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TU Dortmund, 2011."},"page":"197 - 200","quality_controlled":"1","date_published":"2011-01-01T00:00:00Z","conference":{"name":"EuroCG: European Workshop on Computational Geometry","end_date":"2011-03-30","location":"Morschach, Switzerland","start_date":"2011-03-28"},"language":[{"iso":"eng"}],"month":"01","day":"01","_id":"3270","year":"2011","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"publisher":"TU Dortmund","publication_status":"published","title":"Persistent homology computation with a twist","status":"public","author":[{"first_name":"Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao"},{"first_name":"Michael","last_name":"Kerber","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael"}],"oa_version":"None","date_created":"2018-12-11T12:02:22Z","date_updated":"2021-01-12T07:42:17Z","type":"conference","publist_id":"3376","abstract":[{"lang":"eng","text":"The persistence diagram of a filtered simplicial com- plex is usually computed by reducing the boundary matrix of the complex. We introduce a simple op- timization technique: by processing the simplices of the complex in decreasing dimension, we can “kill” columns (i.e., set them to zero) without reducing them. This technique completely avoids reduction on roughly half of the columns. We demonstrate that this idea significantly improves the running time of the reduction algorithm in practice. We also give an output-sensitive complexity analysis for the new al- gorithm which yields to sub-cubic asymptotic bounds under certain assumptions."}]},{"abstract":[{"lang":"eng","text":"We present a new algorithm for enforcing incompressibility for Smoothed Particle Hydrodynamics (SPH) by preserving uniform density across the domain. We propose a hybrid method that uses a Poisson solve on a coarse grid to enforce a divergence free velocity field, followed by a local density correction of the particles. This avoids typical grid artifacts and maintains the Lagrangian nature of SPH by directly transferring pressures onto particles. Our method can be easily integrated with existing SPH techniques such as the incompressible PCISPH method as well as weakly compressible SPH by adding an additional force term. We show that this hybrid method accelerates convergence towards uniform density and permits a significantly larger time step compared to earlier approaches while producing similar results. We demonstrate our approach in a variety of scenarios with significant pressure gradients such as splashing liquids."}],"type":"conference","pubrep_id":"598","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"4769","date_created":"2018-12-12T10:09:44Z","date_updated":"2020-07-14T12:46:06Z","checksum":"6579d27709946e0eefbfa60a456b4913","file_name":"IST-2016-598-v1+1_HybridSPH_Preprint.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2536216,"creator":"system"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3298","title":"Hybrid smoothed particle hydrodynamics","status":"public","ddc":["000"],"day":"05","has_accepted_license":"1","scopus_import":1,"date_published":"2011-08-05T00:00:00Z","citation":{"ista":"Raveendran K, Wojtan C, Turk G. 2011. Hybrid smoothed particle hydrodynamics. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 33–42.","apa":"Raveendran, K., Wojtan, C., & Turk, G. (2011). Hybrid smoothed particle hydrodynamics. In S. Spencer (Ed.) (pp. 33–42). Presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Vancouver, Canada: ACM. https://doi.org/10.1145/2019406.2019411","ieee":"K. Raveendran, C. Wojtan, and G. Turk, “Hybrid smoothed particle hydrodynamics,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Vancouver, Canada, 2011, pp. 33–42.","ama":"Raveendran K, Wojtan C, Turk G. Hybrid smoothed particle hydrodynamics. In: Spencer S, ed. ACM; 2011:33-42. doi:10.1145/2019406.2019411","chicago":"Raveendran, Karthik, Chris Wojtan, and Greg Turk. “Hybrid Smoothed Particle Hydrodynamics.” edited by Stephen Spencer, 33–42. ACM, 2011. https://doi.org/10.1145/2019406.2019411.","mla":"Raveendran, Karthik, et al. Hybrid Smoothed Particle Hydrodynamics. Edited by Stephen Spencer, ACM, 2011, pp. 33–42, doi:10.1145/2019406.2019411.","short":"K. Raveendran, C. Wojtan, G. Turk, in:, S. Spencer (Ed.), ACM, 2011, pp. 33–42."},"page":"33 - 42","file_date_updated":"2020-07-14T12:46:06Z","publist_id":"3343","author":[{"first_name":"Karthik","last_name":"Raveendran","full_name":"Raveendran, Karthik"},{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"},{"last_name":"Turk","first_name":"Greg","full_name":"Turk, Greg"}],"date_updated":"2023-02-23T11:21:05Z","date_created":"2018-12-11T12:02:32Z","year":"2011","publication_status":"published","publisher":"ACM","editor":[{"full_name":"Spencer, Stephen","last_name":"Spencer","first_name":"Stephen"}],"department":[{"_id":"ChWo"}],"month":"08","conference":{"name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","location":"Vancouver, Canada","start_date":"2011-08-05","end_date":"2011-08-07"},"doi":"10.1145/2019406.2019411","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1"},{"file":[{"date_created":"2018-12-12T10:13:34Z","date_updated":"2020-07-14T12:46:06Z","checksum":"8d508ad7c82f50978acbaa4170ee0a75","relation":"main_file","file_id":"5018","content_type":"application/pdf","file_size":34672096,"creator":"system","file_name":"IST-2016-599-v1+1_meshyFluidsCourseSIGGRAPH2011.pdf","access_level":"open_access"}],"oa_version":"Published Version","pubrep_id":"599","status":"public","title":"Liquid simulation with mesh-based surface tracking","ddc":["000"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3297","abstract":[{"lang":"eng","text":"Animating detailed liquid surfaces has always been a challenge for computer graphics researchers and visual effects artists. Over the past few years, researchers in this field have focused on mesh-based surface tracking to synthesize extremely detailed liquid surfaces as efficiently as possible. This course provides a solid understanding of the steps required to create a fluid simulator with a mesh-based liquid surface.\r\n\r\nThe course begins with an overview of several existing liquid-surface-tracking techniques and the pros and cons of each method. Then it explains how to embed a triangle mesh into a finite-difference-based fluid simulator and describes several methods for allowing the liquid surface to merge together or break apart. The final section showcases the benefits and further applications of a mesh-based liquid surface, highlighting state-of-the-art methods for tracking colors and textures, maintaining liquid volume, preserving small surface features, and simulating realistic surface-tension waves."}],"type":"conference","date_published":"2011-08-07T00:00:00Z","citation":{"ama":"Wojtan C, Müller Fischer M, Brochu T. Liquid simulation with mesh-based surface tracking. In: ACM; 2011. doi:10.1145/2037636.2037644","ieee":"C. Wojtan, M. Müller Fischer, and T. Brochu, “Liquid simulation with mesh-based surface tracking,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Vancouver, BC, Canada, 2011.","apa":"Wojtan, C., Müller Fischer, M., & Brochu, T. (2011). Liquid simulation with mesh-based surface tracking. 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Liquid Simulation with Mesh-Based Surface Tracking. 8, ACM, 2011, doi:10.1145/2037636.2037644.","chicago":"Wojtan, Chris, Matthias Müller Fischer, and Tyson Brochu. “Liquid Simulation with Mesh-Based Surface Tracking.” ACM, 2011. https://doi.org/10.1145/2037636.2037644."},"day":"07","has_accepted_license":"1","scopus_import":1,"date_updated":"2023-02-23T11:21:02Z","date_created":"2018-12-11T12:02:31Z","author":[{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J"},{"first_name":"Matthias","last_name":"Müller Fischer","full_name":"Müller Fischer, Matthias"},{"full_name":"Brochu, Tyson","last_name":"Brochu","first_name":"Tyson"}],"publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"ACM","year":"2011","file_date_updated":"2020-07-14T12:46:06Z","publist_id":"3344","article_number":"8","language":[{"iso":"eng"}],"conference":{"end_date":"2011-08-11","location":"Vancouver, BC, Canada","start_date":"2011-08-07","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"doi":"10.1145/2037636.2037644","quality_controlled":"1","oa":1,"month":"08"},{"ec_funded":1,"publist_id":"3355","year":"2011","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"first_name":"Konrad","last_name":"Lohse","full_name":"Lohse, Konrad"},{"full_name":"Harrison, Richard","last_name":"Harrison","first_name":"Richard"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"volume":189,"date_created":"2018-12-11T12:02:29Z","date_updated":"2021-01-12T07:42:26Z","month":"11","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/","open_access":"1"}],"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","doi":"10.1534/genetics.111.129569","language":[{"iso":"eng"}],"type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Analysis of genomic data requires an efficient way to calculate likelihoods across very large numbers of loci. We describe a general method for finding the distribution of genealogies: we allow migration between demes, splitting of demes [as in the isolation-with-migration (IM) model], and recombination between linked loci. These processes are described by a set of linear recursions for the generating function of branch lengths. Under the infinite-sites model, the probability of any configuration of mutations can be found by differentiating this generating function. Such calculations are feasible for small numbers of sampled genomes: as an example, we show how the generating function can be derived explicitly for three genes under the two-deme IM model. This derivation is done automatically, using Mathematica. Given data from a large number of unlinked and nonrecombining blocks of sequence, these results can be used to find maximum-likelihood estimates of model parameters by tabulating the probabilities of all relevant mutational configurations and then multiplying across loci. The feasibility of the method is demonstrated by applying it to simulated data and to a data set previously analyzed by Wang and Hey (2010) consisting of 26,141 loci sampled from Drosophila simulans and D. melanogaster. Our results suggest that such likelihood calculations are scalable to genomic data as long as the numbers of sampled individuals and mutations per sequence block are small."}],"_id":"3290","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 189","status":"public","title":"A general method for calculating likelihoods under the coalescent process","oa_version":"Submitted Version","scopus_import":1,"day":"01","citation":{"short":"K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987.","mla":"Lohse, Konrad, et al. “A General Method for Calculating Likelihoods under the Coalescent Process.” Genetics, vol. 189, no. 3, Genetics Society of America, 2011, pp. 977–87, doi:10.1534/genetics.111.129569.","chicago":"Lohse, Konrad, Richard Harrison, and Nicholas H Barton. “A General Method for Calculating Likelihoods under the Coalescent Process.” Genetics. Genetics Society of America, 2011. https://doi.org/10.1534/genetics.111.129569.","ama":"Lohse K, Harrison R, Barton NH. A general method for calculating likelihoods under the coalescent process. Genetics. 2011;189(3):977-987. doi:10.1534/genetics.111.129569","apa":"Lohse, K., Harrison, R., & Barton, N. H. (2011). A general method for calculating likelihoods under the coalescent process. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.111.129569","ieee":"K. Lohse, R. Harrison, and N. H. Barton, “A general method for calculating likelihoods under the coalescent process,” Genetics, vol. 189, no. 3. Genetics Society of America, pp. 977–987, 2011.","ista":"Lohse K, Harrison R, Barton NH. 2011. A general method for calculating likelihoods under the coalescent process. Genetics. 189(3), 977–987."},"publication":"Genetics","page":"977 - 987","date_published":"2011-11-01T00:00:00Z"},{"year":"2011","acknowledgement":"This research is supported by the National Science Foundation (NSF) under grant DBI-0820624.","department":[{"_id":"HeEd"}],"publisher":"IEEE","publication_status":"published","author":[{"last_name":"Zheng","first_name":"Ying","full_name":"Zheng, Ying"},{"last_name":"Gu","first_name":"Steve","full_name":"Gu, Steve"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"full_name":"Tomasi, Carlo","first_name":"Carlo","last_name":"Tomasi"},{"full_name":"Benfey, Philip","first_name":"Philip","last_name":"Benfey"}],"date_updated":"2020-07-14T23:03:43Z","date_created":"2018-12-11T12:02:36Z","article_number":"6126475","publist_id":"3328","file_date_updated":"2020-07-14T12:46:07Z","oa":1,"quality_controlled":"1","doi":"10.1109/ICCV.2011.6126475","conference":{"start_date":"2011-11-06","location":"Barcelona, Spain","end_date":"2011-11-13","name":"ICCV: International Conference on Computer Vision"},"language":[{"iso":"eng"}],"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3312","title":"Detailed reconstruction of 3D plant root shape","ddc":["000"],"status":"public","pubrep_id":"541","file":[{"creator":"system","file_size":5622728,"content_type":"application/pdf","file_name":"IST-2016-541-v1+1_2011-P-07-RootReconstruction.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:07Z","date_created":"2018-12-12T10:09:04Z","checksum":"30a33564b7b45a7ee31610898267fd0e","file_id":"4727","relation":"main_file"}],"oa_version":"Submitted Version","type":"conference_poster","abstract":[{"lang":"eng","text":"We study the 3D reconstruction of plant roots from multiple 2D images. To meet the challenge caused by the delicate nature of thin branches, we make three innovations to cope with the sensitivity to image quality and calibration. First, we model the background as a harmonic function to improve the segmentation of the root in each 2D image. Second, we develop the concept of the regularized visual hull which reduces the effect of jittering and refraction by ensuring consistency with one 2D image. Third, we guarantee connectedness through adjustments to the 3D reconstruction that minimize global error. Our software is part of a biological phenotype/genotype study of agricultural root systems. It has been tested on more than 40 plant roots and results are promising in terms of reconstruction quality and efficiency."}],"citation":{"short":"Y. Zheng, S. Gu, H. Edelsbrunner, C. Tomasi, P. Benfey, Detailed Reconstruction of 3D Plant Root Shape, IEEE, 2011.","mla":"Zheng, Ying, et al. “Detailed Reconstruction of 3D Plant Root Shape.” Proceedings of the IEEE International Conference on Computer Vision, 6126475, IEEE, 2011, doi:10.1109/ICCV.2011.6126475.","chicago":"Zheng, Ying, Steve Gu, Herbert Edelsbrunner, Carlo Tomasi, and Philip Benfey. Detailed Reconstruction of 3D Plant Root Shape. Proceedings of the IEEE International Conference on Computer Vision. IEEE, 2011. https://doi.org/10.1109/ICCV.2011.6126475.","ama":"Zheng Y, Gu S, Edelsbrunner H, Tomasi C, Benfey P. Detailed Reconstruction of 3D Plant Root Shape. IEEE; 2011. doi:10.1109/ICCV.2011.6126475","apa":"Zheng, Y., Gu, S., Edelsbrunner, H., Tomasi, C., & Benfey, P. (2011). Detailed reconstruction of 3D plant root shape. Proceedings of the IEEE International Conference on Computer Vision. Barcelona, Spain: IEEE. https://doi.org/10.1109/ICCV.2011.6126475","ieee":"Y. Zheng, S. Gu, H. Edelsbrunner, C. Tomasi, and P. Benfey, Detailed reconstruction of 3D plant root shape. IEEE, 2011.","ista":"Zheng Y, Gu S, Edelsbrunner H, Tomasi C, Benfey P. 2011. Detailed reconstruction of 3D plant root shape, IEEE,p."},"publication":"Proceedings of the IEEE International Conference on Computer Vision","date_published":"2011-12-31T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"31"},{"oa":1,"quality_controlled":"1","doi":"10.1109/ICCV.2011.6126271","conference":{"end_date":"2011-11-13","start_date":"2011-11-06","location":"Barcelona, Spain","name":"ICCV: International Conference on Computer Vision"},"language":[{"iso":"eng"}],"month":"11","year":"2011","publisher":"IEEE","department":[{"_id":"HeEd"}],"publication_status":"published","author":[{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chao","full_name":"Chen, Chao"},{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"date_updated":"2021-01-12T07:42:35Z","date_created":"2018-12-11T12:02:37Z","article_number":"6126271","publist_id":"3327","file_date_updated":"2020-07-14T12:46:07Z","citation":{"ista":"Chen C, Edelsbrunner H. 2011. Diffusion runs low on persistence fast. Proceedings of the IEEE International Conference on Computer Vision. ICCV: International Conference on Computer Vision, 6126271.","apa":"Chen, C., & Edelsbrunner, H. (2011). Diffusion runs low on persistence fast. In Proceedings of the IEEE International Conference on Computer Vision. Barcelona, Spain: IEEE. https://doi.org/10.1109/ICCV.2011.6126271","ieee":"C. Chen and H. Edelsbrunner, “Diffusion runs low on persistence fast,” in Proceedings of the IEEE International Conference on Computer Vision, Barcelona, Spain, 2011.","ama":"Chen C, Edelsbrunner H. Diffusion runs low on persistence fast. In: Proceedings of the IEEE International Conference on Computer Vision. IEEE; 2011. doi:10.1109/ICCV.2011.6126271","chicago":"Chen, Chao, and Herbert Edelsbrunner. “Diffusion Runs Low on Persistence Fast.” In Proceedings of the IEEE International Conference on Computer Vision. IEEE, 2011. https://doi.org/10.1109/ICCV.2011.6126271.","mla":"Chen, Chao, and Herbert Edelsbrunner. “Diffusion Runs Low on Persistence Fast.” Proceedings of the IEEE International Conference on Computer Vision, 6126271, IEEE, 2011, doi:10.1109/ICCV.2011.6126271.","short":"C. Chen, H. Edelsbrunner, in:, Proceedings of the IEEE International Conference on Computer Vision, IEEE, 2011."},"publication":"Proceedings of the IEEE International Conference on Computer Vision","date_published":"2011-11-06T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"06","_id":"3313","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Diffusion runs low on persistence fast","status":"public","ddc":["000"],"pubrep_id":"540","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:46:07Z","date_created":"2018-12-12T10:17:28Z","checksum":"6984684081ba123808b344f9f2e64a8f","file_id":"5282","relation":"main_file","creator":"system","file_size":614050,"content_type":"application/pdf","file_name":"IST-2016-540-v1+1_2011-P-08-RunEmpty.pdf","access_level":"open_access"}],"type":"conference","abstract":[{"lang":"eng","text":"Interpreting an image as a function on a compact sub- set of the Euclidean plane, we get its scale-space by diffu- sion, spreading the image over the entire plane. This gener- ates a 1-parameter family of functions alternatively defined as convolutions with a progressively wider Gaussian ker- nel. We prove that the corresponding 1-parameter family of persistence diagrams have norms that go rapidly to zero as time goes to infinity. This result rationalizes experimental observations about scale-space. We hope this will lead to targeted improvements of related computer vision methods."}]},{"file":[{"creator":"dernst","content_type":"application/pdf","file_size":475254,"file_name":"2010_AlphaShapes.pdf","access_level":"open_access","date_updated":"2022-05-24T07:55:05Z","date_created":"2022-05-24T07:55:05Z","success":1,"checksum":"a592ea438351e7280eea993a7713ab8f","file_id":"11408","relation":"main_file"}],"oa_version":"Submitted Version","date_created":"2018-12-11T12:02:36Z","date_updated":"2022-05-24T07:56:30Z","author":[{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"publisher":"Springer","department":[{"_id":"HeEd"}],"editor":[{"first_name":"R","last_name":"van de Weygaert","full_name":"van de Weygaert, R"},{"last_name":"Vegter","first_name":"G","full_name":"Vegter, G"},{"first_name":"J","last_name":"Ritzerveld","full_name":"Ritzerveld, J"},{"last_name":"Icke","first_name":"V","full_name":"Icke, V"}],"ddc":["510"],"publication_status":"inpress","status":"public","title":"Alpha shapes - a survey","year":"2011","_id":"3311","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3329","file_date_updated":"2022-05-24T07:55:05Z","abstract":[{"text":"Alpha shapes have been conceived in 1981 as an attempt to define the shape of a finite set of point in the plane. Since then, connections to diverse areas in the sciences and engineering have developed, including to pattern recognition, digital shape sampling and processing, and structural molecular biology. This survey begins with a historical account and discusses geometric, algorithmic, topological, and combinatorial aspects of alpha shapes in this sequence.","lang":"eng"}],"type":"book_chapter","language":[{"iso":"eng"}],"date_published":"2011-12-31T00:00:00Z","quality_controlled":"1","oa":1,"citation":{"short":"H. Edelsbrunner, in:, R. van de Weygaert, G. Vegter, J. Ritzerveld, V. Icke (Eds.), Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings, Springer, n.d.","mla":"Edelsbrunner, Herbert. “Alpha Shapes - a Survey.” Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings, edited by R van de Weygaert et al., Springer.","chicago":"Edelsbrunner, Herbert. “Alpha Shapes - a Survey.” In Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings, edited by R van de Weygaert, G Vegter, J Ritzerveld, and V Icke. Springer, n.d.","ama":"Edelsbrunner H. Alpha shapes - a survey. In: van de Weygaert R, Vegter G, Ritzerveld J, Icke V, eds. Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings. Springer.","ieee":"H. Edelsbrunner, “Alpha shapes - a survey,” in Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings, R. van de Weygaert, G. Vegter, J. Ritzerveld, and V. Icke, Eds. Springer.","apa":"Edelsbrunner, H. (n.d.). Alpha shapes - a survey. In R. van de Weygaert, G. Vegter, J. Ritzerveld, & V. Icke (Eds.), Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings. Springer.","ista":"Edelsbrunner H.Alpha shapes - a survey. In: Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings. ."