[{"doi":"10.1038/ncb2154","date_published":"2011-01-23T00:00:00Z","language":[{"iso":"eng"}],"citation":{"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","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.","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","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.","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.","short":"N. Plachta, M.T. Bollenbach, S. Pease, S. Fraser, P. Pantazis, Nature Cell Biology 13 (2011) 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."},"publication":"Nature Cell Biology","page":"117 - 123","day":"23","month":"01","scopus_import":1,"author":[{"last_name":"Plachta","first_name":"Nicolas","full_name":"Plachta, Nicolas"},{"full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pease","first_name":"Shirley","full_name":"Pease, Shirley"},{"last_name":"Fraser","first_name":"Scott","full_name":"Fraser, Scott"},{"first_name":"Periklis","last_name":"Pantazis","full_name":"Pantazis, Periklis"}],"oa_version":"None","volume":13,"date_created":"2018-12-11T12:03:17Z","date_updated":"2021-01-12T07:43:24Z","year":"2011","_id":"3429","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","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.","publisher":"Nature Publishing Group","intvolume":" 13","department":[{"_id":"ToBo"}],"publication_status":"published","status":"public","title":"Oct4 kinetics predict cell lineage patterning in the early mammalian embryo","publist_id":"2971","issue":"2","abstract":[{"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.","lang":"eng"}],"type":"journal_article"},{"author":[{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"},{"full_name":"Lämmermann, Tim","first_name":"Tim","last_name":"Lämmermann"}],"volume":769,"date_updated":"2021-01-12T07:43:55Z","date_created":"2018-12-11T12:03:41Z","year":"2011","publisher":"Springer","department":[{"_id":"MiSi"}],"publication_status":"published","publist_id":"2882","doi":"10.1007/978-1-61779-207-6_11","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://pure.mpg.de/pubman/item/item_3219628_1/component/file_3219630/Sixt%20et%20al..pdf"}],"quality_controlled":"1","month":"05","oa_version":"Published Version","_id":"3505","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 769","status":"public","title":"In vitro analysis of chemotactic leukocyte migration in 3D environments","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"}],"type":"journal_article","alternative_title":["Methods in Molecular Biology"],"date_published":"2011-05-17T00:00:00Z","citation":{"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","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.","ista":"Sixt MK, Lämmermann T. 2011. In vitro analysis of chemotactic leukocyte migration in 3D environments. Cell Migration. 769, 149–165.","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","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.","short":"M.K. Sixt, T. Lämmermann, Cell Migration 769 (2011) 149–165.","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."},"publication":"Cell Migration","page":"149 - 165","article_type":"original","article_processing_charge":"No","day":"17"},{"date_published":"2011-03-01T00:00:00Z","citation":{"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","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.","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","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.","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.","short":"F. Palero, G. Guerao, P. Clark, P. Abello, Journal of the Marine Biological Association of the United Kingdom 91 (2011) 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."},"publication":"Journal of the Marine Biological Association of the United Kingdom","page":"485 - 492","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":1,"oa_version":"Published Version","_id":"3784","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 91","status":"public","title":"Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description","issue":"2","abstract":[{"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.","lang":"eng"}],"type":"journal_article","doi":"10.1017/S0025315410000287","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://digital.csic.es/bitstream/10261/32783/3/Palero_et_al_2011.pdf","open_access":"1"}],"quality_controlled":"1","month":"03","author":[{"full_name":"Palero, Ferran","first_name":"Ferran","last_name":"Palero","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329"},{"last_name":"Guerao","first_name":"Guillermo","full_name":"Guerao, Guillermo"},{"first_name":"Paul","last_name":"Clark","full_name":"Clark, Paul"},{"last_name":"Abello","first_name":"Pere","full_name":"Abello, Pere"}],"volume":91,"date_created":"2018-12-11T12:05:09Z","date_updated":"2021-01-12T07:52:10Z","year":"2011","department":[{"_id":"NiBa"}],"publisher":"Cambridge University Press","publication_status":"published","publist_id":"2443"},{"day":"01","month":"01","language":[{"iso":"eng"}],"date_published":"2011-01-01T00:00:00Z","page":"359 - 367","quality_controlled":"1","citation":{"ista":"Fasy BT. 2011. The difference in length of curves in R^n. Acta Sci. Math. (Szeged). 77(1–2), 359–367.","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.","apa":"Fasy, B. T. (2011). The difference in length of curves in R^n. Acta Sci. Math. (Szeged). Szegedi Tudományegyetem.","ama":"Fasy BT. The difference in length of curves in R^n. Acta Sci Math (Szeged). 2011;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.","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.","short":"B.T. Fasy, Acta Sci. Math. (Szeged) 77 (2011) 359–367."