[{"abstract":[{"lang":"eng","text":"Transcription factors are central to sustaining pluripotency, yet little is known about transcription factor dynamics in defining pluripotency in the early mammalian embryo. Here, we establish a fluorescence decay after photoactivation (FDAP) assay to quantitatively study the kinetic behaviour of Oct4, a key transcription factor controlling pre-implantation development in the mouse embryo. FDAP measurements reveal that each cell in a developing embryo shows one of two distinct Oct4 kinetics, before there are any morphologically distinguishable differences or outward signs of lineage patterning. The differences revealed by FDAP are due to differences in the accessibility of Oct4 to its DNA binding sites in the nucleus. Lineage tracing of the cells in the two distinct sub-populations demonstrates that the Oct4 kinetics predict lineages of the early embryo. Cells with slower Oct4 kinetics are more likely to give rise to the pluripotent cell lineage that contributes to the inner cell mass. Those with faster Oct4 kinetics contribute mostly to the extra-embryonic lineage. Our findings identify Oct4 kinetics, rather than differences in total transcription factor expression levels, as a predictive measure of developmental cell lineage patterning in the early mouse embryo."}],"acknowledgement":"This work was supported by the Beckman Institute and Biological Imaging Center at the California Institute of Technology and by the NHGRI Center of Excellence in Genomic Science grant P50HG004071.","oa_version":"None","scopus_import":1,"publisher":"Nature Publishing Group","intvolume":" 13","month":"01","publication_status":"published","year":"2011","publication":"Nature Cell Biology","language":[{"iso":"eng"}],"day":"23","page":"117 - 123","date_created":"2018-12-11T12:03:17Z","doi":"10.1038/ncb2154","date_published":"2011-01-23T00:00:00Z","issue":"2","volume":13,"_id":"3429","type":"journal_article","status":"public","citation":{"short":"N. Plachta, M.T. Bollenbach, S. Pease, S. Fraser, P. Pantazis, Nature Cell Biology 13 (2011) 117–123.","ieee":"N. Plachta, M. T. Bollenbach, S. Pease, S. Fraser, and P. Pantazis, “Oct4 kinetics predict cell lineage patterning in the early mammalian embryo,” Nature Cell Biology, vol. 13, no. 2. Nature Publishing Group, pp. 117–123, 2011.","ama":"Plachta N, Bollenbach MT, Pease S, Fraser S, Pantazis P. Oct4 kinetics predict cell lineage patterning in the early mammalian embryo. Nature Cell Biology. 2011;13(2):117-123. doi:10.1038/ncb2154","apa":"Plachta, N., Bollenbach, M. T., Pease, S., Fraser, S., & Pantazis, P. (2011). Oct4 kinetics predict cell lineage patterning in the early mammalian embryo. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2154","mla":"Plachta, Nicolas, et al. “Oct4 Kinetics Predict Cell Lineage Patterning in the Early Mammalian Embryo.” Nature Cell Biology, vol. 13, no. 2, Nature Publishing Group, 2011, pp. 117–23, doi:10.1038/ncb2154.","ista":"Plachta N, Bollenbach MT, Pease S, Fraser S, Pantazis P. 2011. Oct4 kinetics predict cell lineage patterning in the early mammalian embryo. Nature Cell Biology. 13(2), 117–123.","chicago":"Plachta, Nicolas, Mark Tobias Bollenbach, Shirley Pease, Scott Fraser, and Periklis Pantazis. “Oct4 Kinetics Predict Cell Lineage Patterning in the Early Mammalian Embryo.” Nature Cell Biology. Nature Publishing Group, 2011. https://doi.org/10.1038/ncb2154."},"date_updated":"2021-01-12T07:43:24Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"2971","author":[{"last_name":"Plachta","full_name":"Plachta, Nicolas","first_name":"Nicolas"},{"orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pease","full_name":"Pease, Shirley","first_name":"Shirley"},{"first_name":"Scott","last_name":"Fraser","full_name":"Fraser, Scott"},{"first_name":"Periklis","last_name":"Pantazis","full_name":"Pantazis, Periklis"}],"title":"Oct4 kinetics predict cell lineage patterning in the early mammalian embryo","department":[{"_id":"ToBo"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Sixt, Michael K., and Tim Lämmermann. “In Vitro Analysis of Chemotactic Leukocyte Migration in 3D Environments.” Cell Migration, vol. 769, Springer, 2011, pp. 149–65, doi:10.1007/978-1-61779-207-6_11.","ama":"Sixt MK, Lämmermann T. In vitro analysis of chemotactic leukocyte migration in 3D environments. Cell Migration. 2011;769:149-165. doi:10.1007/978-1-61779-207-6_11","apa":"Sixt, M. K., & Lämmermann, T. (2011). In vitro analysis of chemotactic leukocyte migration in 3D environments. Cell Migration. Springer. https://doi.org/10.1007/978-1-61779-207-6_11","short":"M.K. Sixt, T. Lämmermann, Cell Migration 769 (2011) 149–165.","ieee":"M. K. Sixt and T. Lämmermann, “In vitro analysis of chemotactic leukocyte migration in 3D environments,” Cell Migration, vol. 769. Springer, pp. 149–165, 2011.","chicago":"Sixt, Michael K, and Tim Lämmermann. “In Vitro Analysis of Chemotactic Leukocyte Migration in 3D Environments.” Cell Migration. Springer, 2011. https://doi.org/10.1007/978-1-61779-207-6_11.","ista":"Sixt MK, Lämmermann T. 2011. In vitro analysis of chemotactic leukocyte migration in 3D environments. Cell Migration. 769, 149–165."},"title":"In vitro analysis of chemotactic leukocyte migration in 3D environments","article_processing_charge":"No","author":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"full_name":"Lämmermann, Tim","last_name":"Lämmermann","first_name":"Tim"}],"publist_id":"2882","publication":"Cell Migration","day":"17","year":"2011","date_created":"2018-12-11T12:03:41Z","doi":"10.1007/978-1-61779-207-6_11","date_published":"2011-05-17T00:00:00Z","page":"149 - 165","oa":1,"quality_controlled":"1","publisher":"Springer","date_updated":"2021-01-12T07:43:55Z","department":[{"_id":"MiSi"}],"_id":"3505","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","volume":769,"oa_version":"Published Version","abstract":[{"text":"Cell migration on two-dimensional (2D) substrates follows entirely different rules than cell migration in three-dimensional (3D) environments. This is especially relevant for leukocytes that are able to migrate in the absence of adhesion receptors within the confined geometry of artificial 3D extracellular matrix scaffolds and within the interstitial space in vivo. Here, we describe in detail a simple and economical protocol to visualize dendritic cell migration in 3D collagen scaffolds along chemotactic gradients. This method can be adapted to other cell types and may serve as a physiologically relevant paradigm for the directed locomotion of most amoeboid cells.","lang":"eng"}],"intvolume":" 769","month":"05","main_file_link":[{"open_access":"1","url":"https://pure.mpg.de/pubman/item/item_3219628_1/component/file_3219630/Sixt%20et%20al..pdf"}],"alternative_title":["Methods in Molecular Biology"]},{"title":"Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description","publist_id":"2443","author":[{"first_name":"Ferran","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329","full_name":"Palero, Ferran","last_name":"Palero"},{"first_name":"Guillermo","full_name":"Guerao, Guillermo","last_name":"Guerao"},{"full_name":"Clark, Paul","last_name":"Clark","first_name":"Paul"},{"first_name":"Pere","last_name":"Abello","full_name":"Abello, Pere"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Palero F, Guerao G, Clark P, Abello P. 2011. Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. 91(2), 485–492.","chicago":"Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.” Journal of the Marine Biological Association of the United Kingdom. Cambridge University Press, 2011. https://doi.org/10.1017/S0025315410000287.","short":"F. Palero, G. Guerao, P. Clark, P. Abello, Journal of the Marine Biological Association of the United Kingdom 91 (2011) 485–492.","ieee":"F. Palero, G. Guerao, P. Clark, and P. Abello, “Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description,” Journal of the Marine Biological Association of the United Kingdom, vol. 91, no. 2. Cambridge University Press, pp. 485–492, 2011.","ama":"Palero F, Guerao G, Clark P, Abello P. Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. 2011;91(2):485-492. doi:10.1017/S0025315410000287","apa":"Palero, F., Guerao, G., Clark, P., & Abello, P. (2011). Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description. Journal of the Marine Biological Association of the United Kingdom. Cambridge University Press. https://doi.org/10.1017/S0025315410000287","mla":"Palero, Ferran, et al. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.” Journal of the Marine Biological Association of the United Kingdom, vol. 91, no. 2, Cambridge University Press, 2011, pp. 485–92, doi:10.1017/S0025315410000287."},"publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"date_published":"2011-03-01T00:00:00Z","doi":"10.1017/S0025315410000287","date_created":"2018-12-11T12:05:09Z","page":"485 - 492","day":"01","publication":"Journal of the Marine Biological Association of the United Kingdom","year":"2011","status":"public","article_type":"original","type":"journal_article","_id":"3784","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:52:10Z","month":"03","intvolume":" 91","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://digital.csic.es/bitstream/10261/32783/3/Palero_et_al_2011.pdf"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Advanced stages of Scyllarus phyllosoma larvae were collected by demersal trawling during fishery research surveys in the western Mediterranean Sea in 2003–2005. Nucleotide sequence analysis of the mitochondrial 16S rDNA gene allowed the final-stage phyllosoma of Scyllarus arctus to be identified among these larvae. Its morphology is described and illustrated. This constitutes the second complete description of a Scyllaridae phyllosoma with its specific identity being validated by molecular techniques (the first was S. pygmaeus). These results also solved a long lasting taxonomic anomaly of several species assigned to the ancient genus Phyllosoma Leach, 1814. Detailed examination indicated that the final-stage phyllosoma of S. arctus shows closer affinities with the American scyllarid Scyllarus depressus or with the Australian Scyllarus sp. b (sensu Phillips et al., 1981) than to its sympatric species S. pygmaeus."}],"issue":"2","volume":91,"language":[{"iso":"eng"}],"publication_status":"published"},{"volume":77,"issue":"1-2","date_published":"2011-01-01T00:00:00Z","date_created":"2018-12-11T12:05:08Z","page":"359 - 367","day":"01","publication":"Acta Sci. Math. (Szeged)","language":[{"iso":"eng"}],"year":"2011","publication_status":"published","month":"01","intvolume":" 77","publisher":"Szegedi Tudományegyetem","quality_controlled":"1","oa_version":"None","acknowledgement":"Funded by Graduate Aid in Areas of National Need (GAANN) Fellowship.","abstract":[{"text":"We bound the difference in length of two curves in terms of their total curvatures and the Fréchet distance. The bound is independent of the dimension of the ambient Euclidean space, it improves upon a bound by Cohen-Steiner and Edelsbrunner, and it generalizes a result by Fáry and Chakerian.","lang":"eng"}],"title":"The difference in length of curves in R^n","department":[{"_id":"HeEd"}],"author":[{"full_name":"Fasy, Brittany Terese","last_name":"Fasy","id":"F65D502E-E68D-11E9-9252-C644099818F6","first_name":"Brittany Terese"}],"publist_id":"2446","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:52:09Z","citation":{"ieee":"B. T. Fasy, “The difference in length of curves in R^n,” Acta Sci. Math. (Szeged), vol. 77, no. 1–2. Szegedi Tudományegyetem, pp. 359–367, 2011.","short":"B.T. Fasy, Acta Sci. Math. (Szeged) 77 (2011) 359–367.","ama":"Fasy BT. The difference in length of curves in R^n. Acta Sci Math (Szeged). 2011;77(1-2):359-367.","apa":"Fasy, B. T. (2011). The difference in length of curves in R^n. Acta Sci. Math. (Szeged). Szegedi Tudományegyetem.","mla":"Fasy, Brittany Terese. “The Difference in Length of Curves in R^n.” Acta Sci. Math. (Szeged), vol. 77, no. 1–2, Szegedi Tudományegyetem, 2011, pp. 359–67.","ista":"Fasy BT. 2011. The difference in length of curves in R^n. Acta Sci. Math. (Szeged). 77(1–2), 359–367.","chicago":"Fasy, Brittany Terese. “The Difference in Length of Curves in R^n.” Acta Sci. Math. (Szeged). Szegedi Tudományegyetem, 2011."},"status":"public","type":"journal_article","_id":"3781"},{"publisher":"Springer","quality_controlled":"1","oa":1,"day":"03","publication":"Rainbow of Computer Science","has_accepted_license":"1","year":"2011","doi":"10.1007/978-3-642-19391-0_2","date_published":"2011-05-03T00:00:00Z","date_created":"2018-12-11T12:05:13Z","page":"20 - 35","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Edelsbrunner, Herbert, and Michael Kerber. “Covering and Packing with Spheres by Diagonal Distortion in R^n.” Rainbow of Computer Science, edited by Cristian Calude et al., vol. 6570, Springer, 2011, pp. 20–35, doi:10.1007/978-3-642-19391-0_2.","short":"H. Edelsbrunner, M. Kerber, in:, C. Calude, G. Rozenberg, A. Salomaa (Eds.), Rainbow of Computer Science, Springer, 2011, pp. 20–35.","ieee":"H. Edelsbrunner and M. Kerber, “Covering and packing with spheres by diagonal distortion in R^n,” in Rainbow of Computer Science, vol. 6570, C. Calude, G. Rozenberg, and A. Salomaa, Eds. Springer, 2011, pp. 20–35.","apa":"Edelsbrunner, H., & Kerber, M. (2011). Covering and packing with spheres by diagonal distortion in R^n. In C. Calude, G. Rozenberg, & A. Salomaa (Eds.), Rainbow of Computer Science (Vol. 6570, pp. 20–35). Springer. https://doi.org/10.1007/978-3-642-19391-0_2","ama":"Edelsbrunner H, Kerber M. Covering and packing with spheres by diagonal distortion in R^n. In: Calude C, Rozenberg G, Salomaa A, eds. Rainbow of Computer Science. Vol 6570. Dedicated to Hermann Maurer on the Occasion of His 70th Birthday. Springer; 2011:20-35. doi:10.1007/978-3-642-19391-0_2","chicago":"Edelsbrunner, Herbert, and Michael Kerber. “Covering and Packing with Spheres by Diagonal Distortion in R^n.” In Rainbow of Computer Science, edited by Cristian Calude, Grzegorz Rozenberg, and Arto Salomaa, 6570:20–35. Dedicated to Hermann Maurer on the Occasion of His 70th Birthday. Springer, 2011. https://doi.org/10.1007/978-3-642-19391-0_2.","ista":"Edelsbrunner H, Kerber M. 2011.Covering and packing with spheres by diagonal distortion in R^n. In: Rainbow of Computer Science. LNCS, vol. 6570, 20–35."},"editor":[{"full_name":"Calude, Cristian","last_name":"Calude","first_name":"Cristian"},{"first_name":"Grzegorz","last_name":"Rozenberg","full_name":"Rozenberg, Grzegorz"},{"first_name":"Arto","full_name":"Salomaa, Arto","last_name":"Salomaa"}],"title":"Covering and packing with spheres by diagonal distortion in R^n","author":[{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"last_name":"Kerber","full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"}],"publist_id":"2427","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We address the problem of covering ℝ n with congruent balls, while minimizing the number of balls that contain an average point. Considering the 1-parameter family of lattices defined by stretching or compressing the integer grid in diagonal direction, we give a closed formula for the covering density that depends on the distortion parameter. We observe that our family contains the thinnest lattice coverings in dimensions 2 to 5. We also consider the problem of packing congruent balls in ℝ n , for which we give a closed formula for the packing density as well. Again we observe that our family contains optimal configurations, this time densest packings in dimensions 2 and 3."}],"month":"05","intvolume":" 6570","alternative_title":["LNCS"],"file":[{"file_id":"4640","checksum":"aaf22b4d7bd4277ffe8db532119cf474","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:07:42Z","file_name":"IST-2016-539-v1+1_2011-B-01-CoveringPacking.pdf","creator":"system","date_updated":"2020-07-14T12:46:16Z","file_size":436875}],"language":[{"iso":"eng"}],"publication_status":"published","volume":6570,"series_title":"Dedicated to Hermann Maurer on the Occasion of His 70th Birthday","_id":"3796","status":"public","pubrep_id":"539","type":"book_chapter","ddc":["000"],"date_updated":"2021-01-12T07:52:15Z","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:46:16Z"},{"publication":"IJFCS: International Journal of Foundations of Computer Science","day":"01","year":"2011","has_accepted_license":"1","date_created":"2018-12-11T12:03:00Z","date_published":"2011-06-01T00:00:00Z","doi":"10.1142/S0129054111008441","page":"823 - 841","oa":1,"publisher":"World Scientific Publishing","quality_controlled":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Henzinger TA, Jobstmann B, Wolf V. 2011. Formalisms for specifying Markovian population models. IJFCS: International Journal of Foundations of Computer Science. 22(4), 823–841.","chicago":"Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for Specifying Markovian Population Models.” IJFCS: International Journal of Foundations of Computer Science. World Scientific Publishing, 2011. https://doi.org/10.1142/S0129054111008441.","ieee":"T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian population models,” IJFCS: International Journal of Foundations of Computer Science, vol. 22, no. 4. World Scientific Publishing, pp. 823–841, 2011.","short":"T.A. Henzinger, B. Jobstmann, V. Wolf, IJFCS: International Journal of Foundations of Computer Science 22 (2011) 823–841.","apa":"Henzinger, T. A., Jobstmann, B., & Wolf, V. (2011). Formalisms for specifying Markovian population models. IJFCS: International Journal of Foundations of Computer Science. World Scientific Publishing. https://doi.org/10.1142/S0129054111008441","ama":"Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population models. IJFCS: International Journal of Foundations of Computer Science. 2011;22(4):823-841. doi:10.1142/S0129054111008441","mla":"Henzinger, Thomas A., et al. “Formalisms for Specifying Markovian Population Models.” IJFCS: International Journal of Foundations of Computer Science, vol. 22, no. 4, World Scientific Publishing, 2011, pp. 823–41, doi:10.1142/S0129054111008441."},"title":"Formalisms for specifying Markovian population models","author":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Jobstmann, Barbara","last_name":"Jobstmann","first_name":"Barbara"},{"full_name":"Wolf, Verena","last_name":"Wolf","first_name":"Verena"}],"publist_id":"3226","language":[{"iso":"eng"}],"file":[{"file_size":222840,"date_updated":"2020-07-14T12:46:11Z","creator":"system","file_name":"IST-2016-628-v1+1_journals-ijfcs-HenzingerJW11.pdf","date_created":"2018-12-12T10:08:45Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"df88431872586c773fbcfea37d7b36a2","file_id":"4707"}],"publication_status":"published","issue":"4","related_material":{"record":[{"status":"public","id":"3841","relation":"earlier_version"}]},"volume":22,"oa_version":"Submitted Version","abstract":[{"text":"In this survey, we compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. All these languages — matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models — describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, and ease of use. Moreover, they provide different support for checking the well-formedness of a model and for analyzing a model.","lang":"eng"}],"intvolume":" 22","month":"06","scopus_import":1,"ddc":["000"],"date_updated":"2023-02-23T11:45:03Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:11Z","_id":"3381","pubrep_id":"628","status":"public","type":"journal_article"},{"abstract":[{"text":"We present a detailed study of the local density of states (LDOS) associated with the surface-state band near a step edge of the strong topological insulator Bi2Te3 and reveal a one-dimensional bound state that runs parallel to the step edge and is bound to it at some characteristic distance. This bound state is clearly observed in the bulk gap region, while it becomes entangled with the oscillations of the warped surface band at high energy, and with the valence-band states near the Dirac point. We obtain excellent fits to theoretical predictions [Alpichshev, 2011] that properly incorporate the three-dimensional nature of the problem to the surface state. Fitting the data at different energies, we can recalculate the LDOS originating from the Dirac band without the contribution of the bulk bands or incoherent tunneling effects. ","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1003.2233","open_access":"1"}],"intvolume":" 84","month":"07","publication_status":"published","language":[{"iso":"eng"}],"volume":84,"issue":"4","_id":"386","type":"journal_article","article_type":"original","status":"public","date_updated":"2021-01-12T07:52:44Z","extern":"1","oa":1,"publisher":"American Physical Society","quality_controlled":"1","year":"2011","publication":"Physical Review B - Condensed Matter and Materials Physics","day":"21","date_created":"2018-12-11T11:46:10Z","date_published":"2011-07-21T00:00:00Z","doi":"10.1103/PhysRevB.84.041104","citation":{"chicago":"Alpichshev, Zhanybek, J G Analytis, J H Chu, I R Fisher, and A Kapitulnik. “STM Imaging of a Bound State along a Step on the Surface of the Topological Insulator Bi2Te3.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevB.84.041104.","ista":"Alpichshev Z, Analytis JG, Chu JH, Fisher IR, Kapitulnik A. 2011. STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3. Physical Review B - Condensed Matter and Materials Physics. 84(4).","mla":"Alpichshev, Zhanybek, et al. “STM Imaging of a Bound State along a Step on the Surface of the Topological Insulator Bi2Te3.” Physical Review B - Condensed Matter and Materials Physics, vol. 84, no. 4, American Physical Society, 2011, doi:10.1103/PhysRevB.84.041104.","short":"Z. Alpichshev, J.G. Analytis, J.H. Chu, I.R. Fisher, A. Kapitulnik, Physical Review B - Condensed Matter and Materials Physics 84 (2011).","ieee":"Z. Alpichshev, J. G. Analytis, J. H. Chu, I. R. Fisher, and A. Kapitulnik, “STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3,” Physical Review B - Condensed Matter and Materials Physics, vol. 84, no. 4. American Physical Society, 2011.","ama":"Alpichshev Z, Analytis JG, Chu JH, Fisher IR, Kapitulnik A. STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3. Physical Review B - Condensed Matter and Materials Physics. 2011;84(4). doi:10.1103/PhysRevB.84.041104","apa":"Alpichshev, Z., Analytis, J. G., Chu, J. H., Fisher, I. R., & Kapitulnik, A. (2011). STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.84.041104"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1003.2233"]},"publist_id":"7443","author":[{"first_name":"Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Alpichshev, Zhanybek","orcid":"0000-0002-7183-5203","last_name":"Alpichshev"},{"full_name":"Analytis, J G","last_name":"Analytis","first_name":"J G"},{"last_name":"Chu","full_name":"Chu, J H","first_name":"J H"},{"first_name":"I R","full_name":"Fisher, I R","last_name":"Fisher"},{"first_name":"A","full_name":"Kapitulnik, A","last_name":"Kapitulnik"}],"title":"STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3"},{"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:07Z","date_updated":"2023-02-23T11:46:35Z","ddc":["000","005"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"type":"journal_article","pubrep_id":"506","status":"public","_id":"3315","license":"https://creativecommons.org/licenses/by-nd/4.0/","ec_funded":1,"issue":"4","volume":7,"related_material":{"record":[{"status":"public","id":"3876","relation":"earlier_version"}]},"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":588863,"date_updated":"2020-07-14T12:46:07Z","creator":"system","file_name":"IST-2016-86-v2+1_1011.0688_3_.pdf","date_created":"2018-12-12T10:16:42Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"3480e1594bbef25ff7462fa93a8a814e","file_id":"5231"}],"scopus_import":1,"intvolume":" 7","month":"12","abstract":[{"text":"We consider two-player games played in real time on game structures with clocks where the objectives of players are described using parity conditions. The games are concurrent in that at each turn, both players independently propose a time delay and an action, and the action with the shorter delay is chosen. To prevent a player from winning by blocking time, we restrict each player to play strategies that ensure that the player cannot be responsible for causing a zeno run. First, we present an efficient reduction of these games to turn-based (i.e., not concurrent) finite-state (i.e., untimed) parity games. Our reduction improves the best known complexity for solving timed parity games. Moreover, the rich class of algorithms for classical parity games can now be applied to timed parity games. The states of the resulting game are based on clock regions of the original game, and the state space of the finite game is linear in the size of the region graph. Second, we consider two restricted classes of strategies for the player that represents the controller in a real-time synthesis problem, namely, limit-robust and bounded-robust winning strategies. Using a limit-robust winning strategy, the controller cannot choose an exact real-valued time delay but must allow for some nonzero jitter in each of its actions. If there is a given lower bound on the jitter, then the strategy is bounded-robust winning. We show that exact strategies are more powerful than limit-robust strategies, which are more powerful than bounded-robust winning strategies for any bound. For both kinds of robust strategies, we present efficient reductions to standard timed automaton games. These reductions provide algorithms for the synthesis of robust real-time controllers.","lang":"eng"}],"oa_version":"Published Version","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Prabhu, Vinayak","last_name":"Prabhu","first_name":"Vinayak"}],"publist_id":"3324","title":"Timed parity games: Complexity and robustness","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Vinayak Prabhu. “Timed Parity Games: Complexity and Robustness.” Logical Methods in Computer Science. International Federation of Computational Logic, 2011. https://doi.org/10.2168/LMCS-7(4:8)2011.","ista":"Chatterjee K, Henzinger TA, Prabhu V. 2011. Timed parity games: Complexity and robustness. Logical Methods in Computer Science. 7(4).","mla":"Chatterjee, Krishnendu, et al. “Timed Parity Games: Complexity and Robustness.” Logical Methods in Computer Science, vol. 7, no. 4, International Federation of Computational Logic, 2011, doi:10.2168/LMCS-7(4:8)2011.","short":"K. Chatterjee, T.A. Henzinger, V. Prabhu, Logical Methods in Computer Science 7 (2011).","ieee":"K. Chatterjee, T. A. Henzinger, and V. Prabhu, “Timed parity games: Complexity and robustness,” Logical Methods in Computer Science, vol. 7, no. 4. International Federation of Computational Logic, 2011.","apa":"Chatterjee, K., Henzinger, T. A., & Prabhu, V. (2011). Timed parity games: Complexity and robustness. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.2168/LMCS-7(4:8)2011","ama":"Chatterjee K, Henzinger TA, Prabhu V. Timed parity games: Complexity and robustness. Logical Methods in Computer Science. 2011;7(4). doi:10.2168/LMCS-7(4:8)2011"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"}],"date_created":"2018-12-11T12:02:37Z","doi":"10.2168/LMCS-7(4:8)2011","date_published":"2011-12-14T00:00:00Z","year":"2011","has_accepted_license":"1","publication":"Logical Methods in Computer Science","day":"14","oa":1,"publisher":"International Federation of Computational Logic","quality_controlled":"1"},{"volume":16,"issue":"2.2","date_published":"2011-05-01T00:00:00Z","doi":"10.1145/1963190.1970375","date_created":"2018-12-11T12:06:09Z","page":"1 - 13","day":"01","publication":"Journal of Experimental Algorithmics","language":[{"iso":"eng"}],"publication_status":"published","year":"2011","month":"05","intvolume":" 16","quality_controlled":"1","scopus_import":1,"publisher":"ACM","oa_version":"None","abstract":[{"text":"The elevation function on a smoothly embedded 2-manifold in R-3 reflects the multiscale topography of cavities and protrusions as local maxima. The function has been useful in identifying coarse docking configurations for protein pairs. Transporting the concept from the smooth to the piecewise linear category, this paper describes an algorithm for finding all local maxima. While its worst-case running time is the same as of the algorithm used in prior work, its performance in practice is orders of magnitudes superior. We cast light on this improvement by relating the running time to the total absolute Gaussian curvature of the 2-manifold.","lang":"eng"}],"department":[{"_id":"HeEd"}],"title":"Computing elevation maxima by searching the Gauss sphere","author":[{"first_name":"Bei","last_name":"Wang","full_name":"Wang, Bei"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dmitriy","last_name":"Morozov","full_name":"Morozov, Dmitriy"}],"publist_id":"2161","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Wang B, Edelsbrunner H, Morozov D. Computing elevation maxima by searching the Gauss sphere. Journal of Experimental Algorithmics. 2011;16(2.2):1-13. doi:10.1145/1963190.1970375","apa":"Wang, B., Edelsbrunner, H., & Morozov, D. (2011). Computing elevation maxima by searching the Gauss sphere. Journal of Experimental Algorithmics. ACM. https://doi.org/10.1145/1963190.1970375","ieee":"B. Wang, H. Edelsbrunner, and D. Morozov, “Computing elevation maxima by searching the Gauss sphere,” Journal of Experimental Algorithmics, vol. 16, no. 2.2. ACM, pp. 1–13, 2011.","short":"B. Wang, H. Edelsbrunner, D. Morozov, Journal of Experimental Algorithmics 16 (2011) 1–13.","mla":"Wang, Bei, et al. “Computing Elevation Maxima by Searching the Gauss Sphere.” Journal of Experimental Algorithmics, vol. 16, no. 2.2, ACM, 2011, pp. 1–13, doi:10.1145/1963190.1970375.","ista":"Wang B, Edelsbrunner H, Morozov D. 2011. Computing elevation maxima by searching the Gauss sphere. Journal of Experimental Algorithmics. 16(2.2), 1–13.","chicago":"Wang, Bei, Herbert Edelsbrunner, and Dmitriy Morozov. “Computing Elevation Maxima by Searching the Gauss Sphere.” Journal of Experimental Algorithmics. ACM, 2011. https://doi.org/10.1145/1963190.1970375."},"date_updated":"2021-01-12T07:53:31Z","status":"public","type":"journal_article","_id":"3965"},{"_id":"3086","type":"journal_article","status":"public","citation":{"ista":"Furutani M, Sakamoto N, Yoshida S, Kajiwara T, Robert H, Friml J, Tasaka M. 2011. Polar localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers. Development. 138(10), 2069–2078.","chicago":"Furutani, Masahiko, Norihito Sakamoto, Shuhei Yoshida, Takahito Kajiwara, Hélène Robert, Jiří Friml, and Masao Tasaka. “Polar Localized NPH3-like Proteins Regulate Polarity and Endocytosis of PIN-FORMED Auxin Efflux Carriers.” Development. Company of Biologists, 2011. https://doi.org/10.1242/dev.057745.","short":"M. Furutani, N. Sakamoto, S. Yoshida, T. Kajiwara, H. Robert, J. Friml, M. Tasaka, Development 138 (2011) 2069–2078.","ieee":"M. Furutani et al., “Polar localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers,” Development, vol. 138, no. 10. Company of Biologists, pp. 2069–2078, 2011.","apa":"Furutani, M., Sakamoto, N., Yoshida, S., Kajiwara, T., Robert, H., Friml, J., & Tasaka, M. (2011). Polar localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers. Development. Company of Biologists. https://doi.org/10.1242/dev.057745","ama":"Furutani M, Sakamoto N, Yoshida S, et al. Polar localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers. Development. 2011;138(10):2069-2078. doi:10.1242/dev.057745","mla":"Furutani, Masahiko, et al. “Polar Localized NPH3-like Proteins Regulate Polarity and Endocytosis of PIN-FORMED Auxin Efflux Carriers.” Development, vol. 138, no. 10, Company of Biologists, 2011, pp. 2069–78, doi:10.1242/dev.057745."