[{"abstract":[{"lang":"eng","text":"Termination of a heap-manipulating program generally depends on preconditions that express heap assumptions (i.e., assertions describing reachability, aliasing, separation and sharing in the heap). We present an algorithm for the inference of such preconditions. The algorithm exploits a unique interplay between counterexample-producing abstract termination checker and shape analysis. The shape analysis produces heap assumptions on demand to eliminate counterexamples, i.e., non-terminating abstract computations. The experiments with our prototype implementation indicate its practical potential."}],"publisher":"Springer","quality_controlled":0,"alternative_title":["LNCS"],"intvolume":" 5123","month":"01","publication_status":"published","year":"2008","day":"01","page":"314 - 327","date_created":"2018-12-11T12:08:29Z","date_published":"2008-01-01T00:00:00Z","volume":5123,"doi":"10.1007/978-3-540-70545-1_31","_id":"4366","conference":{"name":"CAV: Computer Aided Verification"},"type":"conference","status":"public","date_updated":"2021-01-12T07:56:26Z","citation":{"short":"A. Podelski, A. Rybalchenko, T. Wies, in:, Springer, 2008, pp. 314–327.","ieee":"A. Podelski, A. Rybalchenko, and T. Wies, “Heap Assumptions on Demand,” presented at the CAV: Computer Aided Verification, 2008, vol. 5123, pp. 314–327.","apa":"Podelski, A., Rybalchenko, A., & Wies, T. (2008). Heap Assumptions on Demand (Vol. 5123, pp. 314–327). Presented at the CAV: Computer Aided Verification, Springer. https://doi.org/10.1007/978-3-540-70545-1_31","ama":"Podelski A, Rybalchenko A, Wies T. Heap Assumptions on Demand. In: Vol 5123. Springer; 2008:314-327. doi:10.1007/978-3-540-70545-1_31","mla":"Podelski, Andreas, et al. Heap Assumptions on Demand. Vol. 5123, Springer, 2008, pp. 314–27, doi:10.1007/978-3-540-70545-1_31.","ista":"Podelski A, Rybalchenko A, Wies T. 2008. Heap Assumptions on Demand. CAV: Computer Aided Verification, LNCS, vol. 5123, 314–327.","chicago":"Podelski, Andreas, Andrey Rybalchenko, and Thomas Wies. “Heap Assumptions on Demand,” 5123:314–27. Springer, 2008. https://doi.org/10.1007/978-3-540-70545-1_31."},"extern":1,"publist_id":"1091","author":[{"last_name":"Podelski","full_name":"Podelski,Andreas","first_name":"Andreas"},{"first_name":"Andrey","last_name":"Rybalchenko","full_name":"Rybalchenko, Andrey"},{"last_name":"Wies","full_name":"Thomas Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"}],"title":"Heap Assumptions on Demand"},{"author":[{"first_name":"Kamal","full_name":"Swarup, Kamal","last_name":"Swarup"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Eva Benková"},{"last_name":"Swarup","full_name":"Swarup, Ranjan","first_name":"Ranjan"},{"first_name":"Ilda","last_name":"Casimiro","full_name":"Casimiro, Ilda"},{"full_name":"Péret, Benjamin","last_name":"Péret","first_name":"Benjamin"},{"first_name":"Yaodong","full_name":"Yang, Yaodong","last_name":"Yang"},{"full_name":"Parry, Geraint","last_name":"Parry","first_name":"Geraint"},{"full_name":"Nielsen, Erik","last_name":"Nielsen","first_name":"Erik"},{"first_name":"Ive","last_name":"De Smet","full_name":"De Smet, Ive"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"first_name":"Mitchell","last_name":"Levesque","full_name":"Levesque, Mitchell P"},{"first_name":"David","full_name":"Carrier, David","last_name":"Carrier"},{"first_name":"Nicholas","last_name":"James","full_name":"James, Nicholas"},{"first_name":"Vanessa","full_name":"Calvo, Vanessa","last_name":"Calvo"},{"full_name":"Ljung, Karin","last_name":"Ljung","first_name":"Karin"},{"full_name":"Kramer, Eric","last_name":"Kramer","first_name":"Eric"},{"last_name":"Roberts","full_name":"Roberts, Rebecca","first_name":"Rebecca"},{"full_name":"Graham, Neil","last_name":"Graham","first_name":"Neil"},{"last_name":"Marillonnet","full_name":"Marillonnet, Sylvestre","first_name":"Sylvestre"},{"first_name":"Kanu","last_name":"Patel","full_name":"Patel, Kanu"},{"full_name":"Jones, Jonathan D","last_name":"Jones","first_name":"Jonathan"},{"full_name":"Taylor, Christopher G","last_name":"Taylor","first_name":"Christopher"},{"first_name":"Daniel","full_name":"Schachtman, Daniel P","last_name":"Schachtman"},{"first_name":"Sean","last_name":"May","full_name":"May, Sean"},{"full_name":"Sandberg, Göran","last_name":"Sandberg","first_name":"Göran"},{"last_name":"Benfey","full_name":"Benfey, Philip N","first_name":"Philip"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Kerr, Ian","last_name":"Kerr","first_name":"Ian"},{"last_name":"Beeckman","full_name":"Beeckman, Tom","first_name":"Tom"},{"first_name":"Laurent","full_name":"Laplaze, Laurent","last_name":"Laplaze"},{"first_name":"Malcolm","last_name":"Bennett","full_name":"Bennett, Malcolm J"}],"publist_id":"3665","title":"The auxin influx carrier LAX3 promotes lateral root emergence","date_updated":"2021-01-12T07:40:37Z","citation":{"mla":"Swarup, Kamal, et al. “The Auxin Influx Carrier LAX3 Promotes Lateral Root Emergence.” Nature Cell Biology, vol. 10, no. 8, Nature Publishing Group, 2008, pp. 946–54, doi:10.1038/ncb1754.","ieee":"K. Swarup et al., “The auxin influx carrier LAX3 promotes lateral root emergence,” Nature Cell Biology, vol. 10, no. 8. Nature Publishing Group, pp. 946–954, 2008.","short":"K. Swarup, E. Benková, R. Swarup, I. Casimiro, B. Péret, Y. Yang, G. Parry, E. Nielsen, I. De Smet, S. Vanneste, M. Levesque, D. Carrier, N. James, V. Calvo, K. Ljung, E. Kramer, R. Roberts, N. Graham, S. Marillonnet, K. Patel, J. Jones, C. Taylor, D. Schachtman, S. May, G. Sandberg, P. Benfey, J. Friml, I. Kerr, T. Beeckman, L. Laplaze, M. Bennett, Nature Cell Biology 10 (2008) 946–954.","apa":"Swarup, K., Benková, E., Swarup, R., Casimiro, I., Péret, B., Yang, Y., … Bennett, M. (2008). The auxin influx carrier LAX3 promotes lateral root emergence. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb1754","ama":"Swarup K, Benková E, Swarup R, et al. The auxin influx carrier LAX3 promotes lateral root emergence. Nature Cell Biology. 2008;10(8):946-954. doi:10.1038/ncb1754","chicago":"Swarup, Kamal, Eva Benková, Ranjan Swarup, Ilda Casimiro, Benjamin Péret, Yaodong Yang, Geraint Parry, et al. “The Auxin Influx Carrier LAX3 Promotes Lateral Root Emergence.” Nature Cell Biology. Nature Publishing Group, 2008. https://doi.org/10.1038/ncb1754.","ista":"Swarup K, Benková E, Swarup R, Casimiro I, Péret B, Yang Y, Parry G, Nielsen E, De Smet I, Vanneste S, Levesque M, Carrier D, James N, Calvo V, Ljung K, Kramer E, Roberts R, Graham N, Marillonnet S, Patel K, Jones J, Taylor C, Schachtman D, May S, Sandberg G, Benfey P, Friml J, Kerr I, Beeckman T, Laplaze L, Bennett M. 2008. The auxin influx carrier LAX3 promotes lateral root emergence. Nature Cell Biology. 10(8), 946–954."},"extern":1,"type":"journal_article","status":"public","_id":"3038","page":"946 - 954","date_created":"2018-12-11T12:01:00Z","issue":"8","date_published":"2008-07-11T00:00:00Z","doi":"10.1038/ncb1754","volume":10,"publication_status":"published","year":"2008","publication":"Nature Cell Biology","day":"11","quality_controlled":0,"publisher":"Nature Publishing Group","intvolume":" 10","month":"07","abstract":[{"text":"Lateral roots originate deep within the parental root from a small number of founder cells at the periphery of vascular tissues and must emerge through intervening layers of tissues. We describe how the hormone auxin, which originates from the developing lateral root, acts as a local inductive signal which re-programmes adjacent cells. Auxin induces the expression of a previously uncharacterized auxin influx carrier LAX3 in cortical and epidermal cells directly overlaying new primordia. Increased LAX3 activity reinforces the auxin-dependent induction of a selection of cell-wall-remodelling enzymes, which are likely to promote cell separation in advance of developing lateral root primordia.","lang":"eng"}]},{"_id":"3036","type":"journal_article","status":"public","date_updated":"2021-01-12T07:40:36Z","citation":{"short":"J. Dubrovsky, M. Sauer, S. Napsucialy Mendivil, M. Ivanchenko, J. Friml, S. Shishkova, J. Celenza, E. Benková, PNAS 105 (2008) 8790–8794.","ieee":"J. Dubrovsky et al., “Auxin acts as a local morphogenetic trigger to specify lateral root founder cells,” PNAS, vol. 105, no. 25. National Academy of Sciences, pp. 8790–8794, 2008.","ama":"Dubrovsky J, Sauer M, Napsucialy Mendivil S, et al. Auxin acts as a local morphogenetic trigger to specify lateral root founder cells. PNAS. 2008;105(25):8790-8794. doi:10.1073/pnas.0712307105","apa":"Dubrovsky, J., Sauer, M., Napsucialy Mendivil, S., Ivanchenko, M., Friml, J., Shishkova, S., … Benková, E. (2008). Auxin acts as a local morphogenetic trigger to specify lateral root founder cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0712307105","mla":"Dubrovsky, Joseph, et al. “Auxin Acts as a Local Morphogenetic Trigger to Specify Lateral Root Founder Cells.” PNAS, vol. 105, no. 25, National Academy of Sciences, 2008, pp. 8790–94, doi:10.1073/pnas.0712307105.","ista":"Dubrovsky J, Sauer M, Napsucialy Mendivil S, Ivanchenko M, Friml J, Shishkova S, Celenza J, Benková E. 2008. Auxin acts as a local morphogenetic trigger to specify lateral root founder cells. PNAS. 105(25), 8790–8794.","chicago":"Dubrovsky, Joseph, Michael Sauer, Selene Napsucialy Mendivil, Maria Ivanchenko, Jiří Friml, Svetlana Shishkova, John Celenza, and Eva Benková. “Auxin Acts as a Local Morphogenetic Trigger to Specify Lateral Root Founder Cells.” PNAS. National Academy of Sciences, 2008. https://doi.org/10.1073/pnas.0712307105."},"extern":1,"author":[{"first_name":"Joseph","last_name":"Dubrovsky","full_name":"Dubrovsky, Joseph G"},{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"first_name":"Selene","full_name":"Napsucialy-Mendivil, Selene","last_name":"Napsucialy Mendivil"},{"last_name":"Ivanchenko","full_name":"Ivanchenko, Maria G","first_name":"Maria"},{"full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"last_name":"Shishkova","full_name":"Shishkova, Svetlana","first_name":"Svetlana"},{"last_name":"Celenza","full_name":"Celenza, John","first_name":"John"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková","orcid":"0000-0002-8510-9739","last_name":"Benková"}],"publist_id":"3666","title":"Auxin acts as a local morphogenetic trigger to specify lateral root founder cells","abstract":[{"lang":"eng","text":"Plants exhibit an exceptional adaptability to different environmental conditions. To a large extent, this adaptability depends on their ability to initiate and form new organs throughout their entire postembryonic life. Plant shoot and root systems unceasingly branch and form axillary shoots or lateral roots, respectively. The first event in the formation of a new organ is specification of founder cells. Several plant hormones, prominent among them auxin, have been implicated in the acquisition of founder cell identity by differentiated cells, but the mechanisms underlying this process are largely elusive. Here, we show that auxin and its local accumulation in root pericycle cells is a necessary and sufficient signal to respecify these cells into lateral root founder cells. Analysis of the alf4-1 mutant suggests that specification of founder cells and the subsequent activation of cell division leading to primordium formation represent two genetically separable events. Time-lapse experiments show that the activation of an auxin response is the earliest detectable event in founder cell specification. Accordingly, local activation of auxin response correlates absolutely with the acquisition of founder cell identity and precedes the actual formation of a lateral root primordium through patterned cell division. Local production and subsequent accumulation of auxin in single pericycle cells induced by Cre-Lox-based activation of auxin synthesis converts them into founder cells. Thus, auxin is the local instructive signal that is sufficient for acquisition of founder cell identity and can be considered a morphogenetic trigger in postembryonic plant organogenesis."}],"publisher":"National Academy of Sciences","quality_controlled":0,"month":"06","intvolume":" 105","year":"2008","publication_status":"published","day":"24","publication":"PNAS","page":"8790 - 8794","doi":"10.1073/pnas.0712307105","volume":105,"issue":"25","date_published":"2008-06-24T00:00:00Z","date_created":"2018-12-11T12:00:59Z"},{"author":[{"first_name":"Eva","last_name":"Růčková","full_name":"Růčková, Eva"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"full_name":"Procházková Schrumpfová, Petra","last_name":"Procházková Schrumpfová","first_name":"Petra"},{"first_name":"Jiří","last_name":"Fajkus","full_name":"Fajkus, Jiří"}],"publist_id":"3671","title":"Role of alternative telomere lengthening unmasked in telomerase knock-out mutant plants","citation":{"chicago":"Růčková, Eva, Jiří Friml, Petra Procházková Schrumpfová, and Jiří Fajkus. “Role of Alternative Telomere Lengthening Unmasked in Telomerase Knock-out Mutant Plants.” Plant Molecular Biology. Springer, 2008. https://doi.org/10.1007/s11103-008-9295-7.","ista":"Růčková E, Friml J, Procházková Schrumpfová P, Fajkus J. 2008. Role of alternative telomere lengthening unmasked in telomerase knock-out mutant plants. Plant Molecular Biology. 66(6), 637–646.","mla":"Růčková, Eva, et al. “Role of Alternative Telomere Lengthening Unmasked in Telomerase Knock-out Mutant Plants.” Plant Molecular Biology, vol. 66, no. 6, Springer, 2008, pp. 637–46, doi:10.1007/s11103-008-9295-7.","apa":"Růčková, E., Friml, J., Procházková Schrumpfová, P., & Fajkus, J. (2008). Role of alternative telomere lengthening unmasked in telomerase knock-out mutant plants. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-008-9295-7","ama":"Růčková E, Friml J, Procházková Schrumpfová P, Fajkus J. Role of alternative telomere lengthening unmasked in telomerase knock-out mutant plants. Plant Molecular Biology. 2008;66(6):637-646. doi:10.1007/s11103-008-9295-7","short":"E. Růčková, J. Friml, P. Procházková Schrumpfová, J. Fajkus, Plant Molecular Biology 66 (2008) 637–646.","ieee":"E. Růčková, J. Friml, P. Procházková Schrumpfová, and J. Fajkus, “Role of alternative telomere lengthening unmasked in telomerase knock-out mutant plants,” Plant Molecular Biology, vol. 66, no. 6. Springer, pp. 637–646, 2008."},"date_updated":"2021-01-12T07:40:34Z","extern":1,"type":"journal_article","status":"public","_id":"3030","page":"637 - 646","date_created":"2018-12-11T12:00:57Z","volume":66,"date_published":"2008-04-01T00:00:00Z","issue":"6","doi":"10.1007/s11103-008-9295-7","year":"2008","publication_status":"published","publication":"Plant Molecular Biology","day":"01","quality_controlled":0,"publisher":"Springer","intvolume":" 66","month":"04","abstract":[{"text":"Telomeres in many eukaryotes are maintained by telomerase in whose absence telomere shortening occurs. However, telomerase-deficient Arabidopsis thaliana mutants (Attert -/-) show extremely low rates of telomere shortening per plant generation (250-500 bp), which does not correspond to the expected outcome of replicative telomere shortening resulting from ca. 1,000 meristem cell divisions per seed-to-seed generation. To investigate the influence of the number of cell divisions per seed-to-seed generation, Attert -/- mutant plants were propagated from seeds coming either from the lower-most or the upper-most siliques (L- and U-plants) and the length of their telomeres were followed over several generations. The rate of telomere shortening was faster in U-plants, than in L-plants, as would be expected from their higher number of cell divisions per generation. However, this trend was observed only in telomeres whose initial length is relatively high and the differences decreased with progressive general telomere shortening over generations. But in generation 4, the L-plants frequently show a net telomere elongation, while the U-plants fail to do so. We propose that this is due to the activation of alternative telomere lengthening (ALT), a process which is activated in early embryonic development in both U- and L-plants, but is overridden in U-plants due to their higher number of cell divisions per generation. These data demonstrate what so far has only been speculated, that in the absence of telomerase, the number of cell divisions within one generation influences the control of telomere lengths. These results also reveal a fast and efficient activation of ALT mechanism(s) in response to the loss of telomerase activity and imply that ALT is probably involved also in normal plant development.","lang":"eng"}]},{"abstract":[{"text":"\n\nCell polarity manifested by the polar cargo delivery to different plasma-membrane domains is a fundamental feature of multicellular organisms. Pathways for polar delivery have been identified in animals; prominent among them is transcytosis, which involves cargo movement between different sides of the cell [1]. PIN transporters are prominent polar cargoes in plants, whose polar subcellular localization determines the directional flow of the signaling molecule auxin [2, 3]. In this study, we address the cellular mechanisms of PIN polar targeting and dynamic polarity changes. We show that apical and basal PIN targeting pathways are interconnected but molecularly distinct by means of ARF GEF vesicle-trafficking regulators. Pharmacological or genetic interference with the Arabidopsis ARF GEF GNOM leads specifically to apicalization of basal cargoes such as PIN1. We visualize the translocation of PIN proteins between the opposite sides of polarized cells in vivo and show that this PIN transcytosis occurs by endocytic recycling and alternative recruitment of the same cargo molecules by apical and basal targeting machineries. Our data suggest that an ARF GEF-dependent transcytosis-like mechanism is operational in plants and provides a plausible mechanism to trigger changes in PIN polarity and hence auxin fluxes during embryogenesis and organogenesis.","lang":"eng"}],"publisher":"Cell Press","quality_controlled":0,"intvolume":" 18","month":"04","publication_status":"published","year":"2008","publication":"Current Biology","day":"08","page":"526 - 531","date_created":"2018-12-11T12:00:58Z","date_published":"2008-04-08T00:00:00Z","issue":"7","volume":18,"doi":"10.1016/j.cub.2008.03.021","_id":"3032","type":"journal_article","status":"public","citation":{"mla":"Kleine Vehn, Jürgen, et al. “ARF GEF Dependent Transcytosis and Polar Delivery of PIN Auxin Carriers in Arabidopsis.” Current Biology, vol. 18, no. 7, Cell Press, 2008, pp. 526–31, doi:10.1016/j.cub.2008.03.021.","ama":"Kleine Vehn J, Dhonukshe P, Sauer M, et al. ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis. Current Biology. 2008;18(7):526-531. doi:10.1016/j.cub.2008.03.021","apa":"Kleine Vehn, J., Dhonukshe, P., Sauer, M., Brewer, P., Wiśniewska, J., Paciorek, T., … Friml, J. (2008). ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2008.03.021","ieee":"J. Kleine Vehn et al., “ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis,” Current Biology, vol. 18, no. 7. Cell Press, pp. 526–531, 2008.","short":"J. Kleine Vehn, P. Dhonukshe, M. Sauer, P. Brewer, J. Wiśniewska, T. Paciorek, E. Benková, J. Friml, Current Biology 18 (2008) 526–531.","chicago":"Kleine Vehn, Jürgen, Pankaj Dhonukshe, Michael Sauer, Philip Brewer, Justyna Wiśniewska, Tomasz Paciorek, Eva Benková, and Jiří Friml. “ARF GEF Dependent Transcytosis and Polar Delivery of PIN Auxin Carriers in Arabidopsis.” Current Biology. Cell Press, 2008. https://doi.org/10.1016/j.cub.2008.03.021.","ista":"Kleine Vehn J, Dhonukshe P, Sauer M, Brewer P, Wiśniewska J, Paciorek T, Benková E, Friml J. 2008. ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis. Current Biology. 18(7), 526–531."},"date_updated":"2021-01-12T07:40:34Z","extern":1,"publist_id":"3670","author":[{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen"},{"first_name":"Pankaj","full_name":"Dhonukshe, Pankaj","last_name":"Dhonukshe"},{"first_name":"Michael","full_name":"Sauer, Michael","last_name":"Sauer"},{"full_name":"Brewer, Philip B","last_name":"Brewer","first_name":"Philip"},{"first_name":"Justyna","last_name":"Wiśniewska","full_name":"Wiśniewska, Justyna"},{"last_name":"Paciorek","full_name":"Paciorek, Tomasz","first_name":"Tomasz"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Eva Benková"},{"last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"title":"ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis"},{"date_updated":"2021-01-12T07:40:35Z","citation":{"ieee":"M. Sauer and J. Friml, “In vitro culture of Arabidopsis embryos ,” in Plant Embryogenesis, vol. 427, M. Suárez and P. Bozhkov, Eds. Humana Press, 2008, pp. 71–76.","short":"M. Sauer, J. Friml, in:, M. Suárez, P. Bozhkov (Eds.), Plant Embryogenesis, Humana Press, 2008, pp. 71–76.","ama":"Sauer M, Friml J. In vitro culture of Arabidopsis embryos . In: Suárez M, Bozhkov P, eds. Plant Embryogenesis. Vol 427. Humana Press; 2008:71-76. doi:10.1007/978-1-59745-273-1_5","apa":"Sauer, M., & Friml, J. (2008). In vitro culture of Arabidopsis embryos . In M. Suárez & P. Bozhkov (Eds.), Plant Embryogenesis (Vol. 427, pp. 71–76). Humana Press. https://doi.org/10.1007/978-1-59745-273-1_5","mla":"Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos .” Plant Embryogenesis, edited by María Suárez and Peter Bozhkov, vol. 427, Humana Press, 2008, pp. 71–76, doi:10.1007/978-1-59745-273-1_5.","ista":"Sauer M, Friml J. 2008.In vitro culture of Arabidopsis embryos . In: Plant Embryogenesis. Methods In Molecular Biology, vol. 427, 71–76.","chicago":"Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos .” In Plant Embryogenesis, edited by María Suárez and Peter Bozhkov, 427:71–76. Humana Press, 2008. https://doi.org/10.1007/978-1-59745-273-1_5."},"extern":1,"author":[{"last_name":"Sauer","full_name":"Sauer, Michael","first_name":"Michael"},{"full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"3667","title":"In vitro culture of Arabidopsis embryos ","editor":[{"first_name":"María","last_name":"Suárez","full_name":"Suárez, María F"},{"last_name":"Bozhkov","full_name":"Bozhkov, Peter V","first_name":"Peter"}],"_id":"3035","type":"book_chapter","status":"public","year":"2008","publication_status":"published","publication":"Plant Embryogenesis","day":"07","page":"71 - 76","date_created":"2018-12-11T12:00:59Z","doi":"10.1007/978-1-59745-273-1_5","volume":427,"date_published":"2008-03-07T00:00:00Z","abstract":[{"text":"Embryogenesis of Arabidopsis thaliana follows a nearly invariant cell division pattern and provides an ideal system for studies of early plant development. However, experimental manipulation with embryogenesis is difficult, as the embryo develops deeply inside maternal tissues. Here, we present a method to culture zygotic Arabidopsis embryos in vitro. It enables culturing for prolonged periods of time from the first developmental stages on. The technique omits excision of the embryo by culturing the entire ovule, which facilitates the manual procedure. It allows pharmacological manipulation of embryo development and does not interfere with standard techniques for localizing gene expression and protein localization in the cultivated embryos.","lang":"eng"}],"alternative_title":["Methods In Molecular Biology"],"quality_controlled":0,"publisher":"Humana Press","intvolume":" 427","month":"03"},{"publication":"Plant Embryogenesis","day":"01","year":"2008","publication_status":"published","date_created":"2018-12-11T12:00:58Z","doi":"10.1007/978-1-59745-273-1_11","volume":427,"date_published":"2008-01-01T00:00:00Z","page":"137 - 144","abstract":[{"text":"\nEmbryogenesis in Arabidopsis thaliana depends on the proper establishment and maintenance of local auxin accumulation. In the course of elucidating the connections between developmental progress and auxin distribution, several techniques have been developed to investigate spatial and temporal distribution of auxin response or accumulation in Arabidopsis embryos. This chapter reviews and describes two independent methods, the detection of the activity of auxin responsive transgenes and immunolocalization of auxin itself.","lang":"eng"}],"intvolume":" 427","month":"01","alternative_title":["Methods In Molecular Biology"],"quality_controlled":0,"publisher":"Humana Press","extern":1,"date_updated":"2021-01-12T07:40:35Z","citation":{"apa":"Sauer, M., & Friml, J. (2008). Visualization of auxin gradients in embryogenesis . In M. Suárez & P. Bozhkov (Eds.), Plant Embryogenesis (Vol. 427, pp. 137–144). Humana Press. https://doi.org/10.1007/978-1-59745-273-1_11","ama":"Sauer M, Friml J. Visualization of auxin gradients in embryogenesis . In: Suárez M, Bozhkov P, eds. Plant Embryogenesis. Vol 427. Humana Press; 2008:137-144. doi:10.1007/978-1-59745-273-1_11","short":"M. Sauer, J. Friml, in:, M. Suárez, P. Bozhkov (Eds.), Plant Embryogenesis, Humana Press, 2008, pp. 137–144.","ieee":"M. Sauer and J. Friml, “Visualization of auxin gradients in embryogenesis ,” in Plant Embryogenesis, vol. 427, M. Suárez and P. Bozhkov, Eds. Humana Press, 2008, pp. 137–144.","mla":"Sauer, Michael, and Jiří Friml. “Visualization of Auxin Gradients in Embryogenesis .” Plant Embryogenesis, edited by María Suárez and Peter Bozhkov, vol. 427, Humana Press, 2008, pp. 137–44, doi:10.1007/978-1-59745-273-1_11.","ista":"Sauer M, Friml J. 2008.Visualization of auxin gradients in embryogenesis . In: Plant Embryogenesis. Methods In Molecular Biology, vol. 427, 137–144.","chicago":"Sauer, Michael, and Jiří Friml. “Visualization of Auxin Gradients in Embryogenesis .” In Plant Embryogenesis, edited by María Suárez and Peter Bozhkov, 427:137–44. Humana Press, 2008. https://doi.org/10.1007/978-1-59745-273-1_11."},"editor":[{"full_name":"Suárez, María F","last_name":"Suárez","first_name":"María"},{"first_name":"Peter","full_name":"Bozhkov, Peter V","last_name":"Bozhkov"}],"title":"Visualization of auxin gradients in embryogenesis ","author":[{"first_name":"Michael","full_name":"Sauer, Michael","last_name":"Sauer"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"publist_id":"3668","_id":"3033","status":"public","type":"book_chapter"},{"external_id":{"pmid":["18678746"]},"author":[{"full_name":"Feraru, Elena","last_name":"Feraru","first_name":"Elena"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"3664","title":"PIN polar targeting","citation":{"chicago":"Feraru, Elena, and Jiří Friml. “PIN Polar Targeting.” Plant Physiology. American Society of Plant Biologists, 2008. https://doi.org/10.1104/pp.108.121756.","ista":"Feraru E, Friml J. 2008. PIN polar targeting. Plant Physiology. 147(4), 1553–1559.","mla":"Feraru, Elena, and Jiří Friml. “PIN Polar Targeting.” Plant Physiology, vol. 147, no. 4, American Society of Plant Biologists, 2008, pp. 1553–59, doi:10.1104/pp.108.121756.","ama":"Feraru E, Friml J. PIN polar targeting. Plant Physiology. 2008;147(4):1553-1559. doi:10.1104/pp.108.121756","apa":"Feraru, E., & Friml, J. (2008). PIN polar targeting. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.108.121756","short":"E. Feraru, J. Friml, Plant Physiology 147 (2008) 1553–1559.","ieee":"E. Feraru and J. Friml, “PIN polar targeting,” Plant Physiology, vol. 147, no. 4. American Society of Plant Biologists, pp. 1553–1559, 2008."},"date_updated":"2021-01-12T07:40:36Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","type":"journal_article","status":"public","_id":"3037","page":"1553 - 1559","date_created":"2018-12-11T12:01:00Z","doi":"10.1104/pp.108.121756","volume":147,"date_published":"2008-08-04T00:00:00Z","issue":"4","publication_status":"published","year":"2008","publication":"Plant Physiology","language":[{"iso":"eng"}],"day":"04","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2492634/","open_access":"1"}],"oa":1,"publisher":"American Society of Plant Biologists","quality_controlled":"1","intvolume":" 147","month":"08","oa_version":"Published Version","pmid":1},{"_id":"3034","status":"public","article_type":"letter_note","type":"journal_article","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:40:35Z","citation":{"short":"J. Friml, M. Sauer, Nature 453 (2008) 298–299.","ieee":"J. Friml and M. Sauer, “Plant biology: In their neighbour’s shadow,” Nature, vol. 453, no. 7193. Nature Publishing Group, pp. 298–299, 2008.","ama":"Friml J, Sauer M. Plant biology: In their neighbour’s shadow. Nature. 2008;453(7193):298-299. doi:10.1038/453298a","apa":"Friml, J., & Sauer, M. (2008). Plant biology: In their neighbour’s shadow. Nature. Nature Publishing Group. https://doi.org/10.1038/453298a","mla":"Friml, Jiří, and Michael Sauer. “Plant Biology: In Their Neighbour’s Shadow.” Nature, vol. 453, no. 7193, Nature Publishing Group, 2008, pp. 298–99, doi:10.1038/453298a.","ista":"Friml J, Sauer M. 2008. Plant biology: In their neighbour’s shadow. Nature. 453(7193), 298–299.","chicago":"Friml, Jiří, and Michael Sauer. “Plant Biology: In Their Neighbour’s Shadow.” Nature. Nature Publishing Group, 2008. https://doi.org/10.1038/453298a."},"title":"Plant biology: In their neighbour's shadow","author":[{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","last_name":"Sauer","full_name":"Sauer, Michael"}],"publist_id":"3669","oa_version":"None","abstract":[{"lang":"eng","text":"They can't move away from shade, so plants resort to a molecular solution to find a place in the sun. The action they take is quite radical, and involves a reprogramming of their development. "}],"month":"05","intvolume":" 453","publisher":"Nature Publishing Group","quality_controlled":"1","day":"15","publication":"Nature","language":[{"iso":"eng"}],"publication_status":"published","year":"2008","date_published":"2008-05-15T00:00:00Z","doi":"10.1038/453298a","volume":453,"issue":"7193","date_created":"2018-12-11T12:00:59Z","page":"298 - 299"},{"quality_controlled":0,"publisher":"IEEE","month":"06","intvolume":" 30","abstract":[{"text":"Among the most exciting advances in early vision has been the development of efficient energy minimization algorithms for pixel-labeling tasks such as depth or texture computation. It has been known for decades that such problems can be elegantly expressed as Markov random fields, yet the resulting energy minimization problems have been widely viewed as intractable. Algorithms such as graph cuts and loopy belief propagation (LBP) have proven to be very powerful: For example, such methods form the basis for almost all the top-performing stereo methods. However, the trade-offs among different energy minimization algorithms are still not well understood. In this paper, we describe a set of energy minimization benchmarks and use them to compare the solution quality and runtime of several common energy minimization algorithms. We investigate three promising methods-graph cuts, LBP, and tree-reweighted message passing-in addition to the well-known older iterated conditional mode (ICM) algorithm. Our benchmark problems are drawn from published energy functions used for stereo, image stitching, interactive segmentation, and denoising. We also provide a general-purpose software interface that allows vision researchers to easily switch between optimization methods. The benchmarks, code, images, and results are available at http://vision.middlebury.edu/MRF/.","lang":"eng"}],"page":"1068 - 1080","date_published":"2008-06-01T00:00:00Z","issue":"6","doi":"10.1109/TPAMI.2007.70844","volume":30,"date_created":"2018-12-11T12:01:57Z","publication_status":"published","year":"2008","day":"01","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","type":"journal_article","status":"public","_id":"3196","publist_id":"3488","author":[{"full_name":"Szeliski, Richard S","last_name":"Szeliski","first_name":"Richard"},{"full_name":"Zabih, Ramin","last_name":"Zabih","first_name":"Ramin"},{"first_name":"Daniel","last_name":"Scharstein","full_name":"Scharstein, Daniel"},{"full_name":"Veksler, Olga","last_name":"Veksler","first_name":"Olga"},{"full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"},{"first_name":"Aseem","full_name":"Agarwala, Aseem","last_name":"Agarwala"},{"first_name":"Marshall","full_name":"Tappen, Marshall F","last_name":"Tappen"},{"first_name":"Carsten","full_name":"Rother, Carsten","last_name":"Rother"}],"title":"A comparative study of energy minimization methods for Markov random fields with smoothness-based priors","date_updated":"2021-01-12T07:41:43Z","citation":{"ista":"Szeliski R, Zabih R, Scharstein D, Veksler O, Kolmogorov V, Agarwala A, Tappen M, Rother C. 2008. A comparative study of energy minimization methods for Markov random fields with smoothness-based priors. IEEE Transactions on Pattern Analysis and Machine Intelligence. 30(6), 1068–1080.","chicago":"Szeliski, Richard, Ramin Zabih, Daniel Scharstein, Olga Veksler, Vladimir Kolmogorov, Aseem Agarwala, Marshall Tappen, and Carsten Rother. “A Comparative Study of Energy Minimization Methods for Markov Random Fields with Smoothness-Based Priors.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2008. https://doi.org/10.1109/TPAMI.2007.70844.","apa":"Szeliski, R., Zabih, R., Scharstein, D., Veksler, O., Kolmogorov, V., Agarwala, A., … Rother, C. (2008). A comparative study of energy minimization methods for Markov random fields with smoothness-based priors. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2007.70844","ama":"Szeliski R, Zabih R, Scharstein D, et al. A comparative study of energy minimization methods for Markov random fields with smoothness-based priors. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2008;30(6):1068-1080. doi:10.1109/TPAMI.2007.70844","short":"R. Szeliski, R. Zabih, D. Scharstein, O. Veksler, V. Kolmogorov, A. Agarwala, M. Tappen, C. Rother, IEEE Transactions on Pattern Analysis and Machine Intelligence 30 (2008) 1068–1080.","ieee":"R. Szeliski et al., “A comparative study of energy minimization methods for Markov random fields with smoothness-based priors,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 30, no. 6. IEEE, pp. 1068–1080, 2008.","mla":"Szeliski, Richard, et al. “A Comparative Study of Energy Minimization Methods for Markov Random Fields with Smoothness-Based Priors.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 30, no. 6, IEEE, 2008, pp. 1068–80, doi:10.1109/TPAMI.2007.70844."},"extern":1},{"status":"public","type":"conference","conference":{"name":"ECCV: European Conference on Computer Vision"},"_id":"3198","title":"Feature correspondence via graph matching: Models and global optimization","publist_id":"3485","author":[{"full_name":"Torresani, Lorenzo","last_name":"Torresani","first_name":"Lorenzo"},{"full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"}],"extern":1,"citation":{"apa":"Torresani, L., Kolmogorov, V., & Rother, C. (2008). Feature correspondence via graph matching: Models and global optimization (Vol. 5303, pp. 596–609). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/978-3-540-88688-4_44","ama":"Torresani L, Kolmogorov V, Rother C. Feature correspondence via graph matching: Models and global optimization. In: Vol 5303. Springer; 2008:596-609. doi:10.1007/978-3-540-88688-4_44","short":"L. Torresani, V. Kolmogorov, C. Rother, in:, Springer, 2008, pp. 596–609.","ieee":"L. Torresani, V. Kolmogorov, and C. Rother, “Feature correspondence via graph matching: Models and global optimization,” presented at the ECCV: European Conference on Computer Vision, 2008, vol. 5303, pp. 596–609.","mla":"Torresani, Lorenzo, et al. Feature Correspondence via Graph Matching: Models and Global Optimization. Vol. 5303, Springer, 2008, pp. 596–609, doi:10.1007/978-3-540-88688-4_44.","ista":"Torresani L, Kolmogorov V, Rother C. 2008. Feature correspondence via graph matching: Models and global optimization. ECCV: European Conference on Computer Vision, LNCS, vol. 5303, 596–609.","chicago":"Torresani, Lorenzo, Vladimir Kolmogorov, and Carsten Rother. “Feature Correspondence via Graph Matching: Models and Global Optimization,” 5303:596–609. Springer, 2008. https://doi.org/10.1007/978-3-540-88688-4_44."},"date_updated":"2021-01-12T07:41:44Z","month":"01","intvolume":" 5303","alternative_title":["LNCS"],"quality_controlled":0,"publisher":"Springer","main_file_link":[{"open_access":"0","url":"http://research-srv.microsoft.com/pubs/70610/eccv08-MatchingMRF.pdf"}],"abstract":[{"lang":"eng","text":"In this paper we present a new approach for establishing correspondences between sparse image features related by an unknown non-rigid mapping and corrupted by clutter and occlusion, such as points extracted from a pair of images containing a human figure in distinct poses. We formulate this matching task as an energy minimization problem by defining a complex objective function of the appearance and the spatial arrangement of the features. Optimization of this energy is an instance of graph matching, which is in general a NP-hard problem. We describe a novel graph matching optimization technique, which we refer to as dual decomposition (DD), and demonstrate on a variety of examples that this method outperforms existing graph matching algorithms. In the majority of our examples DD is able to find the global minimum within a minute. The ability to globally optimize the objective allows us to accurately learn the parameters of our matching model from training examples. We show on several matching tasks that our learned model yields results superior to those of state-of-the-art methods. "}],"volume":5303,"date_published":"2008-01-01T00:00:00Z","doi":"10.1007/978-3-540-88688-4_44","date_created":"2018-12-11T12:01:58Z","page":"596 - 609","day":"01","publication_status":"published","year":"2008"},{"abstract":[{"lang":"eng","text":"Graph cut is a popular technique for interactive image segmentation. However, it has certain shortcomings. In particular, graph cut has problems with segmenting thin elongated objects due to the ldquoshrinking biasrdquo. To overcome this problem, we propose to impose an additional connectivity prior, which is a very natural assumption about objects. We formulate several versions of the connectivity constraint and show that the corresponding optimization problems are all NP-hard. For some of these versions we propose two optimization algorithms: (i) a practical heuristic technique which we call DijkstraGC, and (ii) a slow method based on problem decomposition which provides a lower bound on the problem. We use the second technique to verify that for some practical examples DijkstraGC is able to find the global minimum."}],"quality_controlled":0,"publisher":"IEEE","main_file_link":[{"open_access":"0","url":"http://research.microsoft.com/pubs/80485/CVPR08-ConnectedGC.pdf"}],"month":"08","publication_status":"published","year":"2008","day":"05","doi":"10.1109/CVPR.2008.4587440","date_published":"2008-08-05T00:00:00Z","date_created":"2018-12-11T12:01:57Z","_id":"3195","type":"conference","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"status":"public","date_updated":"2021-01-12T07:41:43Z","citation":{"ista":"Vicente S, Kolmogorov V, Rother C. 2008. Graph cut based image segmentation with connectivity priors. CVPR: Computer Vision and Pattern Recognition.","chicago":"Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Graph Cut Based Image Segmentation with Connectivity Priors.” IEEE, 2008. https://doi.org/10.1109/CVPR.2008.4587440.","short":"S. Vicente, V. Kolmogorov, C. Rother, in:, IEEE, 2008.","ieee":"S. Vicente, V. Kolmogorov, and C. Rother, “Graph cut based image segmentation with connectivity priors,” presented at the CVPR: Computer Vision and Pattern Recognition, 2008.","ama":"Vicente S, Kolmogorov V, Rother C. Graph cut based image segmentation with connectivity priors. In: IEEE; 2008. doi:10.1109/CVPR.2008.4587440","apa":"Vicente, S., Kolmogorov, V., & Rother, C. (2008). Graph cut based image segmentation with connectivity priors. Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2008.4587440","mla":"Vicente, Sara, et al. Graph Cut Based Image Segmentation with Connectivity Priors. IEEE, 2008, doi:10.1109/CVPR.2008.4587440."},"extern":1,"publist_id":"3487","author":[{"first_name":"Sara","last_name":"Vicente","full_name":"Vicente, Sara"},{"last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"},{"first_name":"Carsten","full_name":"Rother, Carsten","last_name":"Rother"}],"title":"Graph cut based image segmentation with connectivity priors"},{"_id":"3224","type":"conference","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"status":"public","citation":{"chicago":"Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Prashant Puniya. “A New Mode of Operation for Block Ciphers and Length Preserving MACs,” 4965:198–219. Springer, 2008. https://doi.org/10.1007/978-3-540-78967-3_12.","ista":"Dodis Y, Pietrzak KZ, Puniya P. 2008. A new mode of operation for block ciphers and length preserving MACs. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 4965, 198–219.","mla":"Dodis, Yevgeniy, et al. A New Mode of Operation for Block Ciphers and Length Preserving MACs. Vol. 4965, Springer, 2008, pp. 198–219, doi:10.1007/978-3-540-78967-3_12.","apa":"Dodis, Y., Pietrzak, K. Z., & Puniya, P. (2008). A new mode of operation for block ciphers and length preserving MACs (Vol. 4965, pp. 198–219). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/978-3-540-78967-3_12","ama":"Dodis Y, Pietrzak KZ, Puniya P. A new mode of operation for block ciphers and length preserving MACs. In: Vol 4965. Springer; 2008:198-219. doi:10.1007/978-3-540-78967-3_12","ieee":"Y. Dodis, K. Z. Pietrzak, and P. Puniya, “A new mode of operation for block ciphers and length preserving MACs,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2008, vol. 4965, pp. 198–219.","short":"Y. Dodis, K.Z. Pietrzak, P. Puniya, in:, Springer, 2008, pp. 198–219."