--- _id: '2970' abstract: - lang: eng text: Morphogen gradients regulate the patterning and growth of many tissues, hence a key question is how they are established and maintained during development. Theoretical descriptions have helped to explain how gradient shape is controlled by the rates of morphogen production, spreading and degradation. These effective rates have been measured using fluorescence recovery after photobleaching (FRAP) and photoactivation. To unravel which molecular events determine the effective rates, such tissue-level assays have been combined with genetic analysis, high-resolution assays, and models that take into account interactions with receptors, extracellular components and trafficking. Nevertheless, because of the natural and experimental data variability, and the underlying assumptions of transport models, it remains challenging to conclusively distinguish between cellular mechanisms. acknowledgement: AK is currently supported by an MRC CDF. MGG and OW were supported by the Swiss National Science Foundation, grants from the Swiss SystemsX.ch initiative, LipidX-2008/011, an ERC advanced investigator grant and the Polish-Swiss research program. author: - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X - first_name: Ortrud full_name: Wartlick, Ortrud last_name: Wartlick - first_name: Frank full_name: Julicher, Frank last_name: Julicher - first_name: Marcos full_name: Gonzalez Gaitan, Marcos last_name: Gonzalez Gaitan citation: ama: 'Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics & Development. 2012;22(6):527-532. doi:10.1016/j.gde.2012.08.004' apa: 'Kicheva, A., Bollenbach, M. T., Wartlick, O., Julicher, F., & Gonzalez Gaitan, M. (2012). Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2012.08.004' chicago: 'Kicheva, Anna, Mark Tobias Bollenbach, Ortrud Wartlick, Frank Julicher, and Marcos Gonzalez Gaitan. “Investigating the Principles of Morphogen Gradient Formation: From Tissues to Cells.” Current Opinion in Genetics & Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.08.004.' ieee: 'A. Kicheva, M. T. Bollenbach, O. Wartlick, F. Julicher, and M. Gonzalez Gaitan, “Investigating the principles of morphogen gradient formation: from tissues to cells,” Current Opinion in Genetics & Development, vol. 22, no. 6. Elsevier, pp. 527–532, 2012.' ista: 'Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. 2012. Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics & Development. 22(6), 527–532.' mla: 'Kicheva, Anna, et al. “Investigating the Principles of Morphogen Gradient Formation: From Tissues to Cells.” Current Opinion in Genetics & Development, vol. 22, no. 6, Elsevier, 2012, pp. 527–32, doi:10.1016/j.gde.2012.08.004.' short: A. Kicheva, M.T. Bollenbach, O. Wartlick, F. Julicher, M. Gonzalez Gaitan, Current Opinion in Genetics & Development 22 (2012) 527–532. date_created: 2018-12-11T12:00:37Z date_published: 2012-12-01T00:00:00Z date_updated: 2021-01-12T07:40:09Z day: '01' department: - _id: ToBo doi: 10.1016/j.gde.2012.08.004 intvolume: ' 22' issue: '6' language: - iso: eng month: '12' oa_version: None page: 527 - 532 publication: Current Opinion in Genetics & Development publication_status: published publisher: Elsevier publist_id: '3739' quality_controlled: '1' scopus_import: 1 status: public title: 'Investigating the principles of morphogen gradient formation: from tissues to cells' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2012' ... --- _id: '2971' abstract: - lang: eng text: 'We study the task of interactive semantic labeling of a segmentation hierarchy. To this end we propose a framework interleaving two components: an automatic labeling step, based on a Conditional Random Field whose dependencies are defined by the inclusion tree of the segmentation hierarchy, and an interaction step that integrates incremental input from a human user. Evaluated on two distinct datasets, the proposed interactive approach efficiently integrates human interventions and illustrates the advantages of structured prediction in an interactive framework. ' author: - first_name: Georg full_name: Zankl, Georg last_name: Zankl - first_name: Yll full_name: Haxhimusa, Yll last_name: Haxhimusa - first_name: Adrian full_name: Ion, Adrian id: 29F89302-F248-11E8-B48F-1D18A9856A87 last_name: Ion citation: ama: 'Zankl G, Haxhimusa Y, Ion A. Interactive labeling of image segmentation hierarchies. In: Vol 7476. Springer; 2012:11-20. doi:10.1007/978-3-642-32717-9_2' apa: 'Zankl, G., Haxhimusa, Y., & Ion, A. (2012). Interactive labeling of image segmentation hierarchies (Vol. 7476, pp. 11–20). Presented at the Pattern Recognition, Graz, Austria: Springer. https://doi.org/10.1007/978-3-642-32717-9_2' chicago: Zankl, Georg, Yll Haxhimusa, and Adrian Ion. “Interactive Labeling of Image Segmentation Hierarchies,” 7476:11–20. Springer, 2012. https://doi.org/10.1007/978-3-642-32717-9_2. ieee: G. Zankl, Y. Haxhimusa, and A. Ion, “Interactive labeling of image segmentation hierarchies,” presented at the Pattern Recognition, Graz, Austria, 2012, vol. 7476, pp. 11–20. ista: Zankl G, Haxhimusa Y, Ion A. 2012. Interactive labeling of image segmentation hierarchies. Pattern Recognition vol. 7476, 11–20. mla: Zankl, Georg, et al. Interactive Labeling of Image Segmentation Hierarchies. Vol. 7476, Springer, 2012, pp. 11–20, doi:10.1007/978-3-642-32717-9_2. short: G. Zankl, Y. Haxhimusa, A. Ion, in:, Springer, 2012, pp. 11–20. conference: end_date: 2012-08-31 location: Graz, Austria name: Pattern Recognition start_date: 2012-08-28 date_created: 2018-12-11T12:00:37Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T07:40:10Z day: '01' department: - _id: HeEd doi: 10.1007/978-3-642-32717-9_2 intvolume: ' 7476' language: - iso: eng month: '01' oa_version: None page: 11 - 20 publication_status: published publisher: Springer publist_id: '3737' quality_controlled: '1' scopus_import: 1 status: public title: Interactive labeling of image segmentation hierarchies type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7476 year: '2012' ... --- _id: '3105' abstract: - lang: eng text: Growth and development are coordinated by an array of intercellular communications. Known plant signaling molecules include phytohormones and hormone peptides. Although both classes can be implicated in the same developmental processes, little is known about the interplay between phytohormone action and peptide signaling within the cellular microenvironment. We show that genes coding for small secretory peptides, designated GOLVEN (GLV), modulate the distribution of the phytohormone auxin. The deregulation of the GLV function impairs the formation of auxin gradients and alters the reorientation of shoots and roots after a gravity stimulus. Specifically, the GLV signal modulates the trafficking dynamics of the auxin efflux carrier PIN-FORMED2 involved in root tropic responses and meristem organization. Our work links the local action of secretory peptides with phytohormone transport. Root growth factor (RGF) or GOLVEN (GLV) secreted peptides have previously been implicated in meristem regulation. Whitford et al. now show that RGF/GLV peptides induce rapid relocalization of the auxin efflux regulator PIN2, regulate auxin gradients, and modulate auxin-dependent root responses to specific stimuli. author: - first_name: Ryan full_name: Whitford, Ryan last_name: Whitford - first_name: Ana full_name: Fernandez, Ana last_name: Fernandez - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Amparo full_name: Pérez, Amparo Cuéllar last_name: Pérez - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Andrzej full_name: Drozdzecki, Andrzej last_name: Drozdzecki - first_name: Johannes full_name: Leitner, Johannes last_name: Leitner - first_name: Lindy full_name: Abas, Lindy last_name: Abas - first_name: Maarten full_name: Aerts, Maarten last_name: Aerts - first_name: Kurt full_name: Hoogewijs, Kurt last_name: Hoogewijs - first_name: Pawel full_name: Pawel Baster id: 3028BD74-F248-11E8-B48F-1D18A9856A87 last_name: Baster - first_name: Ruth full_name: De Groodt, Ruth last_name: De Groodt - first_name: Yao full_name: Lin, Yao-Cheng last_name: Lin - first_name: Véronique full_name: Storme, Véronique last_name: Storme - first_name: Yves full_name: Van de Peer, Yves last_name: Van De Peer - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Annemieke full_name: Madder, Annemieke last_name: Madder - first_name: Bart full_name: Devreese, Bart last_name: Devreese - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Pierre full_name: Hilson, Pierre last_name: Hilson citation: ama: Whitford R, Fernandez A, Tejos R, et al. GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. 2012;22(3):678-685. doi:10.1016/j.devcel.2012.02.002 apa: Whitford, R., Fernandez, A., Tejos, R., Pérez, A., Kleine Vehn, J., Vanneste, S., … Hilson, P. (2012). GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2012.02.002 chicago: Whitford, Ryan, Ana Fernandez, Ricardo Tejos, Amparo Pérez, Jürgen Kleine Vehn, Steffen Vanneste, Andrzej Drozdzecki, et al. “GOLVEN Secretory Peptides Regulate Auxin Carrier Turnover during Plant Gravitropic Responses.” Developmental Cell. Cell Press, 2012. https://doi.org/10.1016/j.devcel.2012.02.002. ieee: R. Whitford et al., “GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses,” Developmental Cell, vol. 22, no. 3. Cell Press, pp. 678–685, 2012. ista: Whitford R, Fernandez A, Tejos R, Pérez A, Kleine Vehn J, Vanneste S, Drozdzecki A, Leitner J, Abas L, Aerts M, Hoogewijs K, Baster P, De Groodt R, Lin Y, Storme V, Van De Peer Y, Beeckman T, Madder A, Devreese B, Luschnig C, Friml J, Hilson P. 2012. GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. 22(3), 678–685. mla: Whitford, Ryan, et al. “GOLVEN Secretory Peptides Regulate Auxin Carrier Turnover during Plant Gravitropic Responses.” Developmental Cell, vol. 22, no. 3, Cell Press, 2012, pp. 678–85, doi:10.1016/j.devcel.2012.02.002. short: R. Whitford, A. Fernandez, R. Tejos, A. Pérez, J. Kleine Vehn, S. Vanneste, A. Drozdzecki, J. Leitner, L. Abas, M. Aerts, K. Hoogewijs, P. Baster, R. De Groodt, Y. Lin, V. Storme, Y. Van De Peer, T. Beeckman, A. Madder, B. Devreese, C. Luschnig, J. Friml, P. Hilson, Developmental Cell 22 (2012) 678–685. date_created: 2018-12-11T12:01:25Z date_published: 2012-03-13T00:00:00Z date_updated: 2021-01-12T07:41:06Z day: '13' doi: 10.1016/j.devcel.2012.02.002 extern: 1 intvolume: ' 22' issue: '3' month: '03' page: 678 - 685 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '3594' quality_controlled: 0 status: public title: GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses type: journal_article volume: 22 year: '2012' ... --- _id: '3109' abstract: - lang: eng text: Receptor-mediated endocytosis is an integral part of signal transduction as it mediates signal attenuation and provides spatial and temporal dimensions to signaling events. One of the best-studied leucine-rich repeat receptor-like kinases in plants, BRASSINOSTEROID INSENSITIVE 1 (BRI1), perceives its ligand, the brassinosteroid (BR) hormone, at the cell surface and is constitutively endocytosed. However, the importance of endocytosis for BR signaling remains unclear. Here we developed a bioactive, fluorescent BR analog, Alexa Fluor 647-castasterone (AFCS), and visualized the endocytosis of BRI1-AFCS complexes in living Arabidopsis thaliana cells. Impairment of endocytosis dependent on clathrin and the guanine nucleotide exchange factor for ARF GTPases (ARF-GEF) GNOM enhanced BR signaling by retaining active BRI1-ligand complexes at the plasma membrane. Increasing the trans-Golgi network/early endosome pool of BRI1-BR complexes did not affect BR signaling. Our findings provide what is to our knowledge the first visualization of receptor-ligand complexes in plants and reveal clathrin-and ARF-GEF-dependent endocytic regulation of BR signaling from the plasma membrane. author: - first_name: Niloufer full_name: Irani, Niloufer G last_name: Irani - first_name: Simone full_name: Di Rubbo, Simone last_name: Di Rubbo - first_name: Evelien full_name: Mylle, Evelien last_name: Mylle - first_name: Jos full_name: Van Den Begin, Jos last_name: Van Den Begin - first_name: Joanna full_name: Schneider-Pizoń, Joanna last_name: Schneider Pizoń - first_name: Jaroslava full_name: Hniliková, Jaroslava last_name: Hniliková - first_name: Miroslav full_name: Šíša, Miroslav last_name: Šíša - first_name: Dieter full_name: Buyst, Dieter last_name: Buyst - first_name: Josep full_name: Vilarrasa-Blasi, Josep last_name: Vilarrasa Blasi - first_name: Anna full_name: Szatmári, Anna-Maria last_name: Szatmári - first_name: Daniël full_name: Van Damme, Daniël last_name: Van Damme - first_name: Kiril full_name: Mishev, Kiril last_name: Mishev - first_name: Mirela full_name: Codreanu, Mirela-Corina last_name: Codreanu - first_name: Ladislav full_name: Kohout, Ladislav last_name: Kohout - first_name: Miroslav full_name: Strnad, Miroslav last_name: Strnad - first_name: Ana full_name: Caño-Delgado, Ana I last_name: Caño Delgado - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Annemieke full_name: Madder, Annemieke last_name: Madder - first_name: Eugenia full_name: Russinova, Eugenia last_name: Russinova citation: ama: Irani N, Di Rubbo S, Mylle E, et al. Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. 2012;8(6):583-589. doi:10.1038/nchembio.958 apa: Irani, N., Di Rubbo, S., Mylle, E., Van Den Begin, J., Schneider Pizoń, J., Hniliková, J., … Russinova, E. (2012). Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.958 chicago: Irani, Niloufer, Simone Di Rubbo, Evelien Mylle, Jos Van Den Begin, Joanna Schneider Pizoń, Jaroslava Hniliková, Miroslav Šíša, et al. “Fluorescent Castasterone Reveals BRI1 Signaling from the Plasma Membrane.” Nature Chemical Biology. Nature Publishing Group, 2012. https://doi.org/10.1038/nchembio.958. ieee: N. Irani et al., “Fluorescent castasterone reveals BRI1 signaling from the plasma membrane,” Nature Chemical Biology, vol. 8, no. 6. Nature Publishing Group, pp. 583–589, 2012. ista: Irani N, Di Rubbo S, Mylle E, Van Den Begin J, Schneider Pizoń J, Hniliková J, Šíša M, Buyst D, Vilarrasa Blasi J, Szatmári A, Van Damme D, Mishev K, Codreanu M, Kohout L, Strnad M, Caño Delgado A, Friml J, Madder A, Russinova E. 2012. Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. 8(6), 583–589. mla: Irani, Niloufer, et al. “Fluorescent Castasterone Reveals BRI1 Signaling from the Plasma Membrane.” Nature Chemical Biology, vol. 8, no. 6, Nature Publishing Group, 2012, pp. 583–89, doi:10.1038/nchembio.958. short: N. Irani, S. Di Rubbo, E. Mylle, J. Van Den Begin, J. Schneider Pizoń, J. Hniliková, M. Šíša, D. Buyst, J. Vilarrasa Blasi, A. Szatmári, D. Van Damme, K. Mishev, M. Codreanu, L. Kohout, M. Strnad, A. Caño Delgado, J. Friml, A. Madder, E. Russinova, Nature Chemical Biology 8 (2012) 583–589. date_created: 2018-12-11T12:01:26Z date_published: 2012-06-01T00:00:00Z date_updated: 2021-01-12T07:41:07Z day: '01' doi: 10.1038/nchembio.958 extern: 1 intvolume: ' 8' issue: '6' month: '06' page: 583 - 589 publication: Nature Chemical Biology publication_status: published publisher: Nature Publishing Group publist_id: '3590' quality_controlled: 0 status: public title: Fluorescent castasterone reveals BRI1 signaling from the plasma membrane type: journal_article volume: 8 year: '2012' ... --- _id: '3104' abstract: - lang: eng text: |2- Gradients of the plant hormone auxin, which depend on its active intercellular transport, are crucial for the maintenance of root meristematic activity. This directional transport is largely orchestrated by a complex interaction of specific influx and efflux carriers that mediate the auxin flow into and out of cells, respectively. Besides these transport proteins, plant-specific polyphenolic compounds knownasflavonols have beenshownto act as endogenous regulators of auxin transport. However, only limited information is available on how flavonol synthesis is developmentally regulated. Using reduction-of-function and overexpression approaches in parallel, we demonstrate that the WRKY23 transcription factor is needed for proper root growth and development by stimulating the local biosynthesis of flavonols. The expression of WRKY23 itself is controlled by auxin through the AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 transcriptional response pathway. Our results suggest a model in which WRKY23 is part of a transcriptional feedback loop of auxin on its own transport through local regulation of flavonol biosynthesis. author: - first_name: Wim full_name: Grunewald, Wim last_name: Grunewald - first_name: Ive full_name: De Smet, Ive last_name: De Smet - first_name: Daniel full_name: Lewis, Daniel R last_name: Lewis - first_name: Christian full_name: Löfke, Christian last_name: Löfke - first_name: Leentje full_name: Jansen, Leentje last_name: Jansen - first_name: Geert full_name: Goeminne, Geert last_name: Goeminne - first_name: Robin full_name: Vanden Bossche, Robin last_name: Vanden Bossche - first_name: Mansour full_name: Karimi, Mansour last_name: Karimi - first_name: Bert full_name: De Rybel, Bert last_name: De Rybel - first_name: Bartel full_name: Vanholme, Bartel last_name: Vanholme - first_name: Thomas full_name: Teichmann, Thomas last_name: Teichmann - first_name: Wout full_name: Boerjan, Wout last_name: Boerjan - first_name: Marc full_name: Van Montagu, Marc C last_name: Van Montagu - first_name: Godelieve full_name: Gheysen, Godelieve last_name: Gheysen - first_name: Gloria full_name: Muday, Gloria K last_name: Muday - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman citation: ama: Grunewald W, De Smet I, Lewis D, et al. Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. 2012;109(5):1554-1559. doi:10.1073/pnas.1121134109 apa: Grunewald, W., De Smet, I., Lewis, D., Löfke, C., Jansen, L., Goeminne, G., … Beeckman, T. (2012). Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1121134109 chicago: Grunewald, Wim, Ive De Smet, Daniel Lewis, Christian Löfke, Leentje Jansen, Geert Goeminne, Robin Vanden Bossche, et al. “Transcription Factor WRKY23 Assists Auxin Distribution Patterns during Arabidopsis Root Development through Local Control on Flavonol Biosynthesis.” PNAS. National Academy of Sciences, 2012. https://doi.org/10.1073/pnas.1121134109. ieee: W. Grunewald et al., “Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis,” PNAS, vol. 109, no. 5. National Academy of Sciences, pp. 1554–1559, 2012. ista: Grunewald W, De Smet I, Lewis D, Löfke C, Jansen L, Goeminne G, Vanden Bossche R, Karimi M, De Rybel B, Vanholme B, Teichmann T, Boerjan W, Van Montagu M, Gheysen G, Muday G, Friml J, Beeckman T. 2012. Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. 109(5), 1554–1559. mla: Grunewald, Wim, et al. “Transcription Factor WRKY23 Assists Auxin Distribution Patterns during Arabidopsis Root Development through Local Control on Flavonol Biosynthesis.” PNAS, vol. 109, no. 5, National Academy of Sciences, 2012, pp. 1554–59, doi:10.1073/pnas.1121134109. short: W. Grunewald, I. De Smet, D. Lewis, C. Löfke, L. Jansen, G. Goeminne, R. Vanden Bossche, M. Karimi, B. De Rybel, B. Vanholme, T. Teichmann, W. Boerjan, M. Van Montagu, G. Gheysen, G. Muday, J. Friml, T. Beeckman, PNAS 109 (2012) 1554–1559. date_created: 2018-12-11T12:01:24Z date_published: 2012-01-31T00:00:00Z date_updated: 2021-01-12T07:41:05Z day: '31' doi: 10.1073/pnas.1121134109 extern: 1 intvolume: ' 109' issue: '5' month: '01' page: 1554 - 1559 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3595' quality_controlled: 0 status: public title: Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis type: journal_article volume: 109 year: '2012' ... --- _id: '3108' abstract: - lang: eng text: The phytohormone auxin acts as a prominent signal, providing, by its local accumulation or depletion in selected cells, a spatial and temporal reference for changes in the developmental program. The distribution of auxin depends on both auxin metabolism (biosynthesis, conjugation and degradation) and cellular auxin transport. We identified in silico a novel putative auxin transport facilitator family, called PIN-LIKES (PILS). Here we illustrate that PILS proteins are required for auxin-dependent regulation of plant growth by determining the cellular sensitivity to auxin. PILS proteins regulate intracellular auxin accumulation at the endoplasmic reticulum and thus auxin availability for nuclear auxin signalling. PILS activity affects the level of endogenous auxin indole-3-acetic acid (IAA), presumably via intracellular accumulation and metabolism. Our findings reveal that the transport machinery to compartmentalize auxin within the cell is of an unexpected molecular complexity and demonstrate this compartmentalization to be functionally important for a number of developmental processes. author: - first_name: Elke full_name: Barbez, Elke last_name: Barbez - first_name: Martin full_name: Kubeš, Martin last_name: Kubeš - first_name: Jakub full_name: Rolčík, Jakub last_name: Rolčík - first_name: Chloe full_name: Béziat, Chloe last_name: Béziat - first_name: Aleš full_name: Pěnčík, Aleš last_name: Pěnčík - first_name: Bangjun full_name: Wang, Bangjun last_name: Wang - first_name: Michel full_name: Rosquete, Michel Ruiz last_name: Rosquete - first_name: Jinsheng full_name: Zhu, Jinsheng last_name: Zhu - first_name: Petre full_name: Dobrev, Petre I last_name: Dobrev - first_name: Yuree full_name: Lee, Yuree last_name: Lee - first_name: Eva full_name: Zašímalová, Eva last_name: Zašímalová - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Markus full_name: Geisler, Markus last_name: Geisler - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn citation: ama: Barbez E, Kubeš M, Rolčík J, et al. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. 2012;485(7396):119-122. doi:10.1038/nature11001 apa: Barbez, E., Kubeš, M., Rolčík, J., Béziat, C., Pěnčík, A., Wang, B., … Kleine Vehn, J. (2012). A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11001 chicago: Barbez, Elke, Martin Kubeš, Jakub Rolčík, Chloe Béziat, Aleš Pěnčík, Bangjun Wang, Michel Rosquete, et al. “A Novel Putative Auxin Carrier Family Regulates Intracellular Auxin Homeostasis in Plants.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11001. ieee: E. Barbez et al., “A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants,” Nature, vol. 485, no. 7396. Nature Publishing Group, pp. 119–122, 2012. ista: Barbez E, Kubeš M, Rolčík J, Béziat C, Pěnčík A, Wang B, Rosquete M, Zhu J, Dobrev P, Lee Y, Zašímalová E, Petrášek J, Geisler M, Friml J, Kleine Vehn J. 2012. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. 485(7396), 119–122. mla: Barbez, Elke, et al. “A Novel Putative Auxin Carrier Family Regulates Intracellular Auxin Homeostasis in Plants.” Nature, vol. 485, no. 7396, Nature Publishing Group, 2012, pp. 119–22, doi:10.1038/nature11001. short: E. Barbez, M. Kubeš, J. Rolčík, C. Béziat, A. Pěnčík, B. Wang, M. Rosquete, J. Zhu, P. Dobrev, Y. Lee, E. Zašímalová, J. Petrášek, M. Geisler, J. Friml, J. Kleine Vehn, Nature 485 (2012) 119–122. date_created: 2018-12-11T12:01:26Z date_published: 2012-05-03T00:00:00Z date_updated: 2021-01-12T07:41:07Z day: '03' doi: 10.1038/nature11001 extern: 1 intvolume: ' 485' issue: '7396' month: '05' page: 119 - 122 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '3591' quality_controlled: 0 status: public title: A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants type: journal_article volume: 485 year: '2012' ... --- _id: '3106' abstract: - lang: eng text: Cell polarization via asymmetrical distribution of structures or molecules is essential for diverse cellular functions and development of organisms, but how polarity is developmentally controlled has been poorly understood. In plants, the asymmetrical distribution of the PIN-FORMED (PIN) proteins involved in the cellular efflux of the quintessential phytohormone auxin plays a central role in developmental patterning, morphogenesis, and differential growth. Recently we showed that auxin promotes cell interdigitation by activating the Rho family ROP GTPases in leaf epidermal pavement cells. Here we found that auxin activation of the ROP2 signaling pathway regulates the asymmetric distribution of PIN1 by inhibiting its endocytosis. ROP2 inhibits PIN1 endocytosis via the accumulation of cortical actin microfilaments induced by the ROP2 effector protein RIC4. Our findings suggest a link between the developmental auxin signal and polar PIN1 distribution via Rho-dependent cytoskeletal reorganization and reveal the conservation of a design principle for cell polarization that is based on Rho GTPase-mediated inhibition of endocytosis. author: - first_name: Shingo full_name: Nagawa, Shingo last_name: Nagawa - first_name: Tongda full_name: Xu, Tongda last_name: Xu - first_name: Deshu full_name: Lin, Deshu last_name: Lin - first_name: Pankaj full_name: Dhonukshe, Pankaj last_name: Dhonukshe - first_name: Xingxing full_name: Zhang, Xingxing last_name: Zhang - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Ben full_name: Scheres, Ben last_name: Scheres - first_name: Ying full_name: Fu, Ying last_name: Fu - first_name: Zhenbiao full_name: Yang, Zhenbiao last_name: Yang citation: ama: Nagawa S, Xu T, Lin D, et al. ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. 2012;10(4). doi:10.1371/journal.pbio.1001299 apa: Nagawa, S., Xu, T., Lin, D., Dhonukshe, P., Zhang, X., Friml, J., … Yang, Z. (2012). ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1001299 chicago: Nagawa, Shingo, Tongda Xu, Deshu Lin, Pankaj Dhonukshe, Xingxing Zhang, Jiří Friml, Ben Scheres, Ying Fu, and Zhenbiao Yang. “ROP GTPase-Dependent Actin Microfilaments Promote PIN1 Polarization by Localized Inhibition of Clathrin-Dependent Endocytosis.” PLoS Biology. Public Library of Science, 2012. https://doi.org/10.1371/journal.pbio.1001299. ieee: S. Nagawa et al., “ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis,” PLoS Biology, vol. 10, no. 4. Public Library of Science, 2012. ista: Nagawa S, Xu T, Lin D, Dhonukshe P, Zhang X, Friml J, Scheres B, Fu Y, Yang Z. 2012. ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. 10(4). mla: Nagawa, Shingo, et al. “ROP GTPase-Dependent Actin Microfilaments Promote PIN1 Polarization by Localized Inhibition of Clathrin-Dependent Endocytosis.” PLoS Biology, vol. 10, no. 4, Public Library of Science, 2012, doi:10.1371/journal.pbio.1001299. short: S. Nagawa, T. Xu, D. Lin, P. Dhonukshe, X. Zhang, J. Friml, B. Scheres, Y. Fu, Z. Yang, PLoS Biology 10 (2012). date_created: 2018-12-11T12:01:25Z date_published: 2012-04-01T00:00:00Z date_updated: 2021-01-12T07:41:06Z day: '01' doi: 10.1371/journal.pbio.1001299 extern: 1 intvolume: ' 10' issue: '4' month: '04' publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '3593' quality_controlled: 0 status: public title: ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 10 year: '2012' ... --- _id: '3107' author: - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Vanneste S, Friml J. Plant Signaling: Deconstructing Auxin Sensing. Vol 8. Nature Publishing Group; 2012:415-416. doi:10.1038/nchembio.943' apa: 'Vanneste, S., & Friml, J. (2012). Plant signaling: Deconstructing auxin sensing. Nature Chemical Biology (Vol. 8, pp. 415–416). Nature Publishing Group. https://doi.org/10.1038/nchembio.943' chicago: 'Vanneste, Steffen, and Jiří Friml. Plant Signaling: Deconstructing Auxin Sensing. Nature Chemical Biology. Vol. 8. Nature Publishing Group, 2012. https://doi.org/10.1038/nchembio.943.' ieee: 'S. Vanneste and J. Friml, Plant signaling: Deconstructing auxin sensing, vol. 8, no. 5. Nature Publishing Group, 2012, pp. 415–416.' ista: 'Vanneste S, Friml J. 2012. Plant signaling: Deconstructing auxin sensing, Nature Publishing Group,p.' mla: 'Vanneste, Steffen, and Jiří Friml. “Plant Signaling: Deconstructing Auxin Sensing.” Nature Chemical Biology, vol. 8, no. 5, Nature Publishing Group, 2012, pp. 415–16, doi:10.1038/nchembio.943.' short: 'S. Vanneste, J. Friml, Plant Signaling: Deconstructing Auxin Sensing, Nature Publishing Group, 2012.' date_created: 2018-12-11T12:01:26Z date_published: 2012-05-01T00:00:00Z date_updated: 2021-01-12T07:41:06Z day: '01' doi: 10.1038/nchembio.943 extern: '1' intvolume: ' 8' issue: '5' language: - iso: eng month: '05' oa_version: None page: 415 - 416 publication: Nature Chemical Biology publication_status: published publisher: Nature Publishing Group publist_id: '3592' quality_controlled: '1' status: public title: 'Plant signaling: Deconstructing auxin sensing' type: other_academic_publication user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2012' ... --- _id: '3119' abstract: - lang: eng text: "We present an approach for artist-directed animation of liquids using multiple levels of control over the simulation, ranging from the overall tracking of desired shapes to highly detailed secondary effects such as dripping streams, separating sheets of fluid, surface waves and ripples. The first portion of our technique is a volume preserving morph that allows the animator to produce a plausible fluid-like motion from a sparse set of control meshes. By rasterizing the resulting control meshes onto the simulation grid, the mesh velocities act as boundary conditions during the projection step of the fluid simulation. We can then blend this motion together with uncontrolled fluid velocities to achieve a more relaxed control over the fluid that captures natural inertial effects. Our method can produce highly detailed liquid surfaces with control over sub-grid details by using a mesh-based surface tracker on top of a coarse grid-based fluid simulation. We can create ripples and waves on the fluid surface attracting the surface mesh to the control mesh with spring-like forces and also by running a wave simulation over the surface mesh. Our video results demonstrate how our control scheme can be used to create animated characters and shapes that are made of water.\r\n" acknowledgement: This work was partially funded by NSF grants CCF-0811485 and IIS-1130934. We would like to thank Scanline VFX for additional funding. We would like to thank Jie Tan as well as our anonymous reviewers for their useful suggestions and feedback. author: - first_name: Karthik full_name: Raveendran, Karthik last_name: Raveendran - first_name: Nils full_name: Thuerey, Nils last_name: Thuerey - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Greg full_name: Turk, Greg last_name: Turk citation: ama: 'Raveendran K, Thuerey N, Wojtan C, Turk G. Controlling liquids using meshes. In: Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. ACM; 2012:255-264.' apa: 'Raveendran, K., Thuerey, N., Wojtan, C., & Turk, G. (2012). Controlling liquids using meshes. In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation (pp. 255–264). Aire-la-Ville, Switzerland: ACM.' chicago: Raveendran, Karthik, Nils Thuerey, Chris Wojtan, and Greg Turk. “Controlling Liquids Using Meshes.” In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, 255–64. ACM, 2012. ieee: K. Raveendran, N. Thuerey, C. Wojtan, and G. Turk, “Controlling liquids using meshes,” in Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, Aire-la-Ville, Switzerland, 2012, pp. 255–264. ista: 'Raveendran K, Thuerey N, Wojtan C, Turk G. 2012. Controlling liquids using meshes. Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 255–264.' mla: Raveendran, Karthik, et al. “Controlling Liquids Using Meshes.” Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–64. short: K. Raveendran, N. Thuerey, C. Wojtan, G. Turk, in:, Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–264. conference: end_date: 2012-07-31 location: Aire-la-Ville, Switzerland name: 'SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation' start_date: 2012-07-29 date_created: 2018-12-11T12:01:30Z date_published: 2012-07-29T00:00:00Z date_updated: 2023-02-23T11:13:07Z day: '29' ddc: - '000' department: - _id: ChWo file: - access_level: open_access checksum: babda64c24cf90a4d05ae86d712bed08 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:23Z date_updated: 2020-07-14T12:46:00Z file_id: '4877' file_name: IST-2016-600-v1+1_ControllingLiquids_Preprint.pdf file_size: 4939370 relation: main_file file_date_updated: 2020-07-14T12:46:00Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 255 - 264 publication: Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation publication_status: published publisher: ACM publist_id: '3580' pubrep_id: '600' quality_controlled: '1' related_material: link: - relation: table_of_contents url: http://dl.acm.org/citation.cfm?id=2422393 scopus_import: 1 status: public title: Controlling liquids using meshes type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '3118' abstract: - lang: eng text: We present a method for recovering a temporally coherent, deforming triangle mesh with arbitrarily changing topology from an incoherent sequence of static closed surfaces. We solve this problem using the surface geometry alone, without any prior information like surface templates or velocity fields. Our system combines a proven strategy for triangle mesh improvement, a robust multi-resolution non-rigid registration routine, and a reliable technique for changing surface mesh topology. We also introduce a novel topological constraint enforcement algorithm to ensure that the output and input always have similar topology. We apply our technique to a series of diverse input data from video reconstructions, physics simulations, and artistic morphs. The structured output of our algorithm allows us to efficiently track information like colors and displacement maps, recover velocity information, and solve PDEs on the mesh as a post process. acknowledgement: "This work is supported by the SNF fellowship PBEZP2-134464.\r\nWe would like to thank Xiaochen Hu for implementing mesh con- version tools, Duygu Ceylan for helping with the rendering, and Art Tevs for the human performance data comparison. We also thank Nils Thuerey and Christopher Batty for helpful discussions. " alternative_title: - SIGGRAPH article_number: '53' article_processing_charge: No article_type: original author: - first_name: Morten full_name: Bojsen-Hansen, Morten id: 439F0C8C-F248-11E8-B48F-1D18A9856A87 last_name: Bojsen-Hansen orcid: 0000-0002-4417-3224 - first_name: Hao full_name: Li, Hao last_name: Li - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Bojsen-Hansen M, Li H, Wojtan C. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 2012;31(4). doi:10.1145/2185520.2185549 apa: Bojsen-Hansen, M., Li, H., & Wojtan, C. (2012). Tracking surfaces with evolving topology. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2185520.2185549 chicago: Bojsen-Hansen, Morten, Hao Li, and Chris Wojtan. “Tracking Surfaces with Evolving Topology.” ACM Transactions on Graphics. ACM, 2012. https://doi.org/10.1145/2185520.2185549. ieee: M. Bojsen-Hansen, H. Li, and C. Wojtan, “Tracking surfaces with evolving topology,” ACM Transactions on Graphics, vol. 31, no. 4. ACM, 2012. ista: Bojsen-Hansen M, Li H, Wojtan C. 2012. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 31(4), 53. mla: Bojsen-Hansen, Morten, et al. “Tracking Surfaces with Evolving Topology.” ACM Transactions on Graphics, vol. 31, no. 4, 53, ACM, 2012, doi:10.1145/2185520.2185549. short: M. Bojsen-Hansen, H. Li, C. Wojtan, ACM Transactions on Graphics 31 (2012). date_created: 2018-12-11T12:01:29Z date_published: 2012-07-01T00:00:00Z date_updated: 2022-05-24T08:21:11Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1145/2185520.2185549 file: - access_level: open_access checksum: 1e219c5bf4e5552c1290c62eefa5cd60 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:37Z date_updated: 2020-07-14T12:46:00Z file_id: '5359' file_name: IST-2016-602-v1+1_topoReg.pdf file_size: 44538518 relation: main_file file_date_updated: 2020-07-14T12:46:00Z has_accepted_license: '1' intvolume: ' 31' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '3581' pubrep_id: '602' quality_controlled: '1' scopus_import: '1' status: public title: Tracking surfaces with evolving topology type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2012' ... --- _id: '3122' abstract: - lang: eng text: 'Since Darwin''s pioneering research on plant reproductive biology (e.g. Darwin 1877), understanding the mechanisms maintaining the diverse sexual strategies of plants has remained an important challenge for evolutionary biologists. In some species, populations are sexually polymorphic and contain two or more mating morphs (sex phenotypes). Differences in morphology or phenology among the morphs influence patterns of non-random mating. In these populations, negative frequency-dependent selection arising from disassortative (intermorph) mating is usually required for the evolutionary maintenance of sexual polymorphism, but few studies have demonstrated the required patterns of non-random mating. In the current issue of Molecular Ecology, Shang (2012) make an important contribution to our understanding of how disassortative mating influences sex phenotype ratios in Acer pictum subsp. mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They monitored sex expression in 97 adults and used paternity analysis of open-pollinated seed to examine disassortative mating among three sex phenotypes. Using a deterministic ''pollen transfer'' model, Shang et al. present convincing evidence that differences in the degree of disassortative mating in progeny arrays of the sex phenotypes can explain their uneven frequencies in the adult population. This study provides a useful example of how the deployment of genetic markers, demographic monitoring and modelling can be integrated to investigate the maintenance of sexual diversity in plants. ' author: - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Spencer full_name: Barrett, Spencer last_name: Barrett citation: ama: Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 2012;21(15):3640-3643. doi:10.1111/j.1365-294X.2012.05643.x apa: Field, D., & Barrett, S. (2012). Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05643.x chicago: Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05643.x. ieee: D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual polymorphism in painted maple,” Molecular Ecology, vol. 21, no. 15. Wiley-Blackwell, pp. 3640–3643, 2012. ista: Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643. mla: Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology, vol. 21, no. 15, Wiley-Blackwell, 2012, pp. 3640–43, doi:10.1111/j.1365-294X.2012.05643.x. short: D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643. date_created: 2018-12-11T12:01:31Z date_published: 2012-08-01T00:00:00Z date_updated: 2021-01-12T07:41:13Z day: '01' department: - _id: NiBa doi: 10.1111/j.1365-294X.2012.05643.x intvolume: ' 21' issue: '15' language: - iso: eng month: '08' oa_version: None page: 3640 - 3643 publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3577' quality_controlled: '1' scopus_import: 1 status: public title: Disassortative mating and the maintenance of sexual polymorphism in painted maple type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2012' ... --- _id: '3121' abstract: - lang: eng text: Voltage-activated Ca(2+) channels (VACCs) mediate Ca(2+) influx to trigger action potential-evoked neurotransmitter release, but the mechanism by which Ca(2+) regulates spontaneous transmission is unclear. We found that VACCs are the major physiological triggers for spontaneous release at mouse neocortical inhibitory synapses. Moreover, despite the absence of a synchronizing action potential, we found that spontaneous fusion of a GABA-containing vesicle required the activation of multiple tightly coupled VACCs of variable type. acknowledgement: "The work was supported by the US National Institutes of Health (DA027110 and GM097433) and OCTRI. C.W. and N.P.V. were supported by a grant from the National Heart, Lung, and Blood Institute (T32HL033808).\r\nWe thank M. Andresen and K. Khodakhah for helpful comments. " author: - first_name: Courtney full_name: Williams, Courtney last_name: Williams - first_name: Wenyan full_name: Chen, Wenyan last_name: Chen - first_name: Chia full_name: Lee, Chia last_name: Lee - first_name: Daniel full_name: Yaeger, Daniel last_name: Yaeger - first_name: Nicholas full_name: Vyleta, Nicholas id: 36C4978E-F248-11E8-B48F-1D18A9856A87 last_name: Vyleta - first_name: Stephen full_name: Smith, Stephen last_name: Smith citation: ama: Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 2012;15(9):1195-1197. doi:10.1038/nn.3162 apa: Williams, C., Chen, W., Lee, C., Yaeger, D., Vyleta, N., & Smith, S. (2012). Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3162 chicago: Williams, Courtney, Wenyan Chen, Chia Lee, Daniel Yaeger, Nicholas Vyleta, and Stephen Smith. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” Nature Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3162. ieee: C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, and S. Smith, “Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA,” Nature Neuroscience, vol. 15, no. 9. Nature Publishing Group, pp. 1195–1197, 2012. ista: Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. 2012. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 15(9), 1195–1197. mla: Williams, Courtney, et al. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” Nature Neuroscience, vol. 15, no. 9, Nature Publishing Group, 2012, pp. 1195–97, doi:10.1038/nn.3162. short: C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, S. Smith, Nature Neuroscience 15 (2012) 1195–1197. date_created: 2018-12-11T12:01:30Z date_published: 2012-09-01T00:00:00Z date_updated: 2021-01-12T07:41:12Z day: '01' department: - _id: PeJo doi: 10.1038/nn.3162 external_id: pmid: - '22842148' intvolume: ' 15' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431448/ month: '09' oa: 1 oa_version: Submitted Version page: 1195 - 1197 pmid: 1 publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '3578' quality_controlled: '1' scopus_import: 1 status: public title: Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2012' ... --- _id: '3120' abstract: - lang: eng text: We introduce a strategy based on Kustin-Miller unprojection that allows us to construct many hundreds of Gorenstein codimension 4 ideals with 9 × 16 resolutions (that is, nine equations and sixteen first syzygies). Our two basic games are called Tom and Jerry; the main application is the biregular construction of most of the anticanonically polarised Mori Fano 3-folds of Altinok's thesis. There are 115 cases whose numerical data (in effect, the Hilbert series) allow a Type I projection. In every case, at least one Tom and one Jerry construction works, providing at least two deformation families of quasismooth Fano 3-folds having the same numerics but different topology. © 2012 Copyright Foundation Compositio Mathematica. acknowledgement: This research is supported by the Korean Government WCU Grant R33-2008-000-10101-0. author: - first_name: Gavin full_name: Brown, Gavin last_name: Brown - first_name: Michael full_name: Kerber, Michael id: 36E4574A-F248-11E8-B48F-1D18A9856A87 last_name: Kerber orcid: 0000-0002-8030-9299 - first_name: Miles full_name: Reid, Miles last_name: Reid citation: ama: Brown G, Kerber M, Reid M. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 2012;148(4):1171-1194. doi:10.1112/S0010437X11007226 apa: Brown, G., Kerber, M., & Reid, M. (2012). Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/S0010437X11007226 chicago: Brown, Gavin, Michael Kerber, and Miles Reid. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” Compositio Mathematica. Cambridge University Press, 2012. https://doi.org/10.1112/S0010437X11007226. ieee: G. Brown, M. Kerber, and M. Reid, “Fano 3 folds in codimension 4 Tom and Jerry Part I,” Compositio Mathematica, vol. 148, no. 4. Cambridge University Press, pp. 1171–1194, 2012. ista: Brown G, Kerber M, Reid M. 2012. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 148(4), 1171–1194. mla: Brown, Gavin, et al. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” Compositio Mathematica, vol. 148, no. 4, Cambridge University Press, 2012, pp. 1171–94, doi:10.1112/S0010437X11007226. short: G. Brown, M. Kerber, M. Reid, Compositio Mathematica 148 (2012) 1171–1194. date_created: 2018-12-11T12:01:30Z date_published: 2012-07-01T00:00:00Z date_updated: 2021-01-12T07:41:12Z day: '01' department: - _id: HeEd doi: 10.1112/S0010437X11007226 intvolume: ' 148' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1009.4313 month: '07' oa: 1 oa_version: Preprint page: 1171 - 1194 publication: Compositio Mathematica publication_status: published publisher: Cambridge University Press publist_id: '3579' quality_controlled: '1' scopus_import: 1 status: public title: Fano 3 folds in codimension 4 Tom and Jerry Part I type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 148 year: '2012' ... --- _id: '3117' abstract: - lang: eng text: We consider the problem of minimizing a function represented as a sum of submodular terms. We assume each term allows an efficient computation of exchange capacities. This holds, for example, for terms depending on a small number of variables, or for certain cardinality-dependent terms. A naive application of submodular minimization algorithms would not exploit the existence of specialized exchange capacity subroutines for individual terms. To overcome this, we cast the problem as a submodular flow (SF) problem in an auxiliary graph in such a way that applying most existing SF algorithms would rely only on these subroutines. We then explore in more detail Iwata's capacity scaling approach for submodular flows (Iwata 1997 [19]). In particular, we show how to improve its complexity in the case when the function contains cardinality-dependent terms. author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Kolmogorov V. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 2012;160(15):2246-2258. doi:10.1016/j.dam.2012.05.025 apa: Kolmogorov, V. (2012). Minimizing a sum of submodular functions. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2012.05.025 chicago: Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete Applied Mathematics. Elsevier, 2012. https://doi.org/10.1016/j.dam.2012.05.025. ieee: V. Kolmogorov, “Minimizing a sum of submodular functions,” Discrete Applied Mathematics, vol. 160, no. 15. Elsevier, pp. 2246–2258, 2012. ista: Kolmogorov V. 2012. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 160(15), 2246–2258. mla: Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete Applied Mathematics, vol. 160, no. 15, Elsevier, 2012, pp. 2246–58, doi:10.1016/j.dam.2012.05.025. short: V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 2246–2258. date_created: 2018-12-11T12:01:29Z date_published: 2012-10-01T00:00:00Z date_updated: 2021-01-12T07:41:11Z day: '01' department: - _id: VlKo doi: 10.1016/j.dam.2012.05.025 intvolume: ' 160' issue: '15' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1006.1990 month: '10' oa: 1 oa_version: Preprint page: 2246 - 2258 publication: Discrete Applied Mathematics publication_status: published publisher: Elsevier publist_id: '3582' quality_controlled: '1' scopus_import: 1 status: public title: Minimizing a sum of submodular functions type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 160 year: '2012' ... --- _id: '3131' abstract: - lang: eng text: 'In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, Λ, that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage. Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on s, N, U, and R only through the baseline density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R, the rate of adaptation grows above R/2, but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection.' acknowledgement: "The work was funded by ERC grant 250152.\r\nWe thank B. Charlesworth, O. Hallatschek, W. G. Hill, R. A. Neher, S. P. Otto, and the anonymous reviewers for their helpful suggestions." article_number: e1002740 author: - first_name: Daniel full_name: Weissman, Daniel id: 2D0CE020-F248-11E8-B48F-1D18A9856A87 last_name: Weissman - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Weissman D, Barton NH. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002740 apa: Weissman, D., & Barton, N. H. (2012). Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002740 chicago: Weissman, Daniel, and Nicholas H Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002740. ieee: D. Weissman and N. H. Barton, “Limits to the rate of adaptive substitution in sexual populations,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012. ista: Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 8(6), e1002740. mla: Weissman, Daniel, and Nicholas H. Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics, vol. 8, no. 6, e1002740, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002740. short: D. Weissman, N.H. Barton, PLoS Genetics 8 (2012). date_created: 2018-12-11T12:01:34Z date_published: 2012-06-07T00:00:00Z date_updated: 2021-01-12T07:41:17Z day: '07' ddc: - '570' - '576' department: - _id: NiBa doi: 10.1371/journal.pgen.1002740 ec_funded: 1 file: - access_level: open_access checksum: 729a4becda7d786c4c3db8f9a1f77953 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:00Z date_updated: 2020-07-14T12:46:01Z file_id: '4659' file_name: IST-2013-114-v1+1_WeissmanBarton2012.pdf file_size: 1284801 relation: main_file file_date_updated: 2020-07-14T12:46:01Z has_accepted_license: '1' intvolume: ' 8' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '3566' pubrep_id: '114' quality_controlled: '1' scopus_import: 1 status: public title: Limits to the rate of adaptive substitution in sexual populations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2012' ... --- _id: '3130' abstract: - lang: eng text: 'Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes.' acknowledgement: We thank Alex Boehm for discussions and comments. article_number: e1002803 author: - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Martin full_name: Ackermann, Martin last_name: Ackermann - first_name: Olin full_name: Silander, Olin last_name: Silander citation: ama: Bergmiller T, Ackermann M, Silander O. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002803 apa: Bergmiller, T., Ackermann, M., & Silander, O. (2012). Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002803 chicago: Bergmiller, Tobias, Martin Ackermann, and Olin Silander. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002803. ieee: T. Bergmiller, M. Ackermann, and O. Silander, “Patterns of evolutionary conservation of essential genes correlate with their compensability,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012. ista: Bergmiller T, Ackermann M, Silander O. 2012. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 8(6), e1002803. mla: Bergmiller, Tobias, et al. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” PLoS Genetics, vol. 8, no. 6, e1002803, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002803. short: T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012). date_created: 2018-12-11T12:01:34Z date_published: 2012-06-28T00:00:00Z date_updated: 2021-01-12T07:41:16Z day: '28' ddc: - '576' department: - _id: CaGu doi: 10.1371/journal.pgen.1002803 file: - access_level: open_access checksum: f8506fb579eda6fc5613ba9bf421b86a content_type: application/pdf creator: system date_created: 2018-12-12T10:12:52Z date_updated: 2020-07-14T12:46:01Z file_id: '4973' file_name: IST-2015-386-v1+1_journal.pgen.1002803.pdf file_size: 2674138 relation: main_file file_date_updated: 2020-07-14T12:46:01Z has_accepted_license: '1' intvolume: ' 8' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '3567' pubrep_id: '386' quality_controlled: '1' scopus_import: 1 status: public title: Patterns of evolutionary conservation of essential genes correlate with their compensability tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2012' ... --- _id: '3136' abstract: - lang: eng text: 'Continuous-time Markov chains (CTMC) with their rich theory and efficient simulation algorithms have been successfully used in modeling stochastic processes in diverse areas such as computer science, physics, and biology. However, systems that comprise non-instantaneous events cannot be accurately and efficiently modeled with CTMCs. In this paper we define delayed CTMCs, an extension of CTMCs that allows for the specification of a lower bound on the time interval between an event''s initiation and its completion, and we propose an algorithm for the computation of their behavior. Our algorithm effectively decomposes the computation into two stages: a pure CTMC governs event initiations while a deterministic process guarantees lower bounds on event completion times. Furthermore, from the nature of delayed CTMCs, we obtain a parallelized version of our algorithm. We use our formalism to model genetic regulatory circuits (biological systems where delayed events are common) and report on the results of our numerical algorithm as run on a cluster. We compare performance and accuracy of our results with results obtained by using pure CTMCs. © 2012 Springer-Verlag.' acknowledgement: This work was supported by the ERC Advanced Investigator grant on Quantitative Reactive Modeling (QUAREM) and by the Swiss National Science Foundation. alternative_title: - LNCS author: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Maria full_name: Mateescu, Maria id: 3B43276C-F248-11E8-B48F-1D18A9856A87 last_name: Mateescu - first_name: Ali full_name: Sezgin, Ali id: 4C7638DA-F248-11E8-B48F-1D18A9856A87 last_name: Sezgin citation: ama: 'Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. Delayed continuous time Markov chains for genetic regulatory circuits. In: Vol 7358. Springer; 2012:294-309. doi:10.1007/978-3-642-31424-7_24' apa: 'Guet, C. C., Gupta, A., Henzinger, T. A., Mateescu, M., & Sezgin, A. (2012). Delayed continuous time Markov chains for genetic regulatory circuits (Vol. 7358, pp. 294–309). Presented at the CAV: Computer Aided Verification, Berkeley, CA, USA: Springer. https://doi.org/10.1007/978-3-642-31424-7_24' chicago: Guet, Calin C, Ashutosh Gupta, Thomas A Henzinger, Maria Mateescu, and Ali Sezgin. “Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits,” 7358:294–309. Springer, 2012. https://doi.org/10.1007/978-3-642-31424-7_24. ieee: 'C. C. Guet, A. Gupta, T. A. Henzinger, M. Mateescu, and A. Sezgin, “Delayed continuous time Markov chains for genetic regulatory circuits,” presented at the CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 294–309.' ista: 'Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. 2012. Delayed continuous time Markov chains for genetic regulatory circuits. CAV: Computer Aided Verification, LNCS, vol. 7358, 294–309.' mla: Guet, Calin C., et al. Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits. Vol. 7358, Springer, 2012, pp. 294–309, doi:10.1007/978-3-642-31424-7_24. short: C.C. Guet, A. Gupta, T.A. Henzinger, M. Mateescu, A. Sezgin, in:, Springer, 2012, pp. 294–309. conference: end_date: 2012-07-13 location: Berkeley, CA, USA name: 'CAV: Computer Aided Verification' start_date: 2012-07-07 date_created: 2018-12-11T12:01:36Z date_published: 2012-07-01T00:00:00Z date_updated: 2021-01-12T07:41:18Z day: '01' department: - _id: CaGu - _id: ToHe doi: 10.1007/978-3-642-31424-7_24 ec_funded: 1 language: - iso: eng month: '07' oa_version: None page: 294 - 309 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication_status: published publisher: Springer publist_id: '3561' quality_controlled: '1' scopus_import: 1 status: public title: Delayed continuous time Markov chains for genetic regulatory circuits type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: '7358 ' year: '2012' ... --- _id: '3135' abstract: - lang: eng text: 'We introduce consumption games, a model for discrete interactive system with multiple resources that are consumed or reloaded independently. More precisely, a consumption game is a finite-state graph where each transition is labeled by a vector of resource updates, where every update is a non-positive number or ω. The ω updates model the reloading of a given resource. Each vertex belongs either to player □ or player ◇, where the aim of player □ is to play so that the resources are never exhausted. We consider several natural algorithmic problems about consumption games, and show that although these problems are computationally hard in general, they are solvable in polynomial time for every fixed number of resource types (i.e., the dimension of the update vectors) and bounded resource updates. ' acknowledgement: 'Tomas Brazdil, Antonin Kucera, and Petr Novotny are supported by the Czech Science Foundation, grant No. P202/10/1469. Krishnendu Chatterjee is supported by the FWF (Austrian Science Fund) NFN Grant No S11407-N23 (RiSE) and ERC Start grant (279307: Graph Games).' alternative_title: - LNCS author: - first_name: Brázdil full_name: Brázdil, Brázdil last_name: Brázdil - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Antonín full_name: Kučera, Antonín last_name: Kučera - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny citation: ama: 'Brázdil B, Chatterjee K, Kučera A, Novotný P. Efficient controller synthesis for consumption games with multiple resource types. In: Vol 7358. Springer; 2012:23-38. doi:10.1007/978-3-642-31424-7_8' apa: 'Brázdil, B., Chatterjee, K., Kučera, A., & Novotný, P. (2012). Efficient controller synthesis for consumption games with multiple resource types (Vol. 7358, pp. 23–38). Presented at the CAV: Computer Aided Verification, Berkeley, CA, USA: Springer. https://doi.org/10.1007/978-3-642-31424-7_8' chicago: Brázdil, Brázdil, Krishnendu Chatterjee, Antonín Kučera, and Petr Novotný. “Efficient Controller Synthesis for Consumption Games with Multiple Resource Types,” 7358:23–38. Springer, 2012. https://doi.org/10.1007/978-3-642-31424-7_8. ieee: 'B. Brázdil, K. Chatterjee, A. Kučera, and P. Novotný, “Efficient controller synthesis for consumption games with multiple resource types,” presented at the CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 23–38.' ista: 'Brázdil B, Chatterjee K, Kučera A, Novotný P. 2012. Efficient controller synthesis for consumption games with multiple resource types. CAV: Computer Aided Verification, LNCS, vol. 7358, 23–38.' mla: Brázdil, Brázdil, et al. Efficient Controller Synthesis for Consumption Games with Multiple Resource Types. Vol. 7358, Springer, 2012, pp. 23–38, doi:10.1007/978-3-642-31424-7_8. short: B. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, in:, Springer, 2012, pp. 23–38. conference: end_date: 2012-07-13 location: Berkeley, CA, USA name: 'CAV: Computer Aided Verification' start_date: 2012-07-07 date_created: 2018-12-11T12:01:35Z date_published: 2012-07-01T00:00:00Z date_updated: 2021-01-12T07:41:18Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-31424-7_8 ec_funded: 1 intvolume: ' 7358' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1202.0796 month: '07' oa: 1 oa_version: Preprint page: 23 - 38 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '3562' quality_controlled: '1' scopus_import: 1 status: public title: Efficient controller synthesis for consumption games with multiple resource types type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7358 year: '2012' ... --- _id: '3133' abstract: - lang: eng text: 'This note contributes to the point calculus of persistent homology by extending Alexander duality from spaces to real-valued functions. Given a perfect Morse function f: S n+1 →[0, 1 and a decomposition S n+1 = U ∪ V into two (n + 1)-manifolds with common boundary M, we prove elementary relationships between the persistence diagrams of f restricted to U, to V, and to M. ' acknowledgement: "his research is partially supported by the National Science Foundation (NSF) under grant DBI-0820624, the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053.\r\nThe authors thank an anonymous referee for suggesting the simplified proof of the Contravariant PE Theorem given in this paper. They also thank Frederick Cohen, Yuriy Mileyko and Amit Patel for helpful discussions." author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Michael full_name: Kerber, Michael id: 36E4574A-F248-11E8-B48F-1D18A9856A87 last_name: Kerber orcid: 0000-0002-8030-9299 citation: ama: 'Edelsbrunner H, Kerber M. Alexander duality for functions: The persistent behavior of land and water and shore. In: Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry . ACM; 2012:249-258. doi:10.1145/2261250.2261287' apa: 'Edelsbrunner, H., & Kerber, M. (2012). Alexander duality for functions: The persistent behavior of land and water and shore. In Proceedings of the twenty-eighth annual symposium on Computational geometry (pp. 249–258). Chapel Hill, NC, USA: ACM. https://doi.org/10.1145/2261250.2261287' chicago: 'Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions: The Persistent Behavior of Land and Water and Shore.” In Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , 249–58. ACM, 2012. https://doi.org/10.1145/2261250.2261287.' ieee: 'H. Edelsbrunner and M. Kerber, “Alexander duality for functions: The persistent behavior of land and water and shore,” in Proceedings of the twenty-eighth annual symposium on Computational geometry , Chapel Hill, NC, USA, 2012, pp. 249–258.' ista: 'Edelsbrunner H, Kerber M. 2012. Alexander duality for functions: The persistent behavior of land and water and shore. Proceedings of the twenty-eighth annual symposium on Computational geometry . SCG: Symposium on Computational Geometry, 249–258.' mla: 'Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions: The Persistent Behavior of Land and Water and Shore.” Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 249–58, doi:10.1145/2261250.2261287.' short: H. Edelsbrunner, M. Kerber, in:, Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 249–258. conference: end_date: 2012-06-20 location: Chapel Hill, NC, USA name: 'SCG: Symposium on Computational Geometry' start_date: 2012-06-17 date_created: 2018-12-11T12:01:35Z date_published: 2012-06-20T00:00:00Z date_updated: 2021-01-12T07:41:17Z day: '20' department: - _id: HeEd doi: 10.1145/2261250.2261287 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1109.5052 month: '06' oa: 1 oa_version: Preprint page: 249 - 258 publication: 'Proceedings of the twenty-eighth annual symposium on Computational geometry ' publication_status: published publisher: ACM publist_id: '3564' quality_controlled: '1' scopus_import: 1 status: public title: 'Alexander duality for functions: The persistent behavior of land and water and shore' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '3134' abstract: - lang: eng text: 'It has been an open question whether the sum of finitely many isotropic Gaussian kernels in n ≥ 2 dimensions can have more modes than kernels, until in 2003 Carreira-Perpiñán and Williams exhibited n +1 isotropic Gaussian kernels in ℝ n with n + 2 modes. We give a detailed analysis of this example, showing that it has exponentially many critical points and that the resilience of the extra mode grows like √n. In addition, we exhibit finite configurations of isotropic Gaussian kernels with superlinearly many modes. ' acknowledgement: This research is partially supported by the National Science Foun- dation (NSF) under grant DBI-0820624, by the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053. author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Brittany full_name: Fasy, Brittany last_name: Fasy - first_name: Günter full_name: Rote, Günter last_name: Rote citation: ama: 'Edelsbrunner H, Fasy B, Rote G. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. In: Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry . ACM; 2012:91-100. doi:10.1145/2261250.2261265' apa: 'Edelsbrunner, H., Fasy, B., & Rote, G. (2012). Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. In Proceedings of the twenty-eighth annual symposium on Computational geometry (pp. 91–100). Chapel Hill, NC, USA: ACM. https://doi.org/10.1145/2261250.2261265' chicago: 'Edelsbrunner, Herbert, Brittany Fasy, and Günter Rote. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” In Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , 91–100. ACM, 2012. https://doi.org/10.1145/2261250.2261265.' ieee: 'H. Edelsbrunner, B. Fasy, and G. Rote, “Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions,” in Proceedings of the twenty-eighth annual symposium on Computational geometry , Chapel Hill, NC, USA, 2012, pp. 91–100.' ista: 'Edelsbrunner H, Fasy B, Rote G. 2012. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. Proceedings of the twenty-eighth annual symposium on Computational geometry . SCG: Symposium on Computational Geometry, 91–100.' mla: 'Edelsbrunner, Herbert, et al. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 91–100, doi:10.1145/2261250.2261265.' short: H. Edelsbrunner, B. Fasy, G. Rote, in:, Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 91–100. conference: end_date: 2012-06-20 location: Chapel Hill, NC, USA name: 'SCG: Symposium on Computational Geometry' start_date: 2012-06-17 date_created: 2018-12-11T12:01:35Z date_published: 2012-06-20T00:00:00Z date_updated: 2023-02-23T10:59:27Z day: '20' department: - _id: HeEd doi: 10.1145/2261250.2261265 language: - iso: eng month: '06' oa_version: None page: 91 - 100 publication: 'Proceedings of the twenty-eighth annual symposium on Computational geometry ' publication_status: published publisher: ACM publist_id: '3563' quality_controlled: '1' related_material: record: - id: '2815' relation: later_version status: public scopus_import: 1 status: public title: 'Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '3132' abstract: - lang: eng text: 'Reproductive division of labour is a characteristic trait of social insects. The dominant reproductive individual, often the queen, uses chemical communication and/or behaviour to maintain her social status. Queens of many social insects communicate their fertility status via cuticle-bound substances. As these substances usually possess a low volatility, their range in queen–worker communication is potentially limited. Here, we investigate the range and impact of behavioural and chemical queen signals on workers of the ant Temnothorax longispinosus. We compared the behaviour and ovary development of workers subjected to three different treatments: workers with direct chemical and physical contact to the queen, those solely under the influence of volatile queen substances and those entirely separated from the queen. In addition to short-ranged queen signals preventing ovary development in workers, we discovered a novel secondary pathway influencing worker behaviour. Workers with no physical contact to the queen, but exposed to volatile substances, started to develop their ovaries, but did not change their behaviour compared to workers in direct contact to the queen. In contrast, workers in queen-separated groups showed both increased ovary development and aggressive dominance interactions. We conclude that T. longispinosus queens influence worker ovary development and behaviour via two independent signals, both ensuring social harmony within the colony.' acknowledgement: We like to thank the editor and three anonymous reviewers for their time and constructive criticism and Inon Scharf, Volker Witte and Andreas Modlmeier for helpful comments on earlier versions of the manuscript. The first and second authors appear in alphabetical order and contributed equally to this paper. author: - first_name: Matthias full_name: Konrad, Matthias id: 46528076-F248-11E8-B48F-1D18A9856A87 last_name: Konrad - first_name: Tobias full_name: Pamminger, Tobias last_name: Pamminger - first_name: Susanne full_name: Foitzik, Susanne last_name: Foitzik citation: ama: Konrad M, Pamminger T, Foitzik S. Two pathways ensuring social harmony. Naturwissenschaften. 2012;99(8):627-636. doi:10.1007/s00114-012-0943-z apa: Konrad, M., Pamminger, T., & Foitzik, S. (2012). Two pathways ensuring social harmony. Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-012-0943-z chicago: Konrad, Matthias, Tobias Pamminger, and Susanne Foitzik. “Two Pathways Ensuring Social Harmony.” Naturwissenschaften. Springer, 2012. https://doi.org/10.1007/s00114-012-0943-z. ieee: M. Konrad, T. Pamminger, and S. Foitzik, “Two pathways ensuring social harmony,” Naturwissenschaften, vol. 99, no. 8. Springer, pp. 627–636, 2012. ista: Konrad M, Pamminger T, Foitzik S. 2012. Two pathways ensuring social harmony. Naturwissenschaften. 99(8), 627–636. mla: Konrad, Matthias, et al. “Two Pathways Ensuring Social Harmony.” Naturwissenschaften, vol. 99, no. 8, Springer, 2012, pp. 627–36, doi:10.1007/s00114-012-0943-z. short: M. Konrad, T. Pamminger, S. Foitzik, Naturwissenschaften 99 (2012) 627–636. date_created: 2018-12-11T12:01:34Z date_published: 2012-08-01T00:00:00Z date_updated: 2021-01-12T07:41:17Z day: '01' department: - _id: SyCr doi: 10.1007/s00114-012-0943-z intvolume: ' 99' issue: '8' language: - iso: eng month: '08' oa_version: None page: 627 - 636 publication: Naturwissenschaften publication_status: published publisher: Springer publist_id: '3565' quality_controlled: '1' scopus_import: 1 status: public title: Two pathways ensuring social harmony type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 99 year: '2012' ... --- _id: '3161' abstract: - lang: eng text: 'Some inflammatory stimuli trigger activation of the NLRP3 inflammasome by inducing efflux of cellular potassium. Loss of cellular potassium is known to potently suppress protein synthesis, leading us to test whether the inhibition of protein synthesis itself serves as an activating signal for the NLRP3 inflammasome. Murine bone marrow-derived macrophages, either primed by LPS or unprimed, were exposed to a panel of inhibitors of ribosomal function: ricin, cycloheximide, puromycin, pactamycin, and anisomycin. Macrophages were also exposed to nigericin, ATP, monosodium urate (MSU), and poly I:C. Synthesis of pro-IL-ß and release of IL-1ß from cells in response to these agents was detected by immunoblotting and ELISA. Release of intracellular potassium was measured by mass spectrometry. Inhibition of translation by each of the tested translation inhibitors led to processing of IL-1ß, which was released from cells. Processing and release of IL-1ß was reduced or absent from cells deficient in NLRP3, ASC, or caspase-1, demonstrating the role of the NLRP3 inflammasome. Despite the inability of these inhibitors to trigger efflux of intracellular potassium, the addition of high extracellular potassium suppressed activation of the NLRP3 inflammasome. MSU and double-stranded RNA, which are known to activate the NLRP3 inflammasome, also substantially inhibited protein translation, supporting a close association between inhibition of translation and inflammasome activation. These data demonstrate that translational inhibition itself constitutes a heretofore-unrecognized mechanism underlying IL-1ß dependent inflammatory signaling and that other physical, chemical, or pathogen-associated agents that impair translation may lead to IL-1ß-dependent inflammation through activation of the NLRP3 inflammasome. For agents that inhibit translation through decreased cellular potassium, the application of high extracellular potassium restores protein translation and suppresses activation of the NLRP inflammasome. For agents that inhibit translation through mechanisms that do not involve loss of potassium, high extracellular potassium suppresses IL-1ß processing through a mechanism that remains undefined.' acknowledgement: "Supported by National Institutes of Health grants GM071338 (ML) and AI059355 (BM).\r\nWe acknowledge the expertise of Dr. Martina Ralle in Department of Biochemistry and Molecular Biology at OHSU for measurements of potassium using inductively coupled plasma mass spectrometry." article_number: e36044 author: - first_name: Meghan full_name: Vyleta, Meghan id: 418901AA-F248-11E8-B48F-1D18A9856A87 last_name: Vyleta - first_name: John full_name: Wong, John last_name: Wong - first_name: Bruce full_name: Magun, Bruce last_name: Magun citation: ama: Vyleta M, Wong J, Magun B. Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. 2012;7(5). doi:10.1371/journal.pone.0036044 apa: Vyleta, M., Wong, J., & Magun, B. (2012). Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0036044 chicago: Vyleta, Meghan, John Wong, and Bruce Magun. “Suppression of Ribosomal Function Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.” PLoS One. Public Library of Science, 2012. https://doi.org/10.1371/journal.pone.0036044. ieee: M. Vyleta, J. Wong, and B. Magun, “Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome,” PLoS One, vol. 7, no. 5. Public Library of Science, 2012. ista: Vyleta M, Wong J, Magun B. 2012. Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. 7(5), e36044. mla: Vyleta, Meghan, et al. “Suppression of Ribosomal Function Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.” PLoS One, vol. 7, no. 5, e36044, Public Library of Science, 2012, doi:10.1371/journal.pone.0036044. short: M. Vyleta, J. Wong, B. Magun, PLoS One 7 (2012). date_created: 2018-12-11T12:01:45Z date_published: 2012-05-14T00:00:00Z date_updated: 2021-01-12T07:41:29Z day: '14' ddc: - '610' department: - _id: SyCr doi: 10.1371/journal.pone.0036044 file: - access_level: open_access checksum: 30cef37e27eaa467f6571b3640282010 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:30Z date_updated: 2020-07-14T12:46:01Z file_id: '5082' file_name: IST-2012-97-v1+1_journal.pone.0036044.pdf file_size: 2984012 relation: main_file file_date_updated: 2020-07-14T12:46:01Z has_accepted_license: '1' intvolume: ' 7' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '3526' pubrep_id: '97' quality_controlled: '1' scopus_import: 1 status: public title: Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2012' ... --- _id: '3162' abstract: - lang: eng text: Given a dense-time real-valued signal and a parameterized temporal logic formula with both magnitude and timing parameters, we compute the subset of the parameter space that renders the formula satisfied by the trace. We provide two preliminary implementations, one which follows the exact semantics and attempts to compute the validity domain by quantifier elimination in linear arithmetics and one which conducts adaptive search in the parameter space. alternative_title: - LNCS article_processing_charge: No author: - first_name: Eugene full_name: Asarin, Eugene last_name: Asarin - first_name: Alexandre full_name: Donzé, Alexandre last_name: Donzé - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Dejan full_name: Nickovic, Dejan id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic citation: ama: 'Asarin E, Donzé A, Maler O, Nickovic D. Parametric identification of temporal properties. In: Vol 7186. Springer; 2012:147-160. doi:10.1007/978-3-642-29860-8_12' apa: 'Asarin, E., Donzé, A., Maler, O., & Nickovic, D. (2012). Parametric identification of temporal properties (Vol. 7186, pp. 147–160). Presented at the RV: Runtime Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-642-29860-8_12' chicago: Asarin, Eugene, Alexandre Donzé, Oded Maler, and Dejan Nickovic. “Parametric Identification of Temporal Properties,” 7186:147–60. Springer, 2012. https://doi.org/10.1007/978-3-642-29860-8_12. ieee: 'E. Asarin, A. Donzé, O. Maler, and D. Nickovic, “Parametric identification of temporal properties,” presented at the RV: Runtime Verification, San Francisco, CA, United States, 2012, vol. 7186, pp. 147–160.' ista: 'Asarin E, Donzé A, Maler O, Nickovic D. 2012. Parametric identification of temporal properties. RV: Runtime Verification, LNCS, vol. 7186, 147–160.' mla: Asarin, Eugene, et al. Parametric Identification of Temporal Properties. Vol. 7186, Springer, 2012, pp. 147–60, doi:10.1007/978-3-642-29860-8_12. short: E. Asarin, A. Donzé, O. Maler, D. Nickovic, in:, Springer, 2012, pp. 147–160. conference: end_date: 2011-09-30 location: San Francisco, CA, United States name: 'RV: Runtime Verification' start_date: 2011-09-27 date_created: 2018-12-11T12:01:45Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T07:41:29Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-642-29860-8_12 file: - access_level: open_access checksum: ba4a75287008fc64b8fbf78a7476ec32 content_type: application/pdf creator: dernst date_created: 2020-05-15T12:50:15Z date_updated: 2020-07-14T12:46:01Z file_id: '7862' file_name: 2012_RV_Asarin.pdf file_size: 374726 relation: main_file file_date_updated: 2020-07-14T12:46:01Z has_accepted_license: '1' intvolume: ' 7186' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 147 - 160 publication_status: published publisher: Springer publist_id: '3525' quality_controlled: '1' scopus_import: 1 status: public title: Parametric identification of temporal properties type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7186 year: '2012' ... --- _id: '3160' abstract: - lang: eng text: There is a long-running controversy about how early cell fate decisions are made in the developing mammalian embryo. 1,2 In particular, it is controversial when the first events that can predict the establishment of the pluripotent and extra-embryonic lineages in the blastocyst of the pre-implantation embryo occur. It has long been proposed that the position and polarity of cells at the 16- to 32-cell stage embryo influence their decision to either give rise to the pluripotent cell lineage that eventually contributes to the inner cell mass (ICM), comprising the primitive endoderm (PE) and the epiblast (EPI), or the extra-embryonic trophectoderm (TE) surrounding the blastocoel. The positioning of cells in the embryo at this developmental stage could largely be the result of random events, making this a stochastic model of cell lineage allocation. Contrary to such a stochastic model, some studies have detected putative differences in the lineage potential of individual blastomeres before compaction, indicating that the first cell fate decisions may occur as early as at the 4-cell stage. Using a non-invasive, quantitative in vivo imaging assay to study the kinetic behavior of Oct4 (also known as POU5F1), a key transcription factor (TF) controlling pre-implantation development in the mouse embryo, 3-5 a recent study identifies Oct4 kinetics as a predictive measure of cell lineage patterning in the early mouse embryo. 6 Here, we discuss the implications of such molecular heterogeneities in early development and offer potential avenues toward a mechanistic understanding of these observations, contributing to the resolution of the controversy of developmental cell lineage allocation. author: - first_name: Periklis full_name: Pantazis, Periklis last_name: Pantazis - first_name: Tobias full_name: Bollenbach, Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Pantazis P, Bollenbach MT. Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. 2012;11(11):2055-2058. doi:10.4161/cc.20118 apa: Pantazis, P., & Bollenbach, M. T. (2012). Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. Taylor and Francis. https://doi.org/10.4161/cc.20118 chicago: Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics and the Emerging Asymmetry in the Early Mammalian Embryo.” Cell Cycle. Taylor and Francis, 2012. https://doi.org/10.4161/cc.20118. ieee: P. Pantazis and M. T. Bollenbach, “Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo,” Cell Cycle, vol. 11, no. 11. Taylor and Francis, pp. 2055–2058, 2012. ista: Pantazis P, Bollenbach MT. 2012. Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. 11(11), 2055–2058. mla: Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics and the Emerging Asymmetry in the Early Mammalian Embryo.” Cell Cycle, vol. 11, no. 11, Taylor and Francis, 2012, pp. 2055–58, doi:10.4161/cc.20118. short: P. Pantazis, M.T. Bollenbach, Cell Cycle 11 (2012) 2055–2058. date_created: 2018-12-11T12:01:44Z date_published: 2012-06-01T00:00:00Z date_updated: 2021-01-12T07:41:28Z day: '01' department: - _id: ToBo doi: 10.4161/cc.20118 intvolume: ' 11' issue: '11' language: - iso: eng month: '06' oa_version: None page: 2055 - 2058 publication: Cell Cycle publication_status: published publisher: Taylor and Francis publist_id: '3531' quality_controlled: '1' scopus_import: 1 status: public title: Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2012' ... --- _id: '3164' abstract: - lang: eng text: Overview of the Special Issue on structured prediction and inference. author: - first_name: Matthew full_name: Blaschko, Matthew last_name: Blaschko - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Blaschko M, Lampert C. Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. 2012;99(3):257-258. doi:10.1007/s11263-012-0530-y' apa: 'Blaschko, M., & Lampert, C. (2012). Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. Springer. https://doi.org/10.1007/s11263-012-0530-y' chicago: 'Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue on Structured Prediction and Inference.” International Journal of Computer Vision. Springer, 2012. https://doi.org/10.1007/s11263-012-0530-y.' ieee: 'M. Blaschko and C. Lampert, “Guest editorial: Special issue on structured prediction and inference,” International Journal of Computer Vision, vol. 99, no. 3. Springer, pp. 257–258, 2012.' ista: 'Blaschko M, Lampert C. 2012. Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. 99(3), 257–258.' mla: 'Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue on Structured Prediction and Inference.” International Journal of Computer Vision, vol. 99, no. 3, Springer, 2012, pp. 257–58, doi:10.1007/s11263-012-0530-y.' short: M. Blaschko, C. Lampert, International Journal of Computer Vision 99 (2012) 257–258. date_created: 2018-12-11T12:01:46Z date_published: 2012-09-01T00:00:00Z date_updated: 2021-01-12T07:41:30Z day: '01' department: - _id: ChLa doi: 10.1007/s11263-012-0530-y intvolume: ' 99' issue: '3' language: - iso: eng month: '09' oa_version: None page: 257 - 258 publication: International Journal of Computer Vision publication_status: published publisher: Springer publist_id: '3521' quality_controlled: '1' scopus_import: 1 status: public title: 'Guest editorial: Special issue on structured prediction and inference' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 99 year: '2012' ... --- _id: '3166' abstract: - lang: eng text: 'There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eors Szathmary (nominated by Dr. Gaspar Jekely) and Dr. Adam Kun (nominated by Dr. Sandor Pongor)' acknowledgement: 'The author was supported by the ERC-2009-AdG Grant for project 250152 SELECTIONINFORMATION. ' article_number: '6' author: - first_name: Harold full_name: Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: Vladar orcid: 0000-0002-5985-7653 citation: ama: de Vladar H. Amino acid fermentation at the origin of the genetic code. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-6 apa: de Vladar, H. (2012). Amino acid fermentation at the origin of the genetic code. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-6 chicago: Vladar, Harold de. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-6. ieee: H. de Vladar, “Amino acid fermentation at the origin of the genetic code,” Biology Direct, vol. 7. BioMed Central, 2012. ista: de Vladar H. 2012. Amino acid fermentation at the origin of the genetic code. Biology Direct. 7, 6. mla: de Vladar, Harold. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct, vol. 7, 6, BioMed Central, 2012, doi:10.1186/1745-6150-7-6. short: H. de Vladar, Biology Direct 7 (2012). date_created: 2018-12-11T12:01:46Z date_published: 2012-02-10T00:00:00Z date_updated: 2021-01-12T07:41:31Z day: '10' ddc: - '570' - '576' department: - _id: NiBa doi: 10.1186/1745-6150-7-6 ec_funded: 1 file: - access_level: open_access checksum: e511e401e239ef608a7fd79b21a06d78 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:44Z date_updated: 2020-07-14T12:46:02Z file_id: '5166' file_name: IST-2012-99-v1+1_1745-6150-7-6.pdf file_size: 4099536 relation: main_file file_date_updated: 2020-07-14T12:46:02Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Biology Direct publication_status: published publisher: BioMed Central publist_id: '3518' pubrep_id: '99' quality_controlled: '1' status: public title: Amino acid fermentation at the origin of the genetic code tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2012' ... --- _id: '3167' article_type: letter_note author: - first_name: Michele full_name: Weber, Michele id: 3A3FC708-F248-11E8-B48F-1D18A9856A87 last_name: Weber citation: ama: Weber M. NextGen speaks 13 . Science. 2012;336(6077):32-34. doi:10.1126/science.336.6077.32 apa: Weber, M. (2012). NextGen speaks 13 . Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.336.6077.32 chicago: Weber, Michele. “NextGen Speaks 13 .” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.336.6077.32. ieee: M. Weber, “NextGen speaks 13 ,” Science, vol. 336, no. 6077. American Association for the Advancement of Science, pp. 32–34, 2012. ista: Weber M. 2012. NextGen speaks 13 . Science. 336(6077), 32–34. mla: Weber, Michele. “NextGen Speaks 13 .” Science, vol. 336, no. 6077, American Association for the Advancement of Science, 2012, pp. 32–34, doi:10.1126/science.336.6077.32. short: M. Weber, Science 336 (2012) 32–34. date_created: 2018-12-11T12:01:47Z date_published: 2012-04-06T00:00:00Z date_updated: 2021-01-12T07:41:32Z day: '06' department: - _id: MiSi doi: 10.1126/science.336.6077.32 external_id: pmid: - '22491839' intvolume: ' 336' issue: '6077' language: - iso: eng month: '04' oa_version: None page: 32-34 pmid: 1 popular_science: '1' publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '3516' status: public title: 'NextGen speaks 13 ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 336 year: '2012' ... --- _id: '3241' abstract: - lang: eng text: 'We prove a negative result concerning error reduction by parallel repetition for computationally sound protocols, e.g., interactive arguments. Our main result is a complete and computationally sound eight round interactive argument for which k-fold parallel repetition does not reduce the error below a constant for any polynomial k. The starting point for our construction is the work of Bellare, Impagliazzo and Naor (FOCS''97). For any fixed k, they construct a four round protocol for which k-fold parallel repetition does not lower the soundness error. The communication complexity of this protocol is linear in k. By using universal arguments due to Barak and Goldreich (CCC 2002), we turn this protocol into an eight-round protocol whose complexity is basically independent of k. ' author: - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Douglas full_name: Wikström, Douglas last_name: Wikström citation: ama: Pietrzak KZ, Wikström D. Parallel repetition of computationally sound protocols revisited. Journal of Cryptology. 2012;25(1):116-135. doi:10.1007/s00145-010-9090-x apa: Pietrzak, K. Z., & Wikström, D. (2012). Parallel repetition of computationally sound protocols revisited. Journal of Cryptology. Springer. https://doi.org/10.1007/s00145-010-9090-x chicago: Pietrzak, Krzysztof Z, and Douglas Wikström. “Parallel Repetition of Computationally Sound Protocols Revisited.” Journal of Cryptology. Springer, 2012. https://doi.org/10.1007/s00145-010-9090-x. ieee: K. Z. Pietrzak and D. Wikström, “Parallel repetition of computationally sound protocols revisited,” Journal of Cryptology, vol. 25, no. 1. Springer, pp. 116–135, 2012. ista: Pietrzak KZ, Wikström D. 2012. Parallel repetition of computationally sound protocols revisited. Journal of Cryptology. 25(1), 116–135. mla: Pietrzak, Krzysztof Z., and Douglas Wikström. “Parallel Repetition of Computationally Sound Protocols Revisited.” Journal of Cryptology, vol. 25, no. 1, Springer, 2012, pp. 116–35, doi:10.1007/s00145-010-9090-x. short: K.Z. Pietrzak, D. Wikström, Journal of Cryptology 25 (2012) 116–135. date_created: 2018-12-11T12:02:12Z date_published: 2012-11-01T00:00:00Z date_updated: 2021-01-12T07:42:03Z day: '01' doi: 10.1007/s00145-010-9090-x extern: 1 intvolume: ' 25' issue: '1' month: '11' page: 116 - 135 publication: Journal of Cryptology publication_status: published publisher: Springer publist_id: '3439' quality_controlled: 0 status: public title: Parallel repetition of computationally sound protocols revisited type: journal_article volume: 25 year: '2012' ... --- _id: '3252' abstract: - lang: eng text: 'We study the automatic synthesis of fair non-repudiation protocols, a class of fair exchange protocols, used for digital contract signing. First, we show how to specify the objectives of the participating agents, the trusted third party (TTP) and the protocols as path formulas in Linear Temporal Logic (LTL) and prove that the satisfaction of the objectives of the agents and the TTP imply satisfaction of the protocol objectives. We then show that weak (co-operative) co-synthesis and classical (strictly competitive) co-synthesis fail in synthesizing these protocols, whereas assume-guarantee synthesis (AGS) succeeds. We demonstrate the success of assume-guarantee synthesis as follows: (a) any solution of assume-guarantee synthesis is attack-free; no subset of participants can violate the objectives of the other participants without violating their own objectives; (b) the Asokan-Shoup-Waidner (ASW) certified mail protocol that has known vulnerabilities is not a solution of AGS; and (c) the Kremer-Markowitch (KM) non-repudiation protocol is a solution of AGS. To our knowledge this is the first application of synthesis to fair non-repudiation protocols, and our results show how synthesis can generate correct protocols and automatically discover vulnerabilities. The solution to assume-guarantee synthesis can be computed efficiently as the secure equilibrium solution of three-player graph games. © 2012 Springer-Verlag.' acknowledgement: "The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23 (Modern Graph Algorithmic Techniques in Formal Verification), FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.\r\nThe authors would like to thank Avik Chaudhuri for his invaluable help and feedback." alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vishwanath full_name: Raman, Vishwanath last_name: Raman citation: ama: 'Chatterjee K, Raman V. Synthesizing protocols for digital contract signing. In: Vol 7148. Springer; 2012:152-168. doi:10.1007/978-3-642-27940-9_11' apa: 'Chatterjee, K., & Raman, V. (2012). Synthesizing protocols for digital contract signing (Vol. 7148, pp. 152–168). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA: Springer. https://doi.org/10.1007/978-3-642-27940-9_11' chicago: Chatterjee, Krishnendu, and Vishwanath Raman. “Synthesizing Protocols for Digital Contract Signing,” 7148:152–68. Springer, 2012. https://doi.org/10.1007/978-3-642-27940-9_11. ieee: 'K. Chatterjee and V. Raman, “Synthesizing protocols for digital contract signing,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA, 2012, vol. 7148, pp. 152–168.' ista: 'Chatterjee K, Raman V. 2012. Synthesizing protocols for digital contract signing. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 7148, 152–168.' mla: Chatterjee, Krishnendu, and Vishwanath Raman. Synthesizing Protocols for Digital Contract Signing. Vol. 7148, Springer, 2012, pp. 152–68, doi:10.1007/978-3-642-27940-9_11. short: K. Chatterjee, V. Raman, in:, Springer, 2012, pp. 152–168. conference: end_date: 2012-01-24 location: Philadelphia, PA, USA name: 'VMCAI: Verification, Model Checking and Abstract Interpretation' start_date: 2012-01-22 date_created: 2018-12-11T12:02:16Z date_published: 2012-01-20T00:00:00Z date_updated: 2021-01-12T07:42:08Z day: '20' department: - _id: KrCh doi: 10.1007/978-3-642-27940-9_11 ec_funded: 1 intvolume: ' 7148' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1004.2697 month: '01' oa: 1 oa_version: Preprint page: 152 - 168 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '3405' quality_controlled: '1' scopus_import: 1 status: public title: Synthesizing protocols for digital contract signing type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7148 year: '2012' ... --- _id: '3255' abstract: - lang: eng text: In this paper we survey results of two-player games on graphs and Markov decision processes with parity, mean-payoff and energy objectives, and the combination of mean-payoff and energy objectives with parity objectives. These problems have applications in verification and synthesis of reactive systems in resource-constrained environments. acknowledgement: This work was partially supported by FWF NFN Grant S11407-N23 (RiSE) and a Microsoft faculty fellowship. alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen citation: ama: 'Chatterjee K, Doyen L. Games and Markov decision processes with mean payoff parity and energy parity objectives. In: Vol 7119. Springer; 2012:37-46. doi:10.1007/978-3-642-25929-6_3' apa: 'Chatterjee, K., & Doyen, L. (2012). Games and Markov decision processes with mean payoff parity and energy parity objectives (Vol. 7119, pp. 37–46). Presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Lednice, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-25929-6_3' chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Games and Markov Decision Processes with Mean Payoff Parity and Energy Parity Objectives,” 7119:37–46. Springer, 2012. https://doi.org/10.1007/978-3-642-25929-6_3. ieee: 'K. Chatterjee and L. Doyen, “Games and Markov decision processes with mean payoff parity and energy parity objectives,” presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Lednice, Czech Republic, 2012, vol. 7119, pp. 37–46.' ista: 'Chatterjee K, Doyen L. 2012. Games and Markov decision processes with mean payoff parity and energy parity objectives. MEMICS: Mathematical and Engineering Methods in Computer Science, LNCS, vol. 7119, 37–46.' mla: Chatterjee, Krishnendu, and Laurent Doyen. Games and Markov Decision Processes with Mean Payoff Parity and Energy Parity Objectives. Vol. 7119, Springer, 2012, pp. 37–46, doi:10.1007/978-3-642-25929-6_3. short: K. Chatterjee, L. Doyen, in:, Springer, 2012, pp. 37–46. conference: end_date: 2011-10-16 location: Lednice, Czech Republic name: 'MEMICS: Mathematical and Engineering Methods in Computer Science' start_date: 2011-10-14 date_created: 2018-12-11T12:02:17Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T07:42:10Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.1007/978-3-642-25929-6_3 file: - access_level: open_access checksum: eed2cc1e76b160418c977e76e8899a60 content_type: application/pdf creator: dernst date_created: 2020-05-15T12:53:12Z date_updated: 2020-07-14T12:46:05Z file_id: '7863' file_name: 2012_MEMICS_Chatterjee.pdf file_size: 114060 relation: main_file file_date_updated: 2020-07-14T12:46:05Z has_accepted_license: '1' intvolume: ' 7119' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 37 - 46 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '3400' quality_controlled: '1' scopus_import: 1 status: public title: Games and Markov decision processes with mean payoff parity and energy parity objectives type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7119 year: '2012' ... --- _id: '3250' abstract: - lang: eng text: The Learning Parity with Noise (LPN) problem has recently found many applications in cryptography as the hardness assumption underlying the constructions of "provably secure" cryptographic schemes like encryption or authentication protocols. Being provably secure means that the scheme comes with a proof showing that the existence of an efficient adversary against the scheme implies that the underlying hardness assumption is wrong. LPN based schemes are appealing for theoretical and practical reasons. On the theoretical side, LPN based schemes offer a very strong security guarantee. The LPN problem is equivalent to the problem of decoding random linear codes, a problem that has been extensively studied in the last half century. The fastest known algorithms run in exponential time and unlike most number-theoretic problems used in cryptography, the LPN problem does not succumb to known quantum algorithms. On the practical side, LPN based schemes are often extremely simple and efficient in terms of code-size as well as time and space requirements. This makes them prime candidates for light-weight devices like RFID tags, which are too weak to implement standard cryptographic primitives like the AES block-cipher. This talk will be a gentle introduction to provable security using simple LPN based schemes as examples. Starting from pseudorandom generators and symmetric key encryption, over secret-key authentication protocols, and, if time admits, touching on recent constructions of public-key identification, commitments and zero-knowledge proofs. alternative_title: - LNCS author: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Pietrzak KZ. Cryptography from learning parity with noise. In: Vol 7147. Springer; 2012:99-114. doi:10.1007/978-3-642-27660-6_9' apa: 'Pietrzak, K. Z. (2012). Cryptography from learning parity with noise (Vol. 7147, pp. 99–114). Presented at the SOFSEM: Current Trends in Theory and Practice of Computer Science, Špindlerův Mlýn, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-27660-6_9' chicago: Pietrzak, Krzysztof Z. “Cryptography from Learning Parity with Noise,” 7147:99–114. Springer, 2012. https://doi.org/10.1007/978-3-642-27660-6_9. ieee: 'K. Z. Pietrzak, “Cryptography from learning parity with noise,” presented at the SOFSEM: Current Trends in Theory and Practice of Computer Science, Špindlerův Mlýn, Czech Republic, 2012, vol. 7147, pp. 99–114.' ista: 'Pietrzak KZ. 2012. Cryptography from learning parity with noise. SOFSEM: Current Trends in Theory and Practice of Computer Science, LNCS, vol. 7147, 99–114.' mla: Pietrzak, Krzysztof Z. Cryptography from Learning Parity with Noise. Vol. 7147, Springer, 2012, pp. 99–114, doi:10.1007/978-3-642-27660-6_9. short: K.Z. Pietrzak, in:, Springer, 2012, pp. 99–114. conference: end_date: 2012-01-27 location: Špindlerův Mlýn, Czech Republic name: 'SOFSEM: Current Trends in Theory and Practice of Computer Science' start_date: 2012-01-21 date_created: 2018-12-11T12:02:15Z date_published: 2012-02-19T00:00:00Z date_updated: 2021-01-12T07:42:07Z day: '19' department: - _id: KrPi doi: 10.1007/978-3-642-27660-6_9 intvolume: ' 7147' language: - iso: eng month: '02' oa_version: None page: 99 - 114 publication_status: published publisher: Springer publist_id: '3407' quality_controlled: '1' scopus_import: 1 status: public title: Cryptography from learning parity with noise type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7147 year: '2012' ... --- _id: '3256' abstract: - lang: eng text: We use a distortion to define the dual complex of a cubical subdivision of ℝ n as an n-dimensional subcomplex of the nerve of the set of n-cubes. Motivated by the topological analysis of high-dimensional digital image data, we consider such subdivisions defined by generalizations of quad- and oct-trees to n dimensions. Assuming the subdivision is balanced, we show that mapping each vertex to the center of the corresponding n-cube gives a geometric realization of the dual complex in ℝ n. acknowledgement: This research is partially supported by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0057 and HR0011-09-0065 as well as the National Science Foundation (NSF) under grant DBI-0820624. author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Michael full_name: Kerber, Michael id: 36E4574A-F248-11E8-B48F-1D18A9856A87 last_name: Kerber orcid: 0000-0002-8030-9299 citation: ama: Edelsbrunner H, Kerber M. Dual complexes of cubical subdivisions of ℝn. Discrete & Computational Geometry. 2012;47(2):393-414. doi:10.1007/s00454-011-9382-4 apa: Edelsbrunner, H., & Kerber, M. (2012). Dual complexes of cubical subdivisions of ℝn. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-011-9382-4 chicago: Edelsbrunner, Herbert, and Michael Kerber. “Dual Complexes of Cubical Subdivisions of ℝn.” Discrete & Computational Geometry. Springer, 2012. https://doi.org/10.1007/s00454-011-9382-4. ieee: H. Edelsbrunner and M. Kerber, “Dual complexes of cubical subdivisions of ℝn,” Discrete & Computational Geometry, vol. 47, no. 2. Springer, pp. 393–414, 2012. ista: Edelsbrunner H, Kerber M. 2012. Dual complexes of cubical subdivisions of ℝn. Discrete & Computational Geometry. 47(2), 393–414. mla: Edelsbrunner, Herbert, and Michael Kerber. “Dual Complexes of Cubical Subdivisions of ℝn.” Discrete & Computational Geometry, vol. 47, no. 2, Springer, 2012, pp. 393–414, doi:10.1007/s00454-011-9382-4. short: H. Edelsbrunner, M. Kerber, Discrete & Computational Geometry 47 (2012) 393–414. date_created: 2018-12-11T12:02:17Z date_published: 2012-03-01T00:00:00Z date_updated: 2021-01-12T07:42:10Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1007/s00454-011-9382-4 file: - access_level: open_access checksum: 76486f3b2c9e7fd81342f3832ca387e7 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:15Z date_updated: 2020-07-14T12:46:05Z file_id: '4675' file_name: IST-2016-543-v1+1_2012-J-08-HierarchyCubeComplex.pdf file_size: 203636 relation: main_file file_date_updated: 2020-07-14T12:46:05Z has_accepted_license: '1' intvolume: ' 47' issue: '2' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 393 - 414 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '3398' pubrep_id: '543' quality_controlled: '1' scopus_import: 1 status: public title: Dual complexes of cubical subdivisions of ℝn type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2012' ... --- _id: '3254' abstract: - lang: eng text: 'The theory of graph games with ω-regular winning conditions is the foundation for modeling and synthesizing reactive processes. In the case of stochastic reactive processes, the corresponding stochastic graph games have three players, two of them (System and Environment) behaving adversarially, and the third (Uncertainty) behaving probabilistically. We consider two problems for stochastic graph games: the qualitative problem asks for the set of states from which a player can win with probability 1 (almost-sure winning); and the quantitative problem asks for the maximal probability of winning (optimal winning) from each state. We consider ω-regular winning conditions formalized as Müller winning conditions. We present optimal memory bounds for pure (deterministic) almost-sure winning and optimal winning strategies in stochastic graph games with Müller winning conditions. We also study the complexity of stochastic Müller games and show that both the qualitative and quantitative analysis problems are PSPACE-complete. Our results are relevant in synthesis of stochastic reactive processes.' acknowledgement: 'The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: Chatterjee K. The complexity of stochastic Müller games. Information and Computation. 