},"date_updated":"2021-01-12T07:40:57Z","extern":1,"publist_id":"3615","author":[{"last_name":"Furutani","full_name":"Furutani, Masahiko","first_name":"Masahiko"},{"full_name":"Sakamoto, Norihito","last_name":"Sakamoto","first_name":"Norihito"},{"first_name":"Shuhei","last_name":"Yoshida","full_name":"Yoshida, Shuhei"},{"full_name":"Kajiwara, Takahito","last_name":"Kajiwara","first_name":"Takahito"},{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène S"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml"},{"last_name":"Tasaka","full_name":"Tasaka, Masao","first_name":"Masao"}],"title":"Polar localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers","abstract":[{"text":"PIN-FORMED (PIN)-dependent auxin transport is essential for plant development and its modulation in response to the environment or endogenous signals. A NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3)-like protein, MACCHI-BOU 4 (MAB4), has been shown to control PIN1 localization during organ formation, but its contribution is limited. The Arabidopsis genome contains four genes, MAB4/ENP/NPY1-LIKE1 (MEL1), MEL2, MEL3 and MEL4, highly homologous to MAB4. Genetic analysis disclosed functional redundancy between MAB4 and MEL genes in regulation of not only organ formation but also of root gravitropism, revealing that NPH3 family proteins have a wider range of functions than previously suspected. Multiple mutants showed severe reduction in PIN abundance and PIN polar localization, leading to defective expression of an auxin responsive marker DR5rev::GFP. Pharmacological analyses and fluorescence recovery after photo-bleaching experiments showed that mel mutations increase PIN2 internalization from the plasma membrane, but affect neither intracellular PIN2 trafficking nor PIN2 lateral diffusion at the plasma membrane. Notably, all MAB4 subfamily proteins show polar localization at the cell periphery in plants. The MAB4 polarity was almost identical to PIN polarity. Our results suggest that the MAB4 subfamily proteins specifically retain PIN proteins in a polarized manner at the plasma membrane, thus controlling directional auxin transport and plant development.","lang":"eng"}],"publisher":"Company of Biologists","quality_controlled":0,"intvolume":" 138","month":"05","publication_status":"published","year":"2011","publication":"Development","day":"01","page":"2069 - 2078","date_created":"2018-12-11T12:01:17Z","doi":"10.1242/dev.057745","issue":"10","date_published":"2011-05-01T00:00:00Z","volume":138},{"title":"Clathrin mediates endocytosis and polar distribution of PIN auxin transporters in Arabidopsis","publist_id":"3614","author":[{"full_name":"Kitakura, Saeko","last_name":"Kitakura","first_name":"Saeko"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"full_name":"Löfke, Christian","last_name":"Löfke","first_name":"Christian"},{"first_name":"Thomas","full_name":"Teichmann, Thomas","last_name":"Teichmann"},{"full_name":"Tanaka, Hirokazu","last_name":"Tanaka","first_name":"Hirokazu"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"extern":1,"citation":{"ieee":"S. Kitakura et al., “Clathrin mediates endocytosis and polar distribution of PIN auxin transporters in Arabidopsis,” Plant Cell, vol. 23, no. 5. American Society of Plant Biologists, pp. 1920–1931, 2011.","short":"S. Kitakura, S. Vanneste, S. Robert, C. Löfke, T. Teichmann, H. Tanaka, J. Friml, Plant Cell 23 (2011) 1920–1931.","apa":"Kitakura, S., Vanneste, S., Robert, S., Löfke, C., Teichmann, T., Tanaka, H., & Friml, J. (2011). Clathrin mediates endocytosis and polar distribution of PIN auxin transporters in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.111.083030","ama":"Kitakura S, Vanneste S, Robert S, et al. Clathrin mediates endocytosis and polar distribution of PIN auxin transporters in Arabidopsis. Plant Cell. 2011;23(5):1920-1931. doi:10.1105/tpc.111.083030","mla":"Kitakura, Saeko, et al. “Clathrin Mediates Endocytosis and Polar Distribution of PIN Auxin Transporters in Arabidopsis.” Plant Cell, vol. 23, no. 5, American Society of Plant Biologists, 2011, pp. 1920–31, doi:10.1105/tpc.111.083030.","ista":"Kitakura S, Vanneste S, Robert S, Löfke C, Teichmann T, Tanaka H, Friml J. 2011. Clathrin mediates endocytosis and polar distribution of PIN auxin transporters in Arabidopsis. Plant Cell. 23(5), 1920–1931.","chicago":"Kitakura, Saeko, Steffen Vanneste, Stéphanie Robert, Christian Löfke, Thomas Teichmann, Hirokazu Tanaka, and Jiří Friml. “Clathrin Mediates Endocytosis and Polar Distribution of PIN Auxin Transporters in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2011. https://doi.org/10.1105/tpc.111.083030."},"date_updated":"2021-01-12T07:40:57Z","status":"public","type":"journal_article","_id":"3087","date_created":"2018-12-11T12:01:18Z","volume":23,"date_published":"2011-05-01T00:00:00Z","doi":"10.1105/tpc.111.083030","issue":"5","page":"1920 - 1931","publication":"Plant Cell","day":"01","publication_status":"published","year":"2011","intvolume":" 23","month":"05","quality_controlled":0,"publisher":"American Society of Plant Biologists","abstract":[{"text":"Endocytosis is a crucial mechanism by which eukaryotic cells internalize extracellular and plasma membrane material, and it is required for a multitude of cellular and developmental processes in unicellular and multicellular organisms. In animals and yeast, the best characterized pathway for endocytosis depends on the function of the vesicle coat protein clathrin. Clathrinmediated endocytosis has recently been demonstrated also in plant cells, but its physiological and developmental roles remain unclear. Here, we assessed the roles of the clathrin-mediated mechanism of endocytosis in plants by genetic means. We interfered with clathrin heavy chain (CHC) function through mutants and dominant-negative approaches in Arabidopsis thaliana and established tools to manipulate clathrin function in a cell type-specific manner. The chc2 single mutants and dominant-negative CHC1 (HUB) transgenic lines were defective in bulk endocytosis as well as in internalization of prominent plasma membrane proteins. Interference with clathrin-mediated endocytosis led to defects in constitutive endocytic recycling of PIN auxin transporters and their polar distribution in embryos and roots. Consistent with this, these lines had altered auxin distribution patterns and associated auxin transport-related phenotypes, such as aberrant embryo patterning, imperfect cotyledon specification, agravitropic growth, and impaired lateral root organogenesis. Together, these data demonstrate a fundamental role for clathrin function in cell polarity, growth, patterning, and organogenesis in plants.","lang":"eng"}]},{"abstract":[{"lang":"eng","text":"Phototropism is an adaptation response, through which plants grow towards the light. It involves light perception and asymmetric distribution of the plant hormone auxin. Here we identify a crucial part of the mechanism for phototropism, revealing how light perception initiates auxin redistribution that leads to directional growth. We show that light polarizes the cellular localization of the auxin efflux carrier PIN3 in hypocotyl endodermis cells, resulting in changes in auxin distribution and differential growth. In the dark, high expression and activity of the PINOID (PID) kinase correlates with apolar targeting of PIN3 to all cell sides. Following illumination, light represses PINOID transcription and PIN3 is polarized specifically to the inner cell sides by GNOM ARF GTPase GEF (guanine nucleotide exchange factor)-dependent trafficking. Thus, differential trafficking at the shaded and illuminated hypocotyl side aligns PIN3 polarity with the light direction, and presumably redirects auxin flow towards the shaded side, where auxin promotes growth, causing hypocotyls to bend towards the light. Our results imply that PID phosphorylation-dependent recruitment of PIN proteins into distinct trafficking pathways is a mechanism to polarize auxin fluxes in response to different environmental and endogenous cues."}],"quality_controlled":0,"publisher":"Nature Publishing Group","month":"04","intvolume":" 13","year":"2011","publication_status":"published","day":"01","publication":"Nature Cell Biology","page":"447 - 453","doi":"10.1038/ncb2208","issue":"4","volume":13,"date_published":"2011-04-01T00:00:00Z","date_created":"2018-12-11T12:01:17Z","_id":"3085","type":"journal_article","status":"public","citation":{"apa":"Ding, Z., Galván Ampudia, C., Demarsy, E., Łangowski, Ł., Kleine Vehn, J., Fan, Y., … Friml, J. (2011). Light-mediated polarization of the PIN3 auxin transporter for the phototropic response in Arabidopsis. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2208","ama":"Ding Z, Galván Ampudia C, Demarsy E, et al. Light-mediated polarization of the PIN3 auxin transporter for the phototropic response in Arabidopsis. Nature Cell Biology. 2011;13(4):447-453. doi:10.1038/ncb2208","short":"Z. Ding, C. Galván Ampudia, E. Demarsy, Ł. Łangowski, J. Kleine Vehn, Y. Fan, M. Morita, M. Tasaka, C. Fankhauser, R. Offringa, J. Friml, Nature Cell Biology 13 (2011) 447–453.","ieee":"Z. Ding et al., “Light-mediated polarization of the PIN3 auxin transporter for the phototropic response in Arabidopsis,” Nature Cell Biology, vol. 13, no. 4. Nature Publishing Group, pp. 447–453, 2011.","mla":"Ding, Zhaojun, et al. “Light-Mediated Polarization of the PIN3 Auxin Transporter for the Phototropic Response in Arabidopsis.” Nature Cell Biology, vol. 13, no. 4, Nature Publishing Group, 2011, pp. 447–53, doi:10.1038/ncb2208.","ista":"Ding Z, Galván Ampudia C, Demarsy E, Łangowski Ł, Kleine Vehn J, Fan Y, Morita M, Tasaka M, Fankhauser C, Offringa R, Friml J. 2011. Light-mediated polarization of the PIN3 auxin transporter for the phototropic response in Arabidopsis. Nature Cell Biology. 13(4), 447–453.","chicago":"Ding, Zhaojun, Carlos Galván Ampudia, Emilie Demarsy, Łukasz Łangowski, Jürgen Kleine Vehn, Yuanwei Fan, Miyo Morita, et al. “Light-Mediated Polarization of the PIN3 Auxin Transporter for the Phototropic Response in Arabidopsis.” Nature Cell Biology. Nature Publishing Group, 2011. https://doi.org/10.1038/ncb2208."},"date_updated":"2021-01-12T07:40:57Z","extern":1,"author":[{"last_name":"Ding","full_name":"Ding, Zhaojun","first_name":"Zhaojun"},{"first_name":"Carlos","last_name":"Galván Ampudia","full_name":"Galván-Ampudia, Carlos S"},{"first_name":"Emilie","full_name":"Demarsy, Emilie","last_name":"Demarsy"},{"first_name":"Łukasz","last_name":"Łangowski","full_name":"Łangowski, Łukasz"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"first_name":"Yuanwei","last_name":"Fan","full_name":"Fan, Yuanwei"},{"last_name":"Morita","full_name":"Morita, Miyo T","first_name":"Miyo"},{"last_name":"Tasaka","full_name":"Tasaka, Masao","first_name":"Masao"},{"first_name":"Christian","full_name":"Fankhauser, Christian","last_name":"Fankhauser"},{"first_name":"Remko","full_name":"Offringa, Remko","last_name":"Offringa"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"3616","title":"Light-mediated polarization of the PIN3 auxin transporter for the phototropic response in Arabidopsis"},{"extern":1,"date_updated":"2021-01-12T07:40:56Z","citation":{"mla":"Feraru, Elena, et al. “PIN Polarity Maintenance by the Cell Wall in Arabidopsis.” Current Biology, vol. 21, no. 4, Cell Press, 2011, pp. 338–43, doi:10.1016/j.cub.2011.01.036.","ieee":"E. Feraru et al., “PIN polarity maintenance by the cell wall in Arabidopsis,” Current Biology, vol. 21, no. 4. Cell Press, pp. 338–343, 2011.","short":"E. Feraru, M. Feraru, J. Kleine Vehn, A. Martinière, G. Mouille, S. Vanneste, S. Vernhettes, J. Runions, J. Friml, Current Biology 21 (2011) 338–343.","ama":"Feraru E, Feraru M, Kleine Vehn J, et al. PIN polarity maintenance by the cell wall in Arabidopsis. Current Biology. 2011;21(4):338-343. doi:10.1016/j.cub.2011.01.036","apa":"Feraru, E., Feraru, M., Kleine Vehn, J., Martinière, A., Mouille, G., Vanneste, S., … Friml, J. (2011). PIN polarity maintenance by the cell wall in Arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2011.01.036","chicago":"Feraru, Elena, Mugurel Feraru, Jürgen Kleine Vehn, Alexandre Martinière, Grégory Mouille, Steffen Vanneste, Samantha Vernhettes, John Runions, and Jiří Friml. “PIN Polarity Maintenance by the Cell Wall in Arabidopsis.” Current Biology. Cell Press, 2011. https://doi.org/10.1016/j.cub.2011.01.036.","ista":"Feraru E, Feraru M, Kleine Vehn J, Martinière A, Mouille G, Vanneste S, Vernhettes S, Runions J, Friml J. 2011. PIN polarity maintenance by the cell wall in Arabidopsis. Current Biology. 21(4), 338–343."},"title":"PIN polarity maintenance by the cell wall in Arabidopsis","author":[{"full_name":"Feraru, Elena","last_name":"Feraru","first_name":"Elena"},{"full_name":"Feraru, Mugurel I","last_name":"Feraru","first_name":"Mugurel"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen"},{"full_name":"Martinière, Alexandre","last_name":"Martinière","first_name":"Alexandre"},{"first_name":"Grégory","full_name":"Mouille, Grégory","last_name":"Mouille"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"first_name":"Samantha","last_name":"Vernhettes","full_name":"Vernhettes, Samantha"},{"first_name":"John","full_name":"Runions, John","last_name":"Runions"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml"}],"publist_id":"3618","_id":"3084","status":"public","type":"journal_article","day":"22","publication":"Current Biology","publication_status":"published","year":"2011","issue":"4","volume":21,"doi":"10.1016/j.cub.2011.01.036","date_published":"2011-02-22T00:00:00Z","date_created":"2018-12-11T12:01:17Z","page":"338 - 343","abstract":[{"text":"\nA central question in developmental biology concerns the mechanism of generation and maintenance of cell polarity, because these processes are essential for many cellular functions and multicellular development [1]. In plants, cell polarity has an additional role in mediating directional transport of the plant hormone auxin that is crucial for multiple developmental processes [2-4]. In addition, plant cells have a complex extracellular matrix, the cell wall [5, 6], whose role in regulating cellular processes, including cell polarity, is unexplored. We have found that polar distribution of PIN auxin transporters [7] in plant cells is maintained by connections between polar domains at the plasma membrane and the cell wall. Genetic and pharmacological interference with cellulose, the major component of the cell wall, or mechanical interference with the cell wall disrupts these connections and leads to increased lateral diffusion and loss of polar distribution of PIN transporters for the phytohormone auxin. Our results reveal a plant-specific mechanism for cell polarity maintenance and provide a conceptual framework for modulating cell polarity and plant development via endogenous and environmental manipulations of the cellulose-based extracellular matrix.","lang":"eng"}],"month":"02","intvolume":" 21","publisher":"Cell Press","quality_controlled":0},{"abstract":[{"lang":"eng","text":"Shoot branching is one of the major determinants of plant architecture. Polar auxin transport in stems is necessary for the control of bud outgrowth by a dominant apex. Here, we show that following decapitation in pea (Pisum sativum L.), the axillary buds establish directional auxin export by subcellular polarization of PIN auxin transporters. Apical auxin application on the decapitated stem prevents this PIN polarization and canalization of laterally applied auxin. These results support a model in which the apical and lateral auxin sources compete for primary channels of auxin transport in the stem to control the outgrowth of axillary buds."}],"publisher":"Wiley-Blackwell","quality_controlled":0,"intvolume":" 65","month":"02","publication_status":"published","year":"2011","publication":"Plant Journal","day":"01","page":"571 - 577","date_created":"2018-12-11T12:01:16Z","volume":65,"issue":"4","doi":"10.1111/j.1365-313X.2010.04443.x","date_published":"2011-02-01T00:00:00Z","_id":"3082","type":"journal_article","status":"public","date_updated":"2021-01-12T07:40:56Z","citation":{"mla":"Balla, Jozef, et al. “Competitive Canalization of PIN Dependent Auxin Flow from Axillary Buds Controls Pea Bud Outgrowth.” Plant Journal, vol. 65, no. 4, Wiley-Blackwell, 2011, pp. 571–77, doi:10.1111/j.1365-313X.2010.04443.x.","short":"J. Balla, P. Kalousek, V. Reinöhl, J. Friml, S. Procházka, Plant Journal 65 (2011) 571–577.","ieee":"J. Balla, P. Kalousek, V. Reinöhl, J. Friml, and S. Procházka, “Competitive canalization of PIN dependent auxin flow from axillary buds controls pea bud outgrowth,” Plant Journal, vol. 65, no. 4. Wiley-Blackwell, pp. 571–577, 2011.","apa":"Balla, J., Kalousek, P., Reinöhl, V., Friml, J., & Procházka, S. (2011). Competitive canalization of PIN dependent auxin flow from axillary buds controls pea bud outgrowth. Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/j.1365-313X.2010.04443.x","ama":"Balla J, Kalousek P, Reinöhl V, Friml J, Procházka S. Competitive canalization of PIN dependent auxin flow from axillary buds controls pea bud outgrowth. Plant Journal. 2011;65(4):571-577. doi:10.1111/j.1365-313X.2010.04443.x","chicago":"Balla, Jozef, Petr Kalousek, Vilém Reinöhl, Jiří Friml, and Stanislav Procházka. “Competitive Canalization of PIN Dependent Auxin Flow from Axillary Buds Controls Pea Bud Outgrowth.” Plant Journal. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1365-313X.2010.04443.x.","ista":"Balla J, Kalousek P, Reinöhl V, Friml J, Procházka S. 2011. Competitive canalization of PIN dependent auxin flow from axillary buds controls pea bud outgrowth. Plant Journal. 65(4), 571–577."},"extern":1,"author":[{"first_name":"Jozef","last_name":"Balla","full_name":"Balla, Jozef"},{"first_name":"Petr","full_name":"Kalousek, Petr","last_name":"Kalousek"},{"first_name":"Vilém","last_name":"Reinöhl","full_name":"Reinöhl, Vilém"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Stanislav","last_name":"Procházka","full_name":"Procházka, Stanislav"}],"publist_id":"3619","title":"Competitive canalization of PIN dependent auxin flow from axillary buds controls pea bud outgrowth"},{"publication_status":"published","year":"2011","day":"01","publication":"Plant Cell","page":"846 - 849","doi":"10.1105/tpc.110.082099","issue":"3","date_published":"2011-03-01T00:00:00Z","volume":23,"date_created":"2018-12-11T12:01:16Z","publisher":"American Society of Plant Biologists","quality_controlled":0,"month":"03","intvolume":" 23","citation":{"ista":"Robinson D, Scheuring D, Naramoto S, Friml J. 2011. ARF1 localizes to the golgi and the trans Golgi network. Plant Cell. 23(3), 846–849.","chicago":"Robinson, David, David Scheuring, Satoshi Naramoto, and Jiří Friml. “ARF1 Localizes to the Golgi and the Trans Golgi Network.” Plant Cell. American Society of Plant Biologists, 2011. https://doi.org/10.1105/tpc.110.082099.","apa":"Robinson, D., Scheuring, D., Naramoto, S., & Friml, J. (2011). ARF1 localizes to the golgi and the trans Golgi network. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.110.082099","ama":"Robinson D, Scheuring D, Naramoto S, Friml J. ARF1 localizes to the golgi and the trans Golgi network. Plant Cell. 2011;23(3):846-849. doi:10.1105/tpc.110.082099","ieee":"D. Robinson, D. Scheuring, S. Naramoto, and J. Friml, “ARF1 localizes to the golgi and the trans Golgi network,” Plant Cell, vol. 23, no. 3. American Society of Plant Biologists, pp. 846–849, 2011.","short":"D. Robinson, D. Scheuring, S. Naramoto, J. Friml, Plant Cell 23 (2011) 846–849.","mla":"Robinson, David, et al. “ARF1 Localizes to the Golgi and the Trans Golgi Network.” Plant Cell, vol. 23, no. 3, American Society of Plant Biologists, 2011, pp. 846–49, doi:10.1105/tpc.110.082099."},"date_updated":"2021-01-12T07:40:56Z","extern":1,"author":[{"first_name":"David","full_name":"Robinson, David G","last_name":"Robinson"},{"first_name":"David","full_name":"Scheuring, David","last_name":"Scheuring"},{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"publist_id":"3617","title":"ARF1 localizes to the golgi and the trans Golgi network","_id":"3083","type":"journal_article","status":"public"},{"publisher":"Nature Publishing Group","quality_controlled":0,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357998/"}],"oa":1,"month":"01","intvolume":" 21","abstract":[{"text":"Subcellular trafficking is required for a multitude of functions in eukaryotic cells. It involves regulation of cargo sorting, vesicle formation, trafficking and fusion processes at multiple levels. Adaptor protein (AP) complexes are key regulators of cargo sorting into vesicles in yeast and mammals but their existence and function in plants have not been demonstrated. Here we report the identification of the protein-affected trafficking 4 (pat4) mutant defective in the putative δ subunit of the AP-3 complex. pat4 and pat2, a mutant isolated from the same GFP imaging-based forward genetic screen that lacks a functional putative AP-3 β, as well as dominant negative AP-3 μ transgenic lines display undistinguishable phenotypes characterized by largely normal morphology and development, but strong intracellular accumulation of membrane proteins in aberrant vacuolar structures. All mutants are defective in morphology and function of lytic and protein storage vacuoles (PSVs) but show normal sorting of reserve proteins to PSVs. Immunoprecipitation experiments and genetic studies revealed tight functional and physical associations of putative AP-3 β and AP-3 δ subunits. Furthermore, both proteins are closely linked with putative AP-3 μ and σ subunits and several components of the clathrin and dynamin machineries. Taken together, these results demonstrate that AP complexes, similar to those in other eukaryotes, exist in plants, and that AP-3 plays a specific role in the regulation of biogenesis and function of vacuoles in plant cells. © 2011 IBCB, SIBS, CAS All rights reserved","lang":"eng"}],"page":"1711 - 1722","doi":"10.1038/cr.2011.99","issue":"12","volume":21,"date_published":"2011-01-01T00:00:00Z","date_created":"2018-12-11T12:01:23Z","year":"2011","publication_status":"published","day":"01","publication":"Cell Research","type":"journal_article","status":"public","_id":"3101","author":[{"last_name":"Zwiewka","full_name":"Zwiewka, Marta","first_name":"Marta"},{"first_name":"Elena","last_name":"Feraru","full_name":"Feraru, Elena"},{"first_name":"Barbara","full_name":"Möller, Barbara","last_name":"Möller"},{"full_name":"Hwang, Inhwan","last_name":"Hwang","first_name":"Inhwan"},{"first_name":"Mugurel","full_name":"Feraru, Mugurel I","last_name":"Feraru"},{"last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen","first_name":"Jürgen"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"3597","title":"The AP 3 adaptor complex is required for vacuolar function in Arabidopsis","date_updated":"2021-01-12T07:41:04Z","citation":{"ieee":"M. Zwiewka et al., “The AP 3 adaptor complex is required for vacuolar function in Arabidopsis,” Cell Research, vol. 21, no. 12. Nature Publishing Group, pp. 1711–1722, 2011.","short":"M. Zwiewka, E. Feraru, B. Möller, I. Hwang, M. Feraru, J. Kleine Vehn, D. Weijers, J. Friml, Cell Research 21 (2011) 1711–1722.","ama":"Zwiewka M, Feraru E, Möller B, et al. The AP 3 adaptor complex is required for vacuolar function in Arabidopsis. Cell Research. 2011;21(12):1711-1722. doi:10.1038/cr.2011.99","apa":"Zwiewka, M., Feraru, E., Möller, B., Hwang, I., Feraru, M., Kleine Vehn, J., … Friml, J. (2011). The AP 3 adaptor complex is required for vacuolar function in Arabidopsis. Cell Research. Nature Publishing Group. https://doi.org/10.1038/cr.2011.99","mla":"Zwiewka, Marta, et al. “The AP 3 Adaptor Complex Is Required for Vacuolar Function in Arabidopsis.” Cell Research, vol. 21, no. 12, Nature Publishing Group, 2011, pp. 1711–22, doi:10.1038/cr.2011.99.","ista":"Zwiewka M, Feraru E, Möller B, Hwang I, Feraru M, Kleine Vehn J, Weijers D, Friml J. 2011. The AP 3 adaptor complex is required for vacuolar function in Arabidopsis. Cell Research. 21(12), 1711–1722.","chicago":"Zwiewka, Marta, Elena Feraru, Barbara Möller, Inhwan Hwang, Mugurel Feraru, Jürgen Kleine Vehn, Dolf Weijers, and Jiří Friml. “The AP 3 Adaptor Complex Is Required for Vacuolar Function in Arabidopsis.” Cell Research. Nature Publishing Group, 2011. https://doi.org/10.1038/cr.2011.99."},"extern":1},{"date_created":"2018-12-11T12:01:22Z","doi":"10.1038/msb.2011.72","volume":7,"date_published":"2011-10-25T00:00:00Z","publication_status":"published","year":"2011","publication":"Molecular Systems Biology","day":"25","publisher":"Nature Publishing Group","quality_controlled":0,"intvolume":" 7","month":"10","abstract":[{"text":"Cell polarity reflected by asymmetric distribution of proteins at the plasma membrane is a fundamental feature of unicellular and multicellular organisms. It remains conceptually unclear how cell polarity is kept in cell wall-encapsulated plant cells. We have used super-resolution and semi-quantitative live-cell imaging in combination with pharmacological, genetic, and computational approaches to reveal insights into the mechanism of cell polarity maintenance in Arabidopsis thaliana. We show that polar-competent PIN transporters for the phytohormone auxin are delivered to the center of polar domains by super-polar recycling. Within the plasma membrane, PINs are recruited into non-mobile membrane clusters and their lateral diffusion is dramatically reduced, which ensures longer polar retention. At the circumventing edges of the polar domain, spatially defined internalization of escaped cargos occurs by clathrin-dependent endocytosis. Computer simulations confirm that the combination of these processes provides a robust mechanism for polarity maintenance in plant cells. Moreover, our study suggests that the regulation of lateral diffusion and spatially defined endocytosis, but not super-polar exocytosis have primary importance for PIN polarity maintenance.","lang":"eng"}],"publist_id":"3601","author":[{"first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn"},{"orcid":"0000-0001-7263-0560","full_name":"Krzysztof Wabnik","last_name":"Wabnik","first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Martinière","full_name":"Martinière, Alexandre","first_name":"Alexandre"},{"first_name":"Łukasz","last_name":"Łangowski","full_name":"Łangowski, Łukasz"},{"first_name":"Katrin","full_name":"Willig, Katrin","last_name":"Willig"},{"full_name":"Naramoto, Satoshi","last_name":"Naramoto","first_name":"Satoshi"},{"full_name":"Leitner, Johannes","last_name":"Leitner","first_name":"Johannes"},{"full_name":"Tanaka, Hirokazu","last_name":"Tanaka","first_name":"Hirokazu"},{"last_name":"Jakobs","full_name":"Jakobs, Stefan","first_name":"Stefan"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"},{"full_name":"Govaerts, Willy J","last_name":"Govaerts","first_name":"Willy"},{"first_name":"Stefan","full_name":"Hell, Stefan W","last_name":"Hell"},{"full_name":"Runions, John","last_name":"Runions","first_name":"John"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml"}],"title":"Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane","citation":{"short":"J. Kleine Vehn, K.T. Wabnik, A. Martinière, Ł. Łangowski, K. Willig, S. Naramoto, J. Leitner, H. Tanaka, S. Jakobs, S. Robert, C. Luschnig, W. Govaerts, S. Hell, J. Runions, J. Friml, Molecular Systems Biology 7 (2011).","ieee":"J. Kleine Vehn et al., “Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane,” Molecular Systems Biology, vol. 7. Nature Publishing Group, 2011.","apa":"Kleine Vehn, J., Wabnik, K. T., Martinière, A., Łangowski, Ł., Willig, K., Naramoto, S., … Friml, J. (2011). Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.1038/msb.2011.72","ama":"Kleine Vehn J, Wabnik KT, Martinière A, et al. Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane. Molecular Systems Biology. 2011;7. doi:10.1038/msb.2011.72","mla":"Kleine Vehn, Jürgen, et al. “Recycling, Clustering and Endocytosis Jointly Maintain PIN Auxin Carrier Polarity at the Plasma Membrane.” Molecular Systems Biology, vol. 7, Nature Publishing Group, 2011, doi:10.1038/msb.2011.72.","ista":"Kleine Vehn J, Wabnik KT, Martinière A, Łangowski Ł, Willig K, Naramoto S, Leitner J, Tanaka H, Jakobs S, Robert S, Luschnig C, Govaerts W, Hell S, Runions J, Friml J. 2011. Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane. Molecular Systems Biology. 7.","chicago":"Kleine Vehn, Jürgen, Krzysztof T Wabnik, Alexandre Martinière, Łukasz Łangowski, Katrin Willig, Satoshi Naramoto, Johannes Leitner, et al. “Recycling, Clustering and Endocytosis Jointly Maintain PIN Auxin Carrier Polarity at the Plasma Membrane.” Molecular Systems Biology. Nature Publishing Group, 2011. https://doi.org/10.1038/msb.2011.72."},"date_updated":"2021-01-12T07:41:02Z","extern":1,"type":"journal_article","status":"public","_id":"3098"},{"citation":{"mla":"Vanneste, Steffen, et al. “Developmental Regulation of CYCA2s Contributes to Tissue-Specific Proliferation in Arabidopsis .” EMBO Journal, vol. 30, no. 16, Wiley-Blackwell, 2011, pp. 3430–41, doi:10.1038/emboj.2011.240.","ama":"Vanneste S, Coppens F, Lee E, et al. Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis . EMBO Journal. 2011;30(16):3430-3441. doi:10.1038/emboj.2011.240","apa":"Vanneste, S., Coppens, F., Lee, E., Donner, T., Xie, Z., Van Isterdael, G., … Beeckman, T. (2011). Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis . EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2011.240","ieee":"S. Vanneste et al., “Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis ,” EMBO Journal, vol. 30, no. 16. Wiley-Blackwell, pp. 3430–3441, 2011.","short":"S. Vanneste, F. Coppens, E. Lee, T. Donner, Z. Xie, G. Van Isterdael, S. Dhondt, F. De Winter, B. De Rybel, M. Vuylsteke, L. De Veylder, J. Friml, D. Inzé, E. Grotewold, E. Scarpella, F. Sack, G. Beemster, T. Beeckman, EMBO Journal 30 (2011) 3430–3441.","chicago":"Vanneste, Steffen, Frederik Coppens, Eunkyoung Lee, Tyler Donner, Zidian Xie, Gert Van Isterdael, Stijn Dhondt, et al. “Developmental Regulation of CYCA2s Contributes to Tissue-Specific Proliferation in Arabidopsis .” EMBO Journal. Wiley-Blackwell, 2011. https://doi.org/10.1038/emboj.2011.240.","ista":"Vanneste S, Coppens F, Lee E, Donner T, Xie Z, Van Isterdael G, Dhondt S, De Winter F, De Rybel B, Vuylsteke M, De Veylder L, Friml J, Inzé D, Grotewold E, Scarpella E, Sack F, Beemster G, Beeckman T. 2011. Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis . EMBO Journal. 30(16), 3430–3441."