},"publication":"Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings","article_processing_charge":"No","has_accepted_license":"1","day":"31","month":"12"},{"day":"14","article_processing_charge":"No","has_accepted_license":"1","citation":{"chicago":"Almagor, Shaull, Udi Boker, and Orna Kupferman. “What’s Decidable about Weighted Automata ,” 6996:482–91. Springer, 2011. https://doi.org/10.1007/978-3-642-24372-1_37.","short":"S. Almagor, U. Boker, O. Kupferman, in:, Springer, 2011, pp. 482–491.","mla":"Almagor, Shaull, et al. What’s Decidable about Weighted Automata . Vol. 6996, Springer, 2011, pp. 482–91, doi:10.1007/978-3-642-24372-1_37.","apa":"Almagor, S., Boker, U., & Kupferman, O. (2011). What’s decidable about weighted automata (Vol. 6996, pp. 482–491). Presented at the ATVA: Automated Technology for Verification and Analysis, Taipei, Taiwan: Springer. https://doi.org/10.1007/978-3-642-24372-1_37","ieee":"S. Almagor, U. Boker, and O. Kupferman, “What’s decidable about weighted automata ,” presented at the ATVA: Automated Technology for Verification and Analysis, Taipei, Taiwan, 2011, vol. 6996, pp. 482–491.","ista":"Almagor S, Boker U, Kupferman O. 2011. What’s decidable about weighted automata . ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 6996, 482–491.","ama":"Almagor S, Boker U, Kupferman O. What’s decidable about weighted automata . In: Vol 6996. Springer; 2011:482-491. doi:10.1007/978-3-642-24372-1_37"},"page":"482 - 491","date_published":"2011-10-14T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Weighted automata map input words to numerical values. Ap- plications of weighted automata include formal verification of quantitative properties, as well as text, speech, and image processing. A weighted au- tomaton is defined with respect to a semiring. For the tropical semiring, the weight of a run is the sum of the weights of the transitions taken along the run, and the value of a word is the minimal weight of an accepting run on it. In the 90’s, Krob studied the decidability of problems on rational series defined with respect to the tropical semiring. Rational series are strongly related to weighted automata, and Krob’s results apply to them. In par- ticular, it follows from Krob’s results that the universality problem (that is, deciding whether the values of all words are below some threshold) is decidable for weighted automata defined with respect to the tropical semir- ing with domain ∪ {∞}, and that the equality problem is undecidable when the domain is ∪ {∞}. In this paper we continue the study of the borders of decidability in weighted automata, describe alternative and direct proofs of the above results, and tighten them further. Unlike the proofs of Krob, which are algebraic in their nature, our proofs stay in the terrain of state machines, and the reduction is from the halting problem of a two-counter machine. This enables us to significantly simplify Krob’s reasoning, make the un- decidability result accessible to the automata-theoretic community, and strengthen it to apply already to a very simple class of automata: all the states are accepting, there are no initial nor final weights, and all the weights on the transitions are from the set {−1, 0, 1}. The fact we work directly with the automata enables us to tighten also the decidability re- sults and to show that the universality problem for weighted automata defined with respect to the tropical semiring with domain ∪ {∞}, and in fact even with domain ≥0 ∪ {∞}, is PSPACE-complete. Our results thus draw a sharper picture about the decidability of decision problems for weighted automata, in both the front of containment vs. universality and the front of the ∪ {∞} vs. the ∪ {∞} domains.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3326","status":"public","ddc":["000"],"title":"What’s decidable about weighted automata ","intvolume":" 6996","oa_version":"Submitted Version","file":[{"file_name":"2011_LNCS_Almagor.pdf","access_level":"open_access","creator":"dernst","file_size":182309,"content_type":"application/pdf","file_id":"7868","relation":"main_file","date_created":"2020-05-19T16:08:32Z","date_updated":"2020-07-14T12:46:07Z","checksum":"a7ca08a2cb1b6925f4c18a3034ae5659"}],"month":"10","oa":1,"quality_controlled":"1","conference":{"name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2011-10-14","location":"Taipei, Taiwan","start_date":"2011-10-11"},"doi":"10.1007/978-3-642-24372-1_37","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:07Z","publist_id":"3309","year":"2011","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","author":[{"full_name":"Almagor, Shaull","last_name":"Almagor","first_name":"Shaull"},{"id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi","last_name":"Boker","full_name":"Boker, Udi"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"date_updated":"2021-01-12T07:42:40Z","date_created":"2018-12-11T12:02:41Z","volume":6996},{"day":"26","month":"01","article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"conference":{"name":"POPL: Principles of Programming Languages","location":"Texas, USA","start_date":"2011-01-26","end_date":"2011-01-28"},"doi":"10.1145/1926385.1926454","date_published":"2011-01-26T00:00:00Z","quality_controlled":"1","page":"599 - 610","citation":{"chicago":"Alur, Rajeev, and Pavol Cerny. “Streaming Transducers for Algorithmic Verification of Single Pass List Processing Programs,” 46:599–610. ACM, 2011. https://doi.org/10.1145/1926385.1926454.","short":"R. Alur, P. Cerny, in:, ACM, 2011, pp. 599–610.","mla":"Alur, Rajeev, and Pavol Cerny. Streaming Transducers for Algorithmic Verification of Single Pass List Processing Programs. Vol. 46, no. 1, ACM, 2011, pp. 599–610, doi:10.1145/1926385.1926454.","ieee":"R. Alur and P. Cerny, “Streaming transducers for algorithmic verification of single pass list processing programs,” presented at the POPL: Principles of Programming Languages, Texas, USA, 2011, vol. 46, no. 1, pp. 599–610.","apa":"Alur, R., & Cerny, P. (2011). Streaming transducers for algorithmic verification of single pass list processing programs (Vol. 46, pp. 599–610). Presented at the POPL: Principles of Programming Languages, Texas, USA: ACM. https://doi.org/10.1145/1926385.1926454","ista":"Alur R, Cerny P. 2011. Streaming transducers for algorithmic verification of single pass list processing programs. POPL: Principles of Programming Languages vol. 46, 599–610.","ama":"Alur R, Cerny P. Streaming transducers for algorithmic verification of single pass list processing programs. In: Vol 46. ACM; 2011:599-610. doi:10.1145/1926385.1926454"},"abstract":[{"text":"We introduce streaming data string transducers that map input data strings to output data strings in a single left-to-right pass in linear time. Data strings are (unbounded) sequences of data values, tagged with symbols from a finite set, over a potentially infinite data do- main that supports only the operations of equality and ordering. The transducer uses a finite set of states, a finite set of variables ranging over the data domain, and a finite set of variables ranging over data strings. At every step, it can make decisions based on the next in- put symbol, updating its state, remembering the input data value in its data variables, and updating data-string variables by concatenat- ing data-string variables and new symbols formed from data vari- ables, while avoiding duplication. We establish that the problems of checking functional equivalence of two streaming transducers, and of checking whether a streaming transducer satisfies pre/post verification conditions specified by streaming acceptors over in- put/output data-strings, are in PSPACE. We identify a class of imperative and a class of functional pro- grams, manipulating lists of data items, which can be effectively translated to streaming data-string transducers. The imperative pro- grams dynamically modify a singly-linked heap by changing next- pointers of heap-nodes and by adding new nodes. The main re- striction specifies how the next-pointers can be used for traversal. We also identify an expressively equivalent fragment of functional programs that traverse a list using syntactically restricted recursive calls. Our results lead to algorithms for assertion checking and for checking functional equivalence of two programs, written possibly in different programming styles, for commonly used routines such as insert, delete, and reverse.","lang":"eng"}],"publist_id":"3310","issue":"1","type":"conference","date_created":"2018-12-11T12:02:41Z","date_updated":"2022-03-21T08:12:51Z","oa_version":"None","volume":46,"author":[{"first_name":"Rajeev","last_name":"Alur","full_name":"Alur, Rajeev"},{"full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","last_name":"Cerny"}],"publication_status":"published","status":"public","title":"Streaming transducers for algorithmic verification of single pass list processing programs","department":[{"_id":"ToHe"}],"intvolume":" 46","publisher":"ACM","year":"2011","_id":"3325","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2011-01-01T00:00:00Z","page":"371 - 386","citation":{"ama":"Piskac R, Wies T. Decision procedures for automating termination proofs. In: Jhala R, Schmidt D, eds. Vol 6538. Springer; 2011:371-386. doi:10.1007/978-3-642-18275-4_26","apa":"Piskac, R., & Wies, T. (2011). Decision procedures for automating termination proofs. In R. Jhala & D. Schmidt (Eds.) (Vol. 6538, pp. 371–386). Presented at the VMCAI: Verification Model Checking and Abstract Interpretation, Texas, USA: Springer. https://doi.org/10.1007/978-3-642-18275-4_26","ieee":"R. Piskac and T. Wies, “Decision procedures for automating termination proofs,” presented at the VMCAI: Verification Model Checking and Abstract Interpretation, Texas, USA, 2011, vol. 6538, pp. 371–386.","ista":"Piskac R, Wies T. 2011. Decision procedures for automating termination proofs. VMCAI: Verification Model Checking and Abstract Interpretation, LNCS, vol. 6538, 371–386.","short":"R. Piskac, T. Wies, in:, R. Jhala, D. Schmidt (Eds.), Springer, 2011, pp. 371–386.","mla":"Piskac, Ruzica, and Thomas Wies. Decision Procedures for Automating Termination Proofs. Edited by Ranjit Jhala and David Schmidt, vol. 6538, Springer, 2011, pp. 371–86, doi:10.1007/978-3-642-18275-4_26.","chicago":"Piskac, Ruzica, and Thomas Wies. “Decision Procedures for Automating Termination Proofs.” edited by Ranjit Jhala and David Schmidt, 6538:371–86. Springer, 2011. https://doi.org/10.1007/978-3-642-18275-4_26."},"day":"01","scopus_import":1,"oa_version":"Submitted Version","intvolume":" 6538","status":"public","title":"Decision procedures for automating termination proofs","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3324","abstract":[{"text":"Automated termination provers often use the following schema to prove that a program terminates: construct a relational abstraction of the program's transition relation and then show that the relational abstraction is well-founded. The focus of current tools has been on developing sophisticated techniques for constructing the abstractions while relying on known decidable logics (such as linear arithmetic) to express them. We believe we can significantly increase the class of programs that are amenable to automated termination proofs by identifying more expressive decidable logics for reasoning about well-founded relations. We therefore present a new decision procedure for reasoning about multiset orderings, which are among the most powerful orderings used to prove termination. We show that, using our decision procedure, one can automatically prove termination of natural abstractions of programs.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-18275-4_26","conference":{"location":"Texas, USA","start_date":"2011-01-23","end_date":"2011-01-25","name":"VMCAI: Verification Model Checking and Abstract Interpretation"},"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://infoscience.epfl.ch/record/170697/","open_access":"1"}],"month":"01","volume":6538,"date_created":"2018-12-11T12:02:40Z","date_updated":"2021-01-12T07:42:39Z","author":[{"first_name":"Ruzica","last_name":"Piskac","full_name":"Piskac, Ruzica"},{"id":"447BFB88-F248-11E8-B48F-1D18A9856A87","last_name":"Wies","first_name":"Thomas","full_name":"Wies, Thomas"}],"editor":[{"first_name":"Ranjit","last_name":"Jhala","full_name":"Jhala, Ranjit"},{"full_name":"Schmidt, David","last_name":"Schmidt","first_name":"David"}],"department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2011","publist_id":"3311"},{"citation":{"ama":"Boker U, Kupferman O. Co-Büching them all. In: Hofmann M, ed. Vol 6604. Springer; 2011:184-198. doi:10.1007/978-3-642-19805-2_13","ista":"Boker U, Kupferman O. 2011. Co-Büching them all. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 6604, 184–198.","apa":"Boker, U., & Kupferman, O. (2011). Co-Büching them all. In M. Hofmann (Ed.) (Vol. 6604, pp. 184–198). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Saarbrücken, Germany: Springer. https://doi.org/10.1007/978-3-642-19805-2_13","ieee":"U. Boker and O. Kupferman, “Co-Büching them all,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Saarbrücken, Germany, 2011, vol. 6604, pp. 184–198.","mla":"Boker, Udi, and Orna Kupferman. Co-Büching Them All. Edited by Martin Hofmann, vol. 6604, Springer, 2011, pp. 184–98, doi:10.1007/978-3-642-19805-2_13.","short":"U. Boker, O. Kupferman, in:, M. Hofmann (Ed.), Springer, 2011, pp. 184–198.","chicago":"Boker, Udi, and Orna Kupferman. “Co-Büching Them All.” edited by Martin Hofmann, 6604:184–98. Springer, 2011. https://doi.org/10.1007/978-3-642-19805-2_13."},"quality_controlled":"1","page":"184 - 198","conference":{"name":"FoSSaCS: Foundations of Software Science and Computation Structures","start_date":"2011-03-26","location":"Saarbrücken, Germany","end_date":"2011-04-03"},"date_published":"2011-03-29T00:00:00Z","doi":"10.1007/978-3-642-19805-2_13","language":[{"iso":"eng"}],"month":"03","day":"29","_id":"3327","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2011","status":"public","title":"Co-Büching them all","publication_status":"published","editor":[{"full_name":"Hofmann, Martin","last_name":"Hofmann","first_name":"Martin"}],"intvolume":" 6604","publisher":"Springer","author":[{"first_name":"Udi","last_name":"Boker","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"date_created":"2018-12-11T12:02:41Z","date_updated":"2021-01-12T07:42:41Z","volume":6604,"oa_version":"None","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We solve the open problems of translating, when possible, all common classes of nondeterministic word automata to deterministic and nondeterministic co-Büchi word automata. The handled classes include Büchi, parity, Rabin, Streett and Muller automata. The translations follow a unified approach and are all asymptotically tight. The problem of translating Büchi automata to equivalent co-Büchi automata was solved in [2], leaving open the problems of translating automata with richer acceptance conditions. For these classes, one cannot easily extend or use the construction in [2]. In particular, going via an intermediate Büchi automaton is not optimal and might involve a blow-up exponentially higher than the known lower bound. Other known translations are also not optimal and involve a doubly exponential blow-up. We describe direct, simple, and asymptotically tight constructions, involving a 2Θ(n) blow-up. The constructions are variants of the subset construction, and allow for symbolic implementations. Beyond the theoretical importance of the results, the new constructions have various applications, among which is an improved algorithm for translating, when possible, LTL formulas to deterministic Büchi word automata.","lang":"eng"}],"publist_id":"3308","extern":"1"},{"doi":"10.1109/IROS.2011.6094892","date_published":"2011-01-01T00:00:00Z","conference":{"name":"IROS: RSJ International Conference on Intelligent Robots and Systems","end_date":"2011-09-30","location":"San Francisco, USA","start_date":"2011-09-25"},"language":[{"iso":"eng"}],"citation":{"short":"Z. Wang, C. Lampert, K. Mülling, B. Schölkopf, J. Peters, in:, IEEE, 2011, pp. 332–337.","mla":"Wang, Zhikun, et al. Learning Anticipation Policies for Robot Table Tennis. IEEE, 2011, pp. 332–37, doi:10.1109/IROS.2011.6094892.","chicago":"Wang, Zhikun, Christoph Lampert, Katharina Mülling, Bernhard Schölkopf, and Jan Peters. “Learning Anticipation Policies for Robot Table Tennis,” 332–37. IEEE, 2011. https://doi.org/10.1109/IROS.2011.6094892.","ama":"Wang Z, Lampert C, Mülling K, Schölkopf B, Peters J. Learning anticipation policies for robot table tennis. In: IEEE; 2011:332-337. doi:10.1109/IROS.2011.6094892","apa":"Wang, Z., Lampert, C., Mülling, K., Schölkopf, B., & Peters, J. (2011). Learning anticipation policies for robot table tennis (pp. 332–337). Presented at the IROS: RSJ International Conference on Intelligent Robots and Systems, San Francisco, USA: IEEE. https://doi.org/10.1109/IROS.2011.6094892","ieee":"Z. Wang, C. Lampert, K. Mülling, B. Schölkopf, and J. Peters, “Learning anticipation policies for robot table tennis,” presented at the IROS: RSJ International Conference on Intelligent Robots and Systems, San Francisco, USA, 2011, pp. 332–337.","ista":"Wang Z, Lampert C, Mülling K, Schölkopf B, Peters J. 2011. Learning anticipation policies for robot table tennis. IROS: RSJ International Conference on Intelligent Robots and Systems, 332–337."},"page":"332 - 337","quality_controlled":"1","month":"01","day":"01","scopus_import":1,"author":[{"last_name":"Wang","first_name":"Zhikun","full_name":"Wang, Zhikun"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"},{"last_name":"Mülling","first_name":"Katharina","full_name":"Mülling, Katharina"},{"full_name":"Schölkopf, Bernhard","first_name":"Bernhard","last_name":"Schölkopf"},{"first_name":"Jan","last_name":"Peters","full_name":"Peters, Jan"}],"oa_version":"None","date_updated":"2021-01-12T07:42:45Z","date_created":"2018-12-11T12:02:45Z","year":"2011","_id":"3337","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChLa"}],"publisher":"IEEE","status":"public","publication_status":"published","title":"Learning anticipation policies for robot table tennis","publist_id":"3293","abstract":[{"text":"Playing table tennis is a difficult task for robots, especially due to their limitations of acceleration. A key bottleneck is the amount of time needed to reach the desired hitting position and velocity of the racket for returning the incoming ball. Here, it often does not suffice to simply extrapolate the ball's trajectory after the opponent returns it but more information is needed. Humans are able to predict the ball's trajectory based on the opponent's moves and, thus, have a considerable advantage. Hence, we propose to incorporate an anticipation system into robot table tennis players, which enables the robot to react earlier while the opponent is performing the striking movement. Based on visual observation of the opponent's racket movement, the robot can predict the aim of the opponent and adjust its movement generation accordingly. The policies for deciding how and when to react are obtained by reinforcement learning. We conduct experiments with an existing robot player to show that the learned reaction policy can significantly improve the performance of the overall system.","lang":"eng"}],"type":"conference"},{"date_published":"2011-07-11T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1107.2132"}],"citation":{"ama":"Chatterjee K, De Alfaro L, Pritam R. Magnifying lens abstraction for stochastic games with discounted and long-run average objectives. arXiv. 2011.","ista":"Chatterjee K, De Alfaro L, Pritam R. 2011. Magnifying lens abstraction for stochastic games with discounted and long-run average objectives. arXiv, .","apa":"Chatterjee, K., De Alfaro, L., & Pritam, R. (2011). Magnifying lens abstraction for stochastic games with discounted and long-run average objectives. arXiv. ArXiv.","ieee":"K. Chatterjee, L. De Alfaro, and R. Pritam, “Magnifying lens abstraction for stochastic games with discounted and long-run average objectives,” arXiv. ArXiv, 2011.","mla":"Chatterjee, Krishnendu, et al. “Magnifying Lens Abstraction for Stochastic Games with Discounted and Long-Run Average Objectives.” ArXiv, ArXiv, 2011.","short":"K. Chatterjee, L. De Alfaro, R. Pritam, ArXiv (2011).","chicago":"Chatterjee, Krishnendu, Luca De Alfaro, and Roy Pritam. “Magnifying Lens Abstraction for Stochastic Games with Discounted and Long-Run Average Objectives.” ArXiv. ArXiv, 2011."},"external_id":{"arxiv":["1107.2132"]},"publication":"arXiv","page":"17","day":"11","month":"07","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"De Alfaro, Luca","last_name":"De Alfaro","first_name":"Luca"},{"full_name":"Pritam, Roy","last_name":"Pritam","first_name":"Roy"}],"oa_version":"Preprint","date_created":"2018-12-11T12:02:46Z","date_updated":"2021-01-12T07:42:46Z","_id":"3339","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","publisher":"ArXiv","department":[{"_id":"KrCh"}],"title":"Magnifying lens abstraction for stochastic games with discounted and long-run average objectives","publication_status":"published","status":"public","publist_id":"3286","abstract":[{"text":"Turn-based stochastic games and its important subclass Markov decision processes (MDPs) provide models for systems with both probabilistic and nondeterministic behaviors. We consider turn-based stochastic games with two classical quantitative objectives: discounted-sum and long-run average objectives. The game models and the quantitative objectives are widely used in probabilistic verification, planning, optimal inventory control, network protocol and performance analysis. Games and MDPs that model realistic systems often have very large state spaces, and probabilistic abstraction techniques are necessary to handle the state-space explosion. The commonly used full-abstraction techniques do not yield space-savings for systems that have many states with similar value, but does not necessarily have similar transition structure. A semi-abstraction technique, namely Magnifying-lens abstractions (MLA), that clusters states based on value only, disregarding differences in their transition relation was proposed for qualitative objectives (reachability and safety objectives). In this paper we extend the MLA technique to solve stochastic games with discounted-sum and long-run average objectives. We present the MLA technique based abstraction-refinement algorithm for stochastic games and MDPs with discounted-sum objectives. For long-run average objectives, our solution works for all MDPs and a sub-class of stochastic games where every state has the same value. ","lang":"eng"}],"type":"preprint"},{"article_processing_charge":"No","day":"11","page":"260 - 276","citation":{"ista":"Chatterjee K, Henzinger MH, Joglekar M, Nisarg S. 2011. Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives. CAV: Computer Aided Verification, LNCS, vol. 6806, 260–276.","apa":"Chatterjee, K., Henzinger, M. H., Joglekar, M., & Nisarg, S. (2011). Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives. In G. Gopalakrishnan & S. Qadeer (Eds.) (Vol. 6806, pp. 260–276). Presented at the CAV: Computer Aided Verification, Snowbird, USA: Springer. https://doi.org/10.1007/978-3-642-22110-1_21","ieee":"K. Chatterjee, M. H. Henzinger, M. Joglekar, and S. Nisarg, “Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives,” presented at the CAV: Computer Aided Verification, Snowbird, USA, 2011, vol. 6806, pp. 260–276.","ama":"Chatterjee K, Henzinger MH, Joglekar M, Nisarg S. Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives. In: Gopalakrishnan G, Qadeer S, eds. Vol 6806. Springer; 2011:260-276. doi:10.1007/978-3-642-22110-1_21","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Manas Joglekar, and Shah Nisarg. “Symbolic Algorithms for Qualitative Analysis of Markov Decision Processes with Büchi Objectives.” edited by Ganesh Gopalakrishnan and Shaz Qadeer, 6806:260–76. Springer, 2011. https://doi.org/10.1007/978-3-642-22110-1_21.","mla":"Chatterjee, Krishnendu, et al. Symbolic Algorithms for Qualitative Analysis of Markov Decision Processes with Büchi Objectives. Edited by Ganesh Gopalakrishnan and Shaz Qadeer, vol. 6806, Springer, 2011, pp. 260–76, doi:10.1007/978-3-642-22110-1_21.","short":"K. Chatterjee, M.H. Henzinger, M. Joglekar, S. Nisarg, in:, G. Gopalakrishnan, S. Qadeer (Eds.), Springer, 2011, pp. 260–276."},"date_published":"2011-08-11T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) with ω-regular specifications given as parity objectives. We consider the problem of computing the set of almost-sure winning states from where the objective can be ensured with probability 1. The algorithms for the computation of the almost-sure winning set for parity objectives iteratively use the solutions for the almost-sure winning set for Büchi objectives (a special case of parity objectives). Our contributions are as follows: First, we present the first subquadratic symbolic algorithm to compute the almost-sure winning set for MDPs with Büchi objectives; our algorithm takes O(nm) symbolic steps as compared to the previous known algorithm that takes O(n 2) symbolic steps, where n is the number of states and m is the number of edges of the MDP. In practice MDPs often have constant out-degree, and then our symbolic algorithm takes O(nn) symbolic steps, as compared to the previous known O(n 2) symbolic steps algorithm. Second, we present a new algorithm, namely win-lose algorithm, with the following two properties: (a) the algorithm iteratively computes subsets of the almost-sure winning set and its complement, as compared to all previous algorithms that discover the almost-sure winning set upon termination; and (b) requires O(nK) symbolic steps, where K is the maximal number of edges of strongly connected components (scc’s) of the MDP. The win-lose algorithm requires symbolic computation of scc’s. Third, we improve the algorithm for symbolic scc computation; the previous known algorithm takes linear symbolic steps, and our new algorithm improves the constants associated with the linear number of steps. In the worst case the previous known algorithm takes 5·n symbolic steps, whereas our new algorithm takes 4 ·n symbolic steps."}],"intvolume":" 6806","title":"Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives","status":"public","_id":"3342","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","oa_version":"Preprint","month":"08","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","external_id":{"arxiv":["1104.3348"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1104.3348"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-22110-1_21","conference":{"end_date":"2011-07-20","start_date":"2011-07-14","location":"Snowbird, USA","name":"CAV: Computer Aided Verification"},"publist_id":"3282","department":[{"_id":"KrCh"}],"publisher":"Springer","editor":[{"full_name":"Gopalakrishnan, Ganesh","last_name":"Gopalakrishnan","first_name":"Ganesh"},{"last_name":"Qadeer","first_name":"Shaz","full_name":"Qadeer, Shaz"}],"publication_status":"published","year":"2011","volume":6806,"date_updated":"2023-02-23T11:00:13Z","date_created":"2018-12-11T12:02:47Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"2831"}]},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"full_name":"Joglekar, Manas","first_name":"Manas","last_name":"Joglekar"},{"full_name":"Nisarg, Shah","first_name":"Shah","last_name":"Nisarg"}]},{"day":"16","scopus_import":1,"date_published":"2011-06-16T00:00:00Z","page":"216 - 226","citation":{"ista":"Chatterjee K, Fijalkow N. 2011. Finitary languages. LATA: Language and Automata Theory and Applications, LNCS, vol. 6638, 216–226.","apa":"Chatterjee, K., & Fijalkow, N. (2011). Finitary languages (Vol. 6638, pp. 216–226). Presented at the LATA: Language and Automata Theory and Applications, Tarragona, Spain: Springer. https://doi.org/10.1007/978-3-642-21254-3_16","ieee":"K. Chatterjee and N. Fijalkow, “Finitary languages,” presented at the LATA: Language and Automata Theory and Applications, Tarragona, Spain, 2011, vol. 6638, pp. 216–226.","ama":"Chatterjee K, Fijalkow N. Finitary languages. In: Vol 6638. Springer; 2011:216-226. doi:10.1007/978-3-642-21254-3_16","chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Finitary Languages,” 6638:216–26. Springer, 2011. https://doi.org/10.1007/978-3-642-21254-3_16.","mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. Finitary Languages. Vol. 6638, Springer, 2011, pp. 216–26, doi:10.1007/978-3-642-21254-3_16.","short":"K. Chatterjee, N. Fijalkow, in:, Springer, 2011, pp. 216–226."},"abstract":[{"text":"The class of omega-regular languages provides a robust specification language in verification. Every omega-regular condition can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens "eventually". Finitary liveness was proposed by Alur and Henzinger as a stronger formulation of liveness. It requires that there exists an unknown, fixed bound b such that something good happens within b transitions. In this work we consider automata with finitary acceptance conditions defined by finitary Buchi, parity and Streett languages. We study languages expressible by such automata: we give their topological complexity and present a regular-expression characterization. We compare the expressive power of finitary automata and give optimal algorithms for classical decisions questions. We show that the finitary languages are Sigma 2-complete; we present a complete picture of the expressive power of various classes of automata with finitary and infinitary acceptance conditions; we show that the languages defined by finitary parity automata exactly characterize the star-free fragment of omega B-regular languages; and we show that emptiness is NLOGSPACE-complete and universality as well as language inclusion are PSPACE-complete for finitary parity and Streett automata.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","title":"Finitary languages","status":"public","intvolume":" 6638","_id":"3347","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","language":[{"iso":"eng"}],"conference":{"name":"LATA: Language and Automata Theory and Applications","end_date":"2011-05-31","start_date":"2011-05-26","location":"Tarragona, Spain"},"doi":"10.1007/978-3-642-21254-3_16","quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"oa":1,"external_id":{"arxiv":["1101.1727"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1101.1727"}],"publist_id":"3274","date_updated":"2021-01-12T07:42:50Z","date_created":"2018-12-11T12:02:48Z","volume":6638,"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nathanaël","last_name":"Fijalkow","id":"A1B5DD72-E997-11E9-8398-E808B6C6ADC0","full_name":"Fijalkow, Nathanaël"}],"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer","year":"2011"},{"type":"conference","article_number":"5970225","publist_id":"3275","ec_funded":1,"abstract":[{"lang":"eng","text":"We study Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) functions. We consider two different objectives, namely, expectation and satisfaction objectives. Given an MDP with k reward functions, in the expectation objective the goal is to maximize the expected limit-average value, and in the satisfaction objective the goal is to maximize the probability of runs such that the limit-average value stays above a given vector. We show that under the expectation objective, in contrast to the single-objective case, both randomization and memory are necessary for strategies, and that finite-memory randomized strategies are sufficient. Under the satisfaction objective, in contrast to the single-objective case, infinite memory is necessary for strategies, and that randomized memoryless strategies are sufficient for epsilon-approximation, for all epsilon>;0. We further prove that the decision problems for both expectation and satisfaction objectives can be solved in polynomial time and the trade-off curve (Pareto curve) can be epsilon-approximated in time polynomial in the size of the MDP and 1/epsilon, and exponential in the number of reward functions, for all epsilon>;0. Our results also reveal flaws in previous work for MDPs with multiple mean-payoff functions under the expectation objective, correct the flaws and obtain improved results."}],"publisher":"IEEE","department":[{"_id":"KrCh"}],"status":"public","title":"Two views on multiple mean payoff objectives in Markov Decision Processes","publication_status":"published","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3346","year":"2011","oa_version":"Submitted Version","date_updated":"2021-01-12T07:42:49Z","date_created":"2018-12-11T12:02:48Z","author":[{"full_name":"Brázdil, Tomáš","first_name":"Tomáš","last_name":"Brázdil"},{"full_name":"Brožek, Václav","last_name":"Brožek","first_name":"Václav"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Forejt, Vojtěch","first_name":"Vojtěch","last_name":"Forejt"},{"full_name":"Kučera, Antonín","first_name":"Antonín","last_name":"Kučera"}],"scopus_import":1,"day":"21","month":"06","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","citation":{"ieee":"T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, and A. Kučera, “Two views on multiple mean payoff objectives in Markov Decision Processes,” presented at the LICS: Logic in Computer Science, Toronto, Canada, 2011.","apa":"Brázdil, T., Brožek, V., Chatterjee, K., Forejt, V., & Kučera, A. (2011). Two views on multiple mean payoff objectives in Markov Decision Processes. Presented at the LICS: Logic in Computer Science, Toronto, Canada: IEEE. https://doi.org/10.1109/LICS.2011.10","ista":"Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. 2011. Two views on multiple mean payoff objectives in Markov Decision Processes. LICS: Logic in Computer Science, 5970225.","ama":"Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. Two views on multiple mean payoff objectives in Markov Decision Processes. In: IEEE; 2011. doi:10.1109/LICS.2011.10","chicago":"Brázdil, Tomáš, Václav Brožek, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Two Views on Multiple Mean Payoff Objectives in Markov Decision Processes.” IEEE, 2011. https://doi.org/10.1109/LICS.2011.10.","short":"T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, A. Kučera, in:, IEEE, 2011.","mla":"Brázdil, Tomáš, et al. Two Views on Multiple Mean Payoff Objectives in Markov Decision Processes. 5970225, IEEE, 2011, doi:10.1109/LICS.2011.10."},"main_file_link":[{"url":"http://arxiv.org/abs/1104.3489","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1109/LICS.2011.10","date_published":"2011-06-21T00:00:00Z","conference":{"name":"LICS: Logic in Computer Science","start_date":"2011-06-21","location":"Toronto, Canada","end_date":"2011-06-24"}},{"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"page":"221 - 230","quality_controlled":"1","citation":{"ama":"Chatterjee K, Prabhu V. Synthesis of memory efficient real time controllers for safety objectives. In: Springer; 2011:221-230. doi:10.1145/1967701.1967734","ista":"Chatterjee K, Prabhu V. 2011. Synthesis of memory efficient real time controllers for safety objectives. HSCC: Hybrid Systems - Computation and Control, 221–230.","apa":"Chatterjee, K., & Prabhu, V. (2011). Synthesis of memory efficient real time controllers for safety objectives (pp. 221–230). Presented at the HSCC: Hybrid Systems - Computation and Control, Chicago, USA: Springer. https://doi.org/10.1145/1967701.1967734","ieee":"K. Chatterjee and V. Prabhu, “Synthesis of memory efficient real time controllers for safety objectives,” presented at the HSCC: Hybrid Systems - Computation and Control, Chicago, USA, 2011, pp. 221–230.","mla":"Chatterjee, Krishnendu, and Vinayak Prabhu. Synthesis of Memory Efficient Real Time Controllers for Safety Objectives. Springer, 2011, pp. 221–30, doi:10.1145/1967701.1967734.","short":"K. Chatterjee, V. Prabhu, in:, Springer, 2011, pp. 221–230.","chicago":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory Efficient Real Time Controllers for Safety Objectives,” 221–30. Springer, 2011. https://doi.org/10.1145/1967701.1967734."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1101.5842"}],"oa":1,"language":[{"iso":"eng"}],"date_published":"2011-01-31T00:00:00Z","doi":"10.1145/1967701.1967734","conference":{"end_date":"2011-04-14","location":"Chicago, USA","start_date":"2011-04-12","name":"HSCC: Hybrid Systems - Computation and Control"},"scopus_import":1,"day":"31","month":"01","publisher":"Springer","department":[{"_id":"KrCh"}],"status":"public","title":"Synthesis of memory efficient real time controllers for safety objectives","publication_status":"published","_id":"3348","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2011","oa_version":"Submitted Version","date_updated":"2021-01-12T07:42:50Z","date_created":"2018-12-11T12:02:49Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Prabhu, Vinayak","first_name":"Vinayak","last_name":"Prabhu"}],"type":"conference","publist_id":"3273","abstract":[{"lang":"eng","text":"We study synthesis of controllers for real-time systems, where the objective is to stay in a given safe set. The problem is solved by obtaining winning strategies in the setting of concurrent two-player timed automaton games with safety objectives. To prevent a player from winning by blocking time, we restrict each player to strategies that ensure that the player cannot be responsible for causing a zeno run. We construct winning strategies for the controller which require access only to (1) the system clocks (thus, controllers which require their own internal infinitely precise clocks are not necessary), and (2) a linear (in the number of clocks) number of memory bits. Precisely, we show that for safety objectives, a memory of size (3 · |C|+lg(|C|+1)) bits suffices for winning controller strategies, where C is the set of clocks of the timed automaton game, significantly improving the previous known exponential bound. We also settle the open question of whether winning region controller strategies require memory for safety objectives by showing with an example the necessity of memory for region strategies to win for safety objectives."}]},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3344","year":"2011","title":"Graph games with reachability objectives","status":"public","publication_status":"published","editor":[{"last_name":"Delzanno","first_name":"Giorgo","full_name":"Delzanno, Giorgo"},{"last_name":"Potapov","first_name":"Igor","full_name":"Potapov, Igor"}],"department":[{"_id":"KrCh"}],"publisher":"Springer","intvolume":" 6945","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"date_updated":"2021-01-12T07:42:48Z","date_created":"2018-12-11T12:02:47Z","oa_version":"None","volume":6945,"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Games played on graphs provide the mathematical framework to analyze several important problems in computer science as well as mathematics, such as the synthesis problem of Church, model checking of open reactive systems and many others. On the basis of mode of interaction of the players these games can be classified as follows: (a) turn-based (players make moves in turns); and (b) concurrent (players make moves simultaneously). On the basis of the information available to the players these games can be classified as follows: (a) perfect-information (players have perfect view of the game); and (b) partial-information (players have partial view of the game). In this talk we will consider all these classes of games with reachability objectives, where the goal of one player is to reach a set of target vertices of the graph, and the goal of the opponent player is to prevent the player from reaching the target. We will survey the results for various classes of games, and the results range from linear time decision algorithms to EXPTIME-complete problems to undecidable problems."}],"publist_id":"3277","citation":{"ieee":"K. Chatterjee, “Graph games with reachability objectives,” presented at the RP: Reachability Problems, Genoa, Italy, 2011, vol. 6945, pp. 1–1.","apa":"Chatterjee, K. (2011). Graph games with reachability objectives. In G. Delzanno & I. Potapov (Eds.) (Vol. 6945, pp. 1–1). Presented at the RP: Reachability Problems, Genoa, Italy: Springer. https://doi.org/10.1007/978-3-642-24288-5_1","ista":"Chatterjee K. 2011. Graph games with reachability objectives. RP: Reachability Problems, LNCS, vol. 6945, 1–1.","ama":"Chatterjee K. Graph games with reachability objectives. In: Delzanno G, Potapov I, eds. Vol 6945. Springer; 2011:1-1. doi:10.1007/978-3-642-24288-5_1","chicago":"Chatterjee, Krishnendu. “Graph Games with Reachability Objectives.” edited by Giorgo Delzanno and Igor Potapov, 6945:1–1. Springer, 2011. https://doi.org/10.1007/978-3-642-24288-5_1.","short":"K. Chatterjee, in:, G. Delzanno, I. Potapov (Eds.), Springer, 2011, pp. 1–1.","mla":"Chatterjee, Krishnendu. Graph Games with Reachability Objectives. Edited by Giorgo Delzanno and Igor Potapov, vol. 6945, Springer, 2011, pp. 1–1, doi:10.1007/978-3-642-24288-5_1."},"quality_controlled":"1","page":"1 - 1","conference":{"name":"RP: Reachability Problems","end_date":"2011-09-30","location":"Genoa, Italy","start_date":"2011-09-28"},"doi":"10.1007/978-3-642-24288-5_1","date_published":"2011-10-15T00:00:00Z","language":[{"iso":"eng"}],"day":"15","month":"10"},{"publist_id":"3278","abstract":[{"lang":"eng","text":"We present faster and dynamic algorithms for the following problems arising in probabilistic verification: Computation of the maximal end-component (mec) decomposition of Markov decision processes (MDPs), and of the almost sure winning set for reachability and parity objectives in MDPs. We achieve the following running time for static algorithms in MDPs with graphs of n vertices and m edges: (1) O(m · min{ √m, n2/3 }) for the mec decomposition, improving the longstanding O(m·n) bound; (2) O(m·n2/3) for reachability objectives, improving the previous O(m · √m) bound for m > n4/3; and (3) O(m · min{ √m, n2/3 } · log(d)) for parity objectives with d priorities, improving the previous O(m · √m · d) bound. We also give incremental and decremental algorithms in linear time for mec decomposition and reachability objectives and O(m · log d) time for parity ob jectives."}],"type":"conference","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"}],"oa_version":"Submitted Version","date_updated":"2023-02-14T10:36:10Z","date_created":"2018-12-11T12:02:47Z","_id":"3343","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","department":[{"_id":"KrCh"}],"publisher":"SIAM","publication_status":"published","status":"public","title":"Faster and dynamic algorithms for maximal end-component decomposition and related graph problems in probabilistic verification","article_processing_charge":"No","day":"01","month":"01","scopus_import":"1","date_published":"2011-01-01T00:00:00Z","doi":"10.1137/1.9781611973082.101","conference":{"name":"SODA: Symposium on Discrete Algorithms","end_date":"2011-01-25","location":"San Francisco, SA, United States","start_date":"2011-01-23"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://eprints.cs.univie.ac.at/21/","open_access":"1"}],"citation":{"short":"K. Chatterjee, M.H. Henzinger, in:, SIAM, 2011, pp. 1318–1336.","mla":"Chatterjee, Krishnendu, and Monika H. Henzinger. Faster and Dynamic Algorithms for Maximal End-Component Decomposition and Related Graph Problems in Probabilistic Verification. SIAM, 2011, pp. 1318–36, doi:10.1137/1.9781611973082.101.","chicago":"Chatterjee, Krishnendu, and Monika H Henzinger. “Faster and Dynamic Algorithms for Maximal End-Component Decomposition and Related Graph Problems in Probabilistic Verification,” 1318–36. SIAM, 2011. https://doi.org/10.1137/1.9781611973082.101.","ama":"Chatterjee K, Henzinger MH. Faster and dynamic algorithms for maximal end-component decomposition and related graph problems in probabilistic verification. In: SIAM; 2011:1318-1336. doi:10.1137/1.9781611973082.101","apa":"Chatterjee, K., & Henzinger, M. H. (2011). Faster and dynamic algorithms for maximal end-component decomposition and related graph problems in probabilistic verification (pp. 1318–1336). Presented at the SODA: Symposium on Discrete Algorithms, San Francisco, SA, United States: SIAM. https://doi.org/10.1137/1.9781611973082.101","ieee":"K. Chatterjee and M. H. Henzinger, “Faster and dynamic algorithms for maximal end-component decomposition and related graph problems in probabilistic verification,” presented at the SODA: Symposium on Discrete Algorithms, San Francisco, SA, United States, 2011, pp. 1318–1336.","ista":"Chatterjee K, Henzinger MH. 2011. Faster and dynamic algorithms for maximal end-component decomposition and related graph problems in probabilistic verification. SODA: Symposium on Discrete Algorithms, 1318–1336."