberg C-PJ, Julicher F, Grill S. 2016. Determining physical properties of the cell cortex. Biophysical Journal. 110(6), 1421–1429."},"project":[{"name":"Control of Epithelial Cell Layer Spreading in Zebrafish","grant_number":"I 930-B20","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"date_updated":"2021-01-12T06:49:24Z","department":[{"_id":"JiFr"}],"_id":"1251","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":28,"issue":"4","abstract":[{"text":"Plant growth and architecture is regulated by the polar distribution of the hormone auxin. Polarity and flexibility of this process is provided by constant cycling of auxin transporter vesicles along actin filaments, coordinated by a positive auxinactin feedback loop. Both polar auxin transport and vesicle cycling are inhibited by synthetic auxin transport inhibitors, such as 1-Nnaphthylphthalamic acid (NPA), counteracting the effect of auxin; however, underlying targets and mechanisms are unclear. Using NMR, we map the NPA binding surface on the Arabidopsis thaliana ABCB chaperone TWISTED DWARF1 (TWD1).We identify ACTIN7 as a relevant, although likely indirect, TWD1 interactor, and show TWD1-dependent regulation of actin filament organization and dynamics and that TWD1 is required for NPA-mediated actin cytoskeleton remodeling. The TWD1-ACTIN7 axis controls plasma membrane presence of efflux transporters, and as a consequence act7 and twd1 share developmental and physiological phenotypes indicative of defects in auxin transport. These can be phenocopied by NPA treatment or by chemical actin (de)stabilization. We provide evidence that TWD1 determines downstreamlocations of auxin efflux transporters by adjusting actin filament debundling and dynamizing processes and mediating NPA action on the latter. This function appears to be evolutionary conserved since TWD1 expression in budding yeast alters actin polarization and cell polarity and provides NPA sensitivity.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863381/","open_access":"1"}],"scopus_import":1,"intvolume":" 28","month":"04","citation":{"chicago":"Zhu, Jinsheng, Aurélien Bailly, Marta Zwiewka, Valpuri Sovero, Martin Di Donato, Pei Ge, Jacqueline Oehri, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” Plant Cell. American Society of Plant Biologists, 2016. https://doi.org/10.1105/tpc.15.00726.","ista":"Zhu J, Bailly A, Zwiewka M, Sovero V, Di Donato M, Ge P, Oehri J, Aryal B, Hao P, Linnert M, Burgardt N, Lücke C, Weiwad M, Michel M, Weiergräber O, Pollmann S, Azzarello E, Mancuso S, Ferro N, Fukao Y, Hoffmann C, Wedlich Söldner R, Friml J, Thomas C, Geisler M. 2016. TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. Plant Cell. 28(4), 930–948.","mla":"Zhu, Jinsheng, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” Plant Cell, vol. 28, no. 4, American Society of Plant Biologists, 2016, pp. 930–48, doi:10.1105/tpc.15.00726.","ama":"Zhu J, Bailly A, Zwiewka M, et al. TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. Plant Cell. 2016;28(4):930-948. doi:10.1105/tpc.15.00726","apa":"Zhu, J., Bailly, A., Zwiewka, M., Sovero, V., Di Donato, M., Ge, P., … Geisler, M. (2016). TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.15.00726","ieee":"J. Zhu et al., “TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics,” Plant Cell, vol. 28, no. 4. American Society of Plant Biologists, pp. 930–948, 2016.","short":"J. Zhu, A. Bailly, M. Zwiewka, V. Sovero, M. Di Donato, P. Ge, J. Oehri, B. Aryal, P. Hao, M. Linnert, N. Burgardt, C. Lücke, M. Weiwad, M. Michel, O. Weiergräber, S. Pollmann, E. Azzarello, S. Mancuso, N. Ferro, Y. Fukao, C. Hoffmann, R. Wedlich Söldner, J. Friml, C. Thomas, M. Geisler, Plant Cell 28 (2016) 930–948."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6078","author":[{"first_name":"Jinsheng","last_name":"Zhu","full_name":"Zhu, Jinsheng"},{"full_name":"Bailly, Aurélien","last_name":"Bailly","first_name":"Aurélien"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"full_name":"Sovero, Valpuri","last_name":"Sovero","first_name":"Valpuri"},{"last_name":"Di Donato","full_name":"Di Donato, Martin","first_name":"Martin"},{"last_name":"Ge","full_name":"Ge, Pei","first_name":"Pei"},{"last_name":"Oehri","full_name":"Oehri, Jacqueline","first_name":"Jacqueline"},{"full_name":"Aryal, Bibek","last_name":"Aryal","first_name":"Bibek"},{"first_name":"Pengchao","last_name":"Hao","full_name":"Hao, Pengchao"},{"full_name":"Linnert, Miriam","last_name":"Linnert","first_name":"Miriam"},{"last_name":"Burgardt","full_name":"Burgardt, Noelia","first_name":"Noelia"},{"first_name":"Christian","last_name":"Lücke","full_name":"Lücke, Christian"},{"first_name":"Matthias","last_name":"Weiwad","full_name":"Weiwad, Matthias"},{"full_name":"Michel, Max","last_name":"Michel","first_name":"Max"},{"last_name":"Weiergräber","full_name":"Weiergräber, Oliver","first_name":"Oliver"},{"last_name":"Pollmann","full_name":"Pollmann, Stephan","first_name":"Stephan"},{"first_name":"Elisa","last_name":"Azzarello","full_name":"Azzarello, Elisa"},{"full_name":"Mancuso, Stefano","last_name":"Mancuso","first_name":"Stefano"},{"first_name":"Noel","last_name":"Ferro","full_name":"Ferro, Noel"},{"first_name":"Yoichiro","last_name":"Fukao","full_name":"Fukao, Yoichiro"},{"first_name":"Céline","full_name":"Hoffmann, Céline","last_name":"Hoffmann"},{"first_name":"Roland","last_name":"Wedlich Söldner","full_name":"Wedlich Söldner, Roland"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"Clément","last_name":"Thomas","full_name":"Thomas, Clément"},{"full_name":"Geisler, Markus","last_name":"Geisler","first_name":"Markus"}],"title":"TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics","year":"2016","publication":"Plant Cell","day":"01","page":"930 - 948","date_created":"2018-12-11T11:50:57Z","date_published":"2016-04-01T00:00:00Z","doi":"10.1105/tpc.15.00726","acknowledgement":" This work was supported by grants from the European Social Fund (CZ.1.07/2.3.00/20.0043), the Czech Science Foundation GAČR (GA13-40637S) to J.F. and M.Z., the Ministry of Education, Youth, and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) to M.Z., the Ministry for Higher Education and Research of Luxembourg (REC-LOCM-20140703) to C.T., the Partial Funding Program for Short Stays Abroad of CONICET Argentina (to N.I.B.), Swiss National Funds, the Pool de Recherche of the University of Fribourg, and the Novartis Foundation (all to M.G.). ","oa":1,"publisher":"American Society of Plant Biologists","quality_controlled":"1"},{"ec_funded":1,"volume":144,"issue":"4","publication_status":"published","publication_identifier":{"issn":["1088-6826"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1411.7563","open_access":"1"}],"scopus_import":"1","intvolume":" 144","month":"04","abstract":[{"text":"We study the homomorphism induced in homology by a closed correspondence between topological spaces, using projections from the graph of the correspondence to its domain and codomain. We provide assumptions under which the homomorphism induced by an outer approximation of a continuous map coincides with the homomorphism induced in homology by the map. In contrast to more classical results we do not require that the projection to the domain have acyclic preimages. Moreover, we show that it is possible to retrieve correct homological information from a correspondence even if some data is missing or perturbed. Finally, we describe an application to combinatorial maps that are either outer approximations of continuous maps or reconstructions of such maps from a finite set of data points.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"HeEd"}],"date_updated":"2022-05-24T09:35:58Z","article_type":"original","type":"journal_article","status":"public","_id":"1252","page":"1787 - 1801","date_created":"2018-12-11T11:50:57Z","date_published":"2016-04-01T00:00:00Z","doi":"10.1090/proc/12812","year":"2016","publication":"Proceedings of the American Mathematical Society","day":"01","oa":1,"publisher":"American Mathematical Society","quality_controlled":"1","acknowledgement":"The authors gratefully acknowledge the support of the Lorenz Center which\r\nprovided an opportunity for us to discuss in depth the work of this paper. Research leading to these results has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Funda¸c˜ao para a Ciˆencia e a Tecnologia (FCT) in the framework of the research\r\nproject FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008),\r\nas well as from the People Programme (Marie Curie Actions) of the European\r\nUnion’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033 (supporting PP). The work of the first and third author has\r\nbeen partially supported by NSF grants NSF-DMS-0835621, 0915019, 1125174,\r\n1248071, and contracts from AFOSR and DARPA. The work of the second author\r\nwas supported by Grant-in-Aid for Scientific Research (No. 25287029), Ministry of\r\nEducation, Science, Technology, Culture and Sports, Japan.","external_id":{"arxiv":["1411.7563"]},"article_processing_charge":"No","author":[{"full_name":"Harker, Shaun","last_name":"Harker","first_name":"Shaun"},{"first_name":"Hiroshi","full_name":"Kokubu, Hiroshi","last_name":"Kokubu"},{"first_name":"Konstantin","full_name":"Mischaikow, Konstantin","last_name":"Mischaikow"},{"full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk","first_name":"Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6075","title":"Inducing a map on homology from a correspondence","citation":{"mla":"Harker, Shaun, et al. “Inducing a Map on Homology from a Correspondence.” Proceedings of the American Mathematical Society, vol. 144, no. 4, American Mathematical Society, 2016, pp. 1787–801, doi:10.1090/proc/12812.","short":"S. Harker, H. Kokubu, K. Mischaikow, P. Pilarczyk, Proceedings of the American Mathematical Society 144 (2016) 1787–1801.","ieee":"S. Harker, H. Kokubu, K. Mischaikow, and P. Pilarczyk, “Inducing a map on homology from a correspondence,” Proceedings of the American Mathematical Society, vol. 144, no. 4. American Mathematical Society, pp. 1787–1801, 2016.","ama":"Harker S, Kokubu H, Mischaikow K, Pilarczyk P. Inducing a map on homology from a correspondence. Proceedings of the American Mathematical Society. 2016;144(4):1787-1801. doi:10.1090/proc/12812","apa":"Harker, S., Kokubu, H., Mischaikow, K., & Pilarczyk, P. (2016). Inducing a map on homology from a correspondence. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/12812","chicago":"Harker, Shaun, Hiroshi Kokubu, Konstantin Mischaikow, and Pawel Pilarczyk. “Inducing a Map on Homology from a Correspondence.” Proceedings of the American Mathematical Society. American Mathematical Society, 2016. https://doi.org/10.1090/proc/12812.","ista":"Harker S, Kokubu H, Mischaikow K, Pilarczyk P. 2016. Inducing a map on homology from a correspondence. Proceedings of the American Mathematical Society. 144(4), 1787–1801."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"622033","name":"Persistent Homology - Images, Data and Maps","call_identifier":"FP7","_id":"255F06BE-B435-11E9-9278-68D0E5697425"}]},{"_id":"1254","status":"public","type":"journal_article","date_updated":"2021-01-12T06:49:25Z","department":[{"_id":"HeEd"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We use rigorous numerical techniques to compute a lower bound for the exponent of expansivity outside a neighborhood of the critical point for thousands of intervals of parameter values in the quadratic family. We first compute a radius of the critical neighborhood outside which the map is uniformly expanding. This radius is taken as small as possible, yet large enough for our numerical procedure to succeed in proving that the expansivity exponent outside this neighborhood is positive. Then, for each of the intervals, we compute a lower bound for this expansivity exponent, valid for all the parameters in that interval. We illustrate and study the distribution of the radii and the expansivity exponents. The results of our computations are mathematically rigorous. The source code of the software and the results of the computations are made publicly available at http://www.pawelpilarczyk.com/quadratic/."}],"intvolume":" 25","month":"04","main_file_link":[{"url":"https://arxiv.org/abs/1504.00116","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":25,"issue":"2","project":[{"grant_number":"622033","name":"Persistent Homology - Images, Data and Maps","_id":"255F06BE-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Golmakani, A., Luzzatto, S., & Pilarczyk, P. (2016). Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. Taylor and Francis. https://doi.org/10.1080/10586458.2015.1048011","ama":"Golmakani A, Luzzatto S, Pilarczyk P. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 2016;25(2):116-124. doi:10.1080/10586458.2015.1048011","short":"A. Golmakani, S. Luzzatto, P. Pilarczyk, Experimental Mathematics 25 (2016) 116–124.","ieee":"A. Golmakani, S. Luzzatto, and P. Pilarczyk, “Uniform expansivity outside a critical neighborhood in the quadratic family,” Experimental Mathematics, vol. 25, no. 2. Taylor and Francis, pp. 116–124, 2016.","mla":"Golmakani, Ali, et al. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” Experimental Mathematics, vol. 25, no. 2, Taylor and Francis, 2016, pp. 116–24, doi:10.1080/10586458.2015.1048011.","ista":"Golmakani A, Luzzatto S, Pilarczyk P. 2016. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 25(2), 116–124.","chicago":"Golmakani, Ali, Stefano Luzzatto, and Pawel Pilarczyk. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” Experimental Mathematics. Taylor and Francis, 2016. https://doi.org/10.1080/10586458.2015.1048011."