[{"author":[{"first_name":"Seungtae","last_name":"Baek","full_name":"Baek, SeungTae"},{"first_name":"Géraldine","last_name":"Kerjan","full_name":"Kerjan, Géraldine"},{"last_name":"Bielas","full_name":"Bielas, Stephanie L","first_name":"Stephanie"},{"first_name":"Jieun","last_name":"Lee","full_name":"Lee, Jieun"},{"last_name":"Fenstermaker","full_name":"Fenstermaker, Ali G","first_name":"Ali"},{"orcid":"0000-0002-7673-7178","full_name":"Gaia Novarino","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gleeson, Joseph G","last_name":"Gleeson","first_name":"Joseph"}],"publist_id":"5322","title":"Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation","date_updated":"2021-01-12T06:53:13Z","citation":{"chicago":"Baek, Seungtae, Géraldine Kerjan, Stephanie Bielas, Jieun Lee, Ali Fenstermaker, Gaia Novarino, and Joseph Gleeson. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.036.","ista":"Baek S, Kerjan G, Bielas S, Lee J, Fenstermaker A, Novarino G, Gleeson J. 2014. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 82(6), 1255–1262.","mla":"Baek, Seungtae, et al. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron, vol. 82, no. 6, Elsevier, 2014, pp. 1255–62, doi:10.1016/j.neuron.2014.04.036.","apa":"Baek, S., Kerjan, G., Bielas, S., Lee, J., Fenstermaker, A., Novarino, G., & Gleeson, J. (2014). Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.036","ama":"Baek S, Kerjan G, Bielas S, et al. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 2014;82(6):1255-1262. doi:10.1016/j.neuron.2014.04.036","ieee":"S. Baek et al., “Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation,” Neuron, vol. 82, no. 6. Elsevier, pp. 1255–1262, 2014.","short":"S. Baek, G. Kerjan, S. Bielas, J. Lee, A. Fenstermaker, G. Novarino, J. Gleeson, Neuron 82 (2014) 1255–1262."},"extern":1,"type":"journal_article","status":"public","_id":"1791","page":"1255 - 1262","date_created":"2018-12-11T11:54:01Z","date_published":"2014-06-18T00:00:00Z","issue":"6","volume":82,"doi":"10.1016/j.neuron.2014.04.036","publication_status":"published","year":"2014","publication":"Neuron","day":"18","publisher":"Elsevier","quality_controlled":0,"intvolume":" 82","month":"06","abstract":[{"lang":"eng","text":"Acute gene inactivation using short hairpin RNA (shRNA, knockdown) in developing brain is a powerful technique to study genetic function; however, discrepancies between knockdown and knockout murine phenotypes have left unanswered questions. For example, doublecortin (Dcx) knockdown but not knockout shows a neocortical neuronal migration phenotype. Here we report that in utero electroporation of shRNA, but not siRNA or miRNA, to Dcx demonstrates a migration phenotype in Dcx knockouts akin to the effect in wild-type mice, suggestingshRNA-mediated off-target toxicity. This effect wasnot limited to Dcx, as it was observed in Dclk1 knockouts, as well as with a fraction of scrambled shRNAs, suggesting a sequence-dependent but not sequence-specific effect. Profiling RNAs from electroporated cells showed a defect in endogenous let7 miRNA levels, and disruption of let7 or Dicer recapitulated the migration defect. The results suggest that shRNA-mediated knockdown can produce untoward migration effects by altering endogenous miRNA pathways."}],"acknowledgement":"This work was supported by the National Institutes of Health R01NS41537. G.K. was supported by an EMBO Long Term Fellowship, S.L.B. by the A.P. Giannini Fellowship, and A.G.F. by the Brain Behavior Research Foundation"},{"citation":{"ista":"Baster P, Friml J. 2014.Auxin on the road navigated by cellular PIN polarity. In: Auxin and Its Role in Plant Development. , 143–170.","chicago":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” In Auxin and Its Role in Plant Development, edited by Eva Zažímalová, Jan Petrášek, and Eva Benková, 143–70. Springer, 2014. https://doi.org/10.1007/978-3-7091-1526-8_8.","apa":"Baster, P., & Friml, J. (2014). Auxin on the road navigated by cellular PIN polarity. In E. Zažímalová, J. Petrášek, & E. Benková (Eds.), Auxin and Its Role in Plant Development (pp. 143–170). Springer. https://doi.org/10.1007/978-3-7091-1526-8_8","ama":"Baster P, Friml J. Auxin on the road navigated by cellular PIN polarity. In: Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development. Springer; 2014:143-170. doi:10.1007/978-3-7091-1526-8_8","ieee":"P. Baster and J. Friml, “Auxin on the road navigated by cellular PIN polarity,” in Auxin and Its Role in Plant Development, E. Zažímalová, J. Petrášek, and E. Benková, Eds. Springer, 2014, pp. 143–170.","short":"P. Baster, J. Friml, in:, E. Zažímalová, J. Petrášek, E. Benková (Eds.), Auxin and Its Role in Plant Development, Springer, 2014, pp. 143–170.","mla":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” Auxin and Its Role in Plant Development, edited by Eva Zažímalová et al., Springer, 2014, pp. 143–70, doi:10.1007/978-3-7091-1526-8_8."},"date_updated":"2021-01-12T06:53:19Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3028BD74-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","last_name":"Baster","full_name":"Baster, Pawel"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"publist_id":"5304","editor":[{"first_name":"Eva","full_name":"Zažímalová, Eva","last_name":"Zažímalová"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"title":"Auxin on the road navigated by cellular PIN polarity","department":[{"_id":"JiFr"}],"_id":"1806","type":"book_chapter","status":"public","publication_status":"published","year":"2014","day":"01","publication":"Auxin and Its Role in Plant Development","language":[{"iso":"eng"}],"page":"143 - 170","doi":"10.1007/978-3-7091-1526-8_8","date_published":"2014-04-01T00:00:00Z","date_created":"2018-12-11T11:54:07Z","abstract":[{"lang":"eng","text":"The generation of asymmetry, at both cellular and tissue level, is one of the most essential capabilities of all eukaryotic organisms. It mediates basically all multicellular development ranging from embryogenesis and de novo organ formation till responses to various environmental stimuli. In plants, the awe-inspiring number of such processes is regulated by phytohormone auxin and its directional, cell-to-cell transport. The mediators of this transport, PIN auxin transporters, are asymmetrically localized at the plasma membrane, and this polar localization determines the directionality of intercellular auxin flow. Thus, auxin transport contributes crucially to the generation of local auxin gradients or maxima, which instruct given cell to change its developmental program. Here, we introduce and discuss the molecular components and cellular mechanisms regulating the generation and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity in plants."}],"oa_version":"None","publisher":"Springer","quality_controlled":"1","scopus_import":1,"month":"04"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Huber, Stefan, et al. “Topology-Preserving Watermarking of Vector Graphics.” International Journal of Computational Geometry and Applications, vol. 24, no. 1, World Scientific Publishing, 2014, pp. 61–86, doi:10.1142/S0218195914500034.","ama":"Huber S, Held M, Meerwald P, Kwitt R. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 2014;24(1):61-86. doi:10.1142/S0218195914500034","apa":"Huber, S., Held, M., Meerwald, P., & Kwitt, R. (2014). Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195914500034","short":"S. Huber, M. Held, P. Meerwald, R. Kwitt, International Journal of Computational Geometry and Applications 24 (2014) 61–86.","ieee":"S. Huber, M. Held, P. Meerwald, and R. Kwitt, “Topology-preserving watermarking of vector graphics,” International Journal of Computational Geometry and Applications, vol. 24, no. 1. World Scientific Publishing, pp. 61–86, 2014.","chicago":"Huber, Stefan, Martin Held, Peter Meerwald, and Roland Kwitt. “Topology-Preserving Watermarking of Vector Graphics.” International Journal of Computational Geometry and Applications. World Scientific Publishing, 2014. https://doi.org/10.1142/S0218195914500034.","ista":"Huber S, Held M, Meerwald P, Kwitt R. 2014. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 24(1), 61–86."},"title":"Topology-preserving watermarking of vector graphics","publist_id":"5290","author":[{"first_name":"Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan","last_name":"Huber"},{"full_name":"Held, Martin","last_name":"Held","first_name":"Martin"},{"first_name":"Peter","full_name":"Meerwald, Peter","last_name":"Meerwald"},{"last_name":"Kwitt","full_name":"Kwitt, Roland","first_name":"Roland"}],"acknowledgement":"Work by Martin Held and Stefan Huber was supported by Austrian Science Fund (FWF): L367-N15 and P25816-N15.","oa":1,"publisher":"World Scientific Publishing","quality_controlled":"1","publication":"International Journal of Computational Geometry and Applications","day":"16","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:54:10Z","date_published":"2014-03-16T00:00:00Z","doi":"10.1142/S0218195914500034","page":"61 - 86","_id":"1816","pubrep_id":"443","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["000"],"date_updated":"2021-01-12T06:53:23Z","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:45:17Z","oa_version":"Published Version","abstract":[{"text":"Watermarking techniques for vector graphics dislocate vertices in order to embed imperceptible, yet detectable, statistical features into the input data. The embedding process may result in a change of the topology of the input data, e.g., by introducing self-intersections, which is undesirable or even disastrous for many applications. In this paper we present a watermarking framework for two-dimensional vector graphics that employs conventional watermarking techniques but still provides the guarantee that the topology of the input data is preserved. The geometric part of this framework computes so-called maximum perturbation regions (MPR) of vertices. We propose two efficient algorithms to compute MPRs based on Voronoi diagrams and constrained triangulations. Furthermore, we present two algorithms to conditionally correct the watermarked data in order to increase the watermark embedding capacity and still guarantee topological correctness. While we focus on the watermarking of input formed by straight-line segments, one of our approaches can also be extended to circular arcs. We conclude the paper by demonstrating and analyzing the applicability of our framework in conjunction with two well-known watermarking techniques.","lang":"eng"}],"intvolume":" 24","month":"03","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-443-v1+1_S0218195914500034.pdf","date_created":"2018-12-12T10:08:43Z","creator":"system","file_size":991734,"date_updated":"2020-07-14T12:45:17Z","checksum":"be45c133ab4d43351260e21beaa8f4b1","file_id":"4704","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","volume":24,"issue":"1"},{"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5172","checksum":"ed0efc93c10f1341155f0316af617b82","file_size":269171,"date_updated":"2020-07-14T12:45:17Z","creator":"system","file_name":"IST-2016-532-v1+1_J._Mathematical_Phys._2014_Seiringer.pdf","date_created":"2018-12-12T10:15:49Z"}],"publication_status":"published","issue":"7","volume":55,"oa_version":"Submitted Version","abstract":[{"text":"We review recent progress towards a rigorous understanding of the Bogoliubov approximation for bosonic quantum many-body systems. We focus, in particular, on the excitation spectrum of a Bose gas in the mean-field (Hartree) limit. A list of open problems will be discussed at the end.","lang":"eng"}],"intvolume":" 55","month":"06","scopus_import":1,"ddc":["510","530"],"date_updated":"2021-01-12T06:53:25Z","file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"RoSe"}],"_id":"1821","pubrep_id":"532","status":"public","type":"journal_article","publication":"Journal of Mathematical Physics","day":"26","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:54:11Z","date_published":"2014-06-26T00:00:00Z","doi":"10.1063/1.4881536","oa":1,"publisher":"American Institute of Physics","quality_controlled":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Seiringer R. 2014. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 55(7), 1.4881536.","chicago":"Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4881536.","ieee":"R. Seiringer, “Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation,” Journal of Mathematical Physics, vol. 55, no. 7. American Institute of Physics, 2014.","short":"R. Seiringer, Journal of Mathematical Physics 55 (2014).","ama":"Seiringer R. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4881536","apa":"Seiringer, R. (2014). Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4881536","mla":"Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics, vol. 55, no. 7, 1.4881536, American Institute of Physics, 2014, doi:10.1063/1.4881536."},"title":"Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation","publist_id":"5285","author":[{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"article_number":"1.4881536","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}]},{"status":"public","type":"journal_article","article_number":"075101","_id":"1822","department":[{"_id":"RoSe"}],"title":"Introduction","publist_id":"5284","author":[{"last_name":"Jakšić","full_name":"Jakšić, Vojkan","first_name":"Vojkan"},{"last_name":"Pillet","full_name":"Pillet, Claude","first_name":"Claude"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Jakšić, Vojkan, et al. “Introduction.” Journal of Mathematical Physics, vol. 55, no. 7, 075101, American Institute of Physics, 2014, doi:10.1063/1.4884877.","apa":"Jakšić, V., Pillet, C., & Seiringer, R. (2014). Introduction. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4884877","ama":"Jakšić V, Pillet C, Seiringer R. Introduction. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4884877","ieee":"V. Jakšić, C. Pillet, and R. Seiringer, “Introduction,” Journal of Mathematical Physics, vol. 55, no. 7. American Institute of Physics, 2014.","short":"V. Jakšić, C. Pillet, R. Seiringer, Journal of Mathematical Physics 55 (2014).","chicago":"Jakšić, Vojkan, Claude Pillet, and Robert Seiringer. “Introduction.” Journal of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4884877.","ista":"Jakšić V, Pillet C, Seiringer R. 2014. Introduction. Journal of Mathematical Physics. 55(7), 075101."},"date_updated":"2021-01-12T06:53:25Z","month":"07","intvolume":" 55","publisher":"American Institute of Physics","quality_controlled":"1","scopus_import":1,"oa_version":"None","date_published":"2014-07-01T00:00:00Z","issue":"7","doi":"10.1063/1.4884877","volume":55,"date_created":"2018-12-11T11:54:12Z","day":"01","language":[{"iso":"eng"}],"publication":"Journal of Mathematical Physics","year":"2014","publication_status":"published"},{"citation":{"mla":"Muelling, Katharina, et al. “Movement Templates for Learning of Hitting and Batting.” Learning Motor Skills, edited by Jens Kober and Jan Peters, vol. 97, Springer, 2014, pp. 69–82, doi:10.1007/978-3-319-03194-1_3.","short":"K. Muelling, O. Kroemer, C. Lampert, B. Schölkopf, in:, J. Kober, J. Peters (Eds.), Learning Motor Skills, Springer, 2014, pp. 69–82.","ieee":"K. Muelling, O. Kroemer, C. Lampert, and B. Schölkopf, “Movement templates for learning of hitting and batting,” in Learning Motor Skills, vol. 97, J. Kober and J. Peters, Eds. Springer, 2014, pp. 69–82.","apa":"Muelling, K., Kroemer, O., Lampert, C., & Schölkopf, B. (2014). Movement templates for learning of hitting and batting. In J. Kober & J. Peters (Eds.), Learning Motor Skills (Vol. 97, pp. 69–82). Springer. https://doi.org/10.1007/978-3-319-03194-1_3","ama":"Muelling K, Kroemer O, Lampert C, Schölkopf B. Movement templates for learning of hitting and batting. In: Kober J, Peters J, eds. Learning Motor Skills. Vol 97. From Algorithms to Robot Experiments. Springer; 2014:69-82. doi:10.1007/978-3-319-03194-1_3","chicago":"Muelling, Katharina, Oliver Kroemer, Christoph Lampert, and Bernhard Schölkopf. “Movement Templates for Learning of Hitting and Batting.” In Learning Motor Skills, edited by Jens Kober and Jan Peters, 97:69–82. From Algorithms to Robot Experiments. Springer, 2014. https://doi.org/10.1007/978-3-319-03194-1_3.","ista":"Muelling K, Kroemer O, Lampert C, Schölkopf B. 2014.Movement templates for learning of hitting and batting. In: Learning Motor Skills. Springer Tracts in Advanced Robotics, vol. 97, 69–82."},"date_updated":"2021-01-12T06:53:28Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5274","author":[{"first_name":"Katharina","last_name":"Muelling","full_name":"Muelling, Katharina"},{"last_name":"Kroemer","full_name":"Kroemer, Oliver","first_name":"Oliver"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"}],"title":"Movement templates for learning of hitting and batting","editor":[{"first_name":"Jens","full_name":"Kober, Jens","last_name":"Kober"},{"last_name":"Peters","full_name":"Peters, Jan","first_name":"Jan"}],"department":[{"_id":"ChLa"}],"_id":"1829","series_title":"From Algorithms to Robot Experiments","type":"book_chapter","status":"public","year":"2014","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Learning Motor Skills","page":"69 - 82","date_published":"2014-01-01T00:00:00Z","doi":"10.1007/978-3-319-03194-1_3","volume":97,"date_created":"2018-12-11T11:54:14Z","abstract":[{"text":"Hitting and batting tasks, such as tennis forehands, ping-pong strokes, or baseball batting, depend on predictions where the ball can be intercepted and how it can properly be returned to the opponent. These predictions get more accurate over time, hence the behaviors need to be continuously modified. As a result, movement templates with a learned global shape need to be adapted during the execution so that the racket reaches a target position and velocity that will return the ball over to the other side of the net or court. It requires altering learned movements to hit a varying target with the necessary velocity at a specific instant in time. Such a task cannot be incorporated straightforwardly in most movement representations suitable for learning. For example, the standard formulation of the dynamical system based motor primitives (introduced by Ijspeert et al (2002b)) does not satisfy this property despite their flexibility which has allowed learning tasks ranging from locomotion to kendama. In order to fulfill this requirement, we reformulate the Ijspeert framework to incorporate the possibility of specifying a desired hitting point and a desired hitting velocity while maintaining all advantages of the original formulation.We show that the proposed movement template formulation works well in two scenarios, i.e., for hitting a ball on a string with a table tennis racket at a specified velocity and for returning balls launched by a ball gun successfully over the net using forehand movements.","lang":"eng"}],"oa_version":"None","quality_controlled":"1","alternative_title":["Springer Tracts in Advanced Robotics"],"publisher":"Springer","scopus_import":1,"month":"01","intvolume":" 97"},{"quality_controlled":"1","publisher":"Oxford University Press","oa":1,"has_accepted_license":"1","year":"2014","day":"12","publication":"Molecular Biology and Evolution","page":"440 - 455","doi":"10.1093/molbev/msu312","date_published":"2014-11-12T00:00:00Z","date_created":"2018-12-11T11:54:19Z","citation":{"ieee":"V. Risso et al., “Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press, pp. 440–455, 2014.","short":"V. Risso, F. Manssour Triedo, A. Delgado Delgado, R. Arco, A. Barroso Deljesús, Á. Inglés Prieto, R. Godoy Ruiz, J. Gavira, E. Gaucher, B. Ibarra Molero, J. Sánchez Ruiz, Molecular Biology and Evolution 32 (2014) 440–455.","apa":"Risso, V., Manssour Triedo, F., Delgado Delgado, A., Arco, R., Barroso Deljesús, A., Inglés Prieto, Á., … Sánchez Ruiz, J. (2014). Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu312","ama":"Risso V, Manssour Triedo F, Delgado Delgado A, et al. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 2014;32(2):440-455. doi:10.1093/molbev/msu312","mla":"Risso, Valeria, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2014, pp. 440–55, doi:10.1093/molbev/msu312.","ista":"Risso V, Manssour Triedo F, Delgado Delgado A, Arco R, Barroso Deljesús A, Inglés Prieto Á, Godoy Ruiz R, Gavira J, Gaucher E, Ibarra Molero B, Sánchez Ruiz J. 2014. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 32(2), 440–455.","chicago":"Risso, Valeria, Fadia Manssour Triedo, Asuncion Delgado Delgado, Rocio Arco, Alicia Barroso Deljesús, Álvaro Inglés Prieto, Raquel Godoy Ruiz, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu312."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Risso, Valeria","last_name":"Risso","first_name":"Valeria"},{"last_name":"Manssour Triedo","full_name":"Manssour Triedo, Fadia","first_name":"Fadia"},{"first_name":"Asuncion","full_name":"Delgado Delgado, Asuncion","last_name":"Delgado Delgado"},{"first_name":"Rocio","full_name":"Arco, Rocio","last_name":"Arco"},{"first_name":"Alicia","last_name":"Barroso Deljesús","full_name":"Barroso Deljesús, Alicia"},{"first_name":"Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","last_name":"Inglés Prieto","full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571"},{"full_name":"Godoy Ruiz, Raquel","last_name":"Godoy Ruiz","first_name":"Raquel"},{"first_name":"Josè","full_name":"Gavira, Josè","last_name":"Gavira"},{"first_name":"Eric","last_name":"Gaucher","full_name":"Gaucher, Eric"},{"first_name":"Beatriz","last_name":"Ibarra Molero","full_name":"Ibarra Molero, Beatriz"},{"full_name":"Sánchez Ruiz, Jose","last_name":"Sánchez Ruiz","first_name":"Jose"}],"publist_id":"5257","title":"Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history","abstract":[{"lang":"eng","text":"Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations."}],"oa_version":"Published Version","scopus_import":1,"month":"11","intvolume":" 32","publication_status":"published","file":[{"checksum":"06215318e66be8f3e0c33abb07e9d3da","file_id":"5247","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:16:56Z","file_name":"IST-2016-430-v1+1_Mol_Biol_Evol-2015-Risso-440-55.pdf","creator":"system","date_updated":"2020-07-14T12:45:19Z","file_size":1545246}],"language":[{"iso":"eng"}],"volume":32,"issue":"2","license":"https://creativecommons.org/licenses/by-nc/4.0/","_id":"1844","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","pubrep_id":"430","date_updated":"2021-01-12T06:53:34Z","ddc":["571"],"department":[{"_id":"HaJa"}],"file_date_updated":"2020-07-14T12:45:19Z"},{"_id":"1842","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Cibulka J, Gao P, Krcál M, Valla T, Valtr P. 2014. On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. 53(1), 64–79.","chicago":"Cibulka, Josef, Pu Gao, Marek Krcál, Tomáš Valla, and Pavel Valtr. “On the Geometric Ramsey Number of Outerplanar Graphs.