--- _id: '3005' author: - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Philip full_name: Benfey, Philip last_name: Benfey - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Malcolm full_name: Bennett, Malcolm last_name: Bennett - first_name: Thomas full_name: Berleth, Thomas last_name: Berleth - first_name: Niko full_name: Geldner, Niko last_name: Geldner - first_name: Markus full_name: Grebe, Markus last_name: Grebe - first_name: Marcus full_name: Heisler, Marcus last_name: Heisler - first_name: Jan full_name: Hejátko, Jan last_name: Hejátko - first_name: Gerd full_name: Jürgens, Gerd last_name: Jürgens - first_name: Thomas full_name: Laux, Thomas last_name: Laux - first_name: Keith full_name: Lindsey, Keith last_name: Lindsey - first_name: Wolfgang full_name: Lukowitz, Wolfgang last_name: Lukowitz - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig - first_name: Remko full_name: Offringa, Remko last_name: Offringa - first_name: Ben full_name: Scheres, Ben last_name: Scheres - first_name: Ranjan full_name: Swarup, Ranjan last_name: Swarup - first_name: Ramón full_name: Torres Ruiz, Ramón last_name: Torres Ruiz - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová citation: ama: 'Friml J, Benfey P, Benková E, et al. Apical-basal polarity: Why plant cells don’t stand on their heads. Trends in Plant Science. 2006;11(1):12-14. doi:10.1016/j.tplants.2005.11.010' apa: 'Friml, J., Benfey, P., Benková, E., Bennett, M., Berleth, T., Geldner, N., … Zažímalová, E. (2006). Apical-basal polarity: Why plant cells don’t stand on their heads. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2005.11.010' chicago: 'Friml, Jiří, Philip Benfey, Eva Benková, Malcolm Bennett, Thomas Berleth, Niko Geldner, Markus Grebe, et al. “Apical-Basal Polarity: Why Plant Cells Don’t Stand on Their Heads.” Trends in Plant Science. Cell Press, 2006. https://doi.org/10.1016/j.tplants.2005.11.010.' ieee: 'J. Friml et al., “Apical-basal polarity: Why plant cells don’t stand on their heads,” Trends in Plant Science, vol. 11, no. 1. Cell Press, pp. 12–14, 2006.' ista: 'Friml J, Benfey P, Benková E, Bennett M, Berleth T, Geldner N, Grebe M, Heisler M, Hejátko J, Jürgens G, Laux T, Lindsey K, Lukowitz W, Luschnig C, Offringa R, Scheres B, Swarup R, Torres Ruiz R, Weijers D, Zažímalová E. 2006. Apical-basal polarity: Why plant cells don’t stand on their heads. Trends in Plant Science. 11(1), 12–14.' mla: 'Friml, Jiří, et al. “Apical-Basal Polarity: Why Plant Cells Don’t Stand on Their Heads.” Trends in Plant Science, vol. 11, no. 1, Cell Press, 2006, pp. 12–14, doi:10.1016/j.tplants.2005.11.010.' short: J. Friml, P. Benfey, E. Benková, M. Bennett, T. Berleth, N. Geldner, M. Grebe, M. Heisler, J. Hejátko, G. Jürgens, T. Laux, K. Lindsey, W. Lukowitz, C. Luschnig, R. Offringa, B. Scheres, R. Swarup, R. Torres Ruiz, D. Weijers, E. Zažímalová, Trends in Plant Science 11 (2006) 12–14. date_created: 2018-12-11T12:00:49Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:40:24Z day: '01' doi: 10.1016/j.tplants.2005.11.010 extern: '1' intvolume: ' 11' issue: '1' language: - iso: eng month: '01' oa_version: None page: 12 - 14 publication: Trends in Plant Science publication_status: published publisher: Cell Press publist_id: '3697' status: public title: 'Apical-basal polarity: Why plant cells don''t stand on their heads' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2006' ... --- _id: '3008' abstract: - lang: eng text: Plants and some animals have a profound capacity to regenerate organs from adult tissues. Molecular mechanisms for regeneration have, however, been largely unexplored. Here we investigate a local regeneration response in Arabidopsis roots. Laser-induced wounding disrupts the flow of auxin-a cell-fate-instructive plant hormone-in root tips, and we demonstrate that resulting cell-fate changes require the PLETHORA, SHORTROOT, and SCARECROW transcription factors. These transcription factors regulate the expression and polar position of PIN auxin efflux-facilitating membrane proteins to reconstitute auxin transport in renewed root tips. Thus, a regeneration mechanism using embryonic root stem-cell patterning factors first responds to and subsequently stabilizes a new hormone distribution. author: - first_name: Jian full_name: Xu, Jian last_name: Xu - first_name: Hugo full_name: Hofhuis, Hugo last_name: Hofhuis - first_name: Renze full_name: Heidstra, Renze last_name: Heidstra - first_name: Michael full_name: Sauer, Michael last_name: Sauer - 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 citation: ama: Xu J, Hofhuis H, Heidstra R, Sauer M, Friml J, Scheres B. A molecular framework for plant regeneration. Science. 