},"title":"Uniform expansivity outside a critical neighborhood in the quadratic family","publist_id":"6071","author":[{"first_name":"Ali","last_name":"Golmakani","full_name":"Golmakani, Ali"},{"first_name":"Stefano","last_name":"Luzzatto","full_name":"Luzzatto, Stefano"},{"last_name":"Pilarczyk","full_name":"Pilarczyk, Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel"}],"acknowledgement":"AG and PP were partially supported by Abdus Salam International Centre for Theoretical Physics (ICTP). Additionally, AG was supported by BREUDS, and research conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008); and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033. The authors gratefully acknowledge the Department of\r\nMathematics of Kyoto University for providing access\r\nto their server for conducting computations for this\r\nproject.","oa":1,"publisher":"Taylor and Francis","quality_controlled":"1","publication":"Experimental Mathematics","day":"02","year":"2016","date_created":"2018-12-11T11:50:58Z","doi":"10.1080/10586458.2015.1048011","date_published":"2016-04-02T00:00:00Z","page":"116 - 124"},{"title":"Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction","author":[{"first_name":"Robert","full_name":"Peuß, Robert","last_name":"Peuß"},{"first_name":"Kristina","full_name":"Wensing, Kristina","last_name":"Wensing"},{"first_name":"Luisa","last_name":"Woestmann","full_name":"Woestmann, Luisa"},{"first_name":"Hendrik","last_name":"Eggert","full_name":"Eggert, Hendrik"},{"full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","last_name":"Milutinovic","first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sroka, Marlene","last_name":"Sroka","first_name":"Marlene"},{"last_name":"Scharsack","full_name":"Scharsack, Jörn","first_name":"Jörn"},{"last_name":"Kurtz","full_name":"Kurtz, Joachim","first_name":"Joachim"},{"first_name":"Sophie","full_name":"Armitage, Sophie","last_name":"Armitage"}],"publist_id":"6070","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"R. Peuß, K. Wensing, L. Woestmann, H. Eggert, B. Milutinovic, M. Sroka, J. Scharsack, J. Kurtz, S. Armitage, Royal Society Open Science 3 (2016).","ieee":"R. Peuß et al., “Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction,” Royal Society Open Science, vol. 3, no. 4. Royal Society, The, 2016.","ama":"Peuß R, Wensing K, Woestmann L, et al. Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction. Royal Society Open Science. 2016;3(4). doi:10.1098/rsos.160138","apa":"Peuß, R., Wensing, K., Woestmann, L., Eggert, H., Milutinovic, B., Sroka, M., … Armitage, S. (2016). Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction. Royal Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.160138","mla":"Peuß, Robert, et al. “Down Syndrome Cell Adhesion Molecule 1: Testing for a Role in Insect Immunity, Behaviour and Reproduction.” Royal Society Open Science, vol. 3, no. 4, 160138, Royal Society, The, 2016, doi:10.1098/rsos.160138.","ista":"Peuß R, Wensing K, Woestmann L, Eggert H, Milutinovic B, Sroka M, Scharsack J, Kurtz J, Armitage S. 2016. Down syndrome cell adhesion molecule 1: Testing for a role in insect immunity, behaviour and reproduction. Royal Society Open Science. 3(4), 160138.","chicago":"Peuß, Robert, Kristina Wensing, Luisa Woestmann, Hendrik Eggert, Barbara Milutinovic, Marlene Sroka, Jörn Scharsack, Joachim Kurtz, and Sophie Armitage. “Down Syndrome Cell Adhesion Molecule 1: Testing for a Role in Insect Immunity, Behaviour and Reproduction.” Royal Society Open Science. Royal Society, The, 2016. https://doi.org/10.1098/rsos.160138."},"article_number":"160138","date_published":"2016-04-01T00:00:00Z","doi":"10.1098/rsos.160138","date_created":"2018-12-11T11:50:58Z","day":"01","publication":"Royal Society Open Science","has_accepted_license":"1","year":"2016","publisher":"Royal Society, The","quality_controlled":"1","oa":1,"acknowledgement":"We thank Dietmar Schmucker for reading a draft of this manuscript and thank him and his group for\r\nhelpful discussions. We thank Barbara Hasert, Kevin Ferro and Manuel F. Talarico for technical support and helpful\r\ndiscussions. We also thank two anonymous reviewers for their comments. This study was supported by grants from the Volkswagen Stiftung (1/83 516 and AZ 86020: both to S.A.O.A.) and from the DFG priority programme 1399 ‘Host parasite coevolution’ (KU 1929/4-2 to R.P. and J.K.).","department":[{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:44:41Z","ddc":["576","592"],"date_updated":"2021-01-12T06:49:25Z","status":"public","pubrep_id":"704","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1255","volume":3,"issue":"4","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5049","checksum":"c3cd84666c8dc0ce6a784f1c82c1cf68","creator":"system","date_updated":"2020-07-14T12:44:41Z","file_size":627377,"date_created":"2018-12-12T10:14:01Z","file_name":"IST-2016-704-v1+1_160138.full.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"04","intvolume":" 3","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Down syndrome cell adhesion molecule 1 (Dscam1) has widereaching and vital neuronal functions although the role it plays in insect and crustacean immunity is less well understood. In this study, we combine different approaches to understand the roles that Dscam1 plays in fitness-related contexts in two model insect species. Contrary to our expectations, we found no short-term modulation of Dscam1 gene expression after haemocoelic or oral bacterial exposure in Tribolium castaneum, or after haemocoelic bacterial exposure in Drosophila melanogaster. Furthermore, RNAi-mediated Dscam1 knockdown and subsequent bacterial exposure did not reduce T. castaneum survival. However, Dscam1 knockdown in larvae resulted in adult locomotion defects, as well as dramatically reduced fecundity in males and females. We suggest that Dscam1 does not always play a straightforward role in immunity, but strongly influences behaviour and fecundity. This study takes a step towards understanding more about the role of this intriguing gene from different phenotypic perspectives.","lang":"eng"}]},{"month":"04","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Simulink is widely used for model driven development (MDD) of industrial software systems. Typically, the Simulink based development is initiated from Stateflow modeling, followed by simulation, validation and code generation mapped to physical execution platforms. However, recent industrial trends have raised the demands of rigorous verification on safety-critical applications, which is unfortunately challenging for Simulink. In this paper, we present an approach to bridge the Stateflow based model driven development and a well- defined rigorous verification. First, we develop a self- contained toolkit to translate Stateflow model into timed automata, where major advanced modeling features in Stateflow are supported. Taking advantage of the strong verification capability of Uppaal, we can not only find bugs in Stateflow models which are missed by Simulink Design Verifier, but also check more important temporal properties. Next, we customize a runtime verifier for the generated nonintrusive VHDL and C code of Stateflow model for monitoring. The major strength of the customization is the flexibility to collect and analyze runtime properties with a pure software monitor, which opens more opportunities for engineers to achieve high reliability of the target system compared with the traditional act that only relies on Simulink Polyspace. We incorporate these two parts into original Stateflow based MDD seamlessly. In this way, safety-critical properties are both verified at the model level, and at the consistent system implementation level with physical execution environment in consideration. We apply our approach on a train controller design, and the verified implementation is tested and deployed on a real hardware platform."}],"file":[{"file_id":"4949","checksum":"42f0462911cc9957f2356b12fb33b4b6","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-780-v1+1_RTAS-42-Camera-Ready.pdf","date_created":"2018-12-12T10:12:31Z","file_size":1293599,"date_updated":"2020-07-14T12:44:41Z","creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"780","type":"conference","conference":{"name":"RTAS: Real-time and Embedded Technology and Applications Symposium","start_date":"2016-04-11","end_date":"2016-04-14","location":"Vienna, Austria"},"_id":"1256","file_date_updated":"2020-07-14T12:44:41Z","department":[{"_id":"ToHe"}],"ddc":["005"],"date_updated":"2021-01-12T06:49:26Z","quality_controlled":"1","publisher":"IEEE","oa":1,"acknowledgement":"This work is supported in part by NSF CNS 13-30077, NSF CNS 13-29886, NSF CNS 15-45002, NSFC 61303014, NSFC 61202010, and NSFC 91218302.","date_published":"2016-04-27T00:00:00Z","doi":"10.1109/RTAS.2016.7461337","date_created":"2018-12-11T11:50:58Z","day":"27","has_accepted_license":"1","year":"2016","article_number":"7461337","title":"From stateflow simulation to verified implementation: A verification approach and a real-time train controller design","author":[{"first_name":"Yu","full_name":"Jiang, Yu","last_name":"Jiang"},{"last_name":"Yang","full_name":"Yang, Yixiao","first_name":"Yixiao"},{"first_name":"Han","last_name":"Liu","full_name":"Liu, Han"},{"last_name":"Kong","orcid":"0000-0002-3066-6941","full_name":"Kong, Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui"},{"first_name":"Ming","full_name":"Gu, Ming","last_name":"Gu"},{"first_name":"Jiaguang","full_name":"Sun, Jiaguang","last_name":"Sun"},{"last_name":"Sha","full_name":"Sha, Lui","first_name":"Lui"}],"publist_id":"6069","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Jiang Y, Yang Y, Liu H, Kong H, Gu M, Sun J, Sha L. 2016. From stateflow simulation to verified implementation: A verification approach and a real-time train controller design. RTAS: Real-time and Embedded Technology and Applications Symposium, 7461337.","chicago":"Jiang, Yu, Yixiao Yang, Han Liu, Hui Kong, Ming Gu, Jiaguang Sun, and Lui Sha. “From Stateflow Simulation to Verified Implementation: A Verification Approach and a Real-Time Train Controller Design.” IEEE, 2016. https://doi.org/10.1109/RTAS.2016.7461337.","ama":"Jiang Y, Yang Y, Liu H, et al. From stateflow simulation to verified implementation: A verification approach and a real-time train controller design. In: IEEE; 2016. doi:10.1109/RTAS.2016.7461337","apa":"Jiang, Y., Yang, Y., Liu, H., Kong, H., Gu, M., Sun, J., & Sha, L. (2016). From stateflow simulation to verified implementation: A verification approach and a real-time train controller design. Presented at the RTAS: Real-time and Embedded Technology and Applications Symposium, Vienna, Austria: IEEE. https://doi.org/10.1109/RTAS.2016.7461337","short":"Y. Jiang, Y. Yang, H. Liu, H. Kong, M. Gu, J. Sun, L. Sha, in:, IEEE, 2016.","ieee":"Y. Jiang et al., “From stateflow simulation to verified implementation: A verification approach and a real-time train controller design,” presented at the RTAS: Real-time and Embedded Technology and Applications Symposium, Vienna, Austria, 2016.","mla":"Jiang, Yu, et al. From Stateflow Simulation to Verified Implementation: A Verification Approach and a Real-Time Train Controller Design. 7461337, IEEE, 2016, doi:10.1109/RTAS.2016.7461337."}},{"file_date_updated":"2020-07-14T12:44:42Z","department":[{"_id":"LaEr"}],"ddc":["510","539"],"date_updated":"2021-01-12T06:49:26Z","pubrep_id":"703","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1257","ec_funded":1,"issue":"3","volume":343,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-703-v1+1_s00220-016-2600-4.pdf","date_created":"2018-12-12T10:15:02Z","file_size":800792,"date_updated":"2020-07-14T12:44:42Z","creator":"system","checksum":"4fb2411d9c2f56676123165aad46c828","file_id":"5119","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","intvolume":" 343","month":"05","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We consider products of random matrices that are small, independent identically distributed perturbations of a fixed matrix (Formula presented.). Focusing on the eigenvalues of (Formula presented.) of a particular size we obtain a limit to a SDE in a critical scaling. Previous results required (Formula presented.) to be a (conjugated) unitary matrix so it could not have eigenvalues of different modulus. From the result we can also obtain a limit SDE for the Markov process given by the action of the random products on the flag manifold. Applying the result to random Schrödinger operators we can improve some results by Valko and Virag showing GOE statistics for the rescaled eigenvalue process of a sequence of Anderson models on long boxes. In particular, we solve a problem posed in their work."}],"title":"A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes","article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Christian","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","last_name":"Sadel","orcid":"0000-0001-8255-3968","full_name":"Sadel, Christian"},{"first_name":"Bálint","full_name":"Virág, Bálint","last_name":"Virág"}],"publist_id":"6067","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Sadel, Christian, and Bálint Virág. “A Central Limit Theorem for Products of Random Matrices and GOE Statistics for the Anderson Model on Long Boxes.” Communications in Mathematical Physics, vol. 343, no. 3, Springer, 2016, pp. 881–919, doi:10.1007/s00220-016-2600-4.","ieee":"C. Sadel and B. Virág, “A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes,” Communications in Mathematical Physics, vol. 343, no. 3. Springer, pp. 881–919, 2016.","short":"C. Sadel, B. Virág, Communications in Mathematical Physics 343 (2016) 881–919.","apa":"Sadel, C., & Virág, B. (2016). A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-016-2600-4","ama":"Sadel C, Virág B. A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes. Communications in Mathematical Physics. 2016;343(3):881-919. doi:10.1007/s00220-016-2600-4","chicago":"Sadel, Christian, and Bálint Virág. “A Central Limit Theorem for Products of Random Matrices and GOE Statistics for the Anderson Model on Long Boxes.” Communications in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s00220-016-2600-4.","ista":"Sadel C, Virág B. 2016. A central limit theorem for products of random matrices and GOE statistics for the Anderson model on long boxes. Communications in Mathematical Physics. 343(3), 881–919."},"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"date_created":"2018-12-11T11:50:59Z","doi":"10.1007/s00220-016-2600-4","date_published":"2016-05-01T00:00:00Z","page":"881 - 919","publication":"Communications in Mathematical Physics","day":"01","year":"2016","has_accepted_license":"1","oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The work of C. Sadel was supported by NSERC Discovery Grant 92997-2010 RGPIN and by the People Programme (Marie Curie Actions) of the EU 7th Framework Programme FP7/2007-2013, REA Grant 291734."