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-014-9646-x.","ama":"Cibulka J, Gao P, Krcál M, Valla T, Valtr P. On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. 2014;53(1):64-79. doi:10.1007/s00454-014-9646-x","apa":"Cibulka, J., Gao, P., Krcál, M., Valla, T., & Valtr, P. (2014). On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-014-9646-x","ieee":"J. Cibulka, P. Gao, M. Krcál, T. Valla, and P. Valtr, “On the geometric ramsey number of outerplanar graphs,” Discrete & Computational Geometry, vol. 53, no. 1. Springer, pp. 64–79, 2014.","short":"J. Cibulka, P. Gao, M. Krcál, T. Valla, P. Valtr, Discrete & Computational Geometry 53 (2014) 64–79.","mla":"Cibulka, Josef, et al. “On the Geometric Ramsey Number of Outerplanar Graphs.” Discrete & Computational Geometry, vol. 53, no. 1, Springer, 2014, pp. 64–79, doi:10.1007/s00454-014-9646-x."},"date_updated":"2021-01-12T06:53:33Z","title":"On the geometric ramsey number of outerplanar graphs","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"publist_id":"5260","author":[{"first_name":"Josef","full_name":"Cibulka, Josef","last_name":"Cibulka"},{"last_name":"Gao","full_name":"Gao, Pu","first_name":"Pu"},{"last_name":"Krcál","full_name":"Krcál, Marek","first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Valla","full_name":"Valla, Tomáš","first_name":"Tomáš"},{"full_name":"Valtr, Pavel","last_name":"Valtr","first_name":"Pavel"}],"oa_version":"Submitted Version","acknowledgement":"Marek Krčál was supported by the ERC Advanced Grant No. 267165.","abstract":[{"text":"We prove polynomial upper bounds of geometric Ramsey numbers of pathwidth-2 outerplanar triangulations in both convex and general cases. We also prove that the geometric Ramsey numbers of the ladder graph on 2n vertices are bounded by O(n3) and O(n10), in the convex and general case, respectively. We then apply similar methods to prove an (Formula presented.) upper bound on the Ramsey number of a path with n ordered vertices.","lang":"eng"}],"month":"11","intvolume":" 53","scopus_import":1,"publisher":"Springer","main_file_link":[{"url":"http://arxiv.org/abs/1310.7004","open_access":"1"}],"oa":1,"day":"14","publication":"Discrete & Computational Geometry","language":[{"iso":"eng"}],"publication_status":"published","year":"2014","issue":"1","volume":53,"doi":"10.1007/s00454-014-9646-x","date_published":"2014-11-14T00:00:00Z","date_created":"2018-12-11T11:54:18Z","page":"64 - 79"},{"title":"Partial shape matching using transformation parameter similarity","publist_id":"5246","author":[{"first_name":"Paul","full_name":"Guerrero, Paul","last_name":"Guerrero"},{"last_name":"Auzinger","orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","full_name":"Wimmer, Michael","last_name":"Wimmer"},{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Jeschke","full_name":"Jeschke, Stefan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Guerrero, Paul, Thomas Auzinger, Michael Wimmer, and Stefan Jeschke. “Partial Shape Matching Using Transformation Parameter Similarity.” Computer Graphics Forum. Wiley, 2014. https://doi.org/10.1111/cgf.12509.","ista":"Guerrero P, Auzinger T, Wimmer M, Jeschke S. 2014. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 34(1), 239–252.","mla":"Guerrero, Paul, et al. “Partial Shape Matching Using Transformation Parameter Similarity.” Computer Graphics Forum, vol. 34, no. 1, Wiley, 2014, pp. 239–52, doi:10.1111/cgf.12509.","apa":"Guerrero, P., Auzinger, T., Wimmer, M., & Jeschke, S. (2014). Partial shape matching using transformation parameter similarity. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.12509","ama":"Guerrero P, Auzinger T, Wimmer M, Jeschke S. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 2014;34(1):239-252. doi:10.1111/cgf.12509","short":"P. Guerrero, T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum 34 (2014) 239–252.","ieee":"P. Guerrero, T. Auzinger, M. Wimmer, and S. Jeschke, “Partial shape matching using transformation parameter similarity,” Computer Graphics Forum, vol. 34, no. 1. Wiley, pp. 239–252, 2014."},"oa":1,"publisher":"Wiley","quality_controlled":"1","date_created":"2018-12-11T11:54:22Z","doi":"10.1111/cgf.12509","date_published":"2014-11-05T00:00:00Z","page":"239 - 252","publication":"Computer Graphics Forum","day":"05","year":"2014","has_accepted_license":"1","pubrep_id":"574","status":"public","type":"journal_article","_id":"1854","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"ChWo"}],"ddc":["000"],"date_updated":"2021-01-12T06:53:38Z","intvolume":" 34","month":"11","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching. In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching."}],"volume":34,"issue":"1","language":[{"iso":"eng"}],"file":[{"file_id":"5182","checksum":"91946bfc509c77f5fd3151a3ff2b2c8f","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-574-v1+1_Guerrero-2014-TPS-paper.pdf","date_created":"2018-12-12T10:15:58Z","creator":"system","file_size":24817484,"date_updated":"2020-07-14T12:45:19Z"}],"publication_status":"published"},{"author":[{"first_name":"Massimiliano","full_name":"Sassi, Massimiliano","last_name":"Sassi"},{"first_name":"Olivier","full_name":"Ali, Olivier","last_name":"Ali"},{"first_name":"Frédéric","last_name":"Boudon","full_name":"Boudon, Frédéric"},{"full_name":"Cloarec, Gladys","last_name":"Cloarec","first_name":"Gladys"},{"first_name":"Ursula","last_name":"Abad","full_name":"Abad, Ursula"},{"full_name":"Cellier, Coralie","last_name":"Cellier","first_name":"Coralie"},{"first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Xu","last_name":"Chen"},{"full_name":"Gilles, Benjamin","last_name":"Gilles","first_name":"Benjamin"},{"first_name":"Pascale","full_name":"Milani, Pascale","last_name":"Milani"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Teva","full_name":"Vernoux, Teva","last_name":"Vernoux"},{"first_name":"Christophe","last_name":"Godin","full_name":"Godin, Christophe"},{"last_name":"Hamant","full_name":"Hamant, Olivier","first_name":"Olivier"},{"full_name":"Traas, Jan","last_name":"Traas","first_name":"Jan"}],"publist_id":"5248","title":"An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis","citation":{"mla":"Sassi, Massimiliano, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology, vol. 24, no. 19, Cell Press, 2014, pp. 2335–42, doi:10.1016/j.cub.2014.08.036.","apa":"Sassi, M., Ali, O., Boudon, F., Cloarec, G., Abad, U., Cellier, C., … Traas, J. (2014). An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.08.036","ama":"Sassi M, Ali O, Boudon F, et al. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. 2014;24(19):2335-2342. doi:10.1016/j.cub.2014.08.036","ieee":"M. Sassi et al., “An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis,” Current Biology, vol. 24, no. 19. Cell Press, pp. 2335–2342, 2014.","short":"M. Sassi, O. Ali, F. Boudon, G. Cloarec, U. Abad, C. Cellier, X. Chen, B. Gilles, P. Milani, J. Friml, T. Vernoux, C. Godin, O. Hamant, J. Traas, Current Biology 24 (2014) 2335–2342.","chicago":"Sassi, Massimiliano, Olivier Ali, Frédéric Boudon, Gladys Cloarec, Ursula Abad, Coralie Cellier, Xu Chen, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.08.036.","ista":"Sassi M, Ali O, Boudon F, Cloarec G, Abad U, Cellier C, Chen X, Gilles B, Milani P, Friml J, Vernoux T, Godin C, Hamant O, Traas J. 2014. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. 24(19), 2335–2342."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Cell Press","oa":1,"acknowledgement":"This work was funded by grants from EraSysBio+ (iSAM) and ERC (Morphodynamics). ","page":"2335 - 2342","doi":"10.1016/j.cub.2014.08.036","date_published":"2014-10-06T00:00:00Z","date_created":"2018-12-11T11:54:22Z","year":"2014","day":"06","publication":"Current Biology","type":"journal_article","status":"public","_id":"1852","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:53:37Z","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01074821"}],"month":"10","intvolume":" 24","abstract":[{"text":"To control morphogenesis, molecular regulatory networks have to interfere with the mechanical properties of the individual cells of developing organs and tissues, but how this is achieved is not well known. We study this issue here in the shoot meristem of higher plants, a group of undifferentiated cells where complex changes in growth rates and directions lead to the continuous formation of new organs [1, 2]. Here, we show that the plant hormone auxin plays an important role in this process via a dual, local effect on the extracellular matrix, the cell wall, which determines cell shape. Our study reveals that auxin not only causes a limited reduction in wall stiffness but also directly interferes with wall anisotropy via the regulation of cortical microtubule dynamics. We further show that to induce growth isotropy and organ outgrowth, auxin somehow interferes with the cortical microtubule-ordering activity of a network of proteins, including AUXIN BINDING PROTEIN 1 and KATANIN 1. Numerical simulations further indicate that the induced isotropy is sufficient to amplify the effects of the relatively minor changes in wall stiffness to promote organogenesis and the establishment of new growth axes in a robust manner.","lang":"eng"}],"oa_version":"Submitted Version","issue":"19","volume":24,"publication_status":"published","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"day":"03","publication_status":"published","year":"2014","date_created":"2018-12-11T11:54:22Z","date_published":"2014-02-03T00:00:00Z","doi":"10.1109/IOT.2014.7030120","page":"85 - 90","oa_version":"None","abstract":[{"text":"Wireless sensor networks (WSNs) composed of low-power, low-cost sensor nodes are expected to form the backbone of future intelligent networks for a broad range of civil, industrial and military applications. These sensor nodes are often deployed through random spreading, and function in dynamic environments. Many applications of WSNs such as pollution tracking, forest fire detection, and military surveillance require knowledge of the location of constituent nodes. But the use of technologies such as GPS on all nodes is prohibitive due to power and cost constraints. So, the sensor nodes need to autonomously determine their locations. Most localization techniques use anchor nodes with known locations to determine the position of remaining nodes. Localization techniques have two conflicting requirements. On one hand, an ideal localization technique should be computationally simple and on the other hand, it must be resistant to attacks that compromise anchor nodes. In this paper, we propose a computationally light-weight game theoretic secure localization technique and demonstrate its effectiveness in comparison to existing techniques.","lang":"eng"}],"month":"02","publisher":"IEEE","quality_controlled":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Jha, Susmit, Stavros Tripakis, Sanjit Seshia, and Krishnendu Chatterjee. “Game Theoretic Secure Localization in Wireless Sensor Networks,” 85–90. IEEE, 2014. https://doi.org/10.1109/IOT.2014.7030120.","ista":"Jha S, Tripakis S, Seshia S, Chatterjee K. 2014. Game theoretic secure localization in wireless sensor networks. IOT: Internet of Things, 85–90.","mla":"Jha, Susmit, et al. Game Theoretic Secure Localization in Wireless Sensor Networks. IEEE, 2014, pp. 85–90, doi:10.1109/IOT.2014.7030120.","ieee":"S. Jha, S. Tripakis, S. Seshia, and K. Chatterjee, “Game theoretic secure localization in wireless sensor networks,” presented at the IOT: Internet of Things, Cambridge, USA, 2014, pp. 85–90.","short":"S. Jha, S. Tripakis, S. Seshia, K. Chatterjee, in:, IEEE, 2014, pp. 85–90.","apa":"Jha, S., Tripakis, S., Seshia, S., & Chatterjee, K. (2014). Game theoretic secure localization in wireless sensor networks (pp. 85–90). Presented at the IOT: Internet of Things, Cambridge, USA: IEEE. https://doi.org/10.1109/IOT.2014.7030120","ama":"Jha S, Tripakis S, Seshia S, Chatterjee K. Game theoretic secure localization in wireless sensor networks. In: IEEE; 2014:85-90. doi:10.1109/IOT.2014.7030120"},"date_updated":"2021-01-12T06:53:38Z","department":[{"_id":"KrCh"}],"title":"Game theoretic secure localization in wireless sensor networks","author":[{"first_name":"Susmit","full_name":"Jha, Susmit","last_name":"Jha"},{"full_name":"Tripakis, Stavros","last_name":"Tripakis","first_name":"Stavros"},{"last_name":"Seshia","full_name":"Seshia, Sanjit","first_name":"Sanjit"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"publist_id":"5247","_id":"1853","status":"public","conference":{"name":"IOT: Internet of Things","location":"Cambridge, USA","end_date":"2014-10-08","start_date":"2014-10-06"},"type":"conference"},{"status":"public","type":"journal_article","article_type":"original","_id":"1862","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"EvBe"}],"date_updated":"2022-05-23T08:26:44Z","intvolume":" 516","month":"12","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257754/","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"The prominent and evolutionarily ancient role of the plant hormone auxin is the regulation of cell expansion. Cell expansion requires ordered arrangement of the cytoskeleton but molecular mechanisms underlying its regulation by signalling molecules including auxin are unknown. Here we show in the model plant Arabidopsis thaliana that in elongating cells exogenous application of auxin or redistribution of endogenous auxin induces very rapid microtubule re-orientation from transverse to longitudinal, coherent with the inhibition of cell expansion. This fast auxin effect requires auxin binding protein 1 (ABP1) and involves a contribution of downstream signalling components such as ROP6 GTPase, ROP-interactive protein RIC1 and the microtubule-severing protein katanin. These components are required for rapid auxin-and ABP1-mediated re-orientation of microtubules to regulate cell elongation in roots and dark-grown hypocotyls as well as asymmetric growth during gravitropic responses."}],"ec_funded":1,"issue":"729","volume":516,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"title":"Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules","article_processing_charge":"No","external_id":{"pmid":["25409144"]},"author":[{"id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu","full_name":"Chen, Xu","last_name":"Chen"},{"first_name":"Laurie","full_name":"Grandont, Laurie","last_name":"Grandont"},{"first_name":"Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li","orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"first_name":"Sébastien","full_name":"Paque, Sébastien","last_name":"Paque"},{"full_name":"Abuzeineh, Anas","last_name":"Abuzeineh","first_name":"Anas"},{"id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","first_name":"Hana","last_name":"Rakusova","full_name":"Rakusova, Hana"},{"last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Perrot Rechenmann, Catherine","last_name":"Perrot Rechenmann","first_name":"Catherine"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"5237","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chen, Xu, et al. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” Nature, vol. 516, no. 729, Nature Publishing Group, 2014, pp. 90–93, doi:10.1038/nature13889.","ieee":"X. Chen et al., “Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules,” Nature, vol. 516, no. 729. Nature Publishing Group, pp. 90–93, 2014.","short":"X. Chen, L. Grandont, H. Li, R. Hauschild, S. Paque, A. Abuzeineh, H. Rakusova, E. Benková, C. Perrot Rechenmann, J. Friml, Nature 516 (2014) 90–93.","ama":"Chen X, Grandont L, Li H, et al. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. 2014;516(729):90-93. doi:10.1038/nature13889","apa":"Chen, X., Grandont, L., Li, H., Hauschild, R., Paque, S., Abuzeineh, A., … Friml, J. (2014). Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13889","chicago":"Chen, Xu, Laurie Grandont, Hongjiang Li, Robert Hauschild, Sébastien Paque, Anas Abuzeineh, Hana Rakusova, Eva Benková, Catherine Perrot Rechenmann, and Jiří Friml. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature13889.","ista":"Chen X, Grandont L, Li H, Hauschild R, Paque S, Abuzeineh A, Rakusova H, Benková E, Perrot Rechenmann C, Friml J. 2014. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. 516(729), 90–93."},"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","acknowledgement":"We thank R. Dixit for performing complementary experiments, D. W. Ehrhardt and T. Hashimoto for providing the seeds of TUB6–RFP and EB1b–GFP respectively, E. Zazimalova, J. Petrasek and M. Fendrych for discussing the manuscript and J. Leung for text optimization. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, to J.F.), ANR blanc AuxiWall project (ANR-11-BSV5-0007, to C.P.-R. and L.G.) and the Agency for Innovation by Science and Technology (IWT) (to H.R.). This work benefited from the facilities and expertise of the Imagif Cell Biology platform (http://www.imagif.cnrs.fr), which is supported by the Conseil Général de l’Essonne.","date_created":"2018-12-11T11:54:25Z","date_published":"2014-12-04T00:00:00Z","doi":"10.1038/nature13889","page":"90 - 93","publication":"Nature","day":"04","year":"2014"},{"author":[{"first_name":"Georg","last_name":"Hofferek","full_name":"Hofferek, Georg"},{"last_name":"Gupta","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh"}],"publist_id":"5228","title":"Suraq - a controller synthesis tool using uninterpreted functions","editor":[{"first_name":"Eran","last_name":"Yahav","full_name":"Yahav, Eran"}],"citation":{"apa":"Hofferek, G., & Gupta, A. (2014). Suraq - a controller synthesis tool using uninterpreted functions. In E. Yahav (Ed.), HVC 2014 (Vol. 8855, pp. 68–74). Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-13338-6_6","ama":"Hofferek G, Gupta A. Suraq - a controller synthesis tool using uninterpreted functions. In: Yahav E, ed. HVC 2014. Vol 8855. Springer; 2014:68-74. doi:10.1007/978-3-319-13338-6_6","ieee":"G. Hofferek and A. Gupta, “Suraq - a controller synthesis tool using uninterpreted functions,” in HVC 2014, Haifa, Israel, 2014, vol. 8855, pp. 68–74.","short":"G. Hofferek, A. Gupta, in:, E. Yahav (Ed.), HVC 2014, Springer, 2014, pp. 68–74.","mla":"Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using Uninterpreted Functions.” HVC 2014, edited by Eran Yahav, vol. 8855, Springer, 2014, pp. 68–74, doi:10.1007/978-3-319-13338-6_6.","ista":"Hofferek G, Gupta A. 2014. Suraq - a controller synthesis tool using uninterpreted functions. HVC 2014. HVC: Haifa Verification Conference, LNCS, vol. 8855, 68–74.","chicago":"Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using Uninterpreted Functions.” In HVC 2014, edited by Eran Yahav, 8855:68–74. Springer, 2014. https://doi.org/10.1007/978-3-319-13338-6_6."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"}],"page":"68 - 74","date_published":"2014-01-01T00:00:00Z","doi":"10.1007/978-3-319-13338-6_6","date_created":"2018-12-11T11:54:27Z","year":"2014","day":"01","publication":"HVC 2014","publisher":"Springer","quality_controlled":"1","acknowledgement":"The work presented in this paper was supported in part by the European Research Council (ERC) under grant agreement QUAINT (I774-N23)","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T06:53:44Z","type":"conference","conference":{"name":"HVC: Haifa Verification Conference","start_date":"2014-11-18","end_date":"2014-11-20","location":"Haifa, Israel"},"status":"public","_id":"1869","volume":8855,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"month":"01","intvolume":" 8855","abstract":[{"lang":"eng","text":"Boolean controllers for systems with complex datapaths are often very difficult to implement correctly, in particular when concurrency is involved. Yet, in many instances it is easy to formally specify correctness. For example, the specification for the controller of a pipelined processor only has to state that the pipelined processor gives the same results as a non-pipelined reference design. This makes such controllers a good target for automated synthesis. However, an efficient abstraction for the complex datapath elements is needed, as a bit-precise description is often infeasible. We present Suraq, the first controller synthesis tool which uses uninterpreted functions for the abstraction. Quantified firstorder formulas (with specific quantifier structure) serve as the specification language from which Suraq synthesizes Boolean controllers. Suraq transforms the specification into an unsatisfiable SMT formula, and uses Craig interpolation to compute its results. Using Suraq, we were able to synthesize a controller (consisting of two Boolean signals) for a five-stage pipelined DLX processor in roughly one hour and 15 minutes."}],"oa_version":"None"},{"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:19Z","ddc":["000"],"date_updated":"2021-01-12T06:53:45Z","pubrep_id":"641","status":"public","conference":{"start_date":"2014-11-03","end_date":"2014-11-07","location":"Sydney, Australia","name":"ATVA: Automated Technology for Verification and Analysis"},"type":"conference","_id":"1872","ec_funded":1,"volume":8837,"language":[{"iso":"eng"}],"file":[{"checksum":"af4bd3fc1f4c93075e4dc5cbf625fe7b","file_id":"4801","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-641-v1+1_atva2014.pdf","date_created":"2018-12-12T10:10:15Z","creator":"system","file_size":244294,"date_updated":"2020-07-14T12:45:19Z"}],"publication_status":"published","intvolume":" 8837","month":"01","alternative_title":["LNCS"],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"Extensionality axioms are common when reasoning about data collections, such as arrays and functions in program analysis, or sets in mathematics. An extensionality axiom asserts that two collections are equal if they consist of the same elements at the same indices. Using extensionality is often required to show that two collections are equal. A typical example is the set theory theorem (∀x)(∀y)x∪y = y ∪x. Interestingly, while humans have no problem with proving such set identities using extensionality, they are very hard for superposition theorem provers because of the calculi they use. In this paper we show how addition of a new inference rule, called extensionality resolution, allows first-order theorem provers to easily solve problems no modern first-order theorem prover can solve. We illustrate this by running the VAMPIRE theorem prover with extensionality resolution on a number of set theory and array problems. Extensionality resolution helps VAMPIRE to solve problems from the TPTP library of first-order problems that were never solved before by any prover.","lang":"eng"}],"title":"Extensional crisis and proving identity","editor":[{"first_name":"Franck","full_name":"Cassez, Franck","last_name":"Cassez"},{"full_name":"Raskin, Jean-François","last_name":"Raskin","first_name":"Jean-François"}],"author":[{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","full_name":"Gupta, Ashutosh","last_name":"Gupta"},{"last_name":"Kovács","full_name":"Kovács, Laura","first_name":"Laura"},{"full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Voronkov, Andrei","last_name":"Voronkov","first_name":"Andrei"}],"publist_id":"5226","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Gupta, Ashutosh, Laura Kovács, Bernhard Kragl, and Andrei Voronkov. “Extensional Crisis and Proving Identity.” In ATVA 2014, edited by Franck Cassez and Jean-François Raskin, 8837:185–200. Springer, 2014. https://doi.org/10.1007/978-3-319-11936-6_14.","ista":"Gupta A, Kovács L, Kragl B, Voronkov A. 2014. Extensional crisis and proving identity. ATVA 2014. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 185–200.","mla":"Gupta, Ashutosh, et al. “Extensional Crisis and Proving Identity.” ATVA 2014, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 185–200, doi:10.1007/978-3-319-11936-6_14.","apa":"Gupta, A., Kovács, L., Kragl, B., & Voronkov, A. (2014). Extensional crisis and proving identity. In F. Cassez & J.-F. Raskin (Eds.), ATVA 2014 (Vol. 8837, pp. 185–200). Sydney, Australia: Springer. https://doi.org/10.1007/978-3-319-11936-6_14","ama":"Gupta A, Kovács L, Kragl B, Voronkov A. Extensional crisis and proving identity. In: Cassez F, Raskin J-F, eds. ATVA 2014. Vol 8837. Springer; 2014:185-200. doi:10.1007/978-3-319-11936-6_14","short":"A. Gupta, L. Kovács, B. Kragl, A. Voronkov, in:, F. Cassez, J.-F. Raskin (Eds.), ATVA 2014, Springer, 2014, pp. 185–200.","ieee":"A. Gupta, L. Kovács, B. Kragl, and A. Voronkov, “Extensional crisis and proving identity,” in ATVA 2014, Sydney, Australia, 2014, vol. 8837, pp. 185–200."},"project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:54:28Z","doi":"10.1007/978-3-319-11936-6_14","date_published":"2014-01-01T00:00:00Z","page":"185 - 200","publication":"ATVA 2014","day":"01","year":"2014","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"This research was supported in part by the Austrian National Research Network RiSE (S11410-N23)."},{"type":"conference","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)"},"conference":{"name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","start_date":"2014-12-15","location":"Delhi, India","end_date":"2014-12-17"},"status":"public","pubrep_id":"804","_id":"1870","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T06:53:45Z","ddc":["004"],"alternative_title":["LIPIcs"],"month":"12","intvolume":" 29","abstract":[{"text":"We investigate the problem of checking if a finite-state transducer is robust to uncertainty in its input. Our notion of robustness is based on the analytic notion of Lipschitz continuity - a transducer is K-(Lipschitz) robust if the perturbation in its output is at most K times the perturbation in its input. We quantify input and output perturbation using similarity functions. We show that K-robustness is undecidable even for deterministic transducers. We identify a class of functional transducers, which admits a polynomial time automata-theoretic decision procedure for K-robustness. This class includes Mealy machines and functional letter-to-letter transducers. We also study K-robustness of nondeterministic transducers. Since a nondeterministic transducer generates a set of output words for each input word, we quantify output perturbation using setsimilarity functions. We show that K-robustness of nondeterministic transducers is undecidable, even for letter-to-letter transducers. We identify a class of set-similarity functions which admit decidable K-robustness of letter-to-letter transducers.","lang":"eng"}],"oa_version":"Published Version","volume":29,"publication_status":"published","file":[{"file_id":"4734","checksum":"7b1aff1710a8bffb7080ec07f62d9a17","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-804-v1+1_37.pdf","date_created":"2018-12-12T10:09:11Z","creator":"system","file_size":562151,"date_updated":"2020-07-14T12:45:19Z"}],"language":[{"iso":"eng"}],"publist_id":"5227","author":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Otop, Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"last_name":"Samanta","full_name":"Samanta, Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","first_name":"Roopsha"}],"title":"Lipschitz robustness of finite-state transducers","citation":{"mla":"Henzinger, Thomas A., et al. “Lipschitz Robustness of Finite-State Transducers.” Leibniz International Proceedings in Informatics, LIPIcs, vol. 29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–43, doi:10.4230/LIPIcs.FSTTCS.2014.431.","apa":"Henzinger, T. A., Otop, J., & Samanta, R. (2014). Lipschitz robustness of finite-state transducers. In Leibniz International Proceedings in Informatics, LIPIcs (Vol. 29, pp. 431–443). Delhi, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431","ama":"Henzinger TA, Otop J, Samanta R. Lipschitz robustness of finite-state transducers. In: Leibniz International Proceedings in Informatics, LIPIcs. Vol 29. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:431-443. doi:10.4230/LIPIcs.FSTTCS.2014.431","short":"T.A. Henzinger, J. Otop, R. Samanta, in:, Leibniz International Proceedings in Informatics, LIPIcs, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–443.","ieee":"T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of finite-state transducers,” in Leibniz International Proceedings in Informatics, LIPIcs, Delhi, India, 2014, vol. 29, pp. 431–443.","chicago":"Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness of Finite-State Transducers.” In Leibniz International Proceedings in Informatics, LIPIcs, 29:431–43. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431.","ista":"Henzinger TA, Otop J, Samanta R. 2014. Lipschitz robustness of finite-state transducers. Leibniz International Proceedings in Informatics, LIPIcs. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 29, 431–443."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"page":"431 - 443","date_published":"2014-12-01T00:00:00Z","doi":"10.4230/LIPIcs.FSTTCS.2014.431","date_created":"2018-12-11T11:54:27Z","has_accepted_license":"1","year":"2014","day":"01","publication":"Leibniz International Proceedings in Informatics, LIPIcs"},{"file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T06:53:46Z","ddc":["000","005"],"conference":{"name":"SAS: Static Analysis Symposium","end_date":"2014-09-14","location":"Munich, Germany","start_date":"2014-09-11"},"type":"conference","pubrep_id":"313","status":"public","_id":"1875","volume":8723,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:07:51Z","file_name":"IST-2014-313-v1+1_SOE.SAS14.pdf","creator":"system","date_updated":"2020-07-14T12:45:19Z","file_size":409485,"checksum":"78ec4ea1bdecc676cd3e8cad35c6182c","file_id":"4650","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"alternative_title":["LNCS"],"scopus_import":1,"intvolume":" 8723","month":"09","abstract":[{"lang":"eng","text":"We present a formal framework for repairing infinite-state, imperative, sequential programs, with (possibly recursive) procedures and multiple assertions; the framework can generate repaired programs by modifying the original erroneous program in multiple program locations, and can ensure the readability of the repaired program using user-defined expression templates; the framework also generates a set of inductive assertions that serve as a proof of correctness of the repaired program. As a step toward integrating programmer intent and intuition in automated program repair, we present a cost-aware formulation - given a cost function associated with permissible statement modifications, the goal is to ensure that the total program modification cost does not exceed a given repair budget. As part of our predicate abstractionbased solution framework, we present a sound and complete algorithm for repair of Boolean programs. We have developed a prototype tool based on SMT solving and used it successfully to repair diverse errors in benchmark C programs."}],"oa_version":"Submitted Version","author":[{"first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","last_name":"Samanta","full_name":"Samanta, Roopsha"},{"full_name":"Olivo, Oswaldo","last_name":"Olivo","first_name":"Oswaldo"},{"first_name":"Emerson","last_name":"Allen","full_name":"Allen, Emerson"}],"publist_id":"5221","title":"Cost-aware automatic program repair","editor":[{"full_name":"Müller-Olm, Markus","last_name":"Müller-Olm","first_name":"Markus"},{"first_name":"Helmut","last_name":"Seidl","full_name":"Seidl, Helmut"}],"citation":{"chicago":"Samanta, Roopsha, Oswaldo Olivo, and Emerson Allen. “Cost-Aware Automatic Program Repair.” edited by Markus Müller-Olm and Helmut Seidl, 8723:268–84. Springer, 2014. https://doi.org/10.1007/978-3-319-10936-7_17.","ista":"Samanta R, Olivo O, Allen E. 2014. Cost-aware automatic program repair. SAS: Static Analysis Symposium, LNCS, vol. 8723, 268–284.","mla":"Samanta, Roopsha, et al. Cost-Aware Automatic Program Repair. Edited by Markus Müller-Olm and Helmut Seidl, vol. 8723, Springer, 2014, pp. 268–84, doi:10.1007/978-3-319-10936-7_17.","ieee":"R. Samanta, O. Olivo, and E. Allen, “Cost-aware automatic program repair,” presented at the SAS: Static Analysis Symposium, Munich, Germany, 2014, vol. 8723, pp. 268–284.","short":"R. Samanta, O. Olivo, E. Allen, in:, M. Müller-Olm, H. Seidl (Eds.), Springer, 2014, pp. 268–284.","ama":"Samanta R, Olivo O, Allen E. Cost-aware automatic program repair. In: Müller-Olm M, Seidl H, eds. Vol 8723. Springer; 2014:268-284. doi:10.1007/978-3-319-10936-7_17","apa":"Samanta, R., Olivo, O., & Allen, E. (2014). Cost-aware automatic program repair. In M. Müller-Olm & H. Seidl (Eds.) (Vol. 8723, pp. 268–284). Presented at the SAS: Static Analysis Symposium, Munich, Germany: Springer. https://doi.org/10.1007/978-3-319-10936-7_17"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"268 - 284","date_created":"2018-12-11T11:54:29Z","doi":"10.1007/978-3-319-10936-7_17","date_published":"2014-09-01T00:00:00Z","year":"2014","has_accepted_license":"1","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer"},{"publication_status":"published","publication_identifier":{"issn":["16093321"]},"language":[{"iso":"eng"}],"volume":14,"issue":"3","abstract":[{"text":"We study densities of functionals over uniformly bounded triangulations of a Delaunay set of vertices, and prove that the minimum is attained for the Delaunay triangulation if this is the case for finite sets.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"url":"http://arxiv.org/abs/1211.7053","open_access":"1"}],"scopus_import":"1","intvolume":" 14","month":"07","date_updated":"2022-03-03T11:47:09Z","department":[{"_id":"HeEd"}],"_id":"1876","article_type":"original","type":"journal_article","status":"public","year":"2014","publication":"Moscow Mathematical Journal","day":"01","page":"491 - 504","date_created":"2018-12-11T11:54:29Z","date_published":"2014-07-01T00:00:00Z","doi":"10.17323/1609-4514-2014-14-3-491-504","oa":1,"quality_controlled":"1","publisher":"Independent University of Moscow","citation":{"ista":"Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. 2014. Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. 14(3), 491–504.","chicago":"Dolbilin, Nikolai, Herbert Edelsbrunner, Alexey Glazyrin, and Oleg Musin. “Functionals on Triangulations of Delaunay Sets.” Moscow Mathematical Journal. Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-3-491-504.","short":"N. Dolbilin, H. Edelsbrunner, A. Glazyrin, O. Musin, Moscow Mathematical Journal 14 (2014) 491–504.","ieee":"N. Dolbilin, H. Edelsbrunner, A. Glazyrin, and O. Musin, “Functionals on triangulations of delaunay sets,” Moscow Mathematical Journal, vol. 14, no. 3. Independent University of Moscow, pp. 491–504, 2014.","apa":"Dolbilin, N., Edelsbrunner, H., Glazyrin, A., & Musin, O. (2014). Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-3-491-504","ama":"Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. 2014;14(3):491-504. doi:10.17323/1609-4514-2014-14-3-491-504","mla":"Dolbilin, Nikolai, et al. “Functionals on Triangulations of Delaunay Sets.” Moscow Mathematical Journal, vol. 14, no. 3, Independent University of Moscow, 2014, pp. 491–504, doi:10.17323/1609-4514-2014-14-3-491-504."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1211.7053"]},"article_processing_charge":"No","author":[{"full_name":"Dolbilin, Nikolai","last_name":"Dolbilin","first_name":"Nikolai"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"last_name":"Glazyrin","full_name":"Glazyrin, Alexey","first_name":"Alexey"},{"first_name":"Oleg","full_name":"Musin, Oleg","last_name":"Musin"}],"publist_id":"5220","title":"Functionals on triangulations of delaunay sets"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:47Z","citation":{"ista":"Sixt MK, Vaahtomeri K. 2014. Physiology: Relax and come in. Nature. 514(7523), 441–442.","chicago":"Sixt, Michael K, and Kari Vaahtomeri. “Physiology: Relax and Come In.” Nature. Springer Nature, 2014. https://doi.org/10.1038/514441a.","short":"M.K. Sixt, K. Vaahtomeri, Nature 514 (2014) 441–442.","ieee":"M. K. Sixt and K. Vaahtomeri, “Physiology: Relax and come in,” Nature, vol. 514, no. 7523. Springer Nature, pp. 441–442, 2014.","apa":"Sixt, M. K., & Vaahtomeri, K. (2014). Physiology: Relax and come in. Nature. Springer Nature. https://doi.org/10.1038/514441a","ama":"Sixt MK, Vaahtomeri K. Physiology: Relax and come in. Nature. 2014;514(7523):441-442. doi:10.1038/514441a","mla":"Sixt, Michael K., and Kari Vaahtomeri. “Physiology: Relax and Come In.” Nature, vol. 514, no. 7523, Springer Nature, 2014, pp. 441–42, doi:10.1038/514441a."},"title":"Physiology: Relax and come in","department":[{"_id":"MiSi"}],"publist_id":"5219","author":[{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"},{"full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518","last_name":"Vaahtomeri","first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87"}],"_id":"1877","status":"public","article_type":"letter_note","type":"journal_article","publication":"Nature","language":[{"iso":"eng"}],"day":"23","publication_status":"published","year":"2014","date_created":"2018-12-11T11:54:30Z","volume":514,"issue":"7523","doi":"10.1038/514441a","date_published":"2014-10-23T00:00:00Z","page":"441 - 442","oa_version":"None","abstract":[{"lang":"eng","text":"During inflammation, lymph nodes swell with an influx of immune cells. New findings identify a signalling pathway that induces relaxation in the contractile cells that give structure to these organs."}],"intvolume":" 514","month":"10","publisher":"Springer Nature","quality_controlled":"1","scopus_import":1},{"article_number":"e03722","project":[{"call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26"}],"citation":{"ista":"Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. 2014. Variance predicts salience in central sensory processing. eLife. (November), e03722.","chicago":"Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian, and Gašper Tkačik. “Variance Predicts Salience in Central Sensory Processing.” ELife. eLife Sciences Publications, 2014. https://doi.org/10.7554/eLife.03722.","ieee":"A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and G. Tkačik, “Variance predicts salience in central sensory processing,” eLife, no. November. eLife Sciences Publications, 2014.","short":"A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkačik, ELife (2014).","ama":"Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. Variance predicts salience in central sensory processing. eLife. 2014;(November). doi:10.7554/eLife.03722","apa":"Hermundstad, A., Briguglio, J., Conte, M., Victor, J., Balasubramanian, V., & Tkačik, G. (2014). Variance predicts salience in central sensory processing. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.03722","mla":"Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.” ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5209","author":[{"first_name":"Ann","full_name":"Hermundstad, Ann","last_name":"Hermundstad"},{"full_name":"Briguglio, John","last_name":"Briguglio","first_name":"John"},{"last_name":"Conte","full_name":"Conte, Mary","first_name":"Mary"},{"full_name":"Victor, Jonathan","last_name":"Victor","first_name":"Jonathan"},{"full_name":"Balasubramanian, Vijay","last_name":"Balasubramanian","first_name":"Vijay"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"}],"title":"Variance predicts salience in central sensory processing","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","year":"2014","has_accepted_license":"1","publication":"eLife","day":"14","date_created":"2018-12-11T11:54:32Z","date_published":"2014-11-14T00:00:00Z","doi":"10.7554/eLife.03722","_id":"1886","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"420","status":"public","date_updated":"2021-01-12T06:53:50Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:20Z","department":[{"_id":"GaTk"}],"abstract":[{"text":"Information processing in the sensory periphery is shaped by natural stimulus statistics. In the periphery, a transmission bottleneck constrains performance; thus efficient coding implies that natural signal components with a predictably wider range should be compressed. In a different regime—when sampling limitations constrain performance—efficient coding implies that more resources should be allocated to informative features that are more variable. We propose that this regime is relevant for sensory cortex when it extracts complex features from limited numbers of sensory samples. To test this prediction, we use central visual processing as a model: we show that visual sensitivity for local multi-point spatial correlations, described by dozens of independently-measured parameters, can be quantitatively predicted from the structure of natural images. This suggests that efficient coding applies centrally, where it extends to higher-order sensory features and operates in a regime in which sensitivity increases with feature variability.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"11","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:12:04Z","file_name":"IST-2016-420-v1+1_e03722.full.pdf","creator":"system","date_updated":"2020-07-14T12:45:20Z","file_size":5117086,"file_id":"4922","checksum":"766ac8999ac6e3364f10065a06024b8f","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"issue":"November"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. 2014. Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. Psychophysiology. 51(4), 385–395.","chicago":"Körner, Christof, Verena Braunstein, Matthias Stangl, Alois Schlögl, Christa Neuper, and Anja Ischebeck. “Sequential Effects in Continued Visual Search: Using Fixation-Related Potentials to Compare Distractor Processing before and after Target Detection.” Psychophysiology. Wiley-Blackwell, 2014. https://doi.org/10.1111/psyp.12062.","ieee":"C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, and A. Ischebeck, “Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection,” Psychophysiology, vol. 51, no. 4. Wiley-Blackwell, pp. 385–395, 2014.","short":"C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, A. Ischebeck, Psychophysiology 51 (2014) 385–395.","ama":"Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. Psychophysiology. 2014;51(4):385-395. doi:10.1111/psyp.12062","apa":"Körner, C., Braunstein, V., Stangl, M., Schlögl, A., Neuper, C., & Ischebeck, A. (2014). Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. Psychophysiology. Wiley-Blackwell. https://doi.org/10.1111/psyp.12062","mla":"Körner, Christof, et al. “Sequential Effects in Continued Visual Search: Using Fixation-Related Potentials to Compare Distractor Processing before and after Target Detection.” Psychophysiology, vol. 51, no. 4, Wiley-Blackwell, 2014, pp. 385–95, doi:10.1111/psyp.12062."},"title":"Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection","publist_id":"5205","author":[{"full_name":"Körner, Christof","last_name":"Körner","first_name":"Christof"},{"first_name":"Verena","last_name":"Braunstein","full_name":"Braunstein, Verena"},{"first_name":"Matthias","last_name":"Stangl","full_name":"Stangl, Matthias"},{"last_name":"Schlögl","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christa","last_name":"Neuper","full_name":"Neuper, Christa"},{"first_name":"Anja","full_name":"Ischebeck, Anja","last_name":"Ischebeck"}],"acknowledgement":"Funded by Austrian Science Fund (FWF) Grant Number: P 22189-B18; European Union within the 6th Framework Programme Grant Number: 517590; State government of Styria Grant Number: PN 4055","publisher":"Wiley-Blackwell","oa":1,"day":"11","publication":"Psychophysiology","has_accepted_license":"1","year":"2014","date_published":"2014-02-11T00:00:00Z","doi":"10.1111/psyp.12062","date_created":"2018-12-11T11:54:34Z","page":"385 - 395","_id":"1890","status":"public","pubrep_id":"442","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"date_updated":"2021-01-12T06:53:52Z","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:20Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"To search for a target in a complex environment is an everyday behavior that ends with finding the target. When we search for two identical targets, however, we must continue the search after finding the first target and memorize its location. We used fixation-related potentials to investigate the neural correlates of different stages of the search, that is, before and after finding the first target. Having found the first target influenced subsequent distractor processing. Compared to distractor fixations before the first target fixation, a negative shift was observed for three subsequent distractor fixations. These results suggest that processing a target in continued search modulates the brain's response, either transiently by reflecting temporary working memory processes or permanently by reflecting working memory retention."