},"date_updated":"2021-01-12T07:41:55Z","extern":1,"author":[{"first_name":"Yevgeniy","full_name":"Dodis, Yevgeniy","last_name":"Dodis"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Krzysztof Pietrzak","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"},{"last_name":"Puniya","full_name":"Puniya, Prashant","first_name":"Prashant"}],"publist_id":"3456","title":"A new mode of operation for block ciphers and length preserving MACs","abstract":[{"text":"We propose a new mode of operation, enciphered CBC, for domain extension of length-preserving functions (like block ciphers), which is a variation on the popular CBC mode of operation. Our new mode is twice slower than CBC, but has many (property-preserving) properties not enjoyed by CBC and other known modes. Most notably, it yields the first constant-rate Variable Input Length (VIL) MAC from any length preserving Fixed Input Length (FIL) MAC. This answers the question of Dodis and Puniya from Eurocrypt 2007. Further, our mode is a secure domain extender for PRFs (with basically the same security as encrypted CBC). This provides a hedge against the security of the block cipher: if the block cipher is pseudorandom, one gets a VIL-PRF, while if it is "only" unpredictable, one "at least" gets a VIL-MAC. Additionally, our mode yields a VIL random oracle (and, hence, a collision-resistant hash function) when instantiated with length-preserving random functions, or even random permutations (which can be queried from both sides). This means that one does not have to re-key the block cipher during the computation, which was critically used in most previous constructions (analyzed in the ideal cipher model). ","lang":"eng"}],"publisher":"Springer","alternative_title":["LNCS"],"quality_controlled":0,"month":"04","intvolume":" 4965","publication_status":"published","year":"2008","day":"28","page":"198 - 219","date_published":"2008-04-28T00:00:00Z","doi":"10.1007/978-3-540-78967-3_12","volume":4965,"date_created":"2018-12-11T12:02:07Z"},{"day":"06","year":"2008","publication_status":"published","issue":"PART 2","related_material":{"record":[{"id":"2852","status":"public","relation":"later_version"}]},"volume":5126,"doi":"10.1007/978-3-540-70583-3_53","date_published":"2008-08-06T00:00:00Z","date_created":"2018-12-11T12:02:07Z","page":"655 - 666","abstract":[{"text":"A robust multi-property combiner for a set of security properties merges two hash functions such that the resulting function satisfies each of the properties which at least one of the two starting functions has. Fischlin and Lehmann (TCC 2008) recently constructed a combiner which simultaneously preserves collision-resistance, target collision-resistance, message authentication, pseudorandomness and indifferentiability from a random oracle (IRO). Their combiner produces outputs of 5n bits, where n denotes the output length of the underlying hash functions. In this paper we propose improved combiners with shorter outputs. By sacrificing the indifferentiability from random oracles we obtain a combiner which preserves all of the other aforementioned properties but with output length 2n only. This matches a lower bound for black-box combiners for collision-resistance as the only property, showing that the other properties can be achieved without penalizing the length of the hash values. We then propose a combiner which also preserves the IRO property, slightly increasing the output length to 2n + ω(logn). Finally, we show that a twist on our combiners also makes them robust for one-wayness (but at the price of a fixed input length). ","lang":"eng"}],"month":"08","intvolume":" 5126","publisher":"Springer","quality_controlled":0,"alternative_title":["LNCS"],"extern":1,"citation":{"mla":"Fischlin, Marc, et al. Robust Multi Property Combiners for Hash Functions Revisited. Vol. 5126, no. PART 2, Springer, 2008, pp. 655–66, doi:10.1007/978-3-540-70583-3_53.","apa":"Fischlin, M., Lehmann, A., & Pietrzak, K. Z. (2008). Robust multi property combiners for hash functions revisited (Vol. 5126, pp. 655–666). Presented at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/978-3-540-70583-3_53","ama":"Fischlin M, Lehmann A, Pietrzak KZ. Robust multi property combiners for hash functions revisited. In: Vol 5126. Springer; 2008:655-666. doi:10.1007/978-3-540-70583-3_53","ieee":"M. Fischlin, A. Lehmann, and K. Z. Pietrzak, “Robust multi property combiners for hash functions revisited,” presented at the ICALP: Automata, Languages and Programming, 2008, vol. 5126, no. PART 2, pp. 655–666.","short":"M. Fischlin, A. Lehmann, K.Z. Pietrzak, in:, Springer, 2008, pp. 655–666.","chicago":"Fischlin, Marc, Anja Lehmann, and Krzysztof Z Pietrzak. “Robust Multi Property Combiners for Hash Functions Revisited,” 5126:655–66. Springer, 2008. https://doi.org/10.1007/978-3-540-70583-3_53.","ista":"Fischlin M, Lehmann A, Pietrzak KZ. 2008. Robust multi property combiners for hash functions revisited. ICALP: Automata, Languages and Programming, LNCS, vol. 5126, 655–666."},"date_updated":"2023-02-23T11:01:10Z","title":"Robust multi property combiners for hash functions revisited","publist_id":"3454","author":[{"last_name":"Fischlin","full_name":"Fischlin, Marc","first_name":"Marc"},{"full_name":"Lehmann, Anja","last_name":"Lehmann","first_name":"Anja"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Krzysztof Pietrzak"}],"_id":"3225","status":"public","type":"conference","conference":{"name":"ICALP: Automata, Languages and Programming"}},{"abstract":[{"text":"The filamentous fungus Aspergillus fumigatus is responsible for a lethal disease called Invasive Aspergillosis that affects immunocompromised patients. This disease, like other human fungal diseases, is generally treated by compounds targeting the primary fungal cell membrane sterol. Recently, glucan synthesis inhibitors were added to the limited antifungal arsenal and encouraged the search for novel targets in cell wall biosynthesis. Although galactomannan is a major component of the A. fumigatus cell wall and extracellular matrix, the biosynthesis and role of galactomannan are currently unknown. By a targeted gene deletion approach, we demonstrate that UDP-galactopyranose mutase, a key enzyme of galactofuranose metabolism, controls the biosynthesis of galactomannan and galactofuranose containing glycoconjugates. The glfA deletion mutant generated in this study is devoid of galactofuranose and displays attenuated virulence in a low-dose mouse model of invasive aspergillosis that likely reflects the impaired growth of the mutant at mammalian body temperature. Furthermore, the absence of galactofuranose results in a thinner cell wall that correlates with an increased susceptibility to several antifungal agents. The UDP-galactopyranose mutase thus appears to be an appealing adjunct therapeutic target in combination with other drugs against A. fumigatus. Its absence from mammalian cells indeed offers a considerable advantage to achieve therapeutic selectivity. ","lang":"eng"}],"quality_controlled":0,"publisher":"American Society for Microbiology","month":"06","intvolume":" 7","publication_status":"published","year":"2008","day":"13","publication":"Eukaryotic Cell","page":"1268 - 1277","issue":"8","volume":7,"doi":"10.1128/EC.00065-08","date_published":"2008-06-13T00:00:00Z","date_created":"2018-12-11T12:02:29Z","_id":"3291","type":"journal_article","status":"public","date_updated":"2021-01-12T07:42:26Z","citation":{"chicago":"Schmalhorst, Philipp S, Sven Krappmann, Wouter Vervecken, Manfred Rohde, Meike Müller, Gerhard Braus, Roland Contreras, Armin Braun, Hans Bakker, and Françoise Routier. “Contribution of Galactofuranose to the Virulence of the Opportunistic Pathogen Aspergillus Fumigatus.” Eukaryotic Cell. American Society for Microbiology, 2008. https://doi.org/10.1128/EC.00065-08.","ista":"Schmalhorst PS, Krappmann S, Vervecken W, Rohde M, Müller M, Braus G, Contreras R, Braun A, Bakker H, Routier F. 2008. Contribution of galactofuranose to the virulence of the opportunistic pathogen Aspergillus fumigatus. Eukaryotic Cell. 7(8), 1268–1277.","mla":"Schmalhorst, Philipp S., et al. “Contribution of Galactofuranose to the Virulence of the Opportunistic Pathogen Aspergillus Fumigatus.” Eukaryotic Cell, vol. 7, no. 8, American Society for Microbiology, 2008, pp. 1268–77, doi:10.1128/EC.00065-08.","ieee":"P. S. Schmalhorst et al., “Contribution of galactofuranose to the virulence of the opportunistic pathogen Aspergillus fumigatus,” Eukaryotic Cell, vol. 7, no. 8. American Society for Microbiology, pp. 1268–1277, 2008.","short":"P.S. Schmalhorst, S. Krappmann, W. Vervecken, M. Rohde, M. Müller, G. Braus, R. Contreras, A. Braun, H. Bakker, F. Routier, Eukaryotic Cell 7 (2008) 1268–1277.","ama":"Schmalhorst PS, Krappmann S, Vervecken W, et al. Contribution of galactofuranose to the virulence of the opportunistic pathogen Aspergillus fumigatus. Eukaryotic Cell. 2008;7(8):1268-1277. doi:10.1128/EC.00065-08","apa":"Schmalhorst, P. S., Krappmann, S., Vervecken, W., Rohde, M., Müller, M., Braus, G., … Routier, F. (2008). Contribution of galactofuranose to the virulence of the opportunistic pathogen Aspergillus fumigatus. Eukaryotic Cell. American Society for Microbiology. https://doi.org/10.1128/EC.00065-08"},"extern":1,"author":[{"orcid":"0000-0002-5795-0133","full_name":"Philipp Schmalhorst","last_name":"Schmalhorst","first_name":"Philipp S","id":"309D50DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sven","last_name":"Krappmann","full_name":"Krappmann, Sven"},{"first_name":"Wouter","last_name":"Vervecken","full_name":"Vervecken, Wouter"},{"last_name":"Rohde","full_name":"Rohde, Manfred","first_name":"Manfred"},{"last_name":"Müller","full_name":"Müller, Meike","first_name":"Meike"},{"first_name":"Gerhard","full_name":"Braus, Gerhard H.","last_name":"Braus"},{"first_name":"Roland","last_name":"Contreras","full_name":"Contreras, Roland"},{"first_name":"Armin","full_name":"Braun, Armin","last_name":"Braun"},{"first_name":"Hans","full_name":"Bakker, Hans","last_name":"Bakker"},{"last_name":"Routier","full_name":"Routier, Françoise H","first_name":"Françoise"}],"publist_id":"3354","title":"Contribution of galactofuranose to the virulence of the opportunistic pathogen Aspergillus fumigatus"},{"publist_id":"3333","author":[{"first_name":"Richard","full_name":"Green, Richard E","last_name":"Green"},{"first_name":"Anna","full_name":"Malaspinas, Anna-Sapfo ","last_name":"Malaspinas"},{"first_name":"Johannes","full_name":"Krause, Johannes","last_name":"Krause"},{"first_name":"Adrian","last_name":"Briggs","full_name":"Briggs, Adrian W"},{"full_name":"Johnson, Philip L","last_name":"Johnson","first_name":"Philip"},{"orcid":"0000-0002-7008-0216","full_name":"Caroline Uhler","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"},{"last_name":"Meyer","full_name":"Meyer, Matthias","first_name":"Matthias"},{"last_name":"Good","full_name":"Good, Jeffrey M","first_name":"Jeffrey"},{"first_name":"Tomislav","last_name":"Maricic","full_name":"Maricic, Tomislav"},{"full_name":"Stenzel, Udo","last_name":"Stenzel","first_name":"Udo"},{"last_name":"Prüfer","full_name":"Prüfer, Kay","first_name":"Kay"},{"first_name":"Michael","full_name":"Siebauer, Michael F","last_name":"Siebauer"},{"full_name":"Burbano, Hernän A","last_name":"Burbano","first_name":"Hernän"},{"last_name":"Ronan","full_name":"Ronan, Michael T","first_name":"Michael"},{"first_name":"Jonathan","full_name":"Rothberg, Jonathan M","last_name":"Rothberg"},{"first_name":"Michael","full_name":"Egholm, Michael","last_name":"Egholm"},{"first_name":"Pavao","full_name":"Rudan, Pavao","last_name":"Rudan"},{"last_name":"Brajković","full_name":"Brajković, Dejana","first_name":"Dejana"},{"last_name":"Kućan","full_name":"Kućan, Željko","first_name":"Željko"},{"full_name":"Gušić, Ivan","last_name":"Gušić","first_name":"Ivan"},{"last_name":"Wikström","full_name":"Wikström, Mårten K","first_name":"Mårten"},{"first_name":"Liisa","full_name":"Laakkonen, Liisa J","last_name":"Laakkonen"},{"last_name":"Kelso","full_name":"Kelso, Janet F","first_name":"Janet"},{"full_name":"Slatkin, Montgomery","last_name":"Slatkin","first_name":"Montgomery"},{"first_name":"Svante","full_name":"Pääbo, Svante H","last_name":"Pääbo"}],"title":"A complete neandertal mitochondrial genome sequence determined by highhhroughput sequencing","date_updated":"2021-01-12T07:42:32Z","citation":{"chicago":"Green, Richard, Anna Malaspinas, Johannes Krause, Adrian Briggs, Philip Johnson, Caroline Uhler, Matthias Meyer, et al. “A Complete Neandertal Mitochondrial Genome Sequence Determined by Highhhroughput Sequencing.” Cell. Cell Press, 2008. https://doi.org/10.1016/j.cell.2008.06.021.","ista":"Green R, Malaspinas A, Krause J, Briggs A, Johnson P, Uhler C, Meyer M, Good J, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano H, Ronan M, Rothberg J, Egholm M, Rudan P, Brajković D, Kućan Ž, Gušić I, Wikström M, Laakkonen L, Kelso J, Slatkin M, Pääbo S. 2008. A complete neandertal mitochondrial genome sequence determined by highhhroughput sequencing. Cell. 134, 416–426.","mla":"Green, Richard, et al. “A Complete Neandertal Mitochondrial Genome Sequence Determined by Highhhroughput Sequencing.” Cell, vol. 134, Cell Press, 2008, pp. 416–26, doi:10.1016/j.cell.2008.06.021.","short":"R. Green, A. Malaspinas, J. Krause, A. Briggs, P. Johnson, C. Uhler, M. Meyer, J. Good, T. Maricic, U. Stenzel, K. Prüfer, M. Siebauer, H. Burbano, M. Ronan, J. Rothberg, M. Egholm, P. Rudan, D. Brajković, Ž. Kućan, I. Gušić, M. Wikström, L. Laakkonen, J. Kelso, M. Slatkin, S. Pääbo, Cell 134 (2008) 416–426.","ieee":"R. Green et al., “A complete neandertal mitochondrial genome sequence determined by highhhroughput sequencing,” Cell, vol. 134. Cell Press, pp. 416–426, 2008.","apa":"Green, R., Malaspinas, A., Krause, J., Briggs, A., Johnson, P., Uhler, C., … Pääbo, S. (2008). A complete neandertal mitochondrial genome sequence determined by highhhroughput sequencing. Cell. Cell Press. https://doi.org/10.1016/j.cell.2008.06.021","ama":"Green R, Malaspinas A, Krause J, et al. A complete neandertal mitochondrial genome sequence determined by highhhroughput sequencing. Cell. 2008;134:416-426. doi:10.1016/j.cell.2008.06.021"},"extern":1,"type":"journal_article","status":"public","_id":"3307","page":"416 - 426","date_published":"2008-08-01T00:00:00Z","doi":"10.1016/j.cell.2008.06.021","volume":134,"date_created":"2018-12-11T12:02:35Z","year":"2008","publication_status":"published","day":"01","publication":"Cell","publisher":"Cell Press","quality_controlled":0,"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2602844/"}],"month":"08","intvolume":" 134","abstract":[{"text":"A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.","lang":"eng"}]},{"volume":179,"doi":"10.1534/genetics.107.085019","date_published":"2008-05-01T00:00:00Z","issue":"1","date_created":"2018-12-11T12:03:19Z","page":"497 - 502","day":"01","publication":"Genetics","year":"2008","publication_status":"published","month":"05","intvolume":" 179","quality_controlled":0,"publisher":"Genetics Society of America","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390626"}],"abstract":[{"lang":"eng","text":"We develop a new method for estimating effective population sizes, Ne, and selection coefficients, s, from time-series data of allele frequencies sampled from a single diallelic locus. The method is based on calculating transition probabilities, using a numerical solution of the diffusion process, and assuming independent binomial sampling from this diffusion process at each time point. We apply the method in two example applications. First, we estimate selection coefficients acting on the CCR5-Δ32 mutation on the basis of published samples of contemporary and ancient human DNA. We show that the data are compatible with the assumption of s = 0, although moderate amounts of selection acting on this mutation cannot be excluded. In our second example, we estimate the selection coefficient acting on a mutation segregating in an experimental phage population. We show that the selection coefficient acting on this mutation is ~0.43."}],"title":"Estimation of 2Nes From Temporal Allele Frequency Data","author":[{"full_name":"Jonathan Bollback","orcid":"0000-0002-4624-4612","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"},{"full_name":"York, Thomas L","last_name":"York","first_name":"Thomas"},{"last_name":"Nielsen","full_name":"Nielsen, Rasmus","first_name":"Rasmus"}],"publist_id":"2965","extern":1,"citation":{"ama":"Bollback JP, York T, Nielsen R. Estimation of 2Nes From Temporal Allele Frequency Data. Genetics. 2008;179(1):497-502. doi:10.1534/genetics.107.085019","apa":"Bollback, J. P., York, T., & Nielsen, R. (2008). Estimation of 2Nes From Temporal Allele Frequency Data. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.107.085019","ieee":"J. P. Bollback, T. York, and R. Nielsen, “Estimation of 2Nes From Temporal Allele Frequency Data,” Genetics, vol. 179, no. 1. Genetics Society of America, pp. 497–502, 2008.","short":"J.P. Bollback, T. York, R. Nielsen, Genetics 179 (2008) 497–502.","mla":"Bollback, Jonathan P., et al. “Estimation of 2Nes From Temporal Allele Frequency Data.” Genetics, vol. 179, no. 1, Genetics Society of America, 2008, pp. 497–502, doi:10.1534/genetics.107.085019.","ista":"Bollback JP, York T, Nielsen R. 2008. Estimation of 2Nes From Temporal Allele Frequency Data. Genetics. 179(1), 497–502.","chicago":"Bollback, Jonathan P, Thomas York, and Rasmus Nielsen. “Estimation of 2Nes From Temporal Allele Frequency Data.” Genetics. Genetics Society of America, 2008. https://doi.org/10.1534/genetics.107.085019."},"date_updated":"2021-01-12T07:43:27Z","status":"public","type":"journal_article","_id":"3435"},{"page":"587 - 594","date_created":"2018-12-11T12:03:44Z","doi":"10.1038/nn.2106","date_published":"2008-05-29T00:00:00Z","volume":11,"issue":"5","publication_status":"published","year":"2008","publication":"Nature Neuroscience","day":"29","quality_controlled":0,"publisher":"Nature Publishing Group","intvolume":" 11","month":"05","abstract":[{"lang":"eng","text":"Temporal coding is a means of representing information by the time, as opposed to the rate, at which neurons fire. Evidence of temporal coding in the hippocampus comes from place cells, whose spike times relative to theta oscillations reflect a rat's position while running along stereotyped trajectories. This arises from the backwards shift in cell firing relative to local theta oscillations (phase precession). Here we demonstrate phase precession during place-field crossings in an open-field foraging task. This produced spike sequences in each theta cycle that disambiguate the rat's trajectory through two-dimensional space and can be used to predict movement direction. Furthermore, position and movement direction were maximally predicted from firing in the early and late portions of the theta cycle, respectively. This represents the first direct evidence of a combined representation of position, trajectory and heading in the hippocampus, organized on a fine temporal scale by theta oscillations."}],"author":[{"first_name":"John","last_name":"Huxter","full_name":"Huxter,John R"},{"full_name":"Senior,Timothy J","last_name":"Senior","first_name":"Timothy"},{"full_name":"Allen, Kevin","last_name":"Allen","first_name":"Kevin"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","full_name":"Jozsef Csicsvari","orcid":"0000-0002-5193-4036","last_name":"Csicsvari"}],"publist_id":"2869","title":"Theta phase-specific codes for two-dimensional position, trajectory and heading in the hippocampus","citation":{"ama":"Huxter J, Senior T, Allen K, Csicsvari JL. Theta phase-specific codes for two-dimensional position, trajectory and heading in the hippocampus. Nature Neuroscience. 2008;11(5):587-594. doi:10.1038/nn.2106","apa":"Huxter, J., Senior, T., Allen, K., & Csicsvari, J. L. (2008). Theta phase-specific codes for two-dimensional position, trajectory and heading in the hippocampus. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2106","ieee":"J. Huxter, T. Senior, K. Allen, and J. L. Csicsvari, “Theta phase-specific codes for two-dimensional position, trajectory and heading in the hippocampus,” Nature Neuroscience, vol. 11, no. 5. Nature Publishing Group, pp. 587–594, 2008.","short":"J. Huxter, T. Senior, K. Allen, J.L. Csicsvari, Nature Neuroscience 11 (2008) 587–594.","mla":"Huxter, John, et al. “Theta Phase-Specific Codes for Two-Dimensional Position, Trajectory and Heading in the Hippocampus.” Nature Neuroscience, vol. 11, no. 5, Nature Publishing Group, 2008, pp. 587–94, doi:10.1038/nn.2106.","ista":"Huxter J, Senior T, Allen K, Csicsvari JL. 2008. Theta phase-specific codes for two-dimensional position, trajectory and heading in the hippocampus. Nature Neuroscience. 11(5), 587–594.","chicago":"Huxter, John, Timothy Senior, Kevin Allen, and Jozsef L Csicsvari. “Theta Phase-Specific Codes for Two-Dimensional Position, Trajectory and Heading in the Hippocampus.” Nature Neuroscience. Nature Publishing Group, 2008. https://doi.org/10.1038/nn.2106."},"date_updated":"2021-01-12T07:44:00Z","extern":1,"type":"journal_article","status":"public","_id":"3516"},{"publication_status":"published","year":"2008","day":"27","publication":"Neuron","page":"917 - 929","doi":"10.1016/j.neuron.2008.01.034","issue":"6","date_published":"2008-03-27T00:00:00Z","volume":57,"date_created":"2018-12-11T12:03:49Z","abstract":[{"lang":"eng","text":"In the cerebral cortex, GABAergic interneurons are often regarded as fast-spiking cells. We have identified a type of slow-spiking interneuron that offers distinct contributions to network activity. “Ivy” cells, named after their dense and fine axons innervating mostly basal and oblique pyramidal cell dendrites, are more numerous than the parvalbumin-expressing basket, bistratified, or axo-axonic cells. Ivy cells express nitric oxide synthase, neuropeptide Y, and high levels of GABA(A) receptor alpha 1 subunit; they discharge at a low frequency with wide spikes in vivo, yet are distinctively phase-locked to behaviorally relevant network rhythms including theta, gamma, and ripple oscillations. Paired recordings in vitro showed that Ivy cells receive depressing EPSPs from pyramidal cells, which in turn receive slowly rising and decaying inhibitory input from Ivy cells. In contrast to fast-spiking interneurons operating with millisecond precision, the highly abundant Ivy cells express presynaptically acting neuromodulators and regulate the excitability of pyramidal cell dendrites through slowly rising and decaying GABAergic inputs."}],"publisher":"Elsevier","quality_controlled":0,"month":"03","intvolume":" 57","date_updated":"2021-01-12T07:44:06Z","citation":{"ieee":"P. Fuentealba et al., “Ivy cells: A population of nitric-oxide-producing, slow-spiking GABAergic neurons and their involvement in hippocampal network activity,” Neuron, vol. 57, no. 6. Elsevier, pp. 917–929, 2008.","short":"P. Fuentealba, R. Begum, M. Capogna, S. Jinno, L. Marton, J.L. Csicsvari, A. Thomson, P. Somogyi, T. Klausberger, Neuron 57 (2008) 917–929.","apa":"Fuentealba, P., Begum, R., Capogna, M., Jinno, S., Marton, L., Csicsvari, J. L., … Klausberger, T. (2008). Ivy cells: A population of nitric-oxide-producing, slow-spiking GABAergic neurons and their involvement in hippocampal network activity. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2008.01.034","ama":"Fuentealba P, Begum R, Capogna M, et al. Ivy cells: A population of nitric-oxide-producing, slow-spiking GABAergic neurons and their involvement in hippocampal network activity. Neuron. 2008;57(6):917-929. doi:10.1016/j.neuron.2008.01.034","mla":"Fuentealba, Pablo, et al. “Ivy Cells: A Population of Nitric-Oxide-Producing, Slow-Spiking GABAergic Neurons and Their Involvement in Hippocampal Network Activity.” Neuron, vol. 57, no. 6, Elsevier, 2008, pp. 917–29, doi:10.1016/j.neuron.2008.01.034.","ista":"Fuentealba P, Begum R, Capogna M, Jinno S, Marton L, Csicsvari JL, Thomson A, Somogyi P, Klausberger T. 2008. Ivy cells: A population of nitric-oxide-producing, slow-spiking GABAergic neurons and their involvement in hippocampal network activity. Neuron. 57(6), 917–929.","chicago":"Fuentealba, Pablo, Rahima Begum, Marco Capogna, Shozo Jinno, Laszlo Marton, Jozsef L Csicsvari, Alex Thomson, Péter Somogyi, and Thomas Klausberger. “Ivy Cells: A Population of Nitric-Oxide-Producing, Slow-Spiking GABAergic Neurons and Their Involvement in Hippocampal Network Activity.” Neuron. Elsevier, 2008. https://doi.org/10.1016/j.neuron.2008.01.034."},"extern":1,"publist_id":"2855","author":[{"last_name":"Fuentealba","full_name":"Fuentealba,Pablo","first_name":"Pablo"},{"last_name":"Begum","full_name":"Begum,Rahima","first_name":"Rahima"},{"last_name":"Capogna","full_name":"Capogna,Marco","first_name":"Marco"},{"full_name":"Jinno,Shozo","last_name":"Jinno","first_name":"Shozo"},{"first_name":"Laszlo","full_name":"Marton,Laszlo F","last_name":"Marton"},{"full_name":"Jozsef Csicsvari","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L"},{"full_name":"Thomson,Alex","last_name":"Thomson","first_name":"Alex"},{"first_name":"Péter","full_name":"Somogyi, Péter","last_name":"Somogyi"},{"full_name":"Klausberger,Thomas","last_name":"Klausberger","first_name":"Thomas"}],"title":"Ivy cells: A population of nitric-oxide-producing, slow-spiking GABAergic neurons and their involvement in hippocampal network activity","_id":"3530","type":"journal_article","status":"public"},{"abstract":[{"lang":"eng","text":"In the subthalamic nucleus (STN) of Parkinson's disease (PD) patients, a pronounced synchronization of oscillatory activity at beta frequencies (15-30 Hz) accompanies movement difficulties. Abnormal beta oscillations and motor symptoms are concomitantly and acutely suppressed by dopaminergic therapies, suggesting that these inappropriate rhythms might also emerge acutely from disrupted dopamine transmission. The neural basis of these abnormal beta oscillations is unclear, and how they might compromise information processing, or how they arise, is unknown. Using a 6-hydroxydopamine-lesioned rodent model of PD, we demonstrate that beta oscillations are inappropriately exaggerated, compared with controls, in a brain-state-dependent manner after chronic dopamine loss. Exaggerated beta oscillations are expressed at the levels of single neurons and small neuronal ensembles, and are focally present and spatially distributed within STN. They are also expressed in synchronous population activities, as evinced by oscillatory local field potentials, in STN and cortex. Excessively synchronized beta oscillations reduce the information coding capacity of STN neuronal ensembles, which may contribute to parkinsonian motor impairment. Acute disruption of dopamine transmission in control animals with antagonists of D-1/D-2 receptors did not exaggerate STN or cortical beta oscillations. Moreover, beta oscillations were not exaggerated until several days after 6-hydroxydopamine injections. Thus, contrary to predictions, abnormally amplified beta oscillations in cortico-STN circuits do not result simply from an acute absence of dopamine receptor stimulation, but are instead delayed sequelae of chronic dopamine depletion. Targeting the plastic processes underlying the delayed emergence of pathological beta oscillations after continuing dopaminergic dysfunction may offer considerable therapeutic promise."}],"month":"04","intvolume":" 28","quality_controlled":0,"publisher":"Society for Neuroscience","day":"30","publication":"Journal of Neuroscience","publication_status":"published","year":"2008","volume":28,"doi":"10.1523/JNEUROSCI.0123-08.2008","issue":"18","date_published":"2008-04-30T00:00:00Z","date_created":"2018-12-11T12:03:53Z","page":"4795 - 4806","_id":"3544","status":"public","type":"journal_article","extern":1,"date_updated":"2021-01-12T07:44:12Z","citation":{"chicago":"Mallet, Nicolas, Alek Pogosyan, Andrew Sharott, Jozsef L Csicsvari, John Bolam, Peter Brown, and Peter Magill. “Disrupted Dopamine Transmission and the Emergence of Exaggerated Beta Oscillations in Subthalamic Nucleus and Cerebral Cortex.” Journal of Neuroscience. Society for Neuroscience, 2008. https://doi.org/10.1523/JNEUROSCI.0123-08.2008.","ista":"Mallet N, Pogosyan A, Sharott A, Csicsvari JL, Bolam J, Brown P, Magill P. 2008. Disrupted dopamine transmission and the emergence of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex. Journal of Neuroscience. 28(18), 4795–4806.","mla":"Mallet, Nicolas, et al. “Disrupted Dopamine Transmission and the Emergence of Exaggerated Beta Oscillations in Subthalamic Nucleus and Cerebral Cortex.” Journal of Neuroscience, vol. 28, no. 18, Society for Neuroscience, 2008, pp. 4795–806, doi:10.1523/JNEUROSCI.0123-08.2008.","ama":"Mallet N, Pogosyan A, Sharott A, et al. Disrupted dopamine transmission and the emergence of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex. Journal of Neuroscience. 2008;28(18):4795-4806. doi:10.1523/JNEUROSCI.0123-08.2008","apa":"Mallet, N., Pogosyan, A., Sharott, A., Csicsvari, J. L., Bolam, J., Brown, P., & Magill, P. (2008). Disrupted dopamine transmission and the emergence of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0123-08.2008","short":"N. Mallet, A. Pogosyan, A. Sharott, J.L. Csicsvari, J. Bolam, P. Brown, P. Magill, Journal of Neuroscience 28 (2008) 4795–4806.","ieee":"N. Mallet et al., “Disrupted dopamine transmission and the emergence of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex,” Journal of Neuroscience, vol. 28, no. 18. Society for Neuroscience, pp. 4795–4806, 2008."},"title":"Disrupted dopamine transmission and the emergence of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex","author":[{"last_name":"Mallet","full_name":"Mallet,Nicolas","first_name":"Nicolas"},{"first_name":"Alek","full_name":"Pogosyan,Alek","last_name":"Pogosyan"},{"first_name":"Andrew","last_name":"Sharott","full_name":"Sharott,Andrew"},{"orcid":"0000-0002-5193-4036","full_name":"Jozsef Csicsvari","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bolam, John Paul","last_name":"Bolam","first_name":"John"},{"first_name":"Peter","full_name":"Brown,Peter","last_name":"Brown"},{"first_name":"Peter","last_name":"Magill","full_name":"Magill,Peter J"}],"publist_id":"2842"},{"month":"01","publisher":"Springer","alternative_title":["Mathematics and Visualization"],"quality_controlled":0,"publication":"Shape Analysis and Structuring","day":"01","year":"2008","publication_status":"published","date_created":"2018-12-11T12:04:03Z","doi":"10.1007/978-3-540-33265-7_5","date_published":"2008-01-01T00:00:00Z","page":"145 - 183","_id":"3577","status":"public","type":"book_chapter","extern":1,"citation":{"chicago":"Biasotti, Silvia, Dominique Attali, Jean Boissonnat, Herbert Edelsbrunner, Gershon Elber, Michela Mortara, Gabriella Sanniti Di Baja, Michela Spagnuolo, Mirela Tanase, and Remco Veltkam. “Skeletal Structures.” In Shape Analysis and Structuring, 145–83. Springer, 2008. https://doi.org/10.1007/978-3-540-33265-7_5.","ista":"Biasotti S, Attali D, Boissonnat J, Edelsbrunner H, Elber G, Mortara M, Sanniti Di Baja G, Spagnuolo M, Tanase M, Veltkam R. 2008.Skeletal structures. In: Shape Analysis and Structuring. Mathematics and Visualization, , 145–183.","mla":"Biasotti, Silvia, et al. “Skeletal Structures.” Shape Analysis and Structuring, Springer, 2008, pp. 145–83, doi:10.1007/978-3-540-33265-7_5.","short":"S. Biasotti, D. Attali, J. Boissonnat, H. Edelsbrunner, G. Elber, M. Mortara, G. Sanniti Di Baja, M. Spagnuolo, M. Tanase, R. Veltkam, in:, Shape Analysis and Structuring, Springer, 2008, pp. 145–183.","ieee":"S. Biasotti et al., “Skeletal structures,” in Shape Analysis and Structuring, Springer, 2008, pp. 145–183.","ama":"Biasotti S, Attali D, Boissonnat J, et al. Skeletal structures. In: Shape Analysis and Structuring. Springer; 2008:145-183. doi:10.1007/978-3-540-33265-7_5","apa":"Biasotti, S., Attali, D., Boissonnat, J., Edelsbrunner, H., Elber, G., Mortara, M., … Veltkam, R. (2008). Skeletal structures. In Shape Analysis and Structuring (pp. 145–183). Springer. https://doi.org/10.1007/978-3-540-33265-7_5"},"date_updated":"2021-01-12T07:44:25Z","title":"Skeletal structures","author":[{"first_name":"Silvia","last_name":"Biasotti","full_name":"Biasotti, Silvia"},{"first_name":"Dominique","full_name":"Attali, Dominique","last_name":"Attali"},{"first_name":"Jean","last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Herbert Edelsbrunner","orcid":"0000-0002-9823-6833"},{"first_name":"Gershon","last_name":"Elber","full_name":"Elber, Gershon"},{"last_name":"Mortara","full_name":"Mortara, Michela","first_name":"Michela"},{"full_name":"Sanniti di Baja, Gabriella","last_name":"Sanniti Di Baja","first_name":"Gabriella"},{"first_name":"Michela","full_name":"Spagnuolo, Michela","last_name":"Spagnuolo"},{"last_name":"Tanase","full_name":"Tanase, Mirela","first_name":"Mirela"},{"full_name":"Veltkam, Remco","last_name":"Veltkam","first_name":"Remco"}],"publist_id":"2808"},{"_id":"3591","type":"journal_article","status":"public","citation":{"mla":"Ulrich, Florian, and Carl-Philipp J. Heisenberg. “Probing E-Cadherin Endocytosis by Morpholino-Mediated Rab5 Knock-down in Zebrafish.” Methods in Molecular Biology, vol. 440, Springer, 2008, pp. 371–87, doi:10.1007/978-1-59745-178-9_27.","ama":"Ulrich F, Heisenberg C-PJ. Probing E-cadherin endocytosis by morpholino-mediated Rab5 knock-down in zebrafish. Methods in Molecular Biology. 2008;440:371-387. doi:10.1007/978-1-59745-178-9_27","apa":"Ulrich, F., & Heisenberg, C.-P. J. (2008). Probing E-cadherin endocytosis by morpholino-mediated Rab5 knock-down in zebrafish. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-59745-178-9_27","ieee":"F. Ulrich and C.-P. J. Heisenberg, “Probing E-cadherin endocytosis by morpholino-mediated Rab5 knock-down in zebrafish.,” Methods in Molecular Biology, vol. 440. Springer, pp. 371–387, 2008.","short":"F. Ulrich, C.-P.J. Heisenberg, Methods in Molecular Biology 440 (2008) 371–387.","chicago":"Ulrich, Florian, and Carl-Philipp J Heisenberg. “Probing E-Cadherin Endocytosis by Morpholino-Mediated Rab5 Knock-down in Zebrafish.” Methods in Molecular Biology. Springer, 2008. https://doi.org/10.1007/978-1-59745-178-9_27.","ista":"Ulrich F, Heisenberg C-PJ. 2008. Probing E-cadherin endocytosis by morpholino-mediated Rab5 knock-down in zebrafish. Methods in Molecular Biology. 440, 371–387."},"date_updated":"2021-01-12T07:44:31Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"2792","author":[{"first_name":"Florian","full_name":"Ulrich, Florian","last_name":"Ulrich"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"article_processing_charge":"No","title":"Probing E-cadherin endocytosis by morpholino-mediated Rab5 knock-down in zebrafish.","abstract":[{"lang":"eng","text":"The controlled internalization of membrane receptors and lipids is crucial for cells to control signaling pathways and interact with their environment. During clathrin-mediated endocytosis, membrane constituents are transported via endocytic vesicles into early endosomes, from which they are further distributed within the cell. The small guanosine triphosphatase (GTPase) Rab5 is both required and sufficient for the formation of these early endosomes and can be used to experimentally address endocytic processes. Recent evidence shows that endocytic turnover of E-cadherin regulates the migration of mesendodermal cells during zebrafish gastrulation by modulating their adhesive interactions with neighboring cells. This in turn leads to effective and synchronized movement within the embryo. In this review, we discuss techniques to manipulate E-cadherin endocytosis by morpholino-mediated knockdown of rab5 during zebrafish gastrulation. We describe the use of antibodies specifically directed against zebrafish E-cadherin to detect its intracellular localization and of in situ hybridization and primary cell culture to reveal patterns of cell migration and adhesion, respectively"}],"oa_version":"None","publisher":"Springer","month":"01","intvolume":" 440","year":"2008","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Methods in Molecular Biology","page":"371 - 387","date_published":"2008-01-01T00:00:00Z","doi":"10.1007/978-1-59745-178-9_27","volume":440,"date_created":"2018-12-11T12:04:08Z"},{"publist_id":"2784","author":[{"last_name":"Yang","full_name":"Yang, Erfu","first_name":"Erfu"},{"last_name":"Erdogan","full_name":"Erdogan, Ahmet T","first_name":"Ahmet"},{"last_name":"Arslan","full_name":"Arslan, Tughrul","first_name":"Tughrul"},{"last_name":"Barton","full_name":"Nicholas Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"title":"Adaptive formation control and bio-inspired optimization of a cluster-based satellite wireless sensor network ","date_updated":"2021-01-12T07:44:34Z","citation":{"mla":"Yang, Erfu, et al. Adaptive Formation Control and Bio-Inspired Optimization of a Cluster-Based Satellite Wireless Sensor Network . IEEE, 2008, pp. 432–39, doi:10.1109/AHS.2008.60.","apa":"Yang, E., Erdogan, A., Arslan, T., & Barton, N. H. (2008). Adaptive formation control and bio-inspired optimization of a cluster-based satellite wireless sensor network (pp. 432–439). Presented at the AHS: NASA/ESA Conference on Adaptive Hardware and Systems, IEEE. https://doi.org/10.1109/AHS.2008.60","ama":"Yang E, Erdogan A, Arslan T, Barton NH. Adaptive formation control and bio-inspired optimization of a cluster-based satellite wireless sensor network . In: IEEE; 2008:432-439. doi:10.1109/AHS.2008.60","ieee":"E. Yang, A. Erdogan, T. Arslan, and N. H. Barton, “Adaptive formation control and bio-inspired optimization of a cluster-based satellite wireless sensor network ,” presented at the AHS: NASA/ESA Conference on Adaptive Hardware and Systems, 2008, pp. 432–439.","short":"E. Yang, A. Erdogan, T. Arslan, N.H. Barton, in:, IEEE, 2008, pp. 432–439.","chicago":"Yang, Erfu, Ahmet Erdogan, Tughrul Arslan, and Nicholas H Barton. “Adaptive Formation Control and Bio-Inspired Optimization of a Cluster-Based Satellite Wireless Sensor Network ,” 432–39. IEEE, 2008. https://doi.org/10.1109/AHS.2008.60.","ista":"Yang E, Erdogan A, Arslan T, Barton NH. 2008. Adaptive formation control and bio-inspired optimization of a cluster-based satellite wireless sensor network . AHS: NASA/ESA Conference on Adaptive Hardware and Systems, 432–439."},"extern":1,"type":"conference","conference":{"name":"AHS: NASA/ESA Conference on Adaptive Hardware and Systems"},"status":"public","_id":"3599","page":"432 - 439","date_published":"2008-08-01T00:00:00Z","doi":"10.1109/AHS.2008.60","date_created":"2018-12-11T12:04:10Z","year":"2008","publication_status":"published","day":"01","quality_controlled":0,"publisher":"IEEE","month":"08","abstract":[{"lang":"eng","text":"In this paper, adaptive formation control and bio-inspired optimization are jointly addressed for a cluster-based satellite wireless sensor network in which there are multiple satellites flying in formation (MSFF) in the presence of unknown disturbances. The full nonlinear dynamics model describing the relative positioning of the MSFF system is used to develop an adaptive formation controller. First, the original nonlinear system is transformed into a linear controllable system with aperturbation term by invoking the input-output feedback linearization technique. Second, by using the integral feedback design scheme, the adaptive formation controller is presented for improving the steady-state performance of the MSFF system in the presence of unknown disturbances. Third, as a currently popular bio-inspired algorithm, PSO (particle swarm optimizer) is employed to minimize the total energy consumption under the required quality of service by jointly optimizing the transmission power and rate for each satellite. Simulation results are provided to demonstrate the effectiveness of the adaptive formation controller and the PSO-based optimization for saving the total communication energy."