},{"abstract":[{"lang":"eng","text":"When plants grow in close proximity basic resources such as light can become limiting. Under such conditions plants respond to anticipate and/or adapt to the light shortage, a process known as the shade avoidance syndrome (SAS). Following genetic screening using a shade-responsive luciferase reporter line (PHYB:LUC), we identified DRACULA2 (DRA2), which encodes an Arabidopsis homolog of mammalian nucleoporin 98, a component of the nuclear pore complex (NPC). DRA2, together with other nucleoporins, participates positively in the control of the hypocotyl elongation response to plant proximity, a role that can be considered dependent on the nucleocytoplasmic transport of macromolecules (i.e. is transport dependent). In addition, our results reveal a specific role for DRA2 in controlling shade-induced gene expression. We suggest that this novel regulatory role of DRA2 is transport independent and that it might rely on its dynamic localization within and outside of the NPC. These results provide mechanistic insights in to how SAS responses are rapidly established by light conditions. They also indicate that nucleoporins have an active role in plant signaling."}],"oa_version":"None","acknowledgement":"M.G. received an FPI fellowship from the Spanish Ministerio de Economía y Competitividad (MINECO). A.G. and A.F.-A. received FPU fellowships from the Spanish Ministerio de Educación. S.P. received an FI fellowship from the Agència de Gestió D'ajuts Universitaris i de Recerca (AGAUR - Generalitat de Catalunya). C.T. received a Marie Curie IEF postdoctoral contract funded by the European Commission. I.R.-V. received initially an FPI fellowship from the Spanish MINECO and later a Beatriu de Pinós contract from AGAUR. Our research is supported by grants from the Spanish MINECO-FEDER [BIO2008-00169, BIO2011-23489 and BIO2014-59895-P] and Generalitat de Catalunya [2011-SGR447 and Xarba] to J.F.M.-G., and Generalitat Valenciana [PROMETEO/2009/112, PROMETEOII/2014/006] to M.R.P. and J.L.M. We acknowledge the support of the Spanish MINECO for the ‘Centro de Excelencia Severo Ochoa 2016-2019’ [award SEV-2015-0533]. We thank the CRAG greenhouse service for plant care; Chus Burillo for technical help; Sergi Portolés and Carles Rentero for assistance with mutagenesis; Mark Estelle (UCSD, USA) for providing sar1-4, sar3-1 and sar3-3 seeds; Juanjo López-Moya (CRAG, Barcelona; 35S:HcPro plasmid) and Dolors Ludevid (CRAG; C307 plasmid) for providing DNA plasmids; and Manuel Rodríguez-Concepción (CRAG) and Miguel Blázquez (IBMCP, Valencia, Spain) for comments on the manuscript.","quality_controlled":"1","scopus_import":1,"publisher":"Company of Biologists","month":"05","intvolume":" 143","publication_status":"published","year":"2016","day":"03","language":[{"iso":"eng"}],"publication":"Development","page":"1623 - 1631","date_published":"2016-05-03T00:00:00Z","volume":143,"doi":"10.1242/dev.130211","issue":"9","date_created":"2018-12-11T11:50:59Z","_id":"1258","type":"journal_article","status":"public","citation":{"ista":"Gallemi M, Galstyan A, Paulišić S, Then C, Ferrández Ayela A, Lorenzo Orts L, Roig Villanova I, Wang X, Micol J, Ponce M, Devlin P, Martínez García J. 2016. DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development. 143(9), 1623–1631.","chicago":"Gallemi, Marçal, Anahit Galstyan, Sandi Paulišić, Christiane Then, Almudena Ferrández Ayela, Laura Lorenzo Orts, Irma Roig Villanova, et al. “DRACULA2 Is a Dynamic Nucleoporin with a Role in Regulating the Shade Avoidance Syndrome in Arabidopsis.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.130211.","ama":"Gallemi M, Galstyan A, Paulišić S, et al. DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development. 2016;143(9):1623-1631. doi:10.1242/dev.130211","apa":"Gallemi, M., Galstyan, A., Paulišić, S., Then, C., Ferrández Ayela, A., Lorenzo Orts, L., … Martínez García, J. (2016). DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development. Company of Biologists. https://doi.org/10.1242/dev.130211","ieee":"M. Gallemi et al., “DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis,” Development, vol. 143, no. 9. Company of Biologists, pp. 1623–1631, 2016.","short":"M. Gallemi, A. Galstyan, S. Paulišić, C. Then, A. Ferrández Ayela, L. Lorenzo Orts, I. Roig Villanova, X. Wang, J. Micol, M. Ponce, P. Devlin, J. Martínez García, Development 143 (2016) 1623–1631.","mla":"Gallemi, Marçal, et al. “DRACULA2 Is a Dynamic Nucleoporin with a Role in Regulating the Shade Avoidance Syndrome in Arabidopsis.” Development, vol. 143, no. 9, Company of Biologists, 2016, pp. 1623–31, doi:10.1242/dev.130211."},"date_updated":"2021-01-12T06:49:27Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Gallemi Rovira, Marcal","last_name":"Gallemi Rovira","id":"460C6802-F248-11E8-B48F-1D18A9856A87","first_name":"Marcal"},{"full_name":"Galstyan, Anahit","last_name":"Galstyan","first_name":"Anahit"},{"first_name":"Sandi","full_name":"Paulišić, Sandi","last_name":"Paulišić"},{"first_name":"Christiane","last_name":"Then","full_name":"Then, Christiane"},{"full_name":"Ferrández Ayela, Almudena","last_name":"Ferrández Ayela","first_name":"Almudena"},{"first_name":"Laura","last_name":"Lorenzo Orts","full_name":"Lorenzo Orts, Laura"},{"first_name":"Irma","full_name":"Roig Villanova, Irma","last_name":"Roig Villanova"},{"first_name":"Xuewen","full_name":"Wang, Xuewen","last_name":"Wang"},{"first_name":"José","full_name":"Micol, José","last_name":"Micol"},{"last_name":"Ponce","full_name":"Ponce, Maria","first_name":"Maria"},{"full_name":"Devlin, Paul","last_name":"Devlin","first_name":"Paul"},{"first_name":"Jaime","last_name":"Martínez García","full_name":"Martínez García, Jaime"}],"publist_id":"6068","title":"DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis","department":[{"_id":"EvBe"}]},{"scopus_import":1,"intvolume":" 19","month":"06","abstract":[{"text":"We consider the Bogolubov–Hartree–Fock functional for a fermionic many-body system with two-body interactions. For suitable interaction potentials that have a strong enough attractive tail in order to allow for two-body bound states, but are otherwise sufficiently repulsive to guarantee stability of the system, we show that in the low-density limit the ground state of this model consists of a Bose–Einstein condensate of fermion pairs. The latter can be described by means of the Gross–Pitaevskii energy functional.","lang":"eng"}],"oa_version":"Published Version","volume":19,"issue":"2","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:09:13Z","file_name":"IST-2016-702-v1+1_s11040-016-9209-x.pdf","date_updated":"2020-07-14T12:44:42Z","file_size":506242,"creator":"system","checksum":"9954f685cc25c58d7f1712c67b47ad8d","file_id":"4736","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"702","status":"public","_id":"1259","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:44:42Z","date_updated":"2021-01-12T06:49:27Z","ddc":["510","539"],"oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"Partial financial support from the DFG grant GRK 1838, as well as the Austrian Science Fund (FWF), project Nr. P 27533-N27 (R.S.), is gratefully acknowledged.","date_created":"2018-12-11T11:50:59Z","date_published":"2016-06-01T00:00:00Z","doi":"10.1007/s11040-016-9209-x","year":"2016","has_accepted_license":"1","publication":"Mathematical Physics, Analysis and Geometry","day":"01","project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"article_number":"13","article_processing_charge":"Yes (via OA deal)","publist_id":"6066","author":[{"full_name":"Bräunlich, Gerhard","last_name":"Bräunlich","first_name":"Gerhard"},{"last_name":"Hainzl","full_name":"Hainzl, Christian","first_name":"Christian"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"title":"Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit","citation":{"mla":"Bräunlich, Gerhard, et al. “Bogolubov–Hartree–Fock Theory for Strongly Interacting Fermions in the Low Density Limit.” Mathematical Physics, Analysis and Geometry, vol. 19, no. 2, 13, Springer, 2016, doi:10.1007/s11040-016-9209-x.","ama":"Bräunlich G, Hainzl C, Seiringer R. Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit. Mathematical Physics, Analysis and Geometry. 2016;19(2). doi:10.1007/s11040-016-9209-x","apa":"Bräunlich, G., Hainzl, C., & Seiringer, R. (2016). Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-016-9209-x","ieee":"G. Bräunlich, C. Hainzl, and R. Seiringer, “Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit,” Mathematical Physics, Analysis and Geometry, vol. 19, no. 2. Springer, 2016.","short":"G. Bräunlich, C. Hainzl, R. Seiringer, Mathematical Physics, Analysis and Geometry 19 (2016).","chicago":"Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Bogolubov–Hartree–Fock Theory for Strongly Interacting Fermions in the Low Density Limit.” Mathematical Physics, Analysis and Geometry. Springer, 2016. https://doi.org/10.1007/s11040-016-9209-x.","ista":"Bräunlich G, Hainzl C, Seiringer R. 2016. Bogolubov–Hartree–Fock theory for strongly interacting fermions in the low density limit. Mathematical Physics, Analysis and Geometry. 19(2), 13."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"article_number":"1650067","citation":{"chicago":"De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” International Journal of Modern Physics C. World Scientific Publishing, 2016. https://doi.org/10.1142/S0129183116500674.","ista":"De Martino D. 2016. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 27(6), 1650067.","mla":"De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” International Journal of Modern Physics C, vol. 27, no. 6, 1650067, World Scientific Publishing, 2016, doi:10.1142/S0129183116500674.","ieee":"D. De Martino, “The dual of the space of interactions in neural network models,” International Journal of Modern Physics C, vol. 27, no. 6. World Scientific Publishing, 2016.","short":"D. De Martino, International Journal of Modern Physics C 27 (2016).","apa":"De Martino, D. (2016). The dual of the space of interactions in neural network models. International Journal of Modern Physics C. World Scientific Publishing. https://doi.org/10.1142/S0129183116500674","ama":"De Martino D. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 2016;27(6). doi:10.1142/S0129183116500674"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1505.02963"]},"publist_id":"6065","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","last_name":"De Martino","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele"}],"title":"The dual of the space of interactions in neural network models","oa":1,"quality_controlled":"1","publisher":"World Scientific Publishing","year":"2016","publication":"International Journal of Modern Physics C","day":"01","date_created":"2018-12-11T11:51:00Z","date_published":"2016-06-01T00:00:00Z","doi":"10.1142/S0129183116500674","_id":"1260","article_type":"original","type":"journal_article","status":"public","date_updated":"2021-01-12T06:49:28Z","department":[{"_id":"GaTk"}],"abstract":[{"lang":"eng","text":"In this work, the Gardner problem of inferring interactions and fields for an Ising neural network from given patterns under a local stability hypothesis is addressed under a dual perspective. By means of duality arguments, an integer linear system is defined whose solution space is the dual of the Gardner space and whose solutions represent mutually unstable patterns. We propose and discuss Monte Carlo methods in order to find and remove unstable patterns and uniformly sample the space of interactions thereafter. We illustrate the problem on a set of real data and perform ensemble calculation that shows how the emergence of phase dominated by unstable patterns can be triggered in a nonlinear discontinuous way."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1505.02963"}],"scopus_import":1,"intvolume":" 27","month":"06","publication_status":"published","language":[{"iso":"eng"}],"volume":27,"issue":"6"},{"department":[{"_id":"JaMa"}],"date_updated":"2021-01-12T06:49:28Z","status":"public","type":"journal_article","_id":"1261","volume":29,"issue":"7","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 29","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1505.03178"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"We consider a non-standard finite-volume discretization of a strongly non-linear fourth order diffusion equation on the d-dimensional cube, for arbitrary . The scheme preserves two important structural properties of the equation: the first is the interpretation as a gradient flow in a mass transportation metric, and the second is an intimate relation to a linear Fokker-Planck equation. Thanks to these structural properties, the scheme possesses two discrete Lyapunov functionals. These functionals approximate the entropy and the Fisher information, respectively, and their dissipation rates converge to the optimal ones in the discrete-to-continuous limit. Using the dissipation, we derive estimates on the long-time asymptotics of the discrete solutions. Finally, we present results from numerical experiments which indicate that our discretization is able to capture significant features of the complex original dynamics, even with a rather coarse spatial resolution.","lang":"eng"}],"title":"Long-time behavior of a finite volume discretization for a fourth order diffusion equation","author":[{"last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniel","full_name":"Matthes, Daniel","last_name":"Matthes"}],"publist_id":"6062","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Maas J, Matthes D. 2016. Long-time behavior of a finite volume discretization for a fourth order diffusion equation. Nonlinearity. 29(7), 1992–2023.","chicago":"Maas, Jan, and Daniel Matthes. “Long-Time Behavior of a Finite Volume Discretization for a Fourth Order Diffusion Equation.” Nonlinearity. IOP Publishing Ltd., 2016. https://doi.org/10.1088/0951-7715/29/7/1992.","ama":"Maas J, Matthes D. Long-time behavior of a finite volume discretization for a fourth order diffusion equation. Nonlinearity. 