}],"month":"02","intvolume":" 51","scopus_import":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5233","checksum":"4255b6185e774acce1d99f8e195c564d","file_size":543243,"date_updated":"2020-07-14T12:45:20Z","creator":"system","file_name":"IST-2016-442-v1+1_K-rner_et_al-2014-Psychophysiology.pdf","date_created":"2018-12-12T10:16:44Z"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":51},{"volume":281,"issue":"1794","publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211437/"}],"scopus_import":"1","intvolume":" 281","month":"11","abstract":[{"text":"Behavioural variation among conspecifics is typically contingent on individual state or environmental conditions. Sex-specific genetic polymorphisms are enigmatic because they lack conditionality, and genes causing adaptive trait variation in one sex may reduce Darwinian fitness in the other. One way to avoid such genetic antagonism is to control sex-specific traits by inheritance via sex chromosomes. Here, controlled laboratory crossings suggest that in snail-brooding cichlid fish a single locus, two-allele polymorphism located on a sex-linked chromosome of heterogametic males generates an extreme reproductive dimorphism. Both natural and sexual selection are responsible for exceptionally large body size of bourgeois males, creating a niche for a miniature male phenotype to evolve. This extreme intrasexual dimorphism results from selection on opposite size thresholds caused by a single ecological factor, empty snail shells used as breeding substrate. Paternity analyses reveal that in the field parasitic dwarf males sire the majority of offspring in direct sperm competition with large nest owners exceeding their size more than 40 times. Apparently, use of empty snail shells as breeding substrate and single locus sex-linked inheritance of growth are the major ecological and genetic mechanisms responsible for the extreme intrasexual diversity observed in Lamprologus callipterus.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","department":[{"_id":"CampIT"}],"date_updated":"2022-06-07T09:12:32Z","article_type":"original","type":"journal_article","status":"public","_id":"1892","date_created":"2018-12-11T11:54:34Z","date_published":"2014-11-07T00:00:00Z","doi":"10.1098/rspb.2014.0253","year":"2014","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","day":"07","oa":1,"publisher":"The Royal Society","quality_controlled":"1","acknowledgement":"This research was supported by grants of the Swiss National Science Foundation to M.T.\r\nWe thank Tetsu Sato for providing field samples, Olivier Goffinet for field assistance, Dolores Schütz for vital help in the field and with the manuscript, David Lank, Barbara Taborsky, Suzanne Alonzo and two anonymous referees for comments on earlier manuscript versions, and the Fisheries Department, Ministry of Agriculture and Livestock of Zambia, for permission and support.","external_id":{"pmid":["25232141"]},"article_processing_charge":"No","author":[{"full_name":"Ocana, Sabine","last_name":"Ocana","first_name":"Sabine"},{"first_name":"Patrick","id":"4709BCE6-F248-11E8-B48F-1D18A9856A87","last_name":"Meidl","full_name":"Meidl, Patrick"},{"first_name":"Danielle","last_name":"Bonfils","full_name":"Bonfils, Danielle"},{"last_name":"Taborsky","full_name":"Taborsky, Michael","first_name":"Michael"}],"publist_id":"5203","title":"Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids","citation":{"chicago":"Ocana, Sabine, Patrick Meidl, Danielle Bonfils, and Michael Taborsky. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.” Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society, 2014. https://doi.org/10.1098/rspb.2014.0253.","ista":"Ocana S, Meidl P, Bonfils D, Taborsky M. 2014. Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. 281(1794), 20140253.","mla":"Ocana, Sabine, et al. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794, 20140253, The Royal Society, 2014, doi:10.1098/rspb.2014.0253.","apa":"Ocana, S., Meidl, P., Bonfils, D., & Taborsky, M. (2014). Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2014.0253","ama":"Ocana S, Meidl P, Bonfils D, Taborsky M. Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. 2014;281(1794). doi:10.1098/rspb.2014.0253","short":"S. Ocana, P. Meidl, D. Bonfils, M. Taborsky, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014).","ieee":"S. Ocana, P. Meidl, D. Bonfils, and M. Taborsky, “Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794. The Royal Society, 2014."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"20140253"},{"title":"Theoretical tests of the mechanical protection strategy in protein nanomechanics","department":[{"_id":"CaHe"}],"author":[{"first_name":"Mateusz","last_name":"Chwastyk","full_name":"Chwastyk, Mateusz"},{"first_name":"Albert","full_name":"Galera Prat, Albert","last_name":"Galera Prat"},{"last_name":"Sikora","full_name":"Sikora, Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K"},{"first_name":"Àngel","last_name":"Gómez Sicilia","full_name":"Gómez Sicilia, Àngel"},{"last_name":"Carrión Vázquez","full_name":"Carrión Vázquez, Mariano","first_name":"Mariano"},{"full_name":"Cieplak, Marek","last_name":"Cieplak","first_name":"Marek"}],"publist_id":"5204","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chwastyk, Mateusz, et al. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” Proteins: Structure, Function and Bioinformatics, vol. 82, no. 5, Wiley-Blackwell, 2014, pp. 717–26, doi:10.1002/prot.24436.","apa":"Chwastyk, M., Galera Prat, A., Sikora, M. K., Gómez Sicilia, À., Carrión Vázquez, M., & Cieplak, M. (2014). Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.24436","ama":"Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M, Cieplak M. Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. 2014;82(5):717-726. doi:10.1002/prot.24436","short":"M. Chwastyk, A. Galera Prat, M.K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez, M. Cieplak, Proteins: Structure, Function and Bioinformatics 82 (2014) 717–726.","ieee":"M. Chwastyk, A. Galera Prat, M. K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez, and M. Cieplak, “Theoretical tests of the mechanical protection strategy in protein nanomechanics,” Proteins: Structure, Function and Bioinformatics, vol. 82, no. 5. Wiley-Blackwell, pp. 717–726, 2014.","chicago":"Chwastyk, Mateusz, Albert Galera Prat, Mateusz K Sikora, Àngel Gómez Sicilia, Mariano Carrión Vázquez, and Marek Cieplak. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell, 2014. https://doi.org/10.1002/prot.24436.","ista":"Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M, Cieplak M. 2014. Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. 82(5), 717–726."},"date_updated":"2021-01-12T06:53:52Z","status":"public","type":"journal_article","_id":"1891","date_created":"2018-12-11T11:54:34Z","volume":82,"doi":"10.1002/prot.24436","issue":"5","date_published":"2014-05-01T00:00:00Z","page":"717 - 726","language":[{"iso":"eng"}],"publication":"Proteins: Structure, Function and Bioinformatics","day":"01","publication_status":"published","year":"2014","intvolume":" 82","month":"05","scopus_import":1,"publisher":"Wiley-Blackwell","acknowledgement":"Grant Nr. 2011/01/N/ST3/02475","oa_version":"None","abstract":[{"lang":"eng","text":"We provide theoretical tests of a novel experimental technique to determine mechanostability of proteins based on stretching a mechanically protected protein by single-molecule force spectroscopy. This technique involves stretching a homogeneous or heterogeneous chain of reference proteins (single-molecule markers) in which one of them acts as host to the guest protein under study. The guest protein is grafted into the host through genetic engineering. It is expected that unraveling of the host precedes the unraveling of the guest removing ambiguities in the reading of the force-extension patterns of the guest protein. We study examples of such systems within a coarse-grained structure-based model. We consider systems with various ratios of mechanostability for the host and guest molecules and compare them to experimental results involving cohesin I as the guest molecule. For a comparison, we also study the force-displacement patterns in proteins that are linked in a serial fashion. We find that the mechanostability of the guest is similar to that of the isolated or serially linked protein. We also demonstrate that the ideal configuration of this strategy would be one in which the host is much more mechanostable than the single-molecule markers. We finally show that it is troublesome to use the highly stable cystine knot proteins as a host to graft a guest in stretching studies because this would involve a cleaving procedure."}]},{"year":"2014","publication_status":"published","day":"04","publication":"Blood","language":[{"iso":"eng"}],"page":"1952 - 1952","volume":124,"issue":"21","date_published":"2014-12-04T00:00:00Z","date_created":"2018-12-11T11:54:32Z","abstract":[{"text":"Unbiased high-throughput massively parallel sequencing methods have transformed the process of discovery of novel putative driver gene mutations in cancer. In chronic lymphocytic leukemia (CLL), these methods have yielded several unexpected findings, including the driver genes SF3B1, NOTCH1 and POT1. Recent analysis, utilizing down-sampling of existing datasets, has shown that the discovery process of putative drivers is far from complete across cancer. In CLL, while driver gene mutations affecting >10% of patients were efficiently discovered with previously published CLL cohorts of up to 160 samples subjected to whole exome sequencing (WES), this sample size has only 0.78 power to detect drivers affecting 5% of patients, and only 0.12 power for drivers affecting 2% of patients. These calculations emphasize the need to apply unbiased WES to larger patient cohorts.","lang":"eng"}],"oa_version":"None","publisher":"American Society of Hematology","main_file_link":[{"url":"http://www.bloodjournal.org/content/124/21/1952?sso-checked=true"}],"month":"12","intvolume":" 124","citation":{"ista":"Landau D, Stewart C, Reiter J, Lawrence M, Sougnez C, Brown J, Lopez Guillermo A, Gabriel S, Lander E, Neuberg D, López Otín C, Campo E, Getz G, Wu C. 2014. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. 124(21), 1952–1952.","chicago":"Landau, Dan, Chip Stewart, Johannes Reiter, Michael Lawrence, Carrie Sougnez, Jennifer Brown, Armando Lopez Guillermo, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” Blood. American Society of Hematology, 2014.","ieee":"D. Landau et al., “Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples,” Blood, vol. 124, no. 21. American Society of Hematology, pp. 1952–1952, 2014.","short":"D. Landau, C. Stewart, J. Reiter, M. Lawrence, C. Sougnez, J. Brown, A. Lopez Guillermo, S. Gabriel, E. Lander, D. Neuberg, C. López Otín, E. Campo, G. Getz, C. Wu, Blood 124 (2014) 1952–1952.","ama":"Landau D, Stewart C, Reiter J, et al. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. 2014;124(21):1952-1952.","apa":"Landau, D., Stewart, C., Reiter, J., Lawrence, M., Sougnez, C., Brown, J., … Wu, C. (2014). Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. American Society of Hematology.","mla":"Landau, Dan, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” Blood, vol. 124, no. 21, American Society of Hematology, 2014, pp. 1952–1952."},"date_updated":"2021-01-12T06:53:50Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5211","author":[{"full_name":"Landau, Dan","last_name":"Landau","first_name":"Dan"},{"first_name":"Chip","full_name":"Stewart, Chip","last_name":"Stewart"},{"orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"},{"last_name":"Lawrence","full_name":"Lawrence, Michael","first_name":"Michael"},{"last_name":"Sougnez","full_name":"Sougnez, Carrie","first_name":"Carrie"},{"first_name":"Jennifer","full_name":"Brown, Jennifer","last_name":"Brown"},{"last_name":"Lopez Guillermo","full_name":"Lopez Guillermo, Armando","first_name":"Armando"},{"full_name":"Gabriel, Stacey","last_name":"Gabriel","first_name":"Stacey"},{"first_name":"Eric","last_name":"Lander","full_name":"Lander, Eric"},{"first_name":"Donna","last_name":"Neuberg","full_name":"Neuberg, Donna"},{"full_name":"López Otín, Carlos","last_name":"López Otín","first_name":"Carlos"},{"full_name":"Campo, Elias","last_name":"Campo","first_name":"Elias"},{"first_name":"Gad","full_name":"Getz, Gad","last_name":"Getz"},{"first_name":"Catherine","last_name":"Wu","full_name":"Wu, Catherine"}],"department":[{"_id":"KrCh"}],"title":"Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples","_id":"1884","type":"journal_article","status":"public"},{"article_number":"1450012","author":[{"last_name":"Bräunlich","full_name":"Bräunlich, Gerhard","first_name":"Gerhard"},{"last_name":"Hainzl","full_name":"Hainzl, Christian","first_name":"Christian"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"publist_id":"5206","article_processing_charge":"No","external_id":{"arxiv":["1305.5135"]},"title":"Translation-invariant quasi-free states for fermionic systems and the BCS approximation","citation":{"ama":"Bräunlich G, Hainzl C, Seiringer R. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. 2014;26(7). doi:10.1142/S0129055X14500123","apa":"Bräunlich, G., Hainzl, C., & Seiringer, R. (2014). Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X14500123","ieee":"G. Bräunlich, C. Hainzl, and R. Seiringer, “Translation-invariant quasi-free states for fermionic systems and the BCS approximation,” Reviews in Mathematical Physics, vol. 26, no. 7. World Scientific Publishing, 2014.","short":"G. Bräunlich, C. Hainzl, R. Seiringer, Reviews in Mathematical Physics 26 (2014).","mla":"Bräunlich, Gerhard, et al. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews in Mathematical Physics, vol. 26, no. 7, 1450012, World Scientific Publishing, 2014, doi:10.1142/S0129055X14500123.","ista":"Bräunlich G, Hainzl C, Seiringer R. 2014. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. 26(7), 1450012.","chicago":"Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews in Mathematical Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X14500123."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"World Scientific Publishing","quality_controlled":"1","oa":1,"acknowledgement":"We would like to thank Max Lein and Andreas Deuchert for valuable suggestions and remarks. Partial financial support by the NSERC (R.S.) is gratefully acknowledged.","date_published":"2014-08-01T00:00:00Z","doi":"10.1142/S0129055X14500123","date_created":"2018-12-11T11:54:33Z","year":"2014","day":"01","publication":"Reviews in Mathematical Physics","type":"journal_article","article_type":"original","status":"public","_id":"1889","department":[{"_id":"RoSe"}],"date_updated":"2022-06-07T09:03:09Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1305.5135"}],"month":"08","intvolume":" 26","abstract":[{"text":"We study translation-invariant quasi-free states for a system of fermions with two-particle interactions. The associated energy functional is similar to the BCS functional but also includes direct and exchange energies. We show that for suitable short-range interactions, these latter terms only lead to a renormalization of the chemical potential, with the usual properties of the BCS functional left unchanged. Our analysis thus represents a rigorous justification of part of the BCS approximation. We give bounds on the critical temperature below which the system displays superfluidity.","lang":"eng"}],"oa_version":"Submitted Version","issue":"7","volume":26,"publication_status":"published","language":[{"iso":"eng"}]},{"title":"Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA","publist_id":"5201","author":[{"first_name":"Anna","last_name":"Grabowska","full_name":"Grabowska, Anna"},{"full_name":"Wywiał, Ewa","last_name":"Wywiał","first_name":"Ewa"},{"first_name":"Stanislaw","last_name":"Dunin Horkawicz","full_name":"Dunin Horkawicz, Stanislaw"},{"full_name":"Łasica, Anna","last_name":"Łasica","first_name":"Anna"},{"full_name":"Wösten, Marc","last_name":"Wösten","first_name":"Marc"},{"first_name":"Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","last_name":"Nagy-Staron","full_name":"Nagy-Staron, Anna A"},{"first_name":"Renata","last_name":"Godlewska","full_name":"Godlewska, Renata"},{"first_name":"Katarzyna","last_name":"Bocian Ostrzycka","full_name":"Bocian Ostrzycka, Katarzyna"},{"last_name":"Pieńkowska","full_name":"Pieńkowska, Katarzyna","first_name":"Katarzyna"},{"first_name":"Paweł","last_name":"Łaniewski","full_name":"Łaniewski, Paweł"},{"full_name":"Bujnicki, Janusz","last_name":"Bujnicki","first_name":"Janusz"},{"first_name":"Jos","full_name":"Van Putten, Jos","last_name":"Van Putten"},{"full_name":"Jagusztyn Krynicka, Elzbieta","last_name":"Jagusztyn Krynicka","first_name":"Elzbieta"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Grabowska, Anna, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” PLoS One, vol. 9, no. 9, e106247, Public Library of Science, 2014, doi:10.1371/journal.pone.0106247.","ieee":"A. Grabowska et al., “Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014.","short":"A. Grabowska, E. Wywiał, S. Dunin Horkawicz, A. Łasica, M. Wösten, A.A. Nagy-Staron, R. Godlewska, K. Bocian Ostrzycka, K. Pieńkowska, P. Łaniewski, J. Bujnicki, J. Van Putten, E. Jagusztyn Krynicka, PLoS One 9 (2014).","apa":"Grabowska, A., Wywiał, E., Dunin Horkawicz, S., Łasica, A., Wösten, M., Nagy-Staron, A. A., … Jagusztyn Krynicka, E. (2014). Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0106247","ama":"Grabowska A, Wywiał E, Dunin Horkawicz S, et al. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0106247","chicago":"Grabowska, Anna, Ewa Wywiał, Stanislaw Dunin Horkawicz, Anna Łasica, Marc Wösten, Anna A Nagy-Staron, Renata Godlewska, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0106247.","ista":"Grabowska A, Wywiał E, Dunin Horkawicz S, Łasica A, Wösten M, Nagy-Staron AA, Godlewska R, Bocian Ostrzycka K, Pieńkowska K, Łaniewski P, Bujnicki J, Van Putten J, Jagusztyn Krynicka E. 2014. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. 9(9), e106247."},"article_number":"e106247","date_created":"2018-12-11T11:54:35Z","doi":"10.1371/journal.pone.0106247","date_published":"2014-09-02T00:00:00Z","publication":"PLoS One","day":"02","year":"2014","has_accepted_license":"1","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","file_date_updated":"2020-07-14T12:45:20Z","department":[{"_id":"CaGu"}],"ddc":["570"],"date_updated":"2021-01-12T06:53:54Z","pubrep_id":"438","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1894","issue":"9","volume":9,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:16:19Z","file_name":"IST-2016-438-v1+1_journal.pone.0106247.pdf","date_updated":"2020-07-14T12:45:20Z","file_size":4248801,"creator":"system","checksum":"7d02c3da7f72b82bb5d7932d80c3251f","file_id":"5205","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","intvolume":" 9","month":"09","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Background: Bacterial Dsb enzymes are involved in the oxidative folding of many proteins, through the formation of disulfide bonds between their cysteine residues. The Dsb protein network has been well characterized in cells of the model microorganism Escherichia coli. To gain insight into the functioning of the Dsb system in epsilon-Proteobacteria, where it plays an important role in the colonization process, we studied two homologs of the main Escherichia coli Dsb oxidase (EcDsbA) that are present in the cells of the enteric pathogen Campylobacter jejuni, the most frequently reported bacterial cause of human enteritis in the world. Methods and Results: Phylogenetic analysis suggests the horizontal transfer of the epsilon-Proteobacterial DsbAs from a common ancestor to gamma-Proteobacteria, which then gave rise to the DsbL lineage. Phenotype and enzymatic assays suggest that the two C. jejuni DsbAs play different roles in bacterial cells and have divergent substrate spectra. CjDsbA1 is essential for the motility and autoagglutination phenotypes, while CjDsbA2 has no impact on those processes. CjDsbA1 plays a critical role in the oxidative folding that ensures the activity of alkaline phosphatase CjPhoX, whereas CjDsbA2 is crucial for the activity of arylsulfotransferase CjAstA, encoded within the dsbA2-dsbB-astA operon. Conclusions: Our results show that CjDsbA1 is the primary thiol-oxidoreductase affecting life processes associated with bacterial spread and host colonization, as well as ensuring the oxidative folding of particular protein substrates. In contrast, CjDsbA2 activity does not affect the same processes and so far its oxidative folding activity has been demonstrated for one substrate, arylsulfotransferase CjAstA. The results suggest the cooperation between CjDsbA2 and CjDsbB. In the case of the CjDsbA1, this cooperation is not exclusive and there is probably another protein to be identified in C. jejuni cells that acts to re-oxidize CjDsbA1. Altogether the data presented here constitute the considerable insight to the Epsilonproteobacterial Dsb systems, which have been poorly understood so far.","lang":"eng"}]},{"day":"30","publication":"PLoS One","has_accepted_license":"1","year":"2014","doi":"10.1371/journal.pone.0107099","date_published":"2014-09-30T00:00:00Z","date_created":"2018-12-11T11:54:35Z","acknowledgement":"This work was supported in part by a Grant-in-Aid for Scientific Research on Innovative Areas (Comprehensive Brain Science Network) and (B) 17330153, from the Ministry of Education, Culture, Sports, Science and Technology of Japan.","publisher":"Public Library of Science","oa":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Edamura, Mitsuhiro, Gen Murakami, Hongrui Meng, Makoto Itakura, Ryuichi Shigemoto, Atsuo Fukuda, and Daiichiro Nakahara. “Functional Deficiency of MHC Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0107099.","ista":"Edamura M, Murakami G, Meng H, Itakura M, Shigemoto R, Fukuda A, Nakahara D. 2014. Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. 9(9), e107099.","mla":"Edamura, Mitsuhiro, et al. “Functional Deficiency of MHC Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS One, vol. 9, no. 9, e107099, Public Library of Science, 2014, doi:10.1371/journal.pone.0107099.","ama":"Edamura M, Murakami G, Meng H, et al. Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0107099","apa":"Edamura, M., Murakami, G., Meng, H., Itakura, M., Shigemoto, R., Fukuda, A., & Nakahara, D. (2014). Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0107099","ieee":"M. Edamura et al., “Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014.","short":"M. Edamura, G. Murakami, H. Meng, M. Itakura, R. Shigemoto, A. Fukuda, D. Nakahara, PLoS One 9 (2014)."},"title":"Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice","publist_id":"5200","author":[{"first_name":"Mitsuhiro","full_name":"Edamura, Mitsuhiro","last_name":"Edamura"},{"first_name":"Gen","last_name":"Murakami","full_name":"Murakami, Gen"},{"full_name":"Meng, Hongrui","last_name":"Meng","first_name":"Hongrui"},{"first_name":"Makoto","full_name":"Itakura, Makoto","last_name":"Itakura"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Atsuo","full_name":"Fukuda, Atsuo","last_name":"Fukuda"},{"full_name":"Nakahara, Daiichiro","last_name":"Nakahara","first_name":"Daiichiro"}],"article_number":"e107099","file":[{"date_updated":"2020-07-14T12:45:20Z","file_size":6262085,"creator":"system","date_created":"2018-12-12T10:09:01Z","file_name":"IST-2016-439-v1+1_journal.pone.0107099.