2012;211:29-48. doi:10.1016/j.ic.2011.11.004 apa: Chatterjee, K. (2012). The complexity of stochastic Müller games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2011.11.004 chicago: Chatterjee, Krishnendu. “The Complexity of Stochastic Müller Games.” Information and Computation. Elsevier, 2012. https://doi.org/10.1016/j.ic.2011.11.004. ieee: K. Chatterjee, “The complexity of stochastic Müller games,” Information and Computation, vol. 211. Elsevier, pp. 29–48, 2012. ista: Chatterjee K. 2012. The complexity of stochastic Müller games. Information and Computation. 211, 29–48. mla: Chatterjee, Krishnendu. “The Complexity of Stochastic Müller Games.” Information and Computation, vol. 211, Elsevier, 2012, pp. 29–48, doi:10.1016/j.ic.2011.11.004. short: K. Chatterjee, Information and Computation 211 (2012) 29–48. date_created: 2018-12-11T12:02:17Z date_published: 2012-02-01T00:00:00Z date_updated: 2021-01-12T07:42:09Z day: '01' department: - _id: KrCh doi: 10.1016/j.ic.2011.11.004 ec_funded: 1 intvolume: ' 211' language: - iso: eng main_file_link: - url: http://arise.or.at/pubpdf/The_complexity_of_stochastic_M___u_ller_games.pdf month: '02' oa_version: None page: 29 - 48 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Information and Computation publication_status: published publisher: Elsevier publist_id: '3403' quality_controlled: '1' scopus_import: 1 status: public title: The complexity of stochastic Müller games type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 211 year: '2012' ... --- _id: '3253' abstract: - lang: eng text: We describe a framework for reasoning about programs with lists carrying integer numerical data. We use abstract domains to describe and manipulate complex constraints on configurations of these programs mixing constraints on the shape of the heap, sizes of the lists, on the multisets of data stored in these lists, and on the data at their different positions. Moreover, we provide powerful techniques for automatic validation of Hoare-triples and invariant checking, as well as for automatic synthesis of invariants and procedure summaries using modular inter-procedural analysis. The approach has been implemented in a tool called Celia and experimented successfully on a large benchmark of programs. acknowledgement: This work was partly supported by the French National Research Agency (ANR) project Veridyc (ANR-09-SEGI-016). alternative_title: - LNCS author: - first_name: Ahmed full_name: Bouajjani, Ahmed last_name: Bouajjani - first_name: Cezara full_name: Dragoi, Cezara id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87 last_name: Dragoi - first_name: Constantin full_name: Enea, Constantin last_name: Enea - first_name: Mihaela full_name: Sighireanu, Mihaela last_name: Sighireanu citation: ama: 'Bouajjani A, Dragoi C, Enea C, Sighireanu M. Abstract domains for automated reasoning about list manipulating programs with infinite data. In: Vol 7148. Springer; 2012:1-22. doi:10.1007/978-3-642-27940-9_1' apa: 'Bouajjani, A., Dragoi, C., Enea, C., & Sighireanu, M. (2012). Abstract domains for automated reasoning about list manipulating programs with infinite data (Vol. 7148, pp. 1–22). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA: Springer. https://doi.org/10.1007/978-3-642-27940-9_1' chicago: Bouajjani, Ahmed, Cezara Dragoi, Constantin Enea, and Mihaela Sighireanu. “Abstract Domains for Automated Reasoning about List Manipulating Programs with Infinite Data,” 7148:1–22. Springer, 2012. https://doi.org/10.1007/978-3-642-27940-9_1. ieee: 'A. Bouajjani, C. Dragoi, C. Enea, and M. Sighireanu, “Abstract domains for automated reasoning about list manipulating programs with infinite data,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA, 2012, vol. 7148, pp. 1–22.' ista: 'Bouajjani A, Dragoi C, Enea C, Sighireanu M. 2012. Abstract domains for automated reasoning about list manipulating programs with infinite data. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 7148, 1–22.' mla: Bouajjani, Ahmed, et al. Abstract Domains for Automated Reasoning about List Manipulating Programs with Infinite Data. Vol. 7148, Springer, 2012, pp. 1–22, doi:10.1007/978-3-642-27940-9_1. short: A. Bouajjani, C. Dragoi, C. Enea, M. Sighireanu, in:, Springer, 2012, pp. 1–22. conference: end_date: 2012-01-24 location: Philadelphia, PA, USA name: 'VMCAI: Verification, Model Checking and Abstract Interpretation' start_date: 2012-01-22 date_created: 2018-12-11T12:02:17Z date_published: 2012-02-26T00:00:00Z date_updated: 2021-01-12T07:42:09Z day: '26' department: - _id: ToHe doi: 10.1007/978-3-642-27940-9_1 intvolume: ' 7148' language: - iso: eng month: '02' oa_version: None page: 1 - 22 publication_status: published publisher: Springer publist_id: '3404' quality_controlled: '1' status: public title: Abstract domains for automated reasoning about list manipulating programs with infinite data type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7148 year: '2012' ... --- _id: '3265' abstract: - lang: eng text: We propose a mid-level statistical model for image segmentation that composes multiple figure-ground hypotheses (FG) obtained by applying constraints at different locations and scales, into larger interpretations (tilings) of the entire image. Inference is cast as optimization over sets of maximal cliques sampled from a graph connecting all non-overlapping figure-ground segment hypotheses. Potential functions over cliques combine unary, Gestalt-based figure qualities, and pairwise compatibilities among spatially neighboring segments, constrained by T-junctions and the boundary interface statistics of real scenes. Learning the model parameters is based on maximum likelihood, alternating between sampling image tilings and optimizing their potential function parameters. State of the art results are reported on the Berkeley and Stanford segmentation datasets, as well as VOC2009, where a 28% improvement was achieved. article_number: '6126486' author: - first_name: Adrian full_name: Ion, Adrian id: 29F89302-F248-11E8-B48F-1D18A9856A87 last_name: Ion - first_name: Joao full_name: Carreira, Joao last_name: Carreira - first_name: Cristian full_name: Sminchisescu, Cristian last_name: Sminchisescu citation: ama: 'Ion A, Carreira J, Sminchisescu C. Image segmentation by figure-ground composition into maximal cliques. In: IEEE; 2012. doi:10.1109/ICCV.2011.6126486' apa: 'Ion, A., Carreira, J., & Sminchisescu, C. (2012). Image segmentation by figure-ground composition into maximal cliques. Presented at the ICCV: International Conference on Computer Vision, Barcelona, Spain: IEEE. https://doi.org/10.1109/ICCV.2011.6126486' chicago: Ion, Adrian, Joao Carreira, and Cristian Sminchisescu. “Image Segmentation by Figure-Ground Composition into Maximal Cliques.” IEEE, 2012. https://doi.org/10.1109/ICCV.2011.6126486. ieee: 'A. Ion, J. Carreira, and C. Sminchisescu, “Image segmentation by figure-ground composition into maximal cliques,” presented at the ICCV: International Conference on Computer Vision, Barcelona, Spain, 2012.' ista: 'Ion A, Carreira J, Sminchisescu C. 2012. Image segmentation by figure-ground composition into maximal cliques. ICCV: International Conference on Computer Vision, 6126486.' mla: Ion, Adrian, et al. Image Segmentation by Figure-Ground Composition into Maximal Cliques. 6126486, IEEE, 2012, doi:10.1109/ICCV.2011.6126486. short: A. Ion, J. Carreira, C. Sminchisescu, in:, IEEE, 2012. conference: end_date: 2011-11-13 location: Barcelona, Spain name: 'ICCV: International Conference on Computer Vision' start_date: 2011-11-06 date_created: 2018-12-11T12:02:21Z date_published: 2012-01-12T00:00:00Z date_updated: 2021-01-12T07:42:15Z day: '12' department: - _id: HeEd doi: 10.1109/ICCV.2011.6126486 language: - iso: eng month: '01' oa_version: None publication_status: published publisher: IEEE publist_id: '3382' quality_controlled: '1' status: public title: Image segmentation by figure-ground composition into maximal cliques type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '3282' abstract: - lang: eng text: 'Traditionally, symmetric-key message authentication codes (MACs) are easily built from pseudorandom functions (PRFs). In this work we propose a wide variety of other approaches to building efficient MACs, without going through a PRF first. In particular, unlike deterministic PRF-based MACs, where each message has a unique valid tag, we give a number of probabilistic MAC constructions from various other primitives/assumptions. Our main results are summarized as follows: We show several new probabilistic MAC constructions from a variety of general assumptions, including CCA-secure encryption, Hash Proof Systems and key-homomorphic weak PRFs. By instantiating these frameworks under concrete number theoretic assumptions, we get several schemes which are more efficient than just using a state-of-the-art PRF instantiation under the corresponding assumption. For probabilistic MACs, unlike deterministic ones, unforgeability against a chosen message attack (uf-cma ) alone does not imply security if the adversary can additionally make verification queries (uf-cmva ). We give an efficient generic transformation from any uf-cma secure MAC which is "message-hiding" into a uf-cmva secure MAC. This resolves the main open problem of Kiltz et al. from Eurocrypt''11; By using our transformation on their constructions, we get the first efficient MACs from the LPN assumption. While all our new MAC constructions immediately give efficient actively secure, two-round symmetric-key identification schemes, we also show a very simple, three-round actively secure identification protocol from any weak PRF. In particular, the resulting protocol is much more efficient than the trivial approach of building a regular PRF from a weak PRF. © 2012 International Association for Cryptologic Research.' acknowledgement: Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC) alternative_title: - LNCS author: - first_name: Yevgeniy full_name: Dodis, Yevgeniy last_name: Dodis - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Eike full_name: Kiltz, Eike last_name: Kiltz - first_name: Daniel full_name: Wichs, Daniel last_name: Wichs citation: ama: 'Dodis Y, Pietrzak KZ, Kiltz E, Wichs D. Message authentication, revisited. In: Vol 7237. Springer; 2012:355-374. doi:10.1007/978-3-642-29011-4_22' apa: 'Dodis, Y., Pietrzak, K. Z., Kiltz, E., & Wichs, D. (2012). Message authentication, revisited (Vol. 7237, pp. 355–374). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Cambridge, UK: Springer. https://doi.org/10.1007/978-3-642-29011-4_22' chicago: Dodis, Yevgeniy, Krzysztof Z Pietrzak, Eike Kiltz, and Daniel Wichs. “Message Authentication, Revisited,” 7237:355–74. Springer, 2012. https://doi.org/10.1007/978-3-642-29011-4_22. ieee: 'Y. Dodis, K. Z. Pietrzak, E. Kiltz, and D. Wichs, “Message authentication, revisited,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Cambridge, UK, 2012, vol. 7237, pp. 355–374.' ista: 'Dodis Y, Pietrzak KZ, Kiltz E, Wichs D. 2012. Message authentication, revisited. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 7237, 355–374.' mla: Dodis, Yevgeniy, et al. Message Authentication, Revisited. Vol. 7237, Springer, 2012, pp. 355–74, doi:10.1007/978-3-642-29011-4_22. short: Y. Dodis, K.Z. Pietrzak, E. Kiltz, D. Wichs, in:, Springer, 2012, pp. 355–374. conference: end_date: 2012-04-19 location: Cambridge, UK name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' start_date: 2012-04-15 date_created: 2018-12-11T12:02:27Z date_published: 2012-03-10T00:00:00Z date_updated: 2021-01-12T07:42:22Z day: '10' ddc: - '000' - '004' department: - _id: KrPi doi: 10.1007/978-3-642-29011-4_22 ec_funded: 1 file: - access_level: open_access checksum: 8557c17a8c2586d06ebfe62d934f5c5f content_type: application/pdf creator: system date_created: 2018-12-12T10:14:23Z date_updated: 2020-07-14T12:46:06Z file_id: '5074' file_name: IST-2016-686-v1+1_059.pdf file_size: 372292 relation: main_file file_date_updated: 2020-07-14T12:46:06Z has_accepted_license: '1' intvolume: ' 7237' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 355 - 374 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '3364' pubrep_id: '686' quality_controlled: '1' status: public title: Message authentication, revisited tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7237 year: '2012' ... --- _id: '3280' abstract: - lang: eng text: 'The (decisional) learning with errors problem (LWE) asks to distinguish "noisy" inner products of a secret vector with random vectors from uniform. The learning parities with noise problem (LPN) is the special case where the elements of the vectors are bits. In recent years, the LWE and LPN problems have found many applications in cryptography. In this paper we introduce a (seemingly) much stronger adaptive assumption, called "subspace LWE" (SLWE), where the adversary can learn the inner product of the secret and random vectors after they were projected into an adaptively and adversarially chosen subspace. We prove that, surprisingly, the SLWE problem mapping into subspaces of dimension d is almost as hard as LWE using secrets of length d (the other direction is trivial.) This result immediately implies that several existing cryptosystems whose security is based on the hardness of the LWE/LPN problems are provably secure in a much stronger sense than anticipated. As an illustrative example we show that the standard way of using LPN for symmetric CPA secure encryption is even secure against a very powerful class of related key attacks. ' acknowledgement: Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC). alternative_title: - LNCS author: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Pietrzak KZ. Subspace LWE. In: Vol 7194. Springer; 2012:548-563. doi:10.1007/978-3-642-28914-9_31' apa: 'Pietrzak, K. Z. (2012). Subspace LWE (Vol. 7194, pp. 548–563). Presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy: Springer. https://doi.org/10.1007/978-3-642-28914-9_31' chicago: Pietrzak, Krzysztof Z. “Subspace LWE,” 7194:548–63. Springer, 2012. https://doi.org/10.1007/978-3-642-28914-9_31. ieee: 'K. Z. Pietrzak, “Subspace LWE,” presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy, 2012, vol. 7194, pp. 548–563.' ista: 'Pietrzak KZ. 2012. Subspace LWE. TCC: Theory of Cryptography Conference, LNCS, vol. 7194, 548–563.' mla: Pietrzak, Krzysztof Z. Subspace LWE. Vol. 7194, Springer, 2012, pp. 548–63, doi:10.1007/978-3-642-28914-9_31. short: K.Z. Pietrzak, in:, Springer, 2012, pp. 548–563. conference: end_date: 2012-03-21 location: Taormina, Sicily, Italy name: 'TCC: Theory of Cryptography Conference' start_date: 2012-03-19 date_created: 2018-12-11T12:02:26Z date_published: 2012-05-04T00:00:00Z date_updated: 2021-01-12T07:42:21Z day: '04' department: - _id: KrPi doi: 10.1007/978-3-642-28914-9_31 ec_funded: 1 intvolume: ' 7194' language: - iso: eng main_file_link: - open_access: '1' url: http://www.iacr.org/archive/tcc2012/71940166/71940166.pdf month: '05' oa: 1 oa_version: Submitted Version page: 548 - 563 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '3366' quality_controlled: '1' status: public title: Subspace LWE type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7194 year: '2012' ... --- _id: '3281' abstract: - lang: eng text: 'We consider the problem of amplifying the "lossiness" of functions. We say that an oracle circuit C*: {0,1} m → {0,1}* amplifies relative lossiness from ℓ/n to L/m if for every function f:{0,1} n → {0,1} n it holds that 1 If f is injective then so is C f. 2 If f has image size of at most 2 n-ℓ, then C f has image size at most 2 m-L. The question is whether such C* exists for L/m ≫ ℓ/n. This problem arises naturally in the context of cryptographic "lossy functions," where the relative lossiness is the key parameter. We show that for every circuit C* that makes at most t queries to f, the relative lossiness of C f is at most L/m ≤ ℓ/n + O(log t)/n. In particular, no black-box method making a polynomial t = poly(n) number of queries can amplify relative lossiness by more than an O(logn)/n additive term. We show that this is tight by giving a simple construction (cascading with some randomization) that achieves such amplification.' acknowledgement: "We would like to thank Oded Goldreich and Omer Rein- gold for discussions at an early stage of this project, and Scott Aaronson for clarifications regarding the collision problem.\r\n" alternative_title: - LNCS author: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Alon full_name: Rosen, Alon last_name: Rosen - first_name: Gil full_name: Segev, Gil last_name: Segev citation: ama: 'Pietrzak KZ, Rosen A, Segev G. Lossy functions do not amplify well. In: Vol 7194. Springer; 2012:458-475. doi:10.1007/978-3-642-28914-9_26' apa: 'Pietrzak, K. Z., Rosen, A., & Segev, G. (2012). Lossy functions do not amplify well (Vol. 7194, pp. 458–475). Presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy: Springer. https://doi.org/10.1007/978-3-642-28914-9_26' chicago: Pietrzak, Krzysztof Z, Alon Rosen, and Gil Segev. “Lossy Functions Do Not Amplify Well,” 7194:458–75. Springer, 2012. https://doi.org/10.1007/978-3-642-28914-9_26. ieee: 'K. Z. Pietrzak, A. Rosen, and G. Segev, “Lossy functions do not amplify well,” presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy, 2012, vol. 7194, pp. 458–475.' ista: 'Pietrzak KZ, Rosen A, Segev G. 2012. Lossy functions do not amplify well. TCC: Theory of Cryptography Conference, LNCS, vol. 7194, 458–475.' mla: Pietrzak, Krzysztof Z., et al. Lossy Functions Do Not Amplify Well. Vol. 7194, Springer, 2012, pp. 458–75, doi:10.1007/978-3-642-28914-9_26. short: K.Z. Pietrzak, A. Rosen, G. Segev, in:, Springer, 2012, pp. 458–475. conference: end_date: 2012-03-21 location: Taormina, Sicily, Italy name: 'TCC: Theory of Cryptography Conference' start_date: 2012-03-19 date_created: 2018-12-11T12:02:26Z date_published: 2012-05-04T00:00:00Z date_updated: 2021-01-12T07:42:22Z day: '04' department: - _id: KrPi doi: 10.1007/978-3-642-28914-9_26 intvolume: ' 7194' language: - iso: eng main_file_link: - url: http://www.iacr.org/archive/tcc2012/tcc2012-index.html month: '05' oa_version: None page: 458 - 475 publication_status: published publisher: Springer publist_id: '3365' quality_controlled: '1' status: public title: Lossy functions do not amplify well type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7194 year: '2012' ... --- _id: '3284' abstract: - lang: eng text: |- We study the complexity of valued constraint satisfaction problems (VCSP). A problem from VCSP is characterised by a constraint language, a fixed set of cost functions over a finite domain. An instance of the problem is specified by a sum of cost functions from the language and the goal is to minimise the sum. Under the unique games conjecture, the approximability of finite-valued VCSPs is well-understood, see Raghavendra [FOCS’08]. However, there is no characterisation of finite-valued VCSPs, let alone general-valued VCSPs, that can be solved exactly in polynomial time, thus giving insights from a combinatorial optimisation perspective. We consider the case of languages containing all possible unary cost functions. In the case of languages consisting of only {0, ∞}-valued cost functions (i.e. relations), such languages have been called conservative and studied by Bulatov [LICS’03] and recently by Barto [LICS’11]. Since we study valued languages, we call a language conservative if it contains all finite-valued unary cost functions. The computational complexity of conservative valued languages has been studied by Cohen et al. [AIJ’06] for languages over Boolean domains, by Deineko et al. [JACM’08] for {0,1}-valued languages (a.k.a Max-CSP), and by Takhanov [STACS’10] for {0,∞}-valued languages containing all finite- valued unary cost functions (a.k.a. Min-Cost-Hom). We prove a Schaefer-like dichotomy theorem for conservative valued languages: if all cost functions in the language satisfy a certain condition (specified by a complementary combination of STP and MJN multimorphisms), then any instance can be solved in polynomial time (via a new algorithm developed in this paper), otherwise the language is NP-hard. This is the first complete complexity classification of general-valued constraint languages over non-Boolean domains. It is a common phenomenon that complexity classifications of problems over non-Boolean domains is significantly harder than the Boolean case. The polynomial-time algorithm we present for the tractable cases is a generalisation of the submodular minimisation problem and a result of Cohen et al. [TCS’08]. Our results generalise previous results by Takhanov [STACS’10] and (a subset of results) by Cohen et al. [AIJ’06] and Deineko et al. [JACM’08]. Moreover, our results do not rely on any computer-assisted search as in Deineko et al. [JACM’08], and provide a powerful tool for proving hardness of finite-valued and general-valued languages. acknowledgement: Vladimir Kolmogorov is supported by the Royal Academy of Eng ineering/EPSRC. author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Stanislav full_name: Živný, Stanislav last_name: Živný citation: ama: 'Kolmogorov V, Živný S. The complexity of conservative valued CSPs. In: SIAM; 2012:750-759.' apa: 'Kolmogorov, V., & Živný, S. (2012). The complexity of conservative valued CSPs (pp. 750–759). Presented at the SODA: Symposium on Discrete Algorithms, SIAM.' chicago: Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative Valued CSPs,” 750–59. SIAM, 2012. ieee: 'V. Kolmogorov and S. Živný, “The complexity of conservative valued CSPs,” presented at the SODA: Symposium on Discrete Algorithms, 2012, pp. 750–759.' ista: 'Kolmogorov V, Živný S. 2012. The complexity of conservative valued CSPs. SODA: Symposium on Discrete Algorithms, 750–759.' mla: Kolmogorov, Vladimir, and Stanislav Živný. The Complexity of Conservative Valued CSPs. SIAM, 2012, pp. 750–59. short: V. Kolmogorov, S. Živný, in:, SIAM, 2012, pp. 750–759. conference: name: 'SODA: Symposium on Discrete Algorithms' date_created: 2018-12-11T12:02:27Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T07:42:23Z day: '01' extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/1008.1555 month: '01' oa: 1 page: 750 - 759 publication_status: published publisher: SIAM publist_id: '3362' quality_controlled: 0 status: public title: The complexity of conservative valued CSPs type: conference year: '2012' ... --- _id: '330' abstract: - lang: eng text: 'A procedure for the continuous production of Cu 2ZnSnS 4 (CZTS) nanoparticles with controlled composition is presented. CZTS nanoparticles were prepared through the reaction of the metals'' amino complexes with elemental sulfur in a continuous-flow reactor at moderate temperatures (300-330 °C). High-resolution transmission electron microscopy and X-ray diffraction analysis showed the nanocrystals to have a crystallographic structure compatible with that of the kesterite. Chemical characterization of the materials showed the presence of the four elements in each individual nanocrystal. Composition control was achieved by adjusting the solution flow rate through the reactor and the proper choice of the nominal precursor concentration within the flowing solution. Single-particle analysis revealed a composition distribution within each sample, which was optimized at the highest synthesis temperatures used. ' article_processing_charge: No article_type: original author: - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Alex full_name: Carrete, Alex last_name: Carrete - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Shavel A, Cadavid D, Ibáñez M, Carrete A, Cabot A. Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. 2012;134(3):1438-1441. doi:10.1021/ja209688a apa: Shavel, A., Cadavid, D., Ibáñez, M., Carrete, A., & Cabot, A. (2012). Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja209688a chicago: Shavel, Alexey, Doris Cadavid, Maria Ibáñez, Alex Carrete, and Andreu Cabot. “Continuous Production of Cu Inf 2 Inf ZnSnS Inf 4 Inf Nanocrystals in a Flow Reactor.” Journal of the American Chemical Society. ACS, 2012. https://doi.org/10.1021/ja209688a. ieee: A. Shavel, D. Cadavid, M. Ibáñez, A. Carrete, and A. Cabot, “Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor,” Journal of the American Chemical Society, vol. 134, no. 3. ACS, pp. 1438–1441, 2012. ista: Shavel A, Cadavid D, Ibáñez M, Carrete A, Cabot A. 2012. Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. 134(3), 1438–1441. mla: Shavel, Alexey, et al. “Continuous Production of Cu Inf 2 Inf ZnSnS Inf 4 Inf Nanocrystals in a Flow Reactor.” Journal of the American Chemical Society, vol. 134, no. 3, ACS, 2012, pp. 1438–41, doi:10.1021/ja209688a. short: A. Shavel, D. Cadavid, M. Ibáñez, A. Carrete, A. Cabot, Journal of the American Chemical Society 134 (2012) 1438–1441. date_created: 2018-12-11T11:45:51Z date_published: 2012-01-02T00:00:00Z date_updated: 2021-01-12T07:42:29Z day: '02' doi: 10.1021/ja209688a extern: '1' intvolume: ' 134' issue: '3' language: - iso: eng month: '01' oa_version: None page: 1438 - 1441 publication: Journal of the American Chemical Society publication_status: published publisher: ACS publist_id: '7531' quality_controlled: '1' status: public title: Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2012' ... --- _id: '3317' abstract: - lang: eng text: The physical distance between presynaptic Ca2+ channels and the Ca2+ sensors that trigger exocytosis of neurotransmitter-containing vesicles is a key determinant of the signalling properties of synapses in the nervous system. Recent functional analysis indicates that in some fast central synapses, transmitter release is triggered by a small number of Ca2+ channels that are coupled to Ca2+ sensors at the nanometre scale. Molecular analysis suggests that this tight coupling is generated by protein–protein interactions involving Ca2+ channels, Ca2+ sensors and various other synaptic proteins. Nanodomain coupling has several functional advantages, as it increases the efficacy, speed and energy efficiency of synaptic transmission. acknowledgement: "Work of the authors was funded by grants of the Deutsche Forschungsgemeinschaft to P.J. (grants SFB 780/A5, TR 3/B10 and the Leibniz programme), a European Research Council Advanced grant to P.J. and a Swiss National Foundation fellowship to E.E.\r\nWe thank D. Tsien and E. Neher for their comments on this Review, J. Guzmán and A. Pernía-Andrade for reading earlier versions and E. Kramberger for perfect editorial support. We apologize that owing to space constraints, not all relevant papers could be cited.\r\n" author: - first_name: Emmanuel full_name: Eggermann, Emmanuel id: 34DACA34-E9AE-11E9-849C-D35BD8ADC20C last_name: Eggermann - first_name: Iancu full_name: Bucurenciu, Iancu id: 4BD1D872-E9AE-11E9-9EE9-8BF4597A9E2A last_name: Bucurenciu - first_name: Sarit full_name: Goswami, Sarit id: 3A578F32-F248-11E8-B48F-1D18A9856A87 last_name: Goswami - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Eggermann E, Bucurenciu I, Goswami S, Jonas PM. Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. Nature Reviews Neuroscience. 2012;13(1):7-21. doi:10.1038/nrn3125 apa: Eggermann, E., Bucurenciu, I., Goswami, S., & Jonas, P. M. (2012). Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. Nature Reviews Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nrn3125 chicago: Eggermann, Emmanuel, Iancu Bucurenciu, Sarit Goswami, and Peter M Jonas. “Nanodomain Coupling between Ca(2+) Channels and Sensors of Exocytosis at Fast Mammalian Synapses.” Nature Reviews Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nrn3125. ieee: E. Eggermann, I. Bucurenciu, S. Goswami, and P. M. Jonas, “Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses,” Nature Reviews Neuroscience, vol. 13, no. 1. Nature Publishing Group, pp. 7–21, 2012. ista: Eggermann E, Bucurenciu I, Goswami S, Jonas PM. 2012. Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. Nature Reviews Neuroscience. 13(1), 7–21. mla: Eggermann, Emmanuel, et al. “Nanodomain Coupling between Ca(2+) Channels and Sensors of Exocytosis at Fast Mammalian Synapses.” Nature Reviews Neuroscience, vol. 13, no. 1, Nature Publishing Group, 2012, pp. 7–21, doi:10.1038/nrn3125. short: E. Eggermann, I. Bucurenciu, S. Goswami, P.M. Jonas, Nature Reviews Neuroscience 13 (2012) 7–21. date_created: 2018-12-11T12:02:38Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T07:42:36Z day: '01' ddc: - '570' department: - _id: PeJo doi: 10.1038/nrn3125 file: - access_level: open_access checksum: 4c1c86b2f6e4e1562f5bb800b457ea9f content_type: application/pdf creator: system date_created: 2018-12-12T10:12:13Z date_updated: 2020-07-14T12:46:07Z file_id: '4931' file_name: IST-2017-820-v1+1_17463_3_art_file_109404_ltmxbw.pdf file_size: 314246 relation: main_file - access_level: open_access checksum: bceb2efdd49d115f4dde8486bc1be3f2 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:14Z date_updated: 2020-07-14T12:46:07Z file_id: '4932' file_name: IST-2017-820-v1+2_17463_3_figure_109402_ltmwlp.pdf file_size: 1840216 relation: main_file file_date_updated: 2020-07-14T12:46:07Z has_accepted_license: '1' intvolume: ' 13' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 7 - 21 project: - _id: 25BC64A8-B435-11E9-9278-68D0E5697425 grant_number: JO_780/A5 name: Synaptic Mechanisms of Neuronal Network Function - _id: 25BDE9A4-B435-11E9-9278-68D0E5697425 grant_number: SFB-TR3-TP10B name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen publication: Nature Reviews Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '3322' pubrep_id: '820' quality_controlled: '1' scopus_import: 1 status: public title: Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2012' ... --- _id: '3314' abstract: - lang: eng text: We introduce two-level discounted and mean-payoff games played by two players on a perfect-information stochastic game graph. The upper level game is a discounted or mean-payoff game and the lower level game is a (undiscounted) reachability game. Two-level games model hierarchical and sequential decision making under uncertainty across different time scales. For both discounted and mean-payoff two-level games, we show the existence of pure memoryless optimal strategies for both players and an ordered field property. We show that if there is only one player (Markov decision processes), then the values can be computed in polynomial time. It follows that whether the value of a player is equal to a given rational constant in two-level discounted or mean-payoff games can be decided in NP ∩ coNP. We also give an alternate strategy improvement algorithm to compute the value. © 2012 World Scientific Publishing Company. author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar citation: ama: Chatterjee K, Majumdar R. Discounting and averaging in games across time scales. International Journal of Foundations of Computer Science. 2012;23(3):609-625. doi:10.1142/S0129054112400308 apa: Chatterjee, K., & Majumdar, R. (2012). Discounting and averaging in games across time scales. International Journal of Foundations of Computer Science. World Scientific Publishing. https://doi.org/10.1142/S0129054112400308 chicago: Chatterjee, Krishnendu, and Ritankar Majumdar. “Discounting and Averaging in Games across Time Scales.” International Journal of Foundations of Computer Science. World Scientific Publishing, 2012. https://doi.org/10.1142/S0129054112400308. ieee: K. Chatterjee and R. Majumdar, “Discounting and averaging in games across time scales,” International Journal of Foundations of Computer Science, vol. 23, no. 3. World Scientific Publishing, pp. 609–625, 2012. ista: Chatterjee K, Majumdar R. 2012. Discounting and averaging in games across time scales. International Journal of Foundations of Computer Science. 23(3), 609–625. mla: Chatterjee, Krishnendu, and Ritankar Majumdar. “Discounting and Averaging in Games across Time Scales.” International Journal of Foundations of Computer Science, vol. 23, no. 3, World Scientific Publishing, 2012, pp. 609–25, doi:10.1142/S0129054112400308. short: K. Chatterjee, R. Majumdar, International Journal of Foundations of Computer Science 23 (2012) 609–625. date_created: 2018-12-11T12:02:37Z date_published: 2012-04-01T00:00:00Z date_updated: 2021-01-12T07:42:35Z day: '01' department: - _id: KrCh doi: 10.1142/S0129054112400308 intvolume: ' 23' issue: '3' language: - iso: eng month: '04' oa_version: None page: 609 - 625 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: International Journal of Foundations of Computer Science publication_status: published publisher: World Scientific Publishing publist_id: '3326' quality_controlled: '1' scopus_import: 1 status: public title: Discounting and averaging in games across time scales type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2012' ... --- _id: '3115' abstract: - lang: eng text: 'We consider the offset-deconstruction problem: Given a polygonal shape Q with n vertices, can it be expressed, up to a tolerance ε in Hausdorff distance, as the Minkowski sum of another polygonal shape P with a disk of fixed radius? If it does, we also seek a preferably simple-looking solution P; then, P''s offset constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We give an O(nlogn)-time exact decision algorithm that handles any polygonal shape, assuming the real-RAM model of computation. A variant of the algorithm, which we have implemented using the cgal library, is based on rational arithmetic and answers the same deconstruction problem up to an uncertainty parameter δ its running time additionally depends on δ. If the input shape is found to be approximable, this algorithm also computes an approximate solution for the problem. It also allows us to solve parameter-optimization problems induced by the offset-deconstruction problem. For convex shapes, the complexity of the exact decision algorithm drops to O(n), which is also the time required to compute a solution P with at most one more vertex than a vertex-minimal one.' acknowledgement: "We thank Eyal Flato (Plataine Ltd.) for raising the offset-deconstruction problem in connection with wood cutting. We also thank Tim Bretl (UIUC) for suggesting the digital-pen offset-deconstruction problem. This work has been supported in part by the Israel Science Foundation (grant no. 1102/11), by the German–Israeli Foundation (grant no. 969/07), by the Hermann Minkowski–Minerva Center for Geometry at Tel Aviv University, and by the EU Project under Contract No. 255827 (CGL—Computational Geometry Learning).\r\n" author: - first_name: Eric full_name: Berberich, Eric last_name: Berberich - first_name: Dan full_name: Halperin, Dan last_name: Halperin - first_name: Michael full_name: Kerber, Michael id: 36E4574A-F248-11E8-B48F-1D18A9856A87 last_name: Kerber orcid: 0000-0002-8030-9299 - first_name: Roza full_name: Pogalnikova, Roza last_name: Pogalnikova citation: ama: Berberich E, Halperin D, Kerber M, Pogalnikova R. Deconstructing approximate offsets. Discrete & Computational Geometry. 2012;48(4):964-989. doi:10.1007/s00454-012-9441-5 apa: Berberich, E., Halperin, D., Kerber, M., & Pogalnikova, R. (2012). Deconstructing approximate offsets. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-012-9441-5 chicago: Berberich, Eric, Dan Halperin, Michael Kerber, and Roza Pogalnikova. “Deconstructing Approximate Offsets.” Discrete & Computational Geometry. Springer, 2012. https://doi.org/10.1007/s00454-012-9441-5. ieee: E. Berberich, D. Halperin, M. Kerber, and R. Pogalnikova, “Deconstructing approximate offsets,” Discrete & Computational Geometry, vol. 48, no. 4. Springer, pp. 964–989, 2012. ista: Berberich E, Halperin D, Kerber M, Pogalnikova R. 2012. Deconstructing approximate offsets. Discrete & Computational Geometry. 48(4), 964–989. mla: Berberich, Eric, et al. “Deconstructing Approximate Offsets.” Discrete & Computational Geometry, vol. 48, no. 4, Springer, 2012, pp. 964–89, doi:10.1007/s00454-012-9441-5. short: E. Berberich, D. Halperin, M. Kerber, R. Pogalnikova, Discrete & Computational Geometry 48 (2012) 964–989. date_created: 2018-12-11T12:01:28Z date_published: 2012-12-01T00:00:00Z date_updated: 2023-02-23T11:22:30Z day: '01' department: - _id: HeEd doi: 10.1007/s00454-012-9441-5 external_id: arxiv: - '1109.2158' intvolume: ' 48' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1109.2158 month: '12' oa: 1 oa_version: Preprint page: 964 - 989 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '3584' quality_controlled: '1' related_material: record: - id: '3329' relation: earlier_version status: public scopus_import: 1 status: public title: Deconstructing approximate offsets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2012' ... --- _id: '3331' abstract: - lang: eng text: Computing the topology of an algebraic plane curve C means computing a combinatorial graph that is isotopic to C and thus represents its topology in R2. We prove that, for a polynomial of degree n with integer coefficients bounded by 2ρ, the topology of the induced curve can be computed with bit operations ( indicates that we omit logarithmic factors). Our analysis improves the previous best known complexity bounds by a factor of n2. The improvement is based on new techniques to compute and refine isolating intervals for the real roots of polynomials, and on the consequent amortized analysis of the critical fibers of the algebraic curve. author: - first_name: Michael full_name: Kerber, Michael id: 36E4574A-F248-11E8-B48F-1D18A9856A87 last_name: Kerber orcid: 0000-0002-8030-9299 - first_name: Michael full_name: Sagraloff, Michael last_name: Sagraloff citation: ama: Kerber M, Sagraloff M. A worst case bound for topology computation of algebraic curves. Journal of Symbolic Computation. 2012;47(3):239-258. doi:10.1016/j.jsc.2011.11.001 apa: Kerber, M., & Sagraloff, M. (2012). A worst case bound for topology computation of algebraic curves. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2011.11.001 chicago: Kerber, Michael, and Michael Sagraloff. “A Worst Case Bound for Topology Computation of Algebraic Curves.” Journal of Symbolic Computation. Elsevier, 2012. https://doi.org/10.1016/j.jsc.2011.11.001. ieee: M. Kerber and M. Sagraloff, “A worst case bound for topology computation of algebraic curves,” Journal of Symbolic Computation, vol. 47, no. 3. Elsevier, pp. 239–258, 2012. ista: Kerber M, Sagraloff M. 2012. A worst case bound for topology computation of algebraic curves. Journal of Symbolic Computation. 47(3), 239–258. mla: Kerber, Michael, and Michael Sagraloff. “A Worst Case Bound for Topology Computation of Algebraic Curves.” Journal of Symbolic Computation, vol. 47, no. 3, Elsevier, 2012, pp. 239–58, doi:10.1016/j.jsc.2011.11.001. short: M. Kerber, M. Sagraloff, Journal of Symbolic Computation 47 (2012) 239–258. date_created: 2018-12-11T12:02:43Z date_published: 2012-03-01T00:00:00Z date_updated: 2021-01-12T07:42:43Z day: '01' department: - _id: HeEd doi: 10.1016/j.jsc.2011.11.001 intvolume: ' 47' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1104.1510 month: '03' oa: 1 oa_version: Preprint page: 239 - 258 publication: ' Journal of Symbolic Computation' publication_status: published publisher: Elsevier publist_id: '3303' quality_controlled: '1' scopus_import: 1 status: public title: A worst case bound for topology computation of algebraic curves type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2012' ... --- _id: '346' abstract: - lang: eng text: Arrays of vertically aligned ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires (NWs) were prepared by means of the combination of two solution-growth processes. First, single-crystal ZnO NWs with controlled n-type doping were grown on conducting substrates by a low-cost, high-yield and seed-free electrochemical route. These NWs were covered by a titanium oxide shell of tunable thickness mediating successive adsorption-hydrolysis-condensation steps. Using this atomic-layer growth procedure, titania shells with controlled thickness and the anatase TiO2 phase were obtained after sintering at 450 °C. Higher sintering temperatures resulted in the formation of ZnO : Cl/ZnxTiOy/TiO2 core–shell NWs by the interdiffusion of Zn and Ti ions at the ZnO–TiO2 interface. The performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell NWs towards photoelectrochemical (PEC) water splitting was investigated as a function of the titania shell thickness. Furthermore, the performance of such core–shell NWs as photoelectrodes in dye-sensitized solar cells was also characterized. The TiO2 presence at the ZnO : Cl surface promoted a two-fold increase on the produced photocurrent densities, probing their potential for PEC and optoelectronic applications. Electrochemical impedance spectroscopy was used to corroborate the lower resistance for charge transfer between the NWs and the electrolyte in the presence of the TiO2 shell. acknowledgement: The research was supported by the European Regional Development Funds and the Spanish MICINN projects MAT2010-15138, MAT2010-21510 and CSD2009-00050. JF and AS thank the FI-DGR and BP grants from the Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR) from the Catalan Government. MI and AC thank the Spanish MICINN for the PhD grant and the financial support through the Ramóny Cajal program. article_processing_charge: No article_type: original author: - first_name: Jiandong full_name: Fan, Jiandong last_name: Fan - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Cristina full_name: Fábrega, Cristina last_name: Fábrega - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Cristina full_name: Flox, Cristina last_name: Flox - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Teresa full_name: Andreu, Teresa last_name: Andreu - first_name: Amtonio full_name: López, Amtonio last_name: López - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Joan full_name: Morante, Joan last_name: Morante - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Fan J, Zamani R, Fábrega C, et al. Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness. Journal of Physics D: Applied Physics. 2012;45(41). doi:10.1088/0022-3727/45/41/415301' apa: 'Fan, J., Zamani, R., Fábrega, C., Shavel, A., Flox, C., Ibáñez, M., … Cabot, A. (2012). Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness. Journal of Physics D: Applied Physics. IOP Publishing Ltd. https://doi.org/10.1088/0022-3727/45/41/415301' chicago: 'Fan, Jiandong, Reza Zamani, Cristina Fábrega, Alexey Shavel, Cristina Flox, Maria Ibáñez, Teresa Andreu, et al. “Solution-Growth and Optoelectronic Performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 Core–Shell Nanowires with Tunable Shell Thickness.” Journal of Physics D: Applied Physics. IOP Publishing Ltd., 2012. https://doi.org/10.1088/0022-3727/45/41/415301.' ieee: 'J. Fan et al., “Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness,” Journal of Physics D: Applied Physics, vol. 45, no. 41. IOP Publishing Ltd., 2012.' ista: 'Fan J, Zamani R, Fábrega C, Shavel A, Flox C, Ibáñez M, Andreu T, López A, Arbiol J, Morante J, Cabot A. 2012. Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness. Journal of Physics D: Applied Physics. 45(41).' mla: 'Fan, Jiandong, et al. “Solution-Growth and Optoelectronic Performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 Core–Shell Nanowires with Tunable Shell Thickness.” Journal of Physics D: Applied Physics, vol. 45, no. 41, IOP Publishing Ltd., 2012, doi:10.1088/0022-3727/45/41/415301.' short: 'J. Fan, R. Zamani, C. Fábrega, A. Shavel, C. Flox, M. Ibáñez, T. Andreu, A. López, J. Arbiol, J. Morante, A. Cabot, Journal of Physics D: Applied Physics 45 (2012).' date_created: 2018-12-11T11:45:56Z date_published: 2012-10-17T00:00:00Z date_updated: 2021-01-12T07:43:36Z day: '17' doi: 10.1088/0022-3727/45/41/415301 extern: '1' intvolume: ' 45' issue: '41' language: - iso: eng month: '10' oa_version: None publication: 'Journal of Physics D: Applied Physics' publication_status: published publisher: IOP Publishing Ltd. publist_id: '7486' quality_controlled: '1' status: public title: Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2012' ... --- _id: '3168' abstract: - lang: eng text: The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a mathematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the combinatorial complexity by quotienting the reachable set of molecular species into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently, we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper, we prove that this quotienting yields a sufficient condition for weak lumpability (that is to say that the quotient system is still Markovian for a given set of initial distributions) and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system (which means that the conditional probability of being in a given state in the original system knowing that we are in its equivalence class is an invariant of the system). We illustrate the framework on a case study of the epidermal growth factor (EGF)/insulin receptor crosstalk. acknowledgement: "We would like to thank the anonymous reviewers for their comments on the different versions of the paper. We would also like to thank Ferdinanda Camporesi for her careful reading and the useful insights that she gave us about the paper.\r\nJérôme Feret’s contribution was partially supported by the AbstractCell ANR-Chair of Excellence. Heinz Koeppl’s research is supported by the Swiss National Science Foundation, grant no. 200020-117975/1. Tatjana Petrov’s research is supported by SystemsX.ch (the Swiss Initiative in Systems Biology)." author: - first_name: Jérôme full_name: Feret, Jérôme last_name: Feret - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Heinz full_name: Koeppl, Heinz last_name: Koeppl - first_name: Tatjana full_name: Petrov, Tatjana id: 3D5811FC-F248-11E8-B48F-1D18A9856A87 last_name: Petrov orcid: 0000-0002-9041-0905 citation: ama: Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule based systems. Theoretical Computer Science. 2012;431:137-164. doi:10.1016/j.tcs.2011.12.059 apa: Feret, J., Henzinger, T. A., Koeppl, H., & Petrov, T. (2012). Lumpability abstractions of rule based systems. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2011.12.059 chicago: Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability Abstractions of Rule Based Systems.” Theoretical Computer Science. Elsevier, 2012. https://doi.org/10.1016/j.tcs.2011.12.059. ieee: J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions of rule based systems,” Theoretical Computer Science, vol. 431. Elsevier, pp. 137–164, 2012. ista: Feret J, Henzinger TA, Koeppl H, Petrov T. 2012. Lumpability abstractions of rule based systems. Theoretical Computer Science. 431, 137–164. mla: Feret, Jérôme, et al. “Lumpability Abstractions of Rule Based Systems.” Theoretical Computer Science, vol. 431, Elsevier, 2012, pp. 137–64, doi:10.1016/j.tcs.2011.12.059. short: J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, Theoretical Computer Science 431 (2012) 137–164. date_created: 2018-12-11T12:01:47Z date_published: 2012-05-04T00:00:00Z date_updated: 2023-02-23T11:39:40Z day: '04' department: - _id: ToHe doi: 10.1016/j.tcs.2011.12.059 intvolume: ' 431' language: - iso: eng month: '05' oa_version: None page: 137 - 164 publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '3515' pubrep_id: '73' quality_controlled: '1' related_material: record: - id: '3719' relation: earlier_version status: public scopus_import: 1 status: public title: Lumpability abstractions of rule based systems type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 431 year: '2012' ... --- _id: '377' abstract: - lang: eng text: The potential to control the composition and crystal phase at the nanometer scale enable the production of nanocrystalline materials with enhanced functionalities and new applications. In the present work, we detail a novel colloidal synthesis route to prepare nanoparticles of the ternary semiconductor Cu2GeSe3 (CGSe) with nanometer-scale control over their crystal phases. We also demonstrate the structural effect on the thermoelectric properties of bottom-up-prepared CGSe nanomaterials. By careful adjustment of the nucleation and growth temperatures, pure orthorhombic CGSe nanoparticles with cationic order or polytypic CGSe nanoparticles with disordered cation positions can be produced. In this second type of nanoparticle, a high density of twins can be created to periodically change the atomic plane stacking, forming a hexagonal wurtzite CGSe phase. The high yield of the synthetic routes reported here allows the production of single-phase and multiphase CGSe nanoparticles in the gram scale, which permits characterization of the thermoelectric properties of these materials. Reduced thermal conductivities and a related 2.5-fold increase of the thermoelectric figure of merit for multiphase nanomaterials compared to pure-phase CGSe are systematically obtained. These results are discussed in terms of the density and efficiency of phonon scattering centers in both types of materials. article_processing_charge: No author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Stéphane full_name: Gorse, Stéphane last_name: Gorse - first_name: Nebll full_name: Katchoi, Nebll last_name: Katchoi - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Antonioo full_name: López, Antonioo last_name: López - first_name: Joan full_name: Morante, Joan last_name: Morante - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Ibáñez M, Zamani R, Li W, et al. Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials. Chemistry of Materials. 2012;24(23):4615-4622. doi:10.1021/cm303252q' apa: 'Ibáñez, M., Zamani, R., Li, W., Cadavid, D., Gorse, S., Katchoi, N., … Cabot, A. (2012). Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/cm303252q' chicago: 'Ibáñez, Maria, Reza Zamani, Wenhua Li, Doris Cadavid, Stéphane Gorse, Nebll Katchoi, Alexey Shavel, et al. “Crystallographic Control at the Nanoscale to Enhance Functionality: Polytypic Cu2GeSe3 Nanoparticles as Thermoelectric Materials.” Chemistry of Materials. American Chemical Society, 2012. https://doi.org/10.1021/cm303252q.' ieee: 'M. Ibáñez et al., “Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials,” Chemistry of Materials, vol. 24, no. 23. American Chemical Society, pp. 4615–4622, 2012.' ista: 'Ibáñez M, Zamani R, Li W, Cadavid D, Gorse S, Katchoi N, Shavel A, López A, Morante J, Arbiol J, Cabot A. 2012. Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials. Chemistry of Materials. 24(23), 4615–4622.' mla: 'Ibáñez, Maria, et al. “Crystallographic Control at the Nanoscale to Enhance Functionality: Polytypic Cu2GeSe3 Nanoparticles as Thermoelectric Materials.” Chemistry of Materials, vol. 24, no. 23, American Chemical Society, 2012, pp. 4615–22, doi:10.1021/cm303252q.' short: M. Ibáñez, R. Zamani, W. Li, D. Cadavid, S. Gorse, N. Katchoi, A. Shavel, A. López, J. Morante, J. Arbiol, A. Cabot, Chemistry of Materials 24 (2012) 4615–4622. date_created: 2018-12-11T11:46:07Z date_published: 2012-11-14T00:00:00Z date_updated: 2021-01-12T07:52:04Z day: '14' doi: 10.1021/cm303252q extern: '1' intvolume: ' 24' issue: '23' language: - iso: eng month: '11' oa_version: None page: 4615 - 4622 publication: Chemistry of Materials publication_status: published publisher: American Chemical Society publist_id: '7452' status: public title: 'Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2012' ... --- _id: '3846' abstract: - lang: eng text: We summarize classical and recent results about two-player games played on graphs with ω-regular objectives. These games have applications in the verification and synthesis of reactive systems. Important distinctions are whether a graph game is turn-based or concurrent; deterministic or stochastic; zero-sum or not. We cluster known results and open problems according to these classifications. acknowledgement: This research was supported in part by the ONR grant N00014-02-1-0671, by the AFOSR MURI grant F49620-00-1-0327, and by the NSF grants CCR-9988172, CCR-0085949, and CCR-0225610. article_processing_charge: No article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: Chatterjee K, Henzinger TA. A survey of stochastic ω regular games. Journal of Computer and System Sciences. 2012;78(2):394-413. doi:10.1016/j.jcss.2011.05.002 apa: Chatterjee, K., & Henzinger, T. A. (2012). A survey of stochastic ω regular games. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2011.05.002 chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “A Survey of Stochastic ω Regular Games.” Journal of Computer and System Sciences. Elsevier, 2012. https://doi.org/10.1016/j.jcss.2011.05.002. ieee: K. Chatterjee and T. A. Henzinger, “A survey of stochastic ω regular games,” Journal of Computer and System Sciences, vol. 78, no. 2. Elsevier, pp. 394–413, 2012. ista: Chatterjee K, Henzinger TA. 2012. A survey of stochastic ω regular games. Journal of Computer and System Sciences. 78(2), 394–413. mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. “A Survey of Stochastic ω Regular Games.” Journal of Computer and System Sciences, vol. 78, no. 2, Elsevier, 2012, pp. 394–413, doi:10.1016/j.jcss.2011.05.002. short: K. Chatterjee, T.A. Henzinger, Journal of Computer and System Sciences 78 (2012) 394–413. date_created: 2018-12-11T12:05:29Z date_published: 2012-03-02T00:00:00Z date_updated: 2022-05-24T08:00:54Z day: '02' ddc: - '000' department: - _id: KrCh - _id: ToHe doi: 10.1016/j.jcss.2011.05.002 file: - access_level: open_access checksum: 241b939deb4517cdd4426d49c67e3fa2 content_type: application/pdf creator: kschuh date_created: 2019-01-29T10:54:28Z date_updated: 2020-07-14T12:46:17Z file_id: '5897' file_name: a_survey_of_stochastic_omega-regular_games.pdf file_size: 336450 relation: main_file file_date_updated: 2020-07-14T12:46:17Z has_accepted_license: '1' intvolume: ' 78' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.jcss.2011.05.002 month: '03' oa: 1 oa_version: Submitted Version page: 394 - 413 publication: Journal of Computer and System Sciences publication_status: published publisher: Elsevier publist_id: '2341' quality_controlled: '1' scopus_import: '1' status: public title: A survey of stochastic ω regular games type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 78 year: '2012' ... --- _id: '387' abstract: - lang: eng text: In this Letter we present detailed study of the density of states near defects in Bi 2Se 3. In particular, we present data on the commonly found triangular defects in this system. While we do not find any measurable quasiparticle scattering interference effects, we do find localized resonances, which can be well fitted by theory once the potential is taken to be extended to properly account for the observed defects. The data together with the fits confirm that while the local density of states around the Dirac point of the electronic spectrum at the surface is significantly disrupted near the impurity by the creation of low-energy resonance state, the Dirac point is not locally destroyed. We discuss our results in terms of the expected protected surface state of topological insulators. © 2012 American Physical Society. author: - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 - first_name: Rudro full_name: Biswas, Rudro last_name: Biswas - first_name: Alexander full_name: Balatsky, Alexander last_name: Balatsky - first_name: James full_name: Analytis, James last_name: Analytis - first_name: Jiunhaw full_name: Chu, Jiunhaw last_name: Chu - first_name: Ian full_name: Fisher, Ian last_name: Fisher - first_name: Aharon full_name: Kapitulnik, Aharon last_name: Kapitulnik citation: ama: Alpichshev Z, Biswas R, Balatsky A, et al. STM imaging of impurity resonances on Bi 2Se 3. Physical Review Letters. 2012;108(20). doi:10.1103/PhysRevLett.108.206402 apa: Alpichshev, Z., Biswas, R., Balatsky, A., Analytis, J., Chu, J., Fisher, I., & Kapitulnik, A. (2012). STM imaging of impurity resonances on Bi 2Se 3. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.108.206402 chicago: Alpichshev, Zhanybek, Rudro Biswas, Alexander Balatsky, James Analytis, Jiunhaw Chu, Ian Fisher, and Aharon Kapitulnik. “STM Imaging of Impurity Resonances on Bi 2Se 3.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.108.206402. ieee: Z. Alpichshev et al., “STM imaging of impurity resonances on Bi 2Se 3,” Physical Review Letters, vol. 108, no. 20. American Physical Society, 2012. ista: Alpichshev Z, Biswas R, Balatsky A, Analytis J, Chu J, Fisher I, Kapitulnik A. 2012. STM imaging of impurity resonances on Bi 2Se 3. Physical Review Letters. 108(20). mla: Alpichshev, Zhanybek, et al. “STM Imaging of Impurity Resonances on Bi 2Se 3.” Physical Review Letters, vol. 108, no. 20, American Physical Society, 2012, doi:10.1103/PhysRevLett.108.206402. short: Z. Alpichshev, R. Biswas, A. Balatsky, J. Analytis, J. Chu, I. Fisher, A. Kapitulnik, Physical Review Letters 108 (2012). date_created: 2018-12-11T11:46:11Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T07:52:49Z day: '01' doi: 10.1103/PhysRevLett.108.206402 extern: '1' intvolume: ' 108' issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1108.0022 month: '01' oa: 1 oa_version: None publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7442' status: public title: STM imaging of impurity resonances on Bi 2Se 3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2012' ... --- _id: '3110' abstract: - lang: eng text: 'The directional transport of the phytohormone auxin depends on the phosphorylation status and polar localization of PIN-FORMED (PIN) auxin efflux proteins. While PINIOD (PID) kinase is directly involved in the phosphorylation of PIN proteins, the phosphatase holoenzyme complexes that dephosphorylate PIN proteins remain elusive. Here, we demonstrate that mutations simultaneously disrupting the function of Arabidopsis thaliana FyPP1 (for Phytochrome-associated serine/threonine protein phosphatase1) and FyPP3, two homologous genes encoding the catalytic subunits of protein phosphatase6 (PP6), cause elevated accumulation of phosphorylated PIN proteins, correlating with a basal-to-apical shift in subcellular PIN localization. The changes in PIN polarity result in increased root basipetal auxin transport and severe defects, including shorter roots, fewer lateral roots, defective columella cells, root meristem collapse, abnormal cotyledons (small, cup-shaped, or fused cotyledons), and altered leaf venation. Our molecular, biochemical, and genetic data support the notion that FyPP1/3, SAL (for SAPS DOMAIN-LIKE), and PP2AA proteins (RCN1 [for ROOTS CURL IN NAPHTHYLPHTHALAMIC ACID1] or PP2AA1, PP2AA2, and PP2AA3) physically interact to form a novel PP6-type heterotrimeric holoenzyme complex. We also show that FyPP1/3, SAL, and PP2AA interact with a subset of PIN proteins and that for SAL the strength of the interaction depends on the PIN phosphorylation status. Thus, an Arabidopsis PP6-type phosphatase holoenzyme acts antagonistically with PID to direct auxin transport polarity and plant development by directly regulating PIN phosphorylation. ' author: - first_name: Mingqiu full_name: Dai, Mingqiu last_name: Dai - first_name: Chen full_name: Zhang, Chen last_name: Zhang - first_name: Urszula full_name: Urszula Kania id: 4AE5C486-F248-11E8-B48F-1D18A9856A87 last_name: Kania - first_name: Fang full_name: Chen, Fang last_name: Chen - first_name: Qin full_name: Xue, Qin last_name: Xue - first_name: Tyra full_name: McCray, Tyra last_name: Mccray - first_name: Gang full_name: Li, Gang last_name: Li - first_name: Genji full_name: Qin, Genji last_name: Qin - first_name: Michelle full_name: Wakeley, Michelle last_name: Wakeley - first_name: William full_name: Terzaghi, William last_name: Terzaghi - first_name: Jianmin full_name: Wan, Jianmin last_name: Wan - first_name: Yunde full_name: Zhao, Yunde last_name: Zhao - first_name: Jian full_name: Xu, Jian last_name: Xu - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Xing full_name: Deng, Xing W last_name: Deng - first_name: Haiyang full_name: Wang, Haiyang last_name: Wang citation: ama: Dai M, Zhang C, Kania U, et al. A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell. 2012;24(6):2497-2514. doi:10.1105/tpc.112.098905 apa: Dai, M., Zhang, C., Kania, U., Chen, F., Xue, Q., Mccray, T., … Wang, H. (2012). A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.112.098905 chicago: Dai, Mingqiu, Chen Zhang, Urszula Kania, Fang Chen, Qin Xue, Tyra Mccray, Gang Li, et al. “A PP6 Type Phosphatase Holoenzyme Directly Regulates PIN Phosphorylation and Auxin Efflux in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2012. https://doi.org/10.1105/tpc.112.098905. ieee: M. Dai et al., “A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis,” Plant Cell, vol. 24, no. 6. American Society of Plant Biologists, pp. 2497–2514, 2012. ista: Dai M, Zhang C, Kania U, Chen F, Xue Q, Mccray T, Li G, Qin G, Wakeley M, Terzaghi W, Wan J, Zhao Y, Xu J, Friml J, Deng X, Wang H. 2012. A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell. 24(6), 2497–2514. mla: Dai, Mingqiu, et al. “A PP6 Type Phosphatase Holoenzyme Directly Regulates PIN Phosphorylation and Auxin Efflux in Arabidopsis.” Plant Cell, vol. 24, no. 6, American Society of Plant Biologists, 2012, pp. 2497–514, doi:10.1105/tpc.112.098905. short: M. Dai, C. Zhang, U. Kania, F. Chen, Q. Xue, T. Mccray, G. Li, G. Qin, M. Wakeley, W. Terzaghi, J. Wan, Y. Zhao, J. Xu, J. Friml, X. Deng, H. Wang, Plant Cell 24 (2012) 2497–2514. date_created: 2018-12-11T12:01:27Z date_published: 2012-06-01T00:00:00Z date_updated: 2021-01-12T07:41:08Z day: '01' doi: 10.1105/tpc.112.098905 extern: 1 intvolume: ' 24' issue: '6' month: '06' page: 2497 - 2514 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3589' quality_controlled: 0 status: public title: A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis type: journal_article volume: 24 year: '2012' ...