2016;29(7):1992-2023. doi:10.1088/0951-7715/29/7/1992","apa":"Maas, J., & Matthes, D. (2016). Long-time behavior of a finite volume discretization for a fourth order diffusion equation. Nonlinearity. IOP Publishing Ltd. https://doi.org/10.1088/0951-7715/29/7/1992","ieee":"J. Maas and D. Matthes, “Long-time behavior of a finite volume discretization for a fourth order diffusion equation,” Nonlinearity, vol. 29, no. 7. IOP Publishing Ltd., pp. 1992–2023, 2016.","short":"J. Maas, D. Matthes, Nonlinearity 29 (2016) 1992–2023.","mla":"Maas, Jan, and Daniel Matthes. “Long-Time Behavior of a Finite Volume Discretization for a Fourth Order Diffusion Equation.” Nonlinearity, vol. 29, no. 7, IOP Publishing Ltd., 2016, pp. 1992–2023, doi:10.1088/0951-7715/29/7/1992."},"date_created":"2018-12-11T11:51:00Z","doi":"10.1088/0951-7715/29/7/1992","date_published":"2016-06-10T00:00:00Z","page":"1992 - 2023","publication":"Nonlinearity","day":"10","year":"2016","oa":1,"publisher":"IOP Publishing Ltd.","quality_controlled":"1","acknowledgement":"This research was supported by the DFG Collaborative Research Centers TRR 109, ‘ Discretization in Geometry and Dynamics ’ and 1060 ‘ The Mathematics of Emergent Effects ’ ."},{"project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Sancho Andrés, Gloria, Esther Soriano Ortega, Caiji Gao, Joan Bernabé Orts, Madhumitha Narasimhan, Anna Müller, Ricardo Tejos, et al. “Sorting Motifs Involved in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.00373.","ista":"Sancho Andrés G, Soriano Ortega E, Gao C, Bernabé Orts J, Narasimhan M, Müller A, Tejos R, Jiang L, Friml J, Aniento F, Marcote M. 2016. Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. 171(3), 1965–1982.","mla":"Sancho Andrés, Gloria, et al. “Sorting Motifs Involved in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” Plant Physiology, vol. 171, no. 3, American Society of Plant Biologists, 2016, pp. 1965–82, doi:10.1104/pp.16.00373.","ama":"Sancho Andrés G, Soriano Ortega E, Gao C, et al. Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. 2016;171(3):1965-1982. doi:10.1104/pp.16.00373","apa":"Sancho Andrés, G., Soriano Ortega, E., Gao, C., Bernabé Orts, J., Narasimhan, M., Müller, A., … Marcote, M. (2016). Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00373","ieee":"G. Sancho Andrés et al., “Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier,” Plant Physiology, vol. 171, no. 3. American Society of Plant Biologists, pp. 1965–1982, 2016.","short":"G. Sancho Andrés, E. Soriano Ortega, C. Gao, J. Bernabé Orts, M. Narasimhan, A. Müller, R. Tejos, L. Jiang, J. Friml, F. Aniento, M. Marcote, Plant Physiology 171 (2016) 1965–1982."},"title":"Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier","publist_id":"6059","author":[{"first_name":"Gloria","last_name":"Sancho Andrés","full_name":"Sancho Andrés, Gloria"},{"first_name":"Esther","full_name":"Soriano Ortega, Esther","last_name":"Soriano Ortega"},{"full_name":"Gao, Caiji","last_name":"Gao","first_name":"Caiji"},{"first_name":"Joan","full_name":"Bernabé Orts, Joan","last_name":"Bernabé Orts"},{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671"},{"full_name":"Müller, Anna","last_name":"Müller","first_name":"Anna","id":"420AB15A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ricardo","full_name":"Tejos, Ricardo","last_name":"Tejos"},{"first_name":"Liwen","last_name":"Jiang","full_name":"Jiang, Liwen"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"full_name":"Aniento, Fernando","last_name":"Aniento","first_name":"Fernando"},{"full_name":"Marcote, Maria","last_name":"Marcote","first_name":"Maria"}],"acknowledgement":"We thank Dr. R. Offringa (Leiden University) for providing the GST-\r\nPIN-CL construct; Sandra Richter and Gerd Jurgens (University of Tübin-\r\ngen) for providing the estradiol-inducible PIN1-RFP construct and the\r\ngnl1 mutant expressing BFA-sensitive GNL1; F.J. Santonja (University of Valencia)\r\nfor help with the statistical analysis; Jurgen Kleine-Vehn, Elke Barbez, and\r\nEva Benkova for helpful discussions; the Salk Institute Genomic Analysis\r\nLaboratory for providing the sequence-indexed Arabidopsis T-DNA in-\r\nsertion mutants; and the greenhouse section and the microscopy section\r\nof SCSIE (University of Valencia) and Pilar Selvi for excellent technical\r\nassistance.","oa":1,"publisher":"American Society of Plant Biologists","quality_controlled":"1","publication":"Plant Physiology","day":"01","year":"2016","date_created":"2018-12-11T11:51:01Z","date_published":"2016-07-01T00:00:00Z","doi":"10.1104/pp.16.00373","page":"1965 - 1982","_id":"1264","status":"public","type":"journal_article","date_updated":"2021-01-12T06:49:29Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"oa_version":"Submitted Version","abstract":[{"text":"n contrast with the wealth of recent reports about the function of μ-adaptins and clathrin adaptor protein (AP) complexes, there is very little information about the motifs that determine the sorting of membrane proteins within clathrin-coated vesicles in plants. Here, we investigated putative sorting signals in the large cytosolic loop of the Arabidopsis (Arabidopsis thaliana) PIN-FORMED1 (PIN1) auxin transporter, which are involved in binding μ-adaptins and thus in PIN1 trafficking and localization. We found that Phe-165 and Tyr-280, Tyr-328, and Tyr-394 are involved in the binding of different μ-adaptins in vitro. However, only Phe-165, which binds μA(μ2)- and μD(μ3)-adaptin, was found to be essential for PIN1 trafficking and localization in vivo. The PIN1:GFP-F165A mutant showed reduced endocytosis but also localized to intracellular structures containing several layers of membranes and endoplasmic reticulum (ER) markers, suggesting that they correspond to ER or ER-derived membranes. While PIN1:GFP localized normally in a μA (μ2)-adaptin mutant, it accumulated in big intracellular structures containing LysoTracker in a μD (μ3)-adaptin mutant, consistent with previous results obtained with mutants of other subunits of the AP-3 complex. Our data suggest that Phe-165, through the binding of μA (μ2)- and μD (μ3)-adaptin, is important for PIN1 endocytosis and for PIN1 trafficking along the secretory pathway, respectively.","lang":"eng"}],"intvolume":" 171","month":"07","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936568/","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"issue":"3","volume":171},{"_id":"1265","article_number":"rs5","type":"journal_article","status":"public","citation":{"ista":"Elsayad K, Werner S, Gallemi M, Kong J, Guajardo E, Zhang L, Jaillais Y, Greb T, Belkhadir Y. 2016. Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. 9(435), rs5.","chicago":"Elsayad, Kareem, Stephanie Werner, Marçal Gallemi, Jixiang Kong, Edmundo Guajardo, Lijuan Zhang, Yvon Jaillais, Thomas Greb, and Youssef Belkhadir. “Mapping the Subcellular Mechanical Properties of Live Cells in Tissues with Fluorescence Emission-Brillouin Imaging.” Science Signaling. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/scisignal.aaf6326.","apa":"Elsayad, K., Werner, S., Gallemi, M., Kong, J., Guajardo, E., Zhang, L., … Belkhadir, Y. (2016). Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. American Association for the Advancement of Science. https://doi.org/10.1126/scisignal.aaf6326","ama":"Elsayad K, Werner S, Gallemi M, et al. Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. 2016;9(435). doi:10.1126/scisignal.aaf6326","ieee":"K. Elsayad et al., “Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging,” Science Signaling, vol. 9, no. 435. American Association for the Advancement of Science, 2016.","short":"K. Elsayad, S. Werner, M. Gallemi, J. Kong, E. Guajardo, L. Zhang, Y. Jaillais, T. Greb, Y. Belkhadir, Science Signaling 9 (2016).","mla":"Elsayad, Kareem, et al. “Mapping the Subcellular Mechanical Properties of Live Cells in Tissues with Fluorescence Emission-Brillouin Imaging.” Science Signaling, vol. 9, no. 435, rs5, American Association for the Advancement of Science, 2016, doi:10.1126/scisignal.aaf6326."},"date_updated":"2021-01-12T06:49:29Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Elsayad, Kareem","last_name":"Elsayad","first_name":"Kareem"},{"full_name":"Werner, Stephanie","last_name":"Werner","first_name":"Stephanie"},{"full_name":"Gallemi Rovira, Marcal","last_name":"Gallemi Rovira","id":"460C6802-F248-11E8-B48F-1D18A9856A87","first_name":"Marcal"},{"last_name":"Kong","full_name":"Kong, Jixiang","first_name":"Jixiang"},{"full_name":"Guajardo, Edmundo","last_name":"Guajardo","first_name":"Edmundo"},{"first_name":"Lijuan","last_name":"Zhang","full_name":"Zhang, Lijuan"},{"first_name":"Yvon","full_name":"Jaillais, Yvon","last_name":"Jaillais"},{"full_name":"Greb, Thomas","last_name":"Greb","first_name":"Thomas"},{"last_name":"Belkhadir","full_name":"Belkhadir, Youssef","first_name":"Youssef"}],"publist_id":"6057","department":[{"_id":"EvBe"}],"title":"Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging","abstract":[{"lang":"eng","text":"Extracellular matrices (ECMs) are central to the advent of multicellular life, and their mechanical propertiesare modulated by and impinge on intracellular signaling pathways that regulate vital cellular functions. High spatial-resolution mapping of mechanical properties in live cells is, however, extremely challenging. Thus, our understanding of how signaling pathways process physiological signals to generate appropriate mechanical responses is limited. We introduce fluorescence emission-Brillouin scattering imaging (FBi), a method for the parallel and all-optical measurements of mechanical properties and fluorescence at the submicrometer scale in living organisms. Using FBi, we showed thatchanges in cellular hydrostatic pressure and cytoplasm viscoelasticity modulate the mechanical signatures of plant ECMs. We further established that the measured "stiffness" of plant ECMs is symmetrically patternedin hypocotyl cells undergoing directional growth. Finally, application of this method to Arabidopsis thaliana with photoreceptor mutants revealed that red and far-red light signals are essential modulators of ECM viscoelasticity. By mapping the viscoelastic signatures of a complex ECM, we provide proof of principlefor the organism-wide applicability of FBi for measuring the mechanical outputs of intracellular signaling pathways. As such, our work has implications for investigations of mechanosignaling pathways and developmental biology."}],"oa_version":"None","scopus_import":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","intvolume":" 9","month":"07","publication_status":"published","year":"2016","language":[{"iso":"eng"}],"publication":"Science Signaling","day":"05","date_created":"2018-12-11T11:51:02Z","doi":"10.1126/scisignal.aaf6326","volume":9,"issue":"435","date_published":"2016-07-05T00:00:00Z"},{"issue":"2016JULY","volume":5,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":2819055,"date_updated":"2020-07-14T12:44:42Z","file_name":"IST-2016-700-v1+1_e13824-download.pdf","date_created":"2018-12-12T10:11:20Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4874","checksum":"dc52d967dc76174477bb258d84be2899"}],"scopus_import":1,"intvolume":" 5","month":"07","abstract":[{"lang":"eng","text":"Cortical networks exhibit ‘global oscillations’, in which neural spike times are entrained to an underlying oscillatory rhythm, but where individual neurons fire irregularly, on only a fraction of cycles. While the network dynamics underlying global oscillations have been well characterised, their function is debated. Here, we show that such global oscillations are a direct consequence of optimal efficient coding in spiking networks with synaptic delays and noise. To avoid firing unnecessary spikes, neurons need to share information about the network state. Ideally, membrane potentials should be strongly correlated and reflect a ‘prediction error’ while the spikes themselves are uncorrelated and occur rarely. We show that the most efficient representation is when: (i) spike times are entrained to a global Gamma rhythm (implying a consistent representation of the error); but (ii) few neurons fire on each cycle (implying high efficiency), while (iii) excitation and inhibition are tightly balanced. This suggests that cortical networks exhibiting such dynamics are tuned to achieve a maximally efficient population code."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:44:42Z","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T06:49:30Z","ddc":["571"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"700","status":"public","_id":"1266","date_created":"2018-12-11T11:51:02Z","date_published":"2016-07-01T00:00:00Z","doi":"10.7554/eLife.13824","year":"2016","has_accepted_license":"1","publication":"eLife","day":"01","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","acknowledgement":"Boris Gutkin acknowledges funding by the Russian Academic Excellence Project '5-100’.","author":[{"last_name":"Chalk","orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J","first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Boris","last_name":"Gutkin","full_name":"Gutkin, Boris"},{"last_name":"Denève","full_name":"Denève, Sophie","first_name":"Sophie"}],"publist_id":"6056","title":"Neural oscillations as a signature of efficient coding in the presence of synaptic delays","citation":{"ista":"Chalk MJ, Gutkin B, Denève S. 2016. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. eLife. 5(2016JULY), e13824.","chicago":"Chalk, Matthew J, Boris Gutkin, and Sophie Denève. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.13824.","short":"M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016).","ieee":"M. J. Chalk, B. Gutkin, and S. Denève, “Neural oscillations as a signature of efficient coding in the presence of synaptic delays,” eLife, vol. 5, no. 2016JULY. eLife Sciences Publications, 2016.","ama":"Chalk MJ, Gutkin B, Denève S. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. eLife. 2016;5(2016JULY). doi:10.7554/eLife.13824","apa":"Chalk, M. J., Gutkin, B., & Denève, S. (2016). Neural oscillations as a signature of efficient coding in the presence of synaptic delays. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.13824","mla":"Chalk, Matthew J., et al. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” ELife, vol. 5, no. 2016JULY, e13824, eLife Sciences Publications, 2016, doi:10.7554/eLife.13824."