},"oa":1,"page":"1318 - 1336","quality_controlled":"1"},{"publist_id":"3255","ec_funded":1,"file_date_updated":"2020-07-14T12:46:10Z","year":"2011","publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","author":[{"full_name":"Boker, Udi","last_name":"Boker","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"volume":12,"date_created":"2018-12-11T12:02:53Z","date_updated":"2021-01-12T07:42:56Z","month":"08","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"COMponent-Based Embedded Systems design Techniques","grant_number":"215543","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Design for Embedded Systems"}],"quality_controlled":"1","doi":"10.4230/LIPIcs.CSL.2011.82","conference":{"name":"CSL: Computer Science Logic","end_date":"2011-09-15","location":"Bergen, Norway","start_date":"2011-09-12"},"language":[{"iso":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"A discounted-sum automaton (NDA) is a nondeterministic finite automaton with edge weights, which values a run by the discounted sum of visited edge weights. More precisely, the weight in the i-th position of the run is divided by lambda^i, where the discount factor lambda is a fixed rational number greater than 1. Discounted summation is a common and useful measuring scheme, especially for infinite sequences, which reflects the assumption that earlier weights are more important than later weights. Determinizing automata is often essential, for example, in formal verification, where there are polynomial algorithms for comparing two deterministic NDAs, while the equivalence problem for NDAs is not known to be decidable. Unfortunately, however, discounted-sum automata are, in general, not determinizable: it is currently known that for every rational discount factor 1 < lambda < 2, there is an NDA with lambda (denoted lambda-NDA) that cannot be determinized. We provide positive news, showing that every NDA with an integral factor is determinizable. We also complete the picture by proving that the integers characterize exactly the discount factors that guarantee determinizability: we show that for every non-integral rational factor lambda, there is a nondeterminizable lambda-NDA. Finally, we prove that the class of NDAs with integral discount factors enjoys closure under the algebraic operations min, max, addition, and subtraction, which is not the case for general NDAs nor for deterministic NDAs. This shows that for integral discount factors, the class of NDAs forms an attractive specification formalism in quantitative formal verification. All our results hold equally for automata over finite words and for automata over infinite words. ","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3360","intvolume":" 12","title":"Determinizing discounted-sum automata","ddc":["004"],"status":"public","pubrep_id":"82","oa_version":"Published Version","file":[{"creator":"system","file_size":504270,"content_type":"application/pdf","file_name":"IST-2012-82-v1+1_Determinizing_discounted-sum_automata.pdf","access_level":"open_access","date_created":"2018-12-12T10:10:17Z","date_updated":"2020-07-14T12:46:10Z","checksum":"250603c6be8ccad4fbd4d7b24221f0ee","file_id":"4803","relation":"main_file"}],"scopus_import":1,"has_accepted_license":"1","day":"31","citation":{"ama":"Boker U, Henzinger TA. Determinizing discounted-sum automata. In: Vol 12. Springer; 2011:82-96. doi:10.4230/LIPIcs.CSL.2011.82","ista":"Boker U, Henzinger TA. 2011. Determinizing discounted-sum automata. CSL: Computer Science Logic, LIPIcs, vol. 12, 82–96.","apa":"Boker, U., & Henzinger, T. A. (2011). Determinizing discounted-sum automata (Vol. 12, pp. 82–96). Presented at the CSL: Computer Science Logic, Bergen, Norway: Springer. https://doi.org/10.4230/LIPIcs.CSL.2011.82","ieee":"U. Boker and T. A. Henzinger, “Determinizing discounted-sum automata,” presented at the CSL: Computer Science Logic, Bergen, Norway, 2011, vol. 12, pp. 82–96.","mla":"Boker, Udi, and Thomas A. Henzinger. Determinizing Discounted-Sum Automata. Vol. 12, Springer, 2011, pp. 82–96, doi:10.4230/LIPIcs.CSL.2011.82.","short":"U. Boker, T.A. Henzinger, in:, Springer, 2011, pp. 82–96.","chicago":"Boker, Udi, and Thomas A Henzinger. “Determinizing Discounted-Sum Automata,” 12:82–96. Springer, 2011. https://doi.org/10.4230/LIPIcs.CSL.2011.82."},"page":"82 - 96","date_published":"2011-08-31T00:00:00Z"},{"language":[{"iso":"eng"}],"doi":"10.1109/CSF.2011.21","conference":{"name":"CSF: Computer Security Foundations","start_date":"2011-06-27","location":"Cernay-la-Ville, France","end_date":"2011-06-29"},"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","oa":1,"month":"06","date_created":"2018-12-11T12:02:54Z","date_updated":"2021-01-12T07:42:56Z","author":[{"full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","last_name":"Cerny"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"publisher":"IEEE","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_status":"published","year":"2011","ec_funded":1,"publist_id":"3254","file_date_updated":"2020-07-14T12:46:10Z","date_published":"2011-06-27T00:00:00Z","page":"205 - 217","citation":{"short":"P. Cerny, K. Chatterjee, T.A. Henzinger, in:, IEEE, 2011, pp. 205–217.","mla":"Cerny, Pavol, et al. The Complexity of Quantitative Information Flow Problems. IEEE, 2011, pp. 205–17, doi:10.1109/CSF.2011.21.","chicago":"Cerny, Pavol, Krishnendu Chatterjee, and Thomas A Henzinger. “The Complexity of Quantitative Information Flow Problems,” 205–17. IEEE, 2011. https://doi.org/10.1109/CSF.2011.21.","ama":"Cerny P, Chatterjee K, Henzinger TA. The complexity of quantitative information flow problems. In: IEEE; 2011:205-217. doi:10.1109/CSF.2011.21","ieee":"P. Cerny, K. Chatterjee, and T. A. Henzinger, “The complexity of quantitative information flow problems,” presented at the CSF: Computer Security Foundations, Cernay-la-Ville, France, 2011, pp. 205–217.","apa":"Cerny, P., Chatterjee, K., & Henzinger, T. A. (2011). The complexity of quantitative information flow problems (pp. 205–217). Presented at the CSF: Computer Security Foundations, Cernay-la-Ville, France: IEEE. https://doi.org/10.1109/CSF.2011.21","ista":"Cerny P, Chatterjee K, Henzinger TA. 2011. The complexity of quantitative information flow problems. CSF: Computer Security Foundations, 205–217."},"has_accepted_license":"1","day":"27","scopus_import":1,"file":[{"file_name":"IST-2012-81-v1+1_The_complexity_of_quantitative_information_flow_problems.pdf","access_level":"open_access","creator":"system","file_size":299069,"content_type":"application/pdf","file_id":"4792","relation":"main_file","date_created":"2018-12-12T10:10:07Z","date_updated":"2020-07-14T12:46:10Z","checksum":"1a25be0c62459fc7640db88af08ff63a"}],"oa_version":"Submitted Version","pubrep_id":"81","status":"public","ddc":["000","005"],"title":"The complexity of quantitative information flow problems","_id":"3361","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"In this paper, we investigate the computational complexity of quantitative information flow (QIF) problems. Information-theoretic quantitative relaxations of noninterference (based on Shannon entropy)have been introduced to enable more fine-grained reasoning about programs in situations where limited information flow is acceptable. The QIF bounding problem asks whether the information flow in a given program is bounded by a constant $d$. Our first result is that the QIF bounding problem is PSPACE-complete. The QIF memoryless synthesis problem asks whether it is possible to resolve nondeterministic choices in a given partial program in such a way that in the resulting deterministic program, the quantitative information flow is bounded by a given constant $d$. Our second result is that the QIF memoryless synthesis problem is also EXPTIME-complete. The QIF memoryless synthesis problem generalizes to QIF general synthesis problem which does not impose the memoryless requirement (that is, by allowing the synthesized program to have more variables then the original partial program). Our third result is that the QIF general synthesis problem is EXPTIME-hard.","lang":"eng"}],"type":"conference"},{"abstract":[{"lang":"eng","text":"The static scheduling problem often arises as a fundamental problem in real-time systems and grid computing. We consider the problem of statically scheduling a large job expressed as a task graph on a large number of computing nodes, such as a data center. This paper solves the large-scale static scheduling problem using abstraction refinement, a technique commonly used in formal verification to efficiently solve computationally hard problems. A scheduler based on abstraction refinement first attempts to solve the scheduling problem with abstract representations of the job and the computing resources. As abstract representations are generally small, the scheduling can be done reasonably fast. If the obtained schedule does not meet specified quality conditions (like data center utilization or schedule makespan) then the scheduler refines the job and data center abstractions and, again solves the scheduling problem. We develop different schedulers based on abstraction refinement. We implemented these schedulers and used them to schedule task graphs from various computing domains on simulated data centers with realistic topologies. We compared the speed of scheduling and the quality of the produced schedules with our abstraction refinement schedulers against a baseline scheduler that does not use any abstraction. We conclude that abstraction refinement techniques give a significant speed-up compared to traditional static scheduling heuristics, at a reasonable cost in the quality of the produced schedules. We further used our static schedulers in an actual system that we deployed on Amazon EC2 and compared it against the Hadoop dynamic scheduler for large MapReduce jobs. Our experiments indicate that there is great potential for static scheduling techniques."}],"publist_id":"3257","type":"conference","author":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Singh, Vasu","last_name":"Singh","first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","full_name":"Wies, Thomas"},{"orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","last_name":"Zufferey","first_name":"Damien","full_name":"Zufferey, Damien"}],"date_created":"2018-12-11T12:02:53Z","date_updated":"2021-01-12T07:42:55Z","oa_version":"Published Version","_id":"3358","year":"2011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Scheduling large jobs by abstraction refinement","department":[{"_id":"ToHe"}],"publisher":"ACM","day":"10","month":"04","article_processing_charge":"No","scopus_import":1,"conference":{"start_date":"2011-04-10","location":"Salzburg, Austria","end_date":"2011-04-13","name":"EuroSys"},"doi":"10.1145/1966445.1966476","date_published":"2011-04-10T00:00:00Z","language":[{"iso":"eng"}],"citation":{"chicago":"Henzinger, Thomas A, Vasu Singh, Thomas Wies, and Damien Zufferey. “Scheduling Large Jobs by Abstraction Refinement,” 329–42. ACM, 2011. https://doi.org/10.1145/1966445.1966476.","short":"T.A. Henzinger, V. Singh, T. Wies, D. Zufferey, in:, ACM, 2011, pp. 329–342.","mla":"Henzinger, Thomas A., et al. Scheduling Large Jobs by Abstraction Refinement. ACM, 2011, pp. 329–42, doi:10.1145/1966445.1966476.","ieee":"T. A. Henzinger, V. Singh, T. Wies, and D. Zufferey, “Scheduling large jobs by abstraction refinement,” presented at the EuroSys, Salzburg, Austria, 2011, pp. 329–342.","apa":"Henzinger, T. A., Singh, V., Wies, T., & Zufferey, D. (2011). Scheduling large jobs by abstraction refinement (pp. 329–342). Presented at the EuroSys, Salzburg, Austria: ACM. https://doi.org/10.1145/1966445.1966476","ista":"Henzinger TA, Singh V, Wies T, Zufferey D. 2011. Scheduling large jobs by abstraction refinement. EuroSys, 329–342.","ama":"Henzinger TA, Singh V, Wies T, Zufferey D. Scheduling large jobs by abstraction refinement. In: ACM; 2011:329-342. doi:10.1145/1966445.1966476"},"main_file_link":[{"url":"http://cs.nyu.edu/wies/publ/scheduling_large_jobs_by_abstraction_refinement.pdf","open_access":"1"}],"oa":1,"quality_controlled":"1","page":"329 - 342"},{"type":"conference","ec_funded":1,"publist_id":"3256","abstract":[{"text":"Motivated by improvements in constraint-solving technology and by the increase of routinely available computational power, partial-program synthesis is emerging as an effective approach for increasing programmer productivity. The goal of the approach is to allow the programmer to specify a part of her intent imperatively (that is, give a partial program) and a part of her intent declaratively, by specifying which conditions need to be achieved or maintained. The task of the synthesizer is to construct a program that satisfies the specification. As an example, consider a partial program where threads access shared data without using any synchronization mechanism, and a declarative specification that excludes data races and deadlocks. The task of the synthesizer is then to place locks into the program code in order for the program to meet the specification.\r\n\r\nIn this paper, we argue that quantitative objectives are needed in partial-program synthesis in order to produce higher-quality programs, while enabling simpler specifications. Returning to the example, the synthesizer could construct a naive solution that uses one global lock for shared data. This can be prevented either by constraining the solution space further (which is error-prone and partly defeats the point of synthesis), or by optimizing a quantitative objective that models performance. Other quantitative notions useful in synthesis include fault tolerance, robustness, resource (memory, power) consumption, and information flow.","lang":"eng"}],"_id":"3359","year":"2011","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was partially supported by the ERC Advanced Grant QUAREM, the FWF NFN Grant S11402-N23 (RiSE), and the EU NOE Grant ArtistDesign.","publisher":"ACM","department":[{"_id":"ToHe"}],"title":"From boolean to quantitative synthesis","status":"public","publication_status":"published","author":[{"last_name":"Cerny","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"oa_version":"None","date_updated":"2021-01-12T07:42:55Z","date_created":"2018-12-11T12:02:53Z","month":"10","day":"09","citation":{"short":"P. Cerny, T.A. Henzinger, in:, ACM, 2011, pp. 149–154.","mla":"Cerny, Pavol, and Thomas A. Henzinger. From Boolean to Quantitative Synthesis. ACM, 2011, pp. 149–54, doi:10.1145/2038642.2038666.","chicago":"Cerny, Pavol, and Thomas A Henzinger. “From Boolean to Quantitative Synthesis,” 149–54. ACM, 2011. https://doi.org/10.1145/2038642.2038666.","ama":"Cerny P, Henzinger TA. From boolean to quantitative synthesis. In: ACM; 2011:149-154. doi:10.1145/2038642.2038666","ieee":"P. Cerny and T. A. Henzinger, “From boolean to quantitative synthesis,” presented at the EMSOFT: Embedded Software , Taipei; Taiwan, 2011, pp. 149–154.","apa":"Cerny, P., & Henzinger, T. A. (2011). From boolean to quantitative synthesis (pp. 149–154). Presented at the EMSOFT: Embedded Software , Taipei; Taiwan: ACM. https://doi.org/10.1145/2038642.2038666","ista":"Cerny P, Henzinger TA. 2011. From boolean to quantitative synthesis. EMSOFT: Embedded Software , 149–154."},"page":"149 - 154","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","grant_number":"214373","call_identifier":"FP7","name":"Design for Embedded Systems"}],"quality_controlled":"1","date_published":"2011-10-09T00:00:00Z","doi":"10.1145/2038642.2038666","conference":{"name":"EMSOFT: Embedded Software ","start_date":"2011-10-09","location":"Taipei; Taiwan","end_date":"2011-10-14"},"language":[{"iso":"eng"}]},{"page":"227 - 237","quality_controlled":"1","citation":{"ama":"Chatterjee K, Henzinger TA, Horn F. The complexity of request-response games. In: Dediu A-H, Inenaga S, Martín-Vide C, eds. Vol 6638. Springer; 2011:227-237. doi:10.1007/978-3-642-21254-3_17","ista":"Chatterjee K, Henzinger TA, Horn F. 2011. The complexity of request-response games. LATA: Language and Automata Theory and Applications, LNCS, vol. 6638, 227–237.","apa":"Chatterjee, K., Henzinger, T. A., & Horn, F. (2011). The complexity of request-response games. In A.-H. Dediu, S. Inenaga, & C. Martín-Vide (Eds.) (Vol. 6638, pp. 227–237). Presented at the LATA: Language and Automata Theory and Applications, Tarragona, Spain: Springer. https://doi.org/10.1007/978-3-642-21254-3_17","ieee":"K. Chatterjee, T. A. Henzinger, and F. Horn, “The complexity of request-response games,” presented at the LATA: Language and Automata Theory and Applications, Tarragona, Spain, 2011, vol. 6638, pp. 227–237.","mla":"Chatterjee, Krishnendu, et al. The Complexity of Request-Response Games. Edited by Adrian-Horia Dediu et al., vol. 6638, Springer, 2011, pp. 227–37, doi:10.1007/978-3-642-21254-3_17.","short":"K. Chatterjee, T.A. Henzinger, F. Horn, in:, A.-H. Dediu, S. Inenaga, C. Martín-Vide (Eds.), Springer, 2011, pp. 227–237.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “The Complexity of Request-Response Games.” edited by Adrian-Horia Dediu, Shunsuke Inenaga, and Carlos Martín-Vide, 6638:227–37. Springer, 2011. https://doi.org/10.1007/978-3-642-21254-3_17."},"language":[{"iso":"eng"}],"date_published":"2011-01-01T00:00:00Z","doi":"10.1007/978-3-642-21254-3_17","conference":{"name":"LATA: Language and Automata Theory and Applications","location":"Tarragona, Spain","start_date":"2011-05-26","end_date":"2011-05-31"},"scopus_import":1,"month":"01","day":"01","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"editor":[{"full_name":"Dediu, Adrian-Horia","first_name":"Adrian-Horia","last_name":"Dediu"},{"full_name":"Inenaga, Shunsuke","first_name":"Shunsuke","last_name":"Inenaga"},{"first_name":"Carlos","last_name":"Martín-Vide","full_name":"Martín-Vide, Carlos"}],"publisher":"Springer","intvolume":" 6638","publication_status":"published","title":"The complexity of request-response games","status":"public","year":"2011","_id":"3357","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","volume":6638,"oa_version":"None","date_created":"2018-12-11T12:02:52Z","date_updated":"2021-01-12T07:42:54Z","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"37327ACE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Horn","full_name":"Horn, Florian"}],"alternative_title":["LNCS"],"type":"conference","publist_id":"3258","abstract":[{"lang":"eng","text":"We consider two-player graph games whose objectives are request-response condition, i.e conjunctions of conditions of the form \"if a state with property Rq is visited, then later a state with property Rp is visited\". The winner of such games can be decided in EXPTIME and the problem is known to be NP-hard. In this paper, we close this gap by showing that this problem is, in fact, EXPTIME-complete. We show that the problem becomes PSPACE-complete if we only consider games played on DAGs, and NP-complete or PTIME-complete if there is only one player (depending on whether he wants to enforce or spoil the request-response condition). We also present near-optimal bounds on the memory needed to design winning strategies for each player, in each case."}]},{"language":[{"iso":"eng"}],"doi":"10.1021/jp2002904","date_published":"2011-04-28T00:00:00Z","quality_controlled":"1","article_type":"original","page":"7947 - 7955","publication":"Journal of Physical Chemistry C","citation":{"ama":"Ibáñez M, Guardia P, Shavel A, et al. Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods. Journal of Physical Chemistry C. 2011;115(16):7947-7955. doi:10.1021/jp2002904","apa":"Ibáñez, M., Guardia, P., Shavel, A., Cadavid, D., Arbiol, J., Morante, J., & Cabot, A. (2011). Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods. Journal of Physical Chemistry C. American Chemical Society. https://doi.org/10.1021/jp2002904","ieee":"M. Ibáñez et al., “Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods,” Journal of Physical Chemistry C, vol. 115, no. 16. American Chemical Society, pp. 7947–7955, 2011.","ista":"Ibáñez M, Guardia P, Shavel A, Cadavid D, Arbiol J, Morante J, Cabot A. 2011. Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods. Journal of Physical Chemistry C. 115(16), 7947–7955.","short":"M. Ibáñez, P. Guardia, A. Shavel, D. Cadavid, J. Arbiol, J. Morante, A. Cabot, Journal of Physical Chemistry C 115 (2011) 7947–7955.","mla":"Ibáñez, Maria, et al. “Growth Kinetics of Asymmetric Bi2S3 Nanocrystals: Size Distribution Focusing in Nanorods.” Journal of Physical Chemistry C, vol. 115, no. 16, American Chemical Society, 2011, pp. 7947–55, doi:10.1021/jp2002904.","chicago":"Ibáñez, Maria, Pablo Guardia, Alexey Shavel, Doris Cadavid, Jordi Arbiol, Joan Morante, and Andreu Cabot. “Growth Kinetics of Asymmetric Bi2S3 Nanocrystals: Size Distribution Focusing in Nanorods.” Journal of Physical Chemistry C. American Chemical Society, 2011. https://doi.org/10.1021/jp2002904."},"day":"28","month":"04","article_processing_charge":"No","date_created":"2018-12-11T11:45:53Z","date_updated":"2021-01-12T07:42:56Z","volume":115,"oa_version":"None","author":[{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"full_name":"Guardia, Pablo","first_name":"Pablo","last_name":"Guardia"},{"first_name":"Alexey","last_name":"Shavel","full_name":"Shavel, Alexey"},{"full_name":"Cadavid, Doris","first_name":"Doris","last_name":"Cadavid"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"last_name":"Morante","first_name":"Joan","full_name":"Morante, Joan"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"status":"public","title":"Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods","publication_status":"published","intvolume":" 115","publisher":"American Chemical Society","_id":"336","year":"2011","acknowledgement":"This work was supported by the Spanish MICINN Projects MAT2008-05779, MAT2008-03400-E/MAT, and ENE2008-03277-E/CON. Maria Ibáñez thanks the Ph.D. grant from the Spanish MICINN.