},"date_updated":"2021-01-12T07:41:04Z","extern":1,"publist_id":"3600","author":[{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"last_name":"Coppens","full_name":"Coppens, Frederik","first_name":"Frederik"},{"last_name":"Lee","full_name":"Lee, EunKyoung","first_name":"Eunkyoung"},{"first_name":"Tyler","full_name":"Donner, Tyler J","last_name":"Donner"},{"first_name":"Zidian","full_name":"Xie, Zidian","last_name":"Xie"},{"first_name":"Gert","last_name":"Van Isterdael","full_name":"Van Isterdael, Gert"},{"first_name":"Stijn","last_name":"Dhondt","full_name":"Dhondt, Stijn"},{"last_name":"De Winter","full_name":"De Winter, Freya","first_name":"Freya"},{"full_name":"De Rybel, Bert","last_name":"De Rybel","first_name":"Bert"},{"first_name":"Marnik","last_name":"Vuylsteke","full_name":"Vuylsteke, Marnik"},{"first_name":"Lieven","full_name":"De Veylder, Lieven","last_name":"De Veylder"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dirk","full_name":"Inzé, Dirk","last_name":"Inzé"},{"last_name":"Grotewold","full_name":"Grotewold, Erich","first_name":"Erich"},{"first_name":"Enrico","full_name":"Scarpella, Enrico","last_name":"Scarpella"},{"full_name":"Sack, Fred","last_name":"Sack","first_name":"Fred"},{"last_name":"Beemster","full_name":"Beemster, Gerrit T","first_name":"Gerrit"},{"first_name":"Tom","full_name":"Beeckman, Tom","last_name":"Beeckman"}],"title":"Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis ","_id":"3100","type":"journal_article","status":"public","year":"2011","publication_status":"published","publication":"EMBO Journal","day":"17","page":"3430 - 3441","date_created":"2018-12-11T12:01:23Z","date_published":"2011-08-17T00:00:00Z","volume":30,"issue":"16","doi":"10.1038/emboj.2011.240","abstract":[{"text":"In multicellular organisms, morphogenesis relies on a strict coordination in time and space of cell proliferation and differentiation. In contrast to animals, plant development displays continuous organ formation and adaptive growth responses during their lifespan relying on a tight coordination of cell proliferation. How developmental signals interact with the plant cell-cycle machinery is largely unknown. Here, we characterize plant A2-type cyclins, a small gene family of mitotic cyclins, and show how they contribute to the fine-tuning of local proliferation during plant development. Moreover, the timely repression of CYCA2;3 expression in newly formed guard cells is shown to require the stomatal transcription factors FOUR LIPS/MYB124 and MYB88, providing a direct link between developmental programming and cell-cycle exit in plants. Thus, transcriptional downregulation of CYCA2s represents a critical mechanism to coordinate proliferation during plant development.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160660/"}],"oa":1,"publisher":"Wiley-Blackwell","quality_controlled":0,"intvolume":" 30","month":"08"},{"publisher":"National Academy of Sciences","quality_controlled":0,"intvolume":" 108","month":"10","abstract":[{"lang":"eng","text":"Endomembrane trafficking relies on the coordination of a highly complex, dynamic network of intracellular vesicles. Understanding the network will require a dissection of cargo and vesicle dynamics at the cellular level in vivo. This is also a key to establishing a link between vesicular networks and their functional roles in development. We used a high-content intracellular screen to discover small molecules targeting endomembrane trafficking in vivo in a complex eukaryote, Arabidopsis thaliana. Tens of thousands of molecules were prescreened and a selected subset was interrogated against a panel of plasma membrane (PM) and other endomembrane compartment markers to identify molecules that altered vesicle trafficking. The extensive image dataset was transformed by a flexible algorithm into a marker-by-phenotype-by-treatment time matrix and revealed groups of molecules that induced similar subcellular fingerprints (clusters). This matrix provides a platform for a systems view of trafficking. Molecules from distinct clusters presented avenues and enabled an entry point to dissect recycling at the PM, vacuolar sorting, and cell-plate maturation. Bioactivity in human cells indicated the value of the approach to identifying small molecules that are active in diverse organisms for biology and drug discovery."}],"page":"17850 - 17855","date_created":"2018-12-11T12:01:23Z","doi":"10.1073/pnas.1108581108","issue":"43","volume":108,"date_published":"2011-10-25T00:00:00Z","publication_status":"published","year":"2011","publication":"PNAS","day":"25","type":"journal_article","status":"public","_id":"3099","author":[{"first_name":"Georgia","full_name":"Drakakaki, Georgia","last_name":"Drakakaki"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"first_name":"Anna","last_name":"Szatmári","full_name":"Szatmári, Anna-Maria"},{"first_name":"Michelle","last_name":"Brown","full_name":"Brown, Michelle Q"},{"full_name":"Nagawa, Shingo","last_name":"Nagawa","first_name":"Shingo"},{"first_name":"Daniël","full_name":"Van Damme, Daniël","last_name":"Van Damme"},{"first_name":"Marylin","full_name":"Leonard, Marylin","last_name":"Leonard"},{"first_name":"Zhenbiao","full_name":"Yang, Zhenbiao","last_name":"Yang"},{"last_name":"Girke","full_name":"Girke, Thomas","first_name":"Thomas"},{"full_name":"Schmid, Sandra L","last_name":"Schmid","first_name":"Sandra"},{"last_name":"Russinova","full_name":"Russinova, Eugenia","first_name":"Eugenia"},{"full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"last_name":"Raikhel","full_name":"Raikhel, Natasha V","first_name":"Natasha"},{"first_name":"Glen","last_name":"Hicks","full_name":"Hicks, Glen R"}],"publist_id":"3602","title":"Clusters of bioactive compounds target dynamic endomembrane networks in vivo","date_updated":"2021-01-12T07:41:02Z","citation":{"ieee":"G. Drakakaki et al., “Clusters of bioactive compounds target dynamic endomembrane networks in vivo,” PNAS, vol. 108, no. 43. National Academy of Sciences, pp. 17850–17855, 2011.","short":"G. Drakakaki, S. Robert, A. Szatmári, M. Brown, S. Nagawa, D. Van Damme, M. Leonard, Z. Yang, T. Girke, S. Schmid, E. Russinova, J. Friml, N. Raikhel, G. Hicks, PNAS 108 (2011) 17850–17855.","ama":"Drakakaki G, Robert S, Szatmári A, et al. Clusters of bioactive compounds target dynamic endomembrane networks in vivo. PNAS. 2011;108(43):17850-17855. doi:10.1073/pnas.1108581108","apa":"Drakakaki, G., Robert, S., Szatmári, A., Brown, M., Nagawa, S., Van Damme, D., … Hicks, G. (2011). Clusters of bioactive compounds target dynamic endomembrane networks in vivo. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1108581108","mla":"Drakakaki, Georgia, et al. “Clusters of Bioactive Compounds Target Dynamic Endomembrane Networks in Vivo.” PNAS, vol. 108, no. 43, National Academy of Sciences, 2011, pp. 17850–55, doi:10.1073/pnas.1108581108.","ista":"Drakakaki G, Robert S, Szatmári A, Brown M, Nagawa S, Van Damme D, Leonard M, Yang Z, Girke T, Schmid S, Russinova E, Friml J, Raikhel N, Hicks G. 2011. Clusters of bioactive compounds target dynamic endomembrane networks in vivo. PNAS. 108(43), 17850–17855.","chicago":"Drakakaki, Georgia, Stéphanie Robert, Anna Szatmári, Michelle Brown, Shingo Nagawa, Daniël Van Damme, Marylin Leonard, et al. “Clusters of Bioactive Compounds Target Dynamic Endomembrane Networks in Vivo.” PNAS. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1108581108."},"extern":1},{"status":"public","type":"journal_article","_id":"3095","title":"Auxin minimum defines a developmental window for lateral root initiation","author":[{"first_name":"Joseph","last_name":"Dubrovsky","full_name":"Dubrovsky, Joseph G"},{"first_name":"Selene","last_name":"Napsucialy Mendivil","full_name":"Napsucialy-Mendivil, Selene"},{"first_name":"Jérôme","last_name":"Duclercq","full_name":"Duclercq, Jérôme"},{"first_name":"Yan","last_name":"Cheng","full_name":"Cheng, Yan"},{"first_name":"Svetlana","last_name":"Shishkova","full_name":"Shishkova, Svetlana O"},{"last_name":"Ivanchenko","full_name":"Ivanchenko, Maria G","first_name":"Maria"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml"},{"full_name":"Murphy, Angus S","last_name":"Murphy","first_name":"Angus"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","full_name":"Eva Benková","orcid":"0000-0002-8510-9739"}],"publist_id":"3605","extern":1,"citation":{"ama":"Dubrovsky J, Napsucialy Mendivil S, Duclercq J, et al. Auxin minimum defines a developmental window for lateral root initiation. New Phytologist. 2011;191(4):970-983. doi: 10.1111/j.1469-8137.2011.03757.x","apa":"Dubrovsky, J., Napsucialy Mendivil, S., Duclercq, J., Cheng, Y., Shishkova, S., Ivanchenko, M., … Benková, E. (2011). Auxin minimum defines a developmental window for lateral root initiation. New Phytologist. Wiley-Blackwell. https://doi.org/ 10.1111/j.1469-8137.2011.03757.x","ieee":"J. Dubrovsky et al., “Auxin minimum defines a developmental window for lateral root initiation,” New Phytologist, vol. 191, no. 4. Wiley-Blackwell, pp. 970–983, 2011.","short":"J. Dubrovsky, S. Napsucialy Mendivil, J. Duclercq, Y. Cheng, S. Shishkova, M. Ivanchenko, J. Friml, A. Murphy, E. Benková, New Phytologist 191 (2011) 970–983.","mla":"Dubrovsky, Joseph, et al. “Auxin Minimum Defines a Developmental Window for Lateral Root Initiation.” New Phytologist, vol. 191, no. 4, Wiley-Blackwell, 2011, pp. 970–83, doi: 10.1111/j.1469-8137.2011.03757.x.","ista":"Dubrovsky J, Napsucialy Mendivil S, Duclercq J, Cheng Y, Shishkova S, Ivanchenko M, Friml J, Murphy A, Benková E. 2011. Auxin minimum defines a developmental window for lateral root initiation. New Phytologist. 191(4), 970–983.","chicago":"Dubrovsky, Joseph, Selene Napsucialy Mendivil, Jérôme Duclercq, Yan Cheng, Svetlana Shishkova, Maria Ivanchenko, Jiří Friml, Angus Murphy, and Eva Benková. “Auxin Minimum Defines a Developmental Window for Lateral Root Initiation.” New Phytologist. Wiley-Blackwell, 2011. https://doi.org/ 10.1111/j.1469-8137.2011.03757.x."},"date_updated":"2021-01-12T07:41:01Z","intvolume":" 191","month":"01","quality_controlled":0,"publisher":"Wiley-Blackwell","abstract":[{"text":"Root system architecture depends on lateral root (LR) initiation that takes place in a relatively narrow developmental window (DW). Here, we analyzed the role of auxin gradients established along the parent root in defining this DW for LR initiation. Correlations between auxin distribution and response, and spatiotemporal control of LR initiation were analyzed in Arabidopsis thaliana and tomato (Solanum lycopersicum). In both Arabidopsis and tomato roots, a well defined zone, where auxin content and response are minimal, demarcates the position of a DW for founder cell specification and LR initiation. We show that in the zone of auxin minimum pericycle cells have highest probability to become founder cells and that auxin perception via the TIR1/AFB pathway, and polar auxin transport, are essential for the establishment of this zone. Altogether, this study reveals that the same morphogen-like molecule, auxin, can act simultaneously as a morphogenetic trigger of LR founder cell identity and as a gradient-dependent signal defining positioning of the founder cell specification. This auxin minimum zone might represent an important control mechanism ensuring the LR initiation steadiness and the acropetal LR initiation pattern. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.","lang":"eng"}],"date_created":"2018-12-11T12:01:21Z","volume":191,"issue":"4","doi":" 10.1111/j.1469-8137.2011.03757.x","date_published":"2011-01-01T00:00:00Z","page":"970 - 983","publication":"New Phytologist","day":"01","publication_status":"published","year":"2011"},{"abstract":[{"lang":"eng","text":"Cytokinin is an important regulator of plant growth and development. In Arabidopsis thaliana, the two-component phosphorelay mediated through a family of histidine kinases and response regulators is recognized as the principal cytokinin signal transduction mechanism activating the complex transcriptional response to control various developmental processes. Here, we identified an alternative mode of cytokinin action that uses endocytic trafficking as a means to direct plant organogenesis. This activity occurs downstream of known cytokinin receptors but through a branch of the cytokinin signaling pathway that does not involve transcriptional regulation. We show that cytokinin regulates endocytic recycling of the auxin efflux carrier PINFORMED1 (PIN1) by redirecting it for lytic degradation in vacuoles. Stimulation of the lytic PIN1 degradation is not a default effect for general downregulation of proteins from plasma membranes, but a specific mechanism to rapidly modulate the auxin distribution in cytokinin-mediated developmental processes."}],"intvolume":" 21","month":"10","publisher":"Cell Press","quality_controlled":0,"publication":"Developmental Cell","day":"18","publication_status":"published","year":"2011","date_created":"2018-12-11T12:01:22Z","date_published":"2011-10-18T00:00:00Z","doi":"10.1016/j.devcel.2011.08.014","volume":21,"issue":"4","page":"796 - 804","_id":"3097","status":"public","type":"journal_article","extern":1,"citation":{"chicago":"Marhavý, Peter, Agnieszka Bielach, Lindy Abas, Anas Abuzeineh, Jérôme Duclercq, Hirokazu Tanaka, Markéta Pařezová, et al. “Cytokinin Modulates Endocytic Trafficking of PIN1 Auxin Efflux Carrier to Control Plant Organogenesis.” Developmental Cell. Cell Press, 2011. https://doi.org/10.1016/j.devcel.2011.08.014.","ista":"Marhavý P, Bielach A, Abas L, Abuzeineh A, Duclercq J, Tanaka H, Pařezová M, Petrášek J, Friml J, Kleine Vehn J, Benková E. 2011. Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis. Developmental Cell. 21(4), 796–804.","mla":"Marhavý, Peter, et al. “Cytokinin Modulates Endocytic Trafficking of PIN1 Auxin Efflux Carrier to Control Plant Organogenesis.” Developmental Cell, vol. 21, no. 4, Cell Press, 2011, pp. 796–804, doi:10.1016/j.devcel.2011.08.014.","short":"P. Marhavý, A. Bielach, L. Abas, A. Abuzeineh, J. Duclercq, H. Tanaka, M. Pařezová, J. Petrášek, J. Friml, J. Kleine Vehn, E. Benková, Developmental Cell 21 (2011) 796–804.","ieee":"P. Marhavý et al., “Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis,” Developmental Cell, vol. 21, no. 4. Cell Press, pp. 796–804, 2011.","apa":"Marhavý, P., Bielach, A., Abas, L., Abuzeineh, A., Duclercq, J., Tanaka, H., … Benková, E. (2011). Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2011.08.014","ama":"Marhavý P, Bielach A, Abas L, et al. Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis. Developmental Cell. 2011;21(4):796-804. doi:10.1016/j.devcel.2011.08.014"},"date_updated":"2021-01-12T07:41:02Z","title":"Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis","publist_id":"3603","author":[{"last_name":"Marhavy","full_name":"Peter Marhavy","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"last_name":"Bielach","full_name":"Bielach, Agnieszka","first_name":"Agnieszka"},{"last_name":"Abas","full_name":"Abas, Lindy","first_name":"Lindy"},{"first_name":"Anas","last_name":"Abuzeineh","full_name":"Abuzeineh, Anas"},{"first_name":"Jérôme","full_name":"Duclercq, Jérôme","last_name":"Duclercq"},{"first_name":"Hirokazu","last_name":"Tanaka","full_name":"Tanaka, Hirokazu"},{"last_name":"Pařezová","full_name":"Pařezová, Markéta","first_name":"Markéta"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen"},{"last_name":"Benková","full_name":"Eva Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}]},{"date_created":"2018-12-11T12:01:21Z","date_published":"2011-09-01T00:00:00Z","doi":"10.1016/j.tplants.2011.05.002","issue":"9","volume":16,"page":"468 - 475","publication":"Trends in Plant Science","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2011","intvolume":" 16","month":"09","quality_controlled":"1","publisher":"Cell Press","oa_version":"None","abstract":[{"lang":"eng","text":"Carrier-dependent, intercellular auxin transport is central to the developmental patterning of higher plants (tracheophytes). The evolution of this polar auxin transport might be linked to the translocation of some PIN auxin efflux carriers from their presumably ancestral localization at the endoplasmic reticulum (ER) to the polar domains at the plasma membrane. Here we propose an eventually ancient mechanism of intercellular auxin distribution by ER-localized auxin transporters involving intracellular auxin retention and switch-like release from the ER. The proposed model integrates feedback circuits utilizing the conserved nuclear auxin signaling for the regulation of PIN transcription and a hypothetical ER-based signaling for the regulation of PIN-dependent transport activity at the ER. Computer simulations of the model revealed its plausibility for generating auxin channels and localized auxin maxima highlighting the possibility of this alternative mechanism for polar auxin transport."}],"title":"Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization","author":[{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","last_name":"Wabnik"},{"first_name":"Jürgen","full_name":"Kleine Vehn, Jürgen","last_name":"Kleine Vehn"},{"first_name":"Willy","last_name":"Govaerts","full_name":"Govaerts, Willy"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"publist_id":"3604","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T07:41:01Z","citation":{"short":"K.T. Wabnik, J. Kleine Vehn, W. Govaerts, J. Friml, Trends in Plant Science 16 (2011) 468–475.","ieee":"K. T. Wabnik, J. Kleine Vehn, W. Govaerts, and J. Friml, “Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization,” Trends in Plant Science, vol. 16, no. 9. Cell Press, pp. 468–475, 2011.","apa":"Wabnik, K. T., Kleine Vehn, J., Govaerts, W., & Friml, J. (2011). Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2011.05.002","ama":"Wabnik KT, Kleine Vehn J, Govaerts W, Friml J. Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization. Trends in Plant Science. 2011;16(9):468-475. doi:10.1016/j.tplants.2011.05.002","mla":"Wabnik, Krzysztof T., et al. “Prototype Cell-to-Cell Auxin Transport Mechanism by Intracellular Auxin Compartmentalization.” Trends in Plant Science, vol. 16, no. 9, Cell Press, 2011, pp. 468–75, doi:10.1016/j.tplants.2011.05.002.","ista":"Wabnik KT, Kleine Vehn J, Govaerts W, Friml J. 2011. Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization. Trends in Plant Science. 16(9), 468–475.","chicago":"Wabnik, Krzysztof T, Jürgen Kleine Vehn, Willy Govaerts, and Jiří Friml. “Prototype Cell-to-Cell Auxin Transport Mechanism by Intracellular Auxin Compartmentalization.” Trends in Plant Science. Cell Press, 2011. https://doi.org/10.1016/j.tplants.2011.05.002."},"status":"public","type":"journal_article","_id":"3096"},{"day":"08","publication":"Journal of Neuroscience","publication_status":"published","year":"2011","volume":31,"doi":"10.1523/JNEUROSCI.0294-11.2011","issue":"23","date_published":"2011-06-08T00:00:00Z","date_created":"2018-12-11T12:01:36Z","page":"8605 - 8616","abstract":[{"text":"Hippocampal sharp waves (SPWs) and associated fast ("ripple") oscillations (SPW-Rs) in the CA1 region are among the most synchronous physiological patterns in the mammalian brain. Using two-dimensional arrays of electrodes for recording local field potentials and unit discharges in freely moving rats, we studied the emergence of ripple oscillations (140-220 Hz) and compared their origin and cellular-synaptic mechanisms with fast gamma oscillations (90-140 Hz). We show that (1) hippocampal SPW-Rs and fast gamma oscillations are quantitatively distinct patterns but involve the same networks and share similar mechanisms; (2) both the frequency and magnitude of fast oscillations are positively correlated with the magnitude of SPWs; (3) during both ripples and fast gamma oscillations the frequency of network oscillation is higher in CA1 than in CA3; and (4) the emergence of CA3 population bursts, a prerequisite for SPW-Rs, is biased by activity patterns in the dentate gyrus and entorhinal cortex, with the highest probability of ripples associated with an "optimum" level of dentate gamma power. We hypothesize that each hippocampal subnetwork possesses distinct resonant properties, tuned by the magnitude of the excitatory drive.","lang":"eng"}],"month":"06","intvolume":" 31","quality_controlled":0,"publisher":"Society for Neuroscience","extern":1,"citation":{"short":"D. Sullivan, J.L. Csicsvari, K. Mizuseki, S. Montgomery, K. Diba, G. Buzsáki, Journal of Neuroscience 31 (2011) 8605–8616.","ieee":"D. Sullivan, J. L. Csicsvari, K. Mizuseki, S. Montgomery, K. Diba, and G. Buzsáki, “Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity,” Journal of Neuroscience, vol. 31, no. 23. Society for Neuroscience, pp. 8605–8616, 2011.","apa":"Sullivan, D., Csicsvari, J. L., Mizuseki, K., Montgomery, S., Diba, K., & Buzsáki, G. (2011). Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0294-11.2011","ama":"Sullivan D, Csicsvari JL, Mizuseki K, Montgomery S, Diba K, Buzsáki G. Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity. Journal of Neuroscience. 2011;31(23):8605-8616. doi:10.1523/JNEUROSCI.0294-11.2011","mla":"Sullivan, David, et al. “Relationships between Hippocampal Sharp Waves Ripples and Fast Gamma Oscillation Influence of Dentate and Entorhinal Cortical Activity.” Journal of Neuroscience, vol. 31, no. 23, Society for Neuroscience, 2011, pp. 8605–16, doi:10.1523/JNEUROSCI.0294-11.2011.","ista":"Sullivan D, Csicsvari JL, Mizuseki K, Montgomery S, Diba K, Buzsáki G. 2011. Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity. Journal of Neuroscience. 31(23), 8605–8616.","chicago":"Sullivan, David, Jozsef L Csicsvari, Kenji Mizuseki, Sean Montgomery, Kamran Diba, and György Buzsáki. “Relationships between Hippocampal Sharp Waves Ripples and Fast Gamma Oscillation Influence of Dentate and Entorhinal Cortical Activity.” Journal of Neuroscience. Society for Neuroscience, 2011. https://doi.org/10.1523/JNEUROSCI.0294-11.2011."},"date_updated":"2021-01-12T07:41:19Z","title":"Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity","publist_id":"3559","author":[{"first_name":"David","last_name":"Sullivan","full_name":"Sullivan, David W"},{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Jozsef Csicsvari","orcid":"0000-0002-5193-4036"},{"first_name":"Kenji","last_name":"Mizuseki","full_name":"Mizuseki, Kenji"},{"first_name":"Sean","last_name":"Montgomery","full_name":"Montgomery, Sean M"},{"full_name":"Diba, Kamran","last_name":"Diba","first_name":"Kamran"},{"full_name":"Buzsáki, György","last_name":"Buzsáki","first_name":"György"}],"_id":"3138","status":"public","type":"journal_article"},{"month":"05","intvolume":" 108","quality_controlled":0,"publisher":"National Academy of Sciences","abstract":[{"text":"Microinjection of recombinant DNA into zygotic pronuclei has been widely used for producing transgenic mice. However, with this method, the insertion site, integrity, and copy number of the transgene cannot be controlled. Here, we present an integrase-based approach to produce transgenic mice via pronuclear injection, whereby an intact single-copy transgene can be inserted into predetermined chromosomal loci with high efficiency (up to 40%), and faithfully transmitted through generations. We show that neighboring transgenic elements and bacterial DNA within the transgene cause profound silencing and expression variability of the transgenic marker. Removal of these undesirable elements leads to global high-level marker expression from transgenes driven by a ubiquitous promoter. We also obtained faithful marker expression from a tissue-specific promoter. The technique presented here will greatly facilitate murine transgenesis and precise structure/function dissection of mammalian gene function and regulation in vivo.","lang":"eng"}],"volume":108,"issue":"19","date_published":"2011-05-10T00:00:00Z","doi":"10.1073/pnas.1019507108","date_created":"2018-12-11T12:01:39Z","page":"7902 - 7907","day":"10","publication":"PNAS","publication_status":"published","year":"2011","status":"public","type":"journal_article","_id":"3145","title":"Site specific integrase mediated transgenesis in mice via pronuclear injection","author":[{"first_name":"Bosiljka","full_name":"Tasic, Bosiljka","last_name":"Tasic"},{"last_name":"Hippenmeyer","full_name":"Simon Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wang, Charlene","last_name":"Wang","first_name":"Charlene"},{"last_name":"Gamboa","full_name":"Gamboa, Matthew","first_name":"Matthew"},{"first_name":"Hui","full_name":"Zong, Hui","last_name":"Zong"},{"full_name":"Chen-Tsai, Yanru","last_name":"Chen Tsai","first_name":"Yanru"},{"last_name":"Luo","full_name":"Luo, Liqun","first_name":"Liqun"}],"publist_id":"3549","extern":1,"date_updated":"2021-01-12T07:41:22Z","citation":{"chicago":"Tasic, Bosiljka, Simon Hippenmeyer, Charlene Wang, Matthew Gamboa, Hui Zong, Yanru Chen Tsai, and Liqun Luo. “Site Specific Integrase Mediated Transgenesis in Mice via Pronuclear Injection.” PNAS. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1019507108.","ista":"Tasic B, Hippenmeyer S, Wang C, Gamboa M, Zong H, Chen Tsai Y, Luo L. 2011. Site specific integrase mediated transgenesis in mice via pronuclear injection. PNAS. 108(19), 7902–7907.","mla":"Tasic, Bosiljka, et al. “Site Specific Integrase Mediated Transgenesis in Mice via Pronuclear Injection.” PNAS, vol. 108, no. 19, National Academy of Sciences, 2011, pp. 7902–07, doi:10.1073/pnas.1019507108.","ama":"Tasic B, Hippenmeyer S, Wang C, et al. Site specific integrase mediated transgenesis in mice via pronuclear injection. PNAS. 2011;108(19):7902-7907. doi:10.1073/pnas.1019507108","apa":"Tasic, B., Hippenmeyer, S., Wang, C., Gamboa, M., Zong, H., Chen Tsai, Y., & Luo, L. (2011). Site specific integrase mediated transgenesis in mice via pronuclear injection. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1019507108","short":"B. Tasic, S. Hippenmeyer, C. Wang, M. Gamboa, H. Zong, Y. Chen Tsai, L. Luo, PNAS 108 (2011) 7902–7907.","ieee":"B. Tasic et al., “Site specific integrase mediated transgenesis in mice via pronuclear injection,” PNAS, vol. 108, no. 19. National Academy of Sciences, pp. 7902–7907, 2011."}},{"title":"Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion","author":[{"full_name":"DeGennaro, Matthew","last_name":"Degennaro","first_name":"Matthew"},{"first_name":"Thomas","full_name":"Hurd, Thomas R","last_name":"Hurd"},{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","full_name":"Daria Siekhaus","orcid":"0000-0001-8323-8353"},{"first_name":"Benoit","last_name":"Biteau","full_name":"Biteau, Benoit"},{"first_name":"Heinrich","full_name":"Jasper, Heinrich","last_name":"Jasper"},{"first_name":"Ruth","last_name":"Lehmann","full_name":"Lehmann, Ruth"}],"publist_id":"3541","extern":1,"date_updated":"2021-01-12T07:41:26Z","citation":{"chicago":"Degennaro, Matthew, Thomas Hurd, Daria E Siekhaus, Benoit Biteau, Heinrich Jasper, and Ruth Lehmann. “Peroxiredoxin Stabilization of DE-Cadherin Promotes Primordial Germ Cell Adhesion.” Developmental Cell. Cell Press, 2011. https://doi.org/10.1016/j.devcel.2010.12.007.","ista":"Degennaro M, Hurd T, Siekhaus DE, Biteau B, Jasper H, Lehmann R. 2011. Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion. Developmental Cell. 20(2), 233–243.","mla":"Degennaro, Matthew, et al. “Peroxiredoxin Stabilization of DE-Cadherin Promotes Primordial Germ Cell Adhesion.” Developmental Cell, vol. 20, no. 2, Cell Press, 2011, pp. 233–43, doi:10.1016/j.devcel.2010.12.007.","short":"M. Degennaro, T. Hurd, D.E. Siekhaus, B. Biteau, H. Jasper, R. Lehmann, Developmental Cell 20 (2011) 233–243.","ieee":"M. Degennaro, T. Hurd, D. E. Siekhaus, B. Biteau, H. Jasper, and R. Lehmann, “Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion,” Developmental Cell, vol. 20, no. 2. Cell Press, pp. 233–243, 2011.","ama":"Degennaro M, Hurd T, Siekhaus DE, Biteau B, Jasper H, Lehmann R. Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion. Developmental Cell. 2011;20(2):233-243. doi:10.1016/j.devcel.2010.12.007","apa":"Degennaro, M., Hurd, T., Siekhaus, D. E., Biteau, B., Jasper, H., & Lehmann, R. (2011). Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2010.12.007"},"status":"public","type":"journal_article","_id":"3154","date_created":"2018-12-11T12:01:42Z","volume":20,"issue":"2","doi":"10.1016/j.devcel.2010.12.007","date_published":"2011-02-15T00:00:00Z","page":"233 - 243","publication":"Developmental Cell","day":"15","year":"2011","publication_status":"published","intvolume":" 20","month":"02","quality_controlled":0,"publisher":"Cell Press","abstract":[{"lang":"eng","text":"Regulated adhesion between cells and their environment is critical for normal cell migration. We have identified mutations in a gene encoding the Drosophila hydrogen peroxide (H2O2)-degrading enzyme Jafrac1, which lead to germ cell adhesion defects. During gastrulation, primordial germ cells (PGCs) associate tightly with the invaginating midgut primordium as it enters the embryo; however, in embryos from jafrac1 mutant mothers this association is disrupted, leaving some PGCs trailing on the outside of the embryo. We observed similar phenotypes in embryos from DE-cadherin/shotgun (shg) mutant mothers and were able to rescue the jafrac1 phenotype by increasing DE-cadherin levels. This and our biochemical evidence strongly suggest that Jafrac1-mediated reduction of H2O2 is required to maintain DE-cadherin protein levels in the early embryo. Our results present in vivo evidence of a peroxiredoxin regulating DE-cadherin-mediated adhesion."}]},{"_id":"3239","status":"public","conference":{"name":"ICALP: Automata, Languages and Programming"},"type":"conference","extern":1,"citation":{"chicago":"Faust, Sebastian, Krzysztof Z Pietrzak, and Daniele Venturi. “Tamper Proof Circuits How to Trade Leakage for Tamper Resilience,” 6755:391–402. Springer, 2011. https://doi.org/10.1007/978-3-642-22006-7_33.","ista":"Faust S, Pietrzak KZ, Venturi D. 2011. Tamper proof circuits How to trade leakage for tamper resilience. ICALP: Automata, Languages and Programming, LNCS, vol. 6755, 391–402.","mla":"Faust, Sebastian, et al. Tamper Proof Circuits How to Trade Leakage for Tamper Resilience. Vol. 6755, no. Part 1, Springer, 2011, pp. 391–402, doi:10.1007/978-3-642-22006-7_33.","ama":"Faust S, Pietrzak KZ, Venturi D. Tamper proof circuits How to trade leakage for tamper resilience. In: Vol 6755. Springer; 2011:391-402. doi:10.1007/978-3-642-22006-7_33","apa":"Faust, S., Pietrzak, K. Z., & Venturi, D. (2011). Tamper proof circuits How to trade leakage for tamper resilience (Vol. 6755, pp. 391–402). Presented at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/978-3-642-22006-7_33","ieee":"S. Faust, K. Z. Pietrzak, and D. Venturi, “Tamper proof circuits How to trade leakage for tamper resilience,” presented at the ICALP: Automata, Languages and Programming, 2011, vol. 6755, no. Part 1, pp. 391–402.","short":"S. Faust, K.Z. Pietrzak, D. Venturi, in:, Springer, 2011, pp. 391–402."},"date_updated":"2021-01-12T07:42:02Z","title":"Tamper proof circuits How to trade leakage for tamper resilience","publist_id":"3441","author":[{"last_name":"Faust","full_name":"Faust, Sebastian","first_name":"Sebastian"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Krzysztof Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"first_name":"Daniele","last_name":"Venturi","full_name":"Venturi, Daniele"}],"abstract":[{"lang":"eng","text":"Tampering attacks are cryptanalytic attacks on the implementation of cryptographic algorithms (e.g., smart cards), where an adversary introduces faults with the hope that the tampered device will reveal secret information. Inspired by the work of Ishai et al. [Eurocrypt'06], we propose a compiler that transforms any circuit into a new circuit with the same functionality, but which is resilient against a well-defined and powerful tampering adversary. More concretely, our transformed circuits remain secure even if the adversary can adaptively tamper with every wire in the circuit as long as the tampering fails with some probability δ>0. This additional requirement is motivated by practical tampering attacks, where it is often difficult to guarantee the success of a specific attack. Formally, we show that a q-query tampering attack against the transformed circuit can be "simulated" with only black-box access to the original circuit and log(q) bits of additional auxiliary information. Thus, if the implemented cryptographic scheme is secure against log(q) bits of leakage, then our implementation is tamper-proof in the above sense. Surprisingly, allowing for this small amount of information leakage allows for much more efficient compilers, which moreover do not require randomness during evaluation. Similar to earlier works our compiler requires small, stateless and computation-independent tamper-proof gadgets. Thus, our result can be interpreted as reducing the problem of shielding arbitrary complex computation to protecting simple components. © 2011 Springer-Verlag."