}]},{"abstract":[{"text":"Kernel canonical correlation analysis (KCCA) is a dimensionality reduction technique for paired data. By finding directions that maximize correlation, KCCA learns representations that are more closely tied to the underlying semantics of the data rather than noise. However, meaningful directions are not only those that have high correlation to another modality, but also those that capture the manifold structure of the data. We propose a method that is simultaneously able to find highly correlated directions that are also located on high variance directions along the data manifold. This is achieved by the use of semi-supervised Laplacian regularization of KCCA. We show experimentally that Laplacian regularized training improves class separation over KCCA with only Tikhonov regularization, while causing no degradation in the correlation between modalities. We propose a model selection criterion based on the Hilbert-Schmidt norm of the semi-supervised Laplacian regularized cross-covariance operator, which we compute in closed form.","lang":"eng"}],"month":"10","intvolume":" 5211","quality_controlled":0,"publisher":"Springer","alternative_title":["LNCS"],"day":"21","publication_status":"published","year":"2008","date_published":"2008-10-21T00:00:00Z","issue":"Part 1","volume":5211,"doi":"10.1007/978-3-540-87479-9_27","date_created":"2018-12-11T12:04:41Z","page":"133 - 145","_id":"3698","status":"public","type":"conference","conference":{"name":"ECML: European Conference on Machine Learning"},"extern":1,"date_updated":"2021-01-12T07:49:02Z","citation":{"chicago":"Blaschko, Matthew, Christoph Lampert, and Arthur Gretton. “Semi-Supervised Laplacian Regularization of Kernel Canonical Correlation Analysis,” 5211:133–45. Springer, 2008. https://doi.org/10.1007/978-3-540-87479-9_27.","ista":"Blaschko M, Lampert C, Gretton A. 2008. Semi-supervised Laplacian regularization of kernel canonical correlation analysis. ECML: European Conference on Machine Learning, LNCS, vol. 5211, 133–145.","mla":"Blaschko, Matthew, et al. Semi-Supervised Laplacian Regularization of Kernel Canonical Correlation Analysis. Vol. 5211, no. Part 1, Springer, 2008, pp. 133–45, doi:10.1007/978-3-540-87479-9_27.","ieee":"M. Blaschko, C. Lampert, and A. Gretton, “Semi-supervised Laplacian regularization of kernel canonical correlation analysis,” presented at the ECML: European Conference on Machine Learning, 2008, vol. 5211, no. Part 1, pp. 133–145.","short":"M. Blaschko, C. Lampert, A. Gretton, in:, Springer, 2008, pp. 133–145.","apa":"Blaschko, M., Lampert, C., & Gretton, A. (2008). Semi-supervised Laplacian regularization of kernel canonical correlation analysis (Vol. 5211, pp. 133–145). Presented at the ECML: European Conference on Machine Learning, Springer. https://doi.org/10.1007/978-3-540-87479-9_27","ama":"Blaschko M, Lampert C, Gretton A. Semi-supervised Laplacian regularization of kernel canonical correlation analysis. In: Vol 5211. Springer; 2008:133-145. doi:10.1007/978-3-540-87479-9_27"},"title":"Semi-supervised Laplacian regularization of kernel canonical correlation analysis","publist_id":"2662","author":[{"first_name":"Matthew","full_name":"Blaschko,Matthew B","last_name":"Blaschko"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Christoph Lampert","orcid":"0000-0001-8622-7887","last_name":"Lampert"},{"last_name":"Gretton","full_name":"Gretton,Arthur","first_name":"Arthur"}]},{"publication_status":"published","year":"2008","day":"13","page":"174 - 179","doi":"10.1109/ICN.2008.64","date_published":"2008-04-13T00:00:00Z","date_created":"2018-12-11T12:04:39Z","abstract":[{"text":"Distributed Denial of Service (DDoS) attacks are today the most destabilizing factor in the global internet and there is a strong need for sophisticated solutions. We introduce a formal statistical framework and derive a Bayes optimal packet classifier from it. Our proposed practical algorithm "Adaptive History-Based IP Filtering" (AHIF) mitigates DDoS attacks near the victim and outperforms existing methods by at least 32% in terms of collateral damage. Furthermore, it adjusts to the strength of an ongoing attack and ensures availability of the attacked server. In contrast to other adaptive solutions, firewall rulesets used to resist an attack can be precalculated before an attack takes place. This ensures an immediate response in a DDoS emergency. For evaluation, simulated DDoS attacks and two real-world user traffic datasets are used.","lang":"eng"}],"quality_controlled":0,"publisher":"IEEE","main_file_link":[{"url":"http://pub.ist.ac.at/~chl/papers/goldstein-icn2008.pdf","open_access":"0"}],"month":"04","date_updated":"2021-01-12T07:49:01Z","citation":{"mla":"Goldstein, Markus, et al. Bayes Optimal DDoS Mitigation by Adaptive History-Based IP Filtering. IEEE, 2008, pp. 174–79, doi:10.1109/ICN.2008.64.","ama":"Goldstein M, Lampert C, Reif M, Stahl A, Breuel T. Bayes optimal DDoS mitigation by adaptive history-based IP filtering. In: IEEE; 2008:174-179. doi:10.1109/ICN.2008.64","apa":"Goldstein, M., Lampert, C., Reif, M., Stahl, A., & Breuel, T. (2008). Bayes optimal DDoS mitigation by adaptive history-based IP filtering (pp. 174–179). Presented at the ICN: International Conference on Networking, IEEE. https://doi.org/10.1109/ICN.2008.64","short":"M. Goldstein, C. Lampert, M. Reif, A. Stahl, T. Breuel, in:, IEEE, 2008, pp. 174–179.","ieee":"M. Goldstein, C. Lampert, M. Reif, A. Stahl, and T. Breuel, “Bayes optimal DDoS mitigation by adaptive history-based IP filtering,” presented at the ICN: International Conference on Networking, 2008, pp. 174–179.","chicago":"Goldstein, Markus, Christoph Lampert, Matthias Reif, Armin Stahl, and Thomas Breuel. “Bayes Optimal DDoS Mitigation by Adaptive History-Based IP Filtering,” 174–79. IEEE, 2008. https://doi.org/10.1109/ICN.2008.64.","ista":"Goldstein M, Lampert C, Reif M, Stahl A, Breuel T. 2008. Bayes optimal DDoS mitigation by adaptive history-based IP filtering. ICN: International Conference on Networking, 174–179."},"extern":1,"publist_id":"2671","author":[{"last_name":"Goldstein","full_name":"Goldstein,Markus","first_name":"Markus"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Christoph Lampert"},{"first_name":"Matthias","last_name":"Reif","full_name":"Reif,Matthias"},{"first_name":"Armin","full_name":"Stahl,Armin","last_name":"Stahl"},{"first_name":"Thomas","last_name":"Breuel","full_name":"Breuel,Thomas M"}],"title":"Bayes optimal DDoS mitigation by adaptive history-based IP filtering","_id":"3694","type":"conference","conference":{"name":"ICN: International Conference on Networking"},"status":"public"},{"title":"Joint kernel support estimation for structured prediction","publist_id":"2650","author":[{"orcid":"0000-0001-8622-7887","full_name":"Christoph Lampert","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"first_name":"Matthew","full_name":"Blaschko,Matthew B","last_name":"Blaschko"}],"extern":1,"date_updated":"2021-01-12T07:51:37Z","citation":{"ista":"Lampert C, Blaschko M. 2008. Joint kernel support estimation for structured prediction. NIPS SISO: NIPS Workshop on ‘Structured Input - Structured Output’, 1–4.","chicago":"Lampert, Christoph, and Matthew Blaschko. “Joint Kernel Support Estimation for Structured Prediction,” 1–4. Curran Associates, Inc., 2008.","ieee":"C. Lampert and M. Blaschko, “Joint kernel support estimation for structured prediction,” presented at the NIPS SISO: NIPS Workshop on “Structured Input - Structured Output,” 2008, pp. 1–4.","short":"C. Lampert, M. Blaschko, in:, Curran Associates, Inc., 2008, pp. 1–4.","ama":"Lampert C, Blaschko M. Joint kernel support estimation for structured prediction. In: Curran Associates, Inc.; 2008:1-4.","apa":"Lampert, C., & Blaschko, M. (2008). Joint kernel support estimation for structured prediction (pp. 1–4). Presented at the NIPS SISO: NIPS Workshop on “Structured Input - Structured Output,” Curran Associates, Inc.","mla":"Lampert, Christoph, and Matthew Blaschko. Joint Kernel Support Estimation for Structured Prediction. Curran Associates, Inc., 2008, pp. 1–4."},"status":"public","conference":{"name":"NIPS SISO: NIPS Workshop on \"Structured Input - Structured Output\""},"type":"conference","_id":"3706","date_created":"2018-12-11T12:04:43Z","date_published":"2008-12-12T00:00:00Z","page":"1 - 4","day":"12","year":"2008","publication_status":"published","month":"12","main_file_link":[{"open_access":"0","url":"http://agbs.kyb.tuebingen.mpg.de/wikis/bg/siso2008/Blaschkoetal.pdf"}],"publisher":"Curran Associates, Inc.","quality_controlled":0,"abstract":[{"lang":"eng","text":"We present a new technique for structured prediction that works in a hybrid generative/discriminative way, using a one-class support vector machine to model the joint probability of (input, output)-pairs in a joint reproducing kernel Hilbert space. Compared to discriminative techniques, like conditional random fields or structured output SVMs?, the proposed method has the advantage that its training time depends only on the number of training examples, not on the size of the label space. Due to its generative aspect, it is also very tolerant against ambiguous, incomplete or incorrect labels. Experiments on realistic data show that our method works efficiently and robustly in situations that discriminative techniques have problems with or that are computationally infeasible for them."}]},{"abstract":[{"lang":"eng","text":"We present a new method for spectral clustering with paired data based on kernel canonical correlation analysis, called correlational spectral clustering. Paired data are common in real world data sources, such as images with text captions. Traditional spectral clustering algorithms either assume that data can be represented by a single similarity measure, or by co-occurrence matrices that are then used in biclustering. In contrast, the proposed method uses separate similarity measures for each data representation, and allows for projection of previously unseen data that are only observed in one representation (e.g. images but not text). We show that this algorithm generalizes traditional spectral clustering algorithms and show consistent empirical improvement over spectral clustering on a variety of datasets of images with associated text."}],"month":"09","quality_controlled":0,"publisher":"IEEE","day":"18","year":"2008","publication_status":"published","doi":"10.1109/CVPR.2008.4587353","date_published":"2008-09-18T00:00:00Z","date_created":"2018-12-11T12:04:45Z","page":"1 - 8","_id":"3712","status":"public","type":"conference","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"extern":1,"date_updated":"2021-01-12T07:51:40Z","citation":{"chicago":"Blaschko, Matthew, and Christoph Lampert. “Correlational Spectral Clustering,” 1–8. IEEE, 2008. https://doi.org/10.1109/CVPR.2008.4587353.","ista":"Blaschko M, Lampert C. 2008. Correlational spectral clustering. CVPR: Computer Vision and Pattern Recognition, 1–8.","mla":"Blaschko, Matthew, and Christoph Lampert. Correlational Spectral Clustering. IEEE, 2008, pp. 1–8, doi:10.1109/CVPR.2008.4587353.","ieee":"M. Blaschko and C. Lampert, “Correlational spectral clustering,” presented at the CVPR: Computer Vision and Pattern Recognition, 2008, pp. 1–8.","short":"M. Blaschko, C. Lampert, in:, IEEE, 2008, pp. 1–8.","ama":"Blaschko M, Lampert C. Correlational spectral clustering. In: IEEE; 2008:1-8. doi:10.1109/CVPR.2008.4587353","apa":"Blaschko, M., & Lampert, C. (2008). Correlational spectral clustering (pp. 1–8). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2008.4587353"},"title":"Correlational spectral clustering","author":[{"first_name":"Matthew","full_name":"Blaschko,Matthew B","last_name":"Blaschko"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Christoph Lampert","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"publist_id":"2646"},{"abstract":[{"text":"Single-molecule atomic force microscopy (AFM) provides novel ways to characterize the structure-function relationship of native membrane proteins. High-resolution AFM topographs allow observing the structure of single proteins at sub-nanometer resolution as well as their conformational changes, oligomeric state, molecular dynamics and assembly. We will review these feasibilities illustrating examples of membrane proteins in native and reconstituted membranes. Classification of individual topographs of single proteins allows understanding the principles of motions of their extrinsic domains, to learn about their local structural flexibilities and to find the entropy minima of certain conformations. Combined with the visualization of functionally related conformational changes these insights allow understanding why certain flexibilities are required for the protein to function and how structurally flexible regions allow certain conformational changes. Complementary to AFM imaging, single-molecule force spectroscopy (SMFS) experiments detect molecular interactions established within and between membrane proteins. The sensitivity of this method makes it possible to measure interactions that stabilize secondary structures such as transmembrane α-helices, polypeptide loops and segments within. Changes in temperature or protein-protein assembly do not change the locations of stable structural segments, but influence their stability established by collective molecular interactions. Such changes alter the probability of proteins to choose a certain unfolding pathway. Recent examples have elucidated unfolding and refolding pathways of membrane proteins as well as their energy landscapes.","lang":"eng"}],"quality_controlled":0,"publisher":"Springer","month":"01","intvolume":" 12","publication_status":"published","year":"2008","day":"08","publication":"Single Molecules and Nanotechnology","page":"279 - 311","date_published":"2008-01-08T00:00:00Z","volume":12,"doi":"10.1007/978-3-540-73924-1_11","date_created":"2018-12-11T12:04:50Z","_id":"3726","type":"book_chapter","status":"public","date_updated":"2021-01-12T07:51:45Z","citation":{"chicago":"Engel, Andreas, Harald L Janovjak, Dimtrios Fotiadis, Alexej Kedrov, David Cisneros, and Daniel Mueller. “Single-Molecule Microscopy and Force Spectroscopy of Membrane Proteins.” In Single Molecules and Nanotechnology, 12:279–311. Springer, 2008. https://doi.org/10.1007/978-3-540-73924-1_11.","ista":"Engel A, Janovjak HL, Fotiadis D, Kedrov A, Cisneros D, Mueller D. 2008.Single-molecule microscopy and force spectroscopy of membrane proteins. In: Single Molecules and Nanotechnology. vol. 12, 279–311.","mla":"Engel, Andreas, et al. “Single-Molecule Microscopy and Force Spectroscopy of Membrane Proteins.” Single Molecules and Nanotechnology, vol. 12, Springer, 2008, pp. 279–311, doi:10.1007/978-3-540-73924-1_11.","ama":"Engel A, Janovjak HL, Fotiadis D, Kedrov A, Cisneros D, Mueller D. Single-molecule microscopy and force spectroscopy of membrane proteins. In: Single Molecules and Nanotechnology. Vol 12. Springer; 2008:279-311. doi:10.1007/978-3-540-73924-1_11","apa":"Engel, A., Janovjak, H. L., Fotiadis, D., Kedrov, A., Cisneros, D., & Mueller, D. (2008). Single-molecule microscopy and force spectroscopy of membrane proteins. In Single Molecules and Nanotechnology (Vol. 12, pp. 279–311). Springer. https://doi.org/10.1007/978-3-540-73924-1_11","ieee":"A. Engel, H. L. Janovjak, D. Fotiadis, A. Kedrov, D. Cisneros, and D. Mueller, “Single-molecule microscopy and force spectroscopy of membrane proteins,” in Single Molecules and Nanotechnology, vol. 12, Springer, 2008, pp. 279–311.","short":"A. Engel, H.L. Janovjak, D. Fotiadis, A. Kedrov, D. Cisneros, D. Mueller, in:, Single Molecules and Nanotechnology, Springer, 2008, pp. 279–311."},"extern":1,"author":[{"last_name":"Engel","full_name":"Engel, Andreas","first_name":"Andreas"},{"orcid":"0000-0002-8023-9315","full_name":"Harald Janovjak","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fotiadis, Dimtrios","last_name":"Fotiadis","first_name":"Dimtrios"},{"first_name":"Alexej","last_name":"Kedrov","full_name":"Kedrov, Alexej"},{"first_name":"David","last_name":"Cisneros","full_name":"Cisneros, David"},{"last_name":"Mueller","full_name":"Mueller, Daniel J","first_name":"Daniel"}],"publist_id":"2503","title":"Single-molecule microscopy and force spectroscopy of membrane proteins"},{"issue":"1","volume":78,"doi":"10.1103/PhysRevE.78.011910","date_published":"2008-07-21T00:00:00Z","date_created":"2018-12-11T12:04:54Z","day":"21","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","publication_status":"published","year":"2008","month":"07","intvolume":" 78","quality_controlled":0,"publisher":"American Institute of Physics","abstract":[{"text":"Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need to perform nontrivial computations that integrate several inputs and affect multiple genes. At the same time, the activities of the regulated genes would fluctuate even if the inputs were held fixed, as a consequence of the intrinsic noise in the system, and such noise must fundamentally limit the reliability of any genetic computation. Here we use information theory to formalize the notion of information transmission in simple genetic regulatory elements in the presence of physically realistic noise sources. The dependence of this "channel capacity" on noise parameters, cooperativity and cost of making signaling molecules is explored systematically. We find that, in the range of parameters probed by recent in vivo measurements, capacities higher than one bit should be achievable. It is of course generally accepted that gene regulatory elements must, in order to function properly, have a capacity of at least one bit. The central point of our analysis is the demonstration that simple physical models of noisy gene transcription, with realistic parameters, can indeed achieve this capacity: it was not self-evident that this should be so. We also demonstrate that capacities significantly greater than one bit are possible, so that transcriptional regulation need not be limited to simple "on-off" components. The question whether real systems actually exploit this richer possibility is beyond the scope of this investigation.","lang":"eng"}],"title":"Information capacity of genetic regulatory elements","author":[{"full_name":"Gasper Tkacik","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Callan","full_name":"Callan,Curtis G","first_name":"Curtis"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William S"}],"publist_id":"2488","extern":1,"date_updated":"2021-01-12T07:51:51Z","citation":{"mla":"Tkačik, Gašper, et al. “Information Capacity of Genetic Regulatory Elements.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78, no. 1, American Institute of Physics, 2008, doi:10.1103/PhysRevE.78.011910.","ieee":"G. Tkačik, C. Callan, and W. Bialek, “Information capacity of genetic regulatory elements,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78, no. 1. American Institute of Physics, 2008.","short":"G. Tkačik, C. Callan, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 78 (2008).","ama":"Tkačik G, Callan C, Bialek W. Information capacity of genetic regulatory elements. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2008;78(1). doi:10.1103/PhysRevE.78.011910","apa":"Tkačik, G., Callan, C., & Bialek, W. (2008). Information capacity of genetic regulatory elements. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.78.011910","chicago":"Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Capacity of Genetic Regulatory Elements.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2008. https://doi.org/10.1103/PhysRevE.78.011910.","ista":"Tkačik G, Callan C, Bialek W. 2008. Information capacity of genetic regulatory elements. Physical Review E Statistical Nonlinear and Soft Matter Physics. 78(1)."},"status":"public","type":"journal_article","_id":"3739"},{"status":"public","type":"journal_article","_id":"3740","title":"Information flow and optimization in transcriptional regulation","publist_id":"2489","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Gasper Tkacik","orcid":"0000-0002-6699-1455","last_name":"Tkacik"},{"first_name":"Curtis","last_name":"Callan","full_name":"Callan,Curtis G"},{"first_name":"William","full_name":"Bialek, William S","last_name":"Bialek"}],"extern":1,"citation":{"mla":"Tkačik, Gašper, et al. “Information Flow and Optimization in Transcriptional Regulation.” PNAS, vol. 105, no. 34, National Academy of Sciences, 2008, pp. 12265–70, doi:10.1073/pnas.0806077105.","apa":"Tkačik, G., Callan, C., & Bialek, W. (2008). Information flow and optimization in transcriptional regulation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0806077105","ama":"Tkačik G, Callan C, Bialek W. Information flow and optimization in transcriptional regulation. PNAS. 2008;105(34):12265-12270. doi:10.1073/pnas.0806077105","short":"G. Tkačik, C. Callan, W. Bialek, PNAS 105 (2008) 12265–12270.","ieee":"G. Tkačik, C. Callan, and W. Bialek, “Information flow and optimization in transcriptional regulation,” PNAS, vol. 105, no. 34. National Academy of Sciences, pp. 12265–12270, 2008.","chicago":"Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Flow and Optimization in Transcriptional Regulation.” PNAS. National Academy of Sciences, 2008. https://doi.org/10.1073/pnas.0806077105.","ista":"Tkačik G, Callan C, Bialek W. 2008. Information flow and optimization in transcriptional regulation. PNAS. 105(34), 12265–12270."},"date_updated":"2021-01-12T07:51:52Z","month":"01","intvolume":" 105","quality_controlled":0,"publisher":"National Academy of Sciences","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527900","open_access":"1"}],"acknowledgement":"P50 GM071508/GM/NIGMS NIH HHS/United States; R01 GM077599/GM/NIGMS NIH HHS/United States","abstract":[{"text":"In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be possible to transmit much more than just one regulatory bit. Realizing this optimal information capacity would require that the dynamic range of TF concentrations used by the cell, the input/output relation of the regulatory module, and the noise in gene expression satisfy certain matching relations, which we derive. These results provide parameter-free, quantitative predictions connecting independently measurable quantities. Although we have considered only the simplified problem of a single gene responding to a single TF, we find that these predictions are in surprisingly good agreement with recent experiments on the Bicoid/Hunchback system in the early Drosophila embryo and that this system achieves approximately 90% of its theoretical maximum information transmission.","lang":"eng"}],"date_published":"2008-01-01T00:00:00Z","volume":105,"issue":"34","doi":"10.1073/pnas.0806077105","date_created":"2018-12-11T12:04:54Z","page":"12265 - 12270","day":"01","publication":"PNAS","year":"2008","publication_status":"published"},{"publist_id":"2482","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Gasper Tkacik","last_name":"Tkacik"},{"first_name":"Marcelo","full_name":"Magnasco, Marcelo O","last_name":"Magnasco"}],"title":"Decoding spike timing: The differential reverse-correlation method","date_updated":"2021-01-12T07:51:53Z","citation":{"ista":"Tkačik G, Magnasco M. 2008. Decoding spike timing: The differential reverse-correlation method. Biosystems. 93(1–2), 90–100.","chicago":"Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential Reverse-Correlation Method.” Biosystems. Elsevier, 2008. https://doi.org/10.1016/j.biosystems.2008.04.011.","apa":"Tkačik, G., & Magnasco, M. (2008). Decoding spike timing: The differential reverse-correlation method. Biosystems. Elsevier. https://doi.org/10.1016/j.biosystems.2008.04.011","ama":"Tkačik G, Magnasco M. Decoding spike timing: The differential reverse-correlation method. Biosystems. 2008;93(1-2):90-100. doi:10.1016/j.biosystems.2008.04.011","ieee":"G. Tkačik and M. Magnasco, “Decoding spike timing: The differential reverse-correlation method,” Biosystems, vol. 93, no. 1–2. Elsevier, pp. 90–100, 2008.","short":"G. Tkačik, M. Magnasco, Biosystems 93 (2008) 90–100.","mla":"Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential Reverse-Correlation Method.” Biosystems, vol. 93, no. 1–2, Elsevier, 2008, pp. 90–100, doi:10.1016/j.biosystems.2008.04.011."},"extern":1,"type":"journal_article","status":"public","_id":"3744","page":"90 - 100","doi":"10.1016/j.biosystems.2008.04.011","issue":"1-2","volume":93,"date_published":"2008-07-01T00:00:00Z","date_created":"2018-12-11T12:04:56Z","year":"2008","publication_status":"published","day":"01","publication":"Biosystems","quality_controlled":0,"publisher":"Elsevier","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2792887","open_access":"1"}],"month":"07","intvolume":" 93","abstract":[{"text":"It is widely acknowledged that detailed timing of action potentials is used to encode information, for example, in auditory pathways; however, the computational tools required to analyze encoding through timing are still in their infancy. We present a simple example of encoding, based on a recent model of time-frequency analysis, in which units fire action potentials when a certain condition is met, but the timing of the action potential depends also on other features of the stimulus. We show that, as a result, spike-triggered averages are smoothed so much that they do not represent the true features of the encoding. Inspired by this example, we present a simple method, differential reverse correlations, that can separate an analysis of what causes a neuron to spike, and what controls its timing. We analyze with this method the leaky integrate-and-fire neuron and show the method accurately reconstructs the model's kernel.","lang":"eng"}]},{"_id":"3760","status":"public","type":"journal_article","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T11:41:29Z","citation":{"ama":"Wojtan C, Turk G. Fast viscoelastic behavior with thin features. ACM Transactions on Graphics. 2008;27(3). doi:10.1145/1360612.1360646","apa":"Wojtan, C., & Turk, G. (2008). Fast viscoelastic behavior with thin features. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/1360612.1360646","short":"C. Wojtan, G. Turk, ACM Transactions on Graphics 27 (2008).","ieee":"C. Wojtan and G. Turk, “Fast viscoelastic behavior with thin features,” ACM Transactions on Graphics, vol. 27, no. 3. ACM, 2008.","mla":"Wojtan, Chris, and Greg Turk. “Fast Viscoelastic Behavior with Thin Features.” ACM Transactions on Graphics, vol. 27, no. 3, ACM, 2008, doi:10.1145/1360612.1360646.","ista":"Wojtan C, Turk G. 2008. Fast viscoelastic behavior with thin features. ACM Transactions on Graphics. 27(3).","chicago":"Wojtan, Chris, and Greg Turk. “Fast Viscoelastic Behavior with Thin Features.” ACM Transactions on Graphics. ACM, 2008. https://doi.org/10.1145/1360612.1360646."},"title":"Fast viscoelastic behavior with thin features","publist_id":"2467","author":[{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Turk, Greg","last_name":"Turk","first_name":"Greg"}],"article_processing_charge":"No","oa_version":"None","abstract":[{"text":"We introduce a method for efficiently animating a wide range of deformable materials. We combine a high resolution surface mesh with a tetrahedral finite element simulator that makes use of frequent re-meshing. This combination allows for fast and detailed simulations of complex elastic and plastic behavior. We significantly expand the range of physical parameters that can be simulated with a single technique, and the results are free from common artifacts such as volume-loss, smoothing, popping, and the absence of thin features like strands and sheets. Our decision to couple a high resolution surface with low-resolution physics leads to efficient simulation and detailed surface features, and our approach to creating the tetrahedral mesh leads to an order-of-magnitude speedup over previous techniques in the time spent re-meshing. We compute masses, collisions, and surface tension forces on the scale of the fine mesh, which helps avoid visual artifacts due to the differing mesh resolutions. The result is a method that can simulate a large array of different material behaviors with high resolution features in a short amount of time.","lang":"eng"}],"month":"08","intvolume":" 27","publisher":"ACM","main_file_link":[{"url":"http://www.cc.gatech.edu/~turk/my_papers/fast_goop_2008.pdf"}],"day":"01","language":[{"iso":"eng"}],"publication":"ACM Transactions on Graphics","publication_status":"published","year":"2008","doi":"10.1145/1360612.1360646","volume":27,"issue":"3","date_published":"2008-08-01T00:00:00Z","date_created":"2018-12-11T12:05:01Z"},{"_id":"3825","status":"public","type":"journal_article","extern":1,"citation":{"mla":"Aponte, Yexica, et al. “Efficient Ca(2+) Buffering in Fast-Spiking Basket Cells of Rat Hippocampus.” Journal of Physiology, vol. 586, no. 8, Wiley-Blackwell, 2008, pp. 2061–75, doi:10.1113/jphysiol.2007.147298.","short":"Y. Aponte, J. Bischofberger, P.M. Jonas, Journal of Physiology 586 (2008) 2061–75.","ieee":"Y. Aponte, J. Bischofberger, and P. M. Jonas, “Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus,” Journal of Physiology, vol. 586, no. 8. Wiley-Blackwell, pp. 2061–75, 2008.","apa":"Aponte, Y., Bischofberger, J., & Jonas, P. M. (2008). Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2007.147298","ama":"Aponte Y, Bischofberger J, Jonas PM. Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus. Journal of Physiology. 2008;586(8):2061-2075. doi:10.1113/jphysiol.2007.147298","chicago":"Aponte, Yexica, Josef Bischofberger, and Peter M Jonas. “Efficient Ca(2+) Buffering in Fast-Spiking Basket Cells of Rat Hippocampus.” Journal of Physiology. Wiley-Blackwell, 2008. https://doi.org/10.1113/jphysiol.2007.147298.","ista":"Aponte Y, Bischofberger J, Jonas PM. 2008. Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus. Journal of Physiology. 586(8), 2061–75."},"date_updated":"2021-01-12T07:52:28Z","title":"Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus","publist_id":"2386","author":[{"first_name":"Yexica","full_name":"Aponte, Yexica","last_name":"Aponte"},{"first_name":"Josef","full_name":"Bischofberger, Josef","last_name":"Bischofberger"},{"full_name":"Peter Jonas","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"abstract":[{"lang":"eng","text":"Fast-spiking parvalbumin-expressing basket cells (BCs) represent a major type of inhibitory interneuron in the hippocampus. These cells inhibit principal cells in a temporally precise manner and are involved in the generation of network oscillations. Although BCs show a unique expression profile of Ca(2+)-permeable receptors, Ca(2+)-binding proteins and Ca(2+)-dependent signalling molecules, physiological Ca(2+) signalling in these interneurons has not been investigated. To study action potential (AP)-induced dendritic Ca(2+) influx and buffering, we combined whole-cell patch-clamp recordings with ratiometric Ca(2+) imaging from the proximal apical dendrites of rigorously identified BCs in acute slices, using the high-affinity Ca(2+) indicator fura-2 or the low-affinity dye fura-FF. Single APs evoked dendritic Ca(2+) transients with small amplitude. Bursts of APs evoked Ca(2+) transients with amplitudes that increased linearly with AP number. Analysis of Ca(2+) transients under steady-state conditions with different fura-2 concentrations and during loading with 200 microm fura-2 indicated that the endogenous Ca(2+)-binding ratio was approximately 200 (kappa(S) = 202 +/- 26 for the loading experiments). The peak amplitude of the Ca(2+) transients measured directly with 100 microm fura-FF was 39 nm AP(-1). At approximately 23 degrees C, the decay time constant of the Ca(2+) transients was 390 ms, corresponding to an extrusion rate of approximately 600 s(-1). At 34 degrees C, the decay time constant was 203 ms and the corresponding extrusion rate was approximately 1100 s(-1). At both temperatures, continuous theta-burst activity with three to five APs per theta cycle, as occurs in vivo during exploration, led to a moderate increase in the global Ca(2+) concentration that was proportional to AP number, whereas more intense stimulation was required to reach micromolar Ca(2+) concentrations and to shift Ca(2+) signalling into a non-linear regime. In conclusion, dentate gyrus BCs show a high endogenous Ca(2+)-binding ratio, a small AP-induced dendritic Ca(2+) influx, and a relatively slow Ca(2+) extrusion. These specific buffering properties of BCs will sharpen the time course of local Ca(2+) signals, while prolonging the decay of global Ca(2+) signals."}],"month":"01","intvolume":" 586","quality_controlled":0,"publisher":"Wiley-Blackwell","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2465201/"}],"oa":1,"day":"01","publication":"Journal of Physiology","publication_status":"published","year":"2008","doi":"10.1113/jphysiol.2007.147298","issue":"8","volume":586,"date_published":"2008-01-01T00:00:00Z","date_created":"2018-12-11T12:05:22Z","page":"2061 - 75"},{"abstract":[{"text":"Dentate gyrus granule cells transmit action potentials (APs) along their unmyelinated mossy fibre axons to the CA3 region. Although the initiation and propagation of APs are fundamental steps during neural computation, little is known about the site of AP initiation and the speed of propagation in mossy fibre axons. To address these questions, we performed simultaneous somatic and axonal whole-cell recordings from granule cells in acute hippocampal slices of adult mice at approximately 23 degrees C. Injection of short current pulses or synaptic stimulation evoked axonal and somatic APs with similar amplitudes. By contrast, the time course was significantly different, as axonal APs had a higher maximal rate of rise (464 +/- 30 V s(-1) in the axon versus 297 +/- 12 V s(-1) in the soma, mean +/- s.e.m.). Furthermore, analysis of latencies between the axonal and somatic signals showed that APs were initiated in the proximal axon at approximately 20-30 mum distance from the soma, and propagated orthodromically with a velocity of 0.24 m s(-1). Qualitatively similar results were obtained at a recording temperature of approximately 34 degrees C. Modelling of AP propagation in detailed cable models of granule cells suggested that a approximately 4 times higher Na(+) channel density ( approximately 1000 pS mum(-2)) in the axon might account for both the higher rate of rise of axonal APs and the robust AP initiation in the proximal mossy fibre axon. This may be of critical importance to separate dendritic integration of thousands of synaptic inputs from the generation and transmission of a common AP output.","lang":"eng"}],"intvolume":" 586","month":"01","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375716/","open_access":"1"}],"publisher":"Wiley-Blackwell","quality_controlled":0,"publication":"Journal of Physiology","day":"01","year":"2008","publication_status":"published","date_created":"2018-12-11T12:05:21Z","issue":"7","date_published":"2008-01-01T00:00:00Z","volume":586,"doi":"10.1113/jphysiol.2007.150151 ","page":"1849 - 57","_id":"3822","status":"public","type":"journal_article","extern":1,"citation":{"ama":"Schmidt Hieber C, Jonas PM, Bischofberger J. Action potential initiation and propagation in hippocampal mossy fibre axons. Journal of Physiology. 2008;586(7):1849-1857. doi:10.1113/jphysiol.2007.150151 ","apa":"Schmidt Hieber, C., Jonas, P. M., & Bischofberger, J. (2008). Action potential initiation and propagation in hippocampal mossy fibre axons. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2007.150151 ","ieee":"C. Schmidt Hieber, P. M. Jonas, and J. Bischofberger, “Action potential initiation and propagation in hippocampal mossy fibre axons,” Journal of Physiology, vol. 586, no. 7. Wiley-Blackwell, pp. 1849–57, 2008.","short":"C. Schmidt Hieber, P.M. Jonas, J. Bischofberger, Journal of Physiology 586 (2008) 1849–57.","mla":"Schmidt Hieber, Christoph, et al. “Action Potential Initiation and Propagation in Hippocampal Mossy Fibre Axons.” Journal of Physiology, vol. 586, no. 7, Wiley-Blackwell, 2008, pp. 1849–57, doi:10.1113/jphysiol.2007.150151 .","ista":"Schmidt Hieber C, Jonas PM, Bischofberger J. 2008. Action potential initiation and propagation in hippocampal mossy fibre axons. Journal of Physiology. 586(7), 1849–57.","chicago":"Schmidt Hieber, Christoph, Peter M Jonas, and Josef Bischofberger. “Action Potential Initiation and Propagation in Hippocampal Mossy Fibre Axons.” Journal of Physiology. Wiley-Blackwell, 2008. https://doi.org/10.1113/jphysiol.2007.150151 ."},"date_updated":"2021-01-12T07:52:27Z","title":"Action potential initiation and propagation in hippocampal mossy fibre axons","author":[{"first_name":"Christoph","full_name":"Schmidt-Hieber, Christoph","last_name":"Schmidt Hieber"},{"full_name":"Peter Jonas","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bischofberger, Josef","last_name":"Bischofberger","first_name":"Josef"}],"publist_id":"2387"},{"publication_status":"published","year":"2008","day":"01","publication":"Neuron","page":"536 - 45","volume":57,"issue":"4","date_published":"2008-01-01T00:00:00Z","doi":"10.1016/j.neuron.2007.12.026","date_created":"2018-12-11T12:05:22Z","abstract":[{"lang":"eng","text":"It is generally thought that transmitter release at mammalian central synapses is triggered by Ca2+ microdomains, implying loose coupling between presynaptic Ca2+ channels and Ca2+ sensors of exocytosis. Here we show that Ca2+ channel subunit immunoreactivity is highly concentrated in the active zone of GABAergic presynaptic terminals of putative parvalbumin-containing basket cells in the hippocampus. Paired recording combined with presynaptic patch pipette perfusion revealed that GABA release at basket cell-granule cell synapses is sensitive to millimolar concentrations of the fast Ca2+ chelator BAPTA but insensitive to the slow Ca2+ chelator EGTA. These results show that Ca2+ source and Ca2+ sensor are tightly coupled at this synapse, with distances in the range of 10-20 nm. Models of Ca2+ inflow-exocytosis coupling further reveal that the tightness of coupling increases efficacy, speed, and temporal precision of transmitter release. Thus, tight coupling contributes to fast feedforward and feedback inhibition in the hippocampal network."}],"publisher":"Elsevier","quality_controlled":0,"month":"01","intvolume":" 57","citation":{"ista":"Bucurenciu I, Kulik Á, Schwaller B, Frotscher M, Jonas PM. 2008. Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter release at a cortical GABAergic synapse. Neuron. 57(4), 536–45.","chicago":"Bucurenciu, Iancu, Ákos Kulik, Beat Schwaller, Michael Frotscher, and Peter M Jonas. “Nanodomain Coupling between Ca(2+) Channels and Ca2+ Sensors Promotes Fast and Efficient Transmitter Release at a Cortical GABAergic Synapse.” Neuron. Elsevier, 2008. https://doi.org/10.1016/j.neuron.2007.12.026.","ama":"Bucurenciu I, Kulik Á, Schwaller B, Frotscher M, Jonas PM. Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter release at a cortical GABAergic synapse. Neuron. 2008;57(4):536-545. doi:10.1016/j.neuron.2007.12.026","apa":"Bucurenciu, I., Kulik, Á., Schwaller, B., Frotscher, M., & Jonas, P. M. (2008). Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter release at a cortical GABAergic synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2007.12.026","short":"I. Bucurenciu, Á. Kulik, B. Schwaller, M. Frotscher, P.M. Jonas, Neuron 57 (2008) 536–45.","ieee":"I. Bucurenciu, Á. Kulik, B. Schwaller, M. Frotscher, and P. M. Jonas, “Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter release at a cortical GABAergic synapse,” Neuron, vol. 57, no. 4. Elsevier, pp. 536–45, 2008.","mla":"Bucurenciu, Iancu, et al. “Nanodomain Coupling between Ca(2+) Channels and Ca2+ Sensors Promotes Fast and Efficient Transmitter Release at a Cortical GABAergic Synapse.” Neuron, vol. 57, no. 4, Elsevier, 2008, pp. 536–45, doi:10.1016/j.neuron.2007.12.026."},"date_updated":"2021-01-12T07:52:27Z","extern":1,"publist_id":"2385","author":[{"last_name":"Bucurenciu","full_name":"Bucurenciu, Iancu","first_name":"Iancu"},{"first_name":"Ákos","full_name":"Kulik, Ákos","last_name":"Kulik"},{"first_name":"Beat","last_name":"Schwaller","full_name":"Schwaller, Beat"},{"full_name":"Frotscher, Michael","last_name":"Frotscher","first_name":"Michael"},{"last_name":"Jonas","full_name":"Peter Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"title":"Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter release at a cortical GABAergic synapse","_id":"3824","type":"journal_article","status":"public"},{"_id":"3823","type":"journal_article","status":"public","citation":{"ama":"Kerr A, Jonas PM. The two sides of hippocampal mossy fiber plasticity (Review). Neuron. 2008;57(1):5-7. doi:10.1016/j.neuron.2007.12.015","apa":"Kerr, A., & Jonas, P. M. (2008). The two sides of hippocampal mossy fiber plasticity (Review). Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2007.12.015","short":"A. Kerr, P.M. Jonas, Neuron 57 (2008) 5–7.","ieee":"A. Kerr and P. M. Jonas, “The two sides of hippocampal mossy fiber plasticity (Review),” Neuron, vol. 57, no. 1. Elsevier, pp. 5–7, 2008.","mla":"Kerr, Angharad, and Peter M. Jonas. “The Two Sides of Hippocampal Mossy Fiber Plasticity (Review).” Neuron, vol. 57, no. 1, Elsevier, 2008, pp. 5–7, doi:10.1016/j.neuron.2007.12.015.","ista":"Kerr A, Jonas PM. 2008. The two sides of hippocampal mossy fiber plasticity (Review). Neuron. 57(1), 5–7.","chicago":"Kerr, Angharad, and Peter M Jonas. “The Two Sides of Hippocampal Mossy Fiber Plasticity (Review).” Neuron. Elsevier, 2008. https://doi.org/10.1016/j.neuron.2007.12.015."},"date_updated":"2021-01-12T07:52:27Z","extern":1,"author":[{"first_name":"Angharad","full_name":"Kerr, Angharad M","last_name":"Kerr"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Peter Jonas"}],"publist_id":"2388","title":"The two sides of hippocampal mossy fiber plasticity (Review)","abstract":[{"lang":"eng","text":"Two studies in this issue of Neuron (Kwon and Castillo and Rebola et al.) show that the mossy fiber-CA3 pyramidal neuron synapse, a hippocampal synapse well known for its presynaptic plasticity, exhibits a novel form of long-term potentiation of NMDAR-mediated currents, which is induced and expressed postsynaptically."}],"quality_controlled":0,"publisher":"Elsevier","month":"01","intvolume":" 57","publication_status":"published","year":"2008","day":"10","publication":"Neuron","page":"5 - 7","date_published":"2008-01-10T00:00:00Z","issue":"1","volume":57,"doi":"10.1016/j.neuron.2007.12.015","date_created":"2018-12-11T12:05:22Z"},{"status":"public","type":"conference","conference":{"name":"CONCUR: Concurrency Theory"},"_id":"3880","title":"Strategy construction for parity games with imperfect information","author":[{"last_name":"Berwanger","full_name":"Berwanger, Dietmar","first_name":"Dietmar"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger"},{"last_name":"Raje","full_name":"Raje, Sangram","first_name":"Sangram"}],"publist_id":"2291","extern":1,"citation":{"chicago":"Berwanger, Dietmar, Krishnendu Chatterjee, Laurent Doyen, Thomas A Henzinger, and Sangram Raje. “Strategy Construction for Parity Games with Imperfect Information,” 5201:325–39. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008. https://doi.org/10.1007/978-3-540-85361-9.","ista":"Berwanger D, Chatterjee K, Doyen L, Henzinger TA, Raje S. 2008. Strategy construction for parity games with imperfect information. CONCUR: Concurrency Theory, LNCS, vol. 5201, 325–339.","mla":"Berwanger, Dietmar, et al. Strategy Construction for Parity Games with Imperfect Information. Vol. 5201, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 325–39, doi:10.1007/978-3-540-85361-9.","apa":"Berwanger, D., Chatterjee, K., Doyen, L., Henzinger, T. A., & Raje, S. (2008). Strategy construction for parity games with imperfect information (Vol. 5201, pp. 325–339). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-540-85361-9","ama":"Berwanger D, Chatterjee K, Doyen L, Henzinger TA, Raje S. Strategy construction for parity games with imperfect information. In: Vol 5201. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2008:325-339. doi:10.1007/978-3-540-85361-9","short":"D. Berwanger, K. Chatterjee, L. Doyen, T.A. Henzinger, S. Raje, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 325–339.","ieee":"D. Berwanger, K. Chatterjee, L. Doyen, T. A. Henzinger, and S. Raje, “Strategy construction for parity games with imperfect information,” presented at the CONCUR: Concurrency Theory, 2008, vol. 5201, pp. 325–339."