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"e13824"},{"status":"public","pubrep_id":"697","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1269","file_date_updated":"2020-07-14T12:44:42Z","department":[{"_id":"EvBe"}],"ddc":["581"],"date_updated":"2021-01-12T06:49:31Z","month":"08","intvolume":" 91","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Plants are continuously exposed to a myriad of external signals such as fluctuating nutrients availability, drought, heat, cold, high salinity, or pathogen/pest attacks that can severely affect their development, growth, and fertility. As sessile organisms, plants must therefore be able to sense and rapidly react to these external inputs, activate efficient responses, and adjust development to changing conditions. In recent years, significant progress has been made towards understanding the molecular mechanisms underlying the intricate and complex communication between plants and the environment. It is now becoming increasingly evident that hormones have an important regulatory role in plant adaptation and defense mechanisms.","lang":"eng"}],"volume":91,"issue":"6","file":[{"date_created":"2018-12-12T10:18:28Z","file_name":"IST-2016-697-v1+1_s11103-016-0501-8.pdf","date_updated":"2020-07-14T12:44:42Z","file_size":297282,"creator":"system","file_id":"5349","checksum":"0ffb7a15c5336b3a55248cc67021a825","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_status":"published","title":"Plant hormones in interactions with the environment","author":[{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6052","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"E. Benková, “Plant hormones in interactions with the environment,” Plant Molecular Biology, vol. 91, no. 6. Springer, p. 597, 2016.","short":"E. Benková, Plant Molecular Biology 91 (2016) 597.","apa":"Benková, E. (2016). Plant hormones in interactions with the environment. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-016-0501-8","ama":"Benková E. Plant hormones in interactions with the environment. Plant Molecular Biology. 2016;91(6):597. doi:10.1007/s11103-016-0501-8","mla":"Benková, Eva. “Plant Hormones in Interactions with the Environment.” Plant Molecular Biology, vol. 91, no. 6, Springer, 2016, p. 597, doi:10.1007/s11103-016-0501-8.","ista":"Benková E. 2016. Plant hormones in interactions with the environment. Plant Molecular Biology. 91(6), 597.","chicago":"Benková, Eva. “Plant Hormones in Interactions with the Environment.” Plant Molecular Biology. Springer, 2016. https://doi.org/10.1007/s11103-016-0501-8."},"publisher":"Springer","quality_controlled":"1","oa":1,"date_published":"2016-08-01T00:00:00Z","doi":"10.1007/s11103-016-0501-8","date_created":"2018-12-11T11:51:03Z","page":"597","day":"01","publication":"Plant Molecular Biology","has_accepted_license":"1","year":"2016"},{"ddc":["510","539"],"date_updated":"2021-01-12T06:49:30Z","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:44:42Z","_id":"1267","pubrep_id":"698","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"checksum":"d740a6a226e0f5f864f40e3e269d3cc0","file_id":"4863","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:11:09Z","file_name":"IST-2016-698-v1+1_s11005-016-0860-8.pdf","creator":"system","date_updated":"2020-07-14T12:44:42Z","file_size":349464}],"publication_status":"published","volume":106,"issue":"8","oa_version":"Published Version","abstract":[{"text":"We give a simplified proof of the nonexistence of large nuclei in the liquid drop model and provide an explicit bound. Our bound is within a factor of 2.3 of the conjectured value and seems to be the first quantitative result.","lang":"eng"}],"intvolume":" 106","month":"08","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Frank, Rupert, et al. “Nonexistence of Large Nuclei in the Liquid Drop Model.” Letters in Mathematical Physics, vol. 106, no. 8, Springer, 2016, pp. 1033–36, doi:10.1007/s11005-016-0860-8.","apa":"Frank, R., Killip, R., & Nam, P. (2016). Nonexistence of large nuclei in the liquid drop model. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0860-8","ama":"Frank R, Killip R, Nam P. Nonexistence of large nuclei in the liquid drop model. Letters in Mathematical Physics. 2016;106(8):1033-1036. doi:10.1007/s11005-016-0860-8","ieee":"R. Frank, R. Killip, and P. Nam, “Nonexistence of large nuclei in the liquid drop model,” Letters in Mathematical Physics, vol. 106, no. 8. Springer, pp. 1033–1036, 2016.","short":"R. Frank, R. Killip, P. Nam, Letters in Mathematical Physics 106 (2016) 1033–1036.","chicago":"Frank, Rupert, Rowan Killip, and Phan Nam. “Nonexistence of Large Nuclei in the Liquid Drop Model.” Letters in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s11005-016-0860-8.","ista":"Frank R, Killip R, Nam P. 2016. Nonexistence of large nuclei in the liquid drop model. Letters in Mathematical Physics. 106(8), 1033–1036."},"title":"Nonexistence of large nuclei in the liquid drop model","author":[{"full_name":"Frank, Rupert","last_name":"Frank","first_name":"Rupert"},{"first_name":"Rowan","full_name":"Killip, Rowan","last_name":"Killip"},{"full_name":"Nam, Phan","last_name":"Nam","first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6054","project":[{"grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"publication":"Letters in Mathematical Physics","day":"01","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:51:02Z","doi":"10.1007/s11005-016-0860-8","date_published":"2016-08-01T00:00:00Z","page":"1033 - 1036","acknowledgement":"Open access funding provided by Institute of Science and Technology Austria.\r\n","oa":1,"publisher":"Springer","quality_controlled":"1"},{"acknowledgement":"We would like to thank Mihai Netea for inviting us to contribute to this Theme Issue.","oa_version":"None","intvolume":" 28","month":"08","quality_controlled":"1","publisher":"Academic Press","scopus_import":1,"language":[{"iso":"eng"}],"publication":"Seminars in Immunology","day":"01","publication_status":"published","year":"2016","date_created":"2018-12-11T11:51:03Z","date_published":"2016-08-01T00:00:00Z","doi":"10.1016/j.smim.2016.05.004","volume":28,"issue":"4","page":"328 - 342","_id":"1268","status":"public","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Milutinovic, Barbara, and Joachim Kurtz. “Immune Memory in Invertebrates.” Seminars in Immunology. Academic Press, 2016. https://doi.org/10.1016/j.smim.2016.05.004.","ista":"Milutinovic B, Kurtz J. 2016. Immune memory in invertebrates. Seminars in Immunology. 28(4), 328–342.","mla":"Milutinovic, Barbara, and Joachim Kurtz. “Immune Memory in Invertebrates.” Seminars in Immunology, vol. 28, no. 4, Academic Press, 2016, pp. 328–42, doi:10.1016/j.smim.2016.05.004.","short":"B. Milutinovic, J. Kurtz, Seminars in Immunology 28 (2016) 328–342.","ieee":"B. Milutinovic and J. Kurtz, “Immune memory in invertebrates,” Seminars in Immunology, vol. 28, no. 4. Academic Press, pp. 328–342, 2016.","ama":"Milutinovic B, Kurtz J. Immune memory in invertebrates. Seminars in Immunology. 2016;28(4):328-342. doi:10.1016/j.smim.2016.05.004","apa":"Milutinovic, B., & Kurtz, J. (2016). Immune memory in invertebrates. Seminars in Immunology. Academic Press. https://doi.org/10.1016/j.smim.2016.05.004"},"date_updated":"2021-01-12T06:49:30Z","department":[{"_id":"SyCr"}],"title":"Immune memory in invertebrates","publist_id":"6053","author":[{"full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","last_name":"Milutinovic","first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Joachim","last_name":"Kurtz","full_name":"Kurtz, Joachim"}]},{"issue":"1","volume":14,"language":[{"iso":"eng"}],"file":[{"checksum":"0bfa484ac69a0a560fb9a4589aeda7f6","file_id":"5002","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:13:20Z","file_name":"IST-2016-695-v1+1_s12915-016-0294-x.pdf","creator":"system","date_updated":"2020-07-14T12:44:42Z","file_size":1875695}],"publication_status":"published","intvolume":" 14","month":"09","scopus_import":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Background: High directional persistence is often assumed to enhance the efficiency of chemotactic migration. Yet, cells in vivo usually display meandering trajectories with relatively low directional persistence, and the control and function of directional persistence during cell migration in three-dimensional environments are poorly understood. Results: Here, we use mesendoderm progenitors migrating during zebrafish gastrulation as a model system to investigate the control of directional persistence during migration in vivo. We show that progenitor cells alternate persistent run phases with tumble phases that result in cell reorientation. Runs are characterized by the formation of directed actin-rich protrusions and tumbles by enhanced blebbing. Increasing the proportion of actin-rich protrusions or blebs leads to longer or shorter run phases, respectively. Importantly, both reducing and increasing run phases result in larger spatial dispersion of the cells, indicative of reduced migration precision. A physical model quantitatively recapitulating the migratory behavior of mesendoderm progenitors indicates that the ratio of tumbling to run times, and thus the specific degree of directional persistence of migration, are critical for optimizing migration precision. Conclusions: Together, our experiments and model provide mechanistic insight into the control of migration directionality for cells moving in three-dimensional environments that combine different protrusion types, whereby the proportion of blebs to actin-rich protrusions determines the directional persistence and precision of movement by regulating the ratio of tumbling to run times."}],"department":[{"_id":"CaHe"}],"file_date_updated":"2020-07-14T12:44:42Z","ddc":["572","576"],"date_updated":"2021-01-12T06:49:32Z","pubrep_id":"695","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1271","date_created":"2018-12-11T11:51:04Z","doi":"10.1186/s12915-016-0294-x","date_published":"2016-09-02T00:00:00Z","publication":"BMC Biology","day":"02","year":"2016","has_accepted_license":"1","oa":1,"publisher":"BioMed Central","quality_controlled":"1","acknowledgement":"We thank K. Lee, C. Norden, A. Webb, and the members of the Paluch lab for\r\ncomments on the manuscript. We are grateful to P. Rørth and Peter Dieterich\r\nfor discussions, S. Ares, Y. Arboleda-Estudillo and S. Schneider for technical help,\r\nM. Biro for help with programming, and the BIOTEC/MPI-CBG and IST zebrafish\r\nand imaging facilities for help and advice at various stages of this project. This work was supported by the Max Planck Society, the Medical Research Council UK (core funding to the MRC LMCB), and by grants from the Polish Ministry of Science and Higher Education (454/N-MPG/2009/0) to EKP, the Deutsche Forschungsgemeinschaft (HE 3231/6-1 and PA 1590/1-1) to CPH and EKP, a A*Star JCO career development award (12302FG010) to WY and a Damon Runyon fellowship award to ADM (DRG 2157-12). This work was also supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001317), the UK Medical Research Council (FC001317), and the Wellcome Trust (FC001317) to GS.","title":"Steering cell migration by alternating blebs and actin-rich protrusions","publist_id":"6049","author":[{"first_name":"Alba","full_name":"Diz Muñoz, Alba","last_name":"Diz Muñoz"},{"first_name":"Pawel","last_name":"Romanczuk","full_name":"Romanczuk, Pawel"},{"full_name":"Yu, Weimiao","last_name":"Yu","first_name":"Weimiao"},{"full_name":"Bergert, Martin","last_name":"Bergert","first_name":"Martin"},{"full_name":"Ivanovitch, Kenzo","last_name":"Ivanovitch","first_name":"Kenzo"},{"full_name":"Salbreux, Guillame","last_name":"Salbreux","first_name":"Guillame"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"first_name":"Ewa","last_name":"Paluch","full_name":"Paluch, Ewa"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Diz Muñoz, Alba, Pawel Romanczuk, Weimiao Yu, Martin Bergert, Kenzo Ivanovitch, Guillame Salbreux, Carl-Philipp J Heisenberg, and Ewa Paluch. “Steering Cell Migration by Alternating Blebs and Actin-Rich Protrusions.” BMC Biology. BioMed Central, 2016. https://doi.org/10.1186/s12915-016-0294-x.","ista":"Diz Muñoz A, Romanczuk P, Yu W, Bergert M, Ivanovitch K, Salbreux G, Heisenberg C-PJ, Paluch E. 2016. Steering cell migration by alternating blebs and actin-rich protrusions. BMC Biology. 14(1), 74.","mla":"Diz Muñoz, Alba, et al. “Steering Cell Migration by Alternating Blebs and Actin-Rich Protrusions.” BMC Biology, vol. 14, no. 1, 74, BioMed Central, 2016, doi:10.1186/s12915-016-0294-x.","short":"A. Diz Muñoz, P. Romanczuk, W. Yu, M. Bergert, K. Ivanovitch, G. Salbreux, C.-P.J. Heisenberg, E. Paluch, BMC Biology 14 (2016).","ieee":"A. Diz Muñoz et al., “Steering cell migration by alternating blebs and actin-rich protrusions,” BMC Biology, vol. 14, no. 1. BioMed Central, 2016.","ama":"Diz Muñoz A, Romanczuk P, Yu W, et al. Steering cell migration by alternating blebs and actin-rich protrusions. BMC Biology. 2016;14(1). doi:10.1186/s12915-016-0294-x","apa":"Diz Muñoz, A., Romanczuk, P., Yu, W., Bergert, M., Ivanovitch, K., Salbreux, G., … Paluch, E. (2016). Steering cell migration by alternating blebs and actin-rich protrusions. BMC Biology. BioMed Central. https://doi.org/10.1186/s12915-016-0294-x"},"project":[{"_id":"252064B8-B435-11E9-9278-68D0E5697425","grant_number":"HE_3231/6-1","name":"Analysis of the Formation and Function of Different Cell Protusion Types During Cell Migration in Vivo"}],"article_number":"74"},{"acknowledgement":"We acknowledge the support of glasshouse technicians at the University of\r\nNottingham for help with plant growth and the Nottingham\r\nArabidopsis\r\nStock Centre\r\n(NASC) for providing\r\nArabidopsis\r\nlines. This research was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (to A.B. and M.J.B.); the European Research Council (ERC) Advanced Grant SysArc (to B.S.) and FUTUREROOTS (to M.J.B.); The Royal Society for University and Wolfson Research Fellowship awards (to A.B. and M.J.B.); a Federation of European Biochemical Societies (FEBS) Long-Term Fellowship (to B.P.); an Intra-European Fellowship for Career Development under the 7th framework of the European Commission [IEF-2008-220506 to B.P.]; a European Molecular Biology Organization (EMBO) Long-Term Fellowship (to B.P.); and a European Reintegration Grant under the 7th framework of the European Commission [ERG-2010-276662 to B.P.]; Interuniversity Attraction Poles Programme [initiated by the Belgian Science Policy Office (Federaal Wetenschapsbeleid)] (to M.J.B.); The Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan: Grants-in-Aid for Scientific Research on Innovative Areas [25110330 to H.F.] and a JSPS Research Fellowship for Young Scientists [12J02079 to T.G.]; funds for research performed by S.M.B. and A.G. were provided by University of California, Davis startup funds.","quality_controlled":"1","publisher":"Company of Biologists","oa":1,"day":"13","publication":"Development","year":"2016","date_published":"2016-09-13T00:00:00Z","doi":"10.1242/dev.136283","date_created":"2018-12-11T11:51:04Z","page":"3340 - 3349","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Porco, Silvana, et al. “Lateral Root Emergence in Arabidopsis Is Dependent on Transcription Factor LBD29 Regulation of Auxin Influx Carrier LAX3.” Development, vol. 143, no. 18, Company of Biologists, 2016, pp. 3340–49, doi:10.1242/dev.136283.","short":"S. Porco, A. Larrieu, Y. Du, A. Gaudinier, T. Goh, K. Swarup, R. Swarup, B. Kuempers, A. Bishopp, J. Lavenus, I. Casimiro, K. Hill, E. Benková, H. Fukaki, S. Brady, B. Scheres, B. Peéet, M. Bennett, Development 143 (2016) 3340–3349.","ieee":"S. Porco et al., “Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3,” Development, vol. 143, no. 18. Company of Biologists, pp. 3340–3349, 2016.","ama":"Porco S, Larrieu A, Du Y, et al. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. 2016;143(18):3340-3349. doi:10.1242/dev.136283","apa":"Porco, S., Larrieu, A., Du, Y., Gaudinier, A., Goh, T., Swarup, K., … Bennett, M. (2016). Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. Company of Biologists. https://doi.org/10.1242/dev.136283","chicago":"Porco, Silvana, Antoine Larrieu, Yujuan Du, Allison Gaudinier, Tatsuaki Goh, Kamal Swarup, Ranjan Swarup, et al. “Lateral Root Emergence in Arabidopsis Is Dependent on Transcription Factor LBD29 Regulation of Auxin Influx Carrier LAX3.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.136283.","ista":"Porco S, Larrieu A, Du Y, Gaudinier A, Goh T, Swarup K, Swarup R, Kuempers B, Bishopp A, Lavenus J, Casimiro I, Hill K, Benková E, Fukaki H, Brady S, Scheres B, Peéet B, Bennett M. 2016. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. 143(18), 3340–3349."},"title":"Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3","publist_id":"6044","author":[{"first_name":"Silvana","last_name":"Porco","full_name":"Porco, Silvana"},{"full_name":"Larrieu, Antoine","last_name":"Larrieu","first_name":"Antoine"},{"full_name":"Du, Yujuan","last_name":"Du","first_name":"Yujuan"},{"first_name":"Allison","full_name":"Gaudinier, Allison","last_name":"Gaudinier"},{"first_name":"Tatsuaki","full_name":"Goh, Tatsuaki","last_name":"Goh"},{"last_name":"Swarup","full_name":"Swarup, Kamal","first_name":"Kamal"},{"full_name":"Swarup, Ranjan","last_name":"Swarup","first_name":"Ranjan"},{"last_name":"Kuempers","full_name":"Kuempers, Britta","first_name":"Britta"},{"last_name":"Bishopp","full_name":"Bishopp, Anthony","first_name":"Anthony"},{"last_name":"Lavenus","full_name":"Lavenus, Julien","first_name":"Julien"},{"full_name":"Casimiro, Ilda","last_name":"Casimiro","first_name":"Ilda"},{"first_name":"Kristine","full_name":"Hill, Kristine","last_name":"Hill"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"last_name":"Fukaki","full_name":"Fukaki, Hidehiro","first_name":"Hidehiro"},{"full_name":"Brady, Siobhan","last_name":"Brady","first_name":"Siobhan"},{"first_name":"Ben","last_name":"Scheres","full_name":"Scheres, Ben"},{"last_name":"Peéet","full_name":"Peéet, Benjamin","first_name":"Benjamin"},{"full_name":"Bennett, Malcolm","last_name":"Bennett","first_name":"Malcolm"}],"oa_version":"Preprint","abstract":[{"text":"Lateral root primordia (LRP) originate from pericycle stem cells located deep within parental root tissues. LRP emerge through overlying root tissues by inducing auxin-dependent cell separation and hydraulic changes in adjacent cells. The auxin-inducible auxin influx carrier LAX3 plays a key role concentrating this signal in cells overlying LRP. Delimiting LAX3 expression to two adjacent cell files overlying new LRP is crucial to ensure that auxin-regulated cell separation occurs solely along their shared walls. Multiscale modeling has predicted that this highly focused pattern of expression requires auxin to sequentially induce auxin efflux and influx carriers PIN3 and LAX3, respectively. Consistent with model predictions, we report that auxin-inducible LAX3 expression is regulated indirectly by AUXIN RESPONSE FACTOR 7 (ARF7). Yeast one-hybrid screens revealed that the LAX3 promoter is bound by the transcription factor LBD29, which is a direct target for regulation by ARF7. Disrupting auxin-inducible LBD29 expression or expressing an LBD29-SRDX transcriptional repressor phenocopied the lax3 mutant, resulting in delayed lateral root emergence. We conclude that sequential LBD29 and LAX3 induction by auxin is required to coordinate cell separation and organ emergence.","lang":"eng"}],"month":"09","intvolume":" 143","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01595056/"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":143,"issue":"18","_id":"1273","status":"public","type":"journal_article","date_updated":"2021-01-12T06:49:32Z","department":[{"_id":"EvBe"}]},{"day":"02","publication":"Computer-Aided Design and Applications","has_accepted_license":"1","year":"2016","doi":"10.1080/16864360.2016.1150718","date_published":"2016-09-02T00:00:00Z","date_created":"2018-12-11T11:51:04Z","page":"712 - 721","acknowledgement":"This work was supported by Austrian Science Fund (FWF): P25816-N15.","publisher":"Taylor and Francis","quality_controlled":"1","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Held, S. Huber, P. Palfrader, Computer-Aided Design and Applications 13 (2016) 712–721.","ieee":"M. Held, S. Huber, and P. Palfrader, “Generalized offsetting of planar structures using skeletons,” Computer-Aided Design and Applications, vol. 13, no. 5. Taylor and Francis, pp. 712–721, 2016.","apa":"Held, M., Huber, S., & Palfrader, P. (2016). Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. Taylor and Francis. https://doi.org/10.1080/16864360.2016.1150718","ama":"Held M, Huber S, Palfrader P. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 2016;13(5):712-721. doi:10.1080/16864360.2016.1150718","mla":"Held, Martin, et al. “Generalized Offsetting of Planar Structures Using Skeletons.” Computer-Aided Design and Applications, vol. 13, no. 5, Taylor and Francis, 2016, pp. 712–21, doi:10.1080/16864360.2016.1150718.","ista":"Held M, Huber S, Palfrader P. 2016. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 13(5), 712–721.","chicago":"Held, Martin, Stefan Huber, and Peter Palfrader. “Generalized Offsetting of Planar Structures Using Skeletons.” Computer-Aided Design and Applications. Taylor and Francis, 2016. https://doi.org/10.1080/16864360.2016.1150718."},"title":"Generalized offsetting of planar structures using skeletons","publist_id":"6048","author":[{"last_name":"Held","full_name":"Held, Martin","first_name":"Martin"},{"first_name":"Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87","last_name":"Huber","orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan"},{"first_name":"Peter","full_name":"Palfrader, Peter","last_name":"Palfrader"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:44:42Z","file_size":1678369,"date_created":"2018-12-12T10:16:20Z","file_name":"IST-2016-694-v1+1_Generalized_offsetting_of_planar_structures_using_skeletons.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"c746f3a48edb62b588d92ea5d0fd2c0e","file_id":"5206"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":13,"issue":"5","oa_version":"Published Version","abstract":[{"text":"We study different means to extend offsetting based on skeletal structures beyond the well-known constant-radius and mitered offsets supported by Voronoi diagrams and straight skeletons, for which the orthogonal distance of offset elements to their respective input elements is constant and uniform over all input elements. Our main contribution is a new geometric structure, called variable-radius Voronoi diagram, which supports the computation of variable-radius offsets, i.e., offsets whose distance to the input is allowed to vary along the input. We discuss properties of this structure and sketch a prototype implementation that supports the computation of variable-radius offsets based on this new variant of Voronoi diagrams.","lang":"eng"}],"month":"09","intvolume":" 13","scopus_import":1,"ddc":["004","516"],"date_updated":"2021-01-12T06:49:32Z","file_date_updated":"2020-07-14T12:44:42Z","department":[{"_id":"HeEd"}],"_id":"1272","status":"public","pubrep_id":"694","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"}},{"article_number":"e0164675","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7","_id":"257A4776-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kovács, Krisztián, et al. “Optogenetically Blocking Sharp Wave Ripple Events in Sleep Does Not Interfere with the Formation of Stable Spatial Representation in the CA1 Area of the Hippocampus.” PLoS One, vol. 11, no. 10, e0164675, Public Library of Science, 2016, doi:10.1371/journal.pone.0164675.","short":"K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D.K. Rangel Guerrero, J.L. Csicsvari, PLoS One 11 (2016).","ieee":"K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D. K. Rangel Guerrero, and J. L. Csicsvari, “Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus,” PLoS One, vol. 11, no. 10. Public Library of Science, 2016.","apa":"Kovács, K., O’Neill, J., Schönenberger, P., Penttonen, M., Rangel Guerrero, D. K., & Csicsvari, J. L. (2016). Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0164675","ama":"Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari JL. Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. PLoS One. 2016;11(10). doi:10.1371/journal.pone.0164675","chicago":"Kovács, Krisztián, Joseph O’Neill, Philipp Schönenberger, Markku Penttonen, Dámaris K Rangel Guerrero, and Jozsef L Csicsvari. “Optogenetically Blocking Sharp Wave Ripple Events in Sleep Does Not Interfere with the Formation of Stable Spatial Representation in the CA1 Area of the Hippocampus.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0164675.","ista":"Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari JL. 2016. Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. PLoS One. 11(10), e0164675."},"title":"Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus","publist_id":"6037","author":[{"id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztián","last_name":"Kovács","full_name":"Kovács, Krisztián"},{"full_name":"O'Neill, Joseph","last_name":"O'Neill","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schönenberger","full_name":"Schönenberger, Philipp","first_name":"Philipp","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Markku","full_name":"Penttonen, Markku","last_name":"Penttonen"},{"last_name":"Rangel Guerrero","orcid":"0000-0002-8602-4374","full_name":"Rangel Guerrero, Dámaris K","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","first_name":"Dámaris K"},{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari"}],"acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734] via the IST FELLOWSHIP awarded to Dr. Krisztián A. Kovács and the European Research Council starting grant (acronym: HIPECMEM Project reference: 281511) awarded to Dr. Jozsef Csicsvari. We thank Lauri Viljanto for technical help in building the ripple detector.","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","publication":"PLoS One","day":"19","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:51:06Z","date_published":"2016-10-19T00:00:00Z","doi":"10.1371/journal.pone.0164675","_id":"1279","pubrep_id":"690","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570","571"],"date_updated":"2021-01-12T06:49:35Z","file_date_updated":"2020-07-14T12:44:42Z","department":[{"_id":"JoCs"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"During hippocampal sharp wave/ripple (SWR) events, previously occurring, sensory inputdriven neuronal firing patterns are replayed. Such replay is thought to be important for plasticity- related processes and consolidation of memory traces. It has previously been shown that the electrical stimulation-induced disruption of SWR events interferes with learning in rodents in different experimental paradigms. On the other hand, the cognitive map theory posits that the plastic changes of the firing of hippocampal place cells constitute the electrophysiological counterpart of the spatial learning, observable at the behavioral level. Therefore, we tested whether intact SWR events occurring during the sleep/rest session after the first exploration of a novel environment are needed for the stabilization of the CA1 code, which process requires plasticity. We found that the newly-formed representation in the CA1 has the same level of stability with optogenetic SWR blockade as with a control manipulation that delivered the same amount of light into the brain. Therefore our results suggest that at least in the case of passive exploratory behavior, SWR-related plasticity is dispensable for the stability of CA1 ensembles."