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","abstract":[{"lang":"eng","text":"The growth kinetics of colloidal Bi2S3 nanorods was investigated. After nucleation, the length distribution of the growing Bi 2S3 nanorods narrows with the reaction time until a bimodal length distribution appears. From this critical reaction time on, the smallest nanorods of the ensemble dissolve, feeding with monomer the growth of the largest ones. A comprehensive characterization of the size-distribution evolution of Bi2S3 nanorods is used here to illustrate the dependences of the anisotropic growth rates of cylindrical nanoparticles on the nanoparticle dimensions and the monomer concentration in solution. With this goal in mind, a diffusion-reaction model is presented to explain the origin of the experimentally obtained length distribution focusing mechanism. The model is able to reproduce the decrease of the growth rate in the nanorod axial direction with both its thickness and length. On the other hand, low lateral reaction rates prevent the nanorod thickness distribution to be focused. In both crystallographic growth directions, a concentration-dependent critical thickness exists, which discriminates between nanorods with positive growth rates and those dissolving in the reaction solution. "}],"publist_id":"7493","issue":"16","type":"journal_article"},{"day":"01","scopus_import":1,"date_published":"2011-06-01T00:00:00Z","article_type":"original","page":"102 - 110","publication":"Developmental Biology","citation":{"short":"R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P.J. Heisenberg, D. Kimelman, Developmental Biology 354 (2011) 102–110.","mla":"Row, Richard, et al. “Completion of the Epithelial to Mesenchymal Transition in Zebrafish Mesoderm Requires Spadetail.” Developmental Biology, vol. 354, no. 1, Elsevier, 2011, pp. 102–10, doi:10.1016/j.ydbio.2011.03.025.","chicago":"Row, Richard, Jean-Léon Maître, Benjamin Martin, Petra Stockinger, Carl-Philipp J Heisenberg, and David Kimelman. “Completion of the Epithelial to Mesenchymal Transition in Zebrafish Mesoderm Requires Spadetail.” Developmental Biology. Elsevier, 2011. https://doi.org/10.1016/j.ydbio.2011.03.025.","ama":"Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. Developmental Biology. 2011;354(1):102-110. doi:10.1016/j.ydbio.2011.03.025","ieee":"R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P. J. Heisenberg, and D. Kimelman, “Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail,” Developmental Biology, vol. 354, no. 1. Elsevier, pp. 102–110, 2011.","apa":"Row, R., Maître, J.-L., Martin, B., Stockinger, P., Heisenberg, C.-P. J., & Kimelman, D. (2011). Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. Developmental Biology. Elsevier. https://doi.org/10.1016/j.ydbio.2011.03.025","ista":"Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. 2011. Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. Developmental Biology. 354(1), 102–110."},"abstract":[{"text":"The process of gastrulation is highly conserved across vertebrates on both the genetic and morphological levels, despite great variety in embryonic shape and speed of development. This mechanism spatially separates the germ layers and establishes the organizational foundation for future development. Mesodermal identity is specified in a superficial layer of cells, the epiblast, where cells maintain an epithelioid morphology. These cells involute to join the deeper hypoblast layer where they adopt a migratory, mesenchymal morphology. Expression of a cascade of related transcription factors orchestrates the parallel genetic transition from primitive to mature mesoderm. Although the early and late stages of this process are increasingly well understood, the transition between them has remained largely mysterious. We present here the first high resolution in vivo observations of the blebby transitional morphology of involuting mesodermal cells in a vertebrate embryo. We further demonstrate that the zebrafish spadetail mutation creates a reversible block in the maturation program, stalling cells in the transition state. This mutation creates an ideal system for dissecting the specific properties of cells undergoing the morphological transition of maturing mesoderm, as we demonstrate with a direct measurement of cell–cell adhesion.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Submitted Version","status":"public","title":"Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail","intvolume":" 354","_id":"3379","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","language":[{"iso":"eng"}],"doi":"10.1016/j.ydbio.2011.03.025","quality_controlled":"1","oa":1,"external_id":{"pmid":["1463614"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090540/","open_access":"1"}],"publist_id":"3228","date_created":"2018-12-11T12:03:00Z","date_updated":"2021-01-12T07:43:04Z","volume":354,"author":[{"full_name":"Row, Richard","first_name":"Richard","last_name":"Row"},{"id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3688-1474","first_name":"Jean-Léon","last_name":"Maître","full_name":"Maître, Jean-Léon"},{"full_name":"Martin, Benjamin","first_name":"Benjamin","last_name":"Martin"},{"full_name":"Stockinger, Petra","last_name":"Stockinger","first_name":"Petra","id":"261CB030-E90D-11E9-B182-F697D44B663C"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Kimelman, David","last_name":"Kimelman","first_name":"David"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"CaHe"}],"year":"2011","pmid":1},{"month":"05","language":[{"iso":"eng"}],"doi":"10.1016/j.molcel.2011.04.016","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143497/","open_access":"1"}],"publist_id":"3231","volume":42,"date_created":"2018-12-11T12:02:59Z","date_updated":"2021-01-12T07:43:03Z","author":[{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"}],"publisher":"Cell Press","department":[{"_id":"ToBo"}],"publication_status":"published","year":"2011","acknowledgement":"This work was supported by a Feodor Lynen Fellowship of the Alexander von Humboldt Foundation (to T.B.).","day":"20","scopus_import":1,"date_published":"2011-05-20T00:00:00Z","page":"413 - 425","citation":{"ama":"Bollenbach MT, Kishony R. Resolution of gene regulatory conflicts caused by combinations of antibiotics. Molecular Cell. 2011;42(4):413-425. doi:10.1016/j.molcel.2011.04.016","ista":"Bollenbach MT, Kishony R. 2011. Resolution of gene regulatory conflicts caused by combinations of antibiotics. Molecular Cell. 42(4), 413–425.","ieee":"M. T. Bollenbach and R. Kishony, “Resolution of gene regulatory conflicts caused by combinations of antibiotics,” Molecular Cell, vol. 42, no. 4. Cell Press, pp. 413–425, 2011.","apa":"Bollenbach, M. T., & Kishony, R. (2011). Resolution of gene regulatory conflicts caused by combinations of antibiotics. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2011.04.016","mla":"Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” Molecular Cell, vol. 42, no. 4, Cell Press, 2011, pp. 413–25, doi:10.1016/j.molcel.2011.04.016.","short":"M.T. Bollenbach, R. Kishony, Molecular Cell 42 (2011) 413–425.","chicago":"Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” Molecular Cell. Cell Press, 2011. https://doi.org/10.1016/j.molcel.2011.04.016."},"publication":"Molecular Cell","issue":"4","abstract":[{"text":"Regulatory conflicts occur when two signals that individually trigger opposite cellular responses are present simultaneously. Here, we investigate regulatory conflicts in the bacterial response to antibiotic combinations. We use an Escherichia coli promoter-GFP library to study the transcriptional response of many promoters to either additive or antagonistic drug pairs at fine two-dimensional (2D) resolution of drug concentration. Surprisingly, we find that this data set can be characterized as a linear sum of only two principal components. Component one, accounting for over 70% of the response, represents the response to growth inhibition by the drugs. Component two describes how regulatory conflicts are resolved. For the additive drug pair, conflicts are resolved by linearly interpolating the single drug responses, while for the antagonistic drug pair, the growth-limiting drug dominates the response. Importantly, for a given drug pair, the same conflict resolution strategy applies to almost all genes. These results provide a recipe for predicting gene expression responses to antibiotic combinations.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 42","status":"public","title":"Resolution of gene regulatory conflicts caused by combinations of antibiotics","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3376"},{"language":[{"iso":"eng"}],"doi":"10.1017/S0016672311000115","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.pure.ed.ac.uk/ws/files/8144621/GR_2011_Barton.pdf"}],"oa":1,"month":"05","volume":93,"date_created":"2018-12-11T12:03:00Z","date_updated":"2021-01-12T07:43:05Z","author":[{"first_name":"Sayanthan","last_name":"Logeswaran","full_name":"Logeswaran, Sayanthan"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"publisher":"Cambridge University Press","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2011","publist_id":"3227","date_published":"2011-05-18T00:00:00Z","page":"221 - 232","article_type":"original","citation":{"short":"S. Logeswaran, N.H. Barton, Genetical Research 93 (2011) 221–232.","mla":"Logeswaran, Sayanthan, and Nicholas H. Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research, vol. 93, no. 3, Cambridge University Press, 2011, pp. 221–32, doi:10.1017/S0016672311000115.","chicago":"Logeswaran, Sayanthan, and Nicholas H Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research. Cambridge University Press, 2011. https://doi.org/10.1017/S0016672311000115.","ama":"Logeswaran S, Barton NH. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 2011;93(3):221-232. doi:10.1017/S0016672311000115","ieee":"S. Logeswaran and N. H. Barton, “Mapping Mendelian traits in asexual progeny using changes in marker allele frequency,” Genetical Research, vol. 93, no. 3. Cambridge University Press, pp. 221–232, 2011.","apa":"Logeswaran, S., & Barton, N. H. (2011). Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. Cambridge University Press. https://doi.org/10.1017/S0016672311000115","ista":"Logeswaran S, Barton NH. 2011. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 93(3), 221–232."},"publication":"Genetical Research","article_processing_charge":"No","day":"18","scopus_import":1,"oa_version":"Published Version","intvolume":" 93","status":"public","title":"Mapping Mendelian traits in asexual progeny using changes in marker allele frequency","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3380","issue":"3","abstract":[{"lang":"eng","text":"Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual, the extreme progeny may be selected by multiple generations of asexual reproduction and selection. We analyse this method of measuring phenotype in asexual progeny and examine the changes in marker allele frequency due to selection over many generations. Stochasticity in marker frequency in the selected population arises due to the finite initial population size. We derive the distribution of marker frequency as a result of selection at a single major locus, and show that in order to avoid spurious changes in marker allele frequency in the selected population, the initial population size should be in the low to mid hundreds."}],"type":"journal_article"},{"citation":{"apa":"Edelsbrunner, H., Morozov, D., & Patel, A. (2011). Quantifying transversality by measuring the robustness of intersections. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-011-9090-8","ieee":"H. Edelsbrunner, D. Morozov, and A. Patel, “Quantifying transversality by measuring the robustness of intersections,” Foundations of Computational Mathematics, vol. 11, no. 3. Springer, pp. 345–361, 2011.","ista":"Edelsbrunner H, Morozov D, Patel A. 2011. Quantifying transversality by measuring the robustness of intersections. Foundations of Computational Mathematics. 11(3), 345–361.","ama":"Edelsbrunner H, Morozov D, Patel A. Quantifying transversality by measuring the robustness of intersections. Foundations of Computational Mathematics. 2011;11(3):345-361. doi:10.1007/s10208-011-9090-8","chicago":"Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “Quantifying Transversality by Measuring the Robustness of Intersections.” Foundations of Computational Mathematics. Springer, 2011. https://doi.org/10.1007/s10208-011-9090-8.","short":"H. Edelsbrunner, D. Morozov, A. Patel, Foundations of Computational Mathematics 11 (2011) 345–361.","mla":"Edelsbrunner, Herbert, et al. “Quantifying Transversality by Measuring the Robustness of Intersections.” Foundations of Computational Mathematics, vol. 11, no. 3, Springer, 2011, pp. 345–61, doi:10.1007/s10208-011-9090-8."},"publication":"Foundations of Computational Mathematics","page":"345 - 361","date_published":"2011-06-01T00:00:00Z","scopus_import":1,"day":"01","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3377","intvolume":" 11","status":"public","title":"Quantifying transversality by measuring the robustness of intersections","oa_version":"Submitted Version","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"By definition, transverse intersections are stable under in- finitesimal perturbations. Using persistent homology, we ex- tend this notion to sizeable perturbations. Specifically, we assign to each homology class of the intersection its robust- ness, the magnitude of a perturbation necessary to kill it, and prove that robustness is stable. Among the applications of this result is a stable notion of robustness for fixed points of continuous mappings and a statement of stability for con- tours of smooth mappings."}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0911.2142"}],"quality_controlled":"1","doi":"10.1007/s10208-011-9090-8","language":[{"iso":"eng"}],"month":"06","acknowledgement":"This research is partially supported by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.","year":"2011","department":[{"_id":"HeEd"}],"publisher":"Springer","publication_status":"published","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"full_name":"Morozov, Dmitriy","last_name":"Morozov","first_name":"Dmitriy"},{"full_name":"Patel, Amit","id":"34A254A0-F248-11E8-B48F-1D18A9856A87","first_name":"Amit","last_name":"Patel"}],"volume":11,"date_created":"2018-12-11T12:02:59Z","date_updated":"2021-01-12T07:43:04Z","publist_id":"3230"},{"type":"journal_article","abstract":[{"text":"The theory of intersection homology was developed to study the singularities of a topologically stratified space. This paper in- corporates this theory into the already developed framework of persistent homology. We demonstrate that persistent intersec- tion homology gives useful information about the relationship between an embedded stratified space and its singularities. We give, and prove the correctness of, an algorithm for the computa- tion of the persistent intersection homology groups of a filtered simplicial complex equipped with a stratification by subcom- plexes. We also derive, from Poincare ́ Duality, some structural results about persistent intersection homology.","lang":"eng"}],"issue":"3","publist_id":"3229","status":"public","title":"Persistent intersection homology","publication_status":"published","intvolume":" 11","department":[{"_id":"HeEd"}],"publisher":"Springer","year":"2011","_id":"3378","acknowledgement":"This research was partially supported by the Defense Advanced Research Projects Agency (DARPA) under grant HR0011-05-1-0007.","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:02:59Z","date_updated":"2021-01-12T07:43:04Z","oa_version":"None","volume":11,"author":[{"full_name":"Bendich, Paul","id":"43F6EC54-F248-11E8-B48F-1D18A9856A87","last_name":"Bendich","first_name":"Paul"},{"last_name":"Harer","first_name":"John","full_name":"Harer, John"}],"scopus_import":1,"month":"06","day":"01","quality_controlled":"1","page":"305 - 336","publication":"Foundations of Computational Mathematics","citation":{"ieee":"P. Bendich and J. Harer, “Persistent intersection homology,” Foundations of Computational Mathematics, vol. 11, no. 3. Springer, pp. 305–336, 2011.","apa":"Bendich, P., & Harer, J. (2011). Persistent intersection homology. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-010-9081-1","ista":"Bendich P, Harer J. 2011. Persistent intersection homology. Foundations of Computational Mathematics. 11(3), 305–336.","ama":"Bendich P, Harer J. Persistent intersection homology. Foundations of Computational Mathematics. 2011;11(3):305-336. doi:10.1007/s10208-010-9081-1","chicago":"Bendich, Paul, and John Harer. “Persistent Intersection Homology.” Foundations of Computational Mathematics. Springer, 2011. https://doi.org/10.1007/s10208-010-9081-1.","short":"P. Bendich, J. Harer, Foundations of Computational Mathematics 11 (2011) 305–336.","mla":"Bendich, Paul, and John Harer. “Persistent Intersection Homology.” Foundations of Computational Mathematics, vol. 11, no. 3, Springer, 2011, pp. 305–36, doi:10.1007/s10208-010-9081-1."},"language":[{"iso":"eng"}],"date_published":"2011-06-01T00:00:00Z","doi":"10.1007/s10208-010-9081-1"},{"doi":"10.1186/1471-2148-11-201","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"07","author":[{"orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","first_name":"Line V","full_name":"Ugelvig, Line V"},{"first_name":"Per","last_name":"Nielsen","full_name":"Nielsen, Per"},{"full_name":"Boomsma, Jacobus","last_name":"Boomsma","first_name":"Jacobus"},{"full_name":"Nash, David","last_name":"Nash","first_name":"David"}],"volume":11,"date_updated":"2021-01-12T07:43:08Z","date_created":"2018-12-11T12:03:03Z","year":"2011","publisher":"BioMed Central","department":[{"_id":"SyCr"}],"publication_status":"published","publist_id":"3220","file_date_updated":"2020-07-14T12:46:11Z","article_number":"201","date_published":"2011-07-11T00:00:00Z","citation":{"ista":"Ugelvig LV, Nielsen P, Boomsma J, Nash D. 2011. Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion. BMC Evolutionary Biology. 11(201), 201.","ieee":"L. V. Ugelvig, P. Nielsen, J. Boomsma, and D. Nash, “Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion,” BMC Evolutionary Biology, vol. 11, no. 201. BioMed Central, 2011.","apa":"Ugelvig, L. V., Nielsen, P., Boomsma, J., & Nash, D. (2011). Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-11-201","ama":"Ugelvig LV, Nielsen P, Boomsma J, Nash D. Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion. BMC Evolutionary Biology. 2011;11(201). doi:10.1186/1471-2148-11-201","chicago":"Ugelvig, Line V, Per Nielsen, Jacobus Boomsma, and David Nash. “Reconstructing Eight Decades of Genetic Variation in an Isolated Danish Population of the Large Blue Butterfly Maculinea Arion.” BMC Evolutionary Biology. BioMed Central, 2011. https://doi.org/10.1186/1471-2148-11-201.","mla":"Ugelvig, Line V., et al. “Reconstructing Eight Decades of Genetic Variation in an Isolated Danish Population of the Large Blue Butterfly Maculinea Arion.” BMC Evolutionary Biology, vol. 11, no. 201, 201, BioMed Central, 2011, doi:10.1186/1471-2148-11-201.","short":"L.V. Ugelvig, P. Nielsen, J. Boomsma, D. Nash, BMC Evolutionary Biology 11 (2011)."},"publication":"BMC Evolutionary Biology","has_accepted_license":"1","day":"11","scopus_import":1,"pubrep_id":"371","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":2166556,"access_level":"open_access","file_name":"IST-2015-371-v1+1_1471-2148-11-201.pdf","checksum":"9ebfed0740f1fa071d02ec32c2b8c17f","date_updated":"2020-07-14T12:46:11Z","date_created":"2018-12-12T10:14:18Z","file_id":"5069","relation":"main_file"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3388","intvolume":" 11","title":"Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion","status":"public","ddc":["576"],"issue":"201","abstract":[{"text":"Background: Fragmentation of terrestrial ecosystems has had detrimental effects on metapopulations of habitat specialists. Maculinea butterflies have been particularly affected because of their specialized lifecycles, requiring both specific food-plants and host-ants. However, the interaction between dispersal, effective population size, and long-term genetic erosion of these endangered butterflies remains unknown. Using non-destructive sampling, we investigated the genetic diversity of the last extant population of M. arion in Denmark, which experienced critically low numbers in the 1980s. Results: Using nine microsatellite markers, we show that the population is genetically impoverished compared to nearby populations in Sweden, but less so than monitoring programs suggested. Ten additional short repeat microsatellites were used to reconstruct changes in genetic diversity and population structure over the last 77 years from museum specimens. We also tested amplification efficiency in such historical samples as a function of repeat length and sample age. Low population numbers in the 1980s did not affect genetic diversity, but considerable turnover of alleles has characterized this population throughout the time-span of our analysis. Conclusions: Our results suggest that M. arion is less sensitive to genetic erosion via population bottlenecks than previously thought, and that managing clusters of high quality habitat may be key for long-term conservation.","lang":"eng"}],"type":"journal_article"},{"_id":"3384","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Natural images from the birthplace of the human eye","status":"public","intvolume":" 6","pubrep_id":"379","oa_version":"Published Version","file":[{"creator":"system","file_size":1424768,"content_type":"application/pdf","file_name":"IST-2015-379-v1+1_journal.pone.0020409.pdf","access_level":"open_access","date_created":"2018-12-12T10:09:25Z","date_updated":"2020-07-14T12:46:11Z","checksum":"307d4356916471306e3705ac65b82fa1","file_id":"4749","relation":"main_file"}],"type":"journal_article","abstract":[{"text":"Here we introduce a database of calibrated natural images publicly available through an easy-to-use web interface. Using a Nikon D70 digital SLR camera, we acquired about six-megapixel images of Okavango Delta of Botswana, a tropical savanna habitat similar to where the human eye is thought to have evolved. Some sequences of images were captured unsystematically while following a baboon troop, while others were designed to vary a single parameter such as aperture, object distance, time of day or position on the horizon. Images are available in the raw RGB format and in grayscale. Images are also available in units relevant to the physiology of human cone photoreceptors, where pixel values represent the expected number of photoisomerizations per second for cones sensitive to long (L), medium (M) and short (S) wavelengths. This database is distributed under a Creative Commons Attribution-Noncommercial Unported license to facilitate research in computer vision, psychophysics of perception, and visual neuroscience.","lang":"eng"}],"issue":"6","publication":"PLoS One","citation":{"ista":"Tkačik G, Garrigan P, Ratliff C, Milcinski G, Klein J, Seyfarth L, Sterling P, Brainard D, Balasubramanian V. 2011. Natural images from the birthplace of the human eye. PLoS One. 6(6), e20409.","apa":"Tkačik, G., Garrigan, P., Ratliff, C., Milcinski, G., Klein, J., Seyfarth, L., … Balasubramanian, V. (2011). Natural images from the birthplace of the human eye. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0020409","ieee":"G. Tkačik et al., “Natural images from the birthplace of the human eye,” PLoS One, vol. 6, no. 6. Public Library of Science, 2011.","ama":"Tkačik G, Garrigan P, Ratliff C, et al. Natural images from the birthplace of the human eye. PLoS One. 2011;6(6). doi:10.1371/journal.pone.0020409","chicago":"Tkačik, Gašper, Patrick Garrigan, Charles Ratliff, Grega Milcinski, Jennifer Klein, Lucia Seyfarth, Peter Sterling, David Brainard, and Vijay Balasubramanian. “Natural Images from the Birthplace of the Human Eye.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0020409.","mla":"Tkačik, Gašper, et al. “Natural Images from the Birthplace of the Human Eye.” PLoS One, vol. 6, no. 6, e20409, Public Library of Science, 2011, doi:10.1371/journal.pone.0020409.","short":"G. Tkačik, P. Garrigan, C. Ratliff, G. Milcinski, J. Klein, L. Seyfarth, P. Sterling, D. Brainard, V. Balasubramanian, PLoS One 6 (2011)."},"date_published":"2011-06-16T00:00:00Z","scopus_import":1,"day":"16","has_accepted_license":"1","year":"2011","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","author":[{"first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"full_name":"Garrigan, Patrick","first_name":"Patrick","last_name":"Garrigan"},{"first_name":"Charles","last_name":"Ratliff","full_name":"Ratliff, Charles"},{"full_name":"Milcinski, Grega","last_name":"Milcinski","first_name":"Grega"},{"full_name":"Klein, Jennifer","first_name":"Jennifer","last_name":"Klein"},{"first_name":"Lucia","last_name":"Seyfarth","full_name":"Seyfarth, Lucia"},{"full_name":"Sterling, Peter","first_name":"Peter","last_name":"Sterling"},{"full_name":"Brainard, David","last_name":"Brainard","first_name":"David"},{"first_name":"Vijay","last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay"}],"date_updated":"2021-01-12T07:43:07Z","date_created":"2018-12-11T12:03:01Z","volume":6,"article_number":"e20409","file_date_updated":"2020-07-14T12:46:11Z","publist_id":"3223","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1371/journal.pone.0020409","language":[{"iso":"eng"}],"month":"06"},{"month":"07","doi":"10.1186/1471-2148-11-205","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","file_date_updated":"2020-07-14T12:46:11Z","publist_id":"3219","article_number":"205","author":[{"full_name":"Kupczok, Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Kupczok","first_name":"Anne"}],"date_created":"2018-12-11T12:03:03Z","date_updated":"2021-01-12T07:43:08Z","volume":11,"year":"2011","publication_status":"published","publisher":"BioMed Central","department":[{"_id":"JoBo"}],"day":"13","has_accepted_license":"1","scopus_import":1,"date_published":"2011-07-13T00:00:00Z","publication":"BMC Evolutionary Biology","citation":{"ista":"Kupczok A. 2011. Split based computation of majority rule supertrees. BMC Evolutionary Biology. 11(205), 205.","ieee":"A. Kupczok, “Split based computation of majority rule supertrees,” BMC Evolutionary Biology, vol. 11, no. 205. BioMed Central, 2011.","apa":"Kupczok, A. (2011). Split based computation of majority rule supertrees. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-11-205","ama":"Kupczok A. Split based computation of majority rule supertrees. BMC Evolutionary Biology. 2011;11(205). doi:10.1186/1471-2148-11-205","chicago":"Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” BMC Evolutionary Biology. BioMed Central, 2011. https://doi.org/10.1186/1471-2148-11-205.","mla":"Kupczok, Anne. “Split Based Computation of Majority Rule Supertrees.” BMC Evolutionary Biology, vol. 11, no. 205, 205, BioMed Central, 2011, doi:10.1186/1471-2148-11-205.","short":"A. Kupczok, BMC Evolutionary Biology 11 (2011)."},"abstract":[{"text":"Background: Supertree methods combine overlapping input trees into a larger supertree. Here, I consider split-based supertree methods that first extract the split information of the input trees and subsequently combine this split information into a phylogeny. Well known split-based supertree methods are matrix representation with parsimony and matrix representation with compatibility. Combining input trees on the same taxon set, as in the consensus setting, is a well-studied task and it is thus desirable to generalize consensus methods to supertree methods. Results: Here, three variants of majority-rule (MR) supertrees that generalize majority-rule consensus trees are investigated. I provide simple formulas for computing the respective score for bifurcating input- and supertrees. These score computations, together with a heuristic tree search minmizing the scores, were implemented in the python program PluMiST (Plus- and Minus SuperTrees) available from http://www.cibiv.at/software/ plumist. The different MR methods were tested by simulation and on real data sets. The search heuristic was successful in combining compatible input trees. When combining incompatible input trees, especially one variant, MR(-) supertrees, performed well. Conclusions: The presented framework allows for an efficient score computation of three majority-rule supertree variants and input trees. I combined the score computation with a heuristic search over the supertree space. The implementation was tested by simulation and on real data sets and showed promising results. Especially the MR(-) variant seems to be a reasonable score for supertree reconstruction. Generalizing these computations to multifurcating trees is an open problem, which may be tackled using this framework.","lang":"eng"}],"issue":"205","type":"journal_article","pubrep_id":"372","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:46:11Z","date_created":"2018-12-12T10:14:09Z","checksum":"68da8d04af1b97b4cbe8606e2f92ddd8","relation":"main_file","file_id":"5058","file_size":465042,"content_type":"application/pdf","creator":"system","file_name":"IST-2015-372-v1+1_1471-2148-11-205.pdf","access_level":"open_access"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3387","ddc":["576"],"status":"public","title":"Split based computation of majority rule supertrees","intvolume":" 11"},{"publist_id":"3218","issue":"11","abstract":[{"lang":"eng","text":"Kernel canonical correlation analysis (KCCA) is a general technique for subspace learning that incorporates principal components analysis (PCA) and Fisher linear discriminant analysis (LDA) as special cases. By finding directions that maximize correlation, KCCA learns representations that are more closely tied to the underlying process that generates the data and can ignore high-variance noise directions. However, for data where acquisition in one or more modalities is expensive or otherwise limited, KCCA may suffer from small sample effects. We propose to use semi-supervised Laplacian regularization to utilize data that are present in only one modality. This approach is able to find highly correlated directions that also lie along the data manifold, resulting in a more robust estimate of correlated subspaces. Functional magnetic resonance imaging (fMRI) acquired data are naturally amenable to subspace techniques as data are well aligned. fMRI data of the human brain are a particularly interesting candidate. In this study we implemented various supervised and semi-supervised versions of KCCA on human fMRI data, with regression to single and multi-variate labels (corresponding to video content subjects viewed during the image acquisition). In each variate condition, the semi-supervised variants of KCCA performed better than the supervised variants, including a supervised variant with Laplacian regularization. We additionally analyze the weights learned by the regression in order to infer brain regions that are important to different types of visual processing."}],"type":"journal_article","author":[{"full_name":"Blaschko, Matthew","last_name":"Blaschko","first_name":"Matthew"},{"first_name":"Jacquelyn","last_name":"Shelton","full_name":"Shelton, Jacquelyn"},{"full_name":"Bartels, Andreas","first_name":"Andreas","last_name":"Bartels"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"},{"full_name":"Gretton, Arthur","last_name":"Gretton","first_name":"Arthur"}],"volume":32,"oa_version":"None","date_updated":"2021-01-12T07:43:09Z","date_created":"2018-12-11T12:03:03Z","_id":"3389","acknowledgement":"The research leading to these results has received funding from the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 228180. This work was funded in part by the EC project CLASS, IST 027978, and the PASCAL2 network of excellence, IST 2002-506778.","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2011","intvolume":" 32","publisher":"Elsevier","department":[{"_id":"ChLa"}],"publication_status":"published","status":"public","title":"Semi supervised kernel canonical correlation analysis with application to human fMRI","month":"08","day":"01","scopus_import":1,"date_published":"2011-08-01T00:00:00Z","doi":"10.1016/j.patrec.2011.02.011","language":[{"iso":"eng"}],"citation":{"ama":"Blaschko M, Shelton J, Bartels A, Lampert C, Gretton A. Semi supervised kernel canonical correlation analysis with application to human fMRI. Pattern Recognition Letters. 2011;32(11):1572-1583. doi:10.1016/j.patrec.2011.02.011","ista":"Blaschko M, Shelton J, Bartels A, Lampert C, Gretton A. 2011. Semi supervised kernel canonical correlation analysis with application to human fMRI. Pattern Recognition Letters. 32(11), 1572–1583.","apa":"Blaschko, M., Shelton, J., Bartels, A., Lampert, C., & Gretton, A. (2011). Semi supervised kernel canonical correlation analysis with application to human fMRI. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2011.02.011","ieee":"M. Blaschko, J. Shelton, A. Bartels, C. Lampert, and A. Gretton, “Semi supervised kernel canonical correlation analysis with application to human fMRI,” Pattern Recognition Letters, vol. 32, no. 11. Elsevier, pp. 1572–1583, 2011.","mla":"Blaschko, Matthew, et al. “Semi Supervised Kernel Canonical Correlation Analysis with Application to Human FMRI.” Pattern Recognition Letters, vol. 32, no. 11, Elsevier, 2011, pp. 1572–83, doi:10.1016/j.patrec.2011.02.011.","short":"M. Blaschko, J. Shelton, A. Bartels, C. Lampert, A. Gretton, Pattern Recognition Letters 32 (2011) 1572–1583.","chicago":"Blaschko, Matthew, Jacquelyn Shelton, Andreas Bartels, Christoph Lampert, and Arthur Gretton. “Semi Supervised Kernel Canonical Correlation Analysis with Application to Human FMRI.” Pattern Recognition Letters. Elsevier, 2011. https://doi.org/10.1016/j.patrec.2011.02.011."},"publication":"Pattern Recognition Letters","page":"1572 - 1583","quality_controlled":"1"},{"doi":"10.1109/TRO.2011.2121130","date_published":"2011-05-21T00:00:00Z","language":[{"iso":"eng"}],"publication":"IEEE Transactions on Robotics","citation":{"ista":"Kroemer O, Lampert C, Peters J. 2011. Learning dynamic tactile sensing with robust vision based training. IEEE Transactions on Robotics. 27(3), 545–557.","ieee":"O. Kroemer, C. Lampert, and J. Peters, “Learning dynamic tactile sensing with robust vision based training,” IEEE Transactions on Robotics, vol. 27, no. 3. IEEE, pp. 545–557, 2011.","apa":"Kroemer, O., Lampert, C., & Peters, J. (2011). Learning dynamic tactile sensing with robust vision based training. IEEE Transactions on Robotics. IEEE. https://doi.org/10.1109/TRO.2011.2121130","ama":"Kroemer O, Lampert C, Peters J. Learning dynamic tactile sensing with robust vision based training. IEEE Transactions on Robotics. 2011;27(3):545-557. doi:10.1109/TRO.2011.2121130","chicago":"Kroemer, Oliver, Christoph Lampert, and Jan Peters. “Learning Dynamic Tactile Sensing with Robust Vision Based Training.” IEEE Transactions on Robotics. IEEE, 2011. https://doi.org/10.1109/TRO.2011.2121130.","mla":"Kroemer, Oliver, et al. “Learning Dynamic Tactile Sensing with Robust Vision Based Training.” IEEE Transactions on Robotics, vol. 27, no. 3, IEEE, 2011, pp. 545–57, doi:10.1109/TRO.2011.2121130.","short":"O. Kroemer, C. Lampert, J. Peters, IEEE Transactions on Robotics 27 (2011) 545–557."},"quality_controlled":"1","page":"545 - 557","day":"21","month":"05","scopus_import":1,"author":[{"full_name":"Kroemer, Oliver","first_name":"Oliver","last_name":"Kroemer"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"},{"full_name":"Peters, Jan","last_name":"Peters","first_name":"Jan"}],"date_created":"2018-12-11T12:03:01Z","date_updated":"2021-01-12T07:43:06Z","oa_version":"None","volume":27,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3382","year":"2011","status":"public","publication_status":"published","title":"Learning dynamic tactile sensing with robust vision based training","publisher":"IEEE","department":[{"_id":"ChLa"}],"intvolume":" 27","abstract":[{"text":"Dynamic tactile sensing is a fundamental ability to recognize materials and objects. However, while humans are born with partially developed dynamic tactile sensing and quickly master this skill, today's robots remain in their infancy. The development of such a sense requires not only better sensors but the right algorithms to deal with these sensors' data as well. For example, when classifying a material based on touch, the data are noisy, high-dimensional, and contain irrelevant signals as well as essential ones. Few classification methods from machine learning can deal with such problems. In this paper, we propose an efficient approach to infer suitable lower dimensional representations of the tactile data. In order to classify materials based on only the sense of touch, these representations are autonomously discovered using visual information of the surfaces during training. However, accurately pairing vision and tactile samples in real-robot applications is a difficult problem. The proposed approach, therefore, works with weak pairings between the modalities. Experiments show that the resulting approach is very robust and yields significantly higher classification performance based on only dynamic tactile sensing.","lang":"eng"}],"publist_id":"3225","issue":"3","type":"journal_article"},{"publist_id":"3221","issue":"7","abstract":[{"lang":"eng","text":"Evolutionary theories of ageing predict that life span increases with decreasing extrinsic mortality, and life span variation among queens in ant species seems to corroborate this prediction: queens, which are the only reproductive in a colony, live much longer than queens in multi-queen colonies. The latter often inhabit ephemeral nest sites and accordingly are assumed to experience a higher mortality risk. Yet, all prior studies compared queens from different single- and multi-queen species. Here, we demonstrate an effect of queen number on longevity and fecundity within a single, socially plastic species, where queens experience the similar level of extrinsic mortality. Queens from single- and two-queen colonies had significantly longer lifespan and higher fecundity than queens living in associations of eight queens. As queens also differ neither in morphology nor the mode of colony foundation, our study shows that the social environment itself strongly affects ageing rate."}],"type":"journal_article","author":[{"last_name":"Schrempf","first_name":"Alexandra","full_name":"Schrempf, Alexandra"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer"},{"full_name":"Heinze, Jürgen","last_name":"Heinze","first_name":"Jürgen"}],"oa_version":"None","volume":24,"date_created":"2018-12-11T12:03:02Z","date_updated":"2021-01-12T07:43:08Z","_id":"3386","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","department":[{"_id":"SyCr"}],"publisher":"Wiley-Blackwell","intvolume":" 24","status":"public","publication_status":"published","title":"Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies","month":"04","day":"21","scopus_import":1,"doi":"10.1111/j.1420-9101.2011.02278.x","date_published":"2011-04-21T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ieee":"A. Schrempf, S. Cremer, and J. Heinze, “Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies,” Journal of Evolutionary Biology, vol. 24, no. 7. Wiley-Blackwell, pp. 1455–1461, 2011.","apa":"Schrempf, A., Cremer, S., & Heinze, J. (2011). Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies. Journal of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/j.1420-9101.2011.02278.x","ista":"Schrempf A, Cremer S, Heinze J. 2011. Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies. Journal of Evolutionary Biology. 24(7), 1455–1461.","ama":"Schrempf A, Cremer S, Heinze J. Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies. Journal of Evolutionary Biology. 2011;24(7):1455-1461. doi:10.1111/j.1420-9101.2011.02278.x","chicago":"Schrempf, Alexandra, Sylvia Cremer, and Jürgen Heinze. “Social Influence on Age and Reproduction Reduced Lifespan and Fecundity in Multi Queen Ant Colonies.” Journal of Evolutionary Biology. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1420-9101.2011.02278.x.","short":"A. Schrempf, S. Cremer, J. Heinze, Journal of Evolutionary Biology 24 (2011) 1455–1461.","mla":"Schrempf, Alexandra, et al. “Social Influence on Age and Reproduction Reduced Lifespan and Fecundity in Multi Queen Ant Colonies.” Journal of Evolutionary Biology, vol. 24, no. 7, Wiley-Blackwell, 2011, pp. 1455–61, doi:10.1111/j.1420-9101.2011.02278.x."},"publication":"Journal of Evolutionary Biology","page":"1455 - 1461","quality_controlled":"1"},{"scopus_import":1,"month":"07","day":"01","publication":"Immunology Letters","citation":{"ista":"Sixt MK. 2011. Interstitial locomotion of leukocytes. Immunology Letters. 138(1), 32–34.","ieee":"M. K. Sixt, “Interstitial locomotion of leukocytes,” Immunology Letters, vol. 138, no. 1. Elsevier, pp. 32–34, 2011.","apa":"Sixt, M. K. (2011). Interstitial locomotion of leukocytes. Immunology Letters. Elsevier. https://doi.org/10.1016/j.imlet.2011.02.013","ama":"Sixt MK. Interstitial locomotion of leukocytes. Immunology Letters. 2011;138(1):32-34. doi:10.1016/j.imlet.2011.02.013","chicago":"Sixt, Michael K. “Interstitial Locomotion of Leukocytes.” Immunology Letters. Elsevier, 2011. https://doi.org/10.1016/j.imlet.2011.02.013.","mla":"Sixt, Michael K. “Interstitial Locomotion of Leukocytes.” Immunology Letters, vol. 138, no. 1, Elsevier, 2011, pp. 32–34, doi:10.1016/j.imlet.2011.02.013.","short":"M.K. Sixt, Immunology Letters 138 (2011) 32–34."},"quality_controlled":"1","article_type":"review","page":"32 - 34","date_published":"2011-07-01T00:00:00Z","doi":"10.1016/j.imlet.2011.02.013","language":[{"iso":"eng"}],"type":"journal_article","issue":"1","publist_id":"3222","_id":"3385","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","title":"Interstitial locomotion of leukocytes","publication_status":"published","status":"public","department":[{"_id":"MiSi"}],"intvolume":" 138","publisher":"Elsevier","author":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"}],"date_created":"2018-12-11T12:03:02Z","date_updated":"2021-01-12T07:43:07Z","volume":138,"oa_version":"None"},{"type":"journal_article","issue":"S1","publist_id":"3224","_id":"3383","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2011","publication_status":"published","title":"Invited Lectures ‐ Symposia Area","status":"public","intvolume":" 278","publisher":"Wiley-Blackwell","department":[{"_id":"CaHe"}],"author":[{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"date_updated":"2021-01-12T07:43:06Z","date_created":"2018-12-11T12:03:01Z","volume":278,"oa_version":"None","month":"07","day":"01","publication":"FEBS Journal","citation":{"ama":"Heisenberg C-PJ. Invited Lectures ‐ Symposia Area. FEBS Journal. 2011;278(S1):24-24. doi:10.1111/j.1742-4658.2011.08136.x","ieee":"C.-P. J. Heisenberg, “Invited Lectures ‐ Symposia Area,” FEBS Journal, vol. 278, no. S1. Wiley-Blackwell, pp. 24–24, 2011.","apa":"Heisenberg, C.-P. J. (2011). Invited Lectures ‐ Symposia Area. FEBS Journal. Wiley-Blackwell. https://doi.org/10.1111/j.1742-4658.2011.08136.x","ista":"Heisenberg C-PJ. 2011. Invited Lectures ‐ Symposia Area. FEBS Journal. 278(S1), 24–24.","short":"C.-P.J. Heisenberg, FEBS Journal 278 (2011) 24–24.","mla":"Heisenberg, Carl-Philipp J. “Invited Lectures ‐ Symposia Area.” FEBS Journal, vol. 278, no. S1, Wiley-Blackwell, 2011, pp. 24–24, doi:10.1111/j.1742-4658.2011.08136.x.","chicago":"Heisenberg, Carl-Philipp J. “Invited Lectures ‐ Symposia Area.” FEBS Journal. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1742-4658.2011.08136.x."},"page":"24 - 24","doi":"10.1111/j.1742-4658.2011.08136.x","date_published":"2011-07-01T00:00:00Z","language":[{"iso":"eng"}]},{"month":"03","language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0017323","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2020-07-14T12:46:12Z","publist_id":"3059","article_number":"e17323","date_updated":"2021-01-12T07:43:12Z","date_created":"2018-12-11T12:03:07Z","volume":6,"author":[{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"},{"last_name":"Schrempf","first_name":"Alexandra","full_name":"Schrempf, Alexandra"},{"last_name":"Heinze","first_name":"Jürgen","full_name":"Heinze, Jürgen"}],"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"SyCr"}],"year":"2011","acknowledgement":"This work was supported by the German Science Foundation (www.dfg.de, He 1623/23).","day":"29","has_accepted_license":"1","scopus_import":1,"date_published":"2011-03-29T00:00:00Z","publication":"PLoS One","citation":{"ieee":"S. Cremer, A. Schrempf, and J. Heinze, “Competition and opportunity shape the reproductive tactics of males in the ant Cardiocondyla obscurior,” PLoS One, vol. 6, no. 3. Public Library of Science, 2011.","apa":"Cremer, S., Schrempf, A., & Heinze, J. (2011). Competition and opportunity shape the reproductive tactics of males in the ant Cardiocondyla obscurior. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0017323","ista":"Cremer S, Schrempf A, Heinze J. 2011. Competition and opportunity shape the reproductive tactics of males in the ant Cardiocondyla obscurior. PLoS One. 6(3), e17323.","ama":"Cremer S, Schrempf A, Heinze J. Competition and opportunity shape the reproductive tactics of males in the ant Cardiocondyla obscurior. PLoS One. 2011;6(3). doi:10.1371/journal.pone.0017323","chicago":"Cremer, Sylvia, Alexandra Schrempf, and Jürgen Heinze. “Competition and Opportunity Shape the Reproductive Tactics of Males in the Ant Cardiocondyla Obscurior.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0017323.","short":"S. Cremer, A. Schrempf, J. Heinze, PLoS One 6 (2011).","mla":"Cremer, Sylvia, et al. “Competition and Opportunity Shape the Reproductive Tactics of Males in the Ant Cardiocondyla Obscurior.” PLoS One, vol. 6, no. 3, e17323, Public Library of Science, 2011, doi:10.1371/journal.pone.0017323."},"abstract":[{"lang":"eng","text":"Context-dependent adjustment of mating tactics can drastically increase the mating success of behaviourally flexible animals. We used the ant Cardiocondyla obscurior as a model system to study adaptive adjustment of male mating tactics. This species shows a male diphenism of wingless fighter males and peaceful winged males. Whereas the wingless males stay and exclusively mate in the maternal colony, the mating behaviour of winged males is plastic. They copulate with female sexuals in their natal nests early in life but later disperse in search for sexuals outside. In this study, we observed the nest-leaving behaviour of winged males under different conditions and found that they adaptively adjust the timing of their dispersal to the availability of mating partners, as well as the presence, and even the type of competitors in their natal nests. In colonies with virgin female queens winged males stayed longest when they were the only male in the nest. They left earlier when mating partners were not available or when other males were present. In the presence of wingless, locally mating fighter males, winged males dispersed earlier than in the presence of docile, winged competitors. This suggests that C. obscurior males are capable of estimating their local breeding chances and adaptively adjust their dispersal behaviour in both an opportunistic and a risk-sensitive way, thus showing hitherto unknown behavioural plasticity in social insect males."}],"issue":"3","type":"journal_article","oa_version":"Published Version","file":[{"checksum":"46f8cbde61f06fcacf8fa297cacfa0e5","date_created":"2018-12-12T10:15:40Z","date_updated":"2020-07-14T12:46:12Z","relation":"main_file","file_id":"5162","content_type":"application/pdf","file_size":147367,"creator":"system","access_level":"open_access","file_name":"IST-2015-377-v1+1_journal.pone.0017323.pdf"}],"pubrep_id":"377","title":"Competition and opportunity shape the reproductive tactics of males in the ant Cardiocondyla obscurior","ddc":["576"],"status":"public","intvolume":" 6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3399"},{"day":"01","month":"03","citation":{"chicago":"Little, Shawn, Gašper Tkačik, Thomas Kneeland, Eric Wieschaus, and Thomas Gregor. “The Formation of the Bicoid Morphogen Gradient Requires Protein Movement from Anteriorly Localized Source.” PLoS Biology. Public Library of Science, 2011. https://doi.org/10.1371/journal.pbio.1000596.","mla":"Little, Shawn, et al. “The Formation of the Bicoid Morphogen Gradient Requires Protein Movement from Anteriorly Localized Source.” PLoS Biology, vol. 9, no. 3, e1000596, Public Library of Science, 2011, doi:10.1371/journal.pbio.1000596.","short":"S. Little, G. Tkačik, T. Kneeland, E. Wieschaus, T. Gregor, PLoS Biology 9 (2011).","ista":"Little S, Tkačik G, Kneeland T, Wieschaus E, Gregor T. 2011. The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source. PLoS Biology. 9(3), e1000596.","ieee":"S. Little, G. Tkačik, T. Kneeland, E. Wieschaus, and T. Gregor, “The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source,” PLoS Biology, vol. 9, no. 3. Public Library of Science, 2011.","apa":"Little, S., Tkačik, G., Kneeland, T., Wieschaus, E., & Gregor, T. (2011). The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000596","ama":"Little S, Tkačik G, Kneeland T, Wieschaus E, Gregor T. The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source. PLoS Biology. 2011;9(3). doi:10.1371/journal.pbio.1000596"},"publication":"PLoS Biology","quality_controlled":"1","article_type":"original","doi":"10.1371/journal.pbio.1000596","date_published":"2011-03-01T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","article_number":"e1000596","issue":"3","publist_id":"3057","abstract":[{"lang":"eng","text":"The Bicoid morphogen gradient directs the patterning of cell fates along the anterior-posterior axis of the syncytial Drosophila embryo and serves as a paradigm of morphogen-mediated patterning. The simplest models of gradient formation rely on constant protein synthesis and diffusion from anteriorly localized source mRNA, coupled with uniform protein degradation. However, currently such models cannot account for all known gradient characteristics. Recent work has proposed that bicoid mRNA spatial distribution is sufficient to produce the observed protein gradient, minimizing the role of protein transport. Here, we adapt a novel method of fluorescent in situ hybridization to quantify the global spatio-temporal dynamics of bicoid mRNA particles. We determine that >90% of all bicoid mRNA is continuously present within the anterior 20% of the embryo. bicoid mRNA distribution along the body axis remains nearly unchanged despite dynamic mRNA translocation from the embryo core to the cortex. To evaluate the impact of mRNA distribution on protein gradient dynamics, we provide detailed quantitative measurements of nuclear Bicoid levels during the formation of the protein gradient. We find that gradient establishment begins 45 minutes after fertilization and that the gradient requires about 50 minutes to reach peak levels. In numerical simulations of gradient formation, we find that incorporating the actual bicoid mRNA distribution yields a closer prediction of the observed protein dynamics compared to modeling protein production from a point source at the anterior pole. We conclude that the spatial distribution of bicoid mRNA contributes to, but cannot account for, protein gradient formation, and therefore that protein movement, either active or passive, is required for gradient formation."}],"extern":"1","_id":"3401","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","intvolume":" 9","publisher":"Public Library of Science","title":"The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source","status":"public","publication_status":"published","author":[{"first_name":"Shawn","last_name":"Little","full_name":"Little, Shawn"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"full_name":"Kneeland, Thomas","last_name":"Kneeland","first_name":"Thomas"},{"full_name":"Wieschaus, Eric","first_name":"Eric","last_name":"Wieschaus"},{"full_name":"Gregor, Thomas","last_name":"Gregor","first_name":"Thomas"}],"oa_version":"None","volume":9,"date_created":"2018-12-11T12:03:08Z","date_updated":"2021-01-12T07:43:14Z"},{"volume":55,"date_updated":"2021-01-12T07:51:45Z","date_created":"2018-12-11T12:04:49Z","author":[{"full_name":"Harald Janovjak","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"},{"first_name":"Ehud","last_name":"Isacoff","full_name":"Isacoff, Ehud Y"}],"publisher":"Springer","intvolume":" 55","publication_status":"published","status":"public","title":"Structure-based design of light-controlled proteins","_id":"3724","year":"2011","extern":1,"publist_id":"2504","abstract":[{"text":"Small photochromic molecules are widespread in nature and serve as switches for a plethora of light-controlled processes. In a typical photoreceptor, the different geometries and polarities of the photochrome isomers are tightly coupled to functionally relevant conformational changes in the proteins. The past decade has seen extensive efforts to mimic nature and create proteins controlled by synthetic photochromes in the laboratory. Here, we discuss the role of molecular modeling to gain a structural understanding of photochromes and to design light-controlled peptides and proteins. We address several fundamental questions: What are the molecular structures of photochromes, particularly for metastable isomers that cannot be addressed experimentally? How are the structures of bistable photoisomers coupled to the conformational states of peptides and proteins? Can we design light-controlled proteins rapidly and reliably? After an introduction to the principles of molecular modeling, we answer these questions by examining systems that range from the size of isolated photochromes, to that of peptides and large cell surface receptors, each from its unique computational perspective.","lang":"eng"}],"type":"book_chapter","doi":"10.1007/978-1-61779-031-7_13","date_published":"2011-03-16T00:00:00Z","page":"233 - 266","quality_controlled":0,"citation":{"ama":"Janovjak HL, Isacoff E. Structure-based design of light-controlled proteins. In: Photosensitive Molecules for the Control of Biological Function. Vol 55. Springer; 2011:233-266. doi:10.1007/978-1-61779-031-7_13","ista":"Janovjak HL, Isacoff E. 2011.Structure-based design of light-controlled proteins. In: Photosensitive Molecules for the Control of Biological Function. vol. 55, 233–266.","ieee":"H. L. Janovjak and E. Isacoff, “Structure-based design of light-controlled proteins,” in Photosensitive Molecules for the Control of Biological Function, vol. 55, Springer, 2011, pp. 233–266.","apa":"Janovjak, H. L., & Isacoff, E. (2011). Structure-based design of light-controlled proteins. In Photosensitive Molecules for the Control of Biological Function (Vol. 55, pp. 233–266). Springer. https://doi.org/10.1007/978-1-61779-031-7_13","mla":"Janovjak, Harald L., and Ehud Isacoff. “Structure-Based Design of Light-Controlled Proteins.” Photosensitive Molecules for the Control of Biological Function, vol. 55, Springer, 2011, pp. 233–66, doi:10.1007/978-1-61779-031-7_13.","short":"H.L. Janovjak, E. Isacoff, in:, Photosensitive Molecules for the Control of Biological Function, Springer, 2011, pp. 233–266.","chicago":"Janovjak, Harald L, and Ehud Isacoff. “Structure-Based Design of Light-Controlled Proteins.” In Photosensitive Molecules for the Control of Biological Function, 55:233–66. Springer, 2011. https://doi.org/10.1007/978-1-61779-031-7_13."},"publication":"Photosensitive Molecules for the Control of Biological Function","month":"03","day":"16"},{"year":"2011","_id":"3770","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","intvolume":" 102","status":"public","publication_status":"published","title":"The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis)","author":[{"last_name":"Hollatz","first_name":"Claudia","full_name":"Hollatz, Claudia"},{"first_name":"Sibelle","last_name":"Vilaça","full_name":"Vilaça, Sibelle"},{"full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo","first_name":"Rodrigo A"},{"first_name":"Míriam","last_name":"Marmontel","full_name":"Marmontel, Míriam"},{"last_name":"Baker","first_name":"Cyndi","full_name":"Baker, Cyndi"},{"first_name":"Fabrício","last_name":"Santos","full_name":"Santos, Fabrício"}],"oa_version":"None","volume":102,"date_updated":"2021-01-12T07:52:05Z","date_created":"2018-12-11T12:05:04Z","type":"journal_article","issue":"4","publist_id":"2457","abstract":[{"lang":"eng","text":"The pink dolphin (Inia geoffrensis) is widely distributed along the Amazon and Orinoco basins, covering an area of approximately 7 million km2. Previous morphological and genetic studies have proposed the existence of at least two evolutionary significant units: one distributed across the Orinoco and Amazon basins and another confined to the Bolivian Amazon. The presence of barriers in the riverine environment has been suggested to play a significant role in shaping present-day patterns of ecological and genetic structure for this species. In the present study, we examined the phylogeographic structure, lineage divergence time and historical demography using mitochondrial (mt)DNA sequences in different pink dolphin populations distributed in large and small spatial scales, including two neighbouring Brazilian Amazon populations. mtDNA control region (CR) analysis revealed that the Brazilian haplotypes occupy an intermediate position compared to three previously studied geographic locations: the Colombian Amazon, the Colombian Orinoco, and the Bolivian Amazon. On a local scale, we have identified a pattern of maternal isolation between two neighbouring populations from Brazil. Six mtDNA CR haplotypes were identified in Brazil with no sharing between the two populations, as well as specific cytochrome b (cyt b) haplotypes identified in each locality. In addition, we analyzed autosomal microsatellites to investigate male-mediated gene flow and demographic changes within the study area in Brazil. Data analysis of 14 microsatellite loci failed to detect significant population subdivision, suggesting that male-mediated gene flow may maintain homogeneity between these two locations. Moreover, both mtDNA and microsatellite data indicate a major demographic collapse within Brazil in the late Pleistocene. Bayesian skyline plots (BSP) of mtDNA data revealed a stable population for Colombian and Brazilian Amazon lineages through time, whereas a population decline was demonstrated in the Colombian Orinoco lineage. Moreover, BSP and Tajima's D and Fu's Fs tests revealed a recent population expansion exclusively in the Bolivian sample. Finally, we estimated that the diversification of the Inia sp. lineage began in the Late Pliocene (approximately 3.1 Mya) and continued throughout the Pleistocene."}],"extern":"1","citation":{"short":"C. Hollatz, S. Vilaça, R.A. Fernandes Redondo, M. Marmontel, C. Baker, F. Santos, Biological Journal of the Linnean Society 102 (2011) 812–827.","mla":"Hollatz, Claudia, et al. “The Amazon River System as an Ecological Barrier Driving Genetic Differentiation of the Pink Dolphin (Inia Geoffrensis).” Biological Journal of the Linnean Society, vol. 102, no. 4, Wiley, 2011, pp. 812–27, doi:10.1111/j.1095-8312.2011.01616.x.","chicago":"Hollatz, Claudia, Sibelle Vilaça, Rodrigo A Fernandes Redondo, Míriam Marmontel, Cyndi Baker, and Fabrício Santos. “The Amazon River System as an Ecological Barrier Driving Genetic Differentiation of the Pink Dolphin (Inia Geoffrensis).” Biological Journal of the Linnean Society. Wiley, 2011. https://doi.org/10.1111/j.1095-8312.2011.01616.x.","ama":"Hollatz C, Vilaça S, Fernandes Redondo RA, Marmontel M, Baker C, Santos F. The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis). Biological Journal of the Linnean Society. 2011;102(4):812-827. doi:10.1111/j.1095-8312.2011.01616.x","ieee":"C. Hollatz, S. Vilaça, R. A. Fernandes Redondo, M. Marmontel, C. Baker, and F. Santos, “The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis),” Biological Journal of the Linnean Society, vol. 102, no. 4. Wiley, pp. 812–827, 2011.","apa":"Hollatz, C., Vilaça, S., Fernandes Redondo, R. A., Marmontel, M., Baker, C., & Santos, F. (2011). The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis). Biological Journal of the Linnean Society. Wiley. https://doi.org/10.1111/j.1095-8312.2011.01616.x","ista":"Hollatz C, Vilaça S, Fernandes Redondo RA, Marmontel M, Baker C, Santos F. 2011. The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis). Biological Journal of the Linnean Society. 102(4), 812–827."},"publication":"Biological Journal of the Linnean Society","page":"812 - 827","date_published":"2011-04-01T00:00:00Z","doi":"10.1111/j.1095-8312.2011.01616.x","language":[{"iso":"eng"}],"article_processing_charge":"No","day":"01","month":"04"},{"author":[{"full_name":"Pavan, Ana","last_name":"Pavan","first_name":"Ana"},{"first_name":"Felipe","last_name":"Martins","full_name":"Martins, Felipe"},{"first_name":"Fabrício","last_name":"Santos","full_name":"Santos, Fabrício"},{"last_name":"Ditchfield","first_name":"Albert","full_name":"Ditchfield, Albert"},{"orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A"}],"date_created":"2018-12-11T12:05:05Z","date_updated":"2021-01-12T07:52:05Z","oa_version":"None","volume":102,"year":"2011","_id":"3771","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.","department":[{"_id":"FyKo"}],"intvolume":" 102","publisher":"Wiley-Blackwell","abstract":[{"text":"The small-sized frugivorous bat Carollia perspicillata is an understory specialist and occurs in a wide range of lowland habitats, tending to be more common in tropical dry or moist forests of South and Central America. Its sister species, Carollia brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic study proposed a hypothesis of origin and subsequent diversification for C. perspicillata along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene sequences and a more extensive sampling to test hypotheses related to the origin and diversification of C. perspicillata plus C. brevicauda clade in South America. The results obtained indicate that there are two sympatric evolutionary lineages within each species. In C. perspicillata, one lineage is limited to the Southern Atlantic Forest, whereas the other is widely distributed. Coalescent analysis points to a simultaneous origin for C. perspicillata and C. brevicauda, although no place for the diversification of each species can be firmly suggested. The phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene refugia hypothesis as a likely vicariant phenomenon shaping the present distribution of its intraspecific lineages.","lang":"eng"}],"publist_id":"2456","issue":"3","type":"journal_article","date_published":"2011-02-10T00:00:00Z","doi":"10.1111/j.1095-8312.2010.01601.x","language":[{"iso":"eng"}],"publication":"Biological Journal of the Linnean Society","citation":{"ista":"Pavan A, Martins F, Santos F, Ditchfield A, Fernandes Redondo RA. 2011. Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. Biological Journal of the Linnean Society. 102(3), 527–539.","ieee":"A. Pavan, F. Martins, F. Santos, A. Ditchfield, and R. A. Fernandes Redondo, “Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.,” Biological Journal of the Linnean Society, vol. 102, no. 3. Wiley-Blackwell, pp. 527–539, 2011.","apa":"Pavan, A., Martins, F., Santos, F., Ditchfield, A., & Fernandes Redondo, R. A. (2011). Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. Biological Journal of the Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2010.01601.x","ama":"Pavan A, Martins F, Santos F, Ditchfield A, Fernandes Redondo RA. Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. Biological Journal of the Linnean Society. 2011;102(3):527-539. doi:10.1111/j.1095-8312.2010.01601.x","chicago":"Pavan, Ana, Felipe Martins, Fabrício Santos, Albert Ditchfield, and Rodrigo A Fernandes Redondo. “Patterns of Diversification in Two Species of Short-Tailed Bats (Carollia Gray, 1838): The Effects of Historical Fragmentation of Brazilian Rainforests.” Biological Journal of the Linnean Society. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1095-8312.2010.01601.x.","mla":"Pavan, Ana, et al. “Patterns of Diversification in Two Species of Short-Tailed Bats (Carollia Gray, 1838): The Effects of Historical Fragmentation of Brazilian Rainforests.” Biological Journal of the Linnean Society, vol. 102, no. 3, Wiley-Blackwell, 2011, pp. 527–39, doi:10.1111/j.1095-8312.2010.01601.x.","short":"A. Pavan, F. Martins, F. Santos, A. Ditchfield, R.A. Fernandes Redondo, Biological Journal of the Linnean Society 102 (2011) 527–539."},"quality_controlled":"1","page":"527 - 539","day":"10","month":"02","scopus_import":1},{"language":[{"iso":"eng"}],"doi":"10.1038/hdy.2010.67","date_published":"2011-02-01T00:00:00Z","page":"205 - 206","external_id":{"pmid":["20502479"]},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183869/"}],"oa":1,"citation":{"apa":"Barton, N. H. (2011). Estimating linkage disequilibria. Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2010.67","ieee":"N. H. Barton, “Estimating linkage disequilibria,” Heredity, vol. 106, no. 2. Nature Publishing Group, pp. 205–206, 2011.","ista":"Barton NH. 2011. Estimating linkage disequilibria. Heredity. 106(2), 205–206.","ama":"Barton NH. Estimating linkage disequilibria. Heredity. 2011;106(2):205-206. doi:10.1038/hdy.2010.67","chicago":"Barton, Nicholas H. “Estimating Linkage Disequilibria.” Heredity. Nature Publishing Group, 2011. https://doi.org/10.1038/hdy.2010.67.","short":"N.H. Barton, Heredity 106 (2011) 205–206.","mla":"Barton, Nicholas H. “Estimating Linkage Disequilibria.” Heredity, vol. 106, no. 2, Nature Publishing Group, 2011, pp. 205–06, doi:10.1038/hdy.2010.67."},"publication":"Heredity","day":"01","month":"02","scopus_import":1,"volume":106,"oa_version":"Submitted Version","date_created":"2018-12-11T12:05:07Z","date_updated":"2021-01-12T07:52:08Z","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"department":[{"_id":"NiBa"}],"intvolume":" 106","publisher":"Nature Publishing Group","status":"public","publication_status":"published","title":"Estimating linkage disequilibria","pmid":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3778","year":"2011","publist_id":"2449","issue":"2","type":"journal_article"},{"page":"189 - 213","quality_controlled":"1","citation":{"ieee":"G. Krens and C.-P. J. Heisenberg, “Cell sorting in development,” in Forces and Tension in Development, vol. 95, M. Labouesse, Ed. Elsevier, 2011, pp. 189–213.","apa":"Krens, G., & Heisenberg, C.