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"1f3be936be93114596d61ba44cacee69","file_id":"4724"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":9,"issue":"9","oa_version":"Published Version","abstract":[{"text":"Major histocompatibility complex class I (MHCI) molecules were recently identified as novel regulators of synaptic plasticity. These molecules are expressed in various brain areas, especially in regions undergoing activity-dependent synaptic plasticity, but their role in the nucleus accumbens (NAc) is unknown. In this study, we investigated the effects of genetic disruption of MHCI function, through deletion of β2-microblobulin, which causes lack of cell surface expression of MHCI. First, we confirmed that MHCI molecules are expressed in the NAc core in wild-type mice. Second, we performed electrophysiological recordings with NAc core slices from wild-type and β2-microglobulin knock-out mice lacking cell surface expression of MHCI. We found that low frequency stimulation induced long-term depression in wild-type but not knock-out mice, whereas high frequency stimulation induced long-term potentiation in both genotypes, with a larger magnitude in knock-out mice. Furthermore, we demonstrated that knock-out mice showed more persistent behavioral sensitization to cocaine, which is a NAc-related behavior. Using this model, we analyzed the density of total AMPA receptors and their subunits GluR1 and GluR2 in the NAc core, by SDS-digested freeze-fracture replica labeling. After repeated cocaine exposure, the density of GluR1 was increased, but there was no change in total AMPA receptors and GluR2 levels in wildtype mice. In contrast, following repeated cocaine exposure, increased densities of total AMPA receptors, GluR1 and GluR2 were observed in knock-out mice. These results indicate that functional deficiency of MHCI enhances synaptic potentiation, induced by electrical and pharmacological stimulation.","lang":"eng"}],"month":"09","intvolume":" 9","scopus_import":1,"ddc":["570"],"date_updated":"2021-01-12T06:53:54Z","file_date_updated":"2020-07-14T12:45:20Z","department":[{"_id":"RySh"}],"_id":"1895","status":"public","pubrep_id":"439","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)"}},{"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932866/","open_access":"1"}],"scopus_import":1,"intvolume":" 111","month":"02","abstract":[{"lang":"eng","text":"Phosphatidylinositol (PtdIns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, PtdIns3P and PtdIns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vacuolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with PtdIns3P, the presumable product of their activity. In SAC gain- and loss-of-function mutants, the levels of PtdIns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with PtdIns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants."}],"oa_version":"Submitted Version","ec_funded":1,"issue":"7","volume":111,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1893","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:53:53Z","oa":1,"publisher":"National Academy of Sciences","acknowledgement":"This work was supported by grants from the Research Foundation-Flanders (Odysseus).","page":"2818 - 2823","date_created":"2018-12-11T11:54:34Z","date_published":"2014-02-18T00:00:00Z","doi":"10.1073/pnas.1324264111","year":"2014","publication":"PNAS","day":"18","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"author":[{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra","full_name":"Nováková, Petra","last_name":"Nováková"},{"first_name":"Sibylle","last_name":"Hirsch","full_name":"Hirsch, Sibylle"},{"first_name":"Elena","last_name":"Feraru","full_name":"Feraru, Elena"},{"first_name":"Ricardo","full_name":"Tejos, Ricardo","last_name":"Tejos"},{"first_name":"Ringo","full_name":"Van Wijk, Ringo","last_name":"Van Wijk"},{"first_name":"Tom","last_name":"Viaene","full_name":"Viaene, Tom"},{"first_name":"Mareike","last_name":"Heilmann","full_name":"Heilmann, Mareike"},{"first_name":"Jennifer","last_name":"Lerche","full_name":"Lerche, Jennifer"},{"first_name":"Riet","last_name":"De Rycke","full_name":"De Rycke, Riet"},{"first_name":"Mugurel","full_name":"Feraru, Mugurel","last_name":"Feraru"},{"first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","last_name":"Grones","full_name":"Grones, Peter"},{"first_name":"Marc","full_name":"Van Montagu, Marc","last_name":"Van Montagu"},{"full_name":"Heilmann, Ingo","last_name":"Heilmann","first_name":"Ingo"},{"full_name":"Munnik, Teun","last_name":"Munnik","first_name":"Teun"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5202","title":"SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis","citation":{"short":"P. Marhavá, S. Hirsch, E. Feraru, R. Tejos, R. Van Wijk, T. Viaene, M. Heilmann, J. Lerche, R. De Rycke, M. Feraru, P. Grones, M. Van Montagu, I. Heilmann, T. Munnik, J. Friml, PNAS 111 (2014) 2818–2823.","ieee":"P. Marhavá et al., “SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis,” PNAS, vol. 111, no. 7. National Academy of Sciences, pp. 2818–2823, 2014.","ama":"Marhavá P, Hirsch S, Feraru E, et al. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 2014;111(7):2818-2823. doi:10.1073/pnas.1324264111","apa":"Marhavá, P., Hirsch, S., Feraru, E., Tejos, R., Van Wijk, R., Viaene, T., … Friml, J. (2014). SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1324264111","mla":"Marhavá, Petra, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS, vol. 111, no. 7, National Academy of Sciences, 2014, pp. 2818–23, doi:10.1073/pnas.1324264111.","ista":"Marhavá P, Hirsch S, Feraru E, Tejos R, Van Wijk R, Viaene T, Heilmann M, Lerche J, De Rycke R, Feraru M, Grones P, Van Montagu M, Heilmann I, Munnik T, Friml J. 2014. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 111(7), 2818–2823.","chicago":"Marhavá, Petra, Sibylle Hirsch, Elena Feraru, Ricardo Tejos, Ringo Van Wijk, Tom Viaene, Mareike Heilmann, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1324264111."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"1896","status":"public","type":"journal_article","date_updated":"2022-08-01T10:50:10Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings."}],"month":"03","intvolume":" 89","scopus_import":"1","main_file_link":[{"url":"http://arxiv.org/abs/1402.0430","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":89,"article_number":"032701","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.032701.","ista":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701.","mla":"Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701.","apa":"Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.032701","ama":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701","short":"R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","ieee":"R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014."},"title":"Mathematical model of alternative mechanism of telomere length maintenance","publist_id":"5198","author":[{"full_name":"Kollár, Richard","last_name":"Kollár","first_name":"Richard"},{"orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína","last_name":"Bod'ová","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína"},{"full_name":"Nosek, Jozef","last_name":"Nosek","first_name":"Jozef"},{"last_name":"Tomáška","full_name":"Tomáška, Ľubomír","first_name":"Ľubomír"}],"article_processing_charge":"No","acknowledgement":"The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.).","publisher":"American Institute of Physics","oa":1,"day":"04","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","year":"2014","doi":"10.1103/PhysRevE.89.032701","date_published":"2014-03-04T00:00:00Z","date_created":"2018-12-11T11:54:35Z"},{"volume":26,"doi":"10.1105/tpc.114.125880","issue":"7","date_published":"2014-07-01T00:00:00Z","date_created":"2018-12-11T11:54:36Z","page":"3062 - 3076","day":"01","language":[{"iso":"eng"}],"publication":"Plant Cell","year":"2014","publication_status":"published","month":"07","intvolume":" 26","publisher":"American Society of Plant Biologists","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145132/"}],"oa":1,"oa_version":"Submitted Version","acknowledgement":"This work was supported by the Odysseus Program of the Research Foundation-Flanders (J.F.).","abstract":[{"text":"GNOM is one of the most characterized membrane trafficking regulators in plants, with crucial roles in development. GNOM encodes an ARF-guanine nucleotide exchange factor (ARF-GEF) that activates small GTPases of the ARF (ADP ribosylation factor) class to mediate vesicle budding at endomembranes. The crucial role of GNOM in recycling of PIN auxin transporters and other proteins to the plasma membrane was identified in studies using the ARF-GEF inhibitor brefeldin A (BFA). GNOM, the most prominent regulator of recycling in plants, has been proposed to act and localize at so far elusive recycling endosomes. Here, we report the GNOM localization in context of its cellular function in Arabidopsis thaliana. State-of-the-art imaging, pharmacological interference, and ultrastructure analysis show that GNOM predominantly localizes to Golgi apparatus. Super-resolution confocal live imaging microscopy identified GNOM and its closest homolog GNOM-like 1 at distinct subdomains on Golgi cisternae. Short-term BFA treatment stabilizes GNOM at the Golgi apparatus, whereas prolonged exposures results in GNOM translocation to trans-Golgi network (TGN)/early endosomes (EEs). Malformed TGN/EE in gnom mutants suggests a role for GNOM in maintaining TGN/EE function. Our results redefine the subcellular action of GNOM and reevaluate the identity and function of recycling endosomes in plants.","lang":"eng"}],"title":"Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis","department":[{"_id":"JiFr"}],"publist_id":"5199","author":[{"first_name":"Satoshi","full_name":"Naramoto, Satoshi","last_name":"Naramoto"},{"full_name":"Otegui, Marisa","last_name":"Otegui","first_name":"Marisa"},{"first_name":"Natsumaro","last_name":"Kutsuna","full_name":"Kutsuna, Natsumaro"},{"last_name":"De Rycke","full_name":"De Rycke, Riet","first_name":"Riet"},{"first_name":"Tomoko","full_name":"Dainobu, Tomoko","last_name":"Dainobu"},{"first_name":"Michael","full_name":"Karampelias, Michael","last_name":"Karampelias"},{"last_name":"Fujimoto","full_name":"Fujimoto, Masaru","first_name":"Masaru"},{"first_name":"Elena","full_name":"Feraru, Elena","last_name":"Feraru"},{"last_name":"Miki","full_name":"Miki, Daisuke","first_name":"Daisuke"},{"last_name":"Fukuda","full_name":"Fukuda, Hiroo","first_name":"Hiroo"},{"first_name":"Akihiko","last_name":"Nakano","full_name":"Nakano, Akihiko"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Naramoto, Satoshi, Marisa Otegui, Natsumaro Kutsuna, Riet De Rycke, Tomoko Dainobu, Michael Karampelias, Masaru Fujimoto, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2014. https://doi.org/10.1105/tpc.114.125880.","ista":"Naramoto S, Otegui M, Kutsuna N, De Rycke R, Dainobu T, Karampelias M, Fujimoto M, Feraru E, Miki D, Fukuda H, Nakano A, Friml J. 2014. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 26(7), 3062–3076.","mla":"Naramoto, Satoshi, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” Plant Cell, vol. 26, no. 7, American Society of Plant Biologists, 2014, pp. 3062–76, doi:10.1105/tpc.114.125880.","apa":"Naramoto, S., Otegui, M., Kutsuna, N., De Rycke, R., Dainobu, T., Karampelias, M., … Friml, J. (2014). Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.125880","ama":"Naramoto S, Otegui M, Kutsuna N, et al. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 2014;26(7):3062-3076. doi:10.1105/tpc.114.125880","short":"S. Naramoto, M. Otegui, N. Kutsuna, R. De Rycke, T. Dainobu, M. Karampelias, M. Fujimoto, E. Feraru, D. Miki, H. Fukuda, A. Nakano, J. Friml, Plant Cell 26 (2014) 3062–3076.","ieee":"S. Naramoto et al., “Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis,” Plant Cell, vol. 26, no. 7. American Society of Plant Biologists, pp. 3062–3076, 2014."},"date_updated":"2021-01-12T06:53:55Z","status":"public","type":"journal_article","_id":"1897"},{"article_type":"original","type":"journal_article","status":"public","_id":"1899","department":[{"_id":"SiHi"}],"date_updated":"2021-01-12T06:53:55Z","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159251/"}],"month":"07","intvolume":" 16","abstract":[{"lang":"eng","text":"Asymmetric cell divisions allow stem cells to balance proliferation and differentiation. During embryogenesis, murine epidermis expands rapidly from a single layer of unspecified basal layer progenitors to a stratified, differentiated epithelium. Morphogenesis involves perpendicular (asymmetric) divisions and the spindle orientation protein LGN, but little is known about how the apical localization of LGN is regulated. Here, we combine conventional genetics and lentiviral-mediated in vivo RNAi to explore the functions of the LGN-interacting proteins Par3, mInsc and Gα i3. Whereas loss of each gene alone leads to randomized division angles, combined loss of Gnai3 and mInsc causes a phenotype of mostly planar divisions, akin to loss of LGN. These findings lend experimental support for the hitherto untested model that Par3-mInsc and Gα i3 act cooperatively to polarize LGN and promote perpendicular divisions. Finally, we uncover a developmental switch between delamination-driven early stratification and spindle-orientation-dependent differentiation that occurs around E15, revealing a two-step mechanism underlying epidermal maturation."}],"oa_version":"Submitted Version","pmid":1,"volume":16,"issue":"8","publication_status":"published","language":[{"iso":"eng"}],"publist_id":"5196","author":[{"full_name":"Williams, Scott","last_name":"Williams","first_name":"Scott"},{"first_name":"Lyndsay","last_name":"Ratliff","full_name":"Ratliff, Lyndsay"},{"last_name":"Postiglione","full_name":"Postiglione, Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87","first_name":"Maria P"},{"full_name":"Knoblich, Juergen","last_name":"Knoblich","first_name":"Juergen"},{"full_name":"Fuchs, Elaine","last_name":"Fuchs","first_name":"Elaine"}],"article_processing_charge":"No","external_id":{"pmid":["25016959"]},"title":"Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN","citation":{"chicago":"Williams, Scott, Lyndsay Ratliff, Maria P Postiglione, Juergen Knoblich, and Elaine Fuchs. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” Nature Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb3001.","ista":"Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. 2014. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. 16(8), 758–769.","mla":"Williams, Scott, et al. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” Nature Cell Biology, vol. 16, no. 8, Nature Publishing Group, 2014, pp. 758–69, doi:10.1038/ncb3001.","ieee":"S. Williams, L. Ratliff, M. P. Postiglione, J. Knoblich, and E. Fuchs, “Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN,” Nature Cell Biology, vol. 16, no. 8. Nature Publishing Group, pp. 758–769, 2014.","short":"S. Williams, L. Ratliff, M.P. Postiglione, J. Knoblich, E. Fuchs, Nature Cell Biology 16 (2014) 758–769.","ama":"Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. 2014;16(8):758-769. doi:10.1038/ncb3001","apa":"Williams, S., Ratliff, L., Postiglione, M. P., Knoblich, J., & Fuchs, E. (2014). Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3001"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"page":"758 - 769","doi":"10.1038/ncb3001","date_published":"2014-07-13T00:00:00Z","date_created":"2018-12-11T11:54:36Z","year":"2014","day":"13","publication":"Nature Cell Biology"},{"oa_version":"None","abstract":[{"text":"Fast synaptic transmission is important for rapid information processing. To explore the maximal rate of neuronal signaling and to analyze the presynaptic mechanisms, we focused on the input layer of the cerebellar cortex, where exceptionally high action potential (AP) frequencies have been reported invivo. With paired recordings between presynaptic cerebellar mossy fiber boutons and postsynaptic granule cells, we demonstrate reliable neurotransmission upto ~1 kHz. Presynaptic APs are ultrafast, with ~100μs half-duration. Both Kv1 and Kv3 potassium channels mediate the fast repolarization, rapidly inactivating sodium channels ensure metabolic efficiency, and little AP broadening occurs during bursts of up to 1.5 kHz. Presynaptic Cav2.1 (P/Q-type) calcium channels open efficiently during ultrafast APs. Furthermore, a subset of synaptic vesicles is tightly coupled to Ca2+ channels, and vesicles are rapidly recruited to the release site. These data reveal mechanisms of presynaptic AP generation and transmitter release underlying neuronal kHz signaling.","lang":"eng"}],"month":"10","intvolume":" 84","quality_controlled":"1","publisher":"Elsevier","scopus_import":1,"day":"01","publication":"Neuron","language":[{"iso":"eng"}],"publication_status":"published","year":"2014","doi":"10.1016/j.neuron.2014.08.036","volume":84,"date_published":"2014-10-01T00:00:00Z","issue":"1","date_created":"2018-12-11T11:54:36Z","page":"152 - 163","_id":"1898","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Ritzau Jost A, Delvendahl I, Rings A, Byczkowicz N, Harada H, Shigemoto R, Hirrlinger J, Eilers J, Hallermann S. 2014. Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. 84(1), 152–163.","chicago":"Ritzau Jost, Andreas, Igor Delvendahl, Annika Rings, Niklas Byczkowicz, Harumi Harada, Ryuichi Shigemoto, Johannes Hirrlinger, Jens Eilers, and Stefan Hallermann. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.08.036.","ama":"Ritzau Jost A, Delvendahl I, Rings A, et al. Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. 2014;84(1):152-163. doi:10.1016/j.neuron.2014.08.036","apa":"Ritzau Jost, A., Delvendahl, I., Rings, A., Byczkowicz, N., Harada, H., Shigemoto, R., … Hallermann, S. (2014). Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.08.036","short":"A. Ritzau Jost, I. Delvendahl, A. Rings, N. Byczkowicz, H. Harada, R. Shigemoto, J. Hirrlinger, J. Eilers, S. Hallermann, Neuron 84 (2014) 152–163.","ieee":"A. Ritzau Jost et al., “Ultrafast action potentials mediate kilohertz signaling at a central synapse,” Neuron, vol. 84, no. 1. Elsevier, pp. 152–163, 2014.","mla":"Ritzau Jost, Andreas, et al. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” Neuron, vol. 84, no. 1, Elsevier, 2014, pp. 152–63, doi:10.1016/j.neuron.2014.08.036."},"date_updated":"2021-01-12T06:53:55Z","department":[{"_id":"RySh"}],"title":"Ultrafast action potentials mediate kilohertz signaling at a central synapse","publist_id":"5197","author":[{"last_name":"Ritzau Jost","full_name":"Ritzau Jost, Andreas","first_name":"Andreas"},{"last_name":"Delvendahl","full_name":"Delvendahl, Igor","first_name":"Igor"},{"full_name":"Rings, Annika","last_name":"Rings","first_name":"Annika"},{"first_name":"Niklas","last_name":"Byczkowicz","full_name":"Byczkowicz, Niklas"},{"first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","full_name":"Harada, Harumi","orcid":"0000-0001-7429-7896"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"first_name":"Johannes","full_name":"Hirrlinger, Johannes","last_name":"Hirrlinger"},{"last_name":"Eilers","full_name":"Eilers, Jens","first_name":"Jens"},{"first_name":"Stefan","last_name":"Hallermann","full_name":"Hallermann, Stefan"}]},{"file_date_updated":"2020-07-14T12:45:20Z","department":[{"_id":"ChWo"}],"date_updated":"2021-01-12T06:53:59Z","ddc":["000"],"type":"journal_article","status":"public","pubrep_id":"573","_id":"1906","issue":"9","volume":20,"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"5bf58942d2eb20adf03c7f9ea2e68124","file_id":"5297","creator":"system","date_updated":"2020-07-14T12:45:20Z","file_size":13594598,"date_created":"2018-12-12T10:17:41Z","file_name":"IST-2016-573-v1+1_arikan-2014-pcvis-draft.pdf"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"09","intvolume":" 20","abstract":[{"text":"In this paper, we introduce a novel scene representation for the visualization of large-scale point clouds accompanied by a set of high-resolution photographs. Many real-world applications deal with very densely sampled point-cloud data, which are augmented with photographs that often reveal lighting variations and inaccuracies in registration. Consequently, the high-quality representation of the captured data, i.e., both point clouds and photographs together, is a challenging and time-consuming task. We propose a two-phase approach, in which the first (preprocessing) phase generates multiple overlapping surface patches and handles the problem of seamless texture generation locally for each patch. The second phase stitches these patches at render-time to produce a high-quality visualization of the data. As a result of the proposed localization of the global texturing problem, our algorithm is more than an order of magnitude faster than equivalent mesh-based texturing techniques. Furthermore, since our preprocessing phase requires only a minor fraction of the whole data set at once, we provide maximum flexibility when dealing with growing data sets.","lang":"eng"}],"oa_version":"Submitted Version","author":[{"full_name":"Arikan, Murat","last_name":"Arikan","first_name":"Murat"},{"full_name":"Preiner, Reinhold","last_name":"Preiner","first_name":"Reinhold"},{"first_name":"Claus","full_name":"Scheiblauer, Claus","last_name":"Scheiblauer"},{"full_name":"Jeschke, Stefan","last_name":"Jeschke","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"last_name":"Wimmer","full_name":"Wimmer, Michael","first_name":"Michael"}],"publist_id":"5189","title":"Large-scale point-cloud visualization through localized textured surface reconstruction","citation":{"ista":"Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. 2014. Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. 20(9), 1280–1292.","chicago":"Arikan, Murat, Reinhold Preiner, Claus Scheiblauer, Stefan Jeschke, and Michael Wimmer. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2014. https://doi.org/10.1109/TVCG.2014.2312011.","ieee":"M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, and M. Wimmer, “Large-scale point-cloud visualization through localized textured surface reconstruction,” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 9. IEEE, pp. 1280–1292, 2014.","short":"M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, M. Wimmer, IEEE Transactions on Visualization and Computer Graphics 20 (2014) 1280–1292.","ama":"Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. 2014;20(9):1280-1292. doi:10.1109/TVCG.2014.2312011","apa":"Arikan, M., Preiner, R., Scheiblauer, C., Jeschke, S., & Wimmer, M. (2014). Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2014.2312011","mla":"Arikan, Murat, et al. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 9, IEEE, 2014, pp. 1280–92, doi:10.1109/TVCG.2014.2312011."