},"date_updated":"2023-02-23T11:46:01Z","month":"07","intvolume":" 5201","quality_controlled":0,"alternative_title":["LNCS"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","abstract":[{"text":"We consider imperfect-information parity games in which strategies rely on observations that provide imperfect information about the history of a play. To solve such games, i.e., to determine the winning regions of players and corresponding winning strategies, one can use the subset construction to build an equivalent perfect-information game. Recently, an algorithm that avoids the inefficient subset construction has been proposed. The algorithm performs a fixed-point computation in a lattice of antichains, thus maintaining a succinct representation of state sets. However, this representation does not allow to recover winning strategies. In this paper, we build on the antichain approach to develop an algorithm for constructing the winning strategies in parity games of imperfect information. We have implemented this algorithm as a prototype. To our knowledge, this is the first implementation of a procedure for solving imperfect-information parity games on graphs.","lang":"eng"}],"doi":"10.1007/978-3-540-85361-9","date_published":"2008-07-30T00:00:00Z","related_material":{"record":[{"status":"public","id":"3863","relation":"later_version"}]},"volume":5201,"date_created":"2018-12-11T12:05:40Z","page":"325 - 339","day":"30","publication_status":"published","year":"2008"},{"oa_version":"None","abstract":[{"text":"Background\r\n\r\nThe invasive garden ant, Lasius neglectus, is the most recently detected pest ant and the first known invasive ant able to become established and thrive in the temperate regions of Eurasia. In this study, we aim to reconstruct the invasion history of this ant in Europe analysing 14 populations with three complementary approaches: genetic microsatellite analysis, chemical analysis of cuticular hydrocarbon profiles and behavioural observations of aggression behaviour. We evaluate the relative informative power of the three methodological approaches and estimate both the number of independent introduction events from a yet unknown native range somewhere in the Black Sea area, and the invasive potential of the existing introduced populations.\r\n\r\nResults\r\n\r\nThree clusters of genetically similar populations were detected, and all but one population had a similar chemical profile. Aggression between populations could be predicted from their genetic and chemical distance, and two major clusters of non-aggressive groups of populations were found. However, populations of L. neglectus did not separate into clear supercolonial associations, as is typical for other invasive ants.\r\n\r\nConclusion\r\n\r\nThe three methodological approaches gave consistent and complementary results. All joint evidence supports the inference that the 14 introduced populations of L. neglectus in Europe likely arose from only very few independent introductions from the native range, and that new infestations were typically started through introductions from other invasive populations. This indicates that existing introduced populations have a very high invasive potential when the ants are inadvertently spread by human transport. ","lang":"eng"}],"intvolume":" 6","month":"02","publisher":"BioMed Central","publication":"BMC Biology","language":[{"iso":"eng"}],"day":"26","publication_status":"published","year":"2008","license":"https://creativecommons.org/licenses/by/4.0/","date_created":"2018-12-11T12:05:48Z","volume":6,"issue":"11","date_published":"2008-02-26T00:00:00Z","doi":"10.1186/1741-7007-6-11","_id":"3903","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","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"apa":"Ugelvig, L. V., Drijfhout, F., Kronauer, D., Boomsma, J., Pedersen, J., & Cremer, S. (2008). The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches. BMC Biology. BioMed Central. https://doi.org/10.1186/1741-7007-6-11","ama":"Ugelvig LV, Drijfhout F, Kronauer D, Boomsma J, Pedersen J, Cremer S. The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches. BMC Biology. 2008;6(11). doi:10.1186/1741-7007-6-11","short":"L.V. Ugelvig, F. Drijfhout, D. Kronauer, J. Boomsma, J. Pedersen, S. Cremer, BMC Biology 6 (2008).","ieee":"L. V. Ugelvig, F. Drijfhout, D. Kronauer, J. Boomsma, J. Pedersen, and S. Cremer, “The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches,” BMC Biology, vol. 6, no. 11. BioMed Central, 2008.","mla":"Ugelvig, Line V., et al. “The Introduction History of Invasive Garden Ants in Europe: Integrating Genetic, Chemical and Behavioural Approaches.” BMC Biology, vol. 6, no. 11, BioMed Central, 2008, doi:10.1186/1741-7007-6-11.","ista":"Ugelvig LV, Drijfhout F, Kronauer D, Boomsma J, Pedersen J, Cremer S. 2008. The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches. BMC Biology. 6(11).","chicago":"Ugelvig, Line V, Falko Drijfhout, Daniel Kronauer, Jacobus Boomsma, Jes Pedersen, and Sylvia Cremer. “The Introduction History of Invasive Garden Ants in Europe: Integrating Genetic, Chemical and Behavioural Approaches.” BMC Biology. BioMed Central, 2008. https://doi.org/10.1186/1741-7007-6-11."},"date_updated":"2021-01-12T07:53:05Z","title":"The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches","publist_id":"2249","author":[{"full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","last_name":"Ugelvig","first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Falko","full_name":"Drijfhout, Falko","last_name":"Drijfhout"},{"first_name":"Daniel","last_name":"Kronauer","full_name":"Kronauer, Daniel"},{"first_name":"Jacobus","full_name":"Boomsma, Jacobus","last_name":"Boomsma"},{"first_name":"Jes","last_name":"Pedersen","full_name":"Pedersen, Jes"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer"}]},{"month":"08","intvolume":" 95","publisher":"Springer","oa_version":"None","abstract":[{"text":"Winged and wingless males coexist in the ant Cardiocondyla obscurior. Wingless (“ergatoid”) males never leave their maternal colony and fight remorselessly among each other for the access to emerging females. The peaceful winged males disperse after about 10 days, but beforehand also mate in the nest. In the first 5 days of their life, winged males perform a chemical female mimicry that protects them against attack and even makes them sexually attractive to ergatoid males. When older, the chemical profile of winged males no longer matches that of virgin females; nevertheless, they are still tolerated, which so far has been puzzling. Contrasting this general pattern, we have identified a single aberrant colony in which all winged males were attacked and killed by the ergatoid males. A comparative analysis of the morphology and chemical profile of these untypical attacked winged males and the tolerated males from several normal colonies revealed that normal old males are still performing some chemical mimicry to the virgin queens, though less perfect than in their young ages. The anomalous attacked winged males, on the other hand, had a very different odour to the females. Our study thus exemplifies that the analysis of rare malfunctioning can add valuable insight on functioning under normal conditions and allows the conclusion that older winged males from normal colonies of the ant C. obscurior are guarded through an imperfect chemical female mimicry, still close enough to protect against attacks by the wingless fighters yet dissimilar enough not to elicit their sexual interest.","lang":"eng"}],"doi":"10.1007/s00114-008-0430-8","issue":"11","volume":95,"date_published":"2008-08-05T00:00:00Z","date_created":"2018-12-11T12:05:48Z","page":"1101 - 1105","day":"05","language":[{"iso":"eng"}],"publication":"Naturwissenschaften","year":"2008","publication_status":"published","status":"public","type":"journal_article","_id":"3905","title":"Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior","author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"},{"first_name":"Patrizia","last_name":"D'Ettorre","full_name":"D'Ettorre, Patrizia"},{"full_name":"Drijfhout, Falko","last_name":"Drijfhout","first_name":"Falko"},{"full_name":"Sledge, Matthew","last_name":"Sledge","first_name":"Matthew"},{"first_name":"Stefano","last_name":"Turillazzi","full_name":"Turillazzi, Stefano"},{"last_name":"Heinze","full_name":"Heinze, Jürgen","first_name":"Jürgen"}],"publist_id":"2246","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"S. Cremer, P. D’Ettorre, F. Drijfhout, M. Sledge, S. Turillazzi, J. Heinze, Naturwissenschaften 95 (2008) 1101–1105.","ieee":"S. Cremer, P. D’Ettorre, F. Drijfhout, M. Sledge, S. Turillazzi, and J. Heinze, “Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior,” Naturwissenschaften, vol. 95, no. 11. Springer, pp. 1101–1105, 2008.","ama":"Cremer S, D’Ettorre P, Drijfhout F, Sledge M, Turillazzi S, Heinze J. Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior. Naturwissenschaften. 2008;95(11):1101-1105. doi:10.1007/s00114-008-0430-8","apa":"Cremer, S., D’Ettorre, P., Drijfhout, F., Sledge, M., Turillazzi, S., & Heinze, J. (2008). Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior. Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-008-0430-8","mla":"Cremer, Sylvia, et al. “Imperfect Chemical Female Mimicry in Males of the Ant Cardiocondyla Obscurior.” Naturwissenschaften, vol. 95, no. 11, Springer, 2008, pp. 1101–05, doi:10.1007/s00114-008-0430-8.","ista":"Cremer S, D’Ettorre P, Drijfhout F, Sledge M, Turillazzi S, Heinze J. 2008. Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior. Naturwissenschaften. 95(11), 1101–1105.","chicago":"Cremer, Sylvia, Patrizia D’Ettorre, Falko Drijfhout, Matthew Sledge, Stefano Turillazzi, and Jürgen Heinze. “Imperfect Chemical Female Mimicry in Males of the Ant Cardiocondyla Obscurior.” Naturwissenschaften. Springer, 2008. https://doi.org/10.1007/s00114-008-0430-8."},"date_updated":"2021-01-12T07:53:06Z"},{"date_created":"2018-12-11T12:05:49Z","doi":"10.1098/rsbl.2008.0355","date_published":"2008-12-23T00:00:00Z","issue":"6","volume":4,"page":"670 - 673","publication":"Biology Letters","language":[{"iso":"eng"}],"day":"23","publication_status":"published","year":"2008","intvolume":" 4","month":"12","publisher":"Royal Society, The","oa_version":"None","abstract":[{"text":"Wingless males of the ant genus Cardiocondyla engage in fatal fighting for access to female sexual nestmates. Older, heavily sclerotized males are usually capable of eliminating all younger rivals, whose cuticle is still soft. In Cardiocondyla sp. A, this type of local mate competition (LMC) has turned the standard pattern of brood production of social insects upside down, in that mother queens in multi-queen colonies produce extremely long-lived sons very early in the life cycle of the colony. Here, we investigated the emergence pattern of sexuals in two species with LMC, in which males are much less long-lived. Queens of Cardiocondyla obscurior and Cardiocondyla minutior reared their first sons significantly earlier in multi-queen than in single-queen societies. In addition, first female sexuals also emerged earlier in multi-queen colonies, so that early males had mating opportunities. Hence, the timing of sexual production appears to be well predicted by evolutionary theory, in particular by local mate and queen–queen competition. ","lang":"eng"}],"title":"Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants","publist_id":"2248","author":[{"first_name":"Masaki","last_name":"Suefuji","full_name":"Suefuji, Masaki"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"},{"first_name":"Jan","last_name":"Oettler","full_name":"Oettler, Jan"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"apa":"Suefuji, M., Cremer, S., Oettler, J., & Heinze, J. (2008). Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants. Biology Letters. Royal Society, The. https://doi.org/10.1098/rsbl.2008.0355","ama":"Suefuji M, Cremer S, Oettler J, Heinze J. Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants. Biology Letters. 2008;4(6):670-673. doi:10.1098/rsbl.2008.0355","ieee":"M. Suefuji, S. Cremer, J. Oettler, and J. Heinze, “Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants,” Biology Letters, vol. 4, no. 6. Royal Society, The, pp. 670–673, 2008.","short":"M. Suefuji, S. Cremer, J. Oettler, J. Heinze, Biology Letters 4 (2008) 670–673.","mla":"Suefuji, Masaki, et al. “Queen Number Influences the Timing of the Sexual Production in Colonies of Cardiocondyla Ants.” Biology Letters, vol. 4, no. 6, Royal Society, The, 2008, pp. 670–73, doi:10.1098/rsbl.2008.0355.","ista":"Suefuji M, Cremer S, Oettler J, Heinze J. 2008. Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants. Biology Letters. 4(6), 670–673.","chicago":"Suefuji, Masaki, Sylvia Cremer, Jan Oettler, and Jürgen Heinze. “Queen Number Influences the Timing of the Sexual Production in Colonies of Cardiocondyla Ants.” Biology Letters. Royal Society, The, 2008. https://doi.org/10.1098/rsbl.2008.0355."},"date_updated":"2021-01-12T07:53:07Z","status":"public","type":"journal_article","_id":"3907"},{"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Cremer, Sylvia, et al. “The Evolution of Invasiveness in Garden Ants.” PLoS One, vol. 3, no. 12, Public Library of Science, 2008, doi:10.1371/journal.pone.0003838.","ama":"Cremer S, Ugelvig LV, Drijfhout F, et al. The evolution of invasiveness in garden ants. PLoS One. 2008;3(12). doi:10.1371/journal.pone.0003838","apa":"Cremer, S., Ugelvig, L. V., Drijfhout, F., Schlick Steiner, B., Steiner, F., Seifert, B., … Boomsma, J. (2008). The evolution of invasiveness in garden ants. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0003838","ieee":"S. Cremer et al., “The evolution of invasiveness in garden ants,” PLoS One, vol. 3, no. 12. Public Library of Science, 2008.","short":"S. Cremer, L.V. Ugelvig, F. Drijfhout, B. Schlick Steiner, F. Steiner, B. Seifert, D. Hughes, A. Schulz, K. Petersen, H. Konrad, C. Stauffer, K. Kiran, X. Espadaler, P. D’Ettorre, N. Aktaç, J. Eilenberg, G. Jones, D. Nash, J. Pedersen, J. Boomsma, PLoS One 3 (2008).","chicago":"Cremer, Sylvia, Line V Ugelvig, Falko Drijfhout, Birgit Schlick Steiner, Florian Steiner, Bernhard Seifert, David Hughes, et al. “The Evolution of Invasiveness in Garden Ants.” PLoS One. Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0003838.","ista":"Cremer S, Ugelvig LV, Drijfhout F, Schlick Steiner B, Steiner F, Seifert B, Hughes D, Schulz A, Petersen K, Konrad H, Stauffer C, Kiran K, Espadaler X, D’Ettorre P, Aktaç N, Eilenberg J, Jones G, Nash D, Pedersen J, Boomsma J. 2008. The evolution of invasiveness in garden ants. PLoS One. 3(12)."},"date_updated":"2021-01-12T07:53:06Z","title":"The evolution of invasiveness in garden ants","publist_id":"2247","author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"},{"last_name":"Ugelvig","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V"},{"full_name":"Drijfhout, Falko","last_name":"Drijfhout","first_name":"Falko"},{"first_name":"Birgit","last_name":"Schlick Steiner","full_name":"Schlick Steiner, Birgit"},{"first_name":"Florian","full_name":"Steiner, Florian","last_name":"Steiner"},{"first_name":"Bernhard","full_name":"Seifert, Bernhard","last_name":"Seifert"},{"full_name":"Hughes, David","last_name":"Hughes","first_name":"David"},{"last_name":"Schulz","full_name":"Schulz, Andreas","first_name":"Andreas"},{"full_name":"Petersen, Klaus","last_name":"Petersen","first_name":"Klaus"},{"full_name":"Konrad, Heino","last_name":"Konrad","first_name":"Heino"},{"last_name":"Stauffer","full_name":"Stauffer, Christian","first_name":"Christian"},{"first_name":"Kadri","last_name":"Kiran","full_name":"Kiran, Kadri"},{"first_name":"Xavier","last_name":"Espadaler","full_name":"Espadaler, Xavier"},{"full_name":"D'Ettorre, Patrizia","last_name":"D'Ettorre","first_name":"Patrizia"},{"full_name":"Aktaç, Nihat","last_name":"Aktaç","first_name":"Nihat"},{"full_name":"Eilenberg, Jørgen","last_name":"Eilenberg","first_name":"Jørgen"},{"first_name":"Graeme","last_name":"Jones","full_name":"Jones, Graeme"},{"full_name":"Nash, David","last_name":"Nash","first_name":"David"},{"last_name":"Pedersen","full_name":"Pedersen, Jes","first_name":"Jes"},{"last_name":"Boomsma","full_name":"Boomsma, Jacobus","first_name":"Jacobus"}],"_id":"3906","status":"public","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)"},"day":"03","language":[{"iso":"eng"}],"publication":"PLoS One","publication_status":"published","year":"2008","issue":"12","date_published":"2008-12-03T00:00:00Z","volume":3,"doi":"10.1371/journal.pone.0003838","date_created":"2018-12-11T12:05:49Z","oa_version":"None","acknowledgement":"Funding was obtained from the European Community: FP5 EU research-training network ‘INSECTS’ (JJB SC PD FPD DPH) and FP6 Individual Marie Curie EIF grant (SC), the Alexander-von-Humboldt Foundation (Feodor-Lynen postdoctoral stipend to SC), the Danish Natural Science Research Council (JSP), the Danish National Research Foundation (JJB DRN JSP), and the Austrian Science Fund (BCS FMS CS HK).","month":"12","intvolume":" 3","publisher":"Public Library of Science"},{"_id":"3939","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"apa":"Lämmermann, T., & Sixt, M. K. (2008). The microanatomy of T-cell responses. Immunological Reviews. Wiley-Blackwell. https://doi.org/10.1111/j.1600-065X.2008.00592.x","ama":"Lämmermann T, Sixt MK. The microanatomy of T-cell responses. Immunological Reviews. 2008;221(1):26-43. doi:10.1111/j.1600-065X.2008.00592.x","short":"T. Lämmermann, M.K. Sixt, Immunological Reviews 221 (2008) 26–43.","ieee":"T. Lämmermann and M. K. Sixt, “The microanatomy of T-cell responses,” Immunological Reviews, vol. 221, no. 1. Wiley-Blackwell, pp. 26–43, 2008.","mla":"Lämmermann, Tim, and Michael K. Sixt. “The Microanatomy of T-Cell Responses.” Immunological Reviews, vol. 221, no. 1, Wiley-Blackwell, 2008, pp. 26–43, doi:10.1111/j.1600-065X.2008.00592.x.","ista":"Lämmermann T, Sixt MK. 2008. The microanatomy of T-cell responses. Immunological Reviews. 221(1), 26–43.","chicago":"Lämmermann, Tim, and Michael K Sixt. “The Microanatomy of T-Cell Responses.” Immunological Reviews. Wiley-Blackwell, 2008. https://doi.org/10.1111/j.1600-065X.2008.00592.x."},"date_updated":"2021-01-12T07:53:20Z","title":"The microanatomy of T-cell responses","author":[{"first_name":"Tim","full_name":"Lämmermann, Tim","last_name":"Lämmermann"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"publist_id":"2187","oa_version":"None","abstract":[{"lang":"eng","text":"The priming of a T cell results from its physical interaction with a dendritic cell (DC) that presents the cognate antigenic peptide. The success rate of such interactions is extremely low, because the precursor frequency of a naive T cell recognizing a specific antigen is in the range of 1:10(5)-10(6). To make this principle practicable, encounter frequencies between DCs and T cells are maximized within lymph nodes (LNs) that are compact immunological projections of the peripheral tissue they drain. But LNs are more than passive meeting places for DCs that immigrated from the tissue and lymphocytes that recirculated via the blood. The microanatomy of the LN stroma actively organizes the cellular encounters by providing preformed migration tracks that create dynamic but highly ordered movement patterns. LN architecture further acts as a sophisticated filtration system that sieves the incoming interstitial fluid at different levels and guarantees that immunologically relevant antigens are loaded on DCs or B cells while inert substances are channeled back into the blood circulation. This review focuses on the non-hematopoietic infrastructure of the lymph node. We describe the association between fibroblastic reticular cell, conduit, DC, and T cell as the essential functional unit of the T-cell cortex."}],"intvolume":" 221","month":"02","publisher":"Wiley-Blackwell","language":[{"iso":"eng"}],"publication":"Immunological Reviews","day":"07","year":"2008","publication_status":"published","date_created":"2018-12-11T12:06:00Z","doi":"10.1111/j.1600-065X.2008.00592.x","issue":"1","date_published":"2008-02-07T00:00:00Z","volume":221,"page":"26 - 43"},{"month":"02","intvolume":" 20","quality_controlled":0,"publisher":"Academic Press","abstract":[{"text":"Until recently little information was available on the molecular details of the extracellular matrix (ECM) of secondary lymphoid tissues. There is now growing evidence that these ECMs are unique structures, combining characteristics of basement membranes and interstitial or fibrillar matrices, resulting in scaffolds that are strong and highly flexible and, in certain secondary lymphoid compartments, also forming conduit networks for rapid fluid transport. This review will address the structural characteristics of the ECM of the murine spleen and its potential role as an organizer of immune cell compartments, with reference to the lymph node where relevant.","lang":"eng"}],"issue":"1","volume":20,"doi":"10.1016/j.smim.2007.12.009","date_published":"2008-02-01T00:00:00Z","date_created":"2018-12-11T12:06:00Z","page":"4 - 13","day":"01","publication":"Seminars in Immunology","year":"2008","publication_status":"published","status":"public","type":"journal_article","_id":"3940","title":"The extracellular matrix of the spleen as a potential organizer of immune cell compartments","publist_id":"2188","author":[{"full_name":"Lokmic, Zerina","last_name":"Lokmic","first_name":"Zerina"},{"full_name":"Lämmermann, Tim","last_name":"Lämmermann","first_name":"Tim"},{"full_name":"Michael Sixt","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Susanna","last_name":"Cardell","full_name":"Cardell, Susanna"},{"first_name":"Rupert","last_name":"Hallmann","full_name":"Hallmann, Rupert"},{"first_name":"Lydia","full_name":"Sorokin, Lydia","last_name":"Sorokin"}],"extern":1,"citation":{"chicago":"Lokmic, Zerina, Tim Lämmermann, Michael K Sixt, Susanna Cardell, Rupert Hallmann, and Lydia Sorokin. “The Extracellular Matrix of the Spleen as a Potential Organizer of Immune Cell Compartments.” Seminars in Immunology. Academic Press, 2008. https://doi.org/10.1016/j.smim.2007.12.009.","ista":"Lokmic Z, Lämmermann T, Sixt MK, Cardell S, Hallmann R, Sorokin L. 2008. The extracellular matrix of the spleen as a potential organizer of immune cell compartments. Seminars in Immunology. 20(1), 4–13.","mla":"Lokmic, Zerina, et al. “The Extracellular Matrix of the Spleen as a Potential Organizer of Immune Cell Compartments.” Seminars in Immunology, vol. 20, no. 1, Academic Press, 2008, pp. 4–13, doi:10.1016/j.smim.2007.12.009.","short":"Z. Lokmic, T. Lämmermann, M.K. Sixt, S. Cardell, R. Hallmann, L. Sorokin, Seminars in Immunology 20 (2008) 4–13.","ieee":"Z. Lokmic, T. Lämmermann, M. K. Sixt, S. Cardell, R. Hallmann, and L. Sorokin, “The extracellular matrix of the spleen as a potential organizer of immune cell compartments,” Seminars in Immunology, vol. 20, no. 1. Academic Press, pp. 4–13, 2008.","apa":"Lokmic, Z., Lämmermann, T., Sixt, M. K., Cardell, S., Hallmann, R., & Sorokin, L. (2008). The extracellular matrix of the spleen as a potential organizer of immune cell compartments. Seminars in Immunology. Academic Press. https://doi.org/10.1016/j.smim.2007.12.009","ama":"Lokmic Z, Lämmermann T, Sixt MK, Cardell S, Hallmann R, Sorokin L. The extracellular matrix of the spleen as a potential organizer of immune cell compartments. Seminars in Immunology. 2008;20(1):4-13. doi:10.1016/j.smim.2007.12.009"},"date_updated":"2021-01-12T07:53:20Z"},{"publication_status":"published","year":"2008","day":"06","publication":"PLoS One","volume":3,"date_published":"2008-08-06T00:00:00Z","issue":"8","doi":"10.1371/journal.pone.0002856","date_created":"2018-12-11T12:06:11Z","abstract":[{"text":"While genome-wide gene expression data are generated at an increasing rate, the repertoire of approaches for pattern discovery in these data is still limited. Identifying subtle patterns of interest in large amounts of data (tens of thousands of profiles) associated with a certain level of noise remains a challenge. A microarray time series was recently generated to study the transcriptional program of the mouse segmentation clock, a biological oscillator associated with the periodic formation of the segments of the body axis. A method related to Fourier analysis, the Lomb-Scargle periodogram, was used to detect periodic profiles in the dataset, leading to the identification of a novel set of cyclic genes associated with the segmentation clock. Here, we applied to the same microarray time series dataset four distinct mathematical methods to identify significant patterns in gene expression profiles. These methods are called: Phase consistency, Address reduction, Cyclohedron test and Stable persistence, and are based on different conceptual frameworks that are either hypothesis- or data-driven. Some of the methods, unlike Fourier transforms, are not dependent on the assumption of periodicity of the pattern of interest. Remarkably, these methods identified blindly the expression profiles of known cyclic genes as the most significant patterns in the dataset. Many candidate genes predicted by more than one approach appeared to be true positive cyclic genes and will be of particular interest for future research. In addition, these methods predicted novel candidate cyclic genes that were consistent with previous biological knowledge and experimental validation in mouse embryos. Our results demonstrate the utility of these novel pattern detection strategies, notably for detection of periodic profiles, and suggest that combining several distinct mathematical approaches to analyze microarray datasets is a valuable strategy for identifying genes that exhibit novel, interesting transcriptional patterns.","lang":"eng"}],"acknowledgement":"This research was partially supported by DARPA grant HR 0011-05-1-0057. HE and YM mathematical work was supported by DARPA grant HR0011-05-1-0007. AS research was supported by a Lucent Technologies Bell Labs Graduate Research. Fellowship; AK and MR research was supported by NIH grant GM U54 GM74942; and SA research was supported by Association pour la Recherche sur le Cancer (ARC), France. OP, AM, MLD, EG and GH research was supported by the Stowers Institute for Medical Research. OP is a Howard Hughes Medical Institute Investigator.","quality_controlled":0,"publisher":"Public Library of Science","month":"08","intvolume":" 3","citation":{"mla":"Dequéant, Mary, et al. “Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock.” PLoS One, vol. 3, no. 8, Public Library of Science, 2008, doi:10.1371/journal.pone.0002856.","ama":"Dequéant M, Ahnert S, Edelsbrunner H, et al. Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One. 2008;3(8). doi:10.1371/journal.pone.0002856","apa":"Dequéant, M., Ahnert, S., Edelsbrunner, H., Fink, T., Glynn, E., Hattem, G., … Pourquie, O. (2008). Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0002856","short":"M. Dequéant, S. Ahnert, H. Edelsbrunner, T. Fink, E. Glynn, G. Hattem, A. Kudlicki, Y. Mileyko, J. Morton, A. Mushegian, L. Pachter, M. Rowicka, A. Shiu, B. Sturmfels, O. Pourquie, PLoS One 3 (2008).","ieee":"M. Dequéant et al., “Comparison of pattern detection methods in microarray time series of the segmentation clock,” PLoS One, vol. 3, no. 8. Public Library of Science, 2008.","chicago":"Dequéant, Mary, Sebastian Ahnert, Herbert Edelsbrunner, Thomas Fink, Earl Glynn, Gaye Hattem, Andrzej Kudlicki, et al. “Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock.” PLoS One. Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0002856.","ista":"Dequéant M, Ahnert S, Edelsbrunner H, Fink T, Glynn E, Hattem G, Kudlicki A, Mileyko Y, Morton J, Mushegian A, Pachter L, Rowicka M, Shiu A, Sturmfels B, Pourquie O. 2008. Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One. 3(8)."},"date_updated":"2021-01-12T07:53:33Z","extern":1,"publist_id":"2157","author":[{"full_name":"Dequéant, Mary-Lee","last_name":"Dequéant","first_name":"Mary"},{"first_name":"Sebastian","full_name":"Ahnert, Sebastian","last_name":"Ahnert"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Herbert Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fink, Thomas M","last_name":"Fink","first_name":"Thomas"},{"first_name":"Earl","full_name":"Glynn, Earl F","last_name":"Glynn"},{"first_name":"Gaye","full_name":"Hattem, Gaye","last_name":"Hattem"},{"full_name":"Kudlicki, Andrzej","last_name":"Kudlicki","first_name":"Andrzej"},{"last_name":"Mileyko","full_name":"Mileyko, Yuriy","first_name":"Yuriy"},{"last_name":"Morton","full_name":"Morton, Jason","first_name":"Jason"},{"first_name":"Arcady","last_name":"Mushegian","full_name":"Mushegian, Arcady R"},{"last_name":"Pachter","full_name":"Pachter, Lior","first_name":"Lior"},{"first_name":"Maga","full_name":"Rowicka, Maga","last_name":"Rowicka"},{"first_name":"Anne","full_name":"Shiu, Anne","last_name":"Shiu"},{"first_name":"Bernd","last_name":"Sturmfels","full_name":"Sturmfels, Bernd"},{"last_name":"Pourquie","full_name":"Pourquie, Olivier","first_name":"Olivier"}],"title":"Comparison of pattern detection methods in microarray time series of the segmentation clock","_id":"3970","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"_id":"3971","type":"journal_article","status":"public","citation":{"chicago":"Edelsbrunner, Herbert, John Harer, Ajith Mascarenhas, Valerio Pascucci, and Jack Snoeyink. “Time-Varying Reeb Graphs for Continuous Space-Time Data.” Computational Geometry: Theory and Applications. Elsevier, 2008. https://doi.org/10.1016/j.comgeo.2007.11.001.","ista":"Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. 2008. Time-varying Reeb graphs for continuous space-time data. Computational Geometry: Theory and Applications. 41(3), 149–166.","mla":"Edelsbrunner, Herbert, et al. “Time-Varying Reeb Graphs for Continuous Space-Time Data.” Computational Geometry: Theory and Applications, vol. 41, no. 3, Elsevier, 2008, pp. 149–66, doi:10.1016/j.comgeo.2007.11.001.","apa":"Edelsbrunner, H., Harer, J., Mascarenhas, A., Pascucci, V., & Snoeyink, J. (2008). Time-varying Reeb graphs for continuous space-time data. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2007.11.001","ama":"Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. Time-varying Reeb graphs for continuous space-time data. Computational Geometry: Theory and Applications. 2008;41(3):149-166. doi:10.1016/j.comgeo.2007.11.001","short":"H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, J. Snoeyink, Computational Geometry: Theory and Applications 41 (2008) 149–166.","ieee":"H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, and J. Snoeyink, “Time-varying Reeb graphs for continuous space-time data,” Computational Geometry: Theory and Applications, vol. 41, no. 3. Elsevier, pp. 149–166, 2008."},"date_updated":"2021-01-12T07:53:34Z","extern":1,"author":[{"full_name":"Herbert Edelsbrunner","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Harer, John","last_name":"Harer","first_name":"John"},{"first_name":"Ajith","last_name":"Mascarenhas","full_name":"Mascarenhas, Ajith"},{"last_name":"Pascucci","full_name":"Pascucci, Valerio","first_name":"Valerio"},{"last_name":"Snoeyink","full_name":"Snoeyink, Jack","first_name":"Jack"}],"publist_id":"2158","title":"Time-varying Reeb graphs for continuous space-time data","abstract":[{"lang":"eng","text":"The Reeb graph is a useful tool in visualizing real-valued data obtained from computational simulations of physical processes. We characterize the evolution of the Reeb graph of a time-varying continuous function defined in three-dimensional space. We show how to maintain the Reeb graph over time and compress the entire sequence of Reeb graphs into a single, partially persistent data structure, and augment this data structure with Betti numbers to describe the topology of level sets and with path seeds to assist in the fast extraction of level sets for visualization."}],"quality_controlled":0,"publisher":"Elsevier","intvolume":" 41","month":"11","year":"2008","publication_status":"published","publication":"Computational Geometry: Theory and Applications","day":"01","page":"149 - 166","date_created":"2018-12-11T12:06:12Z","date_published":"2008-11-01T00:00:00Z","doi":"10.1016/j.comgeo.2007.11.001","volume":41,"issue":"3"},{"title":"Persistent homology - a survey","author":[{"full_name":"Herbert Edelsbrunner","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"first_name":"John","last_name":"Harer","full_name":"Harer, John"}],"publist_id":"2156","extern":1,"date_updated":"2021-01-12T07:53:33Z","citation":{"mla":"Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.” Surveys on Discrete and Computational Geometry: Twenty Years Later, American Mathematical Society, 2008, pp. 257–82.","short":"H. Edelsbrunner, J. Harer, in:, Surveys on Discrete and Computational Geometry: Twenty Years Later, American Mathematical Society, 2008, pp. 257–282.","ieee":"H. Edelsbrunner and J. Harer, “Persistent homology - a survey,” in Surveys on Discrete and Computational Geometry: Twenty Years Later, American Mathematical Society, 2008, pp. 257–282.","apa":"Edelsbrunner, H., & Harer, J. (2008). Persistent homology - a survey. In Surveys on Discrete and Computational Geometry: Twenty Years Later (pp. 257–282). American Mathematical Society.","ama":"Edelsbrunner H, Harer J. Persistent homology - a survey. In: Surveys on Discrete and Computational Geometry: Twenty Years Later. American Mathematical Society; 2008:257-282.","chicago":"Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.” In Surveys on Discrete and Computational Geometry: Twenty Years Later, 257–82. American Mathematical Society, 2008.","ista":"Edelsbrunner H, Harer J. 2008.Persistent homology - a survey. In: Surveys on Discrete and Computational Geometry: Twenty Years Later. Contemporary Mathematics, , 257–282."},"status":"public","type":"book_chapter","_id":"3969","date_created":"2018-12-11T12:06:11Z","date_published":"2008-03-28T00:00:00Z","page":"257 - 282","publication":"Surveys on Discrete and Computational Geometry: Twenty Years Later","day":"28","year":"2008","publication_status":"published","month":"03","quality_controlled":0,"alternative_title":["Contemporary Mathematics"],"publisher":"American Mathematical Society","acknowledgement":"Supported in part by DARPA under grants HR0011-05-1-0007 and HR0011-05-0057 and by the NSF under grant DBI-06-06873.","abstract":[{"lang":"eng","text":"Persistent homology is an algebraic tool for measuring topological features of shapes and functions. It casts the multi-scale organization we frequently observe in nature into a mathematical formalism. Here we give a record of the short history of persistent homology and present its basic concepts. Besides the mathematics we focus on algorithms and mention the various connections to applications, including to biomolecules, biological networks, data analysis, and geometric modeling."}]},{"status":"public","type":"journal_article","_id":"4141","title":"Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation","article_processing_charge":"No","author":[{"full_name":"Vervenne, Hilke","last_name":"Vervenne","first_name":"Hilke"},{"last_name":"Crombez","full_name":"Crombez, Koen","first_name":"Koen"},{"first_name":"Kathleen","last_name":"Lambaerts","full_name":"Lambaerts, Kathleen"},{"first_name":"Lara","full_name":"Carvalho, Lara","last_name":"Carvalho"},{"first_name":"Mathias","full_name":"Köppen, Mathias","last_name":"Köppen"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Van De Ven","full_name":"Van De Ven, Wim","first_name":"Wim"},{"first_name":"Marleen","full_name":"Petit, Marleen","last_name":"Petit"}],"publist_id":"1978","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"ista":"Vervenne H, Crombez K, Lambaerts K, Carvalho L, Köppen M, Heisenberg C-PJ, Van De Ven W, Petit M. 2008. Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation. Developmental Biology. 320(1), 267–277.","chicago":"Vervenne, Hilke, Koen Crombez, Kathleen Lambaerts, Lara Carvalho, Mathias Köppen, Carl-Philipp J Heisenberg, Wim Van De Ven, and Marleen Petit. “Lpp Is Involved in Wnt/PCP Signaling and Acts Together with Scrib to Mediate Convergence and Extension Movements during Zebrafish Gastrulation.” Developmental Biology. Elsevier, 2008. https://doi.org/10.1016/j.ydbio.2008.05.529.","ama":"Vervenne H, Crombez K, Lambaerts K, et al. Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation. Developmental Biology. 2008;320(1):267-277. doi:10.1016/j.ydbio.2008.05.529","apa":"Vervenne, H., Crombez, K., Lambaerts, K., Carvalho, L., Köppen, M., Heisenberg, C.-P. J., … Petit, M. (2008). Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation. Developmental Biology. Elsevier. https://doi.org/10.1016/j.ydbio.2008.05.529","short":"H. Vervenne, K. Crombez, K. Lambaerts, L. Carvalho, M. Köppen, C.-P.J. Heisenberg, W. Van De Ven, M. Petit, Developmental Biology 320 (2008) 267–277.","ieee":"H. Vervenne et al., “Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation,” Developmental Biology, vol. 320, no. 1. Elsevier, pp. 267–277, 2008.","mla":"Vervenne, Hilke, et al. “Lpp Is Involved in Wnt/PCP Signaling and Acts Together with Scrib to Mediate Convergence and Extension Movements during Zebrafish Gastrulation.” Developmental Biology, vol. 320, no. 1, Elsevier, 2008, pp. 267–77, doi:10.1016/j.ydbio.2008.05.529."},"date_updated":"2021-01-12T07:54:48Z","intvolume":" 320","month":"08","publisher":"Elsevier","oa_version":"None","abstract":[{"lang":"eng","text":"The zyxin-related LPP protein is localized at focal adhesions and cell-cell contacts and is involved in the regulation of smooth muscle cell migration. A known interaction partner of LPP in human is the tumor suppressor protein SCRIB. Knocking down scrib expression c uring zebrafish embryonic development results in defects of convergence and extension (C&E) movements, which occur during gastrulation and mediate elongation of the anterior-posterior body axis. Mediolateral cell polarization underlying C&E is regulated by a noncanonical Writ signaling pathway constituting the vertebrate planar cell polarity (PCP) pathway. Here, we investigated the role of Lpp during early zebrafish development. We show that morpholino knockdown of Ipp results in defects of C&E, phenocopying noncanonical Wnt signaling mutants. Time-lapse analysis associates the defective dorsal convergence movements with a reduced ability to migrate along straight paths. In addition, expression of Lpp is significantly reduced in Wnt11 morphants and in embryos overexpressing Wnt11 or a dominant-negative form of Rho kinase 2, which is a downstream effector of Wnt11, Suggesting that Lpp expression is dependent on noncanonical Wnt signaling. Finally, we demonstrate that Lpp interacts with the PCP protein Scrib in zebrafish, and that Lpp and Scrib cooperate for the mediation of C&E. (C) 2008 Elsevier Inc. All rights reserved."}],"date_created":"2018-12-11T12:07:11Z","doi":"10.1016/j.ydbio.2008.05.529","date_published":"2008-08-01T00:00:00Z","issue":"1","volume":320,"page":"267 - 277","language":[{"iso":"eng"}],"publication":"Developmental Biology","day":"01","year":"2008","publication_status":"published"},{"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"P. Oteíza, M. Köppen, M. Concha, and C.-P. J. Heisenberg, “Origin and shaping of the laterality organ in zebrafish,” Development, vol. 135, no. 16. Company of Biologists, pp. 2807–2813, 2008.","short":"P. Oteíza, M. Köppen, M. Concha, C.-P.J. Heisenberg, Development 135 (2008) 2807–2813.","ama":"Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. Origin and shaping of the laterality organ in zebrafish. Development. 2008;135(16):2807-2813. doi:10.1242/dev.022228","apa":"Oteíza, P., Köppen, M., Concha, M., & Heisenberg, C.-P. J. (2008). Origin and shaping of the laterality organ in zebrafish. Development. Company of Biologists. https://doi.org/10.1242/dev.022228","mla":"Oteíza, Pablo, et al. “Origin and Shaping of the Laterality Organ in Zebrafish.” Development, vol. 135, no. 16, Company of Biologists, 2008, pp. 2807–13, doi:10.1242/dev.022228.","ista":"Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. 2008. Origin and shaping of the laterality organ in zebrafish. Development. 135(16), 2807–2813.","chicago":"Oteíza, Pablo, Mathias Köppen, Miguel Concha, and Carl-Philipp J Heisenberg. “Origin and Shaping of the Laterality Organ in Zebrafish.” Development. Company of Biologists, 2008. https://doi.org/10.1242/dev.022228."},"date_updated":"2021-01-12T07:54:57Z","title":"Origin and shaping of the laterality organ in zebrafish","author":[{"first_name":"Pablo","full_name":"Oteíza, Pablo","last_name":"Oteíza"},{"last_name":"Köppen","full_name":"Köppen, Mathias","first_name":"Mathias"},{"first_name":"Miguel","last_name":"Concha","full_name":"Concha, Miguel"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"publist_id":"1956","article_processing_charge":"No","_id":"4161","status":"public","type":"journal_article","day":"15","publication":"Development","language":[{"iso":"eng"}],"year":"2008","publication_status":"published","date_published":"2008-08-15T00:00:00Z","volume":135,"doi":"10.1242/dev.022228","issue":"16","date_created":"2018-12-11T12:07:19Z","page":"2807 - 2813","oa_version":"None","abstract":[{"lang":"eng","text":"Handedness of the vertebrate body plan critically depends on transient embryonic structures/ organs that generate cilia-dependent leftward fluid flow within constrained extracellular environments. Although the function of ciliated organs in laterality determination has been extensively studied, how they are formed during embryogenesis is still poorly understood. Here we show that Kupffer's vesicle (KV), the zebrafish organ of laterality, arises from a surface epithelium previously thought to adopt exclusively extra-embryonic fates. Live multi-photon confocal imaging reveals that surface epithelial cells undergo Nodal/TGF beta signalling-dependent ingression at the dorsal germ ring margin prior to gastrulation, to give rise to dorsal forerunner cells (DFCs), the precursors of KV. DFCs then migrate attached to the overlying surface epithelium and rearrange into rosette-like epithelial structures at the end of gastrulation. During early somitogenesis, these epithelial rosettes coalesce into a single rosette that differentiates into the KV with a ciliated lumen at its apical centre. Our results provide novel insights into the morphogenetic transformations that shape the laterality organ in zebrafish and suggest a conserved progenitor role of the surface epithelium during laterality organ formation in vertebrates."