},"publication":"Acta Sci. Math. (Szeged)","publist_id":"2446","issue":"1-2","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"}],"type":"journal_article","oa_version":"None","volume":77,"date_updated":"2021-01-12T07:52:09Z","date_created":"2018-12-11T12:05:08Z","author":[{"id":"F65D502E-E68D-11E9-9252-C644099818F6","first_name":"Brittany Terese","last_name":"Fasy","full_name":"Fasy, Brittany Terese"}],"department":[{"_id":"HeEd"}],"publisher":"Szegedi Tudományegyetem","intvolume":" 77","publication_status":"published","title":"The difference in length of curves in R^n","status":"public","acknowledgement":"Funded by Graduate Aid in Areas of National Need (GAANN) Fellowship.","_id":"3781","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011"},{"file":[{"checksum":"aaf22b4d7bd4277ffe8db532119cf474","date_created":"2018-12-12T10:07:42Z","date_updated":"2020-07-14T12:46:16Z","relation":"main_file","file_id":"4640","file_size":436875,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-539-v1+1_2011-B-01-CoveringPacking.pdf"}],"oa_version":"Submitted Version","pubrep_id":"539","ddc":["000"],"title":"Covering and packing with spheres by diagonal distortion in R^n","status":"public","intvolume":" 6570","_id":"3796","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"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.","lang":"eng"}],"alternative_title":["LNCS"],"type":"book_chapter","date_published":"2011-05-03T00:00:00Z","page":"20 - 35","publication":"Rainbow of Computer Science","citation":{"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.","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","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.","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.","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."},"day":"03","has_accepted_license":"1","series_title":"Dedicated to Hermann Maurer on the Occasion of His 70th Birthday","date_created":"2018-12-11T12:05:13Z","date_updated":"2021-01-12T07:52:15Z","volume":6570,"author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"first_name":"Michael","last_name":"Kerber","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael"}],"publication_status":"published","editor":[{"full_name":"Calude, Cristian","first_name":"Cristian","last_name":"Calude"},{"full_name":"Rozenberg, Grzegorz","first_name":"Grzegorz","last_name":"Rozenberg"},{"last_name":"Salomaa","first_name":"Arto","full_name":"Salomaa, Arto"}],"publisher":"Springer","department":[{"_id":"HeEd"}],"year":"2011","file_date_updated":"2020-07-14T12:46:16Z","publist_id":"2427","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-19391-0_2","quality_controlled":"1","oa":1,"month":"05"},{"day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2011-06-01T00:00:00Z","page":"823 - 841","publication":"IJFCS: International Journal of Foundations of Computer Science","citation":{"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.","short":"T.A. Henzinger, B. Jobstmann, V. Wolf, IJFCS: International Journal of Foundations of Computer Science 22 (2011) 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.","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","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.","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.","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"},"abstract":[{"lang":"eng","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."}],"issue":"4","type":"journal_article","file":[{"checksum":"df88431872586c773fbcfea37d7b36a2","date_updated":"2020-07-14T12:46:11Z","date_created":"2018-12-12T10:08:45Z","relation":"main_file","file_id":"4707","file_size":222840,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-628-v1+1_journals-ijfcs-HenzingerJW11.pdf"}],"oa_version":"Submitted Version","pubrep_id":"628","status":"public","ddc":["000"],"title":"Formalisms for specifying Markovian population models","intvolume":" 22","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3381","month":"06","language":[{"iso":"eng"}],"doi":"10.1142/S0129054111008441","quality_controlled":"1","oa":1,"file_date_updated":"2020-07-14T12:46:11Z","publist_id":"3226","date_created":"2018-12-11T12:03:00Z","date_updated":"2023-02-23T11:45:03Z","volume":22,"author":[{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Jobstmann, Barbara","first_name":"Barbara","last_name":"Jobstmann"},{"full_name":"Wolf, Verena","first_name":"Verena","last_name":"Wolf"}],"related_material":{"record":[{"id":"3841","relation":"earlier_version","status":"public"}]},"publication_status":"published","publisher":"World Scientific Publishing","department":[{"_id":"ToHe"}],"year":"2011"},{"publist_id":"7443","extern":"1","author":[{"full_name":"Alpichshev, Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203","first_name":"Zhanybek","last_name":"Alpichshev"},{"first_name":"J G","last_name":"Analytis","full_name":"Analytis, J G"},{"full_name":"Chu, J H","first_name":"J H","last_name":"Chu"},{"last_name":"Fisher","first_name":"I R","full_name":"Fisher, I R"},{"last_name":"Kapitulnik","first_name":"A","full_name":"Kapitulnik, A"}],"date_updated":"2021-01-12T07:52:44Z","date_created":"2018-12-11T11:46:10Z","volume":84,"year":"2011","publication_status":"published","publisher":"American Physical Society","month":"07","doi":"10.1103/PhysRevB.84.041104","language":[{"iso":"eng"}],"external_id":{"arxiv":["1003.2233"]},"main_file_link":[{"url":"https://arxiv.org/abs/1003.2233","open_access":"1"}],"oa":1,"quality_controlled":"1","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"}],"issue":"4","type":"journal_article","oa_version":"Preprint","_id":"386","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"STM imaging of a bound state along a step on the surface of the topological insulator Bi2Te3","status":"public","intvolume":" 84","day":"21","article_processing_charge":"No","date_published":"2011-07-21T00:00:00Z","publication":"Physical Review B - Condensed Matter and Materials Physics","citation":{"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","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.","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).","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","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.","short":"Z. Alpichshev, J.G. Analytis, J.H. Chu, I.R. Fisher, A. Kapitulnik, Physical Review B - Condensed Matter and Materials Physics 84 (2011).","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."