}],"intvolume":" 11","month":"10","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-690-v1+1_journal.pone.0164675.PDF","date_created":"2018-12-12T10:13:26Z","file_size":4353592,"date_updated":"2020-07-14T12:44:42Z","creator":"system","file_id":"5009","checksum":"395895ecb2216e9c39135abaa56b28b3","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","ec_funded":1,"issue":"10","volume":11},{"_id":"1278","status":"public","pubrep_id":"689","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570","571"],"date_updated":"2021-01-12T06:49:34Z","department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:44:42Z","oa_version":"Published Version","abstract":[{"text":"Adaptations of vestibulo-ocular and optokinetic response eye movements have been studied as an experimental model of cerebellum-dependent motor learning. Several previous physiological and pharmacological studies have consistently suggested that the cerebellar flocculus (FL) Purkinje cells (P-cells) and the medial vestibular nucleus (MVN) neurons targeted by FL (FL-targeted MVN neurons) may respectively maintain the memory traces of short- and long-term adaptation. To study the basic structures of the FL-MVN synapses by light microscopy (LM) and electron microscopy (EM), we injected green florescence protein (GFP)-expressing lentivirus into FL to anterogradely label the FL P-cell axons in C57BL/6J mice. The FL P-cell axonal boutons were distributed in the magnocellular MVN and in the border region of parvocellular MVN and prepositus hypoglossi (PrH). In the magnocellular MVN, the FL-P cell axons mainly terminated on somata and proximal dendrites. On the other hand, in the parvocellular MVN/PrH, the FL P-cell axonal synaptic boutons mainly terminated on the relatively small-diameter (< 1 μm) distal dendrites of MVN neurons, forming symmetrical synapses. The majority of such parvocellular MVN/PrH neurons were determined to be glutamatergic by immunocytochemistry and in-situ hybridization of GFP expressing transgenic mice. To further examine the spatial relationship between the synapses of FL P-cells and those of vestibular nerve on the neurons of the parvocellular MVN/ PrH, we added injections of biotinylated dextran amine into the semicircular canal and anterogradely labeled vestibular nerve axons in some mice. The MVN dendrites receiving the FL P-cell axonal synaptic boutons often closely apposed vestibular nerve synaptic boutons in both LM and EM studies. Such a partial overlap of synaptic boutons of FL P-cell axons with those of vestibular nerve axons in the distal dendrites of MVN neurons suggests that inhibitory synapses of FL P-cells may influence the function of neighboring excitatory synapses of vestibular nerve in the parvocellular MVN/PrH neurons.","lang":"eng"}],"month":"10","intvolume":" 11","scopus_import":1,"file":[{"checksum":"7c0ba0ca6d79844059158059d2a38d25","file_id":"5269","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:17:16Z","file_name":"IST-2016-689-v1+1_journal.pone.0164037.PDF","date_updated":"2020-07-14T12:44:42Z","file_size":3657084,"creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"10","volume":11,"article_number":"e0164037","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Matsuno, Hitomi, et al. “Distribution and Structure of Synapses on Medial Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” PLoS One, vol. 11, no. 10, e0164037, Public Library of Science, 2016, doi:10.1371/journal.pone.0164037.","ama":"Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. PLoS One. 2016;11(10). doi:10.1371/journal.pone.0164037","apa":"Matsuno, H., Kudoh, M., Watakabe, A., Yamamori, T., Shigemoto, R., & Nagao, S. (2016). Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0164037","ieee":"H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, and S. Nagao, “Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies,” PLoS One, vol. 11, no. 10. Public Library of Science, 2016.","short":"H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, S. Nagao, PLoS One 11 (2016).","chicago":"Matsuno, Hitomi, Moeko Kudoh, Akiya Watakabe, Tetsuo Yamamori, Ryuichi Shigemoto, and Soichi Nagao. “Distribution and Structure of Synapses on Medial Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0164037.","ista":"Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. 2016. Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. PLoS One. 11(10), e0164037."},"title":"Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies","author":[{"first_name":"Hitomi","full_name":"Matsuno, Hitomi","last_name":"Matsuno"},{"first_name":"Moeko","last_name":"Kudoh","full_name":"Kudoh, Moeko"},{"last_name":"Watakabe","full_name":"Watakabe, Akiya","first_name":"Akiya"},{"last_name":"Yamamori","full_name":"Yamamori, Tetsuo","first_name":"Tetsuo"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"first_name":"Soichi","full_name":"Nagao, Soichi","last_name":"Nagao"}],"publist_id":"6038","article_processing_charge":"No","acknowledgement":"This work was supported by RIKEN [to SN]; Grant-in-Aid from the Japan Society for the Promotion of Science, https://www.jsps.go.jp/english/e-grants/ [22300112 to SN].","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"day":"06","publication":"PLoS One","has_accepted_license":"1","year":"2016","date_published":"2016-10-06T00:00:00Z","doi":"10.1371/journal.pone.0164037","date_created":"2018-12-11T11:51:06Z"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"691","status":"public","_id":"1276","file_date_updated":"2020-07-14T12:44:42Z","department":[{"_id":"LeSa"}],"date_updated":"2021-01-12T06:49:34Z","ddc":["576"],"scopus_import":1,"intvolume":" 6","month":"09","abstract":[{"text":"The cytochrome (cyt) bc 1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme's substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Q i-site of the cyt bc 1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Q i-site to facilitate binding of half-protonated semiquinone-a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Q i-site.","lang":"eng"}],"oa_version":"Published Version","volume":6,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:17:09Z","file_name":"IST-2016-691-v1+1_srep33607.pdf","creator":"system","date_updated":"2020-07-14T12:44:42Z","file_size":1960563,"checksum":"07c591c1250ebef266333cbc3228b4dd","file_id":"5261","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"article_number":"33607","author":[{"first_name":"Pekka","full_name":"Postila, Pekka","last_name":"Postila"},{"full_name":"Kaszuba, Karol","last_name":"Kaszuba","first_name":"Karol","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kuleta, Patryk","last_name":"Kuleta","first_name":"Patryk"},{"first_name":"Ilpo","last_name":"Vattulainen","full_name":"Vattulainen, Ilpo"},{"first_name":"Marcin","last_name":"Sarewicz","full_name":"Sarewicz, Marcin"},{"first_name":"Artur","full_name":"Osyczka, Artur","last_name":"Osyczka"},{"last_name":"Róg","full_name":"Róg, Tomasz","first_name":"Tomasz"}],"publist_id":"6040","title":"Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex","citation":{"ieee":"P. Postila et al., “Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","short":"P. Postila, K. Kaszuba, P. Kuleta, I. Vattulainen, M. Sarewicz, A. Osyczka, T. Róg, Scientific Reports 6 (2016).","apa":"Postila, P., Kaszuba, K., Kuleta, P., Vattulainen, I., Sarewicz, M., Osyczka, A., & Róg, T. (2016). Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep33607","ama":"Postila P, Kaszuba K, Kuleta P, et al. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports. 2016;6. doi:10.1038/srep33607","mla":"Postila, Pekka, et al. “Atomistic Determinants of Co-Enzyme Q Reduction at the Qi-Site of the Cytochrome Bc1 Complex.” Scientific Reports, vol. 6, 33607, Nature Publishing Group, 2016, doi:10.1038/srep33607.","ista":"Postila P, Kaszuba K, Kuleta P, Vattulainen I, Sarewicz M, Osyczka A, Róg T. 2016. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports. 6, 33607.","chicago":"Postila, Pekka, Karol Kaszuba, Patryk Kuleta, Ilpo Vattulainen, Marcin Sarewicz, Artur Osyczka, and Tomasz Róg. “Atomistic Determinants of Co-Enzyme Q Reduction at the Qi-Site of the Cytochrome Bc1 Complex.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep33607."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","acknowledgement":"We wish to thank CSC – IT Centre for Science (Espoo, Finland) for computational resources. For financial support, we wish to thank the Academy of Finland (TR, IV and PAP; Center of Excellence in Biomembrane Research (IV, TR)), the Finnish Doctoral Programme in Computational Sciences (KK), the Sigrid Juselius Foundation (IV), the Paulo Foundation (PAP), and the European Research Council (IV, TR; Advanced Grant project CROWDED-PRO-LIPIDS). AO acknowledges The Wellcome Trust International Senior Research Fellowship.","date_created":"2018-12-11T11:51:05Z","date_published":"2016-09-26T00:00:00Z","doi":"10.1038/srep33607","year":"2016","has_accepted_license":"1","publication":"Scientific Reports","day":"26"},{"language":[{"iso":"eng"}],"publication_status":"published","issue":"39","volume":113,"oa_version":"Preprint","abstract":[{"text":"The Arabidopsis thaliana endogenous elicitor peptides (AtPeps) are released into the apoplast after cellular damage caused by pathogens or wounding to induce innate immunity by direct binding to the membrane-localized leucine-rich repeat receptor kinases, PEP RECEPTOR1 (PEPR1) and PEPR2. Although the PEPR-mediated signaling components and responses have been studied extensively, the contributions of the subcellular localization and dynamics of the active PEPRs remain largely unknown. We used live-cell imaging of the fluorescently labeled and bioactive pep1 to visualize the intracellular behavior of the PEPRs in the Arabidopsis root meristem. We found that AtPep1 decorated the plasma membrane (PM) in a receptor-dependent manner and cointernalized with PEPRs. Trafficking of the AtPep1-PEPR1 complexes to the vacuole required neither the trans-Golgi network/early endosome (TGN/EE)-localized vacuolar H+ -ATPase activity nor the function of the brefeldin A-sensitive ADP-ribosylation factor-guanine exchange factors (ARF-GEFs). In addition, AtPep1 and different TGN/EE markers colocalized only rarely, implying that the intracellular route of this receptor-ligand pair is largely independent of the TGN/EE. Inducible overexpression of the Arabidopsis clathrin coat disassembly factor, Auxilin2, which inhibits clathrin-mediated endocytosis (CME), impaired the AtPep1-PEPR1 internalization and compromised AtPep1-mediated responses. Our results show that clathrin function at the PM is required to induce plant defense responses, likely through CME of cell surface-located signaling components.\r\n","lang":"eng"}],"month":"09","intvolume":" 113","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047203/","open_access":"1"}],"date_updated":"2021-01-12T06:49:34Z","department":[{"_id":"JiFr"}],"_id":"1277","status":"public","type":"journal_article","day":"27","publication":"PNAS","year":"2016","doi":"10.1073/pnas.1605588113","date_published":"2016-09-27T00:00:00Z","date_created":"2018-12-11T11:51:06Z","page":"11028 - 11033","acknowledgement":"F.A.O.-M. was supported by special\r\nresearch funding from the Flemish Government for a joint doctorate fellowship\r\nat Ghent University, and funding from the Student Program\r\n–\r\nGraduate Studies\r\nPlan Program from the Coordination for the Improvement of Higher Educa-\r\ntion Personnel, Brazil, for a doctorate fellowship at the University of São Paulo.\r\nX.Z. and Q.L. are indebted to the China Science Council and G.P.d.O. to the\r\n“\r\nCiência sem Fronteiras\r\n”\r\nfor predoctoral fellowships. R.K. and Y.L. have re-\r\nceived postdoctoral fellowships from the Belgian Science Policy Office. This\r\nresearch was supported by Flanders Research Foundation Grant G008416N\r\n(to E.R.) and by the São Paulo Research Foundation and the National Council\r\nfor Scientific and Technological Development (CNPq) (D.S.d.M.). D.S.d.M. is a\r\nresearch fellow of CNPq.\r\nWe thank D. Van Damme, E. Mylle, M. Castro Silva-Filho,\r\nand J. Goeman for providing usefu\r\nl advice and technical assistance;\r\nI. Hara-Nishimura, J. Lin, G. Jürgens, M. A. Johnson, and P. Bozhkov for sharing\r\npublished materials; and M. Nowack and M. Fendrych for kindly donating the\r\npUBQ10::ATG8-YFP\r\n-expressing marker line.","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ortiz Morea, Fausto, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” PNAS, vol. 113, no. 39, National Academy of Sciences, 2016, pp. 11028–33, doi:10.1073/pnas.1605588113.","ieee":"F. Ortiz Morea et al., “Danger-associated peptide signaling in Arabidopsis requires clathrin,” PNAS, vol. 113, no. 39. National Academy of Sciences, pp. 11028–11033, 2016.","short":"F. Ortiz Morea, D. Savatin, W. Dejonghe, R. Kumar, Y. Luo, M. Adamowski, J. Van Begin, K. Dressano, G. De Oliveira, X. Zhao, Q. Lu, A. Madder, J. Friml, D. De Moura, E. Russinova, PNAS 113 (2016) 11028–11033.","ama":"Ortiz Morea F, Savatin D, Dejonghe W, et al. Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. 2016;113(39):11028-11033. doi:10.1073/pnas.1605588113","apa":"Ortiz Morea, F., Savatin, D., Dejonghe, W., Kumar, R., Luo, Y., Adamowski, M., … Russinova, E. (2016). Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1605588113","chicago":"Ortiz Morea, Fausto, Daniel Savatin, Wim Dejonghe, Rahul Kumar, Yu Luo, Maciek Adamowski, Jos Van Begin, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1605588113.","ista":"Ortiz Morea F, Savatin D, Dejonghe W, Kumar R, Luo Y, Adamowski M, Van Begin J, Dressano K, De Oliveira G, Zhao X, Lu Q, Madder A, Friml J, De Moura D, Russinova E. 2016. Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. 113(39), 11028–11033."},"title":"Danger-associated peptide signaling in Arabidopsis requires clathrin","author":[{"first_name":"Fausto","last_name":"Ortiz Morea","full_name":"Ortiz Morea, Fausto"},{"last_name":"Savatin","full_name":"Savatin, Daniel","first_name":"Daniel"},{"full_name":"Dejonghe, Wim","last_name":"Dejonghe","first_name":"Wim"},{"first_name":"Rahul","full_name":"Kumar, Rahul","last_name":"Kumar"},{"last_name":"Luo","full_name":"Luo, Yu","first_name":"Yu"},{"full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","last_name":"Adamowski","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jos","full_name":"Van Begin, Jos","last_name":"Van Begin"},{"first_name":"Keini","full_name":"Dressano, Keini","last_name":"Dressano"},{"first_name":"Guilherme","last_name":"De Oliveira","full_name":"De Oliveira, Guilherme"},{"last_name":"Zhao","full_name":"Zhao, Xiuyang","first_name":"Xiuyang"},{"first_name":"Qing","full_name":"Lu, Qing","last_name":"Lu"},{"first_name":"Annemieke","last_name":"Madder","full_name":"Madder, Annemieke"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"De Moura, Daniel","last_name":"De Moura","first_name":"Daniel"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"}],"publist_id":"6039"},{"department":[{"_id":"EvBe"}],"date_updated":"2021-01-12T06:49:36Z","type":"journal_article","status":"public","_id":"1281","volume":172,"issue":"2","publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047109/"}],"scopus_import":1,"intvolume":" 172","month":"10","abstract":[{"lang":"eng","text":"Plants are able to modulate root growth and development to optimize their nitrogen nutrition. In Arabidopsis (Arabidopsis thaliana), the adaptive root response to nitrate (NO3 -) depends on the NRT1.1/NPF6.3 transporter/sensor. NRT1.1 represses emergence of lateral root primordia (LRPs) at low concentration or absence of NO3 - through its auxin transport activity that lowers auxin accumulation in LR. However, these functional data strongly contrast with the known transcriptional regulation of NRT1.1, which is markedly repressed in LRPs in the absence of NO3 -. To explain this discrepancy, we investigated in detail the spatiotemporal expression pattern of the NRT1.1 protein during LRP development and combined local transcript analysis with the use of transgenic lines expressing tagged NRT1.1 proteins. Our results show that although NO3 - stimulates NRT1.1 transcription and probably mRNA stability both in primary root tissues and in LRPs, it acts differentially on protein accumulation, depending on the tissues considered with stimulation in cortex and epidermis of the primary root and a strong repression in LRPs and to a lower extent at the primary root tip. This demonstrates that NRT1.1 is strongly regulated at the posttranscriptional level by tissue-specific mechanisms. These mechanisms are crucial for controlling the large palette of adaptive responses to NO3 - mediated by NRT1.1 as they ensure that the protein is present in the proper tissue under the specific conditions where it plays a signaling role in this particular tissue."