}],"month":"08","intvolume":" 135","publisher":"Company of Biologists"},{"doi":"10.1242/dev.020396","date_published":"2008-09-15T00:00:00Z","issue":"18","volume":135,"date_created":"2018-12-11T12:07:29Z","page":"3043 - 3051","day":"15","publication":"Development","language":[{"iso":"eng"}],"year":"2008","publication_status":"published","month":"09","intvolume":" 135","publisher":"Company of Biologists","oa_version":"None","abstract":[{"lang":"eng","text":"During vertebrate gastrulation, cells forming the prechordal plate undergo directed migration as a cohesive cluster. Recent studies revealed that E-cadherin-mediated coherence between these cells plays an important role in effective anterior migration, and that platelet-derived growth factor (Pdgf) appears to act as a guidance cue in this process. However, the mechanisms underlying this process at the individual cell level remain poorly understood. We have identified miles apart (mil) as a suppressor of defective anterior migration of the prospective prechordal plate in silberblick (slb)/wnt11 mutant embryos, in which E-cadherin-mediated coherence of cell movement is reduced. mil encodes Edg5, a sphingosine-1-phosphate (S1P) receptor belonging to a family of five G-protein-coupled receptors (S1PRs). S1P is a lipid signalling molecule that has been implicated in regulating cytoskeletal rearrangements, cell motility and cell adhesion in a variety of cell types. We examined the roles of Mil in anterior migration of prechordal plate progenitor cells and found that, in slb embryos injected with mil-MO, cells migrate with increased motility but decreased directionality, without restoring the coherence of cell migration. This indicates that prechordal plate progenitor cells can migrate effectively as individuals, as well as in a coherent cluster of cells. Moreover, we demonstrate that Mil regulates cell motility and polarisation through Pdgf and its intracellular effecter PI3K, but modulates cell coherence independently of the Pdgf/PI3K pathway, thus co-ordinating cell motility and coherence. These results suggest that the net migration of prechordal plate progenitors is determined by different parameters, including motility, persistence and coherence."}],"title":"Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation","author":[{"first_name":"Masatake","last_name":"Kai","full_name":"Kai, Masatake"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Tada, Masazumi","last_name":"Tada","first_name":"Masazumi"}],"publist_id":"1928","article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kai, Masatake, Carl-Philipp J Heisenberg, and Masazumi Tada. “Sphingosine-1-Phosphate Receptors Regulate Individual Cell Behaviours Underlying the Directed Migration of Prechordal Plate Progenitor Cells during Zebrafish Gastrulation.” Development. Company of Biologists, 2008. https://doi.org/10.1242/dev.020396.","ista":"Kai M, Heisenberg C-PJ, Tada M. 2008. Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation. Development. 135(18), 3043–3051.","mla":"Kai, Masatake, et al. “Sphingosine-1-Phosphate Receptors Regulate Individual Cell Behaviours Underlying the Directed Migration of Prechordal Plate Progenitor Cells during Zebrafish Gastrulation.” Development, vol. 135, no. 18, Company of Biologists, 2008, pp. 3043–51, doi:10.1242/dev.020396.","apa":"Kai, M., Heisenberg, C.-P. J., & Tada, M. (2008). Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.020396","ama":"Kai M, Heisenberg C-PJ, Tada M. Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation. Development. 2008;135(18):3043-3051. doi:10.1242/dev.020396","short":"M. Kai, C.-P.J. Heisenberg, M. Tada, Development 135 (2008) 3043–3051.","ieee":"M. Kai, C.-P. J. Heisenberg, and M. Tada, “Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation,” Development, vol. 135, no. 18. Company of Biologists, pp. 3043–3051, 2008."},"date_updated":"2021-01-12T07:55:11Z","status":"public","type":"journal_article","_id":"4190"},{"abstract":[{"text":"Model checking software transactional memories (STMs) is difficult because of the unbounded number, length, and delay of concurrent transactions and the unbounded size of the memory. We show that, under certain conditions, the verification problem can be reduced to a finite-state problem, and we illustrate the use of the method by proving the correctness of several STMs, including two-phase locking, DSTM, TL2, and optimistic concurrency control. The safety properties we consider include strict serializability and opacity; the liveness properties include obstruction freedom, livelock freedom, and wait freedom.\n\nOur main contribution lies in the structure of the proofs, which are largely automated and not restricted to the STMs mentioned above. In a first step we show that every STM that enjoys certain structural properties either violates a safety or liveness requirement on some program with two threads and two shared variables, or satisfies the requirement on all programs. In the second step we use a model checker to prove the requirement for the STM applied to a most general program with two threads and two variables. In the safety case, the model checker constructs a simulation relation between two carefully constructed finite-state transition systems, one representing the given STM applied to a most general program, and the other representing a most liberal safe STM applied to the same program. In the liveness case, the model checker analyzes fairness conditions on the given STM transition system.","lang":"eng"}],"oa":1,"main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/model_checking_transactional_memories.pdf","open_access":"0"}],"publisher":"ACM","quality_controlled":0,"month":"01","publication_status":"published","year":"2008","day":"01","file":[{"checksum":"1238258a27f212fc1a2050a9a246da20","file_id":"5054","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:14:05Z","file_name":"IST-2012-74-v1+1_Model_checking_transactional_memories.pdf","date_updated":"2020-07-14T12:46:28Z","file_size":201583,"creator":"system"}],"page":"372 - 382","date_created":"2018-12-11T12:08:34Z","doi":"10.1145/1375581.1375626","date_published":"2008-01-01T00:00:00Z","_id":"4384","conference":{"name":"PLDI: Programming Languages Design and Implementation"},"type":"conference","status":"public","date_updated":"2021-01-12T07:56:34Z","citation":{"chicago":"Guerraoui, Rachid, Thomas A Henzinger, Barbara Jobstmann, and Vasu Singh. “Model Checking Transactional Memories,” 372–82. ACM, 2008. https://doi.org/10.1145/1375581.1375626.","ista":"Guerraoui R, Henzinger TA, Jobstmann B, Singh V. 2008. Model checking transactional memories. PLDI: Programming Languages Design and Implementation, 372–382.","mla":"Guerraoui, Rachid, et al. Model Checking Transactional Memories. ACM, 2008, pp. 372–82, doi:10.1145/1375581.1375626.","ieee":"R. Guerraoui, T. A. Henzinger, B. Jobstmann, and V. Singh, “Model checking transactional memories,” presented at the PLDI: Programming Languages Design and Implementation, 2008, pp. 372–382.","short":"R. Guerraoui, T.A. Henzinger, B. Jobstmann, V. Singh, in:, ACM, 2008, pp. 372–382.","ama":"Guerraoui R, Henzinger TA, Jobstmann B, Singh V. Model checking transactional memories. In: ACM; 2008:372-382. doi:10.1145/1375581.1375626","apa":"Guerraoui, R., Henzinger, T. A., Jobstmann, B., & Singh, V. (2008). Model checking transactional memories (pp. 372–382). Presented at the PLDI: Programming Languages Design and Implementation, ACM. https://doi.org/10.1145/1375581.1375626"},"extern":1,"author":[{"last_name":"Guerraoui","full_name":"Guerraoui, Rachid","first_name":"Rachid"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"full_name":"Jobstmann, Barbara","last_name":"Jobstmann","first_name":"Barbara"},{"last_name":"Singh","full_name":"Vasu Singh","first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"1073","file_date_updated":"2020-07-14T12:46:28Z","title":"Model checking transactional memories"},{"month":"09","intvolume":" 5218","alternative_title":["LNCS"],"quality_controlled":0,"publisher":"Springer","main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/permissiveness_in_transactional_memories.pdf","open_access":"0"}],"acknowledgement":"This research was supported by the Swiss National Science Foundation.","abstract":[{"lang":"eng","text":"We introduce the notion of permissiveness in transactional memories (TM). Intuitively, a TM is permissive if it never aborts a transaction when it need not. More specifically, a TM is permissive with respect to a safety property p if the TM accepts every history that satisfies p. Permissiveness, like safety and liveness, can be used as a metric to compare TMs. We illustrate that it is impractical to achieve permissiveness deterministically, and then show how randomization can be used to achieve permissiveness efficiently. We introduce Adaptive Validation STM (AVSTM), which is probabilistically permissive with respect to opacity; that is, every opaque history is accepted by AVSTM with positive probability. Moreover, AVSTM guarantees lock freedom. Owing to its permissiveness, AVSTM outperforms other STMs by up to 40% in read dominated workloads in high contention scenarios. But, in low contention scenarios, the book-keeping done by AVSTM to achieve permissiveness makes AVSTM, on average, 20-30% worse than existing STMs."}],"doi":"10.1007/978-3-540-87779-0_21","volume":5218,"date_published":"2008-09-10T00:00:00Z","date_created":"2018-12-11T12:08:35Z","page":"305 - 319","day":"10","publication_status":"published","year":"2008","status":"public","type":"conference","conference":{"name":"DISC: Distributed Computing"},"_id":"4386","title":"Permissiveness in transactional memories","publist_id":"1072","author":[{"full_name":"Guerraoui, Rachid","last_name":"Guerraoui","first_name":"Rachid"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Singh","full_name":"Vasu Singh","first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87"}],"extern":1,"citation":{"mla":"Guerraoui, Rachid, et al. Permissiveness in Transactional Memories. Vol. 5218, Springer, 2008, pp. 305–19, doi:10.1007/978-3-540-87779-0_21.","apa":"Guerraoui, R., Henzinger, T. A., & Singh, V. (2008). Permissiveness in transactional memories (Vol. 5218, pp. 305–319). Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-540-87779-0_21","ama":"Guerraoui R, Henzinger TA, Singh V. Permissiveness in transactional memories. In: Vol 5218. Springer; 2008:305-319. doi:10.1007/978-3-540-87779-0_21","ieee":"R. Guerraoui, T. A. Henzinger, and V. Singh, “Permissiveness in transactional memories,” presented at the DISC: Distributed Computing, 2008, vol. 5218, pp. 305–319.","short":"R. Guerraoui, T.A. Henzinger, V. Singh, in:, Springer, 2008, pp. 305–319.","chicago":"Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Permissiveness in Transactional Memories,” 5218:305–19. Springer, 2008. https://doi.org/10.1007/978-3-540-87779-0_21.","ista":"Guerraoui R, Henzinger TA, Singh V. 2008. Permissiveness in transactional memories. DISC: Distributed Computing, LNCS, vol. 5218, 305–319."},"date_updated":"2021-01-12T07:56:35Z"},{"main_file_link":[{"open_access":"0","url":"http://pub.ist.ac.at/%7Etah/Publications/completeness_and_nondeterminism_in_model_checking_transactional_memories.pdf"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LNCS"],"quality_controlled":0,"intvolume":" 5201","month":"07","abstract":[{"text":"Software transactional memory (STM) offers a disciplined concurrent programming model for exploiting the parallelism of modern processor architectures. This paper presents the first deterministic specification automata for strict serializability and opacity in STMs. Using an antichain-based tool, we show our deterministic specifications to be equivalent to more intuitive, nondeterministic specification automata (which are too large to be determinized automatically). Using deterministic specification automata, we obtain a complete verification tool for STMs. We also show how to model and verify contention management within STMs. We automatically check the opacity of popular STM algorithms, such as TL2 and DSTM, with a universal contention manager. The universal contention manager is nondeterministic and establishes correctness for all possible contention management schemes.","lang":"eng"}],"acknowledgement":"This research was supported by the Swiss National Science Foundation.","page":"21 - 35","date_created":"2018-12-11T12:08:35Z","doi":"10.1007/978-3-540-85361-9_6","volume":5201,"date_published":"2008-07-30T00:00:00Z","year":"2008","publication_status":"published","day":"30","conference":{"name":"CONCUR: Concurrency Theory"},"type":"conference","status":"public","_id":"4387","publist_id":"1071","author":[{"full_name":"Guerraoui, Rachid","last_name":"Guerraoui","first_name":"Rachid"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","last_name":"Henzinger"},{"last_name":"Singh","full_name":"Vasu Singh","first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87"}],"title":"Completeness and nondeterminism in model checking transactional memories","citation":{"mla":"Guerraoui, Rachid, et al. Completeness and Nondeterminism in Model Checking Transactional Memories. Vol. 5201, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 21–35, doi:10.1007/978-3-540-85361-9_6.","apa":"Guerraoui, R., Henzinger, T. A., & Singh, V. (2008). Completeness and nondeterminism in model checking transactional memories (Vol. 5201, pp. 21–35). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-540-85361-9_6","ama":"Guerraoui R, Henzinger TA, Singh V. Completeness and nondeterminism in model checking transactional memories. In: Vol 5201. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2008:21-35. doi:10.1007/978-3-540-85361-9_6","ieee":"R. Guerraoui, T. A. Henzinger, and V. Singh, “Completeness and nondeterminism in model checking transactional memories,” presented at the CONCUR: Concurrency Theory, 2008, vol. 5201, pp. 21–35.","short":"R. Guerraoui, T.A. Henzinger, V. Singh, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 21–35.","chicago":"Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Completeness and Nondeterminism in Model Checking Transactional Memories,” 5201:21–35. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008. https://doi.org/10.1007/978-3-540-85361-9_6.","ista":"Guerraoui R, Henzinger TA, Singh V. 2008. Completeness and nondeterminism in model checking transactional memories. CONCUR: Concurrency Theory, LNCS, vol. 5201, 21–35."},"date_updated":"2021-01-12T07:56:35Z","extern":1},{"quality_controlled":0,"publisher":"Springer","alternative_title":["LNCS 5123"],"month":"01","page":"304 - 308","date_published":"2008-01-01T00:00:00Z","date_created":"2018-12-11T12:08:38Z","year":"2008","publication_status":"published","day":"01","type":"conference","conference":{"name":"CAV: Computer Aided Verification"},"status":"public","_id":"4397","publist_id":"1060","author":[{"last_name":"Beyer","full_name":"Beyer, Dirk","first_name":"Dirk"},{"first_name":"Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","last_name":"Zufferey","full_name":"Damien Zufferey","orcid":"0000-0002-3197-8736"},{"full_name":"Majumdar, Ritankar S","last_name":"Majumdar","first_name":"Ritankar"}],"title":"CSIsat: Interpolation for LA+EUF","citation":{"mla":"Beyer, Dirk, et al. CSIsat: Interpolation for LA+EUF. Springer, 2008, pp. 304–08.","ieee":"D. Beyer, D. Zufferey, and R. Majumdar, “CSIsat: Interpolation for LA+EUF,” presented at the CAV: Computer Aided Verification, 2008, pp. 304–308.","short":"D. Beyer, D. Zufferey, R. Majumdar, in:, Springer, 2008, pp. 304–308.","apa":"Beyer, D., Zufferey, D., & Majumdar, R. (2008). CSIsat: Interpolation for LA+EUF (pp. 304–308). Presented at the CAV: Computer Aided Verification, Springer.","ama":"Beyer D, Zufferey D, Majumdar R. CSIsat: Interpolation for LA+EUF. In: Springer; 2008:304-308.","chicago":"Beyer, Dirk, Damien Zufferey, and Ritankar Majumdar. “CSIsat: Interpolation for LA+EUF,” 304–8. Springer, 2008.","ista":"Beyer D, Zufferey D, Majumdar R. 2008. CSIsat: Interpolation for LA+EUF. CAV: Computer Aided Verification, LNCS 5123, , 304–308."},"date_updated":"2021-01-12T07:56:40Z","extern":1},{"main_file_link":[{"url":"http://www.usenix.org/event/evt08/tech/full_papers/aviv/aviv.pdf","open_access":"0"}],"quality_controlled":0,"publisher":"USENIX","month":"07","date_created":"2018-12-11T12:08:39Z","doi":"1545","date_published":"2008-07-29T00:00:00Z","year":"2008","publication_status":"published","day":"29","conference":{"name":"Usenix/ Accurate Electronic Voting Technology Workshop (EVT) 08"},"type":"conference","status":"public","_id":"4400","author":[{"full_name":"Aviv,Adam J.","last_name":"Aviv","first_name":"Adam"},{"last_name":"Cerny","full_name":"Pavol Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"},{"first_name":"Sandy","last_name":"Clark","full_name":"Clark,Sandy"},{"first_name":"Eric","last_name":"Cronin","full_name":"Cronin,Eric"},{"first_name":"Gaurav","last_name":"Shah","full_name":"Shah,Gaurav"},{"full_name":"Sherr,Micah","last_name":"Sherr","first_name":"Micah"},{"first_name":"Matt","full_name":"Blaze,Matt","last_name":"Blaze"}],"publist_id":"1057","title":"Security Evaluation of ES&S Voting Machines and Election Management System","citation":{"ista":"Aviv A, Cerny P, Clark S, Cronin E, Shah G, Sherr M, Blaze M. 2008. Security Evaluation of ES&S Voting Machines and Election Management System. Usenix/ Accurate Electronic Voting Technology Workshop (EVT) 08.","chicago":"Aviv, Adam, Pavol Cerny, Sandy Clark, Eric Cronin, Gaurav Shah, Micah Sherr, and Matt Blaze. “Security Evaluation of ES&S Voting Machines and Election Management System.” USENIX, 2008. https://doi.org/1545.","ieee":"A. Aviv et al., “Security Evaluation of ES&S Voting Machines and Election Management System,” presented at the Usenix/ Accurate Electronic Voting Technology Workshop (EVT) 08, 2008.","short":"A. Aviv, P. Cerny, S. Clark, E. Cronin, G. Shah, M. Sherr, M. Blaze, in:, USENIX, 2008.","apa":"Aviv, A., Cerny, P., Clark, S., Cronin, E., Shah, G., Sherr, M., & Blaze, M. (2008). Security Evaluation of ES&S Voting Machines and Election Management System. Presented at the Usenix/ Accurate Electronic Voting Technology Workshop (EVT) 08, USENIX. https://doi.org/1545","ama":"Aviv A, Cerny P, Clark S, et al. Security Evaluation of ES&S Voting Machines and Election Management System. In: USENIX; 2008. doi:1545","mla":"Aviv, Adam, et al. Security Evaluation of ES&S Voting Machines and Election Management System. USENIX, 2008, doi:1545."},"date_updated":"2021-01-12T07:56:42Z","extern":1},{"date_created":"2018-12-11T12:08:42Z","date_published":"2008-09-01T00:00:00Z","page":"1 - 137","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2008","degree_awarded":"PhD","month":"09","oa":1,"main_file_link":[{"open_access":"1","url":"https://www2.eecs.berkeley.edu/Pubs/TechRpts/2008/EECS-2008-97.html"}],"publisher":"University of California, Berkeley","oa_version":"None","abstract":[{"text":"Models of timed systems must incorporate not only the sequence of system events, but the timings of these events as well to capture the real-time aspects of physical systems. Timed automata are models of real-time systems in which states consist of discrete locations and values for real-time clocks. The presence of real-time clocks leads to an uncountable state space. This thesis studies verification problems on timed automata in a game theoretic framework.\r\n\r\nFor untimed systems, two systems are close if every sequence of events of one system is also observable in the second system. For timed systems, the difference in timings of the two corresponding sequences is also of importance. We propose the notion of bisimulation distance which quantifies timing differences; if the bisimulation distance between two systems is epsilon, then (a) every sequence of events of one system has a corresponding matching sequence in the other, and (b) the timings of matching events in between the two corresponding traces do not differ by more than epsilon. We show that we can compute the bisimulation distance between two timed automata to within any desired degree of accuracy. We also show that the timed verification logic TCTL is robust with respect to our notion of quantitative bisimilarity, in particular, if a system satisfies a formula, then every close system satisfies a close formula.\r\n\r\nTimed games are used for distinguishing between the actions of several agents, typically a controller and an environment. The controller must achieve its objective against all possible choices of the environment. The modeling of the passage of time leads to the presence of zeno executions, and corresponding unrealizable strategies of the controller which may achieve objectives by blocking time. We disallow such unreasonable strategies by restricting all agents to use only receptive strategies --strategies which while not being required to ensure time divergence by any agent, are such that no agent is responsible for blocking time. Time divergence is guaranteed when all players use receptive strategies. We show that timed automaton games with receptive strategies can be solved by a reduction to finite state turn based game graphs. We define the logic timed alternating-time temporal logic for verification of timed automaton games and show that the logic can be model checked in EXPTIME. We also show that the minimum time required by an agent to reach a desired location, and the maximum time an agent can stay safe within a set of locations, against all possible actions of its adversaries are both computable.\r\n\r\nWe next study the memory requirements of winning strategies for timed automaton games. We prove that finite memory strategies suffice for safety objectives, and that winning strategies for reachability objectives may require infinite memory in general. We introduce randomized strategies in which an agent can propose a probabilistic distribution of moves and show that finite memory randomized strategies suffice for all omega-regular objectives. We also show that while randomization helps in simplifying winning strategies, and thus allows the construction of simpler controllers, it does not help a player in winning at more states, and thus does not allow the construction of more powerful controllers.\r\n\r\nFinally we study robust winning strategies in timed games. In a physical system, a controller may propose an action together with a time delay, but the action cannot be assumed to be executed at the exact proposed time delay. We present robust strategies which incorporate such jitters and show that the set of states from which an agent can win robustly is computable.","lang":"eng"}],"title":"Games for the verification of timed systems","article_processing_charge":"No","author":[{"first_name":"Vinayak","full_name":"Prabhu, Vinayak","last_name":"Prabhu"}],"publist_id":"319","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","date_updated":"2022-02-14T14:35:11Z","citation":{"mla":"Prabhu, Vinayak. Games for the Verification of Timed Systems. University of California, Berkeley, 2008, pp. 1–137.","short":"V. Prabhu, Games for the Verification of Timed Systems, University of California, Berkeley, 2008.","ieee":"V. Prabhu, “Games for the verification of timed systems,” University of California, Berkeley, 2008.","apa":"Prabhu, V. (2008). Games for the verification of timed systems. University of California, Berkeley.","ama":"Prabhu V. Games for the verification of timed systems. 2008:1-137.","chicago":"Prabhu, Vinayak. “Games for the Verification of Timed Systems.” University of California, Berkeley, 2008.","ista":"Prabhu V. 2008. Games for the verification of timed systems. University of California, Berkeley."},"supervisor":[{"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":"John","last_name":"Steel","full_name":"Steel, John"},{"first_name":"Pravin","last_name":"Varaiya","full_name":"Varaiya, Pravin"}],"status":"public","type":"dissertation","_id":"4409"},{"language":[{"iso":"eng"}],"day":"01","degree_awarded":"PhD","publication_status":"published","year":"2008","date_created":"2018-12-11T12:08:44Z","date_published":"2008-01-01T00:00:00Z","page":"1 - 148","acknowledgement":"978-0-549-83480-9","oa_version":"None","abstract":[{"lang":"eng","text":"Many computing applications, especially those in safety critical embedded systems, require highly predictable timing properties. However, time is often not present in the prevailing computing and networking abstractions. In fact, most advances in computer architecture, software, and networking favor average-case performance over timing predictability. This thesis studies several methods for the design of concurrent and/or distributed embedded systems with precise timing guarantees. The focus is on flexible and compositional methods for programming and verification of the timing properties. The presented methods together with related formalisms cover two levels of design: (1) Programming language/model level. We propose the distributed variant of Giotto, a coordination programming language with an explicit temporal semantics—the logical execution time (LET) semantics. The LET of a task is an interval of time that specifies the time instants at which task inputs and outputs become available (task release and termination instants). The LET of a task is always non-zero. This allows us to communicate values across the network without changing the timing information of the task, and without introducing nondeterminism. We show how this methodology supports distributed code generation for distributed real-time systems. The method gives up some performance in favor of composability and predictability. We characterize the tradeoff by comparing the LET semantics with the semantics used in Simulink. (2) Abstract task graph level. We study interface-based design and verification of applications represented with task graphs. We consider task sequence graphs with general event models, and cyclic graphs with periodic event models with jitter and phase. Here an interface of a component exposes time and resource constraints of the component. Together with interfaces we formally define interface composition operations and the refinement relation. For efficient and flexible composability checking two properties are important: incremental design and independent refinement. According to the incremental design property the composition of interfaces can be performed in any order, even if interfaces for some components are not known. The refinement relation is defined such that in a design we can always substitute a refined interface for an abstract one. We show that the framework supports independent refinement, i.e., the refinement relation is preserved under composition operations."}],"month":"01","publisher":"University of California, Berkeley","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","citation":{"mla":"Matic, Slobodan. Compositionality in Deterministic Real-Time Embedded Systems. University of California, Berkeley, 2008, pp. 1–148.","apa":"Matic, S. (2008). Compositionality in deterministic real-time embedded systems. University of California, Berkeley.","ama":"Matic S. Compositionality in deterministic real-time embedded systems. 2008:1-148.","ieee":"S. Matic, “Compositionality in deterministic real-time embedded systems,” University of California, Berkeley, 2008.","short":"S. Matic, Compositionality in Deterministic Real-Time Embedded Systems, University of California, Berkeley, 2008.","chicago":"Matic, Slobodan. “Compositionality in Deterministic Real-Time Embedded Systems.” University of California, Berkeley, 2008.","ista":"Matic S. 2008. Compositionality in deterministic real-time embedded systems. University of California, Berkeley."},"date_updated":"2022-02-14T14:08:50Z","supervisor":[{"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":"Edward","last_name":"Lee","full_name":"Lee, Edward"},{"full_name":"Sengupta, Raja","last_name":"Sengupta","first_name":"Raja"}],"title":"Compositionality in deterministic real-time embedded systems","article_processing_charge":"No","publist_id":"316","author":[{"last_name":"Matic","full_name":"Matic, Slobodan","first_name":"Slobodan"}],"_id":"4415","status":"public","type":"dissertation"},{"month":"11","intvolume":" 5330","alternative_title":["LNCS"],"quality_controlled":0,"publisher":"Springer","main_file_link":[{"open_access":"0","url":"http://pub.ist.ac.at/%7Etah/Publications/valigator.pdf"}],"acknowledgement":"This research was supported by the Swiss NSF.","abstract":[{"text":"We describe Valigator, a software tool for imperative program verification that efficiently combines symbolic computation and automated reasoning in a uniform framework. The system offers support for automatically generating and proving verification conditions and, most importantly, for automatically inferring loop invariants and bound assertions by means of symbolic summation, Gröbner basis computation, and quantifier elimination. We present general principles of the implementation and illustrate them on examples.","lang":"eng"}],"date_published":"2008-11-13T00:00:00Z","volume":5330,"doi":"10.1007/978-3-540-89439-1_24","date_created":"2018-12-11T12:08:55Z","page":"333 - 342","day":"13","publication_status":"published","year":"2008","status":"public","type":"conference","conference":{"name":"LPAR: Logic for Programming, Artificial Intelligence, and Reasoning"},"_id":"4452","title":"Valigator: A verification tool with bound and invariant generation","author":[{"last_name":"Henzinger","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Thibaud","last_name":"Hottelier","full_name":"Hottelier, Thibaud"},{"full_name":"Kovács, Laura","last_name":"Kovács","first_name":"Laura"}],"publist_id":"277","extern":1,"date_updated":"2021-01-12T07:57:04Z","citation":{"ista":"Henzinger TA, Hottelier T, Kovács L. 2008. Valigator: A verification tool with bound and invariant generation. LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol. 5330, 333–342.","chicago":"Henzinger, Thomas A, Thibaud Hottelier, and Laura Kovács. “Valigator: A Verification Tool with Bound and Invariant Generation,” 5330:333–42. Springer, 2008. https://doi.org/10.1007/978-3-540-89439-1_24.","ama":"Henzinger TA, Hottelier T, Kovács L. Valigator: A verification tool with bound and invariant generation. In: Vol 5330. Springer; 2008:333-342. doi:10.1007/978-3-540-89439-1_24","apa":"Henzinger, T. A., Hottelier, T., & Kovács, L. (2008). Valigator: A verification tool with bound and invariant generation (Vol. 5330, pp. 333–342). Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Springer. https://doi.org/10.1007/978-3-540-89439-1_24","ieee":"T. A. Henzinger, T. Hottelier, and L. Kovács, “Valigator: A verification tool with bound and invariant generation,” presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, 2008, vol. 5330, pp. 333–342.","short":"T.A. Henzinger, T. Hottelier, L. Kovács, in:, Springer, 2008, pp. 333–342.","mla":"Henzinger, Thomas A., et al. Valigator: A Verification Tool with Bound and Invariant Generation. Vol. 5330, Springer, 2008, pp. 333–42, doi:10.1007/978-3-540-89439-1_24."}},{"publication":"Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences","day":"31","year":"2008","publication_status":"published","date_created":"2018-12-11T12:09:13Z","date_published":"2008-07-31T00:00:00Z","doi":"10.1098/rsta.2008.0141","issue":"1881","volume":366,"page":"3727 - 3736","abstract":[{"lang":"eng","text":"I discuss two main challenges in embedded systems design: the challenge to build predictable systems, and that to build robust systems. I suggest how predictability can be formalized as a form of determinism, and robustness as a form of continuity."}],"intvolume":" 366","month":"07","main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/two_challenges_in_embedded_systems_design.pdf","open_access":"0"}],"publisher":"Royal Society of London","quality_controlled":0,"extern":1,"date_updated":"2021-01-12T07:59:19Z","citation":{"chicago":"Henzinger, Thomas A. “Two Challenges in Embedded Systems Design: Predictability and Robustness.” Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. Royal Society of London, 2008. https://doi.org/10.1098/rsta.2008.0141.","ista":"Henzinger TA. 2008. Two challenges in embedded systems design: Predictability and robustness. Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. 366(1881), 3727–3736.","mla":"Henzinger, Thomas A. “Two Challenges in Embedded Systems Design: Predictability and Robustness.” Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, vol. 366, no. 1881, Royal Society of London, 2008, pp. 3727–36, doi:10.1098/rsta.2008.0141.","ieee":"T. A. Henzinger, “Two challenges in embedded systems design: Predictability and robustness,” Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, vol. 366, no. 1881. Royal Society of London, pp. 3727–3736, 2008.","short":"T.A. Henzinger, Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences 366 (2008) 3727–3736.","apa":"Henzinger, T. A. (2008). Two challenges in embedded systems design: Predictability and robustness. Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rsta.2008.0141","ama":"Henzinger TA. Two challenges in embedded systems design: Predictability and robustness. Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. 2008;366(1881):3727-3736. doi:10.1098/rsta.2008.0141"},"title":"Two challenges in embedded systems design: Predictability and robustness","publist_id":"219","author":[{"orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"_id":"4509","status":"public","type":"journal_article"},{"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","supervisor":[{"full_name":"Sangiovanni-Vincentelli, Alberto","last_name":"Sangiovanni-Vincentelli","first_name":"Alberto"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"last_name":"Lee","full_name":"Lee, Edward","first_name":"Edward"},{"full_name":"Hedrick, Karl","last_name":"Hedrick","first_name":"Karl"}],"citation":{"ista":"Ghosal A. 2008. A hierarchical coordination language for reliable real-time tasks. University of California, Berkeley.","chicago":"Ghosal, Arkadeb. “A Hierarchical Coordination Language for Reliable Real-Time Tasks.” University of California, Berkeley, 2008.","short":"A. Ghosal, A Hierarchical Coordination Language for Reliable Real-Time Tasks, University of California, Berkeley, 2008.","ieee":"A. Ghosal, “A hierarchical coordination language for reliable real-time tasks,” University of California, Berkeley, 2008.","ama":"Ghosal A. A hierarchical coordination language for reliable real-time tasks. 2008:1-210.","apa":"Ghosal, A. (2008). A hierarchical coordination language for reliable real-time tasks. University of California, Berkeley.","mla":"Ghosal, Arkadeb. A Hierarchical Coordination Language for Reliable Real-Time Tasks. University of California, Berkeley, 2008, pp. 1–210."},"date_updated":"2021-01-12T07:59:26Z","title":"A hierarchical coordination language for reliable real-time tasks","author":[{"full_name":"Ghosal, Arkadeb","last_name":"Ghosal","first_name":"Arkadeb"}],"publist_id":"199","article_processing_charge":"No","_id":"4524","status":"public","type":"dissertation","day":"31","language":[{"iso":"eng"}],"year":"2008","publication_status":"published","date_published":"2008-01-31T00:00:00Z","date_created":"2018-12-11T12:09:18Z","page":"1 - 210","oa_version":"None","acknowledgement":"978-0-549-83679-7","abstract":[{"lang":"eng","text":"Complex requirements, time-to-market pressure and regulatory constraints have made the designing of embedded systems extremely challenging. This is evident by the increase in effort and expenditure for design of safety-driven real-time control-dominated applications like automotive and avionic controllers. Design processes are often challenged by lack of proper programming tools for specifying and verifying critical requirements (e.g. timing and reliability) of such applications. Platform based design, an approach for designing embedded systems, addresses the above concerns by separating requirement from architecture. The requirement specifies the intended behavior of an application while the architecture specifies the guarantees (e.g. execution speed, failure rate etc). An implementation, a mapping of the requirement on the architecture, is then analyzed for correctness. The orthogonalization of concerns makes the specification and analyses simpler. An effective use of such design methodology has been proposed in Logical Execution Time (LET) model of real-time tasks. The model separates the timing requirements (specified by release and termination instances of a task) from the architecture guarantees (specified by worst-case execution time of the task).\r\n\r\nThis dissertation proposes a coordination language, Hierarchical Timing Language (HTL), that captures the timing and reliability requirements of real-time applications. An implementation of the program on an architecture is then analyzed to check whether desired timing and reliability requirements are met or not. The core framework extends the LET model by accounting for reliability and refinement. The reliability model separates the reliability requirements of tasks from the reliability guarantees of the architecture. The requirement expresses the desired long-term reliability while the architecture provides a short-term reliability guarantee (e.g. failure rate for each iteration). The analysis checks if the short-term guarantee ensures the desired long-term reliability. The refinement model allows replacing a task by another task during program execution. Refinement preserves schedulability and reliability, i.e., if a refined task is schedulable and reliable for an implementation, then the refining task is also schedulable and reliable for the implementation. Refinement helps in concise specification without overloading analysis.\r\n\r\nThe work presents the formal model, the analyses (both with and without refinement), and a compiler for HTL programs. The compiler checks composition and refinement constraints, performs schedulability and reliability analyses, and generates code for implementation of an HTL program on a virtual machine. Three real-time controllers, one each from automatic control, automotive control and avionic control, are used to illustrate the steps in modeling and analyzing HTL programs."}],"month":"01","publisher":"University of California, Berkeley"},{"publist_id":"208","author":[{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","full_name":"Ashutosh Gupta","last_name":"Gupta"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","last_name":"Henzinger"},{"last_name":"Majumdar","full_name":"Majumdar, Ritankar S","first_name":"Ritankar"},{"first_name":"Andrey","last_name":"Rybalchenko","full_name":"Rybalchenko, Andrey"},{"last_name":"Xu","full_name":"Xu, Ru-Gang","first_name":"Ru"}],"title":"Proving non-termination","date_updated":"2021-01-12T07:59:25Z","citation":{"mla":"Gupta, Ashutosh, et al. Proving Non-Termination. ACM, 2008, pp. 147–58, doi:10.1145/1328438.1328459.","ama":"Gupta A, Henzinger TA, Majumdar R, Rybalchenko A, Xu R. Proving non-termination. In: ACM; 2008:147-158. doi:10.1145/1328438.1328459","apa":"Gupta, A., Henzinger, T. A., Majumdar, R., Rybalchenko, A., & Xu, R. (2008). Proving non-termination (pp. 147–158). Presented at the POPL: Principles of Programming Languages, ACM. https://doi.org/10.1145/1328438.1328459","short":"A. Gupta, T.A. Henzinger, R. Majumdar, A. Rybalchenko, R. Xu, in:, ACM, 2008, pp. 147–158.","ieee":"A. Gupta, T. A. Henzinger, R. Majumdar, A. Rybalchenko, and R. Xu, “Proving non-termination,” presented at the POPL: Principles of Programming Languages, 2008, pp. 147–158.","chicago":"Gupta, Ashutosh, Thomas A Henzinger, Ritankar Majumdar, Andrey Rybalchenko, and Ru Xu. “Proving Non-Termination,” 147–58. ACM, 2008. https://doi.org/10.1145/1328438.1328459.","ista":"Gupta A, Henzinger TA, Majumdar R, Rybalchenko A, Xu R. 2008. Proving non-termination. POPL: Principles of Programming Languages, 147–158."},"extern":1,"conference":{"name":"POPL: Principles of Programming Languages"},"type":"conference","status":"public","_id":"4521","page":"147 - 158","date_created":"2018-12-11T12:09:17Z","doi":"10.1145/1328438.1328459","date_published":"2008-01-01T00:00:00Z","publication_status":"published","year":"2008","day":"01","main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/proving_non-termination.pdf","open_access":"0"}],"publisher":"ACM","quality_controlled":0,"month":"01","abstract":[{"text":"The search for proof and the search for counterexamples (bugs) are complementary activities that need to be pursued concurrently in order to maximize the practical success rate of verification tools.While this is well-understood in safety verification, the current focus of liveness verification has been almost exclusively on the search for termination proofs. A counterexample to termination is an infinite programexecution. In this paper, we propose a method to search for such counterexamples. The search proceeds in two phases. We first dynamically enumerate lasso-shaped candidate paths for counterexamples, and then statically prove their feasibility. We illustrate the utility of our nontermination prover, called TNT, on several nontrivial examples, some of which require bit-level reasoning about integer representations.","lang":"eng"}]},{"_id":"4527","conference":{"name":"FMSB: Formal Methods in Systems Biology"},"type":"conference","status":"public","citation":{"ista":"Fisher J, Henzinger TA, Mateescu M, Piterman N. 2008. Bounded asynchrony: Concurrency for modeling cell-cell interactions. FMSB: Formal Methods in Systems Biology, LNCS, vol. 5054, 17–32.","chicago":"Fisher, Jasmin, Thomas A Henzinger, Maria Mateescu, and Nir Piterman. “Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions,” 5054:17–32. Springer, 2008. https://doi.org/10.1007/978-3-540-68413-8_2.","ama":"Fisher J, Henzinger TA, Mateescu M, Piterman N. Bounded asynchrony: Concurrency for modeling cell-cell interactions. In: Vol 5054. Springer; 2008:17-32. doi:10.1007/978-3-540-68413-8_2","apa":"Fisher, J., Henzinger, T. A., Mateescu, M., & Piterman, N. (2008). Bounded asynchrony: Concurrency for modeling cell-cell interactions (Vol. 5054, pp. 17–32). Presented at the FMSB: Formal Methods in Systems Biology, Springer. https://doi.org/10.1007/978-3-540-68413-8_2","ieee":"J. Fisher, T. A. Henzinger, M. Mateescu, and N. Piterman, “Bounded asynchrony: Concurrency for modeling cell-cell interactions,” presented at the FMSB: Formal Methods in Systems Biology, 2008, vol. 5054, pp. 17–32.","short":"J. Fisher, T.A. Henzinger, M. Mateescu, N. Piterman, in:, Springer, 2008, pp. 17–32.","mla":"Fisher, Jasmin, et al. Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions. Vol. 5054, Springer, 2008, pp. 17–32, doi:10.1007/978-3-540-68413-8_2."},"date_updated":"2021-01-12T07:59:27Z","extern":1,"author":[{"last_name":"Fisher","full_name":"Fisher, Jasmin","first_name":"Jasmin"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"full_name":"Maria Mateescu","last_name":"Mateescu","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"first_name":"Nir","full_name":"Piterman, Nir","last_name":"Piterman"}],"publist_id":"196","title":"Bounded asynchrony: Concurrency for modeling cell-cell interactions","abstract":[{"lang":"eng","text":"We introduce bounded asynchrony, a notion of concurrency tailored to the modeling of biological cell-cell interactions. Bounded asynchrony is the result of a scheduler that bounds the number of steps that one process gets ahead of other processes; this allows the components of a system to move independently while keeping them coupled. Bounded asynchrony accurately reproduces the experimental observations made about certain cell-cell interactions: its constrained nondeterminism captures the variability observed in cells that, although equally potent, assume distinct fates. Real-life cells are not “scheduled”, but we show that distributed real-time behavior can lead to component interactions that are observationally equivalent to bounded asynchrony; this provides a possible mechanistic explanation for the phenomena observed during cell fate specification.\nWe use model checking to determine cell fates. The nondeterminism of bounded asynchrony causes state explosion during model checking, but partial-order methods are not directly applicable. We present a new algorithm that reduces the number of states that need to be explored: our optimization takes advantage of the bounded-asynchronous progress and the spatially local interactions of components that model cells. We compare our own communication-based reduction with partial-order reduction (on a restricted form of bounded asynchrony) and experiments illustrate that our algorithm leads to significant savings."}],"acknowledgement":"Supported in part by the Swiss National Science Foundation (grant 205321-111840).","main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/bounded_asynchrony.pdf","open_access":"0"}],"publisher":"Springer","alternative_title":["LNCS"],"quality_controlled":0,"intvolume":" 5054","month":"05","year":"2008","publication_status":"published","day":"26","page":"17 - 32","date_created":"2018-12-11T12:09:19Z","doi":"10.1007/978-3-540-68413-8_2","date_published":"2008-05-26T00:00:00Z","volume":5054},{"publication_status":"published","year":"2008","day":"01","publication":"International Journal of Foundations of Computer Science","page":"549 - 563","date_published":"2008-06-01T00:00:00Z","issue":"3","doi":"10.1142/S0129054108005814 ","volume":19,"date_created":"2018-12-11T12:09:20Z","abstract":[{"text":"We consider the equivalence problem for labeled Markov chains (LMCs), where each state is labeled with an observation. Two LMCs are equivalent if every finite sequence of observations has the same probability of occurrence in the two LMCs. We show that equivalence can be decided in polynomial time, using a reduction to the equivalence problem for probabilistic automata, which is known to be solvable in polynomial time. We provide an alternative algorithm to solve the equivalence problem, which is based on a new definition of bisimulation for probabilistic automata. We also extend the technique to decide the equivalence of weighted probabilistic automata.","lang":"eng"}],"quality_controlled":0,"publisher":"World Scientific Publishing","main_file_link":[{"open_access":"0","url":"http://pub.ist.ac.at/%7Etah/Publications/equivalence_of_labeled_markov_chains.pdf"}],"month":"06","intvolume":" 19","date_updated":"2021-01-12T07:59:30Z","citation":{"ista":"Doyen L, Henzinger TA, Raskin J. 2008. Equivalence of labeled Markov chains. International Journal of Foundations of Computer Science. 19(3), 549–563.","chicago":"Doyen, Laurent, Thomas A Henzinger, and Jean Raskin. “Equivalence of Labeled Markov Chains.” International Journal of Foundations of Computer Science. World Scientific Publishing, 2008. https://doi.org/10.1142/S0129054108005814 .","short":"L. Doyen, T.A. Henzinger, J. Raskin, International Journal of Foundations of Computer Science 19 (2008) 549–563.","ieee":"L. Doyen, T. A. Henzinger, and J. Raskin, “Equivalence of labeled Markov chains,” International Journal of Foundations of Computer Science, vol. 19, no. 3. World Scientific Publishing, pp. 549–563, 2008.","apa":"Doyen, L., Henzinger, T. A., & Raskin, J. (2008). Equivalence of labeled Markov chains. International Journal of Foundations of Computer Science. World Scientific Publishing. https://doi.org/10.1142/S0129054108005814 ","ama":"Doyen L, Henzinger TA, Raskin J. Equivalence of labeled Markov chains. International Journal of Foundations of Computer Science. 2008;19(3):549-563. doi:10.1142/S0129054108005814 ","mla":"Doyen, Laurent, et al. “Equivalence of Labeled Markov Chains.” International Journal of Foundations of Computer Science, vol. 19, no. 3, World Scientific Publishing, 2008, pp. 549–63, doi:10.1142/S0129054108005814 ."},"extern":1,"author":[{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger"},{"first_name":"Jean","full_name":"Raskin, Jean-François","last_name":"Raskin"}],"publist_id":"192","title":"Equivalence of labeled Markov chains","_id":"4532","type":"journal_article","status":"public"},{"extern":1,"citation":{"chicago":"Doyen, Laurent, Thomas A Henzinger, Barbara Jobstmann, and Tatjana Petrov. “Interface Theories with Component Reuse,” 79–88. ACM, 2008. https://doi.org/10.1145/1450058.1450070.","ista":"Doyen L, Henzinger TA, Jobstmann B, Petrov T. 2008. Interface theories with component reuse. EMSOFT: Embedded Software , 79–88.","mla":"Doyen, Laurent, et al. Interface Theories with Component Reuse. ACM, 2008, pp. 79–88, doi:10.1145/1450058.1450070.","short":"L. Doyen, T.A. Henzinger, B. Jobstmann, T. Petrov, in:, ACM, 2008, pp. 79–88.","ieee":"L. Doyen, T. A. Henzinger, B. Jobstmann, and T. Petrov, “Interface theories with component reuse,” presented at the EMSOFT: Embedded Software , 2008, pp. 79–88.","ama":"Doyen L, Henzinger TA, Jobstmann B, Petrov T. Interface theories with component reuse. In: ACM; 2008:79-88. doi:10.1145/1450058.1450070","apa":"Doyen, L., Henzinger, T. A., Jobstmann, B., & Petrov, T. (2008). Interface theories with component reuse (pp. 79–88). Presented at the EMSOFT: Embedded Software , ACM. https://doi.org/10.1145/1450058.1450070"},"date_updated":"2021-01-12T07:59:30Z","title":"Interface theories with component reuse","publist_id":"193","author":[{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jobstmann","full_name":"Jobstmann, Barbara","first_name":"Barbara"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","last_name":"Petrov","orcid":"0000-0002-9041-0905","full_name":"Tatjana Petrov"}],"_id":"4533","status":"public","conference":{"name":"EMSOFT: Embedded Software "},"type":"conference","day":"01","publication_status":"published","year":"2008","date_created":"2018-12-11T12:09:21Z","date_published":"2008-10-01T00:00:00Z","doi":"10.1145/1450058.1450070","page":"79 - 88","abstract":[{"lang":"eng","text":"Interface theories have been proposed to support incremental design and independent implementability. Incremental design means that the compatibility checking of interfaces can proceed for partial system descriptions, without knowing the interfaces of all components. Independent implementability means that compatible interfaces can be refined separately, maintaining compatibility. We show that these interface theories provide no formal support for component reuse, meaning that the same component cannot be used to implement several different interfaces in a design. We add a new operation to interface theories in order to support such reuse. For example, different interfaces for the same component may refer to different aspects such as functionality, timing, and power consumption. We give both stateless and stateful examples for interface theories with component reuse. To illustrate component reuse in interface-based design, we show how the stateful theory provides a natural framework for specifying and refining PCI bus clients."}],"month":"10","main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/interface_theories_with_component_reuse.pdf","open_access":"0"}],"publisher":"ACM","quality_controlled":0},{"publist_id":"188","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"title":"Reduction of stochastic parity to stochastic mean-payoff games","citation":{"ama":"Chatterjee K, Henzinger TA. Reduction of stochastic parity to stochastic mean-payoff games. Information Processing Letters. 2008;106(1):1-7. doi:10.1016/j.ipl.2007.08.035","apa":"Chatterjee, K., & Henzinger, T. A. (2008). Reduction of stochastic parity to stochastic mean-payoff games. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2007.08.035","ieee":"K. Chatterjee and T. A. Henzinger, “Reduction of stochastic parity to stochastic mean-payoff games,” Information Processing Letters, vol. 106, no. 1. Elsevier, pp. 1–7, 2008.","short":"K. Chatterjee, T.A. Henzinger, Information Processing Letters 106 (2008) 1–7.","mla":"Chatterjee, Krishnendu, and Thomas A. Henzinger. “Reduction of Stochastic Parity to Stochastic Mean-Payoff Games.” Information Processing Letters, vol. 106, no. 1, Elsevier, 2008, pp. 1–7, doi:10.1016/j.ipl.2007.08.035.","ista":"Chatterjee K, Henzinger TA. 2008. Reduction of stochastic parity to stochastic mean-payoff games. Information Processing Letters. 106(1), 1–7.","chicago":"Chatterjee, Krishnendu, and Thomas A Henzinger. “Reduction of Stochastic Parity to Stochastic Mean-Payoff Games.” Information Processing Letters. Elsevier, 2008. https://doi.org/10.1016/j.ipl.2007.08.035."},"date_updated":"2021-01-12T07:59:30Z","extern":1,"type":"journal_article","status":"public","_id":"4534","page":"1 - 7","date_published":"2008-03-31T00:00:00Z","issue":"1","doi":"10.1016/j.ipl.2007.08.035","volume":106,"date_created":"2018-12-11T12:09:21Z","publication_status":"published","year":"2008","day":"31","publication":"Information Processing Letters","quality_controlled":0,"publisher":"Elsevier","main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/reduction_of_stochastic_parity_to_stochastic_mean-payoff_games.pdf","open_access":"0"}],"month":"03","intvolume":" 106","abstract":[{"text":"A stochastic graph game is played by two players on a game graph with probabilistic transitions. We consider stochastic graph games with ω-regular winning conditions specified as parity objectives, and mean-payoff (or limit-average) objectives. These games lie in NP ∩ coNP. We present a polynomial-time Turing reduction of stochastic parity games to stochastic mean-payoff games.","lang":"eng"}]},{"date_published":"2008-01-01T00:00:00Z","doi":"10.1145/1403375.1403595","date_created":"2018-12-11T12:09:25Z","page":"909 - 914","day":"01","publication_status":"published","year":"2008","month":"01","publisher":"IEEE","quality_controlled":0,"main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/logical_reliability_of_interacting_real-time_tasks.pdf","open_access":"0"}],"abstract":[{"text":"We propose the notion of logical reliability for real-time program tasks that interact through periodically updated program variables. We describe a reliability analysis that checks if the given short-term (e.g., single-period) reliability of a program variable update in an implementation is sufficient to meet the logical reliability requirement (of the program variable) in the long run. We then present a notion of design by refinement where a task can be refined by another task that writes to program variables with less logical reliability. The resulting analysis can be combined with an incremental schedulability analysis for interacting real-time tasks proposed earlier for the Hierarchical Timing Language (HTL), a coordination language for distributed real-time systems. We implemented a logical-reliability-enhanced prototype of the compiler and runtime infrastructure for HTL.","lang":"eng"}],"title":"Logical reliability of interacting real-time tasks","publist_id":"171","author":[{"orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Ghosal, Arkadeb","last_name":"Ghosal","first_name":"Arkadeb"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724"},{"first_name":"Daniel","last_name":"Iercan","full_name":"Iercan, Daniel"},{"last_name":"Kirsch","full_name":"Kirsch, Christoph M","first_name":"Christoph"},{"last_name":"Pinello","full_name":"Pinello, Claudio","first_name":"Claudio"},{"first_name":"Alberto","full_name":"Sangiovanni-Vincentelli, Alberto","last_name":"Sangiovanni Vincentelli"}],"extern":1,"citation":{"chicago":"Chatterjee, Krishnendu, Arkadeb Ghosal, Thomas A Henzinger, Daniel Iercan, Christoph Kirsch, Claudio Pinello, and Alberto Sangiovanni Vincentelli. “Logical Reliability of Interacting Real-Time Tasks,” 909–14. IEEE, 2008. https://doi.org/10.1145/1403375.1403595.","ista":"Chatterjee K, Ghosal A, Henzinger TA, Iercan D, Kirsch C, Pinello C, Sangiovanni Vincentelli A. 2008. Logical reliability of interacting real-time tasks. DATE: Design, Automation and Test in Europe, 909–914.","mla":"Chatterjee, Krishnendu, et al. Logical Reliability of Interacting Real-Time Tasks. IEEE, 2008, pp. 909–14, doi:10.1145/1403375.1403595.","short":"K. Chatterjee, A. Ghosal, T.A. Henzinger, D. Iercan, C. Kirsch, C. Pinello, A. Sangiovanni Vincentelli, in:, IEEE, 2008, pp. 909–914.","ieee":"K. Chatterjee et al., “Logical reliability of interacting real-time tasks,” presented at the DATE: Design, Automation and Test in Europe, 2008, pp. 909–914.","ama":"Chatterjee K, Ghosal A, Henzinger TA, et al. Logical reliability of interacting real-time tasks. In: IEEE; 2008:909-914. doi:10.1145/1403375.1403595","apa":"Chatterjee, K., Ghosal, A., Henzinger, T. A., Iercan, D., Kirsch, C., Pinello, C., & Sangiovanni Vincentelli, A. (2008). Logical reliability of interacting real-time tasks (pp. 909–914). Presented at the DATE: Design, Automation and Test in Europe, IEEE. https://doi.org/10.1145/1403375.1403595"},"date_updated":"2021-01-12T07:59:36Z","status":"public","type":"conference","conference":{"name":"DATE: Design, Automation and Test in Europe"},"_id":"4546"},{"publication_status":"published","year":"2008","publication":"International Journal of Game Theory","day":"01","page":"219 - 234","date_created":"2018-12-11T12:09:25Z","issue":"2","doi":"10.1007/s00182-007-0110-5","volume":37,"date_published":"2008-01-01T00:00:00Z","abstract":[{"text":"The value of a finite-state two-player zero-sum stochastic game with limit-average payoff can be approximated to within ε in time exponential in a polynomial in the size of the game times polynomial in logarithmic in 1/ε, for all ε > 0.","lang":"eng"}],"main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/stochastic_limit-average_games_are_in_exptime.pdf","open_access":"0"}],"publisher":"Springer","quality_controlled":0,"intvolume":" 37","month":"01","date_updated":"2021-01-12T07:59:37Z","citation":{"ista":"Chatterjee K, Majumdar R, Henzinger TA. 2008. Stochastic limit-average games are in EXPTIME. International Journal of Game Theory. 37(2), 219–234.","chicago":"Chatterjee, Krishnendu, Ritankar Majumdar, and Thomas A Henzinger. “Stochastic Limit-Average Games Are in EXPTIME.” International Journal of Game Theory. Springer, 2008. https://doi.org/10.1007/s00182-007-0110-5.","short":"K. Chatterjee, R. Majumdar, T.A. Henzinger, International Journal of Game Theory 37 (2008) 219–234.","ieee":"K. Chatterjee, R. Majumdar, and T. A. Henzinger, “Stochastic limit-average games are in EXPTIME,” International Journal of Game Theory, vol. 37, no. 2. Springer, pp. 219–234, 2008.","ama":"Chatterjee K, Majumdar R, Henzinger TA. Stochastic limit-average games are in EXPTIME. International Journal of Game Theory. 2008;37(2):219-234. doi:10.1007/s00182-007-0110-5","apa":"Chatterjee, K., Majumdar, R., & Henzinger, T. A. (2008). Stochastic limit-average games are in EXPTIME. International Journal of Game Theory. Springer. https://doi.org/10.1007/s00182-007-0110-5","mla":"Chatterjee, Krishnendu, et al. “Stochastic Limit-Average Games Are in EXPTIME.” International Journal of Game Theory, vol. 37, no. 2, Springer, 2008, pp. 219–34, doi:10.1007/s00182-007-0110-5."},"extern":1,"publist_id":"168","author":[{"full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Majumdar, Ritankar S","last_name":"Majumdar","first_name":"Ritankar"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","last_name":"Henzinger"}],"title":"Stochastic limit-average games are in EXPTIME","_id":"4548","type":"journal_article","status":"public"},{"page":"29 - 38","date_created":"2018-12-11T12:09:31Z","date_published":"2008-10-07T00:00:00Z","doi":"10.1109/ASE.2008.13","publication_status":"published","year":"2008","day":"07","main_file_link":[{"open_access":"0","url":"http://pub.ist.ac.at/%7Etah/Publications/program_analysis_with_dynamic_change_of_precision.pdf"}],"quality_controlled":0,"publisher":"ACM","month":"10","abstract":[{"lang":"eng","text":"We present and evaluate a framework and tool for combining multiple program analyses which allows the dynamic (on-line) adjustment of the precision of each analysis depending on the accumulated results. For example, the explicit tracking of the values of a variable may be switched off in favor of a predicate abstraction when and where the number of different variable values that have been encountered has exceeded a specified threshold. The method is evaluated on verifying the SSH client/server software and shows significant gains compared with predicate abstraction-based model checking."}],"publist_id":"140","author":[{"full_name":"Beyer, Dirk","last_name":"Beyer","first_name":"Dirk"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724"},{"first_name":"Grégory","last_name":"Théoduloz","full_name":"Théoduloz, Grégory"}],"title":"Program analysis with dynamic change of precision","date_updated":"2021-01-12T07:59:46Z","citation":{"chicago":"Beyer, Dirk, Thomas A Henzinger, and Grégory Théoduloz. “Program Analysis with Dynamic Change of Precision,” 29–38. ACM, 2008. https://doi.org/10.1109/ASE.2008.13.","ista":"Beyer D, Henzinger TA, Théoduloz G. 2008. Program analysis with dynamic change of precision. ASE: Automated Software Engineering, 29–38.","mla":"Beyer, Dirk, et al. Program Analysis with Dynamic Change of Precision. ACM, 2008, pp. 29–38, doi:10.1109/ASE.2008.13.","ieee":"D. Beyer, T. A. Henzinger, and G. Théoduloz, “Program analysis with dynamic change of precision,” presented at the ASE: Automated Software Engineering, 2008, pp. 29–38.","short":"D. Beyer, T.A. Henzinger, G. Théoduloz, in:, ACM, 2008, pp. 29–38.","apa":"Beyer, D., Henzinger, T. A., & Théoduloz, G. (2008). Program analysis with dynamic change of precision (pp. 29–38). Presented at the ASE: Automated Software Engineering, ACM. https://doi.org/10.1109/ASE.2008.13","ama":"Beyer D, Henzinger TA, Théoduloz G. Program analysis with dynamic change of precision. In: ACM; 2008:29-38. doi:10.1109/ASE.2008.13"},"extern":1,"conference":{"name":"ASE: Automated Software Engineering"},"type":"conference","status":"public","_id":"4568"},{"date_updated":"2021-01-12T08:03:38Z","citation":{"ista":"Hosten O, Kwiat P. 2008. Observation of the spin hall effect of light via weak measurements. Science. 319(5864), 787–790.","chicago":"Hosten, Onur, and Paul Kwiat. “Observation of the Spin Hall Effect of Light via Weak Measurements.” Science. American Association for the Advancement of Science, 2008. https://doi.org/10.1126/science.1152697.","short":"O. Hosten, P. Kwiat, Science 319 (2008) 787–790.","ieee":"O. Hosten and P. Kwiat, “Observation of the spin hall effect of light via weak measurements,” Science, vol. 319, no. 5864. American Association for the Advancement of Science, pp. 787–790, 2008.","apa":"Hosten, O., & Kwiat, P. (2008). Observation of the spin hall effect of light via weak measurements. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1152697","ama":"Hosten O, Kwiat P. Observation of the spin hall effect of light via weak measurements. Science. 2008;319(5864):787-790. doi:10.1126/science.1152697","mla":"Hosten, Onur, and Paul Kwiat. “Observation of the Spin Hall Effect of Light via Weak Measurements.” Science, vol. 319, no. 5864, American Association for the Advancement of Science, 2008, pp. 787–90, doi:10.1126/science.1152697."},"extern":1,"publist_id":"7226","author":[{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur","last_name":"Hosten","orcid":"0000-0002-2031-204X","full_name":"Onur Hosten"},{"first_name":"Paul","full_name":"Kwiat, Paul","last_name":"Kwiat"}],"title":"Observation of the spin hall effect of light via weak measurements","_id":"581","type":"journal_article","status":"public","publication_status":"published","year":"2008","day":"08","publication":"Science","page":"787 - 790","doi":"10.1126/science.1152697","date_published":"2008-02-08T00:00:00Z","volume":319,"issue":"5864","date_created":"2018-12-11T11:47:19Z","abstract":[{"lang":"eng","text":"We have detected a spin-dependent displacement perpendicular to the refractive index gradient for photons passing through an air-glass interface. The effect is the photonic version of the spin Hall effect in electronic systems, indicating the universality of the effect for particles of different nature. Treating the effect as a weak measurement of the spin projection of the photons, we used a preselection and postselection technique on the spin state to enhance the original displacement by nearly four orders of magnitude, attaining sensitivity to displacements of ∼1 angstrom. The spin Hall effect can be used for manipulating photonic angular momentum states, and the measurement technique holds promise for precision metrology."}],"quality_controlled":0,"publisher":"American Association for the Advancement of Science","month":"02","intvolume":" 319"},{"citation":{"ama":"Hosten O, Kwiat P. Spin hall effect of light via weak measurements: Sharp and smooth index variations. In: Optica Publishing Group; 2008.","apa":"Hosten, O., & Kwiat, P. (2008). Spin hall effect of light via weak measurements: Sharp and smooth index variations. Presented at the QELS: Quantum Electronics and Laser Science Conference, San Jose, CA, United States: Optica Publishing Group.","short":"O. Hosten, P. Kwiat, in:, Optica Publishing Group, 2008.","ieee":"O. Hosten and P. Kwiat, “Spin hall effect of light via weak measurements: Sharp and smooth index variations,” presented at the QELS: Quantum Electronics and Laser Science Conference, San Jose, CA, United States, 2008.","mla":"Hosten, Onur, and Paul Kwiat. Spin Hall Effect of Light via Weak Measurements: Sharp and Smooth Index Variations. Optica Publishing Group, 2008.","ista":"Hosten O, Kwiat P. 2008. Spin hall effect of light via weak measurements: Sharp and smooth index variations. QELS: Quantum Electronics and Laser Science Conference, Optics InfoBase Conference Papers, .","chicago":"Hosten, Onur, and Paul Kwiat. “Spin Hall Effect of Light via Weak Measurements: Sharp and Smooth Index Variations.” Optica Publishing Group, 2008."},"date_updated":"2022-05-24T09:10:41Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7227","author":[{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur","last_name":"Hosten","orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur"},{"first_name":"Paul","full_name":"Kwiat, Paul","last_name":"Kwiat"}],"article_processing_charge":"No","title":"Spin hall effect of light via weak measurements: Sharp and smooth index variations","_id":"584","type":"conference","conference":{"name":"QELS: Quantum Electronics and Laser Science Conference","location":"San Jose, CA, United States","end_date":"2008-05-09","start_date":"2008-05-04"},"status":"public","publication_identifier":{"isbn":["978-155752859-9"],"issn":["21622701"]},"publication_status":"published","year":"2008","day":"01","language":[{"iso":"eng"}],"date_published":"2008-01-01T00:00:00Z","date_created":"2018-12-11T11:47:20Z","abstract":[{"text":"Using “quantum weak-measurements” as a coherent enhancement technique for small signals, we have measured the recently proposed “spin Hall effect” of light at an air-glass interface, and are working on the smoothly varying refractive-index case.","lang":"eng"}],"oa_version":"None","scopus_import":"1","quality_controlled":"1","publisher":"Optica Publishing Group","alternative_title":["Optics InfoBase Conference Papers"],"main_file_link":[{"url":"https://opg.optica.org/abstract.cfm?URI=QELS-2008-QFB7"}],"month":"01"},{"title":"A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans","external_id":{"pmid":["18524954"]},"author":[{"first_name":"A. J.","full_name":"Bretscher, A. J.","last_name":"Bretscher"},{"full_name":"Busch, K. E.","last_name":"Busch","first_name":"K. E."},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","last_name":"de Bono"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Bretscher, A. J., K. E. Busch, and Mario de Bono. “A Carbon Dioxide Avoidance Behavior Is Integrated with Responses to Ambient Oxygen and Food in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2008. https://doi.org/10.1073/pnas.0707607105.","ista":"Bretscher AJ, Busch KE, de Bono M. 2008. A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 105(23), 8044–8049.","mla":"Bretscher, A. J., et al. “A Carbon Dioxide Avoidance Behavior Is Integrated with Responses to Ambient Oxygen and Food in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences, vol. 105, no. 23, Proceedings of the National Academy of Sciences, 2008, pp. 8044–49, doi:10.1073/pnas.0707607105.","ieee":"A. J. Bretscher, K. E. Busch, and M. de Bono, “A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans,” Proceedings of the National Academy of Sciences, vol. 105, no. 23. Proceedings of the National Academy of Sciences, pp. 8044–8049, 2008.","short":"A.J. Bretscher, K.E. Busch, M. de Bono, Proceedings of the National Academy of Sciences 105 (2008) 8044–8049.","ama":"Bretscher AJ, Busch KE, de Bono M. A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 2008;105(23):8044-8049. doi:10.1073/pnas.0707607105","apa":"Bretscher, A. J., Busch, K. E., & de Bono, M. (2008). A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0707607105"},"oa":1,"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","date_created":"2019-03-21T08:10:15Z","date_published":"2008-06-10T00:00:00Z","doi":"10.1073/pnas.0707607105","page":"8044-8049","publication":"Proceedings of the National Academy of Sciences","day":"10","year":"2008","has_accepted_license":"1","status":"public","type":"journal_article","_id":"6146","file_date_updated":"2020-07-14T12:47:20Z","ddc":["570"],"extern":"1","date_updated":"2021-01-12T08:06:21Z","intvolume":" 105","month":"06","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Homeostasis of internal carbon dioxide (CO2) and oxygen (O2) levels is fundamental to all animals. Here we examine the CO2 response of the nematode Caenorhabditis elegans. This species inhabits rotting material, which typically has a broad CO2 concentration range. We show that well fed C. elegans avoid CO2 levels above 0.5%. Animals can respond to both absolute CO2 concentrations and changes in CO2 levels within seconds. Responses to CO2 do not reflect avoidance of acid pH but appear to define a new sensory response. Sensation of CO2 is promoted by the cGMP-gated ion channel subunits TAX-2 and TAX-4, but other pathways are also important. Robust CO2 avoidance in well fed animals requires inhibition of the DAF-16 forkhead transcription factor by the insulin-like receptor DAF-2. Starvation, which activates DAF-16, strongly suppresses CO2 avoidance. Exposure to hypoxia (<1% O2) also suppresses CO2 avoidance via activation of the hypoxia-inducible transcription factor HIF-1. The npr-1 215V allele of the naturally polymorphic neuropeptide receptor npr-1, besides inhibiting avoidance of high ambient O2 in feeding C. elegans, also promotes avoidance of high CO2. C. elegans integrates competing O2 and CO2 sensory inputs so that one response dominates. Food and allelic variation at NPR-1 regulate which response prevails. Our results suggest that multiple sensory inputs are coordinated by C. elegans to generate different coherent foraging strategies."}],"volume":105,"issue":"23","language":[{"iso":"eng"}],"file":[{"file_name":"2008_PNAS_Bretscher.pdf","date_created":"2019-03-21T08:14:54Z","file_size":501506,"date_updated":"2020-07-14T12:47:20Z","creator":"kschuh","checksum":"eac0413064b022c1489f7b6719e7228c","file_id":"6147","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["0027-8424","1091-6490"]}},{"type":"journal_article","status":"public","_id":"6148","external_id":{"pmid":["18325626"]},"author":[{"first_name":"Jan E.","full_name":"Kammenga, Jan E.","last_name":"Kammenga"},{"first_name":"Patrick C.","last_name":"Phillips","full_name":"Phillips, Patrick C."},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","last_name":"de Bono"},{"first_name":"Agnieszka","last_name":"Doroszuk","full_name":"Doroszuk, Agnieszka"}],"title":"Beyond induced mutants: using worms to study natural variation in genetic pathways","citation":{"mla":"Kammenga, Jan E., et al. “Beyond Induced Mutants: Using Worms to Study Natural Variation in Genetic Pathways.” Trends in Genetics, vol. 24, no. 4, Elsevier, 2008, pp. 178–85, doi:10.1016/j.tig.2008.01.001.","ieee":"J. E. Kammenga, P. C. Phillips, M. de Bono, and A. Doroszuk, “Beyond induced mutants: using worms to study natural variation in genetic pathways,” Trends in Genetics, vol. 24, no. 4. Elsevier, pp. 178–185, 2008.","short":"J.E. Kammenga, P.C. Phillips, M. de Bono, A. Doroszuk, Trends in Genetics 24 (2008) 178–185.","ama":"Kammenga JE, Phillips PC, de Bono M, Doroszuk A. Beyond induced mutants: using worms to study natural variation in genetic pathways. Trends in Genetics. 2008;24(4):178-185. doi:10.1016/j.tig.2008.01.001","apa":"Kammenga, J. E., Phillips, P. C., de Bono, M., & Doroszuk, A. (2008). Beyond induced mutants: using worms to study natural variation in genetic pathways. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2008.01.001","chicago":"Kammenga, Jan E., Patrick C. Phillips, Mario de Bono, and Agnieszka Doroszuk. “Beyond Induced Mutants: Using Worms to Study Natural Variation in Genetic Pathways.” Trends in Genetics. Elsevier, 2008. https://doi.org/10.1016/j.tig.2008.01.001.","ista":"Kammenga JE, Phillips PC, de Bono M, Doroszuk A. 2008. Beyond induced mutants: using worms to study natural variation in genetic pathways. Trends in Genetics. 24(4), 178–185."},"date_updated":"2021-01-12T08:06:21Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","quality_controlled":"1","publisher":"Elsevier","intvolume":" 24","month":"04","oa_version":"None","pmid":1,"page":"178-185","date_created":"2019-03-21T08:19:45Z","doi":"10.1016/j.tig.2008.01.001","volume":24,"date_published":"2008-04-01T00:00:00Z","issue":"4","publication_status":"published","year":"2008","publication_identifier":{"issn":["0168-9525"]},"language":[{"iso":"eng"}],"publication":"Trends in Genetics","day":"01"},{"article_processing_charge":"No","external_id":{"pmid":["18334193"]},"author":[{"last_name":"Olofsson","full_name":"Olofsson, Birgitta","first_name":"Birgitta"},{"last_name":"de Bono","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario"}],"title":"Sleep: dozy worms and sleepy flies","date_updated":"2022-08-25T15:03:41Z","citation":{"ieee":"B. Olofsson and M. de Bono, “Sleep: dozy worms and sleepy flies,” Current Biology, vol. 18, no. 5. Elsevier, pp. R204–R206, 2008.","short":"B. Olofsson, M. de Bono, Current Biology 18 (2008) R204–R206.","ama":"Olofsson B, de Bono M. Sleep: dozy worms and sleepy flies. Current Biology. 2008;18(5):R204-R206. doi:10.1016/j.cub.2008.01.002","apa":"Olofsson, B., & de Bono, M. (2008). Sleep: dozy worms and sleepy flies. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2008.01.002","mla":"Olofsson, Birgitta, and Mario de Bono. “Sleep: Dozy Worms and Sleepy Flies.” Current Biology, vol. 18, no. 5, Elsevier, 2008, pp. R204–06, doi:10.1016/j.cub.2008.01.002.","ista":"Olofsson B, de Bono M. 2008. Sleep: dozy worms and sleepy flies. Current Biology. 18(5), R204–R206.","chicago":"Olofsson, Birgitta, and Mario de Bono. “Sleep: Dozy Worms and Sleepy Flies.” Current Biology. Elsevier, 2008. https://doi.org/10.1016/j.cub.2008.01.002."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","type":"journal_article","status":"public","_id":"6149","page":"R204-R206","date_created":"2019-03-21T08:23:24Z","date_published":"2008-03-11T00:00:00Z","issue":"5","volume":18,"doi":"10.1016/j.cub.2008.01.002","publication_status":"published","year":"2008","publication_identifier":{"issn":["0960-9822"]},"language":[{"iso":"eng"}],"publication":"Current Biology","day":"11","quality_controlled":"1","publisher":"Elsevier","intvolume":" 18","month":"03","pmid":1,"oa_version":"None"},{"quality_controlled":"1","publisher":"The Electrochemical Society","month":"05","intvolume":" 155","abstract":[{"lang":"eng","text":"Cell interaction phenomena in polymer electrolyte fuel cell stacks that arise from imbalance between adjacent cells are investigated in detail experimentally and theoretically. A specialized two-cell stack with advanced localized diagnostics was developed and used to analyze the mechanism and effect of cell-to-cell coupling as a result of operationally relevant variations in reactant feed flow. Contributions to overall and local voltage changes with respect to uniformly operated cells are scrutinized. Unequal operation of the cells causes in-plane current in the bipolar plate to redistribute current and result in inhomogeneous polarization. Both increasing and decreasing polarization along the air-flow path reduces cell power as compared to isopotential operation. A two-dimensional model based on a commercial computational fluid dynamics code is used to back and extend the experimental results to more general cases. Furthermore, the experimental setup presented allowed for the first time to perform simultaneous localized electrochemical impedance spectroscopy beyond the single-cell level. The mechanism of mutual cell interaction on local and integral spectra is revealed. Results show that virtually identical operation of the cells is essential to obtain meaningful integral spectra."}],"oa_version":"None","date_published":"2008-05-08T00:00:00Z","doi":"10.1149/1.2913095","issue":"7","volume":155,"date_created":"2020-01-15T12:21:47Z","publication_identifier":{"issn":["0013-4651"]},"year":"2008","publication_status":"published","day":"08","publication":"Journal of The Electrochemical Society","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"7321","article_number":"B704","author":[{"last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"first_name":"Ingo A.","last_name":"Schneider","full_name":"Schneider, Ingo A."},{"first_name":"Pang-Chieh","full_name":"Sui, Pang-Chieh","last_name":"Sui"},{"last_name":"Wokaun","full_name":"Wokaun, Alexander","first_name":"Alexander"},{"full_name":"Djilali, Nedjib","last_name":"Djilali","first_name":"Nedjib"},{"first_name":"Felix N.","full_name":"Büchi, Felix N.","last_name":"Büchi"}],"article_processing_charge":"No","title":"Cell interaction phenomena in polymer electrolyte fuel cell stacks","citation":{"chicago":"Freunberger, Stefan Alexander, Ingo A. Schneider, Pang-Chieh Sui, Alexander Wokaun, Nedjib Djilali, and Felix N. Büchi. “Cell Interaction Phenomena in Polymer Electrolyte Fuel Cell Stacks.” Journal of The Electrochemical Society. The Electrochemical Society, 2008. https://doi.org/10.1149/1.2913095.","ista":"Freunberger SA, Schneider IA, Sui P-C, Wokaun A, Djilali N, Büchi FN. 2008. Cell interaction phenomena in polymer electrolyte fuel cell stacks. Journal of The Electrochemical Society. 155(7), B704.","mla":"Freunberger, Stefan Alexander, et al. “Cell Interaction Phenomena in Polymer Electrolyte Fuel Cell Stacks.” Journal of The Electrochemical Society, vol. 155, no. 7, B704, The Electrochemical Society, 2008, doi:10.1149/1.2913095.","apa":"Freunberger, S. A., Schneider, I. A., Sui, P.-C., Wokaun, A., Djilali, N., & Büchi, F. N. (2008). Cell interaction phenomena in polymer electrolyte fuel cell stacks. Journal of The Electrochemical Society. The Electrochemical Society. https://doi.org/10.1149/1.2913095","ama":"Freunberger SA, Schneider IA, Sui P-C, Wokaun A, Djilali N, Büchi FN. Cell interaction phenomena in polymer electrolyte fuel cell stacks. Journal of The Electrochemical Society. 2008;155(7). doi:10.1149/1.2913095","short":"S.A. Freunberger, I.A. Schneider, P.-C. Sui, A. Wokaun, N. Djilali, F.N. Büchi, Journal of The Electrochemical Society 155 (2008).","ieee":"S. A. Freunberger, I. A. Schneider, P.-C. Sui, A. Wokaun, N. Djilali, and F. N. Büchi, “Cell interaction phenomena in polymer electrolyte fuel cell stacks,” Journal of The Electrochemical Society, vol. 155, no. 7. The Electrochemical Society, 2008."},"date_updated":"2021-01-12T08:13:03Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","type":"journal_article","article_type":"original","_id":"7320","title":"Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC","author":[{"first_name":"Reto","full_name":"Flückiger, Reto","last_name":"Flückiger"},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"full_name":"Kramer, Denis","last_name":"Kramer","first_name":"Denis"},{"first_name":"Alexander","last_name":"Wokaun","full_name":"Wokaun, Alexander"},{"first_name":"Günther G.","full_name":"Scherer, Günther G.","last_name":"Scherer"},{"last_name":"Büchi","full_name":"Büchi, Felix N.","first_name":"Felix N."}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:13:02Z","citation":{"chicago":"Flückiger, Reto, Stefan Alexander Freunberger, Denis Kramer, Alexander Wokaun, Günther G. Scherer, and Felix N. Büchi. “Anisotropic, Effective Diffusivity of Porous Gas Diffusion Layer Materials for PEFC.” Electrochimica Acta. Elsevier, 2008. https://doi.org/10.1016/j.electacta.2008.07.034.","ista":"Flückiger R, Freunberger SA, Kramer D, Wokaun A, Scherer GG, Büchi FN. 2008. Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC. Electrochimica Acta. 54(2), 551–559.","mla":"Flückiger, Reto, et al. “Anisotropic, Effective Diffusivity of Porous Gas Diffusion Layer Materials for PEFC.” Electrochimica Acta, vol. 54, no. 2, Elsevier, 2008, pp. 551–59, doi:10.1016/j.electacta.2008.07.034.","short":"R. Flückiger, S.A. Freunberger, D. Kramer, A. Wokaun, G.G. Scherer, F.N. Büchi, Electrochimica Acta 54 (2008) 551–559.","ieee":"R. Flückiger, S. A. Freunberger, D. Kramer, A. Wokaun, G. G. Scherer, and F. N. Büchi, “Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC,” Electrochimica Acta, vol. 54, no. 2. Elsevier, pp. 551–559, 2008.","apa":"Flückiger, R., Freunberger, S. A., Kramer, D., Wokaun, A., Scherer, G. G., & Büchi, F. N. (2008). Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC. Electrochimica Acta. Elsevier. https://doi.org/10.1016/j.electacta.2008.07.034","ama":"Flückiger R, Freunberger SA, Kramer D, Wokaun A, Scherer GG, Büchi FN. Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC. Electrochimica Acta. 2008;54(2):551-559. doi:10.1016/j.electacta.2008.07.034"},"month":"12","intvolume":" 54","quality_controlled":"1","publisher":"Elsevier","oa_version":"None","abstract":[{"text":"A comparative, experimental diffusivity study of gas diffusion layer (GDL) materials for polymer electrolyte fuel cells (PEFC) is presented for the first time. The GDL plays an important role for electrochemical losses due to gas transport limitations at high current densities. Characterization and optimization of these layers is therefore essential to improve power density. A recently developed method which allows for fast diffusimetry is applied and data compared to the literature values. Measurements are made as a function of direction and compression and the effect of different binder structures and hydrophobic treatments on effective diffusivities are discussed. A better understanding of the results is gained by including novel GDL cross-section images and a meaningful unit cell model for the interpretation of the data. The diffusivity data is valuable for GDL manufacturers and future PEFC models. The study reveals that a binder–fiber ratio larger than 50% has a negative impact on the effective diffusion properties. The hydrophobic treatment which is necessary to improve the water management can impede diffusion and thus reduce the power density. Furthermore binder has an isotropic effect while compression pronounces the in-plane orientation of the fibers.","lang":"eng"}],"issue":"2","volume":54,"doi":"10.1016/j.electacta.2008.07.034","date_published":"2008-12-30T00:00:00Z","date_created":"2020-01-15T12:21:36Z","page":"551-559","day":"30","language":[{"iso":"eng"}],"publication":"Electrochimica Acta","publication_identifier":{"issn":["0013-4686"]},"year":"2008","publication_status":"published"},{"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kramer D, Freunberger SA, Flückiger R, Schneider IA, Wokaun A, Büchi FN, Scherer GG. 2008. Electrochemical diffusimetry of fuel cell gas diffusion layers. Journal of Electroanalytical Chemistry. 