}],"month":"01","alternative_title":["LNCS"],"publisher":"Springer","quality_controlled":0,"day":"01","year":"2011","publication_status":"published","date_created":"2018-12-11T12:02:12Z","date_published":"2011-01-01T00:00:00Z","issue":"Part 1","volume":"6755 ","doi":"10.1007/978-3-642-22006-7_33","page":"391 - 402"},{"date_updated":"2021-01-12T07:42:00Z","citation":{"chicago":"Jain, Abhishek, and Krzysztof Z Pietrzak. “Parallel Repetition for Leakage Resilience Amplification Revisited,” 6597:58–69. Springer, 2011. https://doi.org/10.1007/978-3-642-19571-6_5.","ista":"Jain A, Pietrzak KZ. 2011. Parallel repetition for leakage resilience amplification revisited. TCC: Theory of Cryptography Conference, LNCS, vol. 6597, 58–69.","mla":"Jain, Abhishek, and Krzysztof Z. Pietrzak. Parallel Repetition for Leakage Resilience Amplification Revisited. Vol. 6597, Springer, 2011, pp. 58–69, doi:10.1007/978-3-642-19571-6_5.","ieee":"A. Jain and K. Z. Pietrzak, “Parallel repetition for leakage resilience amplification revisited,” presented at the TCC: Theory of Cryptography Conference, 2011, vol. 6597, pp. 58–69.","short":"A. Jain, K.Z. Pietrzak, in:, Springer, 2011, pp. 58–69.","apa":"Jain, A., & Pietrzak, K. Z. (2011). Parallel repetition for leakage resilience amplification revisited (Vol. 6597, pp. 58–69). Presented at the TCC: Theory of Cryptography Conference, Springer. https://doi.org/10.1007/978-3-642-19571-6_5","ama":"Jain A, Pietrzak KZ. Parallel repetition for leakage resilience amplification revisited. In: Vol 6597. Springer; 2011:58-69. doi:10.1007/978-3-642-19571-6_5"},"extern":1,"publist_id":"3443","author":[{"full_name":"Jain, Abhishek","last_name":"Jain","first_name":"Abhishek"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Krzysztof Pietrzak","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"}],"title":"Parallel repetition for leakage resilience amplification revisited","_id":"3236","conference":{"name":"TCC: Theory of Cryptography Conference"},"type":"conference","status":"public","year":"2011","publication_status":"published","day":"01","page":"58 - 69","date_created":"2018-12-11T12:02:11Z","doi":"10.1007/978-3-642-19571-6_5","volume":"6597 ","date_published":"2011-01-01T00:00:00Z","abstract":[{"text":"If a cryptographic primitive remains secure even if ℓ bits about the secret key are leaked to the adversary, one would expect that at least one of n independent instantiations of the scheme remains secure given n·ℓ bits of leakage. This intuition has been proven true for schemes satisfying some special information-theoretic properties by Alwen et al. [Eurocrypt'10]. On the negative side, Lewko and Waters [FOCS'10] construct a CPA secure public-key encryption scheme for which this intuition fails. The counterexample of Lewko and Waters leaves open the interesting possibility that for any scheme there exists a constant c>0, such that n fold repetition remains secure against c·n·ℓ bits of leakage. Furthermore, their counterexample requires the n copies of the encryption scheme to share a common reference parameter, leaving open the possibility that the intuition is true for all schemes without common setup. In this work we give a stronger counterexample ruling out these possibilities. We construct a signature scheme such that: 1. a single instantiation remains secure given ℓ = log(k) bits of leakage where k is a security parameter. 2. any polynomial number of independent instantiations can be broken (in the strongest sense of key-recovery) given ℓ′ = poly(k) bits of leakage. Note that ℓ does not depend on the number of instances. The computational assumption underlying our counterexample is that non-interactive computationally sound proofs exist. Moreover, under a stronger (non-standard) assumption about such proofs, our counterexample does not require a common reference parameter. The underlying idea of our counterexample is rather generic and can be applied to other primitives like encryption schemes. © 2011 International Association for Cryptologic Research.","lang":"eng"}],"publisher":"Springer","quality_controlled":0,"alternative_title":["LNCS"],"month":"01"},{"day":"20","file":[{"file_name":"IST-2015-381-v1+1_journal.pone.0019884.pdf","date_created":"2018-12-12T10:11:38Z","creator":"system","file_size":885464,"date_updated":"2020-07-14T12:46:06Z","checksum":"654464e99683b55a699734213d5356f1","file_id":"4894","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication":"PLoS One","publication_status":"published","year":"2011","date_published":"2011-07-20T00:00:00Z","volume":6,"issue":"7","doi":"10.1371/journal.pone.0019884","date_created":"2018-12-11T12:02:24Z","acknowledgement":"This work was supported by National Science Foundation (NSF) grants IBN-0344678, EF-0928048, National Institutes of Health (NIH) grant RO1 EY08124, NIH training grant T32-07035, and NIH training grant 5T90DA022763-04.\n\nMichael Berry and Olivier Marre have developed an algorithm similar to, but different from, ours (manuscript in preparation). We thank them for discussions of their work, and specifically thank Olivier Marre for suggesting to us that the most complete subtraction of a spike can be obtained by refitting the spike without a prior.\n\n","abstract":[{"lang":"eng","text":"We present an algorithm to identify individual neural spikes observed on high-density multi-electrode arrays (MEAs). Our method can distinguish large numbers of distinct neural units, even when spikes overlap, and accounts for intrinsic variability of spikes from each unit. As MEAs grow larger, it is important to find spike-identification methods that are scalable, that is, the computational cost of spike fitting should scale well with the number of units observed. Our algorithm accomplishes this goal, and is fast, because it exploits the spatial locality of each unit and the basic biophysics of extracellular signal propagation. Human interaction plays a key role in our method; but effort is minimized and streamlined via a graphical interface. We illustrate our method on data from guinea pig retinal ganglion cells and document its performance on simulated data consisting of spikes added to experimentally measured background noise. We present several tests demonstrating that the algorithm is highly accurate: it exhibits low error rates on fits to synthetic data, low refractory violation rates, good receptive field coverage, and consistency across users."}],"month":"07","intvolume":" 6","quality_controlled":0,"publisher":"Public Library of Science","oa":1,"extern":1,"citation":{"ama":"Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One. 2011;6(7). doi:10.1371/journal.pone.0019884","apa":"Prentice, J., Homann, J., Simmons, K., Tkačik, G., Balasubramanian, V., & Nelson, P. (2011). Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0019884","short":"J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, P. Nelson, PLoS One 6 (2011).","ieee":"J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, and P. Nelson, “Fast, scalable, Bayesian spike identification for multi-electrode arrays,” PLoS One, vol. 6, no. 7. Public Library of Science, 2011.","mla":"Prentice, Jason, et al. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” PLoS One, vol. 6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0019884.","ista":"Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. 2011. Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One. 6(7).","chicago":"Prentice, Jason, Jan Homann, Kristina Simmons, Gašper Tkačik, Vijay Balasubramanian, and Philip Nelson. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0019884."},"date_updated":"2021-01-12T07:42:19Z","title":"Fast, scalable, Bayesian spike identification for multi-electrode arrays","file_date_updated":"2020-07-14T12:46:06Z","author":[{"first_name":"Jason","full_name":"Prentice, Jason S","last_name":"Prentice"},{"last_name":"Homann","full_name":"Homann, Jan","first_name":"Jan"},{"first_name":"Kristina","full_name":"Simmons, Kristina D","last_name":"Simmons"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Gasper Tkacik"},{"first_name":"Vijay","full_name":"Balasubramanian, Vijay","last_name":"Balasubramanian"},{"full_name":"Nelson, Philip C","last_name":"Nelson","first_name":"Philip"}],"publist_id":"3370","_id":"3276","status":"public","pubrep_id":"381","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Wagner, Hubert, Chao Chen, and Erald Vuçini. “Efficient Computation of Persistent Homology for Cubical Data.” In Topological Methods in Data Analysis and Visualization II, edited by Ronald Peikert, Helwig Hauser, Hamish Carr, and Raphael Fuchs, 91–106. Springer, 2011. https://doi.org/10.1007/978-3-642-23175-9_7.","ista":"Wagner H, Chen C, Vuçini E. 2011.Efficient computation of persistent homology for cubical data. In: Topological Methods in Data Analysis and Visualization II. Theory, Algorithms, and Applications, , 91–106.","mla":"Wagner, Hubert, et al. “Efficient Computation of Persistent Homology for Cubical Data.” Topological Methods in Data Analysis and Visualization II, edited by Ronald Peikert et al., Springer, 2011, pp. 91–106, doi:10.1007/978-3-642-23175-9_7.","ieee":"H. Wagner, C. Chen, and E. Vuçini, “Efficient computation of persistent homology for cubical data,” in Topological Methods in Data Analysis and Visualization II, R. Peikert, H. Hauser, H. Carr, and R. Fuchs, Eds. Springer, 2011, pp. 91–106.","short":"H. Wagner, C. Chen, E. Vuçini, in:, R. Peikert, H. Hauser, H. Carr, R. Fuchs (Eds.), Topological Methods in Data Analysis and Visualization II, Springer, 2011, pp. 91–106.","apa":"Wagner, H., Chen, C., & Vuçini, E. (2011). Efficient computation of persistent homology for cubical data. In R. Peikert, H. Hauser, H. Carr, & R. Fuchs (Eds.), Topological Methods in Data Analysis and Visualization II (pp. 91–106). Springer. https://doi.org/10.1007/978-3-642-23175-9_7","ama":"Wagner H, Chen C, Vuçini E. Efficient computation of persistent homology for cubical data. In: Peikert R, Hauser H, Carr H, Fuchs R, eds. Topological Methods in Data Analysis and Visualization II. Springer; 2011:91-106. doi:10.1007/978-3-642-23175-9_7"},"date_updated":"2021-01-12T07:42:18Z","department":[{"_id":"HeEd"}],"title":"Efficient computation of persistent homology for cubical data","editor":[{"first_name":"Ronald","full_name":"Peikert, Ronald","last_name":"Peikert"},{"full_name":"Hauser, Helwig","last_name":"Hauser","first_name":"Helwig"},{"first_name":"Hamish","last_name":"Carr","full_name":"Carr, Hamish"},{"last_name":"Fuchs","full_name":"Fuchs, Raphael","first_name":"Raphael"}],"publist_id":"3375","author":[{"full_name":"Wagner, Hubert","last_name":"Wagner","first_name":"Hubert"},{"full_name":"Chen, Chao","last_name":"Chen","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vuçini, Erald","last_name":"Vuçini","first_name":"Erald"}],"_id":"3271","status":"public","type":"book_chapter","day":"14","language":[{"iso":"eng"}],"publication":"Topological Methods in Data Analysis and Visualization II","year":"2011","publication_status":"published","doi":"10.1007/978-3-642-23175-9_7","date_published":"2011-11-14T00:00:00Z","date_created":"2018-12-11T12:02:23Z","page":"91 - 106","oa_version":"None","abstract":[{"lang":"eng","text":"In this paper we present an efficient framework for computation of persis- tent homology of cubical data in arbitrary dimensions. An existing algorithm using simplicial complexes is adapted to the setting of cubical complexes. The proposed approach enables efficient application of persistent homology in domains where the data is naturally given in a cubical form. By avoiding triangulation of the data, we significantly reduce the size of the complex. We also present a data-structure de- signed to compactly store and quickly manipulate cubical complexes. By means of numerical experiments, we show high speed and memory efficiency of our ap- proach. We compare our framework to other available implementations, showing its superiority. Finally, we report performance on selected 3D and 4D data-sets."}],"month":"11","quality_controlled":"1","publisher":"Springer","scopus_import":1,"alternative_title":["Theory, Algorithms, and Applications"]},{"status":"public","type":"journal_article","_id":"3278","title":"A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade","author":[{"last_name":"Vila","full_name":"Vila, Roger","first_name":"Roger"},{"full_name":"Pierce, Naomi E","last_name":"Pierce","first_name":"Naomi"},{"last_name":"Nash","full_name":"Nash, David R","first_name":"David"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V","orcid":"0000-0003-1832-8883","full_name":"Line Ugelvig","last_name":"Ugelvig"}],"publist_id":"3368","extern":1,"date_updated":"2021-01-12T07:42:20Z","citation":{"mla":"Vila, Roger, et al. “A Phylogenetic Revision of the Glaucopsyche Section (Lepidoptera: Lycaenidae), with Special Focus on the Phengaris-Maculinea Clade.” Molecular Phylogenetics and Evolution, vol. 61, no. 1, Elsevier, 2011, pp. 237–43, doi:10.1016/j.ympev.2011.05.016.","ieee":"R. Vila, N. Pierce, D. Nash, and L. V. Ugelvig, “A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade,” Molecular Phylogenetics and Evolution, vol. 61, no. 1. Elsevier, pp. 237–243, 2011.","short":"R. Vila, N. Pierce, D. Nash, L.V. Ugelvig, Molecular Phylogenetics and Evolution 61 (2011) 237–243.","ama":"Vila R, Pierce N, Nash D, Ugelvig LV. A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. Molecular Phylogenetics and Evolution. 2011;61(1):237-243. doi:10.1016/j.ympev.2011.05.016","apa":"Vila, R., Pierce, N., Nash, D., & Ugelvig, L. V. (2011). A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. Molecular Phylogenetics and Evolution. Elsevier. https://doi.org/10.1016/j.ympev.2011.05.016","chicago":"Vila, Roger, Naomi Pierce, David Nash, and Line V Ugelvig. “A Phylogenetic Revision of the Glaucopsyche Section (Lepidoptera: Lycaenidae), with Special Focus on the Phengaris-Maculinea Clade.” Molecular Phylogenetics and Evolution. Elsevier, 2011. https://doi.org/10.1016/j.ympev.2011.05.016.","ista":"Vila R, Pierce N, Nash D, Ugelvig LV. 2011. A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. Molecular Phylogenetics and Evolution. 61(1), 237–243."},"month":"10","intvolume":" 61","quality_controlled":0,"publisher":"Elsevier","abstract":[{"lang":"eng","text":"Despite much research on the socially parasitic large blue butterflies (genus Maculinea) in the past 40 years, their relationship to their closest relatives, Phengaris, is controversial and the relationships among the remaining genera in the Glaucopsyche section are largely unresolved. The evolutionary history of this butterfly section is particularly important to understand the evolution of life history diversity con- nected to food-plant and host-ant associations in the larval stage. In the present study, we use a combi- nation of four nuclear and two mitochondrial genes to reconstruct the phylogeny of the Glaucopsyche section, and in particular, to study the relationships among and within the Phengaris–Maculinea species.\nWe find a clear pattern between the clades recovered in the Glaucopsyche section phylogeny and their food-plant associations, with only the Phengaris–Maculinea clade utilising more than one plant family. Maculinea is, for the first time, recovered with strong support as a monophyletic group nested within Phengaris, with the closest relative being the rare genus Caerulea. The genus Glaucopsyche is polyphyletic, including the genera Sinia and Iolana. Interestingly, we find evidence for additional potential cryptic spe- cies within the highly endangered Maculinea, which has long been suspected from morphological, ecolog- ical and molecular studies."}],"date_published":"2011-10-01T00:00:00Z","issue":"1","volume":61,"doi":"10.1016/j.ympev.2011.05.016","date_created":"2018-12-11T12:02:25Z","page":"237 - 243","day":"01","publication":"Molecular Phylogenetics and Evolution","year":"2011","publication_status":"published"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chen C, Kerber M. 2011. Persistent homology computation with a twist. EuroCG: European Workshop on Computational Geometry, 197–200.","chicago":"Chen, Chao, and Michael Kerber. “Persistent Homology Computation with a Twist,” 197–200. TU Dortmund, 2011.","ama":"Chen C, Kerber M. Persistent homology computation with a twist. In: TU Dortmund; 2011:197-200.","apa":"Chen, C., & Kerber, M. (2011). Persistent homology computation with a twist (pp. 197–200). Presented at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland: TU Dortmund.","short":"C. Chen, M. Kerber, in:, TU Dortmund, 2011, pp. 197–200.","ieee":"C. Chen and M. Kerber, “Persistent homology computation with a twist,” presented at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland, 2011, pp. 197–200.","mla":"Chen, Chao, and Michael Kerber. Persistent Homology Computation with a Twist. TU Dortmund, 2011, pp. 197–200."},"date_updated":"2021-01-12T07:42:17Z","title":"Persistent homology computation with a twist","department":[{"_id":"HeEd"}],"author":[{"first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Chao"},{"last_name":"Kerber","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"}],"publist_id":"3376","_id":"3270","status":"public","conference":{"end_date":"2011-03-30","location":"Morschach, Switzerland","start_date":"2011-03-28","name":"EuroCG: European Workshop on Computational Geometry"},"type":"conference","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2011","date_created":"2018-12-11T12:02:22Z","date_published":"2011-01-01T00:00:00Z","page":"197 - 200","oa_version":"None","abstract":[{"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.","lang":"eng"}],"month":"01","quality_controlled":"1","publisher":"TU Dortmund"},{"ddc":["000"],"date_updated":"2023-02-23T11:21:05Z","file_date_updated":"2020-07-14T12:46:06Z","department":[{"_id":"ChWo"}],"_id":"3298","pubrep_id":"598","status":"public","conference":{"name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","start_date":"2011-08-05","location":"Vancouver, Canada","end_date":"2011-08-07"},"type":"conference","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"6579d27709946e0eefbfa60a456b4913","file_id":"4769","creator":"system","file_size":2536216,"date_updated":"2020-07-14T12:46:06Z","file_name":"IST-2016-598-v1+1_HybridSPH_Preprint.pdf","date_created":"2018-12-12T10:09:44Z"}],"publication_status":"published","oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"month":"08","scopus_import":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Raveendran K, Wojtan C, Turk G. 2011. Hybrid smoothed particle hydrodynamics. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 33–42.","mla":"Raveendran, Karthik, et al. Hybrid Smoothed Particle Hydrodynamics. Edited by Stephen Spencer, ACM, 2011, pp. 33–42, doi:10.1145/2019406.2019411.","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","ama":"Raveendran K, Wojtan C, Turk G. Hybrid smoothed particle hydrodynamics. In: Spencer S, ed. ACM; 2011:33-42. doi:10.1145/2019406.2019411","short":"K. Raveendran, C. Wojtan, G. Turk, in:, S. Spencer (Ed.), ACM, 2011, pp. 33–42.","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."},"editor":[{"first_name":"Stephen","full_name":"Spencer, Stephen","last_name":"Spencer"}],"title":"Hybrid smoothed particle hydrodynamics","author":[{"full_name":"Raveendran, Karthik","last_name":"Raveendran","first_name":"Karthik"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"},{"first_name":"Greg","full_name":"Turk, Greg","last_name":"Turk"}],"publist_id":"3343","day":"05","year":"2011","has_accepted_license":"1","date_created":"2018-12-11T12:02:32Z","doi":"10.1145/2019406.2019411","date_published":"2011-08-05T00:00:00Z","page":"33 - 42","oa":1,"publisher":"ACM","quality_controlled":"1"},{"article_number":"8","title":"Liquid simulation with mesh-based surface tracking","publist_id":"3344","author":[{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","full_name":"Müller Fischer, Matthias","last_name":"Müller Fischer"},{"full_name":"Brochu, Tyson","last_name":"Brochu","first_name":"Tyson"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Wojtan C, Müller Fischer M, Brochu T. 2011. Liquid simulation with mesh-based surface tracking. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, 8.","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.","short":"C. Wojtan, M. Müller Fischer, T. Brochu, in:, ACM, 2011.","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. Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Vancouver, BC, Canada: ACM. https://doi.org/10.1145/2037636.2037644","ama":"Wojtan C, Müller Fischer M, Brochu T. Liquid simulation with mesh-based surface tracking. In: ACM; 2011. doi:10.1145/2037636.2037644","mla":"Wojtan, Chris, et al. Liquid Simulation with Mesh-Based Surface Tracking. 8, ACM, 2011, doi:10.1145/2037636.2037644."},"oa":1,"quality_controlled":"1","publisher":"ACM","date_created":"2018-12-11T12:02:31Z","date_published":"2011-08-07T00:00:00Z","doi":"10.1145/2037636.2037644","day":"07","year":"2011","has_accepted_license":"1","pubrep_id":"599","status":"public","conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","start_date":"2011-08-07","end_date":"2011-08-11","location":"Vancouver, BC, Canada"},"type":"conference","_id":"3297","department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:46:06Z","ddc":["000"],"date_updated":"2023-02-23T11:21:02Z","month":"08","scopus_import":1,"oa_version":"Published Version","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."}],"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:13:34Z","file_name":"IST-2016-599-v1+1_meshyFluidsCourseSIGGRAPH2011.pdf","creator":"system","date_updated":"2020-07-14T12:46:06Z","file_size":34672096,"file_id":"5018","checksum":"8d508ad7c82f50978acbaa4170ee0a75","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published"},{"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/"}],"scopus_import":1,"intvolume":" 189","month":"11","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."}],"oa_version":"Submitted Version","ec_funded":1,"volume":189,"issue":"3","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"3290","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:42:26Z","oa":1,"quality_controlled":"1","publisher":"Genetics Society of America","page":"977 - 987","date_created":"2018-12-11T12:02:29Z","doi":"10.1534/genetics.111.129569","date_published":"2011-11-01T00:00:00Z","year":"2011","publication":"Genetics","day":"01","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"author":[{"first_name":"Konrad","last_name":"Lohse","full_name":"Lohse, Konrad"},{"first_name":"Richard","full_name":"Harrison, Richard","last_name":"Harrison"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publist_id":"3355","title":"A general method for calculating likelihoods under the coalescent process","citation":{"short":"K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987.","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.","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","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.","ista":"Lohse K, Harrison R, Barton NH. 2011. A general method for calculating likelihoods under the coalescent process. Genetics. 189(3), 977–987.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"conference":{"end_date":"2011-11-13","location":"Barcelona, Spain","start_date":"2011-11-06","name":"ICCV: International Conference on Computer Vision"},"type":"conference_poster","pubrep_id":"541","status":"public","_id":"3312","file_date_updated":"2020-07-14T12:46:07Z","department":[{"_id":"HeEd"}],"date_updated":"2020-07-14T23:03:43Z","ddc":["000"],"month":"12","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."}],"oa_version":"Submitted Version","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:46:07Z","file_size":5622728,"creator":"system","date_created":"2018-12-12T10:09:04Z","file_name":"IST-2016-541-v1+1_2011-P-07-RootReconstruction.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"30a33564b7b45a7ee31610898267fd0e","file_id":"4727"}],"article_number":"6126475","article_processing_charge":"No","author":[{"full_name":"Zheng, Ying","last_name":"Zheng","first_name":"Ying"},{"last_name":"Gu","full_name":"Gu, Steve","first_name":"Steve"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"full_name":"Tomasi, Carlo","last_name":"Tomasi","first_name":"Carlo"},{"full_name":"Benfey, Philip","last_name":"Benfey","first_name":"Philip"}],"publist_id":"3328","title":"Detailed reconstruction of 3D plant root shape","citation":{"ieee":"Y. Zheng, S. Gu, H. Edelsbrunner, C. Tomasi, and P. Benfey, Detailed reconstruction of 3D plant root shape. IEEE, 2011.","short":"Y. Zheng, S. Gu, H. Edelsbrunner, C. Tomasi, P. Benfey, Detailed Reconstruction of 3D Plant Root Shape, IEEE, 2011.","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","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.","ista":"Zheng Y, Gu S, Edelsbrunner H, Tomasi C, Benfey P. 2011. Detailed reconstruction of 3D plant root shape, IEEE,p.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"IEEE","quality_controlled":"1","acknowledgement":"This research is supported by the National Science Foundation (NSF) under grant DBI-0820624.","date_created":"2018-12-11T12:02:36Z","date_published":"2011-12-31T00:00:00Z","doi":"10.1109/ICCV.2011.6126475","year":"2011","has_accepted_license":"1","publication":"Proceedings of the IEEE International Conference on Computer Vision","day":"31"},{"department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:46:07Z","ddc":["000"],"date_updated":"2021-01-12T07:42:35Z","status":"public","pubrep_id":"540","type":"conference","conference":{"start_date":"2011-11-06","end_date":"2011-11-13","location":"Barcelona, Spain","name":"ICCV: International Conference on Computer Vision"},"_id":"3313","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5282","checksum":"6984684081ba123808b344f9f2e64a8f","creator":"system","file_size":614050,"date_updated":"2020-07-14T12:46:07Z","file_name":"IST-2016-540-v1+1_2011-P-08-RunEmpty.pdf","date_created":"2018-12-12T10:17:28Z"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"11","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"title":"Diffusion runs low on persistence fast","publist_id":"3327","author":[{"last_name":"Chen","full_name":"Chen, Chao","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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.","short":"C. Chen, H. Edelsbrunner, in:, Proceedings of the IEEE International Conference on Computer Vision, IEEE, 2011.","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.","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."},"article_number":"6126271","date_published":"2011-11-06T00:00:00Z","doi":"10.1109/ICCV.2011.6126271","date_created":"2018-12-11T12:02:37Z","day":"06","publication":"Proceedings of the IEEE International Conference on Computer Vision","has_accepted_license":"1","year":"2011","publisher":"IEEE","quality_controlled":"1","oa":1},{"publisher":"Springer","quality_controlled":"1","oa":1,"month":"12","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"}],"oa_version":"Submitted Version","date_published":"2011-12-31T00:00:00Z","date_created":"2018-12-11T12:02:36Z","has_accepted_license":"1","year":"2011","publication_status":"inpress","day":"31","file":[{"file_name":"2010_AlphaShapes.pdf","date_created":"2022-05-24T07:55:05Z","file_size":475254,"date_updated":"2022-05-24T07:55:05Z","creator":"dernst","success":1,"file_id":"11408","checksum":"a592ea438351e7280eea993a7713ab8f","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication":"Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings","type":"book_chapter","status":"public","_id":"3311","author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"}],"publist_id":"3329","article_processing_charge":"No","department":[{"_id":"HeEd"}],"file_date_updated":"2022-05-24T07:55:05Z","title":"Alpha shapes - a survey","editor":[{"first_name":"R","full_name":"van de Weygaert, R","last_name":"van de Weygaert"},{"full_name":"Vegter, G","last_name":"Vegter","first_name":"G"},{"full_name":"Ritzerveld, J","last_name":"Ritzerveld","first_name":"J"},{"first_name":"V","last_name":"Icke","full_name":"Icke, V"}],"date_updated":"2022-05-24T07:56:30Z","citation":{"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.","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.","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.","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.","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.","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.","ista":"Edelsbrunner H.Alpha shapes - a survey. In: Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings. ."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510"]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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.","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","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","short":"S. Almagor, U. Boker, O. Kupferman, in:, Springer, 2011, pp. 482–491.","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."},"title":"What’s decidable about weighted automata ","article_processing_charge":"No","publist_id":"3309","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","full_name":"Kupferman, Orna","last_name":"Kupferman"}],"day":"14","year":"2011","has_accepted_license":"1","date_created":"2018-12-11T12:02:41Z","date_published":"2011-10-14T00:00:00Z","doi":"10.1007/978-3-642-24372-1_37","page":"482 - 491","oa":1,"publisher":"Springer","quality_controlled":"1","ddc":["000"],"date_updated":"2021-01-12T07:42:40Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:07Z","_id":"3326","status":"public","conference":{"end_date":"2011-10-14","location":"Taipei, Taiwan","start_date":"2011-10-11","name":"ATVA: Automated Technology for Verification and Analysis"},"type":"conference","language":[{"iso":"eng"}],"file":[{"file_size":182309,"date_updated":"2020-07-14T12:46:07Z","creator":"dernst","file_name":"2011_LNCS_Almagor.pdf","date_created":"2020-05-19T16:08:32Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7868","checksum":"a7ca08a2cb1b6925f4c18a3034ae5659"}],"publication_status":"published","volume":6996,"oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}],"intvolume":" 6996","month":"10","alternative_title":["LNCS"]},{"publication_status":"published","year":"2011","language":[{"iso":"eng"}],"day":"26","page":"599 - 610","date_created":"2018-12-11T12:02:41Z","volume":46,"doi":"10.1145/1926385.1926454","issue":"1","date_published":"2011-01-26T00:00:00Z","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"}],"oa_version":"None","scopus_import":"1","publisher":"ACM","quality_controlled":"1","intvolume":" 46","month":"01","citation":{"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.","short":"R. Alur, P. Cerny, in:, ACM, 2011, 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","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","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.","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."