},"article_type":"original"},{"date_published":"2011-12-14T00:00:00Z","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.","short":"K. Chatterjee, T.A. Henzinger, V. Prabhu, Logical Methods in Computer Science 7 (2011).","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.","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","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.","ista":"Chatterjee K, Henzinger TA, Prabhu V. 2011. Timed parity games: Complexity and robustness. Logical Methods in Computer Science. 7(4).","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"},"publication":"Logical Methods in Computer Science","has_accepted_license":"1","day":"14","scopus_import":1,"oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":588863,"file_name":"IST-2016-86-v2+1_1011.0688_3_.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:07Z","date_created":"2018-12-12T10:16:42Z","checksum":"3480e1594bbef25ff7462fa93a8a814e","file_id":"5231","relation":"main_file"}],"pubrep_id":"506","intvolume":" 7","ddc":["000","005"],"title":"Timed parity games: Complexity and robustness","status":"public","_id":"3315","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"4","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"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.2168/LMCS-7(4:8)2011","project":[{"_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","call_identifier":"FP7","name":"COMponent-Based Embedded Systems design Techniques"}],"quality_controlled":"1","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"month":"12","volume":7,"date_updated":"2023-02-23T11:46:35Z","date_created":"2018-12-11T12:02:37Z","related_material":{"record":[{"id":"3876","status":"public","relation":"earlier_version"}]},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"last_name":"Prabhu","first_name":"Vinayak","full_name":"Prabhu, Vinayak"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"International Federation of Computational Logic","publication_status":"published","year":"2011","license":"https://creativecommons.org/licenses/by-nd/4.0/","publist_id":"3324","ec_funded":1,"file_date_updated":"2020-07-14T12:46:07Z"},{"author":[{"full_name":"Wang, Bei","first_name":"Bei","last_name":"Wang"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"full_name":"Morozov, Dmitriy","first_name":"Dmitriy","last_name":"Morozov"}],"date_updated":"2021-01-12T07:53:31Z","date_created":"2018-12-11T12:06:09Z","volume":16,"oa_version":"None","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3965","year":"2011","publication_status":"published","title":"Computing elevation maxima by searching the Gauss sphere","status":"public","department":[{"_id":"HeEd"}],"intvolume":" 16","publisher":"ACM","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"}],"issue":"2.2","publist_id":"2161","type":"journal_article","doi":"10.1145/1963190.1970375","date_published":"2011-05-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Journal of Experimental Algorithmics","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","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.","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","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.","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.","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."},"quality_controlled":"1","page":"1 - 13","month":"05","day":"01","scopus_import":1},{"quality_controlled":0,"page":"2069 - 2078","publication":"Development","citation":{"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.","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.","short":"M. Furutani, N. Sakamoto, S. Yoshida, T. Kajiwara, H. Robert, J. Friml, M. Tasaka, Development 138 (2011) 2069–2078.","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.","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"},"date_published":"2011-05-01T00:00:00Z","doi":"10.1242/dev.057745","day":"01","month":"05","publication_status":"published","title":"Polar localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers","status":"public","publisher":"Company of Biologists","intvolume":" 138","year":"2011","_id":"3086","date_updated":"2021-01-12T07:40:57Z","date_created":"2018-12-11T12:01:17Z","volume":138,"author":[{"full_name":"Furutani, Masahiko","last_name":"Furutani","first_name":"Masahiko"},{"first_name":"Norihito","last_name":"Sakamoto","full_name":"Sakamoto, Norihito"},{"first_name":"Shuhei","last_name":"Yoshida","full_name":"Yoshida, Shuhei"},{"full_name":"Kajiwara, Takahito","first_name":"Takahito","last_name":"Kajiwara"},{"full_name":"Robert, Hélène S","first_name":"Hélène","last_name":"Robert"},{"full_name":"Jirí Friml","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tasaka","first_name":"Masao","full_name":"Tasaka, Masao"}],"type":"journal_article","extern":1,"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"}],"issue":"10","publist_id":"3615"}]