612(1), 63–77.","chicago":"Kramer, Denis, Stefan Alexander Freunberger, Reto Flückiger, Ingo A. Schneider, Alexander Wokaun, Felix N. Büchi, and Günther G. Scherer. “Electrochemical Diffusimetry of Fuel Cell Gas Diffusion Layers.” Journal of Electroanalytical Chemistry. Elsevier, 2008. https://doi.org/10.1016/j.jelechem.2007.09.014.","ama":"Kramer D, Freunberger SA, Flückiger R, et al. Electrochemical diffusimetry of fuel cell gas diffusion layers. Journal of Electroanalytical Chemistry. 2008;612(1):63-77. doi:10.1016/j.jelechem.2007.09.014","apa":"Kramer, D., Freunberger, S. A., Flückiger, R., Schneider, I. A., Wokaun, A., Büchi, F. N., & Scherer, G. G. (2008). Electrochemical diffusimetry of fuel cell gas diffusion layers. Journal of Electroanalytical Chemistry. Elsevier. https://doi.org/10.1016/j.jelechem.2007.09.014","short":"D. Kramer, S.A. Freunberger, R. Flückiger, I.A. Schneider, A. Wokaun, F.N. Büchi, G.G. Scherer, Journal of Electroanalytical Chemistry 612 (2008) 63–77.","ieee":"D. Kramer et al., “Electrochemical diffusimetry of fuel cell gas diffusion layers,” Journal of Electroanalytical Chemistry, vol. 612, no. 1. Elsevier, pp. 63–77, 2008.","mla":"Kramer, Denis, et al. “Electrochemical Diffusimetry of Fuel Cell Gas Diffusion Layers.” Journal of Electroanalytical Chemistry, vol. 612, no. 1, Elsevier, 2008, pp. 63–77, doi:10.1016/j.jelechem.2007.09.014."},"date_updated":"2021-01-12T08:13:03Z","title":"Electrochemical diffusimetry of fuel cell gas diffusion layers","author":[{"last_name":"Kramer","full_name":"Kramer, Denis","first_name":"Denis"},{"last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"full_name":"Flückiger, Reto","last_name":"Flückiger","first_name":"Reto"},{"last_name":"Schneider","full_name":"Schneider, Ingo A.","first_name":"Ingo A."},{"full_name":"Wokaun, Alexander","last_name":"Wokaun","first_name":"Alexander"},{"first_name":"Felix N.","last_name":"Büchi","full_name":"Büchi, Felix N."},{"last_name":"Scherer","full_name":"Scherer, Günther G.","first_name":"Günther G."}],"article_processing_charge":"No","_id":"7322","status":"public","article_type":"original","type":"journal_article","day":"01","language":[{"iso":"eng"}],"publication":"Journal of Electroanalytical Chemistry","publication_identifier":{"issn":["1572-6657"]},"year":"2008","publication_status":"published","volume":612,"date_published":"2008-01-01T00:00:00Z","doi":"10.1016/j.jelechem.2007.09.014","issue":"1","date_created":"2020-01-15T12:21:57Z","page":"63-77","oa_version":"None","abstract":[{"lang":"eng","text":"The gas diffusion layers (GDLs) of a membrane electrode assembly (MEA) serve as link between flow field and porous electrode within a polymer electrolyte fuel cell. Beside ensuring sufficient electrical and thermal contact between the whole electrode area and the flow field, these typically 200–400 μm thick porous structures enable the access of educts to the electrode area which would be occluded by the flow field lands if the flow field is directly attached to the electrode. Hence, the characterisation of properties pertaining to mass transport of educts and products through these structures is indispensable whilst examining the contribution of the GDLs to the overall electrochemical characteristics of a MEA. A fast and cost effective method to measure the effective diffusivity of a GDL is presented. Electrochemical impedance spectroscopy is applied to measure the effective ionic conductivity of an electrolyte-soaked GDL. Taking advantage of the analogy between Ficks and Ohms law, this provides a measure for the effective diffusivity. The method is described in detail, including experimental as well as theoretical aspects, and selected results, highlighting the anisotropy and dependence on the degree of compression, are shown. Moreover, a two-dimensional model consisting of regularly spaced ellipses is developed to represent the porous structure of the GDL, and by using conformal maps, the agreement between this model and experiment with respect to the sensitivity of the effective diffusivity towards compression is shown."}],"month":"01","intvolume":" 612","publisher":"Elsevier","quality_controlled":"1"},{"_id":"7425","status":"public","conference":{"name":"International conference on fuel cell science, engineering and technology","start_date":"2005-05-23","location":"Ypsilanti, MI, United States","end_date":"2005-05-25"},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T08:13:33Z","citation":{"chicago":"Santis, Marco, Stefan Alexander Freunberger, Matthias Papra, and Felix N. Büchi. “Experimental Investigation of the Propagation of Local Current Density Variations to Adjacent Cells in PEFC Stacks.” In 3rd International Conference on Fuel Cell Science, Engineering and Technology, 763–65. ASMEDC, 2008. https://doi.org/10.1115/fuelcell2005-74116.","ista":"Santis M, Freunberger SA, Papra M, Büchi FN. 2008. Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks. 3rd International Conference on Fuel Cell Science, Engineering and Technology. International conference on fuel cell science, engineering and technology, 763–765.","mla":"Santis, Marco, et al. “Experimental Investigation of the Propagation of Local Current Density Variations to Adjacent Cells in PEFC Stacks.” 3rd International Conference on Fuel Cell Science, Engineering and Technology, ASMEDC, 2008, pp. 763–65, doi:10.1115/fuelcell2005-74116.","apa":"Santis, M., Freunberger, S. A., Papra, M., & Büchi, F. N. (2008). Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks. In 3rd International Conference on Fuel Cell Science, Engineering and Technology (pp. 763–765). Ypsilanti, MI, United States: ASMEDC. https://doi.org/10.1115/fuelcell2005-74116","ama":"Santis M, Freunberger SA, Papra M, Büchi FN. Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks. In: 3rd International Conference on Fuel Cell Science, Engineering and Technology. ASMEDC; 2008:763-765. doi:10.1115/fuelcell2005-74116","short":"M. Santis, S.A. Freunberger, M. Papra, F.N. Büchi, in:, 3rd International Conference on Fuel Cell Science, Engineering and Technology, ASMEDC, 2008, pp. 763–765.","ieee":"M. Santis, S. A. Freunberger, M. Papra, and F. N. Büchi, “Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks,” in 3rd International Conference on Fuel Cell Science, Engineering and Technology, Ypsilanti, MI, United States, 2008, pp. 763–765."},"title":"Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks","article_processing_charge":"No","author":[{"last_name":"Santis","full_name":"Santis, Marco","first_name":"Marco"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger"},{"full_name":"Papra, Matthias","last_name":"Papra","first_name":"Matthias"},{"last_name":"Büchi","full_name":"Büchi, Felix N.","first_name":"Felix N."}],"oa_version":"None","abstract":[{"lang":"eng","text":"The propagation of single cell performance losses to adjacent cells in a polymer electrolyte fuel cell stack is studied by means of local current density measurements in a two cell stack. In this stack, the working conditions of adjacent cells can be controlled independently in order to deliberately change the performance of one cell (inducing cell) and study the coupling effects to the adjacent cell (response cell), while keeping the working conditions of the later one unchanged. The experiments have shown that changes in the current density distribution caused by lowering of the air stoichiometry in the inducing cell cause changes in the current density distribution of the response cell in the order of 60% of the change of the inducing cell, even when the air stoichiometry of the response cell is kept constant. The losses in cell voltage of the inducing cell cause losses in cell voltage of the response cell in a magnitude between 30 and 50%."}],"month":"10","publisher":"ASMEDC","quality_controlled":"1","language":[{"iso":"eng"}],"publication":"3rd International Conference on Fuel Cell Science, Engineering and Technology","day":"13","publication_status":"published","year":"2008","publication_identifier":{"isbn":["0791837645","0791837572"]},"date_created":"2020-01-31T10:14:45Z","doi":"10.1115/fuelcell2005-74116","date_published":"2008-10-13T00:00:00Z","page":"763-765"},{"page":"32 - 46","date_created":"2018-12-11T11:48:19Z","date_published":"2008-01-01T00:00:00Z","doi":"10.1007/978-3-540-87779-0_3","volume":"5218 LNCS","publication_status":"published","year":"2008","language":[{"iso":"eng"}],"day":"01","publisher":"Springer","alternative_title":["LNCS"],"month":"01","abstract":[{"lang":"eng","text":"This paper addresses the following question: what is the minimum-sized synchronous window needed to solve consensus in an otherwise asynchronous system? In answer to this question, we present the first optimally-resilient algorithm ASAP that solves consensus as soon as possible in an eventually synchronous system, i.e., a system that from some time GST onwards, delivers messages in a timely fashion. ASAP guarantees that, in an execution with at most f failures, every process decides no later than round GST + f + 2, which is optimal."}],"oa_version":"None","article_processing_charge":"No","author":[{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"Seth","last_name":"Gilbert","full_name":"Gilbert, Seth"},{"first_name":"Rachid","full_name":"Guerraoui, Rachid","last_name":"Guerraoui"},{"first_name":"Corentin","full_name":"Travers, Corentin","last_name":"Travers"}],"publist_id":"6904","title":"How to solve consensus in the smallest window of synchrony","date_updated":"2023-02-23T13:10:13Z","citation":{"short":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, in:, Springer, 2008, pp. 32–46.","ieee":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “How to solve consensus in the smallest window of synchrony,” presented at the DISC: Distributed Computing, 2008, vol. 5218 LNCS, pp. 32–46.","apa":"Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2008). How to solve consensus in the smallest window of synchrony (Vol. 5218 LNCS, pp. 32–46). Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-540-87779-0_3","ama":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. How to solve consensus in the smallest window of synchrony. In: Vol 5218 LNCS. Springer; 2008:32-46. doi:10.1007/978-3-540-87779-0_3","mla":"Alistarh, Dan-Adrian, et al. How to Solve Consensus in the Smallest Window of Synchrony. Vol. 5218 LNCS, Springer, 2008, pp. 32–46, doi:10.1007/978-3-540-87779-0_3.","ista":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2008. How to solve consensus in the smallest window of synchrony. DISC: Distributed Computing, LNCS, vol. 5218 LNCS, 32–46.","chicago":"Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers. “How to Solve Consensus in the Smallest Window of Synchrony,” 5218 LNCS:32–46. Springer, 2008. https://doi.org/10.1007/978-3-540-87779-0_3."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","conference":{"name":"DISC: Distributed Computing"},"type":"conference","status":"public","_id":"753"},{"intvolume":" 18","month":"05","publisher":"Elsevier","quality_controlled":"1","oa_version":"None","date_created":"2020-04-30T11:02:13Z","volume":18,"doi":"10.1016/j.cub.2008.04.059","issue":"10","date_published":"2008-05-20T00:00:00Z","page":"751-757","language":[{"iso":"eng"}],"publication":"Current Biology","day":"20","year":"2008","publication_status":"published","publication_identifier":{"issn":["0960-9822"]},"status":"public","type":"journal_article","article_type":"original","_id":"7752","title":"Environmental heterogeneity generates fluctuating selection on a secondary sexual trait","article_processing_charge":"No","author":[{"last_name":"Robinson","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"full_name":"Pilkington, Jill G.","last_name":"Pilkington","first_name":"Jill G."},{"full_name":"Clutton-Brock, Tim H.","last_name":"Clutton-Brock","first_name":"Tim H."},{"first_name":"Josephine M.","last_name":"Pemberton","full_name":"Pemberton, Josephine M."},{"full_name":"Kruuk, Loeske. E.B.","last_name":"Kruuk","first_name":"Loeske. E.B."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T08:15:17Z","citation":{"ieee":"M. R. Robinson, J. G. Pilkington, T. H. Clutton-Brock, J. M. Pemberton, and L. E. B. Kruuk, “Environmental heterogeneity generates fluctuating selection on a secondary sexual trait,” Current Biology, vol. 18, no. 10. Elsevier, pp. 751–757, 2008.","short":"M.R. Robinson, J.G. Pilkington, T.H. Clutton-Brock, J.M. Pemberton, L.E.B. Kruuk, Current Biology 18 (2008) 751–757.","apa":"Robinson, M. R., Pilkington, J. G., Clutton-Brock, T. H., Pemberton, J. M., & Kruuk, L. E. B. (2008). Environmental heterogeneity generates fluctuating selection on a secondary sexual trait. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2008.04.059","ama":"Robinson MR, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. Environmental heterogeneity generates fluctuating selection on a secondary sexual trait. Current Biology. 2008;18(10):751-757. doi:10.1016/j.cub.2008.04.059","mla":"Robinson, Matthew Richard, et al. “Environmental Heterogeneity Generates Fluctuating Selection on a Secondary Sexual Trait.” Current Biology, vol. 18, no. 10, Elsevier, 2008, pp. 751–57, doi:10.1016/j.cub.2008.04.059.","ista":"Robinson MR, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. 2008. Environmental heterogeneity generates fluctuating selection on a secondary sexual trait. Current Biology. 18(10), 751–757.","chicago":"Robinson, Matthew Richard, Jill G. Pilkington, Tim H. Clutton-Brock, Josephine M. Pemberton, and Loeske. E.B. Kruuk. “Environmental Heterogeneity Generates Fluctuating Selection on a Secondary Sexual Trait.” Current Biology. Elsevier, 2008. https://doi.org/10.1016/j.cub.2008.04.059."}},{"acknowledgement":"This work was supported in part by NIH grants R01 GM078598 and U54 LM008748.","abstract":[{"text":"Mutation rate varies greatly between nucleotide sites of the human genome and depends both on the global genomic location and the local sequence context of a site. In particular, CpG context elevates the mutation rate by an order of magnitude. Mutations also vary widely in their effect on the molecular function, phenotype, and fitness. Independence of the probability of occurrence of a new mutation's effect has been a fundamental premise in genetics. However, highly mutable contexts may be preserved by negative selection at important sites but destroyed by mutation at sites under no selection. Thus, there may be a positive correlation between the rate of mutations at a nucleotide site and the magnitude of their effect on fitness. We studied the impact of CpG context on the rate of human-chimpanzee divergence and on intrahuman nucleotide diversity at non-synonymous coding sites. We compared nucleotides that occupy identical positions within codons of identical amino acids and only differ by being within versus outside CpG context. Nucleotides within CpG context are under a stronger negative selection, as revealed by their lower, proportionally to the mutation rate, rate of evolution and nucleotide diversity. In particular, the probability of fixation of a non-synonymous transition at a CpG site is two times lower than at a CpG site. Thus, sites with different mutation rates are not necessarily selectively equivalent. This suggests that the mutation rate may complement sequence conservation as a characteristic predictive of functional importance of nucleotide sites.","lang":"eng"}],"month":"11","intvolume":" 4","publisher":"Public Library of Science","quality_controlled":0,"day":"01","publication":"PLoS Genetics","publication_status":"published","year":"2008","issue":"11","date_published":"2008-11-01T00:00:00Z","doi":"10.1371/journal.pgen.1000281","volume":4,"date_created":"2018-12-11T11:48:48Z","_id":"844","status":"public","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)"},"extern":1,"citation":{"mla":"Schmidt, Steffen, et al. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” PLoS Genetics, vol. 4, no. 11, Public Library of Science, 2008, doi:10.1371/journal.pgen.1000281.","ieee":"S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, and S. Sunyaev, “Hypermutable non-synonymous sites are under stronger negative selection,” PLoS Genetics, vol. 4, no. 11. Public Library of Science, 2008.","short":"S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, S. Sunyaev, PLoS Genetics 4 (2008).","ama":"Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S. Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genetics. 2008;4(11). doi:10.1371/journal.pgen.1000281","apa":"Schmidt, S., Gerasimova, A., Kondrashov, F., Adzuhbei, I., Kondrashov, A., & Sunyaev, S. (2008). Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000281","chicago":"Schmidt, Steffen, Anna Gerasimova, Fyodor Kondrashov, Ivan Adzuhbei, Alexey Kondrashov, and Shamil Sunyaev. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” PLoS Genetics. Public Library of Science, 2008. https://doi.org/10.1371/journal.pgen.1000281.","ista":"Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S. 2008. Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genetics. 4(11)."},"date_updated":"2021-01-12T08:19:16Z","title":"Hypermutable non-synonymous sites are under stronger negative selection","publist_id":"6800","author":[{"full_name":"Schmidt, Steffen","last_name":"Schmidt","first_name":"Steffen"},{"first_name":"Anna","last_name":"Gerasimova","full_name":"Gerasimova, Anna"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"last_name":"Adzuhbei","full_name":"Adzuhbei, Ivan A","first_name":"Ivan"},{"first_name":"Alexey","full_name":"Kondrashov, Alexey S","last_name":"Kondrashov"},{"first_name":"Shamil","full_name":"Sunyaev, Shamil R","last_name":"Sunyaev"}]},{"intvolume":" 380","month":"07","publisher":"Elsevier","quality_controlled":"1","oa_version":"None","abstract":[{"text":"The copK gene is localized on the pMOL30 plasmid of Cupriavidus metallidurans CH34 within the complex cop cluster of genes, for which 21 genes have been identified. The expression of the corresponding periplasmic CopK protein is strongly upregulated in the presence of copper, leading to a high periplasmic accumulation. The structure and metal-binding properties of CopK were investigated by NMR and mass spectrometry. The protein is dimeric in the apo state with a dissociation constant in the range of 10- 5 M estimated from analytical ultracentrifugation. Mass spectrometry revealed that CopK has two high-affinity Cu(I)-binding sites per monomer with different Cu(I) affinities. Binding of Cu(II) was observed but appeared to be non-specific. The solution structure of apo-CopK revealed an all-β fold formed of two β-sheets in perpendicular orientation with an unstructured C-terminal tail. The dimer interface is formed by the surface of the C-terminal β-sheet. Binding of the first Cu(I)-ion induces a major structural modification involving dissociation of the dimeric apo-protein. Backbone chemical shifts determined for the 1Cu(I)-bound form confirm the conservation of the N-terminal β-sheet, while the last strand of the C-terminal sheet appears in slow conformational exchange. We hypothesize that the partial disruption of the C-terminal β-sheet is related to dimer dissociation. NH-exchange data acquired on the apo-protein are consistent with a lower thermodynamic stability of the C-terminal sheet. CopK contains seven methionine residues, five of which appear highly conserved. Chemical shift data suggest implication of two or three methionines (Met54, Met38, Met28) in the first Cu(I) site. Addition of a second Cu(I) ion further increases protein plasticity. Comparison of the structural and metal-binding properties of CopK with other periplasmic copper-binding proteins reveals two conserved features within these functionally related proteins: the all-β fold and the methionine-rich Cu(I)-binding site.","lang":"eng"}],"date_created":"2020-09-18T10:12:37Z","date_published":"2008-07-04T00:00:00Z","issue":"2","doi":"10.1016/j.jmb.2008.05.017","volume":380,"page":"386-403","publication":"Journal of Molecular Biology","language":[{"iso":"eng"}],"day":"04","publication_status":"published","year":"2008","publication_identifier":{"issn":["0022-2836"]},"keyword":["Molecular Biology"],"status":"public","article_type":"original","type":"journal_article","_id":"8481","title":"Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge","article_processing_charge":"No","author":[{"last_name":"Bersch","full_name":"Bersch, Beate","first_name":"Beate"},{"first_name":"Adrien","last_name":"Favier","full_name":"Favier, Adrien"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"},{"first_name":"Sébastien","full_name":"van Aelst, Sébastien","last_name":"van Aelst"},{"full_name":"Vallaeys, Tatiana","last_name":"Vallaeys","first_name":"Tatiana"},{"full_name":"Covès, Jacques","last_name":"Covès","first_name":"Jacques"},{"first_name":"Max","full_name":"Mergeay, Max","last_name":"Mergeay"},{"first_name":"Ruddy","full_name":"Wattiez, Ruddy","last_name":"Wattiez"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"short":"B. Bersch, A. Favier, P. Schanda, S. van Aelst, T. Vallaeys, J. Covès, M. Mergeay, R. Wattiez, Journal of Molecular Biology 380 (2008) 386–403.","ieee":"B. Bersch et al., “Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge,” Journal of Molecular Biology, vol. 380, no. 2. Elsevier, pp. 386–403, 2008.","apa":"Bersch, B., Favier, A., Schanda, P., van Aelst, S., Vallaeys, T., Covès, J., … Wattiez, R. (2008). Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2008.05.017","ama":"Bersch B, Favier A, Schanda P, et al. Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. Journal of Molecular Biology. 2008;380(2):386-403. doi:10.1016/j.jmb.2008.05.017","mla":"Bersch, Beate, et al. “Molecular Structure and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during Copper Challenge.” Journal of Molecular Biology, vol. 380, no. 2, Elsevier, 2008, pp. 386–403, doi:10.1016/j.jmb.2008.05.017.","ista":"Bersch B, Favier A, Schanda P, van Aelst S, Vallaeys T, Covès J, Mergeay M, Wattiez R. 2008. Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. Journal of Molecular Biology. 380(2), 386–403.","chicago":"Bersch, Beate, Adrien Favier, Paul Schanda, Sébastien van Aelst, Tatiana Vallaeys, Jacques Covès, Max Mergeay, and Ruddy Wattiez. “Molecular Structure and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during Copper Challenge.” Journal of Molecular Biology. Elsevier, 2008. https://doi.org/10.1016/j.jmb.2008.05.017."},"date_updated":"2021-01-12T08:19:34Z"},{"article_processing_charge":"No","author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"},{"full_name":"Brutscher, Bernhard","last_name":"Brutscher","first_name":"Bernhard"},{"first_name":"Robert","full_name":"Konrat, Robert","last_name":"Konrat"},{"first_name":"Martin","last_name":"Tollinger","full_name":"Tollinger, Martin"}],"title":"Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy","citation":{"chicago":"Schanda, Paul, Bernhard Brutscher, Robert Konrat, and Martin Tollinger. “Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange NMR Spectroscopy.” Journal of Molecular Biology. Elsevier, 2008. https://doi.org/10.1016/j.jmb.2008.05.040.","ista":"Schanda P, Brutscher B, Konrat R, Tollinger M. 2008. Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal of Molecular Biology. 380(4), 726–741.","mla":"Schanda, Paul, et al. “Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange NMR Spectroscopy.” Journal of Molecular Biology, vol. 380, no. 4, Elsevier, 2008, pp. 726–41, doi:10.1016/j.jmb.2008.05.040.","ama":"Schanda P, Brutscher B, Konrat R, Tollinger M. Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal of Molecular Biology. 2008;380(4):726-741. doi:10.1016/j.jmb.2008.05.040","apa":"Schanda, P., Brutscher, B., Konrat, R., & Tollinger, M. (2008). Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2008.05.040","short":"P. Schanda, B. Brutscher, R. Konrat, M. Tollinger, Journal of Molecular Biology 380 (2008) 726–741.","ieee":"P. Schanda, B. Brutscher, R. Konrat, and M. Tollinger, “Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy,” Journal of Molecular Biology, vol. 380, no. 4. Elsevier, pp. 726–741, 2008."},"date_updated":"2021-01-12T08:19:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","type":"journal_article","article_type":"original","keyword":["Molecular Biology"],"status":"public","_id":"8480","page":"726-741","date_created":"2020-09-18T10:12:29Z","doi":"10.1016/j.jmb.2008.05.040","issue":"4","date_published":"2008-07-18T00:00:00Z","volume":380,"publication_status":"published","year":"2008","publication_identifier":{"issn":["0022-2836"]},"publication":"Journal of Molecular Biology","language":[{"iso":"eng"}],"day":"18","quality_controlled":"1","publisher":"Elsevier","intvolume":" 380","month":"07","abstract":[{"text":"The KIX domain of the transcription co-activator CBP is a three-helix bundle protein that folds via rapid accumulation of an intermediate state, followed by a slower folding phase. Recent NMR relaxation dispersion studies revealed the presence of a low-populated (excited) state of KIX that exists in equilibrium with the natively folded form under non-denaturing conditions, and likely represents the equilibrium analog of the folding intermediate. Here, we combine amide hydrogen/deuterium exchange measurements using rapid NMR data acquisition techniques with backbone 15N and 13C relaxation dispersion experiments to further investigate the equilibrium folding of the KIX domain. Residual structure within the folding intermediate is detected by both methods, and their combination enables reliable quantification of the amount of persistent residual structure. Three well-defined folding subunits are found, which display variable stability and correspond closely to the individual helices in the native state. While two of the three helices (α2 and α3) are partially formed in the folding intermediate (to ∼ 50% and ∼ 80%, respectively, at 20 °C), the third helix is disordered. The observed helical content within the excited state exceeds the helical propensities predicted for the corresponding peptide regions, suggesting that the two helices are weakly mutually stabilized, while methyl 13C relaxation dispersion data indicate that a defined packing arrangement is unlikely. Temperature-dependent experiments reveal that the largest enthalpy and entropy changes along the folding reaction occur during the final transition from the intermediate to the native state. Our experimental data are consistent with a folding mechanism where helices α2 and α3 form rapidly, although to different extents, while helix α1 consolidates only as folding proceeds to complete the native state-structure.","lang":"eng"}],"oa_version":"None"},{"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Kern, T., Schanda, P., & Brutscher, B. (2008). Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2007.11.015","ama":"Kern T, Schanda P, Brutscher B. Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic Resonance. 2008;190(2):333-338. doi:10.1016/j.jmr.2007.11.015","short":"T. Kern, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 190 (2008) 333–338.","ieee":"T. Kern, P. Schanda, and B. Brutscher, “Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load,” Journal of Magnetic Resonance, vol. 190, no. 2. Elsevier, pp. 333–338, 2008.","mla":"Kern, Thomas, et al. “Sensitivity-Enhanced IPAP-SOFAST-HMQC for Fast-Pulsing 2D NMR with Reduced Radiofrequency Load.” Journal of Magnetic Resonance, vol. 190, no. 2, Elsevier, 2008, pp. 333–38, doi:10.1016/j.jmr.2007.11.015.","ista":"Kern T, Schanda P, Brutscher B. 2008. Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic Resonance. 190(2), 333–338.","chicago":"Kern, Thomas, Paul Schanda, and Bernhard Brutscher. “Sensitivity-Enhanced IPAP-SOFAST-HMQC for Fast-Pulsing 2D NMR with Reduced Radiofrequency Load.” Journal of Magnetic Resonance. Elsevier, 2008. https://doi.org/10.1016/j.jmr.2007.11.015."},"date_updated":"2021-01-12T08:19:35Z","title":"Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load","author":[{"first_name":"Thomas","last_name":"Kern","full_name":"Kern, Thomas"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"},{"first_name":"Bernhard","full_name":"Brutscher, Bernhard","last_name":"Brutscher"}],"article_processing_charge":"No","_id":"8482","status":"public","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"type":"journal_article","article_type":"letter_note","day":"01","publication":"Journal of Magnetic Resonance","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1090-7807"]},"year":"2008","publication_status":"published","date_published":"2008-02-01T00:00:00Z","doi":"10.1016/j.jmr.2007.11.015","volume":190,"issue":"2","date_created":"2020-09-18T10:12:46Z","page":"333-338","oa_version":"None","abstract":[{"lang":"eng","text":"The SOFAST-HMQC experiment [P. Schanda, B. Brutscher, Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds, J. Am. Chem. Soc. 127 (2005) 8014–8015] allows recording two-dimensional correlation spectra of macromolecules such as proteins in only a few seconds acquisition time. To achieve the highest possible sensitivity, SOFAST-HMQC experiments are preferably performed on high-field NMR spectrometers equipped with cryogenically cooled probes. The duty cycle of over 80% in fast-pulsing SOFAST-HMQC experiments, however, may cause problems when using a cryogenic probe. Here we introduce SE-IPAP-SOFAST-HMQC, a new pulse sequence that provides comparable sensitivity to standard SOFAST-HMQC, while avoiding heteronuclear decoupling during 1H detection, and thus significantly reducing the radiofrequency load of the probe during the experiment. The experiment is also attractive for fast and sensitive measurement of heteronuclear one-bond spin coupling constants."}],"month":"02","intvolume":" 190","quality_controlled":"1","publisher":"Elsevier"},{"author":[{"last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"}],"article_processing_charge":"No","external_id":{"pmid":["18774331"]},"title":"The evolving functions of DNA methylation","citation":{"chicago":"Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” Current Opinion in Plant Biology. Elsevier , 2008. https://doi.org/10.1016/j.pbi.2008.07.004.","ista":"Zilberman D. 2008. The evolving functions of DNA methylation. Current Opinion in Plant Biology. 11(5), 554–559.","mla":"Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” Current Opinion in Plant Biology, vol. 11, no. 5, Elsevier , 2008, pp. 554–59, doi:10.1016/j.pbi.2008.07.004.","short":"D. Zilberman, Current Opinion in Plant Biology 11 (2008) 554–559.","ieee":"D. Zilberman, “The evolving functions of DNA methylation,” Current Opinion in Plant Biology, vol. 11, no. 5. Elsevier , pp. 554–559, 2008.","ama":"Zilberman D. The evolving functions of DNA methylation. Current Opinion in Plant Biology. 2008;11(5):554-559. doi:10.1016/j.pbi.2008.07.004","apa":"Zilberman, D. (2008). The evolving functions of DNA methylation. Current Opinion in Plant Biology. Elsevier . https://doi.org/10.1016/j.pbi.2008.07.004"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Elsevier ","quality_controlled":"1","page":"554-559","doi":"10.1016/j.pbi.2008.07.004","date_published":"2008-10-01T00:00:00Z","date_created":"2021-06-08T13:13:37Z","year":"2008","publication":"Current Opinion in Plant Biology","type":"journal_article","article_type":"review","status":"public","_id":"9537","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T08:54:07Z","extern":"1","scopus_import":"1","month":"10","intvolume":" 11","abstract":[{"lang":"eng","text":"DNA methylation is an ancient process found in all domains of life. Although the enzymes that mediate methylation have remained highly conserved, DNA methylation has been adapted for a variety of uses throughout evolution, including defense against transposable elements and control of gene expression. Defects in DNA methylation are linked to human diseases, including cancer. Methylation has been lost several times in the course of animal and fungal evolution, thus limiting the opportunity for study in common model organisms. In the past decade, plants have emerged as a premier model system for genetic dissection of DNA methylation. A recent combination of plant genetics with powerful genomic approaches has led to a number of exciting discoveries and promises many more."}],"pmid":1,"oa_version":"None","issue":"5","volume":11,"publication_identifier":{"issn":["1369-5266"]},"publication_status":"published","language":[{"iso":"eng"}]},{"publisher":"Elsevier","quality_controlled":0,"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/hep-th/0703258"}],"month":"01","intvolume":" 154","abstract":[{"text":"We give many examples of applying Bogoliubov's forest formula to iterative solutions of various nonlinear equations. The same formula describes an extremely wide class of objects, from an ordinary quadratic equation to renormalization in quantum field theory.","lang":"eng"}],"acknowledgement":"This work is supported in part by the Dynasty Foundation (M. N. S.), the\nRussian Foundation for Basic Research (Grant No\ns. 07-02-00878 and 07-02-00645), a joint grant (Grant\nNo. 06-01-92059-CE), the NWO (Project No. 047.011.2004.026), INTAS (Grant No. 05-1000008-7865), the\nProgram for Supporting Leading Scientific School\ns (Grant No. NSh-8004.2006.2), and also by a project\n(Project No. ANR-05-BLAN-0029-01, A. Yu. M.).","page":"270 - 293","issue":"2","date_published":"2008-01-01T00:00:00Z","doi":"10.1007/s11232-008-0026-7","volume":154,"date_created":"2018-12-11T11:49:26Z","publication_status":"published","year":"2008","day":"01","publication":"Theoretical and Mathematical Physics","type":"journal_article","status":"public","_id":"965","author":[{"last_name":"Morozov","full_name":"Morozov, Alexei Y","first_name":"Alexei"},{"orcid":"0000-0002-2399-5827","full_name":"Maksym Serbyn","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6437","title":"Nonlinear algebra and Bogoliubov's recursion","date_updated":"2021-01-12T08:22:17Z","citation":{"mla":"Morozov, Alexei, and Maksym Serbyn. “Nonlinear Algebra and Bogoliubov’s Recursion.” Theoretical and Mathematical Physics, vol. 154, no. 2, Elsevier, 2008, pp. 270–93, doi:10.1007/s11232-008-0026-7.","short":"A. Morozov, M. Serbyn, Theoretical and Mathematical Physics 154 (2008) 270–293.","ieee":"A. Morozov and M. Serbyn, “Nonlinear algebra and Bogoliubov’s recursion,” Theoretical and Mathematical Physics, vol. 154, no. 2. Elsevier, pp. 270–293, 2008.","ama":"Morozov A, Serbyn M. Nonlinear algebra and Bogoliubov’s recursion. Theoretical and Mathematical Physics. 2008;154(2):270-293. doi:10.1007/s11232-008-0026-7","apa":"Morozov, A., & Serbyn, M. (2008). Nonlinear algebra and Bogoliubov’s recursion. Theoretical and Mathematical Physics. Elsevier. https://doi.org/10.1007/s11232-008-0026-7","chicago":"Morozov, Alexei, and Maksym Serbyn. “Nonlinear Algebra and Bogoliubov’s Recursion.” Theoretical and Mathematical Physics. Elsevier, 2008. https://doi.org/10.1007/s11232-008-0026-7.","ista":"Morozov A, Serbyn M. 2008. Nonlinear algebra and Bogoliubov’s recursion. Theoretical and Mathematical Physics. 154(2), 270–293."},"extern":1},{"_id":"8510","type":"journal_article","article_type":"original","status":"public","keyword":["Applied Mathematics","General Mathematics"],"citation":{"ista":"Kaloshin V, Levi M. 2008. An example of Arnold diffusion for near-integrable Hamiltonians. Bulletin of the American Mathematical Society. 45(3), 409–427.","chicago":"Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable Hamiltonians.” Bulletin of the American Mathematical Society. American Mathematical Society, 2008. https://doi.org/10.1090/s0273-0979-08-01211-1.","apa":"Kaloshin, V., & Levi, M. (2008). An example of Arnold diffusion for near-integrable Hamiltonians. Bulletin of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/s0273-0979-08-01211-1","ama":"Kaloshin V, Levi M. An example of Arnold diffusion for near-integrable Hamiltonians. Bulletin of the American Mathematical Society. 2008;45(3):409-427. doi:10.1090/s0273-0979-08-01211-1","ieee":"V. Kaloshin and M. Levi, “An example of Arnold diffusion for near-integrable Hamiltonians,” Bulletin of the American Mathematical Society, vol. 45, no. 3. American Mathematical Society, pp. 409–427, 2008.","short":"V. Kaloshin, M. Levi, Bulletin of the American Mathematical Society 45 (2008) 409–427.","mla":"Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable Hamiltonians.” Bulletin of the American Mathematical Society, vol. 45, no. 3, American Mathematical Society, 2008, pp. 409–27, doi:10.1090/s0273-0979-08-01211-1."},"date_updated":"2021-01-12T08:19:47Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","last_name":"Kaloshin"},{"first_name":"Mark","last_name":"Levi","full_name":"Levi, Mark"}],"article_processing_charge":"No","title":"An example of Arnold diffusion for near-integrable Hamiltonians","abstract":[{"text":"In this paper, using the ideas of Bessi and Mather, we present a simple mechanical system exhibiting Arnold diffusion. This system of a particle in a small periodic potential can be also interpreted as ray propagation in a periodic optical medium with a near-constant index of refraction. Arnold diffusion in this context manifests itself as an arbitrary finite change of direction for nearly constant index of refraction.","lang":"eng"}],"oa_version":"None","quality_controlled":"1","publisher":"American Mathematical Society","month":"07","intvolume":" 45","publication_identifier":{"issn":["0273-0979"]},"year":"2008","publication_status":"published","day":"01","publication":"Bulletin of the American Mathematical Society","language":[{"iso":"eng"}],"page":"409-427","date_published":"2008-07-01T00:00:00Z","volume":45,"doi":"10.1090/s0273-0979-08-01211-1","issue":"3","date_created":"2020-09-18T10:48:20Z"},{"publication_identifier":{"issn":["0036-1445","1095-7200"]},"publication_status":"published","year":"2008","day":"05","language":[{"iso":"eng"}],"publication":"SIAM Review","page":"702-720","date_published":"2008-11-05T00:00:00Z","volume":50,"issue":"4","doi":"10.1137/070703235","date_created":"2020-09-18T10:48:12Z","abstract":[{"text":"The goal of this paper is to present to nonspecialists what is perhaps the simplest possible geometrical picture explaining the mechanism of Arnold diffusion. We choose to speak of a specific model—that of geometric rays in a periodic optical medium. This model is equivalent to that of a particle in a periodic potential in ${\\mathbb R}^{n}$ with energy prescribed and to the geodesic flow in a Riemannian metric on ${\\mathbb R}^{n} $.","lang":"eng"}],"oa_version":"None","publisher":"Society for Industrial & Applied Mathematics","quality_controlled":"1","month":"11","intvolume":" 50","date_updated":"2021-01-12T08:19:46Z","citation":{"chicago":"Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” SIAM Review. Society for Industrial & Applied Mathematics, 2008. https://doi.org/10.1137/070703235.","ista":"Kaloshin V, Levi M. 2008. Geometry of Arnold diffusion. SIAM Review. 50(4), 702–720.","mla":"Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” SIAM Review, vol. 50, no. 4, Society for Industrial & Applied Mathematics, 2008, pp. 702–20, doi:10.1137/070703235.","apa":"Kaloshin, V., & Levi, M. (2008). Geometry of Arnold diffusion. SIAM Review. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/070703235","ama":"Kaloshin V, Levi M. Geometry of Arnold diffusion. SIAM Review. 2008;50(4):702-720. doi:10.1137/070703235","short":"V. Kaloshin, M. Levi, SIAM Review 50 (2008) 702–720.","ieee":"V. Kaloshin and M. Levi, “Geometry of Arnold diffusion,” SIAM Review, vol. 50, no. 4. Society for Industrial & Applied Mathematics, pp. 702–720, 2008."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","last_name":"Kaloshin"},{"first_name":"Mark","full_name":"Levi, Mark","last_name":"Levi"}],"article_processing_charge":"No","title":"Geometry of Arnold diffusion","_id":"8509","article_type":"original","type":"journal_article","status":"public","keyword":["Theoretical Computer Science","Applied Mathematics","Computational Mathematics"]},{"date_updated":"2021-01-12T08:21:29Z","citation":{"ama":"Donaldson Z, Kondrashov F, Putnam A, et al. Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. 2008;8(1). doi:10.1186/1471-2148-8-180","apa":"Donaldson, Z., Kondrashov, F., Putnam, A., Bai, Y., Stoinski, T., Hammock, E., & Young, L. (2008). Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-8-180","ieee":"Z. Donaldson et al., “Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene,” BMC Evolutionary Biology, vol. 8, no. 1. BioMed Central, 2008.","short":"Z. Donaldson, F. Kondrashov, A. Putnam, Y. Bai, T. Stoinski, E. Hammock, L. Young, BMC Evolutionary Biology 8 (2008).","mla":"Donaldson, Zoe, et al. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary Biology, vol. 8, no. 1, BioMed Central, 2008, doi:10.1186/1471-2148-8-180.","ista":"Donaldson Z, Kondrashov F, Putnam A, Bai Y, Stoinski T, Hammock E, Young L. 2008. Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. 8(1).","chicago":"Donaldson, Zoe, Fyodor Kondrashov, Andrea Putnam, Yaohui Bai, Tara Stoinski, Elizabeth Hammock, and Larry Young. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary Biology. BioMed Central, 2008. https://doi.org/10.1186/1471-2148-8-180."