},"date_updated":"2022-03-21T08:12:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publist_id":"3310","author":[{"full_name":"Alur, Rajeev","last_name":"Alur","first_name":"Rajeev"},{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","last_name":"Cerny","full_name":"Cerny, Pavol"}],"department":[{"_id":"ToHe"}],"title":"Streaming transducers for algorithmic verification of single pass list processing programs","_id":"3325","conference":{"location":"Texas, USA","end_date":"2011-01-28","start_date":"2011-01-26","name":"POPL: Principles of Programming Languages"},"type":"conference","status":"public"},{"editor":[{"last_name":"Jhala","full_name":"Jhala, Ranjit","first_name":"Ranjit"},{"full_name":"Schmidt, David","last_name":"Schmidt","first_name":"David"}],"title":"Decision procedures for automating termination proofs","author":[{"first_name":"Ruzica","full_name":"Piskac, Ruzica","last_name":"Piskac"},{"id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Wies","full_name":"Wies, Thomas"}],"publist_id":"3311","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Piskac R, Wies T. 2011. Decision procedures for automating termination proofs. VMCAI: Verification Model Checking and Abstract Interpretation, LNCS, vol. 6538, 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.","short":"R. Piskac, T. Wies, in:, R. Jhala, D. Schmidt (Eds.), Springer, 2011, pp. 371–386.","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.","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","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"},"publisher":"Springer","quality_controlled":"1","oa":1,"date_published":"2011-01-01T00:00:00Z","doi":"10.1007/978-3-642-18275-4_26","date_created":"2018-12-11T12:02:40Z","page":"371 - 386","day":"01","year":"2011","status":"public","type":"conference","conference":{"location":"Texas, USA","end_date":"2011-01-25","start_date":"2011-01-23","name":"VMCAI: Verification Model Checking and Abstract Interpretation"},"_id":"3324","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T07:42:39Z","month":"01","intvolume":" 6538","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"url":"https://infoscience.epfl.ch/record/170697/","open_access":"1"}],"oa_version":"Submitted Version","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"}],"volume":6538,"language":[{"iso":"eng"}],"publication_status":"published"},{"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"}],"oa_version":"None","alternative_title":["LNCS"],"publisher":"Springer","quality_controlled":"1","month":"03","intvolume":" 6604","publication_status":"published","year":"2011","day":"29","language":[{"iso":"eng"}],"page":"184 - 198","volume":6604,"doi":"10.1007/978-3-642-19805-2_13","date_published":"2011-03-29T00:00:00Z","date_created":"2018-12-11T12:02:41Z","_id":"3327","type":"conference","conference":{"name":"FoSSaCS: Foundations of Software Science and Computation Structures","start_date":"2011-03-26","location":"Saarbrücken, Germany","end_date":"2011-04-03"},"status":"public","date_updated":"2021-01-12T07:42:41Z","citation":{"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.","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","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.","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.","ista":"Boker U, Kupferman O. 2011. Co-Büching them all. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 6604, 184–198."},"extern":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Boker","full_name":"Boker, Udi","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Orna","full_name":"Kupferman, Orna","last_name":"Kupferman"}],"publist_id":"3308","title":"Co-Büching them all","editor":[{"first_name":"Martin","full_name":"Hofmann, Martin","last_name":"Hofmann"}]},{"conference":{"name":"IROS: RSJ International Conference on Intelligent Robots and Systems","location":"San Francisco, USA","end_date":"2011-09-30","start_date":"2011-09-25"},"type":"conference","status":"public","_id":"3337","author":[{"full_name":"Wang, Zhikun","last_name":"Wang","first_name":"Zhikun"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mülling","full_name":"Mülling, Katharina","first_name":"Katharina"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"first_name":"Jan","last_name":"Peters","full_name":"Peters, Jan"}],"publist_id":"3293","department":[{"_id":"ChLa"}],"title":"Learning anticipation policies for robot table tennis","date_updated":"2021-01-12T07:42:45Z","citation":{"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.","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.","short":"Z. Wang, C. Lampert, K. Mülling, B. Schölkopf, J. Peters, in:, IEEE, 2011, pp. 332–337.","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.","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","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","mla":"Wang, Zhikun, et al. Learning Anticipation Policies for Robot Table Tennis. IEEE, 2011, pp. 332–37, doi:10.1109/IROS.2011.6094892."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publisher":"IEEE","quality_controlled":"1","month":"01","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"}],"oa_version":"None","page":"332 - 337","date_created":"2018-12-11T12:02:45Z","doi":"10.1109/IROS.2011.6094892","date_published":"2011-01-01T00:00:00Z","publication_status":"published","year":"2011","language":[{"iso":"eng"}],"day":"01"},{"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"}],"oa_version":"Preprint","publisher":"ArXiv","main_file_link":[{"url":"http://arxiv.org/abs/1107.2132","open_access":"1"}],"oa":1,"month":"07","year":"2011","publication_status":"published","day":"11","publication":"arXiv","language":[{"iso":"eng"}],"page":"17","date_published":"2011-07-11T00:00:00Z","date_created":"2018-12-11T12:02:46Z","_id":"3339","type":"preprint","status":"public","citation":{"mla":"Chatterjee, Krishnendu, et al. “Magnifying Lens Abstraction for Stochastic Games with Discounted and Long-Run Average Objectives.” ArXiv, ArXiv, 2011.","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.","short":"K. Chatterjee, L. De Alfaro, R. Pritam, ArXiv (2011).","apa":"Chatterjee, K., De Alfaro, L., & Pritam, R. (2011). Magnifying lens abstraction for stochastic games with discounted and long-run average objectives. arXiv. ArXiv.","ama":"Chatterjee K, De Alfaro L, Pritam R. Magnifying lens abstraction for stochastic games with discounted and long-run average objectives. 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.","ista":"Chatterjee K, De Alfaro L, Pritam R. 2011. Magnifying lens abstraction for stochastic games with discounted and long-run average objectives. arXiv, ."},"date_updated":"2021-01-12T07:42:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3286","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luca","full_name":"De Alfaro, Luca","last_name":"De Alfaro"},{"first_name":"Roy","last_name":"Pritam","full_name":"Pritam, Roy"}],"external_id":{"arxiv":["1107.2132"]},"department":[{"_id":"KrCh"}],"title":"Magnifying lens abstraction for stochastic games with discounted and long-run average objectives"},{"related_material":{"record":[{"relation":"later_version","status":"public","id":"2831"}]},"volume":6806,"language":[{"iso":"eng"}],"publication_status":"published","month":"08","intvolume":" 6806","alternative_title":["LNCS"],"main_file_link":[{"url":"http://arxiv.org/abs/1104.3348","open_access":"1"}],"oa_version":"Preprint","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."}],"department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T11:00:13Z","status":"public","type":"conference","conference":{"name":"CAV: Computer Aided Verification","location":"Snowbird, USA","end_date":"2011-07-20","start_date":"2011-07-14"},"_id":"3342","date_published":"2011-08-11T00:00:00Z","doi":"10.1007/978-3-642-22110-1_21","date_created":"2018-12-11T12:02:47Z","page":"260 - 276","day":"11","year":"2011","publisher":"Springer","quality_controlled":"1","oa":1,"editor":[{"full_name":"Gopalakrishnan, Ganesh","last_name":"Gopalakrishnan","first_name":"Ganesh"},{"last_name":"Qadeer","full_name":"Qadeer, Shaz","first_name":"Shaz"}],"title":"Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"first_name":"Manas","last_name":"Joglekar","full_name":"Joglekar, Manas"},{"first_name":"Shah","last_name":"Nisarg","full_name":"Nisarg, Shah"}],"publist_id":"3282","external_id":{"arxiv":["1104.3348"]},"article_processing_charge":"No","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"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.","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.","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.","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","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","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.","short":"K. Chatterjee, M.H. Henzinger, M. Joglekar, S. Nisarg, in:, G. Gopalakrishnan, S. Qadeer (Eds.), Springer, 2011, pp. 260–276."},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}]},{"oa":1,"quality_controlled":"1","publisher":"Springer","page":"216 - 226","date_created":"2018-12-11T12:02:48Z","date_published":"2011-06-16T00:00:00Z","doi":"10.1007/978-3-642-21254-3_16","year":"2011","day":"16","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["1101.1727"]},"publist_id":"3274","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Nathanaël","id":"A1B5DD72-E997-11E9-8398-E808B6C6ADC0","last_name":"Fijalkow","full_name":"Fijalkow, Nathanaël"}],"title":"Finitary languages","citation":{"mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. Finitary Languages. Vol. 6638, Springer, 2011, pp. 216–26, doi: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.","short":"K. Chatterjee, N. Fijalkow, in:, Springer, 2011, pp. 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","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.","ista":"Chatterjee K, Fijalkow N. 2011. Finitary languages. LATA: Language and Automata Theory and Applications, LNCS, vol. 6638, 216–226."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"http://arxiv.org/abs/1101.1727","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":1,"intvolume":" 6638","month":"06","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","volume":6638,"publication_status":"published","language":[{"iso":"eng"}],"conference":{"location":"Tarragona, Spain","end_date":"2011-05-31","start_date":"2011-05-26","name":"LATA: Language and Automata Theory and Applications"},"type":"conference","status":"public","_id":"3347","department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T07:42:50Z"},{"quality_controlled":"1","publisher":"IEEE","scopus_import":1,"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1104.3489","open_access":"1"}],"month":"06","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","date_published":"2011-06-21T00:00:00Z","doi":"10.1109/LICS.2011.10","ec_funded":1,"date_created":"2018-12-11T12:02:48Z","publication_status":"published","year":"2011","day":"21","language":[{"iso":"eng"}],"type":"conference","conference":{"name":"LICS: Logic in Computer Science","start_date":"2011-06-21","end_date":"2011-06-24","location":"Toronto, Canada"},"status":"public","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"_id":"3346","article_number":"5970225","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"last_name":"Brožek","full_name":"Brožek, Václav","first_name":"Václav"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Forejt, Vojtěch","last_name":"Forejt","first_name":"Vojtěch"},{"first_name":"Antonín","last_name":"Kučera","full_name":"Kučera, Antonín"}],"publist_id":"3275","title":"Two views on multiple mean payoff objectives in Markov Decision Processes","department":[{"_id":"KrCh"}],"citation":{"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.","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.","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.","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","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","short":"T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, A. Kučera, in:, IEEE, 2011.","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."},"date_updated":"2021-01-12T07:42:49Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"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."}],"oa_version":"Submitted Version","scopus_import":1,"publisher":"Springer","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1101.5842","open_access":"1"}],"month":"01","publication_status":"published","year":"2011","day":"31","language":[{"iso":"eng"}],"page":"221 - 230","doi":"10.1145/1967701.1967734","date_published":"2011-01-31T00:00:00Z","date_created":"2018-12-11T12:02:49Z","_id":"3348","type":"conference","conference":{"name":"HSCC: Hybrid Systems - Computation and Control","start_date":"2011-04-12","location":"Chicago, USA","end_date":"2011-04-14"},"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"status":"public","citation":{"ista":"Chatterjee K, Prabhu V. 2011. Synthesis of memory efficient real time controllers for safety objectives. HSCC: Hybrid Systems - Computation and Control, 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.","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.","short":"K. Chatterjee, V. Prabhu, in:, Springer, 2011, pp. 221–230.","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","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","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."},"date_updated":"2021-01-12T07:42:50Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"3273","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Prabhu, Vinayak","last_name":"Prabhu","first_name":"Vinayak"}],"title":"Synthesis of memory efficient real time controllers for safety objectives","department":[{"_id":"KrCh"}]},{"editor":[{"last_name":"Delzanno","full_name":"Delzanno, Giorgo","first_name":"Giorgo"},{"full_name":"Potapov, Igor","last_name":"Potapov","first_name":"Igor"}],"department":[{"_id":"KrCh"}],"title":"Graph games with reachability objectives","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"publist_id":"3277","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Chatterjee K. 2011. Graph games with reachability objectives. RP: Reachability Problems, LNCS, vol. 6945, 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.","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","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","short":"K. Chatterjee, in:, G. Delzanno, I. Potapov (Eds.), Springer, 2011, pp. 1–1.","ieee":"K. Chatterjee, “Graph games with reachability objectives,” presented at the RP: Reachability Problems, Genoa, Italy, 2011, vol. 6945, pp. 1–1."},"date_updated":"2021-01-12T07:42:48Z","status":"public","conference":{"name":"RP: Reachability Problems","start_date":"2011-09-28","end_date":"2011-09-30","location":"Genoa, Italy"},"type":"conference","_id":"3344","date_created":"2018-12-11T12:02:47Z","volume":6945,"doi":"10.1007/978-3-642-24288-5_1","date_published":"2011-10-15T00:00:00Z","page":"1 - 1","language":[{"iso":"eng"}],"day":"15","year":"2011","publication_status":"published","intvolume":" 6945","month":"10","quality_controlled":"1","publisher":"Springer","alternative_title":["LNCS"],"oa_version":"None","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."}]},{"article_processing_charge":"No","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger"}],"publist_id":"3278","department":[{"_id":"KrCh"}],"title":"Faster and dynamic algorithms for maximal end-component decomposition and related graph problems in probabilistic verification","date_updated":"2023-02-14T10:36:10Z","citation":{"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.","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.","short":"K. Chatterjee, M.H. Henzinger, in:, SIAM, 2011, pp. 1318–1336.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"location":"San Francisco, SA, United States","end_date":"2011-01-25","start_date":"2011-01-23","name":"SODA: Symposium on Discrete Algorithms"},"type":"conference","status":"public","_id":"3343","page":"1318 - 1336","date_created":"2018-12-11T12:02:47Z","date_published":"2011-01-01T00:00:00Z","doi":"10.1137/1.9781611973082.101","year":"2011","publication_status":"published","language":[{"iso":"eng"}],"day":"01","oa":1,"main_file_link":[{"url":"https://eprints.cs.univie.ac.at/21/","open_access":"1"}],"publisher":"SIAM","scopus_import":"1","quality_controlled":"1","month":"01","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."}],"oa_version":"Submitted Version"},{"ddc":["004"],"date_updated":"2021-01-12T07:42:56Z","file_date_updated":"2020-07-14T12:46:10Z","department":[{"_id":"ToHe"}],"_id":"3360","pubrep_id":"82","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"conference":{"name":"CSL: Computer Science Logic","start_date":"2011-09-12","end_date":"2011-09-15","location":"Bergen, Norway"},"type":"conference","language":[{"iso":"eng"}],"file":[{"checksum":"250603c6be8ccad4fbd4d7b24221f0ee","file_id":"4803","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:10:17Z","file_name":"IST-2012-82-v1+1_Determinizing_discounted-sum_automata.pdf","creator":"system","date_updated":"2020-07-14T12:46:10Z","file_size":504270}],"publication_status":"published","ec_funded":1,"volume":12,"oa_version":"Published Version","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"}],"intvolume":" 12","month":"08","alternative_title":["LIPIcs"],"scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Boker U, Henzinger TA. 2011. Determinizing discounted-sum automata. CSL: Computer Science Logic, LIPIcs, vol. 12, 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.","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","ama":"Boker U, Henzinger TA. Determinizing discounted-sum automata. In: Vol 12. Springer; 2011:82-96. doi:10.4230/LIPIcs.CSL.2011.82","short":"U. Boker, T.A. Henzinger, in:, Springer, 2011, pp. 82–96.","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."},"title":"Determinizing discounted-sum automata","publist_id":"3255","author":[{"first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi","last_name":"Boker"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"}],"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"COMponent-Based Embedded Systems design Techniques","grant_number":"215543"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Design for Embedded Systems","grant_number":"214373","call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425"}],"day":"31","year":"2011","has_accepted_license":"1","date_created":"2018-12-11T12:02:53Z","date_published":"2011-08-31T00:00:00Z","doi":"10.4230/LIPIcs.CSL.2011.82","page":"82 - 96","oa":1,"publisher":"Springer","quality_controlled":"1"},{"date_published":"2011-06-27T00:00:00Z","doi":"10.1109/CSF.2011.21","date_created":"2018-12-11T12:02:54Z","page":"205 - 217","day":"27","has_accepted_license":"1","year":"2011","publisher":"IEEE","quality_controlled":"1","oa":1,"title":"The complexity of quantitative information flow problems","publist_id":"3254","author":[{"first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","full_name":"Cerny, Pavol"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Cerny P, Chatterjee K, Henzinger TA. 2011. The complexity of quantitative information flow problems. CSF: Computer Security Foundations, 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.","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","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","short":"P. Cerny, K. Chatterjee, T.A. Henzinger, in:, IEEE, 2011, pp. 205–217.","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."},"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"ec_funded":1,"file":[{"file_name":"IST-2012-81-v1+1_The_complexity_of_quantitative_information_flow_problems.pdf","date_created":"2018-12-12T10:10:07Z","creator":"system","file_size":299069,"date_updated":"2020-07-14T12:46:10Z","checksum":"1a25be0c62459fc7640db88af08ff63a","file_id":"4792","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"06","scopus_import":1,"oa_version":"Submitted Version","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"}],"file_date_updated":"2020-07-14T12:46:10Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"ddc":["000","005"],"date_updated":"2021-01-12T07:42:56Z","status":"public","pubrep_id":"81","type":"conference","conference":{"name":"CSF: Computer Security Foundations","end_date":"2011-06-29","location":"Cernay-la-Ville, France","start_date":"2011-06-27"},"_id":"3361"},{"status":"public","conference":{"name":"EuroSys","end_date":"2011-04-13","location":"Salzburg, Austria","start_date":"2011-04-10"},"type":"conference","_id":"3358","title":"Scheduling large jobs by abstraction refinement","department":[{"_id":"ToHe"}],"article_processing_charge":"No","author":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Singh, Vasu","last_name":"Singh","first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wies, Thomas","last_name":"Wies","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"last_name":"Zufferey","orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien","first_name":"Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"3257","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:55Z","citation":{"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.","short":"T.A. Henzinger, V. Singh, T. Wies, D. Zufferey, in:, ACM, 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","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","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.","ista":"Henzinger TA, Singh V, Wies T, Zufferey D. 2011. Scheduling large jobs by abstraction refinement. EuroSys, 329–342."},"month":"04","main_file_link":[{"open_access":"1","url":"http://cs.nyu.edu/wies/publ/scheduling_large_jobs_by_abstraction_refinement.pdf"}],"oa":1,"quality_controlled":"1","publisher":"ACM","scopus_import":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"date_created":"2018-12-11T12:02:53Z","date_published":"2011-04-10T00:00:00Z","doi":"10.1145/1966445.1966476","page":"329 - 342","language":[{"iso":"eng"}],"day":"10","publication_status":"published","year":"2011"},{"quality_controlled":"1","publisher":"ACM","month":"10","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"}],"oa_version":"None","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.","page":"149 - 154","doi":"10.1145/2038642.2038666","date_published":"2011-10-09T00:00:00Z","date_created":"2018-12-11T12:02:53Z","ec_funded":1,"publication_status":"published","year":"2011","day":"09","language":[{"iso":"eng"}],"type":"conference","conference":{"start_date":"2011-10-09","end_date":"2011-10-14","location":"Taipei; Taiwan","name":"EMSOFT: Embedded Software "},"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Design for Embedded Systems","grant_number":"214373"}],"status":"public","_id":"3359","publist_id":"3256","author":[{"first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","last_name":"Cerny"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"title":"From boolean to quantitative synthesis","department":[{"_id":"ToHe"}],"citation":{"chicago":"Cerny, Pavol, and Thomas A Henzinger. “From Boolean to Quantitative Synthesis,” 149–54. ACM, 2011. https://doi.org/10.1145/2038642.2038666.","ista":"Cerny P, Henzinger TA. 2011. From boolean to quantitative synthesis. EMSOFT: Embedded Software , 149–154.","mla":"Cerny, Pavol, and Thomas A. Henzinger. From Boolean to Quantitative Synthesis. ACM, 2011, pp. 149–54, 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.","short":"P. Cerny, T.A. Henzinger, in:, ACM, 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","ama":"Cerny P, Henzinger TA. From boolean to quantitative synthesis. In: ACM; 2011:149-154. doi:10.1145/2038642.2038666"},"date_updated":"2021-01-12T07:42:55Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"status":"public","conference":{"start_date":"2011-05-26","location":"Tarragona, Spain","end_date":"2011-05-31","name":"LATA: Language and Automata Theory and Applications"},"type":"conference","_id":"3357","title":"The complexity of request-response games","editor":[{"last_name":"Dediu","full_name":"Dediu, Adrian-Horia","first_name":"Adrian-Horia"},{"first_name":"Shunsuke","last_name":"Inenaga","full_name":"Inenaga, Shunsuke"},{"first_name":"Carlos","full_name":"Martín-Vide, Carlos","last_name":"Martín-Vide"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publist_id":"3258","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Horn, Florian","last_name":"Horn","id":"37327ACE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:54Z","citation":{"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.","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","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","short":"K. Chatterjee, T.A. Henzinger, F. Horn, in:, A.-H. Dediu, S. Inenaga, C. Martín-Vide (Eds.), Springer, 2011, pp. 227–237.","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.","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.","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."},"intvolume":" 6638","month":"01","publisher":"Springer","scopus_import":1,"quality_controlled":"1","alternative_title":["LNCS"],"oa_version":"None","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."}],"date_created":"2018-12-11T12:02:52Z","date_published":"2011-01-01T00:00:00Z","volume":6638,"doi":"10.1007/978-3-642-21254-3_17","page":"227 - 237","language":[{"iso":"eng"}],"day":"01","year":"2011","publication_status":"published"},{"_id":"336","status":"public","type":"journal_article","article_type":"original","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:56Z","citation":{"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.","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.","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.","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","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","short":"M. Ibáñez, P. Guardia, A. Shavel, D. Cadavid, J. Arbiol, J. Morante, A. Cabot, Journal of Physical Chemistry C 115 (2011) 7947–7955.","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."},"title":"Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods","author":[{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guardia","full_name":"Guardia, Pablo","first_name":"Pablo"},{"first_name":"Alexey","last_name":"Shavel","full_name":"Shavel, Alexey"},{"full_name":"Cadavid, Doris","last_name":"Cadavid","first_name":"Doris"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"full_name":"Morante, Joan","last_name":"Morante","first_name":"Joan"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"publist_id":"7493","article_processing_charge":"No","oa_version":"None","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.","abstract":[{"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. ","lang":"eng"}],"month":"04","intvolume":" 115","publisher":"American Chemical Society","quality_controlled":"1","day":"28","language":[{"iso":"eng"}],"publication":"Journal of Physical Chemistry C","year":"2011","publication_status":"published","volume":115,"doi":"10.1021/jp2002904","issue":"16","date_published":"2011-04-28T00:00:00Z","date_created":"2018-12-11T11:45:53Z","page":"7947 - 7955"},{"_id":"3379","type":"journal_article","article_type":"original","status":"public","date_updated":"2021-01-12T07:43:04Z","department":[{"_id":"CaHe"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version","pmid":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090540/"}],"scopus_import":1,"intvolume":" 354","month":"06","publication_status":"published","language":[{"iso":"eng"}],"issue":"1","volume":354,"citation":{"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","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","short":"R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P.J. Heisenberg, D. Kimelman, Developmental Biology 354 (2011) 102–110.","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["1463614"]},"author":[{"last_name":"Row","full_name":"Row, Richard","first_name":"Richard"},{"orcid":"0000-0002-3688-1474","full_name":"Maître, Jean-Léon","last_name":"Maître","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","first_name":"Jean-Léon"},{"full_name":"Martin, Benjamin","last_name":"Martin","first_name":"Benjamin"},{"first_name":"Petra","id":"261CB030-E90D-11E9-B182-F697D44B663C","last_name":"Stockinger","full_name":"Stockinger, Petra"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"},{"first_name":"David","last_name":"Kimelman","full_name":"Kimelman, David"}],"publist_id":"3228","title":"Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail","oa":1,"publisher":"Elsevier","quality_controlled":"1","year":"2011","publication":"Developmental Biology","day":"01","page":"102 - 110","date_created":"2018-12-11T12:03:00Z","doi":"10.1016/j.ydbio.2011.03.025","date_published":"2011-06-01T00:00:00Z"},{"page":"413 - 425","doi":"10.1016/j.molcel.2011.04.016","date_published":"2011-05-20T00:00:00Z","date_created":"2018-12-11T12:02:59Z","year":"2011","day":"20","publication":"Molecular Cell","quality_controlled":"1","publisher":"Cell Press","oa":1,"acknowledgement":"This work was supported by a Feodor Lynen Fellowship of the Alexander von Humboldt Foundation (to T.B.).","author":[{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roy","full_name":"Kishony, Roy","last_name":"Kishony"}],"publist_id":"3231","title":"Resolution of gene regulatory conflicts caused by combinations of antibiotics","citation":{"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.","ista":"Bollenbach MT, Kishony R. 2011. Resolution of gene regulatory conflicts caused by combinations of antibiotics. Molecular Cell. 42(4), 413–425.","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.","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","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","short":"M.T. Bollenbach, R. Kishony, Molecular Cell 42 (2011) 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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","volume":42,"issue":"4","publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143497/","open_access":"1"}],"month":"05","intvolume":" 42","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"}],"oa_version":"Submitted Version","department":[{"_id":"ToBo"}],"date_updated":"2021-01-12T07:43:03Z","type":"journal_article","status":"public","_id":"3376"},{"citation":{"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","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.","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.","ista":"Logeswaran S, Barton NH. 2011. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 93(3), 221–232.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3227","author":[{"last_name":"Logeswaran","full_name":"Logeswaran, Sayanthan","first_name":"Sayanthan"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Mapping Mendelian traits in asexual progeny using changes in marker allele frequency","year":"2011","day":"18","publication":"Genetical Research","page":"221 - 232","date_published":"2011-05-18T00:00:00Z","doi":"10.1017/S0016672311000115","date_created":"2018-12-11T12:03:00Z","publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"date_updated":"2021-01-12T07:43:05Z","department":[{"_id":"NiBa"}],"_id":"3380","type":"journal_article","article_type":"original","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":93,"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."}],"oa_version":"Published Version","scopus_import":1,"main_file_link":[{"url":"https://www.pure.ed.ac.uk/ws/files/8144621/GR_2011_Barton.pdf","open_access":"1"}],"month":"05","intvolume":" 93"},{"page":"345 - 361","date_created":"2018-12-11T12:02:59Z","date_published":"2011-06-01T00:00:00Z","doi":"10.1007/s10208-011-9090-8","year":"2011","publication":"Foundations of Computational Mathematics","day":"01","oa":1,"publisher":"Springer","quality_controlled":"1","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.","author":[{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dmitriy","last_name":"Morozov","full_name":"Morozov, Dmitriy"},{"full_name":"Patel, Amit","last_name":"Patel","first_name":"Amit","id":"34A254A0-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"3230","title":"Quantifying transversality by measuring the robustness of intersections","citation":{"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.","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.","short":"H. Edelsbrunner, D. Morozov, A. Patel, Foundations of Computational Mathematics 11 (2011) 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","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","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.","ista":"Edelsbrunner H, Morozov D, Patel A. 2011. Quantifying transversality by measuring the robustness of intersections. Foundations of Computational Mathematics. 