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FWF","_id":"25357BD2-B435-11E9-9278-68D0E5697425","name":"Deep Pictures: Creating Visual and Haptic Vector Images","grant_number":"P 24352-N23"}],"page":"1280 - 1292","doi":"10.1109/TVCG.2014.2312011","date_published":"2014-09-09T00:00:00Z","date_created":"2018-12-11T11:54:39Z","has_accepted_license":"1","year":"2014","day":"09","publication":"IEEE Transactions on Visualization and Computer Graphics","publisher":"IEEE","oa":1,"acknowledgement":"This research was supported by the Austrian Research Promotion Agency (FFG) project REPLICATE (no. 835948), the EU FP7 project HARVEST4D (no. 323567)."},{"oa_version":"None","pmid":1,"abstract":[{"text":"The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution).","lang":"eng"}],"intvolume":" 27","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"volume":27,"issue":"5","_id":"1905","status":"public","article_type":"original","type":"journal_article","date_updated":"2022-06-07T09:22:20Z","department":[{"_id":"SyCr"}],"acknowledgement":"This study was funded by grants from the National Science Foundation (NSF) to MT (IOS-1121832) and IS (DEB-0743406) and from the German Science Foundation (DFG; PL 470/1-2) and ‘LOEWE − Landesoffensive zur Entwicklung wissenschaftlich-ökonomischer Exzellenz’ of Hesse's Ministry of Higher Education, Research, and the Arts, to MP.","publisher":"Wiley","quality_controlled":"1","publication":"Journal of Evolutionary Biology","day":"12","year":"2014","date_created":"2018-12-11T11:54:38Z","date_published":"2014-04-12T00:00:00Z","doi":"10.1111/jeb.12370","page":"960 - 974","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Tobler, Michael, et al. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary Biology, vol. 27, no. 5, Wiley, 2014, pp. 960–74, doi:10.1111/jeb.12370.","apa":"Tobler, M., Plath, M., Riesch, R., Schlupp, I., Grasse, A. V., Munimanda, G., … Moodley, Y. (2014). Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.12370","ama":"Tobler M, Plath M, Riesch R, et al. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. 2014;27(5):960-974. doi:10.1111/jeb.12370","ieee":"M. Tobler et al., “Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations,” Journal of Evolutionary Biology, vol. 27, no. 5. Wiley, pp. 960–974, 2014.","short":"M. Tobler, M. Plath, R. Riesch, I. Schlupp, A.V. Grasse, G. Munimanda, C. Setzer, D. Penn, Y. Moodley, Journal of Evolutionary Biology 27 (2014) 960–974.","chicago":"Tobler, Michael, Martin Plath, Rüdiger Riesch, Ingo Schlupp, Anna V Grasse, Gopi Munimanda, C Setzer, Dustin Penn, and Yoshan Moodley. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary Biology. Wiley, 2014. https://doi.org/10.1111/jeb.12370.","ista":"Tobler M, Plath M, Riesch R, Schlupp I, Grasse AV, Munimanda G, Setzer C, Penn D, Moodley Y. 2014. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. 27(5), 960–974."},"title":"Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations","article_processing_charge":"No","external_id":{"pmid":["24725091"]},"publist_id":"5190","author":[{"last_name":"Tobler","full_name":"Tobler, Michael","first_name":"Michael"},{"full_name":"Plath, Martin","last_name":"Plath","first_name":"Martin"},{"full_name":"Riesch, Rüdiger","last_name":"Riesch","first_name":"Rüdiger"},{"first_name":"Ingo","last_name":"Schlupp","full_name":"Schlupp, Ingo"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","full_name":"Grasse, Anna V"},{"full_name":"Munimanda, Gopi","last_name":"Munimanda","first_name":"Gopi"},{"last_name":"Setzer","full_name":"Setzer, C","first_name":"C"},{"last_name":"Penn","full_name":"Penn, Dustin","first_name":"Dustin"},{"full_name":"Moodley, Yoshan","last_name":"Moodley","first_name":"Yoshan"}]},{"publisher":"Oxford University Press","quality_controlled":"1","date_created":"2018-12-11T11:54:37Z","doi":"10.1093/molbev/mst187","date_published":"2014-01-01T00:00:00Z","page":"232 - 238","publication":"Molecular Biology and Evolution","day":"01","year":"2014","title":"Growth rates made easy","article_processing_charge":"No","external_id":{"pmid":["24170494"]},"author":[{"first_name":"Barry","last_name":"Hall","full_name":"Hall, Barry"},{"full_name":"Acar, Hande","orcid":"0000-0003-1986-9753","last_name":"Acar","first_name":"Hande","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nandipati, Anna","last_name":"Nandipati","first_name":"Anna"},{"full_name":"Barlow, Miriam","last_name":"Barlow","first_name":"Miriam"}],"publist_id":"5193","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates Made Easy.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/mst187.","ista":"Hall B, Acar H, Nandipati A, Barlow M. 2014. Growth rates made easy. Molecular Biology and Evolution. 31(1), 232–238.","mla":"Hall, Barry, et al. “Growth Rates Made Easy.” Molecular Biology and Evolution, vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:10.1093/molbev/mst187.","ieee":"B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” Molecular Biology and Evolution, vol. 31, no. 1. Oxford University Press, pp. 232–238, 2014.","short":"B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution 31 (2014) 232–238.","ama":"Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. Molecular Biology and Evolution. 2014;31(1):232-238. doi:10.1093/molbev/mst187","apa":"Hall, B., Acar, H., Nandipati, A., & Barlow, M. (2014). Growth rates made easy. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst187"},"intvolume":" 31","month":"01","scopus_import":"1","oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"In the 1960s-1980s, determination of bacterial growth rates was an important tool in microbial genetics, biochemistry, molecular biology, and microbial physiology. The exciting technical developments of the 1990s and the 2000s eclipsed that tool; as a result, many investigators today lack experience with growth rate measurements. Recently, investigators in a number of areas have started to use measurements of bacterial growth rates for a variety of purposes. Those measurements have been greatly facilitated by the availability of microwell plate readers that permit the simultaneous measurements on up to 384 different cultures. Only the exponential (logarithmic) portions of the resulting growth curves are useful for determining growth rates, and manual determination of that portion and calculation of growth rates can be tedious for high-throughput purposes. Here, we introduce the program GrowthRates that uses plate reader output files to automatically determine the exponential portion of the curve and to automatically calculate the growth rate, the maximum culture density, and the duration of the growth lag phase. GrowthRates is freely available for Macintosh, Windows, and Linux.We discuss the effects of culture volume, the classical bacterial growth curve, and the differences between determinations in rich media and minimal (mineral salts) media. This protocol covers calibration of the plate reader, growth of culture inocula for both rich and minimal media, and experimental setup. As a guide to reliability, we report typical day-to-day variation in growth rates and variation within experiments with respect to position of wells within the plates."}],"volume":31,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"status":"public","type":"journal_article","article_type":"original","_id":"1902","department":[{"_id":"JoBo"}],"date_updated":"2022-06-07T11:08:13Z"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Tian, Huiyu, Krzysztof T Wabnik, Tiantian Niu, Hongjiang Li, Qianqian Yu, Stephan Pollmann, Steffen Vanneste, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular Plant. Oxford University Press, 2014. https://doi.org/10.1093/mp/sst118.","ista":"Tian H, Wabnik KT, Niu T, Li H, Yu Q, Pollmann S, Vanneste S, Govaerts W, Rolčík J, Geisler M, Friml J, Ding Z. 2014. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. 7(2), 277–289.","mla":"Tian, Huiyu, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular Plant, vol. 7, no. 2, Oxford University Press, 2014, pp. 277–89, doi:10.1093/mp/sst118.","ama":"Tian H, Wabnik KT, Niu T, et al. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. 2014;7(2):277-289. doi:10.1093/mp/sst118","apa":"Tian, H., Wabnik, K. T., Niu, T., Li, H., Yu, Q., Pollmann, S., … Ding, Z. (2014). WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. Oxford University Press. https://doi.org/10.1093/mp/sst118","ieee":"H. Tian et al., “WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis,” Molecular Plant, vol. 7, no. 2. Oxford University Press, pp. 277–289, 2014.","short":"H. Tian, K.T. Wabnik, T. Niu, H. Li, Q. Yu, S. Pollmann, S. Vanneste, W. Govaerts, J. Rolčík, M. Geisler, J. Friml, Z. Ding, Molecular Plant 7 (2014) 277–289."},"date_updated":"2021-01-12T06:53:57Z","department":[{"_id":"JiFr"}],"title":"WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis","author":[{"full_name":"Tian, Huiyu","last_name":"Tian","first_name":"Huiyu"},{"last_name":"Wabnik","full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T"},{"first_name":"Tiantian","full_name":"Niu, Tiantian","last_name":"Niu"},{"full_name":"Li, Hongjiang","last_name":"Li","first_name":"Hongjiang"},{"full_name":"Yu, Qianqian","last_name":"Yu","first_name":"Qianqian"},{"last_name":"Pollmann","full_name":"Pollmann, Stephan","first_name":"Stephan"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"first_name":"Willy","last_name":"Govaerts","full_name":"Govaerts, Willy"},{"first_name":"Jakub","full_name":"Rolčík, Jakub","last_name":"Rolčík"},{"full_name":"Geisler, Markus","last_name":"Geisler","first_name":"Markus"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Ding","full_name":"Ding, Zhaojun","first_name":"Zhaojun"}],"publist_id":"5194","_id":"1901","status":"public","type":"journal_article","day":"01","language":[{"iso":"eng"}],"publication":"Molecular Plant","year":"2014","publication_status":"published","volume":7,"doi":"10.1093/mp/sst118","issue":"2","date_published":"2014-02-01T00:00:00Z","date_created":"2018-12-11T11:54:37Z","page":"277 - 289","oa_version":"None","acknowledgement":"This work was supported by funding from the projects CZ.1.07/2.3.00/20.0043 and CZ.1.05/1.1.00/02.0068 (to CEITEC, Central European Institute of Technology) and the Odysseus program of the Research Foundation-Flanders to J.F\r\n","abstract":[{"lang":"eng","text":"In plants, the patterning of stem cell-enriched meristems requires a graded auxin response maximum that emerges from the concerted action of polar auxin transport, auxin biosynthesis, auxin metabolism, and cellular auxin response machinery. However, mechanisms underlying this auxin response maximum-mediated root stem cell maintenance are not fully understood. Here, we present unexpected evidence that WUSCHEL-RELATED HOMEOBOX 5 (WOX5) transcription factor modulates expression of auxin biosynthetic genes in the quiescent center (QC) of the root and thus provides a robust mechanism for the maintenance of auxin response maximum in the root tip. This WOX5 action is balanced through the activity of indole-3-acetic acid 17 (IAA17) auxin response repressor. Our combined genetic, cell biology, and computational modeling studies revealed a previously uncharacterized feedback loop linking WOX5-mediated auxin production to IAA17-dependent repression of auxin responses. This WOX5-IAA17 feedback circuit further assures the maintenance of auxin response maximum in the root tip and thereby contributes to the maintenance of distal stem cell (DSC) populations. Our experimental studies and in silico computer simulations both demonstrate that the WOX5-IAA17 feedback circuit is essential for the maintenance of auxin gradient in the root tip and the auxin-mediated root DSC differentiation."}],"month":"02","intvolume":" 7","scopus_import":1,"publisher":"Oxford University Press"},{"publication":"Journal of the European Mathematical Society","day":"23","year":"2014","date_created":"2018-12-11T11:54:38Z","doi":"10.4171/JEMS/467","date_published":"2014-08-23T00:00:00Z","page":"1507 - 1526","oa":1,"publisher":"European Mathematical Society","quality_controlled":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"short":"R. Frank, M. Lewin, É. Lieb, R. Seiringer, Journal of the European Mathematical Society 16 (2014) 1507–1526.","ieee":"R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “Strichartz inequality for orthonormal functions,” Journal of the European Mathematical Society, vol. 16, no. 7. European Mathematical Society, pp. 1507–1526, 2014.","ama":"Frank R, Lewin M, Lieb É, Seiringer R. Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. 2014;16(7):1507-1526. doi:10.4171/JEMS/467","apa":"Frank, R., Lewin, M., Lieb, É., & Seiringer, R. (2014). Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/467","mla":"Frank, Rupert, et al. “Strichartz Inequality for Orthonormal Functions.” Journal of the European Mathematical Society, vol. 16, no. 7, European Mathematical Society, 2014, pp. 1507–26, doi:10.4171/JEMS/467.","ista":"Frank R, Lewin M, Lieb É, Seiringer R. 2014. Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. 16(7), 1507–1526.","chicago":"Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “Strichartz Inequality for Orthonormal Functions.” Journal of the European Mathematical Society. European Mathematical Society, 2014. https://doi.org/10.4171/JEMS/467."},"title":"Strichartz inequality for orthonormal functions","author":[{"first_name":"Rupert","full_name":"Frank, Rupert","last_name":"Frank"},{"first_name":"Mathieu","last_name":"Lewin","full_name":"Lewin, Mathieu"},{"first_name":"Élliott","last_name":"Lieb","full_name":"Lieb, Élliott"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"publist_id":"5191","project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":16,"issue":"7","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We prove a Strichartz inequality for a system of orthonormal functions, with an optimal behavior of the constant in the limit of a large number of functions. The estimate generalizes the usual Strichartz inequality, in the same fashion as the Lieb-Thirring inequality generalizes the Sobolev inequality. As an application, we consider the Schrödinger equation with a time-dependent potential and we show the existence of the wave operator in Schatten spaces."}],"intvolume":" 16","month":"08","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1306.1309"}],"scopus_import":1,"date_updated":"2021-01-12T06:53:58Z","department":[{"_id":"RoSe"}],"_id":"1904","status":"public","type":"journal_article"},{"page":"127 - 129","doi":"10.1038/ncb2913","issue":"2","date_published":"2014-01-31T00:00:00Z","volume":16,"date_created":"2018-12-11T11:54:37Z","year":"2014","publication_status":"published","day":"31","language":[{"iso":"eng"}],"publication":"Nature Cell Biology","quality_controlled":"1","publisher":"Nature Publishing Group","scopus_import":1,"month":"01","intvolume":" 16","abstract":[{"lang":"eng","text":"Epithelial cell layers need to be tightly regulated to maintain their integrity and correct function. Cell integration into epithelial sheets is now shown to depend on the N-WASP-regulated stabilization of cortical F-actin, which generates distinct patterns of apical-lateral contractility at E-cadherin-based cell-cell junctions."}],"oa_version":"None","author":[{"last_name":"Behrndt","full_name":"Behrndt, Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5195","title":"Lateral junction dynamics lead the way out","department":[{"_id":"CaHe"}],"citation":{"chicago":"Behrndt, Martin, and Carl-Philipp J Heisenberg. “Lateral Junction Dynamics Lead the Way Out.” Nature Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb2913.","ista":"Behrndt M, Heisenberg C-PJ. 2014. Lateral junction dynamics lead the way out. Nature Cell Biology. 16(2), 127–129.","mla":"Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Lateral Junction Dynamics Lead the Way Out.” Nature Cell Biology, vol. 16, no. 2, Nature Publishing Group, 2014, pp. 127–29, doi:10.1038/ncb2913.","apa":"Behrndt, M., & Heisenberg, C.-P. J. (2014). Lateral junction dynamics lead the way out. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2913","ama":"Behrndt M, Heisenberg C-PJ. Lateral junction dynamics lead the way out. Nature Cell Biology. 2014;16(2):127-129. doi:10.1038/ncb2913","ieee":"M. Behrndt and C.-P. J. Heisenberg, “Lateral junction dynamics lead the way out,” Nature Cell Biology, vol. 16, no. 2. Nature Publishing Group, pp. 127–129, 2014.","short":"M. Behrndt, C.-P.J. Heisenberg, Nature Cell Biology 16 (2014) 127–129."},"date_updated":"2021-01-12T06:53:56Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1900"},{"acknowledgement":"Engineering and Physical Sciences Research Council. Grant Number: EP/H031928/1","publisher":"Wiley-Blackwell","oa":1,"has_accepted_license":"1","year":"2014","day":"01","publication":"Functional Ecology","page":"693 - 701","doi":"10.1111/1365-2435.12207","date_published":"2014-06-01T00:00:00Z","date_created":"2018-12-11T11:54:40Z","citation":{"ista":"Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 28(3), 693–701.","chicago":"Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology. Wiley-Blackwell, 2014. https://doi.org/10.1111/1365-2435.12207.","short":"T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.","ieee":"T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell, pp. 693–701, 2014.","ama":"Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701. doi:10.1111/1365-2435.12207","apa":"Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell. https://doi.org/10.1111/1365-2435.12207","mla":"Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell, 2014, pp. 693–701, doi:10.1111/1365-2435.12207."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5186","author":[{"full_name":"Ezard, Thomas","last_name":"Ezard","first_name":"Thomas"},{"last_name":"Prizak","full_name":"Prizak, Roshan","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rebecca","last_name":"Hoyle","full_name":"Hoyle, Rebecca"}],"title":"The fitness costs of adaptation via phenotypic plasticity and maternal effects","abstract":[{"text":"Summary: Phenotypes are often environmentally dependent, which requires organisms to track environmental change. The challenge for organisms is to construct phenotypes using the most accurate environmental cue. Here, we use a quantitative genetic model of adaptation by additive genetic variance, within- and transgenerational plasticity via linear reaction norms and indirect genetic effects respectively. We show how the relative influence on the eventual phenotype of these components depends on the predictability of environmental change (fast or slow, sinusoidal or stochastic) and the developmental lag τ between when the environment is perceived and when selection acts. We then decompose expected mean fitness into three components (variance load, adaptation and fluctuation load) to study the fitness costs of within- and transgenerational plasticity. A strongly negative maternal effect coefficient m minimizes the variance load, but a strongly positive m minimises the fluctuation load. The adaptation term is maximized closer to zero, with positive or negative m preferred under different environmental scenarios. Phenotypic plasticity is higher when τ is shorter and when the environment changes frequently between seasonal extremes. Expected mean population fitness is highest away from highest observed levels of phenotypic plasticity. Within- and transgenerational plasticity act in concert to deliver well-adapted phenotypes, which emphasizes the need to study both simultaneously when investigating phenotypic evolution.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"06","intvolume":" 28","publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5167","checksum":"3cbe8623174709a8ceec2103246f8fe0","date_updated":"2020-07-14T12:45:20Z","file_size":536154,"creator":"system","date_created":"2018-12-12T10:15:45Z","file_name":"IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf"}],"language":[{"iso":"eng"}],"issue":"3","volume":28,"_id":"1909","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"419","date_updated":"2021-01-12T06:54:00Z","ddc":["570"],"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:20Z"},{"month":"02","intvolume":" 44","publisher":"Wiley-Blackwell","scopus_import":1,"oa_version":"None","acknowledgement":"FWF. Grant Number: P22058-B20","abstract":[{"text":"angerhans cells (LCs) are a unique subset of dendritic cells (DCs) that express epithelial adhesion molecules, allowing them to form contacts with epithelial cells and reside in epidermal/epithelial tissues. The dynamic regulation of epithelial adhesion plays a decisive role in the life cycle of LCs. It controls whether LCs remain immature and sessile within the epidermis or mature and egress to initiate immune responses. So far, the molecular machinery regulating epithelial adhesion molecules during LC maturation remains elusive. Here, we generated pure populations of immature human LCs in vitro to systematically probe for gene-expression changes during LC maturation. LCs down-regulate a set of epithelial genes including E-cadherin, while they upregulate the mesenchymal marker N-cadherin known to facilitate cell migration. In addition, N-cadherin is constitutively expressed by monocyte-derived DCs known to exhibit characteristics of both inflammatory-type and interstitial/dermal DCs. Moreover, the transcription factors ZEB1 and ZEB2 (ZEB is zinc-finger E-box-binding homeobox) are upregulated in migratory LCs. ZEB1 and ZEB2 have been shown to induce epithelial-to-mesenchymal transition (EMT) and invasive behavior in cancer cells undergoing metastasis. Our results provide the first hint that the molecular EMT machinery might facilitate LC mobilization. Moreover, our study suggests that N-cadherin plays a role during DC migration.","lang":"eng"}],"date_published":"2014-02-01T00:00:00Z","volume":44,"issue":"2","doi":"10.1002/eji.201343681","date_created":"2018-12-11T11:54:40Z","page":"553 - 560","day":"01","publication":"European Journal of Immunology","language":[{"iso":"eng"}],"publication_status":"published","year":"2014","status":"public","type":"journal_article","_id":"1910","department":[{"_id":"MiSi"}],"title":"Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2","author":[{"full_name":"Konradi, Sabine","last_name":"Konradi","first_name":"Sabine"},{"last_name":"Yasmin","full_name":"Yasmin, Nighat","first_name":"Nighat"},{"first_name":"Denise","full_name":"Haslwanter, Denise","last_name":"Haslwanter"},{"first_name":"Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","last_name":"Weber","full_name":"Weber, Michele"},{"first_name":"Bernd","last_name":"Gesslbauer","full_name":"Gesslbauer, Bernd"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"last_name":"Strobl","full_name":"Strobl, Herbert","first_name":"Herbert"}],"publist_id":"5185","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:01Z","citation":{"chicago":"Konradi, Sabine, Nighat Yasmin, Denise Haslwanter, Michele Weber, Bernd Gesslbauer, Michael K Sixt, and Herbert Strobl. “Langerhans Cell Maturation Is Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition ZEB1/2.” European Journal of Immunology. Wiley-Blackwell, 2014. https://doi.org/10.1002/eji.201343681.","ista":"Konradi S, Yasmin N, Haslwanter D, Weber M, Gesslbauer B, Sixt MK, Strobl H. 2014. Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. 44(2), 553–560.","mla":"Konradi, Sabine, et al. “Langerhans Cell Maturation Is Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition ZEB1/2.” European Journal of Immunology, vol. 44, no. 2, Wiley-Blackwell, 2014, pp. 553–60, doi:10.1002/eji.201343681.","ieee":"S. Konradi et al., “Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2,” European Journal of Immunology, vol. 44, no. 2. Wiley-Blackwell, pp. 553–560, 2014.","short":"S. Konradi, N. Yasmin, D. Haslwanter, M. Weber, B. Gesslbauer, M.K. Sixt, H. Strobl, European Journal of Immunology 44 (2014) 553–560.","apa":"Konradi, S., Yasmin, N., Haslwanter, D., Weber, M., Gesslbauer, B., Sixt, M. K., & Strobl, H. (2014). Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. Wiley-Blackwell. https://doi.org/10.1002/eji.201343681","ama":"Konradi S, Yasmin N, Haslwanter D, et al. Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. 2014;44(2):553-560. doi:10.1002/eji.201343681"}},{"author":[{"last_name":"Demay","full_name":"Demay, Grégory","first_name":"Grégory"},{"first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","last_name":"Gazi","full_name":"Gazi, Peter"},{"last_name":"Maurer","full_name":"Maurer, Ueli","first_name":"Ueli"},{"last_name":"Tackmann","full_name":"Tackmann, Björn","first_name":"Björn"}],"publist_id":"5188","department":[{"_id":"KrPi"}],"title":"Optimality of non-adaptive strategies: The case of parallel games","date_updated":"2021-01-12T06:53:59Z","citation":{"chicago":"Demay, Grégory, Peter Gazi, Ueli Maurer, and Björn Tackmann. “Optimality of Non-Adaptive Strategies: The Case of Parallel Games.” In IEEE International Symposium on Information Theory. IEEE, 2014. https://doi.org/10.1109/ISIT.2014.6875125.","ista":"Demay G, Gazi P, Maurer U, Tackmann B. 2014. Optimality of non-adaptive strategies: The case of parallel games. IEEE International Symposium on Information Theory. IEEE International Symposium on Information Theory Proceedings, 6875125.","mla":"Demay, Grégory, et al. “Optimality of Non-Adaptive Strategies: The Case of Parallel Games.” IEEE International Symposium on Information Theory, 6875125, IEEE, 2014, doi:10.1109/ISIT.2014.6875125.","ieee":"G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Optimality of non-adaptive strategies: The case of parallel games,” in IEEE International Symposium on Information Theory, Honolulu, USA, 2014.","short":"G. Demay, P. Gazi, U. Maurer, B. Tackmann, in:, IEEE International Symposium on Information Theory, IEEE, 2014.","apa":"Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2014). Optimality of non-adaptive strategies: The case of parallel games. In IEEE International Symposium on Information Theory. Honolulu, USA: IEEE. https://doi.org/10.1109/ISIT.2014.6875125","ama":"Demay G, Gazi P, Maurer U, Tackmann B. Optimality of non-adaptive strategies: The case of parallel games. In: IEEE International Symposium on Information Theory. IEEE; 2014. doi:10.1109/ISIT.2014.6875125"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"conference","conference":{"name":"IEEE International Symposium on Information Theory Proceedings","start_date":"2014-06-29","end_date":"2014-07-04","location":"Honolulu, USA"},"status":"public","_id":"1907","article_number":"6875125","date_published":"2014-01-01T00:00:00Z","doi":"10.1109/ISIT.2014.6875125","date_created":"2018-12-11T11:54:39Z","year":"2014","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"IEEE International Symposium on Information Theory","publisher":"IEEE","quality_controlled":"1","scopus_import":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2014/299"}],"month":"01","abstract":[{"text":"Most cryptographic security proofs require showing that two systems are indistinguishable. A central tool in such proofs is that of a game, where winning the game means provoking a certain condition, and it is shown that the two systems considered cannot be distinguished unless this condition is provoked. Upper bounding the probability of winning such a game, i.e., provoking this condition, for an arbitrary strategy is usually hard, except in the special case where the best strategy for winning such a game is known to be non-adaptive. A sufficient criterion for ensuring the optimality of non-adaptive strategies is that of conditional equivalence to a system, a notion introduced in [1]. In this paper, we show that this criterion is not necessary to ensure the optimality of non-adaptive strategies by giving two results of independent interest: 1) the optimality of non-adaptive strategies is not preserved under parallel composition; 2) in contrast, conditional equivalence is preserved under parallel composition.","lang":"eng"}],"oa_version":"Submitted Version"},{"abstract":[{"text":"In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can bring together beneficial alleles from different backgrounds, but tightly linked alleles may still greatly interfere with each other. We show for well-mixed populations that when this interference is strong, the genome can be seen as consisting of many effectively asexual stretches linked together. The rate at which beneficial alleles fix is thus roughly proportional to the rate of recombination and depends only logarithmically on the mutation supply and the strength of selection. Our scaling arguments also allow us to predict, with reasonable accuracy, the fitness distribution of fixed mutations when the mutational effect sizes are broad. We focus on the regime in which crossovers occur more frequently than beneficial mutations, as is likely to be the case for many natural populations.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1307.0737","open_access":"1"}],"month":"04","intvolume":" 196","publication_status":"published","language":[{"iso":"eng"}],"volume":196,"issue":"4","ec_funded":1,"_id":"1908","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:59Z","department":[{"_id":"NiBa"}],"quality_controlled":"1","publisher":"Genetics Society of America","oa":1,"year":"2014","day":"01","publication":"Genetics","page":"1167 - 1183","doi":"10.1534/genetics.113.160705","date_published":"2014-04-01T00:00:00Z","date_created":"2018-12-11T11:54:39Z","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"citation":{"mla":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics, vol. 196, no. 4, Genetics Society of America, 2014, pp. 1167–83, doi:10.1534/genetics.113.160705.","short":"D. Weissman, O. Hallatschek, Genetics 196 (2014) 1167–1183.","ieee":"D. Weissman and O. Hallatschek, “The rate of adaptation in large sexual populations with linear chromosomes,” Genetics, vol. 196, no. 4. Genetics Society of America, pp. 1167–1183, 2014.","ama":"Weissman D, Hallatschek O. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 2014;196(4):1167-1183. doi:10.1534/genetics.113.160705","apa":"Weissman, D., & Hallatschek, O. (2014). The rate of adaptation in large sexual populations with linear chromosomes. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.160705","chicago":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics. Genetics Society of America, 2014. https://doi.org/10.1534/genetics.113.160705.","ista":"Weissman D, Hallatschek O. 2014. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 196(4), 1167–1183."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Weissman","full_name":"Weissman, Daniel","first_name":"Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Oskar","full_name":"Hallatschek, Oskar","last_name":"Hallatschek"}],"publist_id":"5187","title":"The rate of adaptation in large sexual populations with linear chromosomes"},{"acknowledgement":"Patrik Norén gratefully acknowledges support from the Wallenberg foundation","oa_version":"None","abstract":[{"text":"The topological Tverberg theorem has been generalized in several directions by setting extra restrictions on the Tverberg partitions. Restricted Tverberg partitions, defined by the idea that certain points cannot be in the same part, are encoded with graphs. When two points are adjacent in the graph, they are not in the same part. If the restrictions are too harsh, then the topological Tverberg theorem fails. The colored Tverberg theorem corresponds to graphs constructed as disjoint unions of small complete graphs. Hell studied the case of paths and cycles. In graph theory these partitions are usually viewed as graph colorings. As explored by Aharoni, Haxell, Meshulam and others there are fundamental connections between several notions of graph colorings and topological combinatorics. For ordinary graph colorings it is enough to require that the number of colors q satisfy q>Δ, where Δ is the maximal degree of the graph. It was proven by the first author using equivariant topology that if q>Δ 2 then the topological Tverberg theorem still works. It is conjectured that q>KΔ is also enough for some constant K, and in this paper we prove a fixed-parameter version of that conjecture. The required topological connectivity results are proven with shellability, which also strengthens some previous partial results where the topological connectivity was proven with the nerve lemma.","lang":"eng"}],"intvolume":" 51","month":"01","publisher":"Springer","scopus_import":1,"language":[{"iso":"eng"}],"publication":"Discrete & Computational Geometry","day":"01","publication_status":"published","year":"2014","date_created":"2018-12-11T11:54:40Z","doi":"10.1007/s00454-013-9556-3","date_published":"2014-01-01T00:00:00Z","volume":51,"issue":"1","page":"207 - 220","_id":"1911","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:01Z","citation":{"mla":"Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.” Discrete & Computational Geometry, vol. 51, no. 1, Springer, 2014, pp. 207–20, doi:10.1007/s00454-013-9556-3.","ieee":"A. Engström and P. Noren, “Tverberg’s Theorem and Graph Coloring,” Discrete & Computational Geometry, vol. 51, no. 1. Springer, pp. 207–220, 2014.","short":"A. Engström, P. Noren, Discrete & Computational Geometry 51 (2014) 207–220.","ama":"Engström A, Noren P. Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. 2014;51(1):207-220. doi:10.1007/s00454-013-9556-3","apa":"Engström, A., & Noren, P. (2014). Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-013-9556-3","chicago":"Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-013-9556-3.","ista":"Engström A, Noren P. 2014. Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. 51(1), 207–220."},"title":"Tverberg's Theorem and Graph Coloring","department":[{"_id":"CaUh"}],"publist_id":"5183","author":[{"first_name":"Alexander","full_name":"Engström, Alexander","last_name":"Engström"},{"last_name":"Noren","full_name":"Noren, Patrik","id":"46870C74-F248-11E8-B48F-1D18A9856A87","first_name":"Patrik"}]},{"language":[{"iso":"eng"}],"publication_status":"published","issue":"6170","volume":343,"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases characterized by progressive age-dependent loss of corticospinal motor tract function. Although the genetic basis is partly understood, only a fraction of cases can receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome sequencing in combination with network analysis, we identified 18 previously unknown putative HSP genes and validated nearly all of these genes functionally or genetically. The pathways highlighted by these mutations link HSP to cellular transport, nucleotide metabolism, and synapse and axon development. Network analysis revealed a host of further candidate genes, of which three were mutated in our cohort. Our analysis links HSP to other neurodegenerative disorders and can facilitate gene discovery and mechanistic understanding of disease."}],"month":"01","intvolume":" 343","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157572/","open_access":"1"}],"date_updated":"2021-01-12T06:54:03Z","department":[{"_id":"GaNo"}],"_id":"1916","status":"public","article_type":"original","type":"journal_article","day":"31","publication":"Science","year":"2014","date_published":"2014-01-31T00:00:00Z","doi":"10.1126/science.1247363","date_created":"2018-12-11T11:54:42Z","page":"506 - 511","acknowledgement":"Supported by the Deutsche Forschungsgemeinschaft (G.N.)","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Novarino, Gaia, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders.” Science, vol. 343, no. 6170, American Association for the Advancement of Science, 2014, pp. 506–11, doi:10.1126/science.1247363.","apa":"Novarino, G., Fenstermaker, A., Zaki, M., Hofree, M., Silhavy, J., Heiberg, A., … Gleeson, J. (2014). Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1247363","ama":"Novarino G, Fenstermaker A, Zaki M, et al. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 2014;343(6170):506-511. doi:10.1126/science.1247363","short":"G. Novarino, A. Fenstermaker, M. Zaki, M. Hofree, J. Silhavy, A. Heiberg, M. Abdellateef, B. Rosti, E. Scott, L. Mansour, A. Masri, H. Kayserili, J. Al Aama, G. Abdel Salam, A. Karminejad, M. Kara, B. Kara, B. Bozorgmehri, T. Ben Omran, F. Mojahedi, I. Mahmoud, N. Bouslam, A. Bouhouche, A. Benomar, S. Hanein, L. Raymond, S. Forlani, M. Mascaro, L. Selim, N. Shehata, N. Al Allawi, P. Bindu, M. Azam, M. Günel, A. Caglayan, K. Bilgüvar, A. Tolun, M. Issa, J. Schroth, E. Spencer, R. Rosti, N. Akizu, K. Vaux, A. Johansen, A. Koh, H. Megahed, A. Dürr, A. Brice, G. Stévanin, S. Gabriel, T. Ideker, J. Gleeson, Science 343 (2014) 506–511.","ieee":"G. Novarino et al., “Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders,” Science, vol. 343, no. 6170. American Association for the Advancement of Science, pp. 506–511, 2014.","chicago":"Novarino, Gaia, Ali Fenstermaker, Maha Zaki, Matan Hofree, Jennifer Silhavy, Andrew Heiberg, Mostafa Abdellateef, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1247363.","ista":"Novarino G, Fenstermaker A, Zaki M, Hofree M, Silhavy J, Heiberg A, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al Aama J, Abdel Salam G, Karminejad A, Kara M, Kara B, Bozorgmehri B, Ben Omran T, Mojahedi F, Mahmoud I, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro M, Selim L, Shehata N, Al Allawi N, Bindu P, Azam M, Günel M, Caglayan A, Bilgüvar K, Tolun A, Issa M, Schroth J, Spencer E, Rosti R, Akizu N, Vaux K, Johansen A, Koh A, Megahed H, Dürr A, Brice A, Stévanin G, Gabriel S, Ideker T, Gleeson J. 2014. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 343(6170), 506–511."},"title":"Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders","author":[{"last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"first_name":"Ali","full_name":"Fenstermaker, Ali","last_name":"Fenstermaker"},{"first_name":"Maha","last_name":"Zaki","full_name":"Zaki, Maha"},{"full_name":"Hofree, Matan","last_name":"Hofree","first_name":"Matan"},{"last_name":"Silhavy","full_name":"Silhavy, Jennifer","first_name":"Jennifer"},{"full_name":"Heiberg, Andrew","last_name":"Heiberg","first_name":"Andrew"},{"last_name":"Abdellateef","full_name":"Abdellateef, Mostafa","first_name":"Mostafa"},{"last_name":"Rosti","full_name":"Rosti, Başak","first_name":"Başak"},{"last_name":"Scott","full_name":"Scott, Eric","first_name":"Eric"},{"first_name":"Lobna","last_name":"Mansour","full_name":"Mansour, Lobna"},{"full_name":"Masri, Amira","last_name":"Masri","first_name":"Amira"},{"last_name":"Kayserili","full_name":"Kayserili, Hülya","first_name":"Hülya"},{"first_name":"Jumana","full_name":"Al Aama, Jumana","last_name":"Al Aama"},{"last_name":"Abdel Salam","full_name":"Abdel Salam, Ghada","first_name":"Ghada"},{"first_name":"Ariana","full_name":"Karminejad, Ariana","last_name":"Karminejad"},{"first_name":"Majdi","last_name":"Kara","full_name":"Kara, Majdi"},{"full_name":"Kara, Bülent","last_name":"Kara","first_name":"Bülent"},{"first_name":"Bita","full_name":"Bozorgmehri, Bita","last_name":"Bozorgmehri"},{"first_name":"Tawfeg","last_name":"Ben Omran","full_name":"Ben Omran, Tawfeg"},{"first_name":"Faezeh","full_name":"Mojahedi, Faezeh","last_name":"Mojahedi"},{"first_name":"Iman","last_name":"Mahmoud","full_name":"Mahmoud, Iman"},{"full_name":"Bouslam, Naïma","last_name":"Bouslam","first_name":"Naïma"},{"first_name":"Ahmed","full_name":"Bouhouche, Ahmed","last_name":"Bouhouche"},{"first_name":"Ali","last_name":"Benomar","full_name":"Benomar, Ali"},{"full_name":"Hanein, Sylvain","last_name":"Hanein","first_name":"Sylvain"},{"full_name":"Raymond, Laure","last_name":"Raymond","first_name":"Laure"},{"first_name":"Sylvie","full_name":"Forlani, Sylvie","last_name":"Forlani"},{"first_name":"Massimo","full_name":"Mascaro, Massimo","last_name":"Mascaro"},{"first_name":"Laila","last_name":"Selim","full_name":"Selim, Laila"},{"full_name":"Shehata, Nabil","last_name":"Shehata","first_name":"Nabil"},{"first_name":"Nasir","full_name":"Al Allawi, Nasir","last_name":"Al Allawi"},{"last_name":"Bindu","full_name":"Bindu, Parayil","first_name":"Parayil"},{"first_name":"Matloob","full_name":"Azam, Matloob","last_name":"Azam"},{"first_name":"Murat","full_name":"Günel, Murat","last_name":"Günel"},{"last_name":"Caglayan","full_name":"Caglayan, Ahmet","first_name":"Ahmet"},{"full_name":"Bilgüvar, Kaya","last_name":"Bilgüvar","first_name":"Kaya"},{"last_name":"Tolun","full_name":"Tolun, Aslihan","first_name":"Aslihan"},{"last_name":"Issa","full_name":"Issa, Mahmoud","first_name":"Mahmoud"},{"first_name":"Jana","full_name":"Schroth, Jana","last_name":"Schroth"},{"full_name":"Spencer, Emily","last_name":"Spencer","first_name":"Emily"},{"full_name":"Rosti, Rasim","last_name":"Rosti","first_name":"Rasim"},{"first_name":"Naiara","last_name":"Akizu","full_name":"Akizu, Naiara"},{"first_name":"Keith","full_name":"Vaux, Keith","last_name":"Vaux"},{"first_name":"Anide","last_name":"Johansen","full_name":"Johansen, Anide"},{"first_name":"Alice","last_name":"Koh","full_name":"Koh, Alice"},{"full_name":"Megahed, Hisham","last_name":"Megahed","first_name":"Hisham"},{"first_name":"Alexandra","last_name":"Dürr","full_name":"Dürr, Alexandra"},{"last_name":"Brice","full_name":"Brice, Alexis","first_name":"Alexis"},{"first_name":"Giovanni","full_name":"Stévanin, Giovanni","last_name":"Stévanin"},{"first_name":"Stacy","last_name":"Gabriel","full_name":"Gabriel, Stacy"},{"first_name":"Trey","last_name":"Ideker","full_name":"Ideker, Trey"},{"full_name":"Gleeson, Joseph","last_name":"Gleeson","first_name":"Joseph"}],"publist_id":"5178","article_processing_charge":"No","external_id":{"pmid":["24482476"]}},{"citation":{"chicago":"Xu, Tongda, Ning Dai, Jisheng Chen, Shingo Nagawa, Min Cao, Hongjiang Li, Zimin Zhou, et al. “Cell Surface ABP1-TMK Auxin Sensing Complex Activates ROP GTPase Signaling.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1245125.","ista":"Xu T, Dai N, Chen J, Nagawa S, Cao M, Li H, Zhou Z, Chen X, De Rycke R, Rakusová H, Wang W, Jones A, Friml J, Patterson S, Bleecker A, Yang Z. 2014. Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. 343(6174), 1025–1028.","mla":"Xu, Tongda, et al. “Cell Surface ABP1-TMK Auxin Sensing Complex Activates ROP GTPase Signaling.” Science, vol. 343, no. 6174, American Association for the Advancement of Science, 2014, pp. 1025–28, doi:10.1126/science.1245125.","apa":"Xu, T., Dai, N., Chen, J., Nagawa, S., Cao, M., Li, H., … Yang, Z. (2014). Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1245125","ama":"Xu T, Dai N, Chen J, et al. Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. 2014;343(6174):1025-1028. doi:10.1126/science.1245125","ieee":"T. Xu et al., “Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling,” Science, vol. 343, no. 6174. American Association for the Advancement of Science, pp. 1025–1028, 2014.","short":"T. Xu, N. Dai, J. Chen, S. Nagawa, M. Cao, H. Li, Z. Zhou, X. Chen, R. De Rycke, H. Rakusová, W. Wang, A. Jones, J. Friml, S. Patterson, A. Bleecker, Z. Yang, Science 343 (2014) 1025–1028."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["24578577"]},"article_processing_charge":"No","author":[{"first_name":"Tongda","full_name":"Xu, Tongda","last_name":"Xu"},{"full_name":"Dai, Ning","last_name":"Dai","first_name":"Ning"},{"last_name":"Chen","full_name":"Chen, Jisheng","first_name":"Jisheng"},{"first_name":"Shingo","last_name":"Nagawa","full_name":"Nagawa, Shingo"},{"first_name":"Min","full_name":"Cao, Min","last_name":"Cao"},{"last_name":"Li","full_name":"Li, Hongjiang","orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang"},{"full_name":"Zhou, Zimin","last_name":"Zhou","first_name":"Zimin"},{"last_name":"Chen","full_name":"Chen, Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu"},{"first_name":"Riet","full_name":"De Rycke, Riet","last_name":"De Rycke"},{"first_name":"Hana","last_name":"Rakusová","full_name":"Rakusová, Hana"},{"full_name":"Wang, Wen","last_name":"Wang","first_name":"Wen"},{"last_name":"Jones","full_name":"Jones, Alan","first_name":"Alan"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"full_name":"Patterson, Sara","last_name":"Patterson","first_name":"Sara"},{"first_name":"Anthony","full_name":"Bleecker, Anthony","last_name":"Bleecker"},{"first_name":"Zhenbiao","last_name":"Yang","full_name":"Yang, Zhenbiao"}],"publist_id":"5177","title":"Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling","year":"2014","publication":"Science","day":"28","page":"1025 - 1028","date_created":"2018-12-11T11:54:42Z","doi":"10.1126/science.1245125","date_published":"2014-02-28T00:00:00Z","acknowledgement":"Supported by the intramural research program of the National Institute of Arthritis and Musculoskeletal and Skin Diseases and by its Laboratory Animal Care and Use Section and Flow Cytometry Group, Office of Science and Technology","oa":1,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","date_updated":"2021-01-12T06:54:03Z","department":[{"_id":"JiFr"}],"_id":"1917","type":"journal_article","article_type":"original","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":343,"issue":"6174","abstract":[{"text":"Auxin-binding protein 1 (ABP1) was discovered nearly 40 years ago and was shown to be essential for plant development and morphogenesis, but its mode of action remains unclear. Here, we report that the plasma membrane-localized transmembrane kinase (TMK) receptor-like kinases interact with ABP1 and transduce auxin signal to activate plasma membrane-associated ROPs [Rho-like guanosine triphosphatases (GTPase) from plants], leading to changes in the cytoskeleton and the shape of leaf pavement cells in Arabidopsis. The interaction between ABP1 and TMK at the cell surface is induced by auxin and requires ABP1 sensing of auxin. These findings show that TMK proteins and ABP1 form a cell surface auxin perception complex that activates ROP signaling pathways, regulating nontranscriptional cytoplasmic responses and associated fundamental processes.