},"extern":1,"publist_id":"6753","author":[{"first_name":"Zoe","full_name":"Donaldson, Zoe R","last_name":"Donaldson"},{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrea","full_name":"Putnam, Andrea S","last_name":"Putnam"},{"last_name":"Bai","full_name":"Bai, Yaohui","first_name":"Yaohui"},{"first_name":"Tara","last_name":"Stoinski","full_name":"Stoinski, Tara S"},{"first_name":"Elizabeth","last_name":"Hammock","full_name":"Hammock, Elizabeth A"},{"first_name":"Larry","last_name":"Young","full_name":"Young, Larry"}],"title":"Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene","_id":"895","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","year":"2008","publication_status":"published","day":"01","publication":"BMC Evolutionary Biology","volume":8,"issue":"1","doi":"10.1186/1471-2148-8-180","date_published":"2008-01-01T00:00:00Z","date_created":"2018-12-11T11:49:04Z","abstract":[{"text":"Background. The arginine vasopressin V1a receptor (V1aR) modulates social cognition and behavior in a wide variety of species. Variation in a repetitive microsatellite element in the 5′ flanking region of the V1aR gene (AVPR1A) in rodents has been associated with variation in brain V1aR expression and in social behavior. In humans, the 5′ flanking region of AVPR1A contains a tandem duplication of two ∼350 bp, microsatellite-containing elements located approximately 3.5 kb upstream of the transcription start site. The first block, referred to as DupA, contains a polymorphic (GT) 25microsatellite; the second block, DupB, has a complex (CT) 4-(TT)-(CT)8-(GT)24polymorphic motif, known as RS3. Polymorphisms in RS3 have been associated with variation in sociobehavioral traits in humans, including autism spectrum disorders. Thus, evolution of these regions may have contributed to variation in social behavior in primates. We examined the structure of these regions in six ape, six monkey, and one prosimian species. Results. Both tandem repeat blocks are present upstream of the AVPR1A coding region in five of the ape species we investigated, while monkeys have only one copy of this region. As in humans, the microsatellites within DupA and DupB are polymorphic in many primate species. Furthermore, both single (lacking DupB) and duplicated alleles (containing both DupA and DupB) are present in chimpanzee (Pan troglodytes) populations with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles, respectively, based on the analysis of 47 wild-caught individuals. Finally, a phylogenetic reconstruction suggests two alternate evolutionary histories for this locus. Conclusion. There is no obvious relationship between the presence of the RS3 duplication and social organization in primates. However, polymorphisms identified in some species may be useful in future genetic association studies. In particular, the presence of both single and duplicated alleles in chimpanzees provides a unique opportunity to assess the functional role of this duplication in contributing to variation in social behavior in primates. While our initial studies show no signs of directional selection on this locus in chimps, pharmacological and genetic association studies support a potential role for this region in influencing V1aR expression and social behavior.","lang":"eng"}],"acknowledgement":"We thank the caretakers at Zoo Atlanta and Yerkes National Primate Center for help with procuring specimens. Additional DNA samples were supplied by Bill Hopkins, Emory University (chimpanzee), Allyson Bennet, Wake Forest University (chimpanzee, rhesus macaque, bonnet macaque), Mar Sanchez, Emory University (rhesus macaque), and Anne Yoder, Duke University (galago). Susan Lambeth, M.D. Anderson Cancer Center, and Katie Chace, Yerkes National Primate Center, helped provide records regarding the origins of wild born chimps at these centers. We would like to thank Dr Lisa McGraw and two anonymous reviewers for their com- ments on this manuscript. This work was supported by NSF IBN-9876754, NIH RR00165, NIMH56897 (LJY), MH64692 (LJY) and a Howard Hughes Predoctoral Fellowship (ZRD).\n","quality_controlled":0,"publisher":"BioMed Central","month":"01","intvolume":" 8"},{"title":"Nested genes and increasing organizational complexity of metazoan genomes","author":[{"first_name":"Raquel","last_name":"Assis","full_name":"Assis, Raquel"},{"last_name":"Kondrashov","full_name":"Kondrashov, Alexey S","first_name":"Alexey"},{"last_name":"Koonin","full_name":"Koonin, Eugene V","first_name":"Eugene"},{"last_name":"Kondrashov","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"publist_id":"6743","extern":1,"citation":{"ista":"Assis R, Kondrashov A, Koonin E, Kondrashov F. 2008. Nested genes and increasing organizational complexity of metazoan genomes. Trends in Genetics. 24(10), 475–478.","chicago":"Assis, Raquel, Alexey Kondrashov, Eugene Koonin, and Fyodor Kondrashov. “Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” Trends in Genetics. Elsevier, 2008. https://doi.org/10.1016/j.tig.2008.08.003.","apa":"Assis, R., Kondrashov, A., Koonin, E., & Kondrashov, F. (2008). Nested genes and increasing organizational complexity of metazoan genomes. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2008.08.003","ama":"Assis R, Kondrashov A, Koonin E, Kondrashov F. Nested genes and increasing organizational complexity of metazoan genomes. Trends in Genetics. 2008;24(10):475-478. doi:10.1016/j.tig.2008.08.003","ieee":"R. Assis, A. Kondrashov, E. Koonin, and F. Kondrashov, “Nested genes and increasing organizational complexity of metazoan genomes,” Trends in Genetics, vol. 24, no. 10. Elsevier, pp. 475–478, 2008.","short":"R. Assis, A. Kondrashov, E. Koonin, F. Kondrashov, Trends in Genetics 24 (2008) 475–478.","mla":"Assis, Raquel, et al. “Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” Trends in Genetics, vol. 24, no. 10, Elsevier, 2008, pp. 475–78, doi:10.1016/j.tig.2008.08.003."},"date_updated":"2021-01-12T08:21:49Z","status":"public","type":"journal_article","_id":"907","date_created":"2018-12-11T11:49:08Z","issue":"10","doi":"10.1016/j.tig.2008.08.003","volume":24,"date_published":"2008-10-01T00:00:00Z","page":"475 - 478","publication":"Trends in Genetics","day":"01","publication_status":"published","year":"2008","intvolume":" 24","month":"10","quality_controlled":0,"publisher":"Elsevier","abstract":[{"text":"The most common form of protein-coding gene overlap in eukaryotes is a simple nested structure, whereby one gene is embedded in an intron of another. Analysis of nested protein-coding genes in vertebrates, fruit flies and nematodes revealed substantially higher rates of evolutionary gains than losses. The accumulation of nested gene structures could not be attributed to any obvious functional relationships between the genes involved and represents an increase of the organizational complexity of animal genomes via a neutral process.","lang":"eng"}]},{"oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Nature","day":"06","year":"2008","date_created":"2021-06-04T11:49:32Z","date_published":"2008-11-06T00:00:00Z","doi":"10.1038/nature07324","page":"125-129","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Zilberman, D., Coleman-Derr, D., Ballinger, T., & Henikoff, S. (2008). Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. Springer Nature. https://doi.org/10.1038/nature07324","ama":"Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 2008;456(7218):125-129. doi:10.1038/nature07324","short":"D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008) 125–129.","ieee":"D. Zilberman, D. Coleman-Derr, T. Ballinger, and S. Henikoff, “Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks,” Nature, vol. 456, no. 7218. Springer Nature, pp. 125–129, 2008.","mla":"Zilberman, Daniel, et al. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” Nature, vol. 456, no. 7218, Springer Nature, 2008, pp. 125–29, doi:10.1038/nature07324.","ista":"Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. 2008. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 456(7218), 125–129.","chicago":"Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” Nature. Springer Nature, 2008. https://doi.org/10.1038/nature07324."},"title":"Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks","article_processing_charge":"No","external_id":{"pmid":["18815594"]},"author":[{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman"},{"first_name":"Devin","full_name":"Coleman-Derr, Devin","last_name":"Coleman-Derr"},{"last_name":"Ballinger","full_name":"Ballinger, Tracy","first_name":"Tracy"},{"first_name":"Steven","full_name":"Henikoff, Steven","last_name":"Henikoff"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation1–6. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development4,5, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer7. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation."}],"intvolume":" 456","month":"11","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877514/","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"issue":"7218","volume":456,"_id":"9457","keyword":["Multidisciplinary"],"status":"public","type":"journal_article","article_type":"letter_note","extern":"1","date_updated":"2021-12-14T08:54:36Z","department":[{"_id":"DaZi"}]},{"volume":18,"issue":"18","publication_status":"published","publication_identifier":{"eissn":["1616-3028"],"issn":["1616-301X"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 18","month":"09","abstract":[{"lang":"eng","text":"Supraspheres (SS) composed of hundreds to thousands of metal nanoparticles (NPs) and crosslinked by dithiol linkers are assembled into larger structures, which are subsequently converted into nanoporous metals (NMs). Conversion is achieved by heating which removes organic molecules stabilizing the NPs and allows for NP fusion. Heating of SS solutions leads to NMs of overall macroscopic dimensions; localized radiation using collimated electron beam is used to prepare metallized surface micropatterns. Depending on the composition of supraspherical precursors, nanoporous materials composed of up to three metals can be obtained. Strategies for controlling pore size and nanoscale surface roughness of these materials are discussed."}],"oa_version":"None","date_updated":"2023-08-08T11:16:28Z","extern":"1","article_type":"original","type":"journal_article","keyword":["Electrochemistry","Condensed Matter Physics","Biomaterials","Electronic","Optical and Magnetic Materials"],"status":"public","_id":"13423","page":"2763-2769","date_created":"2023-08-01T10:30:57Z","date_published":"2008-09-23T00:00:00Z","doi":"10.1002/adfm.200800293","year":"2008","publication":"Advanced Functional Materials","day":"23","publisher":"Wiley","quality_controlled":"1","article_processing_charge":"No","author":[{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn"},{"first_name":"Timothy P.","full_name":"Gray, Timothy P.","last_name":"Gray"},{"last_name":"Wesson","full_name":"Wesson, Paul J.","first_name":"Paul J."},{"first_name":"Benjamin D.","full_name":"Myers, Benjamin D.","last_name":"Myers"},{"first_name":"Vinayak P.","last_name":"Dravid","full_name":"Dravid, Vinayak P."},{"first_name":"Stoyan K.","last_name":"Smoukov","full_name":"Smoukov, Stoyan K."},{"full_name":"Grzybowski, Bartosz A.","last_name":"Grzybowski","first_name":"Bartosz A."}],"title":"Bulk synthesis and surface patterning of nanoporous metals and alloys from supraspherical nanoparticle aggregates","citation":{"ieee":"R. Klajn et al., “Bulk synthesis and surface patterning of nanoporous metals and alloys from supraspherical nanoparticle aggregates,” Advanced Functional Materials, vol. 18, no. 18. Wiley, pp. 2763–2769, 2008.","short":"R. Klajn, T.P. Gray, P.J. Wesson, B.D. Myers, V.P. Dravid, S.K. Smoukov, B.A. Grzybowski, Advanced Functional Materials 18 (2008) 2763–2769.","apa":"Klajn, R., Gray, T. P., Wesson, P. J., Myers, B. D., Dravid, V. P., Smoukov, S. K., & Grzybowski, B. A. (2008). Bulk synthesis and surface patterning of nanoporous metals and alloys from supraspherical nanoparticle aggregates. Advanced Functional Materials. Wiley. https://doi.org/10.1002/adfm.200800293","ama":"Klajn R, Gray TP, Wesson PJ, et al. Bulk synthesis and surface patterning of nanoporous metals and alloys from supraspherical nanoparticle aggregates. Advanced Functional Materials. 2008;18(18):2763-2769. doi:10.1002/adfm.200800293","mla":"Klajn, Rafal, et al. “Bulk Synthesis and Surface Patterning of Nanoporous Metals and Alloys from Supraspherical Nanoparticle Aggregates.” Advanced Functional Materials, vol. 18, no. 18, Wiley, 2008, pp. 2763–69, doi:10.1002/adfm.200800293.","ista":"Klajn R, Gray TP, Wesson PJ, Myers BD, Dravid VP, Smoukov SK, Grzybowski BA. 2008. Bulk synthesis and surface patterning of nanoporous metals and alloys from supraspherical nanoparticle aggregates. Advanced Functional Materials. 18(18), 2763–2769.","chicago":"Klajn, Rafal, Timothy P. Gray, Paul J. Wesson, Benjamin D. Myers, Vinayak P. Dravid, Stoyan K. Smoukov, and Bartosz A. Grzybowski. “Bulk Synthesis and Surface Patterning of Nanoporous Metals and Alloys from Supraspherical Nanoparticle Aggregates.” Advanced Functional Materials. Wiley, 2008. https://doi.org/10.1002/adfm.200800293."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Wei, Yanhu, et al. “Synthesis, Shape Control, and Optical Properties of Hybrid Au/Fe3O4 ‘Nanoflowers.’” Small, vol. 4, no. 10, Wiley, 2008, pp. 1635–39, doi:10.1002/smll.200800511.","apa":"Wei, Y., Klajn, R., Pinchuk, A. O., & Grzybowski, B. A. (2008). Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers.” Small. Wiley. https://doi.org/10.1002/smll.200800511","ama":"Wei Y, Klajn R, Pinchuk AO, Grzybowski BA. Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers.” Small. 2008;4(10):1635-1639. doi:10.1002/smll.200800511","short":"Y. Wei, R. Klajn, A.O. Pinchuk, B.A. Grzybowski, Small 4 (2008) 1635–1639.","ieee":"Y. Wei, R. Klajn, A. O. Pinchuk, and B. A. Grzybowski, “Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 ‘nanoflowers,’” Small, vol. 4, no. 10. Wiley, pp. 1635–1639, 2008.","chicago":"Wei, Yanhu, Rafal Klajn, Anatoliy O. Pinchuk, and Bartosz A. Grzybowski. “Synthesis, Shape Control, and Optical Properties of Hybrid Au/Fe3O4 ‘Nanoflowers.’” Small. Wiley, 2008. https://doi.org/10.1002/smll.200800511.","ista":"Wei Y, Klajn R, Pinchuk AO, Grzybowski BA. 2008. Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers”. Small. 4(10), 1635–1639."},"title":"Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers”","external_id":{"pmid":["18636405"]},"article_processing_charge":"No","author":[{"last_name":"Wei","full_name":"Wei, Yanhu","first_name":"Yanhu"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","full_name":"Klajn, Rafal","last_name":"Klajn"},{"full_name":"Pinchuk, Anatoliy O.","last_name":"Pinchuk","first_name":"Anatoliy O."},{"last_name":"Grzybowski","full_name":"Grzybowski, Bartosz A.","first_name":"Bartosz A."}],"publisher":"Wiley","quality_controlled":"1","publication":"Small","day":"09","year":"2008","date_created":"2023-08-01T10:30:42Z","doi":"10.1002/smll.200800511","date_published":"2008-10-09T00:00:00Z","page":"1635-1639","_id":"13422","keyword":["Biomaterials","Biotechnology","General Materials Science","General Chemistry"],"status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2023-08-08T11:14:50Z","oa_version":"None","pmid":1,"abstract":[{"text":"Make like a leaf: The synthesis and characterization of a family of “flowerlike” Au/Fe3O4 nanoparticles is described, whereby Fe3O4 “leaves” adhere to a gold core (see image). The size and numbers of iron oxide domains can be adjusted flexibly by changing the proportion of the starting materials and the reaction time.","lang":"eng"}],"intvolume":" 4","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1613-6829"],"issn":["1613-6810"]},"issue":"10","volume":4},{"article_processing_charge":"No","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"publist_id":"7302","department":[{"_id":"NiBa"}],"title":"Identity and coalescence in structured populations: A commentary on 'Inbreeding coefficients and coalescence times' by Montgomery Slatkin","citation":{"chicago":"Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.” Genetics Research. Cambridge University Press, 2008. https://doi.org/10.1017/S0016672308009683.","ista":"Barton NH. 2008. Identity and coalescence in structured populations: A commentary on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin. Genetics Research. 89(5–6), 475–477.","mla":"Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.” Genetics Research, vol. 89, no. 5–6, Cambridge University Press, 2008, pp. 475–77, doi:10.1017/S0016672308009683.","ama":"Barton NH. Identity and coalescence in structured populations: A commentary on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. Genetics Research. 2008;89(5-6):475-477. doi:10.1017/S0016672308009683","apa":"Barton, N. H. (2008). Identity and coalescence in structured populations: A commentary on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. Genetics Research. Cambridge University Press. https://doi.org/10.1017/S0016672308009683","ieee":"N. H. Barton, “Identity and coalescence in structured populations: A commentary on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin,” Genetics Research, vol. 89, no. 5–6. Cambridge University Press, pp. 475–477, 2008.","short":"N.H. Barton, Genetics Research 89 (2008) 475–477."},"date_updated":"2024-02-14T09:51:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"517","page":"475 - 477","date_created":"2018-12-11T11:46:55Z","date_published":"2008-10-29T00:00:00Z","doi":"10.1017/S0016672308009683","issue":"5-6","volume":89,"publication_status":"published","year":"2008","publication":"Genetics Research","language":[{"iso":"eng"}],"day":"29","publisher":"Cambridge University Press","scopus_import":"1","quality_controlled":"1","intvolume":" 89","month":"10","oa_version":"None"},{"abstract":[{"lang":"eng","text":"We explore the rich internal structure of Cs2 Feshbach molecules. Pure ultracold molecular samples are prepared in a CO2 -laser trap, and a multitude of weakly bound states is populated by elaborate magnetic-field ramping techniques. Our methods use different Feshbach resonances as input ports and various internal level crossings for controlled state transfer. We populate higher partial-wave states of up to eight units of rotational angular momentum (l -wave states). We investigate the molecular structure by measurements of the magnetic moments for various states. Avoided level crossings between different molecular states are characterized through the changes in magnetic moment and by a Landau-Zener tunneling method. Based on microwave spectroscopy, we present a precise measurement of the magnetic-field-dependent binding energy of the weakly bound s -wave state that is responsible for the large background scattering length of Cs. This state is of particular interest because of its quantum-halo character."}],"oa_version":"None","acknowledgement":"The authors thank E. Tiesinga, P. Julienne, and C. Williams for providing invaluable theoretical input and J. Hutson and A. Simoni for helpful discussions. The authors acknowledge support by the Austrian Science Fund (FWF) within SFB 15 (project part 16) and by the European Union within the Cold Molecules TMR Network under Contract No. HPRN-CT-2002-00290. One of the authors (M.M.) acknowledges support within the Ph.D. program DOC of the Austrian Academy of Sciences, and two of the authors (F.F., C.C.) acknowledge support within the Lise Meitner program of the FWF. One of the authors (S.K.) is supported by the European Community, Marie Curie Intra-European program.","publisher":"American Physical Society","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/0706.1041"}],"month":"10","intvolume":" 76","year":"2007","publication_status":"published","day":"25","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","language":[{"iso":"eng"}],"volume":76,"issue":"4","doi":"10.1103/PhysRevA.76.042514","date_published":"2007-10-25T00:00:00Z","date_created":"2018-12-11T11:49:48Z","_id":"1035","type":"journal_article","status":"public","citation":{"chicago":"Mark, Michael, Francesca Ferlaino, Steven Knoop, Johann G Danzl, Tobias Kraemer, Cheng Chin, Hanns Nägerl, and Rudolf Grimm. “Spectroscopy of Ultracold Trapped Cesium Feshbach Molecules.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2007. https://doi.org/10.1103/PhysRevA.76.042514.","ista":"Mark M, Ferlaino F, Knoop S, Danzl JG, Kraemer T, Chin C, Nägerl H, Grimm R. 2007. Spectroscopy of ultracold trapped cesium Feshbach molecules. Physical Review A - Atomic, Molecular, and Optical Physics. 76(4).","mla":"Mark, Michael, et al. “Spectroscopy of Ultracold Trapped Cesium Feshbach Molecules.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 76, no. 4, American Physical Society, 2007, doi:10.1103/PhysRevA.76.042514.","apa":"Mark, M., Ferlaino, F., Knoop, S., Danzl, J. G., Kraemer, T., Chin, C., … Grimm, R. (2007). Spectroscopy of ultracold trapped cesium Feshbach molecules. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.76.042514","ama":"Mark M, Ferlaino F, Knoop S, et al. Spectroscopy of ultracold trapped cesium Feshbach molecules. Physical Review A - Atomic, Molecular, and Optical Physics. 2007;76(4). doi:10.1103/PhysRevA.76.042514","ieee":"M. Mark et al., “Spectroscopy of ultracold trapped cesium Feshbach molecules,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 76, no. 4. American Physical Society, 2007.","short":"M. Mark, F. Ferlaino, S. Knoop, J.G. Danzl, T. Kraemer, C. Chin, H. Nägerl, R. Grimm, Physical Review A - Atomic, Molecular, and Optical Physics 76 (2007)."},"date_updated":"2021-01-12T06:47:49Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6354","author":[{"first_name":"Michael","last_name":"Mark","full_name":"Mark, Michael"},{"first_name":"Francesca","last_name":"Ferlaino","full_name":"Ferlaino, Francesca"},{"first_name":"Steven","full_name":"Knoop, Steven","last_name":"Knoop"},{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","last_name":"Kraemer","full_name":"Kraemer, Tobias"},{"first_name":"Cheng","last_name":"Chin","full_name":"Chin, Cheng"},{"first_name":"Hanns","last_name":"Nägerl","full_name":"Nägerl, Hanns"},{"first_name":"Rudolf","last_name":"Grimm","full_name":"Grimm, Rudolf"}],"article_processing_charge":"No","title":"Spectroscopy of ultracold trapped cesium Feshbach molecules"},{"doi":"10.1038/sj.embor.7400889","date_published":"2007-01-19T00:00:00Z","date_created":"2022-04-07T07:56:13Z","page":"165-172","day":"19","publication":"EMBO reports","year":"2007","publisher":"EMBO","quality_controlled":"1","oa":1,"title":"MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly","author":[{"first_name":"Cerstin","full_name":"Franz, Cerstin","last_name":"Franz"},{"first_name":"Rudolf","last_name":"Walczak","full_name":"Walczak, Rudolf"},{"first_name":"Sevil","last_name":"Yavuz","full_name":"Yavuz, Sevil"},{"first_name":"Rachel","last_name":"Santarella","full_name":"Santarella, Rachel"},{"last_name":"Gentzel","full_name":"Gentzel, Marc","first_name":"Marc"},{"last_name":"Askjaer","full_name":"Askjaer, Peter","first_name":"Peter"},{"last_name":"Galy","full_name":"Galy, Vincent","first_name":"Vincent"},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"},{"first_name":"Iain W","last_name":"Mattaj","full_name":"Mattaj, Iain W"},{"last_name":"Antonin","full_name":"Antonin, Wolfram","first_name":"Wolfram"}],"external_id":{"pmid":["17235358"]},"article_processing_charge":"No","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"ista":"Franz C, Walczak R, Yavuz S, Santarella R, Gentzel M, Askjaer P, Galy V, Hetzer M, Mattaj IW, Antonin W. 2007. MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly. EMBO reports. 8(2), 165–172.","chicago":"Franz, Cerstin, Rudolf Walczak, Sevil Yavuz, Rachel Santarella, Marc Gentzel, Peter Askjaer, Vincent Galy, Martin Hetzer, Iain W Mattaj, and Wolfram Antonin. “MEL‐28/ELYS Is Required for the Recruitment of Nucleoporins to Chromatin and Postmitotic Nuclear Pore Complex Assembly.” EMBO Reports. EMBO, 2007. https://doi.org/10.1038/sj.embor.7400889.","ama":"Franz C, Walczak R, Yavuz S, et al. MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly. EMBO reports. 2007;8(2):165-172. doi:10.1038/sj.embor.7400889","apa":"Franz, C., Walczak, R., Yavuz, S., Santarella, R., Gentzel, M., Askjaer, P., … Antonin, W. (2007). MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly. EMBO Reports. EMBO. https://doi.org/10.1038/sj.embor.7400889","ieee":"C. Franz et al., “MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly,” EMBO reports, vol. 8, no. 2. EMBO, pp. 165–172, 2007.","short":"C. Franz, R. Walczak, S. Yavuz, R. Santarella, M. Gentzel, P. Askjaer, V. Galy, M. Hetzer, I.W. Mattaj, W. Antonin, EMBO Reports 8 (2007) 165–172.","mla":"Franz, Cerstin, et al. “MEL‐28/ELYS Is Required for the Recruitment of Nucleoporins to Chromatin and Postmitotic Nuclear Pore Complex Assembly.” EMBO Reports, vol. 8, no. 2, EMBO, 2007, pp. 165–72, doi:10.1038/sj.embor.7400889."},"volume":8,"issue":"2","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"publication_status":"published","month":"01","intvolume":" 8","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/sj.embor.7400889"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"The metazoan nuclear envelope (NE) breaks down and re-forms during each cell cycle. Nuclear pore complexes (NPCs), which allow nucleocytoplasmic transport during interphase, assemble into the re-forming NE at the end of mitosis. Using in vitro NE assembly, we show that the vertebrate homologue of MEL-28 (maternal effect lethal), a recently discovered NE component in Caenorhabditis elegans, functions in postmitotic NPC assembly. MEL-28 interacts with the Nup107–160 complex (Nup for nucleoporin), an important building block of the NPC, and is essential for the recruitment of the Nup107–160 complex to chromatin. We suggest that MEL-28 acts as a seeding point for NPC assembly.","lang":"eng"}],"extern":"1","date_updated":"2022-07-18T08:56:40Z","status":"public","keyword":["Genetics","Molecular Biology","Biochemistry"],"article_type":"original","type":"journal_article","_id":"11116"},{"publisher":"Springer Nature","quality_controlled":"1","date_created":"2022-04-07T07:56:04Z","doi":"10.1038/ncb1636","date_published":"2007-09-09T00:00:00Z","page":"1160-1166","publication":"Nature Cell Biology","day":"09","year":"2007","title":"Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum","external_id":{"pmid":["17828249"]},"article_processing_charge":"No","author":[{"first_name":"Daniel J.","full_name":"Anderson, Daniel J.","last_name":"Anderson"},{"last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"apa":"Anderson, D. J., & Hetzer, M. (2007). Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/ncb1636","ama":"Anderson DJ, Hetzer M. Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum. Nature Cell Biology. 2007;9(10):1160-1166. doi:10.1038/ncb1636","short":"D.J. Anderson, M. Hetzer, Nature Cell Biology 9 (2007) 1160–1166.","ieee":"D. J. Anderson and M. Hetzer, “Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum,” Nature Cell Biology, vol. 9, no. 10. Springer Nature, pp. 1160–1166, 2007.","mla":"Anderson, Daniel J., and Martin Hetzer. “Nuclear Envelope Formation by Chromatin-Mediated Reorganization of the Endoplasmic Reticulum.” Nature Cell Biology, vol. 9, no. 10, Springer Nature, 2007, pp. 1160–66, doi:10.1038/ncb1636.","ista":"Anderson DJ, Hetzer M. 2007. Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum. Nature Cell Biology. 9(10), 1160–1166.","chicago":"Anderson, Daniel J., and Martin Hetzer. “Nuclear Envelope Formation by Chromatin-Mediated Reorganization of the Endoplasmic Reticulum.” Nature Cell Biology. Springer Nature, 2007. https://doi.org/10.1038/ncb1636."},"intvolume":" 9","month":"09","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"text":"The formation of the nuclear envelope (NE) around chromatin is a major membrane-remodelling event that occurs during cell division of metazoa. It is unclear whether the nuclear membrane reforms by the fusion of NE fragments or if it re-emerges from an intact tubular network of the endoplasmic reticulum (ER). Here, we show that NE formation and expansion requires a tubular ER network and occurs efficiently in the presence of the membrane fusion inhibitor GTPγS. Chromatin recruitment of membranes, which is initiated by tubule-end binding, followed by the formation, expansion and sealing of flat membrane sheets, is mediated by DNA-binding proteins residing in the ER. Thus, chromatin plays an active role in reshaping of the ER during NE formation.","lang":"eng"}],"volume":9,"issue":"10","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1476-4679"],"issn":["1465-7392"]},"keyword":["Cell Biology"],"status":"public","article_type":"original","type":"journal_article","_id":"11115","extern":"1","date_updated":"2022-07-18T08:56:38Z"},{"citation":{"ista":"Henzinger MH. 2007. Search technologies for the internet. Science. 317(5837), 468–471.","chicago":"Henzinger, Monika H. “Search Technologies for the Internet.” Science. American Association for the Advancement of Science, 2007. https://doi.org/10.1126/science.1126557.","ieee":"M. H. Henzinger, “Search technologies for the internet,” Science, vol. 317, no. 5837. American Association for the Advancement of Science, pp. 468–471, 2007.","short":"M.H. Henzinger, Science 317 (2007) 468–471.","apa":"Henzinger, M. H. (2007). Search technologies for the internet. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1126557","ama":"Henzinger MH. Search technologies for the internet. Science. 2007;317(5837):468-471. doi:10.1126/science.1126557","mla":"Henzinger, Monika H. “Search Technologies for the Internet.” Science, vol. 317, no. 5837, American Association for the Advancement of Science, 2007, pp. 468–71, doi:10.1126/science.1126557."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger"}],"external_id":{"pmid":["17656714"]},"article_processing_charge":"No","title":"Search technologies for the internet","year":"2007","day":"27","publication":"Science","page":"468-471","date_published":"2007-07-27T00:00:00Z","doi":"10.1126/science.1126557","date_created":"2022-08-17T07:30:07Z","quality_controlled":"1","publisher":"American Association for the Advancement of Science","date_updated":"2023-02-17T14:07:49Z","extern":"1","_id":"11884","article_type":"review","type":"journal_article","status":"public","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"5837","volume":317,"abstract":[{"lang":"eng","text":"About 20% of the world's population uses the Web, and a large majority thereof uses Web search engines to find information. As a result, many Web researchers are devoting much effort to improving the speed and capability of search technology."}],"pmid":1,"oa_version":"None","scopus_import":"1","month":"07","intvolume":" 317"},{"publisher":"Society for Industrial & Applied Mathematics","scopus_import":"1","quality_controlled":"1","month":"01","abstract":[{"text":"How much can smart combinatorial algorithms improve web search engines? To address this question we will describe three algorithms that have had a positive impact on web search engines: The PageRank algorithm, algorithms for finding near-duplicate web pages, and algorithms for index server loadbalancing.","lang":"eng"}],"oa_version":"None","page":"1022-1026","date_created":"2022-08-18T12:37:03Z","date_published":"2007-01-01T00:00:00Z","publication_status":"published","year":"2007","publication_identifier":{"isbn":["9780898716245"]},"publication":"18th Annual ACM-SIAM Symposium on Discrete Algorithms","language":[{"iso":"eng"}],"day":"01","conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2007-01-07","location":"New Orleans, LA, United States","end_date":"2007-01-09"},"type":"conference","status":"public","_id":"11924","article_processing_charge":"No","author":[{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"}],"title":"Combinatorial algorithms for web search engines: three success stories","citation":{"mla":"Henzinger, Monika H. “Combinatorial Algorithms for Web Search Engines: Three Success Stories.” 18th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial & Applied Mathematics, 2007, pp. 1022–26.","apa":"Henzinger, M. H. (2007). Combinatorial algorithms for web search engines: three success stories. In 18th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1022–1026). New Orleans, LA, United States: Society for Industrial & Applied Mathematics.","ama":"Henzinger MH. Combinatorial algorithms for web search engines: three success stories. In: 18th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial & Applied Mathematics; 2007:1022-1026.","short":"M.H. Henzinger, in:, 18th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial & Applied Mathematics, 2007, pp. 1022–1026.","ieee":"M. H. Henzinger, “Combinatorial algorithms for web search engines: three success stories,” in 18th Annual ACM-SIAM Symposium on Discrete Algorithms, New Orleans, LA, United States, 2007, pp. 1022–1026.","chicago":"Henzinger, Monika H. “Combinatorial Algorithms for Web Search Engines: Three Success Stories.” In 18th Annual ACM-SIAM Symposium on Discrete Algorithms, 1022–26. Society for Industrial & Applied Mathematics, 2007.","ista":"Henzinger MH. 2007. Combinatorial algorithms for web search engines: three success stories. 18th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1022–1026."},"date_updated":"2023-02-17T12:06:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Carr A, Serchest Y, Waitukaitis SR, Perreault J, Lonij V, Cronin A. 2007. Cover slip external cavity diode laser. Review of Scientific Instruments. 78(10), 106108.","chicago":"Carr, Adra, Yancey Serchest, Scott R Waitukaitis, John Perreault, Vincent Lonij, and Alexander Cronin. “Cover Slip External Cavity Diode Laser.” Review of Scientific Instruments. American Institute of Physics, 2007. https://doi.org/10.1063/1.2801006.","short":"A. Carr, Y. Serchest, S.R. Waitukaitis, J. Perreault, V. Lonij, A. Cronin, Review of Scientific Instruments 78 (2007).","ieee":"A. Carr, Y. Serchest, S. R. Waitukaitis, J. Perreault, V. Lonij, and A. Cronin, “Cover slip external cavity diode laser,” Review of Scientific Instruments, vol. 78, no. 10. American Institute of Physics, 2007.","apa":"Carr, A., Serchest, Y., Waitukaitis, S. R., Perreault, J., Lonij, V., & Cronin, A. (2007). Cover slip external cavity diode laser. Review of Scientific Instruments. American Institute of Physics. https://doi.org/10.1063/1.2801006","ama":"Carr A, Serchest Y, Waitukaitis SR, Perreault J, Lonij V, Cronin A. Cover slip external cavity diode laser. Review of Scientific Instruments. 2007;78(10). doi:10.1063/1.2801006","mla":"Carr, Adra, et al. “Cover Slip External Cavity Diode Laser.” Review of Scientific Instruments, vol. 78, no. 10, 106108, American Institute of Physics, 2007, doi:10.1063/1.2801006."},"title":"Cover slip external cavity diode laser","author":[{"full_name":"Carr, Adra","last_name":"Carr","first_name":"Adra"},{"full_name":"Serchest, Yancey","last_name":"Serchest","first_name":"Yancey"},{"last_name":"Waitukaitis","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"},{"first_name":"John","full_name":"Perreault, John","last_name":"Perreault"},{"first_name":"Vincent","last_name":"Lonij","full_name":"Lonij, Vincent"},{"first_name":"Alexander","full_name":"Cronin, Alexander","last_name":"Cronin"}],"publist_id":"7925","external_id":{"arxiv":["0708.0014"]},"article_number":"106108","day":"29","publication":"Review of Scientific Instruments","year":"2007","date_published":"2007-10-29T00:00:00Z","doi":"10.1063/1.2801006","date_created":"2018-12-11T11:44:46Z","acknowledgement":"National Science Foundation\r\nThis work was supported with NSF Grant No. PHY-0653623. We thank Dr. W. Bickel and Dr. J. Jones for diagnostic equipment, K. Guerin for assistance with mechanical drawings, and M. Parker of Rincon Research Inc. for optics components.","publisher":"American Institute of Physics","quality_controlled":"1","oa":1,"extern":"1","date_updated":"2021-01-12T06:49:35Z","_id":"128","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"10","volume":78,"oa_version":"Preprint","abstract":[{"text":"A 671 nm diode laser with a mode-hop-free tuning range of 40 GHz is described. This long tuning range is achieved by simultaneously ramping the external cavity length with the laser injection current. The laser output pointing remains fixed, independent of its frequency because of the cover slip cavity design. This system is simple, economical, robust, and easy to use for spectroscopy, as we demonstrate with lithium vapor and lithium atom beam experiments. ","lang":"eng"}],"month":"10","intvolume":" 78","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/0708.0014"}]},{"abstract":[{"text":"In flies, the large tangential cells of the lobula plate represent an important processing center for visual navigation based on optic flow. Although the visual response properties of these cells have been well studied in blowflies, information on their synaptic organization is mostly lacking. Here we study the distribution of presynaptic release and postsynaptic inhibitory sites in the same set of cells in Drosophila melanogaster. By making use of transgenic tools and immunohistochemistry, our results suggest that HS and VS cells of Drosophila express γ-aminobutyric acid (GABA) receptors in their dendritic region within the lobula plate, thus being postsynaptic to inhibitory input there. At their axon terminals in the protocerebrum, both cell types express synaptobrevin, suggesting the presence of presynaptic specializations there. HS- and VS-cell terminals additionally show evidence for postsynaptic GABAergic input, superimposed on this synaptic polarity. Our findings are in line with the general circuit for visual motion detection and receptive field properties as postulated from electrophysiological and optical recordings in blowflies, suggesting a similar functional organization of lobula plate tangential cells in the two species.","lang":"eng"}],"publisher":"Wiley-Blackwell","quality_controlled":0,"intvolume":" 502","month":"06","publication_status":"published","year":"2007","publication":"Journal of Comparative Neurology","day":"01","page":"598 - 610","date_created":"2018-12-11T11:51:13Z","issue":"4","doi":"10.1002/cne.21319","volume":502,"date_published":"2007-06-01T00:00:00Z","_id":"1297","type":"journal_article","status":"public","date_updated":"2021-01-12T06:49:42Z","citation":{"chicago":"Raghu, Shamprasad, Maximilian A Jösch, Alexander Borst, and Dierk Reiff. “Synaptic Organization of Lobula Plate Tangential Cells in Drosophila: γ-Aminobutyric Acid Receptors and Chemical Release Sites.” Journal of Comparative Neurology. Wiley-Blackwell, 2007. https://doi.org/10.1002/cne.21319.","ista":"Raghu S, Jösch MA, Borst A, Reiff D. 2007. Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites. Journal of Comparative Neurology. 502(4), 598–610.","mla":"Raghu, Shamprasad, et al. “Synaptic Organization of Lobula Plate Tangential Cells in Drosophila: γ-Aminobutyric Acid Receptors and Chemical Release Sites.” Journal of Comparative Neurology, vol. 502, no. 4, Wiley-Blackwell, 2007, pp. 598–610, doi:10.1002/cne.21319.","ieee":"S. Raghu, M. A. Jösch, A. Borst, and D. Reiff, “Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites,” Journal of Comparative Neurology, vol. 502, no. 4. Wiley-Blackwell, pp. 598–610, 2007.","short":"S. Raghu, M.A. Jösch, A. Borst, D. Reiff, Journal of Comparative Neurology 502 (2007) 598–610.","apa":"Raghu, S., Jösch, M. A., Borst, A., & Reiff, D. (2007). Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites. Journal of Comparative Neurology. Wiley-Blackwell. https://doi.org/10.1002/cne.21319","ama":"Raghu S, Jösch MA, Borst A, Reiff D. Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites. Journal of Comparative Neurology. 2007;502(4):598-610. doi:10.1002/cne.21319"},"extern":1,"author":[{"first_name":"Shamprasad","full_name":"Raghu, Shamprasad V","last_name":"Raghu"},{"last_name":"Jösch","full_name":"Maximilian Jösch","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander","full_name":"Borst, Alexander","last_name":"Borst"},{"first_name":"Dierk","full_name":"Reiff, Dierk F","last_name":"Reiff"}],"publist_id":"5974","title":"Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites"},{"year":"2007","publication":"Diophantine Geometry","day":"01","page":"93 - 100","date_created":"2018-12-11T11:44:59Z","date_published":"2007-01-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Edizioni della Normale","citation":{"chicago":"Browning, Timothy D, and Roger Heath Brown. “Simultaneous Equal Sums of Three Powers.” In Diophantine Geometry, edited by Umberto Zannier, 4:93–100. Edizioni della Normale, 2007.","ista":"Browning TD, Heath Brown R. 2007.Simultaneous equal sums of three powers. In: Diophantine Geometry. CRM Series, vol. 4, 93–100.","mla":"Browning, Timothy D., and Roger Heath Brown. “Simultaneous Equal Sums of Three Powers.” Diophantine Geometry, edited by Umberto Zannier, vol. 4, Edizioni della Normale, 2007, pp. 93–100.","apa":"Browning, T. D., & Heath Brown, R. (2007). Simultaneous equal sums of three powers. In U. Zannier (Ed.), Diophantine Geometry (Vol. 4, pp. 93–100). Edizioni della Normale.","ama":"Browning TD, Heath Brown R. Simultaneous equal sums of three powers. In: Zannier U, ed. Diophantine Geometry. Vol 4. Edizioni della Normale; 2007:93-100.","short":"T.D. Browning, R. Heath Brown, in:, U. Zannier (Ed.), Diophantine Geometry, Edizioni della Normale, 2007, pp. 93–100.","ieee":"T. D. Browning and R. Heath Brown, “Simultaneous equal sums of three powers,” in Diophantine Geometry, vol. 4, U. Zannier, Ed. Edizioni della Normale, 2007, pp. 93–100."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["0509152"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heath Brown","full_name":"Heath Brown, Roger","first_name":"Roger"}],"publist_id":"7754","title":"Simultaneous equal sums of three powers","editor":[{"last_name":"Zannier","full_name":"Zannier, Umberto","first_name":"Umberto"}],"publication_status":"published","language":[{"iso":"eng"}],"volume":4,"abstract":[{"lang":"eng","text":"This book contains research articles on Diophantine Geometry, written by participants of a research program held at the Ennio De Giorgi Mathematical Research Center in Pisa, Italy, during the period April – July 2005. The authors are eminent experts in the field. Several subfields of the main topic are presented; the volume thus is particularly useful to get a broad overview of recent research developments."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/math/0509152"}],"alternative_title":["CRM Series"],"intvolume":" 4","month":"01","date_updated":"2021-01-12T06:52:24Z","extern":"1","_id":"167","type":"book_chapter","status":"public"}]