-P. J. (2011). Cell sorting in development. In M. Labouesse (Ed.), Forces and Tension in Development (Vol. 95, pp. 189–213). Elsevier. https://doi.org/10.1016/B978-0-12-385065-2.00006-2","ista":"Krens G, Heisenberg C-PJ. 2011.Cell sorting in development. In: Forces and Tension in Development. Current Topics in Developmental Biology, vol. 95, 189–213.","ama":"Krens G, Heisenberg C-PJ. Cell sorting in development. In: Labouesse M, ed. Forces and Tension in Development. Vol 95. Elsevier; 2011:189-213. doi:10.1016/B978-0-12-385065-2.00006-2","chicago":"Krens, Gabriel, and Carl-Philipp J Heisenberg. “Cell Sorting in Development.” In Forces and Tension in Development, edited by Michel Labouesse, 95:189–213. Elsevier, 2011. https://doi.org/10.1016/B978-0-12-385065-2.00006-2.","short":"G. Krens, C.-P.J. Heisenberg, in:, M. Labouesse (Ed.), Forces and Tension in Development, Elsevier, 2011, pp. 189–213.","mla":"Krens, Gabriel, and Carl-Philipp J. Heisenberg. “Cell Sorting in Development.” Forces and Tension in Development, edited by Michel Labouesse, vol. 95, Elsevier, 2011, pp. 189–213, doi:10.1016/B978-0-12-385065-2.00006-2."},"publication":"Forces and Tension in Development","language":[{"iso":"eng"}],"date_published":"2011-01-01T00:00:00Z","doi":"10.1016/B978-0-12-385065-2.00006-2","scopus_import":"1","article_processing_charge":"No","day":"01","month":"01","department":[{"_id":"CaHe"}],"publisher":"Elsevier","editor":[{"first_name":"Michel","last_name":"Labouesse","full_name":"Labouesse, Michel"}],"intvolume":" 95","publication_status":"published","status":"public","title":"Cell sorting in development","_id":"3791","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","oa_version":"None","volume":95,"date_created":"2018-12-11T12:05:11Z","date_updated":"2021-01-12T07:52:13Z","author":[{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","first_name":"Gabriel","last_name":"Krens","full_name":"Krens, Gabriel"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"alternative_title":["Current Topics in Developmental Biology"],"type":"book_chapter","publist_id":"2436","abstract":[{"lang":"eng","text":"During the development of multicellular organisms, cell fate specification is followed by the sorting of different cell types into distinct domains from where the different tissues and organs are formed. Cell sorting involves both the segregation of a mixed population of cells with different fates and properties into distinct domains, and the active maintenance of their segregated state. Because of its biological importance and apparent resemblance to fluid segregation in physics, cell sorting was extensively studied by both biologists and physicists over the last decades. Different theories were developed that try to explain cell sorting on the basis of the physical properties of the constituent cells. However, only recently the molecular and cellular mechanisms that control the physical properties driving cell sorting, have begun to be unraveled. In this review, we will provide an overview of different cell-sorting processes in development and discuss how these processes can be explained by the different sorting theories, and how these theories in turn can be connected to the molecular and cellular mechanisms driving these processes."}]},{"file_date_updated":"2020-07-14T12:46:10Z","publist_id":"3249","publication_status":"published","publisher":"Elsevier","department":[{"_id":"ToHe"}],"year":"2011","date_created":"2018-12-11T12:02:55Z","date_updated":"2023-02-23T12:15:28Z","volume":412,"author":[{"full_name":"Didier, Frédéric","first_name":"Frédéric","last_name":"Didier"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Mateescu, Maria","last_name":"Mateescu","first_name":"Maria"},{"full_name":"Wolf, Verena","last_name":"Wolf","first_name":"Verena"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"4535"}]},"month":"05","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.tcs.2010.10.022","type":"journal_article","abstract":[{"text":"Molecular noise, which arises from the randomness of the discrete events in the cell, significantly influences fundamental biological processes. Discrete-state continuous-time stochastic models (CTMC) can be used to describe such effects, but the calculation of the probabilities of certain events is computationally expensive. We present a comparison of two analysis approaches for CTMC. On one hand, we estimate the probabilities of interest using repeated Gillespie simulation and determine the statistical accuracy that we obtain. On the other hand, we apply a numerical reachability analysis that approximates the probability distributions of the system at several time instances. We use examples of cellular processes to demonstrate the superiority of the reachability analysis if accurate results are required.","lang":"eng"}],"issue":"21","title":"Approximation of event probabilities in noisy cellular processes","status":"public","ddc":["000","004"],"intvolume":" 412","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3364","file":[{"checksum":"e5503e25ce020d753e06b3431e16841e","date_created":"2018-12-12T10:11:09Z","date_updated":"2020-07-14T12:46:10Z","file_id":"4862","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":230503,"access_level":"open_access","file_name":"IST-2012-79-v1+1_Approximation_of_event_probabilities_in_noisy_cellular_processes.pdf"}],"oa_version":"Submitted Version","pubrep_id":"79","scopus_import":1,"day":"06","has_accepted_license":"1","page":"2128 - 2141","publication":"Theoretical Computer Science","citation":{"ama":"Didier F, Henzinger TA, Mateescu M, Wolf V. Approximation of event probabilities in noisy cellular processes. Theoretical Computer Science. 2011;412(21):2128-2141. doi:10.1016/j.tcs.2010.10.022","ista":"Didier F, Henzinger TA, Mateescu M, Wolf V. 2011. Approximation of event probabilities in noisy cellular processes. Theoretical Computer Science. 412(21), 2128–2141.","apa":"Didier, F., Henzinger, T. A., Mateescu, M., & Wolf, V. (2011). Approximation of event probabilities in noisy cellular processes. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2010.10.022","ieee":"F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Approximation of event probabilities in noisy cellular processes,” Theoretical Computer Science, vol. 412, no. 21. Elsevier, pp. 2128–2141, 2011.","mla":"Didier, Frédéric, et al. “Approximation of Event Probabilities in Noisy Cellular Processes.” Theoretical Computer Science, vol. 412, no. 21, Elsevier, 2011, pp. 2128–41, doi:10.1016/j.tcs.2010.10.022.","short":"F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, Theoretical Computer Science 412 (2011) 2128–2141.","chicago":"Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Approximation of Event Probabilities in Noisy Cellular Processes.” Theoretical Computer Science. Elsevier, 2011. https://doi.org/10.1016/j.tcs.2010.10.022."},"date_published":"2011-05-06T00:00:00Z"},{"scopus_import":1,"month":"03","day":"23","page":"4593 - 4606","quality_controlled":"1","oa":1,"citation":{"ieee":"N. Vyleta and S. Smith, “Spontaneous glutamate release is independent of calcium influx and tonically activated by the calcium-sensing receptor,” European Journal of Neuroscience, vol. 31, no. 12. Wiley-Blackwell, pp. 4593–4606, 2011.","apa":"Vyleta, N., & Smith, S. (2011). Spontaneous glutamate release is independent of calcium influx and tonically activated by the calcium-sensing receptor. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1523/JNEUROSCI.6398-10.2011","ista":"Vyleta N, Smith S. 2011. Spontaneous glutamate release is independent of calcium influx and tonically activated by the calcium-sensing receptor. European Journal of Neuroscience. 31(12), 4593–4606.","ama":"Vyleta N, Smith S. Spontaneous glutamate release is independent of calcium influx and tonically activated by the calcium-sensing receptor. European Journal of Neuroscience. 2011;31(12):4593-4606. doi:10.1523/JNEUROSCI.6398-10.2011","chicago":"Vyleta, Nicholas, and Stephen Smith. “Spontaneous Glutamate Release Is Independent of Calcium Influx and Tonically Activated by the Calcium-Sensing Receptor.” European Journal of Neuroscience. Wiley-Blackwell, 2011. https://doi.org/10.1523/JNEUROSCI.6398-10.2011.","short":"N. Vyleta, S. Smith, European Journal of Neuroscience 31 (2011) 4593–4606.","mla":"Vyleta, Nicholas, and Stephen Smith. “Spontaneous Glutamate Release Is Independent of Calcium Influx and Tonically Activated by the Calcium-Sensing Receptor.” European Journal of Neuroscience, vol. 31, no. 12, Wiley-Blackwell, 2011, pp. 4593–606, doi:10.1523/JNEUROSCI.6398-10.2011."},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3097128/"}],"publication":"European Journal of Neuroscience","language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.6398-10.2011","date_published":"2011-03-23T00:00:00Z","type":"journal_article","issue":"12","publist_id":"7353","abstract":[{"text":"Spontaneous release of glutamate is important for maintaining synaptic strength and controlling spike timing in the brain. Mechanisms regulating spontaneous exocytosis remain poorly understood. Extracellular calcium concentration ([Ca2+]o) regulates Ca2+ entry through voltage-activated calcium channels (VACCs) and consequently is a pivotal determinant of action potential-evoked vesicle fusion. Extracellular Ca 2+ also enhances spontaneous release, but via unknown mechanisms. Here we report that external Ca2+ triggers spontaneous glutamate release more weakly than evoked release in mouse neocortical neurons. Blockade of VACCs has no effect on the spontaneous release rate or its dependence on [Ca2+]o. Intracellular [Ca2+] slowly increases in a minority of neurons following increases in [Ca2+]o. Furthermore, the enhancement of spontaneous release by extracellular calcium is insensitive to chelation of intracellular calcium by BAPTA. Activation of the calcium-sensing receptor (CaSR), a G-protein-coupled receptor present in nerve terminals, by several specific agonists increased spontaneous glutamate release. The frequency of spontaneous synaptic transmission was decreased in CaSR mutant neurons. The concentration-effect relationship for extracellular calcium regulation of spontaneous release was well described by a combination of CaSR-dependent and CaSR-independent mechanisms. Overall these results indicate that extracellular Ca2+ does not trigger spontaneous glutamate release by simply increasing calcium influx but stimulates CaSR and thereby promotes resting spontaneous glutamate release. ","lang":"eng"}],"department":[{"_id":"PeJo"}],"intvolume":" 31","publisher":"Wiley-Blackwell","status":"public","publication_status":"published","title":"Spontaneous glutamate release is independent of calcium influx and tonically activated by the calcium-sensing receptor","_id":"469","year":"2011","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","volume":31,"date_updated":"2021-01-12T08:00:49Z","date_created":"2018-12-11T11:46:39Z","author":[{"full_name":"Vyleta, Nicholas","first_name":"Nicholas","last_name":"Vyleta","id":"36C4978E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stephen","last_name":"Smith","full_name":"Smith, Stephen"}]},{"pubrep_id":"947","oa_version":"Published Version","file":[{"checksum":"8263bbf255171f2054f43f3db5f53b6e","date_updated":"2020-07-14T12:46:35Z","date_created":"2018-12-12T10:07:44Z","file_id":"4642","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":2863551,"access_level":"open_access","file_name":"IST-2018-947-v1+1_2011_Schloegl_BioSig.pdf"}],"_id":"490","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 2011","status":"public","ddc":["005"],"title":"BioSig: The free and open source software library for biomedical signal processing","abstract":[{"lang":"eng","text":"BioSig is an open source software library for biomedical signal processing. The aim of the BioSig project is to foster research in biomedical signal processing by providing free and open source software tools for many different application areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research. Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), or respiration signals is a very relevant element of the BioSig project. Specifically, BioSig provides solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, and data visualization, to name a few. In this paper, we highlight several methods to help students and researchers to work more efficiently with biomedical signals. "}],"type":"journal_article","date_published":"2011-01-01T00:00:00Z","citation":{"short":"A. Schlögl, C. Vidaurre, T. Sander, Computational Intelligence and Neuroscience 2011 (2011).","mla":"Schlögl, Alois, et al. “BioSig: The Free and Open Source Software Library for Biomedical Signal Processing.” Computational Intelligence and Neuroscience, vol. 2011, 935364, Hindawi Publishing Corporation, 2011, doi:10.1155/2011/935364.","chicago":"Schlögl, Alois, Carmen Vidaurre, and Tilmann Sander. “BioSig: The Free and Open Source Software Library for Biomedical Signal Processing.” Computational Intelligence and Neuroscience. Hindawi Publishing Corporation, 2011. https://doi.org/10.1155/2011/935364.","ama":"Schlögl A, Vidaurre C, Sander T. BioSig: The free and open source software library for biomedical signal processing. Computational Intelligence and Neuroscience. 2011;2011. doi:10.1155/2011/935364","apa":"Schlögl, A., Vidaurre, C., & Sander, T. (2011). BioSig: The free and open source software library for biomedical signal processing. Computational Intelligence and Neuroscience. Hindawi Publishing Corporation. https://doi.org/10.1155/2011/935364","ieee":"A. Schlögl, C. Vidaurre, and T. Sander, “BioSig: The free and open source software library for biomedical signal processing,” Computational Intelligence and Neuroscience, vol. 2011. Hindawi Publishing Corporation, 2011.","ista":"Schlögl A, Vidaurre C, Sander T. 2011. BioSig: The free and open source software library for biomedical signal processing. Computational Intelligence and Neuroscience. 2011, 935364."},"publication":"Computational Intelligence and Neuroscience","has_accepted_license":"1","day":"01","scopus_import":1,"author":[{"last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois"},{"full_name":"Vidaurre, Carmen","first_name":"Carmen","last_name":"Vidaurre"},{"full_name":"Sander, Tilmann","last_name":"Sander","first_name":"Tilmann"}],"volume":2011,"date_created":"2018-12-11T11:46:45Z","date_updated":"2021-01-12T08:01:02Z","year":"2011","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"publisher":"Hindawi Publishing Corporation","publication_status":"published","publist_id":"7330","file_date_updated":"2020-07-14T12:46:35Z","article_number":"935364","doi":"10.1155/2011/935364","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","month":"01"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"491","year":"2011","publication_status":"published","status":"public","title":"Setting the clock for recirculating lymphocytes","department":[{"_id":"MiSi"}],"publisher":"American Association for the Advancement of Science","intvolume":" 4","author":[{"id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","last_name":"Eichner","first_name":"Alexander","full_name":"Eichner, Alexander"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"}],"date_updated":"2021-01-12T08:01:02Z","date_created":"2018-12-11T11:46:46Z","volume":4,"oa_version":"None","article_number":"pe43","type":"journal_article","abstract":[{"text":"In their search for antigens, lymphocytes continuously shuttle among blood vessels, lymph vessels, and lymphatic tissues. Chemokines mediate entry of lymphocytes into lymphatic tissues, and sphingosine 1-phosphate (S1P) promotes localization of lymphocytes to the vasculature. Both signals are sensed through G protein-coupled receptors (GPCRs). Most GPCRs undergo ligand-dependent homologous receptor desensitization, a process that decreases their signaling output after previous exposure to high ligand concentration. Such desensitization can explain why lymphocytes do not take an intermediate position between two signals but rather oscillate between them. The desensitization of S1P receptor 1 (S1PR1) is mediated by GPCR kinase 2 (GRK2). Deletion of GRK2 in lymphocytes compromises desensitization by high vascular S1P concentrations, thereby reducing responsiveness to the chemokine signal and trapping the cells in the vascular compartment. The desensitization kinetics of S1PR1 allows lymphocytes to dynamically shuttle between vasculature and lymphatic tissue, although the positional information in both compartments is static.","lang":"eng"}],"publist_id":"7329","issue":"198","publication":"Science Signaling","citation":{"ama":"Eichner A, Sixt MK. Setting the clock for recirculating lymphocytes. Science Signaling. 2011;4(198). doi:10.1126/scisignal.2002617","ieee":"A. Eichner and M. K. Sixt, “Setting the clock for recirculating lymphocytes,” Science Signaling, vol. 4, no. 198. American Association for the Advancement of Science, 2011.","apa":"Eichner, A., & Sixt, M. K. (2011). Setting the clock for recirculating lymphocytes. Science Signaling. American Association for the Advancement of Science. https://doi.org/10.1126/scisignal.2002617","ista":"Eichner A, Sixt MK. 2011. Setting the clock for recirculating lymphocytes. Science Signaling. 4(198), pe43.","short":"A. Eichner, M.K. Sixt, Science Signaling 4 (2011).","mla":"Eichner, Alexander, and Michael K. Sixt. “Setting the Clock for Recirculating Lymphocytes.” Science Signaling, vol. 4, no. 198, pe43, American Association for the Advancement of Science, 2011, doi:10.1126/scisignal.2002617.","chicago":"Eichner, Alexander, and Michael K Sixt. “Setting the Clock for Recirculating Lymphocytes.” Science Signaling. American Association for the Advancement of Science, 2011. https://doi.org/10.1126/scisignal.2002617."},"quality_controlled":"1","doi":"10.1126/scisignal.2002617","date_published":"2011-11-08T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"08","month":"11"},{"scopus_import":1,"day":"19","article_processing_charge":"No","publication":"EMBO Journal","citation":{"mla":"Schraivogel, Daniel, et al. “CAMTA1 Is a Novel Tumour Suppressor Regulated by MiR-9/9 * in Glioblastoma Stem Cells.” EMBO Journal, vol. 30, no. 20, Wiley-Blackwell, 2011, pp. 4309–22, doi:10.1038/emboj.2011.301.","short":"D. Schraivogel, L. Weinmann, D. Beier, G. Tabatabai, A. Eichner, J. Zhu, M. Anton, M.K. Sixt, M. Weller, C. Beier, G. Meister, EMBO Journal 30 (2011) 4309–4322.","chicago":"Schraivogel, Daniel, Lasse Weinmann, Dagmar Beier, Ghazaleh Tabatabai, Alexander Eichner, Jia Zhu, Martina Anton, et al. “CAMTA1 Is a Novel Tumour Suppressor Regulated by MiR-9/9 * in Glioblastoma Stem Cells.” EMBO Journal. Wiley-Blackwell, 2011. https://doi.org/10.1038/emboj.2011.301.","ama":"Schraivogel D, Weinmann L, Beier D, et al. CAMTA1 is a novel tumour suppressor regulated by miR-9/9 * in glioblastoma stem cells. EMBO Journal. 2011;30(20):4309-4322. doi:10.1038/emboj.2011.301","ista":"Schraivogel D, Weinmann L, Beier D, Tabatabai G, Eichner A, Zhu J, Anton M, Sixt MK, Weller M, Beier C, Meister G. 2011. CAMTA1 is a novel tumour suppressor regulated by miR-9/9 * in glioblastoma stem cells. EMBO Journal. 30(20), 4309–4322.","apa":"Schraivogel, D., Weinmann, L., Beier, D., Tabatabai, G., Eichner, A., Zhu, J., … Meister, G. (2011). CAMTA1 is a novel tumour suppressor regulated by miR-9/9 * in glioblastoma stem cells. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2011.301","ieee":"D. Schraivogel et al., “CAMTA1 is a novel tumour suppressor regulated by miR-9/9 * in glioblastoma stem cells,” EMBO Journal, vol. 30, no. 20. Wiley-Blackwell, pp. 4309–4322, 2011."},"article_type":"original","page":"4309 - 4322","date_published":"2011-10-19T00:00:00Z","type":"journal_article","abstract":[{"text":"Cancer stem cells or cancer initiating cells are believed to contribute to cancer recurrence after therapy. MicroRNAs (miRNAs) are short RNA molecules with fundamental roles in gene regulation. The role of miRNAs in cancer stem cells is only poorly understood. Here, we report miRNA expression profiles of glioblastoma stem cell-containing CD133 + cell populations. We find that miR-9, miR-9 * (referred to as miR-9/9 *), miR-17 and miR-106b are highly abundant in CD133 + cells. Furthermore, inhibition of miR-9/9 * or miR-17 leads to reduced neurosphere formation and stimulates cell differentiation. Calmodulin-binding transcription activator 1 (CAMTA1) is a putative transcription factor, which induces the expression of the anti-proliferative cardiac hormone natriuretic peptide A (NPPA). We identify CAMTA1 as an miR-9/9 * and miR-17 target. CAMTA1 expression leads to reduced neurosphere formation and tumour growth in nude mice, suggesting that CAMTA1 can function as tumour suppressor. Consistently, CAMTA1 and NPPA expression correlate with patient survival. Our findings could provide a basis for novel strategies of glioblastoma therapy.","lang":"eng"}],"issue":"20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"518","title":"CAMTA1 is a novel tumour suppressor regulated by miR-9/9 * in glioblastoma stem cells","status":"public","intvolume":" 30","oa_version":"Submitted Version","month":"10","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199389/"}],"external_id":{"pmid":["21857646"]},"oa":1,"quality_controlled":"1","doi":"10.1038/emboj.2011.301","language":[{"iso":"eng"}],"publist_id":"7301","year":"2011","pmid":1,"publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"MiSi"}],"author":[{"first_name":"Daniel","last_name":"Schraivogel","full_name":"Schraivogel, Daniel"},{"full_name":"Weinmann, Lasse","last_name":"Weinmann","first_name":"Lasse"},{"full_name":"Beier, Dagmar","first_name":"Dagmar","last_name":"Beier"},{"full_name":"Tabatabai, Ghazaleh","last_name":"Tabatabai","first_name":"Ghazaleh"},{"full_name":"Eichner, Alexander","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","last_name":"Eichner","first_name":"Alexander"},{"last_name":"Zhu","first_name":"Jia","full_name":"Zhu, Jia"},{"full_name":"Anton, Martina","last_name":"Anton","first_name":"Martina"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"full_name":"Weller, Michael","last_name":"Weller","first_name":"Michael"},{"last_name":"Beier","first_name":"Christoph","full_name":"Beier, Christoph"},{"full_name":"Meister, Gunter","last_name":"Meister","first_name":"Gunter"}],"date_created":"2018-12-11T11:46:55Z","date_updated":"2021-01-12T08:01:19Z","volume":30}]