11(3), 345–361."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","volume":11,"issue":"3","publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0911.2142"}],"scopus_import":1,"intvolume":" 11","month":"06","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T07:43:04Z","type":"journal_article","status":"public","_id":"3377"},{"status":"public","type":"journal_article","_id":"3378","title":"Persistent intersection homology","department":[{"_id":"HeEd"}],"publist_id":"3229","author":[{"id":"43F6EC54-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","last_name":"Bendich","full_name":"Bendich, Paul"},{"first_name":"John","full_name":"Harer, John","last_name":"Harer"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bendich P, Harer J. 2011. Persistent intersection homology. Foundations of Computational Mathematics. 11(3), 305–336.","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.","ieee":"P. Bendich and J. Harer, “Persistent intersection homology,” Foundations of Computational Mathematics, vol. 11, no. 3. Springer, pp. 305–336, 2011.","ama":"Bendich P, Harer J. Persistent intersection homology. Foundations of Computational Mathematics. 2011;11(3):305-336. doi:10.1007/s10208-010-9081-1","apa":"Bendich, P., & Harer, J. (2011). Persistent intersection homology. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-010-9081-1","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."},"date_updated":"2021-01-12T07:43:04Z","month":"06","intvolume":" 11","scopus_import":1,"quality_controlled":"1","publisher":"Springer","oa_version":"None","acknowledgement":"This research was partially supported by the Defense Advanced Research Projects Agency (DARPA) under grant HR0011-05-1-0007.","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"}],"doi":"10.1007/s10208-010-9081-1","issue":"3","date_published":"2011-06-01T00:00:00Z","volume":11,"date_created":"2018-12-11T12:02:59Z","page":"305 - 336","day":"01","language":[{"iso":"eng"}],"publication":"Foundations of Computational Mathematics","year":"2011","publication_status":"published"},{"year":"2011","has_accepted_license":"1","publication":"BMC Evolutionary Biology","day":"11","date_created":"2018-12-11T12:03:03Z","date_published":"2011-07-11T00:00:00Z","doi":"10.1186/1471-2148-11-201","oa":1,"publisher":"BioMed Central","quality_controlled":"1","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.","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.","short":"L.V. Ugelvig, P. Nielsen, J. Boomsma, D. Nash, BMC Evolutionary Biology 11 (2011).","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","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Ugelvig","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V"},{"last_name":"Nielsen","full_name":"Nielsen, Per","first_name":"Per"},{"first_name":"Jacobus","last_name":"Boomsma","full_name":"Boomsma, Jacobus"},{"first_name":"David","full_name":"Nash, David","last_name":"Nash"}],"publist_id":"3220","title":"Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion","article_number":"201","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2015-371-v1+1_1471-2148-11-201.pdf","date_created":"2018-12-12T10:14:18Z","file_size":2166556,"date_updated":"2020-07-14T12:46:11Z","creator":"system","checksum":"9ebfed0740f1fa071d02ec32c2b8c17f","file_id":"5069","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"volume":11,"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"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 11","month":"07","date_updated":"2021-01-12T07:43:08Z","ddc":["576"],"department":[{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:46:11Z","_id":"3388","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"371","status":"public"},{"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","publication":"PLoS One","day":"16","year":"2011","has_accepted_license":"1","date_created":"2018-12-11T12:03:01Z","doi":"10.1371/journal.pone.0020409","date_published":"2011-06-16T00:00:00Z","article_number":"e20409","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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).","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.","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","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.","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."},"title":"Natural images from the birthplace of the human eye","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"full_name":"Garrigan, Patrick","last_name":"Garrigan","first_name":"Patrick"},{"first_name":"Charles","full_name":"Ratliff, Charles","last_name":"Ratliff"},{"last_name":"Milcinski","full_name":"Milcinski, Grega","first_name":"Grega"},{"first_name":"Jennifer","full_name":"Klein, Jennifer","last_name":"Klein"},{"last_name":"Seyfarth","full_name":"Seyfarth, Lucia","first_name":"Lucia"},{"first_name":"Peter","last_name":"Sterling","full_name":"Sterling, Peter"},{"first_name":"David","last_name":"Brainard","full_name":"Brainard, David"},{"full_name":"Balasubramanian, Vijay","last_name":"Balasubramanian","first_name":"Vijay"}],"publist_id":"3223","oa_version":"Published Version","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"}],"intvolume":" 6","month":"06","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:46:11Z","file_size":1424768,"date_created":"2018-12-12T10:09:25Z","file_name":"IST-2015-379-v1+1_journal.pone.0020409.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"307d4356916471306e3705ac65b82fa1","file_id":"4749"}],"publication_status":"published","issue":"6","volume":6,"_id":"3384","pubrep_id":"379","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2021-01-12T07:43:07Z","file_date_updated":"2020-07-14T12:46:11Z","department":[{"_id":"GaTk"}]},{"language":[{"iso":"eng"}],"file":[{"checksum":"68da8d04af1b97b4cbe8606e2f92ddd8","file_id":"5058","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:14:09Z","file_name":"IST-2015-372-v1+1_1471-2148-11-205.pdf","date_updated":"2020-07-14T12:46:11Z","file_size":465042,"creator":"system"}],"publication_status":"published","issue":"205","volume":11,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"intvolume":" 11","month":"07","scopus_import":1,"ddc":["576"],"date_updated":"2021-01-12T07:43:08Z","department":[{"_id":"JoBo"}],"file_date_updated":"2020-07-14T12:46:11Z","_id":"3387","pubrep_id":"372","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","publication":"BMC Evolutionary Biology","day":"13","year":"2011","has_accepted_license":"1","date_created":"2018-12-11T12:03:03Z","doi":"10.1186/1471-2148-11-205","date_published":"2011-07-13T00:00:00Z","oa":1,"publisher":"BioMed Central","quality_controlled":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kupczok A. 2011. Split based computation of majority rule supertrees. BMC Evolutionary Biology. 11(205), 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.","short":"A. Kupczok, BMC Evolutionary Biology 11 (2011).","ieee":"A. Kupczok, “Split based computation of majority rule supertrees,” BMC Evolutionary Biology, vol. 11, no. 205. BioMed Central, 2011.","ama":"Kupczok A. Split based computation of majority rule supertrees. BMC Evolutionary Biology. 2011;11(205). doi:10.1186/1471-2148-11-205","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","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."},"title":"Split based computation of majority rule supertrees","author":[{"id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","full_name":"Kupczok, Anne","last_name":"Kupczok"}],"publist_id":"3219","article_number":"205"},{"title":"Semi supervised kernel canonical correlation analysis with application to human fMRI","department":[{"_id":"ChLa"}],"author":[{"first_name":"Matthew","full_name":"Blaschko, Matthew","last_name":"Blaschko"},{"first_name":"Jacquelyn","last_name":"Shelton","full_name":"Shelton, Jacquelyn"},{"full_name":"Bartels, Andreas","last_name":"Bartels","first_name":"Andreas"},{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Arthur","full_name":"Gretton, Arthur","last_name":"Gretton"}],"publist_id":"3218","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:43:09Z","citation":{"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.","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.","short":"M. Blaschko, J. Shelton, A. Bartels, C. Lampert, A. Gretton, Pattern Recognition Letters 32 (2011) 1572–1583.","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.","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","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","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."},"status":"public","type":"journal_article","_id":"3389","date_created":"2018-12-11T12:03:03Z","doi":"10.1016/j.patrec.2011.02.011","volume":32,"issue":"11","date_published":"2011-08-01T00:00:00Z","page":"1572 - 1583","language":[{"iso":"eng"}],"publication":"Pattern Recognition Letters","day":"01","year":"2011","publication_status":"published","intvolume":" 32","month":"08","scopus_import":1,"publisher":"Elsevier","quality_controlled":"1","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.","oa_version":"None","abstract":[{"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.","lang":"eng"}]},{"publication":"IEEE Transactions on Robotics","language":[{"iso":"eng"}],"day":"21","publication_status":"published","year":"2011","date_created":"2018-12-11T12:03:01Z","volume":27,"date_published":"2011-05-21T00:00:00Z","doi":"10.1109/TRO.2011.2121130","issue":"3","page":"545 - 557","oa_version":"None","abstract":[{"lang":"eng","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."}],"intvolume":" 27","month":"05","scopus_import":1,"quality_controlled":"1","publisher":"IEEE","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:43:06Z","citation":{"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.","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.","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.","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","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","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.","short":"O. Kroemer, C. Lampert, J. Peters, IEEE Transactions on Robotics 27 (2011) 545–557."},"department":[{"_id":"ChLa"}],"title":"Learning dynamic tactile sensing with robust vision based training","author":[{"first_name":"Oliver","last_name":"Kroemer","full_name":"Kroemer, Oliver"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"},{"first_name":"Jan","full_name":"Peters, Jan","last_name":"Peters"}],"publist_id":"3225","_id":"3382","status":"public","type":"journal_article"},{"_id":"3386","type":"journal_article","status":"public","date_updated":"2021-01-12T07:43:08Z","citation":{"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.","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.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Alexandra","last_name":"Schrempf","full_name":"Schrempf, Alexandra"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"},{"first_name":"Jürgen","full_name":"Heinze, Jürgen","last_name":"Heinze"}],"publist_id":"3221","department":[{"_id":"SyCr"}],"title":"Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies","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."}],"oa_version":"None","publisher":"Wiley-Blackwell","scopus_import":1,"quality_controlled":"1","intvolume":" 24","month":"04","publication_status":"published","year":"2011","publication":"Journal of Evolutionary Biology","language":[{"iso":"eng"}],"day":"21","page":"1455 - 1461","date_created":"2018-12-11T12:03:02Z","date_published":"2011-04-21T00:00:00Z","doi":"10.1111/j.1420-9101.2011.02278.x","volume":24,"issue":"7"},{"publist_id":"3222","author":[{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"MiSi"}],"title":"Interstitial locomotion of leukocytes","citation":{"ista":"Sixt MK. 2011. Interstitial locomotion of leukocytes. Immunology Letters. 138(1), 32–34.","chicago":"Sixt, Michael K. “Interstitial Locomotion of Leukocytes.” Immunology Letters. Elsevier, 2011. https://doi.org/10.1016/j.imlet.2011.02.013.","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","short":"M.K. Sixt, Immunology Letters 138 (2011) 32–34.","ieee":"M. K. Sixt, “Interstitial locomotion of leukocytes,” Immunology Letters, vol. 138, no. 1. Elsevier, pp. 32–34, 2011.","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."},"date_updated":"2021-01-12T07:43:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"review","type":"journal_article","status":"public","_id":"3385","page":"32 - 34","issue":"1","volume":138,"doi":"10.1016/j.imlet.2011.02.013","date_published":"2011-07-01T00:00:00Z","date_created":"2018-12-11T12:03:02Z","publication_status":"published","year":"2011","day":"01","publication":"Immunology Letters","language":[{"iso":"eng"}],"scopus_import":1,"publisher":"Elsevier","quality_controlled":"1","month":"07","intvolume":" 138","oa_version":"None"},{"oa_version":"None","intvolume":" 278","month":"07","publisher":"Wiley-Blackwell","language":[{"iso":"eng"}],"publication":"FEBS Journal","day":"01","publication_status":"published","year":"2011","date_created":"2018-12-11T12:03:01Z","doi":"10.1111/j.1742-4658.2011.08136.x","issue":"S1","volume":278,"date_published":"2011-07-01T00:00:00Z","page":"24 - 24","_id":"3383","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Heisenberg C-PJ. 2011. Invited Lectures ‐ Symposia Area. FEBS Journal. 278(S1), 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.","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","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.","short":"C.-P.J. Heisenberg, FEBS Journal 278 (2011) 24–24."},"date_updated":"2021-01-12T07:43:06Z","department":[{"_id":"CaHe"}],"title":"Invited Lectures ‐ Symposia Area","author":[{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"3224"},{"ddc":["576"],"date_updated":"2021-01-12T07:43:12Z","department":[{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:46:12Z","_id":"3399","status":"public","pubrep_id":"377","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_created":"2018-12-12T10:15:40Z","file_name":"IST-2015-377-v1+1_journal.pone.0017323.pdf","date_updated":"2020-07-14T12:46:12Z","file_size":147367,"creator":"system","checksum":"46f8cbde61f06fcacf8fa297cacfa0e5","file_id":"5162","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":6,"issue":"3","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"03","intvolume":" 6","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","short":"S. Cremer, A. Schrempf, J. Heinze, PLoS One 6 (2011).","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.","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","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"},"title":"Competition and opportunity shape the reproductive tactics of males in the ant Cardiocondyla obscurior","author":[{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"},{"first_name":"Alexandra","full_name":"Schrempf, Alexandra","last_name":"Schrempf"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"}],"publist_id":"3059","article_number":"e17323","day":"29","publication":"PLoS One","has_accepted_license":"1","year":"2011","doi":"10.1371/journal.pone.0017323","date_published":"2011-03-29T00:00:00Z","date_created":"2018-12-11T12:03:07Z","acknowledgement":"This work was supported by the German Science Foundation (www.dfg.de, He 1623/23).","quality_controlled":"1","publisher":"Public Library of Science","oa":1},{"oa_version":"None","abstract":[{"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.","lang":"eng"}],"intvolume":" 9","month":"03","publisher":"Public Library of Science","quality_controlled":"1","publication":"PLoS Biology","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2011","date_created":"2018-12-11T12:03:08Z","volume":9,"doi":"10.1371/journal.pbio.1000596","date_published":"2011-03-01T00:00:00Z","issue":"3","article_number":"e1000596","_id":"3401","status":"public","article_type":"original","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"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).","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","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.","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."},"date_updated":"2021-01-12T07:43:14Z","title":"The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source","publist_id":"3057","author":[{"first_name":"Shawn","full_name":"Little, Shawn","last_name":"Little"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"},{"last_name":"Kneeland","full_name":"Kneeland, Thomas","first_name":"Thomas"},{"first_name":"Eric","last_name":"Wieschaus","full_name":"Wieschaus, Eric"},{"first_name":"Thomas","full_name":"Gregor, Thomas","last_name":"Gregor"}]},{"type":"book_chapter","status":"public","_id":"3724","author":[{"last_name":"Janovjak","full_name":"Harald Janovjak","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"},{"full_name":"Isacoff, Ehud Y","last_name":"Isacoff","first_name":"Ehud"}],"publist_id":"2504","title":"Structure-based design of light-controlled proteins","citation":{"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.","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.","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.","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","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"},"date_updated":"2021-01-12T07:51:45Z","extern":1,"quality_controlled":0,"publisher":"Springer","intvolume":" 55","month":"03","abstract":[{"lang":"eng","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."}],"page":"233 - 266","date_created":"2018-12-11T12:04:49Z","volume":55,"doi":"10.1007/978-1-61779-031-7_13","date_published":"2011-03-16T00:00:00Z","year":"2011","publication_status":"published","publication":"Photosensitive Molecules for the Control of Biological Function","day":"16"},{"publisher":"Wiley","month":"04","intvolume":" 102","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."}],"oa_version":"None","page":"812 - 827","date_published":"2011-04-01T00:00:00Z","volume":102,"issue":"4","doi":"10.1111/j.1095-8312.2011.01616.x","date_created":"2018-12-11T12:05:04Z","year":"2011","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Biological Journal of the Linnean Society","type":"journal_article","status":"public","_id":"3770","publist_id":"2457","author":[{"first_name":"Claudia","last_name":"Hollatz","full_name":"Hollatz, Claudia"},{"full_name":"Vilaça, Sibelle","last_name":"Vilaça","first_name":"Sibelle"},{"orcid":"0000-0002-5837-2793","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","first_name":"Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Míriam","last_name":"Marmontel","full_name":"Marmontel, Míriam"},{"full_name":"Baker, Cyndi","last_name":"Baker","first_name":"Cyndi"},{"last_name":"Santos","full_name":"Santos, Fabrício","first_name":"Fabrício"}],"article_processing_charge":"No","title":"The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis)","citation":{"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.","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","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","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.","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.","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.","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."},"date_updated":"2021-01-12T07:52:05Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"citation":{"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","short":"A. Pavan, F. Martins, F. Santos, A. Ditchfield, R.A. Fernandes Redondo, Biological Journal of the Linnean Society 102 (2011) 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.","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.","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.","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."},"date_updated":"2021-01-12T07:52:05Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"2456","author":[{"last_name":"Pavan","full_name":"Pavan, Ana","first_name":"Ana"},{"last_name":"Martins","full_name":"Martins, Felipe","first_name":"Felipe"},{"first_name":"Fabrício","last_name":"Santos","full_name":"Santos, Fabrício"},{"full_name":"Ditchfield, Albert","last_name":"Ditchfield","first_name":"Albert"},{"last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793","full_name":"Fernandes Redondo, Rodrigo A","first_name":"Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"FyKo"}],"title":"Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.","_id":"3771","type":"journal_article","status":"public","publication_status":"published","year":"2011","day":"10","language":[{"iso":"eng"}],"publication":"Biological Journal of the Linnean Society","page":"527 - 539","volume":102,"doi":"10.1111/j.1095-8312.2010.01601.x","date_published":"2011-02-10T00:00:00Z","issue":"3","date_created":"2018-12-11T12:05:05Z","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"}],"oa_version":"None","quality_controlled":"1","scopus_import":1,"publisher":"Wiley-Blackwell","month":"02","intvolume":" 102"},{"type":"journal_article","status":"public","_id":"3778","external_id":{"pmid":["20502479"]},"author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"2449","title":"Estimating linkage disequilibria","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:52:08Z","citation":{"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.","ieee":"N. H. Barton, “Estimating linkage disequilibria,” Heredity, vol. 106, no. 2. Nature Publishing Group, pp. 205–206, 2011.","short":"N.H. Barton, Heredity 106 (2011) 205–206.","apa":"Barton, N. H. (2011). Estimating linkage disequilibria. Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2010.67","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.","ista":"Barton NH. 2011. Estimating linkage disequilibria. Heredity. 106(2), 205–206."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183869/","open_access":"1"}],"publisher":"Nature Publishing Group","scopus_import":1,"intvolume":" 106","month":"02","oa_version":"Submitted Version","pmid":1,"page":"205 - 206","date_created":"2018-12-11T12:05:07Z","volume":106,"issue":"2","doi":"10.1038/hdy.2010.67","date_published":"2011-02-01T00:00:00Z","publication_status":"published","year":"2011","language":[{"iso":"eng"}],"publication":"Heredity","day":"01"},{"oa_version":"None","abstract":[{"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.","lang":"eng"}],"intvolume":" 95","month":"01","publisher":"Elsevier","quality_controlled":"1","scopus_import":"1","alternative_title":["Current Topics in Developmental Biology"],"language":[{"iso":"eng"}],"publication":"Forces and Tension in Development","day":"01","publication_status":"published","year":"2011","date_created":"2018-12-11T12:05:11Z","doi":"10.1016/B978-0-12-385065-2.00006-2","volume":95,"date_published":"2011-01-01T00:00:00Z","page":"189 - 213","_id":"3791","status":"public","type":"book_chapter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:52:13Z","citation":{"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.","short":"G. Krens, C.-P.J. Heisenberg, in:, M. Labouesse (Ed.), Forces and Tension in Development, Elsevier, 2011, pp. 189–213.","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","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.","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."},"department":[{"_id":"CaHe"}],"title":"Cell sorting in development","editor":[{"full_name":"Labouesse, Michel","last_name":"Labouesse","first_name":"Michel"}],"article_processing_charge":"No","author":[{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"publist_id":"2436"},{"author":[{"last_name":"Didier","full_name":"Didier, Frédéric","first_name":"Frédéric"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Maria","full_name":"Mateescu, Maria","last_name":"Mateescu"},{"last_name":"Wolf","full_name":"Wolf, Verena","first_name":"Verena"}],"publist_id":"3249","title":"Approximation of event probabilities in noisy cellular processes","citation":{"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.","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.","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.","short":"F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, Theoretical Computer Science 412 (2011) 2128–2141.","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","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","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","quality_controlled":"1","oa":1,"page":"2128 - 2141","doi":"10.1016/j.tcs.2010.10.022","date_published":"2011-05-06T00:00:00Z","date_created":"2018-12-11T12:02:55Z","has_accepted_license":"1","year":"2011","day":"06","publication":"Theoretical Computer Science","type":"journal_article","status":"public","pubrep_id":"79","_id":"3364","file_date_updated":"2020-07-14T12:46:10Z","department":[{"_id":"ToHe"}],"date_updated":"2023-02-23T12:15:28Z","ddc":["000","004"],"scopus_import":1,"month":"05","intvolume":" 412","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"}],"oa_version":"Submitted Version","issue":"21","volume":412,"related_material":{"record":[{"status":"public","id":"4535","relation":"earlier_version"}]},"publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:46:10Z","file_size":230503,"date_created":"2018-12-12T10:11:09Z","file_name":"IST-2012-79-v1+1_Approximation_of_event_probabilities_in_noisy_cellular_processes.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4862","checksum":"e5503e25ce020d753e06b3431e16841e"}],"language":[{"iso":"eng"}]},{"citation":{"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.","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.","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.","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","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","short":"N. Vyleta, S. Smith, European Journal of Neuroscience 31 (2011) 4593–4606.","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."},"date_updated":"2021-01-12T08:00:49Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"7353","author":[{"id":"36C4978E-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas","full_name":"Vyleta, Nicholas","last_name":"Vyleta"},{"full_name":"Smith, Stephen","last_name":"Smith","first_name":"Stephen"}],"department":[{"_id":"PeJo"}],"title":"Spontaneous glutamate release is independent of calcium influx and tonically activated by the calcium-sensing receptor","_id":"469","type":"journal_article","status":"public","year":"2011","publication_status":"published","day":"23","language":[{"iso":"eng"}],"publication":"European Journal of Neuroscience","page":"4593 - 4606","volume":31,"doi":"10.1523/JNEUROSCI.6398-10.2011","issue":"12","date_published":"2011-03-23T00:00:00Z","date_created":"2018-12-11T11:46:39Z","abstract":[{"lang":"eng","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. "}],"oa_version":"Submitted Version","quality_controlled":"1","scopus_import":1,"publisher":"Wiley-Blackwell","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3097128/","open_access":"1"}],"month":"03","intvolume":" 31"},{"doi":"10.1155/2011/935364","date_published":"2011-01-01T00:00:00Z","date_created":"2018-12-11T11:46:45Z","has_accepted_license":"1","year":"2011","day":"01","publication":"Computational Intelligence and Neuroscience","quality_controlled":"1","publisher":"Hindawi Publishing Corporation","oa":1,"publist_id":"7330","author":[{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"first_name":"Carmen","full_name":"Vidaurre, Carmen","last_name":"Vidaurre"},{"first_name":"Tilmann","last_name":"Sander","full_name":"Sander, Tilmann"}],"title":"BioSig: The free and open source software library for biomedical signal processing","citation":{"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","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","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.","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.","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.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","article_number":"935364","volume":2011,"publication_status":"published","file":[{"date_created":"2018-12-12T10:07:44Z","file_name":"IST-2018-947-v1+1_2011_Schloegl_BioSig.pdf","date_updated":"2020-07-14T12:46:35Z","file_size":2863551,"creator":"system","checksum":"8263bbf255171f2054f43f3db5f53b6e","file_id":"4642","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"01","intvolume":" 2011","abstract":[{"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. ","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:35Z","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"date_updated":"2021-01-12T08:01:02Z","ddc":["005"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"947","_id":"490"},{"article_number":"pe43","_id":"491","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:01:02Z","citation":{"ista":"Eichner A, Sixt MK. 2011. Setting the clock for recirculating lymphocytes. Science Signaling. 4(198), pe43.","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.","short":"A. Eichner, M.K. Sixt, Science Signaling 4 (2011).","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","ama":"Eichner A, Sixt MK. Setting the clock for recirculating lymphocytes. Science Signaling. 2011;4(198). doi:10.1126/scisignal.2002617","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."},"department":[{"_id":"MiSi"}],"title":"Setting the clock for recirculating lymphocytes","author":[{"id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","full_name":"Eichner, Alexander","last_name":"Eichner"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"publist_id":"7329","oa_version":"None","abstract":[{"lang":"eng","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."}],"intvolume":" 4","month":"11","publisher":"American Association for the Advancement of Science","quality_controlled":"1","scopus_import":1,"publication":"Science Signaling","language":[{"iso":"eng"}],"day":"08","year":"2011","publication_status":"published","date_created":"2018-12-11T11:46:46Z","issue":"198","date_published":"2011-11-08T00:00:00Z","doi":"10.1126/scisignal.2002617","volume":4},{"_id":"518","status":"public","article_type":"original","type":"journal_article","date_updated":"2021-01-12T08:01:19Z","department":[{"_id":"MiSi"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","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."}],"month":"10","intvolume":" 30","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199389/","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"20","volume":30,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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","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.","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."