}],"oa_version":"Preprint","publist_id":"6035","author":[{"first_name":"Eléonore","full_name":"Bouguyon, Eléonore","last_name":"Bouguyon"},{"full_name":"Perrine Walker, Francine","last_name":"Perrine Walker","first_name":"Francine"},{"first_name":"Marjorie","full_name":"Pervent, Marjorie","last_name":"Pervent"},{"first_name":"Juliette","full_name":"Rochette, Juliette","last_name":"Rochette"},{"full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410","last_name":"Cuesta","first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"first_name":"Alexandre","full_name":"Martinière, Alexandre","last_name":"Martinière"},{"first_name":"Lien","full_name":"Bach, Lien","last_name":"Bach"},{"first_name":"Gabriel","full_name":"Krouk, Gabriel","last_name":"Krouk"},{"full_name":"Gojon, Alain","last_name":"Gojon","first_name":"Alain"},{"last_name":"Nacry","full_name":"Nacry, Philippe","first_name":"Philippe"}],"title":"Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor","citation":{"mla":"Bouguyon, Eléonore, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” Plant Physiology, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1237–48, doi:10.1104/pp.16.01047.","ama":"Bouguyon E, Perrine Walker F, Pervent M, et al. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. 2016;172(2):1237-1248. doi:10.1104/pp.16.01047","apa":"Bouguyon, E., Perrine Walker, F., Pervent, M., Rochette, J., Cuesta, C., Benková, E., … Nacry, P. (2016). Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.01047","short":"E. Bouguyon, F. Perrine Walker, M. Pervent, J. Rochette, C. Cuesta, E. Benková, A. Martinière, L. Bach, G. Krouk, A. Gojon, P. Nacry, Plant Physiology 172 (2016) 1237–1248.","ieee":"E. Bouguyon et al., “Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor,” Plant Physiology, vol. 172, no. 2. American Society of Plant Biologists, pp. 1237–1248, 2016.","chicago":"Bouguyon, Eléonore, Francine Perrine Walker, Marjorie Pervent, Juliette Rochette, Candela Cuesta, Eva Benková, Alexandre Martinière, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.01047.","ista":"Bouguyon E, Perrine Walker F, Pervent M, Rochette J, Cuesta C, Benková E, Martinière A, Bach L, Krouk G, Gojon A, Nacry P. 2016. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. 172(2), 1237–1248."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"1237 - 1248","date_created":"2018-12-11T11:51:07Z","doi":"10.1104/pp.16.01047","date_published":"2016-10-01T00:00:00Z","year":"2016","publication":"Plant Physiology","day":"01","oa":1,"publisher":"American Society of Plant Biologists","quality_controlled":"1","acknowledgement":"This work was supported by the Agropolis Foundation (RHIZOPOLIS project to A.G. and P.N., and RTRA 2009-2011 project to F.P.-W.), the Knowledge Biobase Economy European project (KBBE-005-002 Root enhancement for crop improvement to M.P. and P.N.), and the European EURoot project (FP7-KBBE-2011-5 to J.R., A.G., and P.N.). We thank Carine Alcon for the help with analysis of confocal images, Xavier\r\nDumont for assistance with Arabidopsis transformations, staff members of the\r\nInstitut de Biologie Intégrative des Plantes for technical assistance with biological\r\nmaterial culture, and students and trainees for assistance with laboratory work.\r\nConfocal observations were made at the Montpellier RIO Imaging facility."},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1411.4906"}],"oa":1,"publisher":"Springer","scopus_import":1,"quality_controlled":"1","intvolume":" 216","month":"10","abstract":[{"lang":"eng","text":"We consider higher-dimensional generalizations of the normalized Laplacian and the adjacency matrix of graphs and study their eigenvalues for the Linial–Meshulam model Xk(n, p) of random k-dimensional simplicial complexes on n vertices. We show that for p = Ω(logn/n), the eigenvalues of each of the matrices are a.a.s. concentrated around two values. The main tool, which goes back to the work of Garland, are arguments that relate the eigenvalues of these matrices to those of graphs that arise as links of (k - 2)-dimensional faces. Garland’s result concerns the Laplacian; we develop an analogous result for the adjacency matrix. The same arguments apply to other models of random complexes which allow for dependencies between the choices of k-dimensional simplices. In the second part of the paper, we apply this to the question of possible higher-dimensional analogues of the discrete Cheeger inequality, which in the classical case of graphs relates the eigenvalues of a graph and its edge expansion. It is very natural to ask whether this generalizes to higher dimensions and, in particular, whether the eigenvalues of the higher-dimensional Laplacian capture the notion of coboundary expansion—a higher-dimensional generalization of edge expansion that arose in recent work of Linial and Meshulam and of Gromov; this question was raised, for instance, by Dotterrer and Kahle. We show that this most straightforward version of a higher-dimensional discrete Cheeger inequality fails, in quite a strong way: For every k ≥ 2 and n ∈ N, there is a k-dimensional complex Yn k on n vertices that has strong spectral expansion properties (all nontrivial eigenvalues of the normalised k-dimensional Laplacian lie in the interval [1−O(1/√1), 1+0(1/√1]) but whose coboundary expansion is bounded from above by O(log n/n) and so tends to zero as n → ∞; moreover, Yn k can be taken to have vanishing integer homology in dimension less than k."}],"oa_version":"Preprint","page":"545 - 582","date_created":"2018-12-11T11:51:07Z","volume":216,"issue":"2","doi":"10.1007/s11856-016-1419-1","date_published":"2016-10-01T00:00:00Z","publication_status":"published","year":"2016","language":[{"iso":"eng"}],"publication":"Israel Journal of Mathematics","day":"01","type":"journal_article","status":"public","_id":"1282","publist_id":"6034","author":[{"last_name":"Gundert","full_name":"Gundert, Anna","first_name":"Anna"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner"}],"department":[{"_id":"UlWa"}],"title":"On eigenvalues of random complexes","citation":{"mla":"Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” Israel Journal of Mathematics, vol. 216, no. 2, Springer, 2016, pp. 545–82, doi:10.1007/s11856-016-1419-1.","apa":"Gundert, A., & Wagner, U. (2016). On eigenvalues of random complexes. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1419-1","ama":"Gundert A, Wagner U. On eigenvalues of random complexes. Israel Journal of Mathematics. 2016;216(2):545-582. doi:10.1007/s11856-016-1419-1","ieee":"A. Gundert and U. Wagner, “On eigenvalues of random complexes,” Israel Journal of Mathematics, vol. 216, no. 2. Springer, pp. 545–582, 2016.","short":"A. Gundert, U. Wagner, Israel Journal of Mathematics 216 (2016) 545–582.","chicago":"Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” Israel Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1419-1.","ista":"Gundert A, Wagner U. 2016. On eigenvalues of random complexes. Israel Journal of Mathematics. 216(2), 545–582."},"date_updated":"2021-01-12T06:49:36Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"title":"Fixed energy universality for generalized wigner matrices","publist_id":"6036","author":[{"first_name":"Paul","last_name":"Bourgade","full_name":"Bourgade, Paul"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"full_name":"Yau, Horngtzer","last_name":"Yau","first_name":"Horngtzer"},{"first_name":"Jun","last_name":"Yin","full_name":"Yin, Jun"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bourgade, Paul, et al. “Fixed Energy Universality for Generalized Wigner Matrices.” Communications on Pure and Applied Mathematics, vol. 69, no. 10, Wiley-Blackwell, 2016, pp. 1815–81, doi:10.1002/cpa.21624.","apa":"Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2016). Fixed energy universality for generalized wigner matrices. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21624","ama":"Bourgade P, Erdös L, Yau H, Yin J. Fixed energy universality for generalized wigner matrices. Communications on Pure and Applied Mathematics. 2016;69(10):1815-1881. doi:10.1002/cpa.21624","ieee":"P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Fixed energy universality for generalized wigner matrices,” Communications on Pure and Applied Mathematics, vol. 69, no. 10. Wiley-Blackwell, pp. 1815–1881, 2016.","short":"P. Bourgade, L. Erdös, H. Yau, J. Yin, Communications on Pure and Applied Mathematics 69 (2016) 1815–1881.","chicago":"Bourgade, Paul, László Erdös, Horngtzer Yau, and Jun Yin. “Fixed Energy Universality for Generalized Wigner Matrices.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2016. https://doi.org/10.1002/cpa.21624.","ista":"Bourgade P, Erdös L, Yau H, Yin J. 2016. Fixed energy universality for generalized wigner matrices. Communications on Pure and Applied Mathematics. 69(10), 1815–1881."},"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"doi":"10.1002/cpa.21624","date_published":"2016-10-01T00:00:00Z","date_created":"2018-12-11T11:51:07Z","page":"1815 - 1881","day":"01","publication":"Communications on Pure and Applied Mathematics","year":"2016","publisher":"Wiley-Blackwell","oa":1,"acknowledgement":"The work of P.B. was partially supported by National Sci-\r\nence Foundation Grant DMS-1208859. The work of L.E. was partially supported\r\nby ERC Advanced Grant RANMAT 338804. The work of H.-T. Y. was partially\r\nsupported by National Science Foundation Grant DMS-1307444 and a Simons In-\r\nvestigator award. The work of J.Y. was partially supported by National Science\r\nFoundation Grant DMS-1207961. The major part of this research was conducted\r\nwhen all authors were visiting IAS and were also supported by National Science\r\nFoundation Grant DMS-1128255.","department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T06:49:35Z","status":"public","type":"journal_article","_id":"1280","issue":"10","volume":69,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 69","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1407.5606","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"We prove the Wigner-Dyson-Mehta conjecture at fixed energy in the bulk of the spectrum for generalized symmetric and Hermitian Wigner matrices. Previous results concerning the universality of random matrices either require an averaging in the energy parameter or they hold only for Hermitian matrices if the energy parameter is fixed. We develop a homogenization theory of the Dyson Brownian motion and show that microscopic universality follows from mesoscopic statistics.","lang":"eng"}]},{"oa_version":"None","month":"09","intvolume":" 117","scopus_import":1,"publisher":"American Physical Society","quality_controlled":"1","day":"22","language":[{"iso":"eng"}],"publication":"Physical Review Letters","year":"2016","publication_status":"published","doi":"10.1103/PhysRevLett.117.139802","volume":117,"date_published":"2016-09-22T00:00:00Z","issue":"13","date_created":"2018-12-11T11:51:05Z","article_number":"139802","_id":"1275","status":"public","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"A. Callan Jones, V. Ruprecht, S. Wieser, C.-P. J. Heisenberg, and R. Voituriez, “Callan-Jones et al. Reply,” Physical Review Letters, vol. 117, no. 13. American Physical Society, 2016.","short":"A. Callan Jones, V. Ruprecht, S. Wieser, C.-P.J. Heisenberg, R. Voituriez, Physical Review Letters 117 (2016).","apa":"Callan Jones, A., Ruprecht, V., Wieser, S., Heisenberg, C.-P. J., & Voituriez, R. (2016). Callan-Jones et al. Reply. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.117.139802","ama":"Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. Callan-Jones et al. Reply. Physical Review Letters. 2016;117(13). doi:10.1103/PhysRevLett.117.139802","mla":"Callan Jones, Andrew, et al. “Callan-Jones et Al. Reply.” Physical Review Letters, vol. 117, no. 13, 139802, American Physical Society, 2016, doi:10.1103/PhysRevLett.117.139802.","ista":"Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. 2016. Callan-Jones et al. Reply. Physical Review Letters. 117(13), 139802.","chicago":"Callan Jones, Andrew, Verena Ruprecht, Stefan Wieser, Carl-Philipp J Heisenberg, and Raphaël Voituriez. “Callan-Jones et Al. Reply.” Physical Review Letters. American Physical Society, 2016. https://doi.org/10.1103/PhysRevLett.117.139802."},"date_updated":"2021-01-12T06:49:33Z","title":"Callan-Jones et al. Reply","department":[{"_id":"CaHe"}],"author":[{"full_name":"Callan Jones, Andrew","last_name":"Callan Jones","first_name":"Andrew"},{"first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht","full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633"},{"first_name":"Stefan","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","last_name":"Wieser","orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Voituriez, Raphaël","last_name":"Voituriez","first_name":"Raphaël"}],"publist_id":"6041"}]