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166562/","open_access":"1"}],"scopus_import":1,"intvolume":" 343","month":"02"},{"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890858/","open_access":"1"}],"oa":1,"publisher":"National Academy of Sciences","scopus_import":1,"intvolume":" 111","month":"01","abstract":[{"lang":"eng","text":"Cerebellar motor learning is suggested to be caused by long-term plasticity of excitatory parallel fiber-Purkinje cell (PF-PC) synapses associated with changes in the number of synaptic AMPA-type glutamate receptors (AMPARs). However, whether the AMPARs decrease or increase in individual PF-PC synapses occurs in physiological motor learning and accounts for memory that lasts over days remains elusive. We combined quantitative SDS-digested freeze-fracture replica labeling for AMPAR and physical dissector electron microscopy with a simple model of cerebellar motor learning, adaptation of horizontal optokinetic response (HOKR) in mouse. After 1-h training of HOKR, short-term adaptation (STA) was accompanied with transient decrease in AMPARs by 28% in target PF-PC synapses. STA was well correlated with AMPAR decrease in individual animals and both STA and AMPAR decrease recovered to basal levels within 24 h. Surprisingly, long-termadaptation (LTA) after five consecutive daily trainings of 1-h HOKR did not alter the number of AMPARs in PF-PC synapses but caused gradual and persistent synapse elimination by 45%, with corresponding PC spine loss by the fifth training day. Furthermore, recovery of LTA after 2 wk was well correlated with increase of PF-PC synapses to the control level. Our findings indicate that the AMPARs decrease in PF-PC synapses and the elimination of these synapses are in vivo engrams in short- and long-term motor learning, respectively, showing a unique type of synaptic plasticity that may contribute to memory consolidation."}],"acknowledgement":"This work was supported by Solution-Oriented Research for Science and Technology from the Japan Science and Technology Agency; Ministry of Education, Culture, Sports, Science and Technology of Japan Grant 16300114 (to R.S.).","oa_version":"Submitted Version","page":"E188 - E193","date_created":"2018-12-11T11:54:43Z","volume":111,"issue":"1","date_published":"2014-01-07T00:00:00Z","doi":"10.1073/pnas.1315541111","publication_status":"published","year":"2014","publication":"PNAS","language":[{"iso":"eng"}],"day":"07","type":"journal_article","status":"public","_id":"1920","author":[{"first_name":"Wen","last_name":"Wang","full_name":"Wang, Wen"},{"first_name":"Kazuhiko","full_name":"Nakadate, Kazuhiko","last_name":"Nakadate"},{"first_name":"Miwako","full_name":"Masugi Tokita, Miwako","last_name":"Masugi Tokita"},{"full_name":"Shutoh, Fumihiro","last_name":"Shutoh","first_name":"Fumihiro"},{"last_name":"Aziz","full_name":"Aziz, Wajeeha","first_name":"Wajeeha"},{"first_name":"Etsuko","last_name":"Tarusawa","full_name":"Tarusawa, Etsuko"},{"full_name":"Lörincz, Andrea","last_name":"Lörincz","first_name":"Andrea"},{"first_name":"Elek","last_name":"Molnár","full_name":"Molnár, Elek"},{"first_name":"Sebnem","id":"401AB46C-F248-11E8-B48F-1D18A9856A87","full_name":"Kesaf, Sebnem","last_name":"Kesaf"},{"first_name":"Yunqing","last_name":"Li","full_name":"Li, Yunqing"},{"first_name":"Yugo","full_name":"Fukazawa, Yugo","last_name":"Fukazawa"},{"last_name":"Nagao","full_name":"Nagao, Soichi","first_name":"Soichi"},{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5174","department":[{"_id":"RySh"}],"title":"Distinct cerebellar engrams in short-term and long-term motor learning","citation":{"mla":"Wang, Wen, et al. “Distinct Cerebellar Engrams in Short-Term and Long-Term Motor Learning.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. E188–93, doi:10.1073/pnas.1315541111.","ieee":"W. Wang et al., “Distinct cerebellar engrams in short-term and long-term motor learning,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. E188–E193, 2014.","short":"W. Wang, K. Nakadate, M. Masugi Tokita, F. Shutoh, W. Aziz, E. Tarusawa, A. Lörincz, E. Molnár, S. Kesaf, Y. Li, Y. Fukazawa, S. Nagao, R. Shigemoto, PNAS 111 (2014) E188–E193.","ama":"Wang W, Nakadate K, Masugi Tokita M, et al. Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. 2014;111(1):E188-E193. doi:10.1073/pnas.1315541111","apa":"Wang, W., Nakadate, K., Masugi Tokita, M., Shutoh, F., Aziz, W., Tarusawa, E., … Shigemoto, R. (2014). Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1315541111","chicago":"Wang, Wen, Kazuhiko Nakadate, Miwako Masugi Tokita, Fumihiro Shutoh, Wajeeha Aziz, Etsuko Tarusawa, Andrea Lörincz, et al. “Distinct Cerebellar Engrams in Short-Term and Long-Term Motor Learning.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1315541111.","ista":"Wang W, Nakadate K, Masugi Tokita M, Shutoh F, Aziz W, Tarusawa E, Lörincz A, Molnár E, Kesaf S, Li Y, Fukazawa Y, Nagao S, Shigemoto R. 2014. Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. 111(1), E188–E193."},"date_updated":"2021-01-12T06:54:05Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"date_updated":"2022-06-07T11:20:56Z","department":[{"_id":"JiFr"}],"_id":"1915","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["0300-5127"],"eissn":["1470-8752"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"1","volume":42,"abstract":[{"text":"ROPs (Rho of plants) belong to a large family of plant-specific Rho-like small GTPases that function as essential molecular switches to control diverse cellular processes including cytoskeleton organization, cell polarization, cytokinesis, cell differentiation and vesicle trafficking. Although the machineries of vesicle trafficking and cell polarity in plants have been individually well addressed, how ROPs co-ordinate those processes is still largely unclear. Recent progress has been made towards an understanding of the coordination of ROP signalling and trafficking of PIN (PINFORMED) transporters for the plant hormone auxin in both root and leaf pavement cells. PIN transporters constantly shuttle between the endosomal compartments and the polar plasma membrane domains, therefore the modulation of PIN-dependent auxin transport between cells is a main developmental output of ROP-regulated vesicle trafficking. The present review focuses on these cellular mechanisms, especially the integration of ROP-based vesicle trafficking and plant cell polarity.","lang":"eng"}],"oa_version":"None","pmid":1,"scopus_import":"1","intvolume":" 42","month":"02","citation":{"apa":"Chen, X., & Friml, J. (2014). Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/BST20130269","ama":"Chen X, Friml J. Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. 2014;42(1):212-218. doi:10.1042/BST20130269","ieee":"X. Chen and J. Friml, “Rho-GTPase-regulated vesicle trafficking in plant cell polarity,” Biochemical Society Transactions, vol. 42, no. 1. Portland Press, pp. 212–218, 2014.","short":"X. Chen, J. Friml, Biochemical Society Transactions 42 (2014) 212–218.","mla":"Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant Cell Polarity.” Biochemical Society Transactions, vol. 42, no. 1, Portland Press, 2014, pp. 212–18, doi:10.1042/BST20130269.","ista":"Chen X, Friml J. 2014. Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. 42(1), 212–218.","chicago":"Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant Cell Polarity.” Biochemical Society Transactions. Portland Press, 2014. https://doi.org/10.1042/BST20130269."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["24450654"]},"author":[{"id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu","last_name":"Chen","full_name":"Chen, Xu"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"5179","title":"Rho-GTPase-regulated vesicle trafficking in plant cell polarity","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"year":"2014","publication":"Biochemical Society Transactions","day":"01","page":"212 - 218","date_created":"2018-12-11T11:54:41Z","doi":"10.1042/BST20130269","date_published":"2014-02-01T00:00:00Z","acknowledgement":"This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP], Central European Institute of Technology (CEITEC) [grant number CZ.1.05/1.1.00/02.0068], European Social Fund [grant number CZ.1.07/2.3.00/20.0043] and the Czec","publisher":"Portland Press","quality_controlled":"1"},{"intvolume":" 111","month":"01","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890840/","open_access":"1"}],"publisher":"National Academy of Sciences","scopus_import":1,"acknowledgement":"his work was supported by Solution Oriented Research for Science and Technology (R.S.), Core Research for Evolutional Science and Technology, Japan Science and Technology Agency (Y.F.), and Grants-in-Aid for Scientific Research on Priority Areas-Molecular Brain Sciences 16300114 (to R.S.) and 18022043 (to Y.F.).","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Long-lasting memories are formed when the stimulus is temporally distributed (spacing effect). However, the synaptic mechanisms underlying this robust phenomenon and the precise time course of the synaptic modifications that occur during learning remain unclear. Here we examined the adaptation of horizontal optokinetic response in mice that underwent 1 h of massed and spaced training at varying intervals. Despite similar acquisition by all training protocols, 1 h of spacing produced the highest memory retention at 24 h, which lasted for 1 mo. The distinct kinetics of memory are strongly correlated with the reduction of floccular parallel fiber-Purkinje cell synapses but not with AMPA receptor (AMPAR) number and synapse size. After the spaced training, we observed 25%, 23%, and 12% reduction in AMPAR density, synapse size, and synapse number, respectively. Four hours after the spaced training, half of the synapses and Purkinje cell spines had been eliminated, whereas AMPAR density and synapse size were recovered in remaining synapses. Surprisingly, massed training also produced long-term memory and halving of synapses; however, this occurred slowly over days, and the memory lasted for only 1 wk. This distinct kinetics of structural plasticity may serve as a basis for unique temporal profiles in the formation and decay of memory with or without intervals."}],"date_created":"2018-12-11T11:54:43Z","issue":"1","date_published":"2014-01-07T00:00:00Z","doi":"10.1073/pnas.1303317110","volume":111,"page":"E194 - E202","language":[{"iso":"eng"}],"publication":"PNAS","day":"07","publication_status":"published","year":"2014","status":"public","type":"journal_article","_id":"1919","title":"Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning","department":[{"_id":"RySh"}],"publist_id":"5175","author":[{"full_name":"Aziz, Wajeeha","last_name":"Aziz","first_name":"Wajeeha"},{"full_name":"Wang, Wen","last_name":"Wang","first_name":"Wen"},{"id":"401AB46C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebnem","last_name":"Kesaf","full_name":"Kesaf, Sebnem"},{"first_name":"Alsayed","last_name":"Mohamed","full_name":"Mohamed, Alsayed"},{"first_name":"Yugo","full_name":"Fukazawa, Yugo","last_name":"Fukazawa"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:04Z","citation":{"ama":"Aziz W, Wang W, Kesaf S, Mohamed A, Fukazawa Y, Shigemoto R. Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. 2014;111(1):E194-E202. doi:10.1073/pnas.1303317110","apa":"Aziz, W., Wang, W., Kesaf, S., Mohamed, A., Fukazawa, Y., & Shigemoto, R. (2014). Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1303317110","ieee":"W. Aziz, W. Wang, S. Kesaf, A. Mohamed, Y. Fukazawa, and R. Shigemoto, “Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. E194–E202, 2014.","short":"W. Aziz, W. Wang, S. Kesaf, A. Mohamed, Y. Fukazawa, R. Shigemoto, PNAS 111 (2014) E194–E202.","mla":"Aziz, Wajeeha, et al. “Distinct Kinetics of Synaptic Structural Plasticity, Memory Formation, and Memory Decay in Massed and Spaced Learning.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. E194–202, doi:10.1073/pnas.1303317110.","ista":"Aziz W, Wang W, Kesaf S, Mohamed A, Fukazawa Y, Shigemoto R. 2014. Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. 111(1), E194–E202.","chicago":"Aziz, Wajeeha, Wen Wang, Sebnem Kesaf, Alsayed Mohamed, Yugo Fukazawa, and Ryuichi Shigemoto. “Distinct Kinetics of Synaptic Structural Plasticity, Memory Formation, and Memory Decay in Massed and Spaced Learning.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1303317110."}},{"_id":"1918","status":"public","type":"journal_article","date_updated":"2021-01-12T06:54:04Z","department":[{"_id":"RoSe"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"As the nuclear charge Z is continuously decreased an N-electron atom undergoes a binding-unbinding transition. We investigate whether the electrons remain bound and whether the radius of the system stays finite as the critical value Zc is approached. Existence of a ground state at Zc is shown under the condition Zc < N-K, where K is the maximal number of electrons that can be removed at Zc without changing the energy."}],"month":"02","intvolume":" 26","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1301.5370"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":26,"issue":"1","article_number":"1350021","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bellazzini J, Frank R, Lieb É, Seiringer R. 2014. Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. 26(1), 1350021.","chicago":"Bellazzini, Jacopo, Rupert Frank, Élliott Lieb, and Robert Seiringer. “Existence of Ground States for Negative Ions at the Binding Threshold.” Reviews in Mathematical Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X13500219.","ama":"Bellazzini J, Frank R, Lieb É, Seiringer R. Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. 2014;26(1). doi:10.1142/S0129055X13500219","apa":"Bellazzini, J., Frank, R., Lieb, É., & Seiringer, R. (2014). Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X13500219","ieee":"J. Bellazzini, R. Frank, É. Lieb, and R. Seiringer, “Existence of ground states for negative ions at the binding threshold,” Reviews in Mathematical Physics, vol. 26, no. 1. World Scientific Publishing, 2014.","short":"J. Bellazzini, R. Frank, É. Lieb, R. Seiringer, Reviews in Mathematical Physics 26 (2014).","mla":"Bellazzini, Jacopo, et al. “Existence of Ground States for Negative Ions at the Binding Threshold.” Reviews in Mathematical Physics, vol. 26, no. 1, 1350021, World Scientific Publishing, 2014, doi:10.1142/S0129055X13500219."},"title":"Existence of ground states for negative ions at the binding threshold","publist_id":"5176","author":[{"last_name":"Bellazzini","full_name":"Bellazzini, Jacopo","first_name":"Jacopo"},{"first_name":"Rupert","last_name":"Frank","full_name":"Frank, Rupert"},{"full_name":"Lieb, Élliott","last_name":"Lieb","first_name":"Élliott"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"publisher":"World Scientific Publishing","quality_controlled":"1","oa":1,"day":"01","publication":"Reviews in Mathematical Physics","year":"2014","date_published":"2014-02-01T00:00:00Z","doi":"10.1142/S0129055X13500219","date_created":"2018-12-11T11:54:42Z"},{"_id":"1914","type":"journal_article","status":"public","date_updated":"2021-01-12T06:54:02Z","citation":{"chicago":"Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to Protein Perdition.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2013.11.019.","ista":"Sauer M, Friml J. 2014. Plant biology: Gatekeepers of the road to protein perdition. Current Biology. 24(1), R27–R29.","mla":"Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to Protein Perdition.” Current Biology, vol. 24, no. 1, Cell Press, 2014, pp. R27–29, doi:10.1016/j.cub.2013.11.019.","short":"M. Sauer, J. Friml, Current Biology 24 (2014) R27–R29.","ieee":"M. Sauer and J. Friml, “Plant biology: Gatekeepers of the road to protein perdition,” Current Biology, vol. 24, no. 1. Cell Press, pp. R27–R29, 2014.","ama":"Sauer M, Friml J. Plant biology: Gatekeepers of the road to protein perdition. Current Biology. 2014;24(1):R27-R29. doi:10.1016/j.cub.2013.11.019","apa":"Sauer, M., & Friml, J. (2014). Plant biology: Gatekeepers of the road to protein perdition. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.11.019"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5180","author":[{"last_name":"Sauer","full_name":"Sauer, Michael","first_name":"Michael"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"department":[{"_id":"JiFr"}],"title":"Plant biology: Gatekeepers of the road to protein perdition","abstract":[{"text":"Targeting membrane proteins for degradation requires the sequential action of ESCRT sub-complexes ESCRT-0 to ESCRT-III. Although this machinery is generally conserved among kingdoms, plants lack the essential ESCRT-0 components. A new report closes this gap by identifying a novel protein family that substitutes for ESCRT-0 function in plants.","lang":"eng"}],"oa_version":"None","scopus_import":1,"publisher":"Cell Press","quality_controlled":"1","intvolume":" 24","month":"01","publication_status":"published","year":"2014","language":[{"iso":"eng"}],"publication":"Current Biology","day":"06","page":"R27 - R29","date_created":"2018-12-11T11:54:41Z","doi":"10.1016/j.cub.2013.11.019","volume":24,"issue":"1","date_published":"2014-01-06T00:00:00Z"},{"article_processing_charge":"No","publist_id":"5169","author":[{"first_name":"Constanze","full_name":"Lamprecht, Constanze","last_name":"Lamprecht"},{"full_name":"Plochberger, Birgit","last_name":"Plochberger","first_name":"Birgit"},{"full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633","last_name":"Ruprecht","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","first_name":"Verena"},{"last_name":"Wieser","full_name":"Wieser, Stefan","orcid":"0000-0002-2670-2217","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"last_name":"Rankl","full_name":"Rankl, Christian","first_name":"Christian"},{"last_name":"Heister","full_name":"Heister, Elena","first_name":"Elena"},{"first_name":"Barbara","full_name":"Unterauer, Barbara","last_name":"Unterauer"},{"full_name":"Brameshuber, Mario","last_name":"Brameshuber","first_name":"Mario"},{"full_name":"Danzberger, Jürgen","last_name":"Danzberger","first_name":"Jürgen"},{"first_name":"Petar","full_name":"Lukanov, Petar","last_name":"Lukanov"},{"full_name":"Flahaut, Emmanuel","last_name":"Flahaut","first_name":"Emmanuel"},{"first_name":"Gerhard","full_name":"Schütz, Gerhard","last_name":"Schütz"},{"last_name":"Hinterdorfer","full_name":"Hinterdorfer, Peter","first_name":"Peter"},{"first_name":"Andreas","last_name":"Ebner","full_name":"Ebner, Andreas"}],"title":"A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes","citation":{"ista":"Lamprecht C, Plochberger B, Ruprecht V, Wieser S, Rankl C, Heister E, Unterauer B, Brameshuber M, Danzberger J, Lukanov P, Flahaut E, Schütz G, Hinterdorfer P, Ebner A. 2014. A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. 25(12), 125704.","chicago":"Lamprecht, Constanze, Birgit Plochberger, Verena Ruprecht, Stefan Wieser, Christian Rankl, Elena Heister, Barbara Unterauer, et al. “A Single-Molecule Approach to Explore Binding Uptake and Transport of Cancer Cell Targeting Nanotubes.” Nanotechnology. IOP Publishing, 2014. https://doi.org/10.1088/0957-4484/25/12/125704.","short":"C. Lamprecht, B. Plochberger, V. Ruprecht, S. Wieser, C. Rankl, E. Heister, B. Unterauer, M. Brameshuber, J. Danzberger, P. Lukanov, E. Flahaut, G. Schütz, P. Hinterdorfer, A. Ebner, Nanotechnology 25 (2014).","ieee":"C. Lamprecht et al., “A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes,” Nanotechnology, vol. 25, no. 12. IOP Publishing, 2014.","ama":"Lamprecht C, Plochberger B, Ruprecht V, et al. A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. 2014;25(12). doi:10.1088/0957-4484/25/12/125704","apa":"Lamprecht, C., Plochberger, B., Ruprecht, V., Wieser, S., Rankl, C., Heister, E., … Ebner, A. (2014). A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. IOP Publishing. https://doi.org/10.1088/0957-4484/25/12/125704","mla":"Lamprecht, Constanze, et al. “A Single-Molecule Approach to Explore Binding Uptake and Transport of Cancer Cell Targeting Nanotubes.” Nanotechnology, vol. 25, no. 12, 125704, IOP Publishing, 2014, doi:10.1088/0957-4484/25/12/125704."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"125704","date_created":"2018-12-11T11:54:45Z","doi":"10.1088/0957-4484/25/12/125704","date_published":"2014-03-28T00:00:00Z","year":"2014","has_accepted_license":"1","publication":"Nanotechnology","day":"28","oa":1,"publisher":"IOP Publishing","acknowledgement":"This work was supported by EC grant Marie Curie RTN-CT-2006-035616, CARBIO 'Carbon nanotubes for biomedical applications' and Austrian FFG grant mnt-era.net 823980, 'IntelliTip'.\r\n","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:45:21Z","date_updated":"2021-01-12T06:54:07Z","ddc":["570"],"type":"journal_article","article_type":"original","status":"public","_id":"1925","issue":"12","volume":25,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"7856","checksum":"df4e03d225a19179e7790f6d87a12332","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2014_Nanotechnology_Lamprecht.pdf","date_created":"2020-05-15T09:21:19Z","creator":"dernst","file_size":3804152,"date_updated":"2020-07-14T12:45:21Z"}],"scopus_import":1,"intvolume":" 25","month":"03","abstract":[{"lang":"eng","text":"In the past decade carbon nanotubes (CNTs) have been widely studied as a potential drug-delivery system, especially with functionality for cellular targeting. Yet, little is known about the actual process of docking to cell receptors and transport dynamics after internalization. Here we performed single-particle studies of folic acid (FA) mediated CNT binding to human carcinoma cells and their transport inside the cytosol. In particular, we employed molecular recognition force spectroscopy, an atomic force microscopy based method, to visualize and quantify docking of FA functionalized CNTs to FA binding receptors in terms of binding probability and binding force. We then traced individual fluorescently labeled, FA functionalized CNTs after specific uptake, and created a dynamic 'roadmap' that clearly showed trajectories of directed diffusion and areas of nanotube confinement in the cytosol. Our results demonstrate the potential of a single-molecule approach for investigation of drug-delivery vehicles and their targeting capacity."}],"oa_version":"Submitted Version"}]