},"title":"CAMTA1 is a novel tumour suppressor regulated by miR-9/9 * in glioblastoma stem cells","author":[{"first_name":"Daniel","last_name":"Schraivogel","full_name":"Schraivogel, Daniel"},{"full_name":"Weinmann, Lasse","last_name":"Weinmann","first_name":"Lasse"},{"last_name":"Beier","full_name":"Beier, Dagmar","first_name":"Dagmar"},{"first_name":"Ghazaleh","last_name":"Tabatabai","full_name":"Tabatabai, Ghazaleh"},{"first_name":"Alexander","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","full_name":"Eichner, Alexander","last_name":"Eichner"},{"first_name":"Jia","full_name":"Zhu, Jia","last_name":"Zhu"},{"full_name":"Anton, Martina","last_name":"Anton","first_name":"Martina"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Weller","full_name":"Weller, Michael","first_name":"Michael"},{"last_name":"Beier","full_name":"Beier, Christoph","first_name":"Christoph"},{"first_name":"Gunter","last_name":"Meister","full_name":"Meister, Gunter"}],"publist_id":"7301","article_processing_charge":"No","external_id":{"pmid":["21857646"]},"publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"day":"19","publication":"EMBO Journal","year":"2011","doi":"10.1038/emboj.2011.301","date_published":"2011-10-19T00:00:00Z","date_created":"2018-12-11T11:46:55Z","page":"4309 - 4322"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Guerraoui, Rachid, et al. “Verification of STM on Relaxed Memory Models.” Formal Methods in System Design, vol. 39, no. 3, Springer, 2011, pp. 297–331, doi:10.1007/s10703-011-0131-3.","ama":"Guerraoui R, Henzinger TA, Singh V. Verification of STM on relaxed memory models. Formal Methods in System Design. 2011;39(3):297-331. doi:10.1007/s10703-011-0131-3","apa":"Guerraoui, R., Henzinger, T. A., & Singh, V. (2011). Verification of STM on relaxed memory models. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-011-0131-3","ieee":"R. Guerraoui, T. A. Henzinger, and V. Singh, “Verification of STM on relaxed memory models,” Formal Methods in System Design, vol. 39, no. 3. Springer, pp. 297–331, 2011.","short":"R. Guerraoui, T.A. Henzinger, V. Singh, Formal Methods in System Design 39 (2011) 297–331.","chicago":"Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Verification of STM on Relaxed Memory Models.” Formal Methods in System Design. Springer, 2011. https://doi.org/10.1007/s10703-011-0131-3.","ista":"Guerraoui R, Henzinger TA, Singh V. 2011. Verification of STM on relaxed memory models. Formal Methods in System Design. 39(3), 297–331."},"title":"Verification of STM on relaxed memory models","publist_id":"7288","author":[{"full_name":"Guerraoui, Rachid","last_name":"Guerraoui","first_name":"Rachid"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","full_name":"Singh, Vasu","last_name":"Singh"}],"article_processing_charge":"No","day":"01","publication":"Formal Methods in System Design","year":"2011","date_published":"2011-12-01T00:00:00Z","doi":"10.1007/s10703-011-0131-3","date_created":"2018-12-11T11:47:00Z","page":"297 - 331","publisher":"Springer","quality_controlled":"1","oa":1,"ddc":["000"],"date_updated":"2021-01-12T08:01:27Z","department":[{"_id":"ToHe"}],"_id":"531","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":39,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Software transactional memories (STM) are described in the literature with assumptions of sequentially consistent program execution and atomicity of high level operations like read, write, and abort. However, in a realistic setting, processors use relaxed memory models to optimize hardware performance. Moreover, the atomicity of operations depends on the underlying hardware. This paper presents the first approach to verify STMs under relaxed memory models with atomicity of 32 bit loads and stores, and read-modify-write operations. We describe RML, a simple language for expressing concurrent programs. We develop a semantics of RML parametrized by a relaxed memory model. We then present our tool, FOIL, which takes as input the RML description of an STM algorithm restricted to two threads and two variables, and the description of a memory model, and automatically determines the locations of fences, which if inserted, ensure the correctness of the restricted STM algorithm under the given memory model. We use FOIL to verify DSTM, TL2, and McRT STM under the memory models of sequential consistency, total store order, partial store order, and relaxed memory order for two threads and two variables. Finally, we extend the verification results for DSTM and TL2 to an arbitrary number of threads and variables by manually proving that the structural properties of STMs are satisfied at the hardware level of atomicity under the considered relaxed memory models."}],"month":"12","intvolume":" 39","scopus_import":1,"main_file_link":[{"url":"https://infoscience.epfl.ch/record/178042/files/art3A10.10072Fs10703-011-0131-3.pdf","open_access":"1"}]},{"publisher":"IST Austria","oa":1,"page":"20","date_published":"2011-07-11T00:00:00Z","doi":"10.15479/AT:IST-2011-0009","date_created":"2018-12-12T11:38:59Z","has_accepted_license":"1","year":"2011","day":"11","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger"}],"article_processing_charge":"No","title":"An O(n2) time algorithm for alternating Büchi games","citation":{"chicago":"Chatterjee, Krishnendu, and Monika H Henzinger. An O(N2) Time Algorithm for Alternating Büchi Games. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0009.","ista":"Chatterjee K, Henzinger MH. 2011. An O(n2) time algorithm for alternating Büchi games, IST Austria, 20p.","mla":"Chatterjee, Krishnendu, and Monika H. Henzinger. An O(N2) Time Algorithm for Alternating Büchi Games. IST Austria, 2011, doi:10.15479/AT:IST-2011-0009.","apa":"Chatterjee, K., & Henzinger, M. H. (2011). An O(n2) time algorithm for alternating Büchi games. IST Austria. https://doi.org/10.15479/AT:IST-2011-0009","ama":"Chatterjee K, Henzinger MH. An O(N2) Time Algorithm for Alternating Büchi Games. IST Austria; 2011. doi:10.15479/AT:IST-2011-0009","ieee":"K. Chatterjee and M. H. Henzinger, An O(n2) time algorithm for alternating Büchi games. IST Austria, 2011.","short":"K. Chatterjee, M.H. Henzinger, An O(N2) Time Algorithm for Alternating Büchi Games, IST Austria, 2011."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","alternative_title":["IST Austria Technical Report"],"month":"07","abstract":[{"text":"Computing the winning set for Büchi objectives in alternating games on graphs is a central problem in computer aided verification with a large number of applications. The long standing best known upper bound for solving the problem is ̃O(n·m), where n is the number of vertices and m is the number of edges in the graph. We are the first to break the ̃O(n·m) boundary by presenting a new technique that reduces the running time to O(n2). This bound also leads to O(n2) time algorithms for computing the set of almost-sure winning vertices for Büchi objectives (1) in alternating games with probabilistic transitions (improving an earlier bound of O(n·m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n3)), and (3) in Markov decision processes (improving for m > n4/3 an earlier bound of O(min(m1.5, m·n2/3)). We also show that the same technique can be used to compute the maximal end-component decomposition of a graph in time O(n2), which is an improvement over earlier bounds for m > n4/3. Finally, we show how to maintain the winning set for Büchi objectives in alternating games under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per operation. This is the first dynamic algorithm for this problem.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"3165","relation":"later_version"}]},"publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5504","checksum":"0b354264229045d982332fd2cb5b9a26","date_updated":"2020-07-14T12:46:39Z","file_size":388665,"creator":"system","date_created":"2018-12-12T11:53:43Z","file_name":"IST-2011-0009_IST-2011-0009.pdf"}],"language":[{"iso":"eng"}],"type":"technical_report","status":"public","pubrep_id":"15","_id":"5379","file_date_updated":"2020-07-14T12:46:39Z","department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T11:15:12Z","ddc":["000","004"]},{"page":"43","date_published":"2011-07-05T00:00:00Z","doi":"10.15479/AT:IST-2011-0007","related_material":{"record":[{"relation":"later_version","id":"1903","status":"public"},{"relation":"later_version","status":"public","id":"2211"},{"status":"public","id":"2955","relation":"later_version"}]},"date_created":"2018-12-12T11:39:00Z","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","year":"2011","publication_status":"published","file":[{"file_name":"IST-2011-0007_IST-2011-0007.pdf","date_created":"2018-12-12T11:53:27Z","creator":"system","file_size":574055,"date_updated":"2020-07-14T12:46:39Z","file_id":"5488","checksum":"06bf6dfc97f6006e3fd0e9a3f31bc961","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"day":"05","language":[{"iso":"eng"}],"publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"oa":1,"month":"07","abstract":[{"lang":"eng","text":"In two-player finite-state stochastic games of partial obser- vation on graphs, in every state of the graph, the players simultaneously choose an action, and their joint actions determine a probability distri- bution over the successor states. The game is played for infinitely many rounds and thus the players construct an infinite path in the graph. We consider reachability objectives where the first player tries to ensure a target state to be visited almost-surely (i.e., with probability 1) or pos- itively (i.e., with positive probability), no matter the strategy of the second player.\r\n\r\nWe classify such games according to the information and to the power of randomization available to the players. On the basis of information, the game can be one-sided with either (a) player 1, or (b) player 2 having partial observation (and the other player has perfect observation), or two- sided with (c) both players having partial observation. On the basis of randomization, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization.\r\n\r\nOur main results for pure strategies are as follows: (1) For one-sided games with player 2 perfect observation we show that (in contrast to full randomized strategies) belief-based (subset-construction based) strate- gies are not sufficient, and present an exponential upper bound on mem- ory both for almost-sure and positive winning strategies; we show that the problem of deciding the existence of almost-sure and positive winning strategies for player 1 is EXPTIME-complete and present symbolic algo- rithms that avoid the explicit exponential construction. (2) For one-sided games with player 1 perfect observation we show that non-elementary memory is both necessary and sufficient for both almost-sure and posi- tive winning strategies. (3) We show that for the general (two-sided) case finite-memory strategies are sufficient for both positive and almost-sure winning, and at least non-elementary memory is required. We establish the equivalence of the almost-sure winning problems for pure strategies and for randomized strategies with actions invisible. Our equivalence re- sult exhibit serious flaws in previous results in the literature: we show a non-elementary memory lower bound for almost-sure winning whereas an exponential upper bound was previously claimed."}],"oa_version":"Published Version","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"}],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:39Z","title":"Partial-observation stochastic games: How to win when belief fails","date_updated":"2023-02-23T11:05:48Z","citation":{"ista":"Chatterjee K, Doyen L. 2011. Partial-observation stochastic games: How to win when belief fails, IST Austria, 43p.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. Partial-Observation Stochastic Games: How to Win When Belief Fails. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0007.","ama":"Chatterjee K, Doyen L. Partial-Observation Stochastic Games: How to Win When Belief Fails. IST Austria; 2011. doi:10.15479/AT:IST-2011-0007","apa":"Chatterjee, K., & Doyen, L. (2011). Partial-observation stochastic games: How to win when belief fails. IST Austria. https://doi.org/10.15479/AT:IST-2011-0007","ieee":"K. Chatterjee and L. Doyen, Partial-observation stochastic games: How to win when belief fails. IST Austria, 2011.","short":"K. Chatterjee, L. Doyen, Partial-Observation Stochastic Games: How to Win When Belief Fails, IST Austria, 2011.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. Partial-Observation Stochastic Games: How to Win When Belief Fails. IST Austria, 2011, doi:10.15479/AT:IST-2011-0007."},"ddc":["000","005"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"technical_report","status":"public","pubrep_id":"17","_id":"5381"},{"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:39Z","title":"Bounded rationality in concurrent parity games","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"date_updated":"2023-02-23T11:22:53Z","citation":{"chicago":"Chatterjee, Krishnendu. Bounded Rationality in Concurrent Parity Games. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0008.","ista":"Chatterjee K. 2011. Bounded rationality in concurrent parity games, IST Austria, 53p.","mla":"Chatterjee, Krishnendu. Bounded Rationality in Concurrent Parity Games. IST Austria, 2011, doi:10.15479/AT:IST-2011-0008.","ieee":"K. Chatterjee, Bounded rationality in concurrent parity games. IST Austria, 2011.","short":"K. Chatterjee, Bounded Rationality in Concurrent Parity Games, IST Austria, 2011.","ama":"Chatterjee K. Bounded Rationality in Concurrent Parity Games. IST Austria; 2011. doi:10.15479/AT:IST-2011-0008","apa":"Chatterjee, K. (2011). Bounded rationality in concurrent parity games. IST Austria. https://doi.org/10.15479/AT:IST-2011-0008"},"status":"public","pubrep_id":"16","type":"technical_report","_id":"5380","doi":"10.15479/AT:IST-2011-0008","date_published":"2011-07-11T00:00:00Z","related_material":{"record":[{"relation":"later_version","id":"3338","status":"public"}]},"date_created":"2018-12-12T11:39:00Z","page":"53","day":"11","file":[{"date_updated":"2020-07-14T12:46:39Z","file_size":500399,"creator":"system","date_created":"2018-12-12T11:54:22Z","file_name":"IST-2011-0008_IST-2011-0008.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"0fd38186409be819a911c4990fa79d1f","file_id":"5544"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","year":"2011","month":"07","alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","oa":1,"oa_version":"Published Version","abstract":[{"text":"We consider 2-player games played on a finite state space for an infinite number of rounds. The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine the successor state. We study concurrent games with ω-regular winning conditions specified as parity objectives. We consider the qualitative analysis problems: the computation of the almost-sure and limit-sure winning set of states, where player 1 can ensure to win with probability 1 and with probability arbitrarily close to 1, respectively. In general the almost-sure and limit-sure winning strategies require both infinite-memory as well as infinite-precision (to describe probabilities). We study the bounded-rationality problem for qualitative analysis of concurrent parity games, where the strategy set for player 1 is restricted to bounded-resource strategies. In terms of precision, strategies can be deterministic, uniform, finite-precision or infinite-precision; and in terms of memory, strategies can be memoryless, finite-memory or infinite-memory. We present a precise and complete characterization of the qualitative winning sets for all combinations of classes of strategies. In particular, we show that uniform memoryless strategies are as powerful as finite-precision infinite-memory strategies, and infinite-precision memoryless strategies are as powerful as infinite-precision finite-memory strategies. We show that the winning sets can be computed in O(n2d+3) time, where n is the size of the game structure and 2d is the number of priorities (or colors), and our algorithms are symbolic. The membership problem of whether a state belongs to a winning set can be decided in NP ∩ coNP. While this complexity is the same as for the simpler class of turn-based parity games, where in each state only one of the two players has a choice of moves, our algorithms,that are obtained by characterization of the winning sets as μ-calculus formulas, are considerably more involved than those for turn-based games.","lang":"eng"}]},{"date_created":"2018-12-12T11:39:00Z","doi":"10.15479/AT:IST-2011-0006","related_material":{"record":[{"id":"3341","status":"public","relation":"later_version"}]},"date_published":"2011-06-27T00:00:00Z","page":"18","language":[{"iso":"eng"}],"day":"27","file":[{"file_name":"IST-2011-0006_IST-2011-0006.pdf","date_created":"2018-12-12T11:54:24Z","file_size":335997,"date_updated":"2020-07-14T12:46:40Z","creator":"system","file_id":"5546","checksum":"1322b652d6ab07eb5248298a3f91c1cf","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"year":"2011","publication_status":"published","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"month":"06","oa":1,"publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We consider two-player stochastic games played on a finite state space for an infinite num- ber of rounds. The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine a probability distribution over the successor states. We also consider the important special case of turn-based stochastic games where players make moves in turns, rather than concurrently. We study concurrent games with ω-regular winning conditions specified as parity objectives. The value for player 1 for a parity objective is the maximal probability with which the player can guarantee the satisfaction of the objective against all strategies of the opponent. We study the problem of continuity and robustness of the value function in concurrent and turn-based stochastic parity games with respect to imprecision in the transition probabilities. We present quantitative bounds on the difference of the value function (in terms of the imprecision of the transition probabilities) and show the value continuity for structurally equivalent concurrent games (two games are structurally equivalent if the support of the transition func- tion is same and the probabilities differ). We also show robustness of optimal strategies for structurally equivalent turn-based stochastic parity games. Finally we show that the value continuity property breaks without the structurally equivalent assumption (even for Markov chains) and show that our quantitative bound is asymptotically optimal. Hence our results are tight (the assumption is both necessary and sufficient) and optimal (our quantitative bound is asymptotically optimal)."}],"file_date_updated":"2020-07-14T12:46:40Z","title":"Robustness of structurally equivalent concurrent parity games","department":[{"_id":"KrCh"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000","005"],"date_updated":"2023-02-23T11:23:01Z","citation":{"mla":"Chatterjee, Krishnendu. Robustness of Structurally Equivalent Concurrent Parity Games. IST Austria, 2011, doi:10.15479/AT:IST-2011-0006.","ieee":"K. Chatterjee, Robustness of structurally equivalent concurrent parity games. IST Austria, 2011.","short":"K. Chatterjee, Robustness of Structurally Equivalent Concurrent Parity Games, IST Austria, 2011.","ama":"Chatterjee K. Robustness of Structurally Equivalent Concurrent Parity Games. IST Austria; 2011. doi:10.15479/AT:IST-2011-0006","apa":"Chatterjee, K. (2011). Robustness of structurally equivalent concurrent parity games. IST Austria. https://doi.org/10.15479/AT:IST-2011-0006","chicago":"Chatterjee, Krishnendu. Robustness of Structurally Equivalent Concurrent Parity Games. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0006.","ista":"Chatterjee K. 2011. Robustness of structurally equivalent concurrent parity games, IST Austria, 18p."},"pubrep_id":"18","status":"public","type":"technical_report","_id":"5382"},{"date_created":"2018-12-11T12:02:45Z","related_material":{"record":[{"status":"public","id":"5380","relation":"earlier_version"}]},"date_published":"2011-07-11T00:00:00Z","page":"1 - 51","publication":"arXiv","language":[{"iso":"eng"}],"day":"11","year":"2011","publication_status":"published","month":"07","main_file_link":[{"url":"http://arxiv.org/abs/1107.2146","open_access":"1"}],"oa":1,"publisher":"ArXiv","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider 2-player games played on a finite state space for an infinite number of rounds. The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves inde- pendently and simultaneously; the current state and the two moves determine the successor state. We study concurrent games with ω-regular winning conditions specified as parity objectives. We consider the qualitative analysis problems: the computation of the almost-sure and limit-sure winning set of states, where player 1 can ensure to win with probability 1 and with probability arbitrarily close to 1, respec- tively. In general the almost-sure and limit-sure winning strategies require both infinite-memory as well as infinite-precision (to describe probabilities). We study the bounded-rationality problem for qualitative analysis of concurrent parity games, where the strategy set for player 1 is restricted to bounded-resource strategies. In terms of precision, strategies can be deterministic, uniform, finite-precision or infinite- precision; and in terms of memory, strategies can be memoryless, finite-memory or infinite-memory. We present a precise and complete characterization of the qualitative winning sets for all combinations of classes of strategies. In particular, we show that uniform memoryless strategies are as powerful as finite-precision infinite-memory strategies, and infinite-precision memoryless strategies are as power- ful as infinite-precision finite-memory strategies. We show that the winning sets can be computed in O(n2d+3) time, where n is the size of the game structure and 2d is the number of priorities (or colors), and our algorithms are symbolic. The membership problem of whether a state belongs to a winning set can be decided in NP ∩ coNP. While this complexity is the same as for the simpler class of turn-based parity games, where in each state only one of the two players has a choice of moves, our algorithms, that are obtained by characterization of the winning sets as μ-calculus formulas, are considerably more involved than those for turn-based games."}],"title":"Bounded rationality in concurrent parity games","department":[{"_id":"KrCh"}],"external_id":{"arxiv":["1107.2146"]},"publist_id":"3287","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Chatterjee, K. (2011). Bounded rationality in concurrent parity games. arXiv. ArXiv.","ama":"Chatterjee K. Bounded rationality in concurrent parity games. arXiv. 2011:1-51.","ieee":"K. Chatterjee, “Bounded rationality in concurrent parity games,” arXiv. ArXiv, pp. 1–51, 2011.","short":"K. Chatterjee, ArXiv (2011) 1–51.","mla":"Chatterjee, Krishnendu. “Bounded Rationality in Concurrent Parity Games.” ArXiv, ArXiv, 2011, pp. 1–51.","ista":"Chatterjee K. 2011. Bounded rationality in concurrent parity games. arXiv, 1–51, .","chicago":"Chatterjee, Krishnendu. “Bounded Rationality in Concurrent Parity Games.” ArXiv. ArXiv, 2011."},"date_updated":"2023-02-23T12:23:40Z","status":"public","type":"preprint","_id":"3338"},{"publisher":"IEEE","oa":1,"day":"21","has_accepted_license":"1","year":"2011","date_published":"2011-06-21T00:00:00Z","doi":"10.1109/LICS.2011.33","date_created":"2018-12-11T12:02:52Z","article_number":"5970226","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425","grant_number":"214373","name":"Design for Embedded Systems"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Boker, Udi, et al. Temporal Specifications with Accumulative Values. 5970226, IEEE, 2011, doi:10.1109/LICS.2011.33.","apa":"Boker, U., Chatterjee, K., Henzinger, T. A., & Kupferman, O. (2011). Temporal specifications with accumulative values. Presented at the LICS: Logic in Computer Science, Toronto, Canada: IEEE. https://doi.org/10.1109/LICS.2011.33","ama":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. Temporal specifications with accumulative values. In: IEEE; 2011. doi:10.1109/LICS.2011.33","ieee":"U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, “Temporal specifications with accumulative values,” presented at the LICS: Logic in Computer Science, Toronto, Canada, 2011.","short":"U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, in:, IEEE, 2011.","chicago":"Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman. “Temporal Specifications with Accumulative Values.” IEEE, 2011. https://doi.org/10.1109/LICS.2011.33.","ista":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2011. Temporal specifications with accumulative values. LICS: Logic in Computer Science, 5970226."},"title":"Temporal specifications with accumulative values","publist_id":"3259","author":[{"id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi","full_name":"Boker, Udi","last_name":"Boker"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"There is recently a significant effort to add quantitative objectives to formal verification and synthesis. We introduce and investigate the extension of temporal logics with quantitative atomic assertions, aiming for a general and flexible framework for quantitative-oriented specifications. In the heart of quantitative objectives lies the accumulation of values along a computation. It is either the accumulated summation, as with the energy objectives, or the accumulated average, as with the mean-payoff objectives. We investigate the extension of temporal logics with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric variable of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the accumulated sum and average of the values of v from the beginning of the computation up to the current point of time. We also allow the path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an entire computation. We study the border of decidability for extensions of various temporal logics. In particular, we show that extending the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities by prefix-accumulation assertions and extending LTL with path-accumulation assertions, result in temporal logics whose model-checking problem is decidable. The extended logics allow to significantly extend the currently known energy and mean-payoff objectives. Moreover, the prefix-accumulation assertions may be refined with \"controlled-accumulation\", allowing, for example, to specify constraints on the average waiting time between a request and a grant. On the negative side, we show that the fragment we point to is, in a sense, the maximal logic whose extension with prefix-accumulation assertions permits a decidable model-checking procedure. Extending a temporal logic that has the EG or EU modalities, and in particular CTL and LTL, makes the problem undecidable."}],"month":"06","scopus_import":1,"file":[{"date_updated":"2020-07-14T12:46:09Z","file_size":225426,"creator":"system","date_created":"2018-12-12T10:12:42Z","file_name":"IST-2012-83-v1+1_Temporal_specifications_with_accumulative_values.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"792128f5455f0f40f1105f0398e05fa9","file_id":"4960"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"later_version","status":"public","id":"2038"},{"id":"5385","status":"public","relation":"earlier_version"}]},"ec_funded":1,"_id":"3356","status":"public","pubrep_id":"83","type":"conference","conference":{"name":"LICS: Logic in Computer Science","start_date":"2011-06-21","location":"Toronto, Canada","end_date":"2011-06-24"},"ddc":["000","004"],"date_updated":"2023-02-23T12:23:54Z","file_date_updated":"2020-07-14T12:46:09Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}]},{"ec_funded":1,"related_material":{"record":[{"id":"2038","status":"public","relation":"later_version"},{"status":"public","id":"3356","relation":"later_version"}]},"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2011-0003_IST-2011-0003.pdf","date_created":"2018-12-12T11:53:00Z","file_size":366281,"date_updated":"2020-07-14T12:46:41Z","creator":"system","checksum":"8491d0d48c4911620ecd5350b413c11e","file_id":"5461","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"month":"04","alternative_title":["IST Austria Technical Report"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"There is recently a significant effort to add quantitative objectives to formal verification and synthesis. We introduce and investigate the extension of temporal logics with quantitative atomic assertions, aiming for a general and flexible framework for quantitative-oriented specifications. In the heart of quantitative objectives lies the accumulation of values along a computation. It is either the accumulated summation, as with the energy objectives, or the accumulated average, as with the mean-payoff objectives. We investigate the extension of temporal logics with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric variable of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the accumulated sum and average of the values of v from the beginning of the computation up to the current point of time. We also allow the path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an entire computation. We study the border of decidability for extensions of various temporal logics. In particular, we show that extending the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities by prefix-accumulation assertions and extending LTL with path-accumulation assertions, result in temporal logics whose model-checking problem is decidable. The extended logics allow to significantly extend the currently known energy and mean-payoff objectives. Moreover, the prefix-accumulation assertions may be refined with “controlled-accumulation”, allowing, for example, to specify constraints on the average waiting time between a request and a grant. On the negative side, we show that the fragment we point to is, in a sense, the maximal logic whose extension with prefix-accumulation assertions permits a decidable model-checking procedure. Extending a temporal logic that has the EG or EU modalities, and in particular CTL and LTL, makes the problem undecidable."}],"file_date_updated":"2020-07-14T12:46:41Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"ddc":["000","004"],"date_updated":"2023-02-23T11:23:41Z","pubrep_id":"21","status":"public","type":"technical_report","_id":"5385","date_created":"2018-12-12T11:39:02Z","doi":"10.15479/AT:IST-2011-0003","date_published":"2011-04-04T00:00:00Z","page":"14","day":"04","year":"2011","has_accepted_license":"1","oa":1,"publisher":"IST Austria","title":"Temporal specifications with accumulative values","author":[{"id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi","last_name":"Boker","full_name":"Boker, Udi"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Orna","full_name":"Kupferman, Orna","last_name":"Kupferman"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Boker, Udi, et al. 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Temporal specifications with accumulative values, IST Austria, 14p."},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Design for Embedded Systems","grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}]},{"date_updated":"2023-02-23T11:22:48Z","citation":{"ista":"Chen C, Freedman D, Lampert C. 2011. Enforcing topological constraints in random field image segmentation, IST Austria, 69p.","chicago":"Chen, Chao, Daniel Freedman, and Christoph Lampert. 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Instead of including TPs as additional constraints during minimization of the energy function, we devise an efficient algorithm for modifying the unary potentials such that the resulting segmentation is guaranteed with the desired properties. Our method is more flexible in the sense that it handles more topology constraints than previous methods, which were only able to enforce pairwise or global connectivity. In particular, our method is very fast, making it for the first time possible to enforce global topological properties in practical image segmentation tasks.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","oa":1,"month":"03"},{"month":"04","oa":1,"alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","oa_version":"Published Version","abstract":[{"text":"We present a new decidable logic called TREX for expressing constraints about imperative tree data structures. In particular, TREX supports a transitive closure operator that can express reachability constraints, which often appear in data structure invariants. We show that our logic is closed under weakest precondition computation, which enables its use for automated software verification. We further show that satisfiability of formulas in TREX is decidable in NP. The low complexity makes it an attractive alternative to more expensive logics such as monadic second-order logic (MSOL) over trees, which have been traditionally used for reasoning about tree data structures.","lang":"eng"}],"date_created":"2018-12-12T11:39:01Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"3323"}]},"doi":"10.15479/AT:IST-2011-0005","date_published":"2011-04-26T00:00:00Z","page":"25","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"b20029184c4a819c5f4466a4a3d238b5","file_id":"5462","file_size":619053,"date_updated":"2020-07-14T12:46:40Z","creator":"system","file_name":"IST-2011-0005_IST-2011-0005.pdf","date_created":"2018-12-12T11:53:01Z"}],"day":"26","publication_status":"published","year":"2011","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","pubrep_id":"19","status":"public","type":"technical_report","_id":"5383","title":"On an efficient decision procedure for imperative tree data structures","file_date_updated":"2020-07-14T12:46:40Z","department":[{"_id":"ToHe"}],"author":[{"full_name":"Wies, Thomas","last_name":"Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marco","last_name":"Muñiz","full_name":"Muñiz, Marco"},{"full_name":"Kuncak, Viktor","last_name":"Kuncak","first_name":"Viktor"}],"ddc":["000","006"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Wies, T., Muñiz, M., & Kuncak, V. (2011). On an efficient decision procedure for imperative tree data structures. IST Austria. https://doi.org/10.15479/AT:IST-2011-0005","ama":"Wies T, Muñiz M, Kuncak V. On an Efficient Decision Procedure for Imperative Tree Data Structures. IST Austria; 2011. doi:10.15479/AT:IST-2011-0005","ieee":"T. Wies, M. Muñiz, and V. Kuncak, On an efficient decision procedure for imperative tree data structures. IST Austria, 2011.","short":"T. Wies, M. Muñiz, V. Kuncak, On an Efficient Decision Procedure for Imperative Tree Data Structures, IST Austria, 2011.","mla":"Wies, Thomas, et al. On an Efficient Decision Procedure for Imperative Tree Data Structures. IST Austria, 2011, doi:10.15479/AT:IST-2011-0005.","ista":"Wies T, Muñiz M, Kuncak V. 2011. On an efficient decision procedure for imperative tree data structures, IST Austria, 25p.","chicago":"Wies, Thomas, Marco Muñiz, and Viktor Kuncak. On an Efficient Decision Procedure for Imperative Tree Data Structures. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0005."},"date_updated":"2023-02-23T11:22:16Z"},{"_id":"5384","type":"technical_report","status":"public","pubrep_id":"20","date_updated":"2023-02-23T11:05:53Z","citation":{"chicago":"Chatterjee, Krishnendu, and Mathieu Tracol. Decidable Problems for Probabilistic Automata on Infinite Words. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0004.","ista":"Chatterjee K, Tracol M. 2011. Decidable problems for probabilistic automata on infinite words, IST Austria, 30p.","mla":"Chatterjee, Krishnendu, and Mathieu Tracol. Decidable Problems for Probabilistic Automata on Infinite Words. IST Austria, 2011, doi:10.15479/AT:IST-2011-0004.","apa":"Chatterjee, K., & Tracol, M. (2011). Decidable problems for probabilistic automata on infinite words. IST Austria. https://doi.org/10.15479/AT:IST-2011-0004","ama":"Chatterjee K, Tracol M. Decidable Problems for Probabilistic Automata on Infinite Words. IST Austria; 2011. doi:10.15479/AT:IST-2011-0004","short":"K. Chatterjee, M. Tracol, Decidable Problems for Probabilistic Automata on Infinite Words, IST Austria, 2011.","ieee":"K. Chatterjee and M. Tracol, Decidable problems for probabilistic automata on infinite words. IST Austria, 2011."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000","005"],"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","first_name":"Mathieu","last_name":"Tracol","full_name":"Tracol, Mathieu"}],"department":[{"_id":"KrCh"}],"title":"Decidable problems for probabilistic automata on infinite words","file_date_updated":"2020-07-14T12:46:40Z","abstract":[{"lang":"eng","text":"We consider probabilistic automata on infinite words with acceptance defined by parity conditions. We consider three qualitative decision problems: (i) the positive decision problem asks whether there is a word that is accepted with positive probability; (ii) the almost decision problem asks whether there is a word that is accepted with probability 1; and (iii) the limit decision problem asks whether for every ε > 0 there is a word that is accepted with probability at least 1 − ε. We unify and generalize several decidability results for probabilistic automata over infinite words, and identify a robust (closed under union and intersection) subclass of probabilistic automata for which all the qualitative decision problems are decidable for parity conditions. We also show that if the input words are restricted to lasso shape words, then the positive and almost problems are decidable for all probabilistic automata with parity conditions."}],"oa_version":"Published Version","alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","oa":1,"month":"04","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","year":"2011","publication_status":"published","day":"11","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5545","checksum":"f5a0f664fadc335990f5fcf138df19f1","file_size":570827,"date_updated":"2020-07-14T12:46:40Z","creator":"system","file_name":"IST-2011-004_IST-2011-0004.pdf","date_created":"2018-12-12T11:54:23Z"}],"language":[{"iso":"eng"}],"page":"30","related_material":{"record":[{"relation":"later_version","id":"2957","status":"public"}]},"doi":"10.15479/AT:IST-2011-0004","date_published":"2011-04-11T00:00:00Z","date_created":"2018-12-12T11:39:01Z"},{"article_processing_charge":"No","author":[{"full_name":"Chen, Chao","last_name":"Chen","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Freedman","full_name":"Freedman, Daniel","first_name":"Daniel"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert"}],"publist_id":"3294","title":"Enforcing topological constraints in random field image segmentation","department":[{"_id":"HeEd"},{"_id":"ChLa"}],"date_updated":"2023-02-23T12:23:56Z","citation":{"ama":"Chen C, Freedman D, Lampert C. 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Lampert, in:, CVPR: Computer Vision and Pattern Recognition, IEEE, 2011, pp. 2089–2096.","mla":"Chen, Chao, et al. “Enforcing Topological Constraints in Random Field Image Segmentation.” CVPR: Computer Vision and Pattern Recognition, IEEE, 2011, pp. 2089–96, doi:10.1109/CVPR.2011.5995503.","ista":"Chen C, Freedman D, Lampert C. 2011. Enforcing topological constraints in random field image segmentation. CVPR: Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 2089–2096.","chicago":"Chen, Chao, Daniel Freedman, and Christoph Lampert. “Enforcing Topological Constraints in Random Field Image Segmentation.” In CVPR: Computer Vision and Pattern Recognition, 2089–96. 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Instead of including TPs as additional constraints during minimization of the energy function, we devise an efficient algorithm for modifying the unary potentials such that the resulting segmentation is guaranteed with the desired properties. Our method is more flexible in the sense that it handles more topology constraints than previous methods, which were only able to enforce pairwise or global connectivity. In particular, our method is very fast, making it for the first time possible to enforce global topological properties in practical image segmentation tasks.","lang":"eng"}],"acknowledgement":"The first author is supported by the Austrian Science Fund (FWF) grant No. P20134-N13. The authors would like to thank Sebastian Nowozin for helpful discussions.","oa_version":"None"},{"oa_version":"None","abstract":[{"text":"We present a new decidable logic called TREX for expressing constraints about imperative tree data structures. In particular, TREX supports a transitive closure operator that can express reachability constraints, which often appear in data structure invariants. We show that our logic is closed under weakest precondition computation, which enables its use for automated software verification. We further show that satisfiability of formulas in TREX is decidable in NP. The low complexity makes it an attractive alternative to more expensive logics such as monadic second-order logic (MSOL) over trees, which have been traditionally used for reasoning about tree data structures.","lang":"eng"}],"month":"07","intvolume":" 6803","alternative_title":["LNAI "],"publisher":"Springer","scopus_import":1,"quality_controlled":"1","day":"19","language":[{"iso":"eng"}],"year":"2011","publication_status":"published","doi":"10.1007/978-3-642-22438-6_36","related_material":{"record":[{"status":"public","id":"5383","relation":"earlier_version"}]},"date_published":"2011-07-19T00:00:00Z","volume":6803,"date_created":"2018-12-11T12:02:40Z","page":"476 - 491","_id":"3323","status":"public","type":"conference","conference":{"name":"CADE 23: Automated Deduction ","start_date":"2011-07-31","end_date":"2011-08-05","location":"Wrocław, Poland"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Wies, T., Muñiz, M., & Kuncak, V. (2011). An efficient decision procedure for imperative tree data structures (Vol. 6803, pp. 476–491). Presented at the CADE 23: Automated Deduction , Wrocław, Poland: Springer. https://doi.org/10.1007/978-3-642-22438-6_36","ama":"Wies T, Muñiz M, Kuncak V. An efficient decision procedure for imperative tree data structures. In: Vol 6803. Springer; 2011:476-491. doi:10.1007/978-3-642-22438-6_36","ieee":"T. Wies, M. Muñiz, and V. Kuncak, “An efficient decision procedure for imperative tree data structures,” presented at the CADE 23: Automated Deduction , Wrocław, Poland, 2011, vol. 6803, pp. 476–491.","short":"T. Wies, M. Muñiz, V. Kuncak, in:, Springer, 2011, pp. 476–491.","mla":"Wies, Thomas, et al. An Efficient Decision Procedure for Imperative Tree Data Structures. Vol. 6803, Springer, 2011, pp. 476–91, doi:10.1007/978-3-642-22438-6_36.","ista":"Wies T, Muñiz M, Kuncak V. 2011. An efficient decision procedure for imperative tree data structures. CADE 23: Automated Deduction , LNAI , vol. 6803, 476–491.","chicago":"Wies, Thomas, Marco Muñiz, and Viktor Kuncak. “An Efficient Decision Procedure for Imperative Tree Data Structures,” 6803:476–91. Springer, 2011. https://doi.org/10.1007/978-3-642-22438-6_36."},"date_updated":"2023-02-23T12:23:48Z","department":[{"_id":"ToHe"}],"title":"An efficient decision procedure for imperative tree data structures","author":[{"id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Wies","full_name":"Wies, Thomas"},{"last_name":"Muñiz","full_name":"Muñiz, Marco","first_name":"Marco"},{"last_name":"Kuncak","full_name":"Kuncak, Viktor","first_name":"Viktor"}],"publist_id":"3312"},{"publisher":"Springer","quality_controlled":"1","oa":1,"doi":"10.1007/978-3-642-22110-1_20","date_published":"2011-04-21T00:00:00Z","date_created":"2018-12-11T12:02:55Z","page":"243 - 259","day":"21","has_accepted_license":"1","year":"2011","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Design for Embedded Systems","grant_number":"214373"}],"editor":[{"last_name":"Gopalakrishnan","full_name":"Gopalakrishnan, Ganesh","first_name":"Ganesh"},{"first_name":"Shaz","full_name":"Qadeer, Shaz","last_name":"Qadeer"}],"title":"Quantitative synthesis for concurrent programs","author":[{"first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","full_name":"Cerny, Pavol"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun"},{"full_name":"Singh, Rohit","last_name":"Singh","first_name":"Rohit"}],"publist_id":"3247","article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Cerny P, Chatterjee K, Henzinger TA, Radhakrishna A, Singh R. 2011. Quantitative synthesis for concurrent programs. CAV: Computer Aided Verification, LNCS, vol. 6806, 243–259.","chicago":"Cerny, Pavol, Krishnendu Chatterjee, Thomas A Henzinger, Arjun Radhakrishna, and Rohit Singh. “Quantitative Synthesis for Concurrent Programs.” edited by Ganesh Gopalakrishnan and Shaz Qadeer, 6806:243–59. Springer, 2011. https://doi.org/10.1007/978-3-642-22110-1_20.","ieee":"P. Cerny, K. Chatterjee, T. A. Henzinger, A. Radhakrishna, and R. Singh, “Quantitative synthesis for concurrent programs,” presented at the CAV: Computer Aided Verification, Snowbird, USA, 2011, vol. 6806, pp. 243–259.","short":"P. Cerny, K. Chatterjee, T.A. Henzinger, A. Radhakrishna, R. Singh, in:, G. Gopalakrishnan, S. Qadeer (Eds.), Springer, 2011, pp. 243–259.","ama":"Cerny P, Chatterjee K, Henzinger TA, Radhakrishna A, Singh R. Quantitative synthesis for concurrent programs. In: Gopalakrishnan G, Qadeer S, eds. Vol 6806. Springer; 2011:243-259. doi:10.1007/978-3-642-22110-1_20","apa":"Cerny, P., Chatterjee, K., Henzinger, T. A., Radhakrishna, A., & Singh, R. (2011). Quantitative synthesis for concurrent programs. In G. Gopalakrishnan & S. Qadeer (Eds.) (Vol. 6806, pp. 243–259). Presented at the CAV: Computer Aided Verification, Snowbird, USA: Springer. https://doi.org/10.1007/978-3-642-22110-1_20","mla":"Cerny, Pavol, et al. Quantitative Synthesis for Concurrent Programs. Edited by Ganesh Gopalakrishnan and Shaz Qadeer, vol. 6806, Springer, 2011, pp. 243–59, doi:10.1007/978-3-642-22110-1_20."},"month":"04","intvolume":" 6806","alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"text":"We present an algorithmic method for the quantitative, performance-aware synthesis of concurrent programs. The input consists of a nondeterministic partial program and of a parametric performance model. The nondeterminism allows the programmer to omit which (if any) synchronization construct is used at a particular program location. The performance model, specified as a weighted automaton, can capture system architectures by assigning different costs to actions such as locking, context switching, and memory and cache accesses. The quantitative synthesis problem is to automatically resolve the nondeterminism of the partial program so that both correctness is guaranteed and performance is optimal. As is standard for shared memory concurrency, correctness is formalized "specification free", in particular as race freedom or deadlock freedom. For worst-case (average-case) performance, we show that the problem can be reduced to 2-player graph games (with probabilistic transitions) with quantitative objectives. While we show, using game-theoretic methods, that the synthesis problem is Nexp-complete, we present an algorithmic method and an implementation that works efficiently for concurrent programs and performance models of practical interest. We have implemented a prototype tool and used it to synthesize finite-state concurrent programs that exhibit different programming patterns, for several performance models representing different architectures. ","lang":"eng"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5388"}]},"volume":6806,"ec_funded":1,"file":[{"checksum":"c033689355f45742dc7c99b5af13ce7a","file_id":"5174","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2012-76-v1+1_Quantitative_synthesis_for_concurrent_programs.pdf","date_created":"2018-12-12T10:15:51Z","file_size":508946,"date_updated":"2020-07-14T12:46:10Z","creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"76","type":"conference","conference":{"name":"CAV: Computer Aided Verification","end_date":"2011-07-20","location":"Snowbird, USA","start_date":"2011-07-14"},"_id":"3366","file_date_updated":"2020-07-14T12:46:10Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"ddc":["000","004"],"date_updated":"2023-02-23T12:24:01Z"},{"date_updated":"2023-02-23T12:23:59Z","department":[{"_id":"KrCh"}],"_id":"3345","status":"public","type":"conference","conference":{"start_date":"2011-08-22","location":"Warsaw, Poland","end_date":"2011-08-26","name":"MFCS: Mathematical Foundations of Computer Science"},"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"5387","relation":"earlier_version"}]},"volume":6907,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider Markov Decision Processes (MDPs) with mean-payoff parity and energy parity objectives. In system design, the parity objective is used to encode ω-regular specifications, and the mean-payoff and energy objectives can be used to model quantitative resource constraints. The energy condition re- quires that the resource level never drops below 0, and the mean-payoff condi- tion requires that the limit-average value of the resource consumption is within a threshold. While these two (energy and mean-payoff) classical conditions are equivalent for two-player games, we show that they differ for MDPs. We show that the problem of deciding whether a state is almost-sure winning (i.e., winning with probability 1) in energy parity MDPs is in NP ∩ coNP, while for mean- payoff parity MDPs, the problem is solvable in polynomial time, improving a recent PSPACE bound."}],"month":"09","intvolume":" 6907","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1104.2909","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Energy and Mean-Payoff Parity Markov Decision Processes,” 6907:206–18. Springer, 2011. https://doi.org/10.1007/978-3-642-22993-0_21.","ista":"Chatterjee K, Doyen L. 2011. Energy and mean-payoff parity Markov Decision Processes. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 6907, 206–218.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. Energy and Mean-Payoff Parity Markov Decision Processes. Vol. 6907, Springer, 2011, pp. 206–18, doi:10.1007/978-3-642-22993-0_21.","ieee":"K. Chatterjee and L. Doyen, “Energy and mean-payoff parity Markov Decision Processes,” presented at the MFCS: Mathematical Foundations of Computer Science, Warsaw, Poland, 2011, vol. 6907, pp. 206–218.","short":"K. Chatterjee, L. Doyen, in:, Springer, 2011, pp. 206–218.","apa":"Chatterjee, K., & Doyen, L. (2011). Energy and mean-payoff parity Markov Decision Processes (Vol. 6907, pp. 206–218). Presented at the MFCS: Mathematical Foundations of Computer Science, Warsaw, Poland: Springer. https://doi.org/10.1007/978-3-642-22993-0_21","ama":"Chatterjee K, Doyen L. Energy and mean-payoff parity Markov Decision Processes. In: Vol 6907. Springer; 2011:206-218. doi:10.1007/978-3-642-22993-0_21"},"title":"Energy and mean-payoff parity Markov Decision Processes","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"}],"publist_id":"3276","external_id":{"arxiv":["1104.2909"]},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"day":"28","year":"2011","doi":"10.1007/978-3-642-22993-0_21","date_published":"2011-09-28T00:00:00Z","date_created":"2018-12-11T12:02:48Z","page":"206 - 218","quality_controlled":"1","publisher":"Springer","oa":1},{"date_updated":"2023-02-23T11:23:11Z","citation":{"mla":"Chatterjee, Krishnendu, and Laurent Doyen. Energy and Mean-Payoff Parity Markov Decision Processes. IST Austria, 2011, doi:10.15479/AT:IST-2011-0001.","ieee":"K. Chatterjee and L. Doyen, Energy and mean-payoff parity Markov decision processes. IST Austria, 2011.","short":"K. Chatterjee, L. Doyen, Energy and Mean-Payoff Parity Markov Decision Processes, IST Austria, 2011.","apa":"Chatterjee, K., & Doyen, L. (2011). Energy and mean-payoff parity Markov decision processes. IST Austria. https://doi.org/10.15479/AT:IST-2011-0001","ama":"Chatterjee K, Doyen L. Energy and Mean-Payoff Parity Markov Decision Processes. IST Austria; 2011. doi:10.15479/AT:IST-2011-0001","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. Energy and Mean-Payoff Parity Markov Decision Processes. IST Austria, 2011. https://doi.org/10.15479/AT:IST-2011-0001.","ista":"Chatterjee K, Doyen L. 2011. Energy and mean-payoff parity Markov decision processes, IST Austria, 20p."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000","005"],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"}],"file_date_updated":"2020-07-14T12:46:41Z","department":[{"_id":"KrCh"}],"title":"Energy and mean-payoff parity Markov decision processes","_id":"5387","type":"technical_report","status":"public","pubrep_id":"23","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","year":"2011","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5458","checksum":"824d6c70e6d3feb3e836b009e0b3cf73","file_size":329976,"date_updated":"2020-07-14T12:46:41Z","creator":"system","file_name":"IST-2011-0001_IST-2011-0001.pdf","date_created":"2018-12-12T11:52:57Z"}],"day":"16","language":[{"iso":"eng"}],"page":"20","doi":"10.15479/AT:IST-2011-0001","related_material":{"record":[{"status":"public","id":"3345","relation":"later_version"}]},"date_published":"2011-02-16T00:00:00Z","date_created":"2018-12-12T11:39:02Z","abstract":[{"lang":"eng","text":"We consider Markov Decision Processes (MDPs) with mean-payoff parity and energy parity objectives. In system design, the parity objective is used to encode ω-regular specifications, and the mean-payoff and energy objectives can be used to model quantitative resource constraints. The energy condition re- quires that the resource level never drops below 0, and the mean-payoff condi- tion requires that the limit-average value of the resource consumption is within a threshold. While these two (energy and mean-payoff) classical conditions are equivalent for two-player games, we show that they differ for MDPs. We show that the problem of deciding whether a state is almost-sure winning (i.e., winning with probability 1) in energy parity MDPs is in NP ∩ coNP, while for mean- payoff parity MDPs, the problem is solvable in polynomial time, improving a recent PSPACE bound."}],"oa_version":"Published Version","publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"oa":1,"month":"02"},{"status":"public","type":"journal_article","_id":"580","title":"Quantum physics: How to catch a wave","publist_id":"7224","author":[{"full_name":"Onur Hosten","orcid":"0000-0002-2031-204X","last_name":"Hosten","first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"}],"extern":1,"date_updated":"2021-01-12T08:03:34Z","citation":{"chicago":"Hosten, Onur. “Quantum Physics: How to Catch a Wave.” Nature. Nature Publishing Group, 2011. https://doi.org/10.1038/474170a.","ista":"Hosten O. 2011. Quantum physics: How to catch a wave. Nature. 474(7350), 170–171.","mla":"Hosten, Onur. “Quantum Physics: How to Catch a Wave.” Nature, vol. 474, no. 7350, Nature Publishing Group, 2011, pp. 170–71, doi:10.1038/474170a.","short":"O. Hosten, Nature 474 (2011) 170–171.","ieee":"O. Hosten, “Quantum physics: How to catch a wave,” Nature, vol. 474, no. 7350. Nature Publishing Group, pp. 170–171, 2011.","apa":"Hosten, O. (2011). Quantum physics: How to catch a wave. Nature. Nature Publishing Group. https://doi.org/10.1038/474170a","ama":"Hosten O. Quantum physics: How to catch a wave. Nature. 2011;474(7350):170-171. doi:10.1038/474170a"},"month":"06","intvolume":" 474","publisher":"Nature Publishing Group","quality_controlled":0,"doi":"10.1038/474170a","issue":"7350","volume":474,"date_published":"2011-06-08T00:00:00Z","date_created":"2018-12-11T11:47:18Z","page":"170 - 171","day":"08","publication":"Nature","year":"2011","publication_status":"published"},{"abstract":[{"text":"We present two independent schemes for the precise focusing of orthogonal polarizations of light at arbitrary relative locations. The first scheme uses a polarization Sagnac interferometer, the second a set of three birefringent elements.\n\n","lang":"eng"}],"alternative_title":["Optics InfoBase Conference Papers"],"quality_controlled":0,"publisher":"OSA","month":"01","year":"2011","publication_status":"published","day":"01","date_published":"2011-01-01T00:00:00Z","doi":"10.1364/CLEO_AT.2011.JThB130","date_created":"2018-12-11T11:47:20Z","_id":"585","type":"conference","conference":{"name":"QELS: Quantum Electronics and Laser Science"},"status":"public","date_updated":"2021-01-12T08:03:44Z","citation":{"ista":"Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. 2011. Methods towards achieving precise birefringent focusing. QELS: Quantum Electronics and Laser Science, Optics InfoBase Conference Papers, .","chicago":"Schmid, David, Shiraz Hazrat, Radhika Rangarajan, Onur Hosten, Stephan Quint, and Paul Kwiat. “Methods towards Achieving Precise Birefringent Focusing.” OSA, 2011. https://doi.org/10.1364/CLEO_AT.2011.JThB130.","short":"D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, P. Kwiat, in:, OSA, 2011.","ieee":"D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, and P. Kwiat, “Methods towards achieving precise birefringent focusing,” presented at the QELS: Quantum Electronics and Laser Science, 2011.","apa":"Schmid, D., Hazrat, S., Rangarajan, R., Hosten, O., Quint, S., & Kwiat, P. (2011). Methods towards achieving precise birefringent focusing. Presented at the QELS: Quantum Electronics and Laser Science, OSA. https://doi.org/10.1364/CLEO_AT.2011.JThB130","ama":"Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. Methods towards achieving precise birefringent focusing. In: OSA; 2011. doi:10.1364/CLEO_AT.2011.JThB130","mla":"Schmid, David, et al. Methods towards Achieving Precise Birefringent Focusing. OSA, 2011, doi:10.1364/CLEO_AT.2011.JThB130."},"extern":1,"publist_id":"7220","author":[{"last_name":"Schmid","full_name":"Schmid, David","first_name":"David"},{"full_name":"Hazrat, Shiraz","last_name":"Hazrat","first_name":"Shiraz"},{"first_name":"Radhika","last_name":"Rangarajan","full_name":"Rangarajan, Radhika"},{"first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","orcid":"0000-0002-2031-204X","full_name":"Onur Hosten"},{"last_name":"Quint","full_name":"Quint, Stephan","first_name":"Stephan"},{"full_name":"Kwiat, Paul G","last_name":"Kwiat","first_name":"Paul"}],"title":"Methods towards achieving precise birefringent focusing"},{"publist_id":"7223","author":[{"full_name":"Vrijsen, Geert","last_name":"Vrijsen","first_name":"Geert"},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur","last_name":"Hosten","orcid":"0000-0002-2031-204X","full_name":"Onur Hosten"},{"last_name":"Lee","full_name":"Lee, Jongmin","first_name":"Jongmin"},{"last_name":"Bernon","full_name":"Bernon, Simon","first_name":"Simon"},{"last_name":"Kasevich","full_name":"Kasevich, Mark A","first_name":"Mark"}],"title":"Raman lasing with a cold atom gain medium in a high-finesse optical cavity","date_updated":"2021-01-12T08:05:05Z","citation":{"ista":"Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. 2011. Raman lasing with a cold atom gain medium in a high-finesse optical cavity. Physical Review Letters. 107(6).","chicago":"Vrijsen, Geert, Onur Hosten, Jongmin Lee, Simon Bernon, and Mark Kasevich. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.063904.","ieee":"G. Vrijsen, O. Hosten, J. Lee, S. Bernon, and M. Kasevich, “Raman lasing with a cold atom gain medium in a high-finesse optical cavity,” Physical Review Letters, vol. 107, no. 6. American Physical Society, 2011.","short":"G. Vrijsen, O. Hosten, J. Lee, S. Bernon, M. Kasevich, Physical Review Letters 107 (2011).","ama":"Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. Raman lasing with a cold atom gain medium in a high-finesse optical cavity. Physical Review Letters. 2011;107(6). doi:10.1103/PhysRevLett.107.063904","apa":"Vrijsen, G., Hosten, O., Lee, J., Bernon, S., & Kasevich, M. (2011). Raman lasing with a cold atom gain medium in a high-finesse optical cavity. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.063904","mla":"Vrijsen, Geert, et al. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.” Physical Review Letters, vol. 107, no. 6, American Physical Society, 2011, doi:10.1103/PhysRevLett.107.063904."},"extern":1,"type":"journal_article","status":"public","_id":"586","date_created":"2018-12-11T11:47:20Z","date_published":"2011-08-04T00:00:00Z","issue":"6","doi":"10.1103/PhysRevLett.107.063904","volume":107,"publication_status":"published","year":"2011","publication":"Physical Review Letters","day":"04","publisher":"American Physical Society","quality_controlled":0,"intvolume":" 107","month":"08","abstract":[{"text":"We demonstrate a Raman laser using cold Rb87 atoms as the gain medium in a high-finesse optical cavity. We observe robust continuous wave lasing in the atypical regime where single atoms can considerably affect the cavity field. Consequently, we discover unusual lasing threshold behavior in the system causing jumps in lasing power, and propose a model to explain the effect. We also measure the intermode laser linewidth, and observe values as low as 80Hz. The tunable gain properties of this laser suggest multiple directions for future research.","lang":"eng"}]},{"citation":{"ama":"Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. 2011;9(3). doi:10.1371/journal.pbio.1000603","apa":"Bernecky, C., Grob, P., Ebmeier, C., Nogales, E., & Taatjes, D. (2011). Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000603","short":"C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, D. Taatjes, PLoS Biology 9 (2011).","ieee":"C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, and D. Taatjes, “Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly,” PLoS Biology, vol. 9, no. 3. Public Library of Science, 2011.","mla":"Bernecky, Carrie, et al. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF Assembly.” PLoS Biology, vol. 9, no. 3, Public Library of Science, 2011, doi:10.1371/journal.pbio.1000603.","ista":"Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. 2011. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. 9(3).","chicago":"Bernecky, Carrie, Patricia Grob, Christopher Ebmeier, Eva Nogales, and Dylan Taatjes. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF Assembly.” PLoS Biology. Public Library of Science, 2011. https://doi.org/10.1371/journal.pbio.1000603."},"date_updated":"2021-01-12T08:05:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","publist_id":"7209","author":[{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky"},{"last_name":"Grob","full_name":"Grob, Patricia","first_name":"Patricia"},{"last_name":"Ebmeier","full_name":"Ebmeier, Christopher","first_name":"Christopher"},{"last_name":"Nogales","full_name":"Nogales, Eva","first_name":"Eva"},{"first_name":"Dylan","full_name":"Taatjes, Dylan","last_name":"Taatjes"}],"title":"Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly","_id":"597","type":"journal_article","status":"public","year":"2011","publication_status":"published","language":[{"iso":"eng"}],"publication":"PLoS Biology","day":"01","date_created":"2018-12-11T11:47:24Z","issue":"3","volume":9,"date_published":"2011-03-01T00:00:00Z","doi":"10.1371/journal.pbio.1000603","abstract":[{"lang":"eng","text":"The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol II interface is not well-characterized, whereas attempts to structurally define the Mediator-pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly."}],"oa_version":"None","publisher":"Public Library of Science","intvolume":" 9","month":"03"}]