2006;311(5759):385-388. doi:10.1126/science.1121790 apa: Xu, J., Hofhuis, H., Heidstra, R., Sauer, M., Friml, J., & Scheres, B. (2006). A molecular framework for plant regeneration. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1121790 chicago: Xu, Jian, Hugo Hofhuis, Renze Heidstra, Michael Sauer, Jiří Friml, and Ben Scheres. “A Molecular Framework for Plant Regeneration.” Science. American Association for the Advancement of Science, 2006. https://doi.org/10.1126/science.1121790. ieee: J. Xu, H. Hofhuis, R. Heidstra, M. Sauer, J. Friml, and B. Scheres, “A molecular framework for plant regeneration,” Science, vol. 311, no. 5759. American Association for the Advancement of Science, pp. 385–388, 2006. ista: Xu J, Hofhuis H, Heidstra R, Sauer M, Friml J, Scheres B. 2006. A molecular framework for plant regeneration. Science. 311(5759), 385–388. mla: Xu, Jian, et al. “A Molecular Framework for Plant Regeneration.” Science, vol. 311, no. 5759, American Association for the Advancement of Science, 2006, pp. 385–88, doi:10.1126/science.1121790. short: J. Xu, H. Hofhuis, R. Heidstra, M. Sauer, J. Friml, B. Scheres, Science 311 (2006) 385–388. date_created: 2018-12-11T12:00:50Z date_published: 2006-01-20T00:00:00Z date_updated: 2021-01-12T07:40:25Z day: '20' doi: 10.1126/science.1121790 extern: 1 intvolume: ' 311' issue: '5759' month: '01' page: 385 - 388 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '3695' quality_controlled: 0 status: public title: A molecular framework for plant regeneration type: journal_article volume: 311 year: '2006' ... --- _id: '3009' author: - first_name: Tomasz full_name: Paciorek, Tomasz last_name: Paciorek - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Paciorek T, Friml J. Auxin signaling. Journal of Cell Science. 2006;119(7):1199-1202. doi:10.1242/jcs.02910 apa: Paciorek, T., & Friml, J. (2006). Auxin signaling. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.02910 chicago: Paciorek, Tomasz, and Jiří Friml. “Auxin Signaling.” Journal of Cell Science. Company of Biologists, 2006. https://doi.org/10.1242/jcs.02910. ieee: T. Paciorek and J. Friml, “Auxin signaling,” Journal of Cell Science, vol. 119, no. 7. Company of Biologists, pp. 1199–1202, 2006. ista: Paciorek T, Friml J. 2006. Auxin signaling. Journal of Cell Science. 119(7), 1199–1202. mla: Paciorek, Tomasz, and Jiří Friml. “Auxin Signaling.” Journal of Cell Science, vol. 119, no. 7, Company of Biologists, 2006, pp. 1199–202, doi:10.1242/jcs.02910. short: T. Paciorek, J. Friml, Journal of Cell Science 119 (2006) 1199–1202. date_created: 2018-12-11T12:00:50Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:40:25Z day: '01' doi: 10.1242/jcs.02910 extern: '1' external_id: pmid: - ' 16554435' intvolume: ' 119' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/16554435 month: '01' oa: 1 oa_version: Published Version page: 1199 - 1202 pmid: 1 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '3693' quality_controlled: '1' status: public title: Auxin signaling type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2006' ... --- _id: '3016' abstract: - lang: eng text: Plant development is characterized by a profound ability to regenerate and form tissues with new axes of polarity. An unsolved question concerns how the position within a tissue and cues from neighboring cells are integrated to specify the polarity of individual cells. The canalization hypothesis proposes a feedback effect of the phytohormone auxin on the directionality of intercellular auxin flow as a means to polarize tissues. Here we identify a cellular and molecular mechanism for canalization. Local auxin application, wounding, or auxin accumulation during de novo organ formation lead to rearrangements in the subcellular polar localization of PIN auxin transport components. This auxin effect on PIN polarity is cell-specific, does not depend on PIN transcription, and involves the Aux/IAA-ARF (indole-3-acetic acid-auxin response factor) signaling pathway. Our data suggest that auxin acts as polarizing cue, which links individual cell polarity with tissue and organ polarity through control of PIN polar targeting. This feedback regulation provides a conceptual framework for polarization during multiple regenerative and patterning processes in plants. article_processing_charge: No author: - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jozef full_name: Balla, Jozef last_name: Balla - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig - first_name: Justyna full_name: Wiśniewska, Justyna last_name: Wiśniewska - first_name: Vilém full_name: Reinöhl, Vilém last_name: Reinöhl - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Sauer M, Balla J, Luschnig C, et al. Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity. Genes and Development. 2006;20(20):2902-2911. doi:10.1101/gad.390806 apa: Sauer, M., Balla, J., Luschnig, C., Wiśniewska, J., Reinöhl, V., Friml, J., & Benková, E. (2006). Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.390806 chicago: Sauer, Michael, Jozef Balla, Christian Luschnig, Justyna Wiśniewska, Vilém Reinöhl, Jiří Friml, and Eva Benková. “Canalization of Auxin Flow by Aux/IAA-ARF-Dependent Feedback Regulation of PIN Polarity.” Genes and Development. Cold Spring Harbor Laboratory Press, 2006. https://doi.org/10.1101/gad.390806. ieee: M. Sauer et al., “Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity,” Genes and Development, vol. 20, no. 20. Cold Spring Harbor Laboratory Press, pp. 2902–2911, 2006. ista: Sauer M, Balla J, Luschnig C, Wiśniewska J, Reinöhl V, Friml J, Benková E. 2006. Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity. Genes and Development. 20(20), 2902–2911. mla: Sauer, Michael, et al. “Canalization of Auxin Flow by Aux/IAA-ARF-Dependent Feedback Regulation of PIN Polarity.” Genes and Development, vol. 20, no. 20, Cold Spring Harbor Laboratory Press, 2006, pp. 2902–11, doi:10.1101/gad.390806. short: M. Sauer, J. Balla, C. Luschnig, J. Wiśniewska, V. Reinöhl, J. Friml, E. Benková, Genes and Development 20 (2006) 2902–2911. date_created: 2018-12-11T12:00:53Z date_published: 2006-10-15T00:00:00Z date_updated: 2021-11-16T07:53:09Z day: '15' doi: 10.1101/gad.390806 extern: '1' intvolume: ' 20' issue: '20' language: - iso: eng month: '10' oa_version: None page: 2902 - 2911 publication: Genes and Development publication_status: published publisher: Cold Spring Harbor Laboratory Press publist_id: '3686' related_material: link: - relation: erratum url: http://genesdev.cshlp.org/content/21/11/1431.short status: public title: Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 20 year: '2006' ... --- _id: '3017' abstract: - lang: eng text: The plant hormone auxin plays crucial roles in regulating plant growth development, including embryo and root patterning, organ formation, vascular tissue differentiation and growth responses to environmental stimuli. Asymmetric auxin distribution patterns have been observed within tissues, and these so-called auxin gradients change dynamically during different developmental processes. Most auxin is synthesized in the shoot and distributed directionally throughout the plant. This polar auxin transport is mediated by auxin influx and efflux facilitators, whose subcellular polar localizations guide the direction of auxin flow. The polar localization of PIN auxin efflux carriers changes in response to developmental and external cues in order to channel auxin flow in a regulated manner for organized growth. Auxin itself modulates the expression and subcellular localization of PIN proteins, contributing to a complex pattern of feedback regulation. Here we review the available information mainly from studies of a model plant, Arabidopsis thaliana, on the generation of auxin gradients, the regulation of polar auxin transport and further downstream cellular events. author: - first_name: Hirokazu full_name: Tanaka, Hirokazu last_name: Tanaka - first_name: Pankaj full_name: Dhonukshe, Pankaj last_name: Dhonukshe - first_name: Philip full_name: Brewer, Philip last_name: Brewer - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Tanaka H, Dhonukshe P, Brewer P, Friml J. Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development. Cellular and Molecular Life Sciences. 2006;63(23):2738-2754. doi:10.1007/s00018-006-6116-5' apa: 'Tanaka, H., Dhonukshe, P., Brewer, P., & Friml, J. (2006). Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development. Cellular and Molecular Life Sciences. Birkhäuser. https://doi.org/10.1007/s00018-006-6116-5' chicago: 'Tanaka, Hirokazu, Pankaj Dhonukshe, Philip Brewer, and Jiří Friml. “Spatiotemporal Asymmetric Auxin Distribution: A Means to Coordinate Plant Development.” Cellular and Molecular Life Sciences. Birkhäuser, 2006. https://doi.org/10.1007/s00018-006-6116-5.' ieee: 'H. Tanaka, P. Dhonukshe, P. Brewer, and J. Friml, “Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development,” Cellular and Molecular Life Sciences, vol. 63, no. 23. Birkhäuser, pp. 2738–2754, 2006.' ista: 'Tanaka H, Dhonukshe P, Brewer P, Friml J. 2006. Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development. Cellular and Molecular Life Sciences. 63(23), 2738–2754.' mla: 'Tanaka, Hirokazu, et al. “Spatiotemporal Asymmetric Auxin Distribution: A Means to Coordinate Plant Development.” Cellular and Molecular Life Sciences, vol. 63, no. 23, Birkhäuser, 2006, pp. 2738–54, doi:10.1007/s00018-006-6116-5.' short: H. Tanaka, P. Dhonukshe, P. Brewer, J. Friml, Cellular and Molecular Life Sciences 63 (2006) 2738–2754. date_created: 2018-12-11T12:00:53Z date_published: 2006-12-01T00:00:00Z date_updated: 2021-01-12T07:40:29Z day: '01' doi: 10.1007/s00018-006-6116-5 extern: '1' intvolume: ' 63' issue: '23' language: - iso: eng month: '12' oa_version: None page: 2738 - 2754 publication: Cellular and Molecular Life Sciences publication_status: published publisher: Birkhäuser publist_id: '3685' quality_controlled: '1' status: public title: 'Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 63 year: '2006' ... --- _id: '3018' abstract: - lang: eng text: The directional flow of the plant hormone auxin mediates multiple developmental processes, including patterning and tropisms. Apical and basal plasma membrane localization of AUXIN-RESISTANT1 (AUX1) and PIN-FORMED1 (PIN1) auxin transport components underpins the directionality of intercellular auxin flow in Arabidopsis thaliana roots. Here, we examined the mechanism of polar trafficking of AUX1. Real-time live cell analysis along with subcellular markers revealed that AUX1 resides at the apical plasma membrane of protophloem cells and at highly dynamic subpopulations of Golgi apparatus and endosomes in all cell types. Plasma membrane and intracellular pools of AUX1 are interconnected by actin-dependent constitutive trafficking, which is not sensitive to the vesicle trafficking inhibitor brefeldin A. AUX1 subcellular dynamics are not influenced by the auxin influx inhibitor NOA but are blocked by the auxin efflux inhibitors TIBA and PBA. Furthermore, auxin transport inhibitors and interference with the sterol composition of membranes disrupt polar AUX1 distribution at the plasma membrane. Compared with PIN1 trafficking, AUX1 dynamics display different sensitivities to trafficking inhibitors and are independent of the endosomal trafficking regulator ARF GEF GNOM. Hence, AUX1 uses a novel trafficking pathway in plants that is distinct from PIN trafficking, providing an additional mechanism for the fine regulation of auxin transport. author: - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: Pankaj full_name: Dhonukshe, Pankaj last_name: Dhonukshe - first_name: Ranjan full_name: Swarup, Ranjan last_name: Swarup - first_name: Malcolm full_name: Bennett, Malcolm last_name: Bennett - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Kleine Vehn J, Dhonukshe P, Swarup R, Bennett M, Friml J. Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1. Plant Cell. 2006;18(11):3171-3181. doi:10.1105/tpc.106.042770 apa: Kleine Vehn, J., Dhonukshe, P., Swarup, R., Bennett, M., & Friml, J. (2006). Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.106.042770 chicago: Kleine Vehn, Jürgen, Pankaj Dhonukshe, Ranjan Swarup, Malcolm Bennett, and Jiří Friml. “Subcellular Trafficking of the Arabidopsis Auxin Influx Carrier AUX1 Uses a Novel Pathway Distinct from PIN1.” Plant Cell. American Society of Plant Biologists, 2006. https://doi.org/10.1105/tpc.106.042770. ieee: J. Kleine Vehn, P. Dhonukshe, R. Swarup, M. Bennett, and J. Friml, “Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1,” Plant Cell, vol. 18, no. 11. American Society of Plant Biologists, pp. 3171–3181, 2006. ista: Kleine Vehn J, Dhonukshe P, Swarup R, Bennett M, Friml J. 2006. Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1. Plant Cell. 18(11), 3171–3181. mla: Kleine Vehn, Jürgen, et al. “Subcellular Trafficking of the Arabidopsis Auxin Influx Carrier AUX1 Uses a Novel Pathway Distinct from PIN1.” Plant Cell, vol. 18, no. 11, American Society of Plant Biologists, 2006, pp. 3171–81, doi:10.1105/tpc.106.042770. short: J. Kleine Vehn, P. Dhonukshe, R. Swarup, M. Bennett, J. Friml, Plant Cell 18 (2006) 3171–3181. date_created: 2018-12-11T12:00:53Z date_published: 2006-11-01T00:00:00Z date_updated: 2021-01-12T07:40:29Z day: '01' doi: 10.1105/tpc.106.042770 extern: 1 intvolume: ' 18' issue: '11' month: '11' page: 3171 - 3181 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3684' quality_controlled: 0 status: public title: Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1 type: journal_article volume: 18 year: '2006' ... --- _id: '3020' abstract: - lang: eng text: High throughput microarray transcription analyses provide us with the expression profiles for large amounts of plant genes. However, their tissue and cellular resolution is limited. Thus, for detailed functional analysis, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here, we present an in situ mRNA hybridization method that is routinely used for the analysis of plant gene expression patterns. The protocol is optimized for whole mount mRNA localizations in Arabidopsis seedling tissues including embryos, roots, hypocotyls and young primary leaves. It can also be used for comparable tissues in other species. Part of the protocol can also be automated and performed by a liquid handling robot. Here we present a detailed protocol, recommended controls and troubleshooting, along with examples of several applications. The total time to carry out the entire procedure is ∼7 d, depending on the tissue used. author: - first_name: Jan full_name: Hejátko, Jan last_name: Hejátko - first_name: Ikram full_name: Blilou, Ikram last_name: Blilou - first_name: Philip full_name: Brewer, Philip B last_name: Brewer - 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: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Hejátko J, Blilou I, Brewer P, Friml J, Scheres B, Benková E. In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples. Nature Protocols. 2006;1(4):1939-1946. doi:10.1038/nprot.2006.333 apa: Hejátko, J., Blilou, I., Brewer, P., Friml, J., Scheres, B., & Benková, E. (2006). In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.333 chicago: Hejátko, Jan, Ikram Blilou, Philip Brewer, Jiří Friml, Ben Scheres, and Eva Benková. “In Situ Hybridization Technique for MRNA Detection in Whole Mount Arabidopsis Samples.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.333. ieee: J. Hejátko, I. Blilou, P. Brewer, J. Friml, B. Scheres, and E. Benková, “In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples,” Nature Protocols, vol. 1, no. 4. Nature Publishing Group, pp. 1939–1946, 2006. ista: Hejátko J, Blilou I, Brewer P, Friml J, Scheres B, Benková E. 2006. In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples. Nature Protocols. 1(4), 1939–1946. mla: Hejátko, Jan, et al. “In Situ Hybridization Technique for MRNA Detection in Whole Mount Arabidopsis Samples.” Nature Protocols, vol. 1, no. 4, Nature Publishing Group, 2006, pp. 1939–46, doi:10.1038/nprot.2006.333. short: J. Hejátko, I. Blilou, P. Brewer, J. Friml, B. Scheres, E. Benková, Nature Protocols 1 (2006) 1939–1946. date_created: 2018-12-11T12:00:54Z date_published: 2006-11-01T00:00:00Z date_updated: 2021-01-12T07:40:30Z day: '01' doi: 10.1038/nprot.2006.333 extern: 1 intvolume: ' 1' issue: '4' month: '11' page: 1939 - 1946 publication: Nature Protocols publication_status: published publisher: Nature Publishing Group publist_id: '3683' quality_controlled: 0 status: public title: In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples type: journal_article volume: 1 year: '2006' ... --- _id: '3015' abstract: - lang: eng text: 'As the field of plant molecular biology is swiftly advancing, a need has been created for methods that allow rapid and reliable in situ localization of proteins in plant cells. Here we describe a whole-mount ''immunolocalization'' technique for various plant tissues, including roots, hypocotyls, cotyledons, young primary leaves and embryos of Arabidopsis thaliana and other species. The detailed protocol, recommended controls and troubleshooting are presented, along with examples of applications. The protocol consists of five main procedures: tissue fixation, tissue permeation, blocking, primary and secondary antibody incubation. Notably, the first procedure (tissue fixation) includes several steps (4-12) that are absolutely necessary for protein localization in hypocotyls, cotyledons and young primary leaves but should be omitted for other tissues. The protocol is usually done in 3 days, but could also be completed in 2 days.' author: - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Tomasz full_name: Paciorek, Tomasz last_name: Paciorek - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Sauer M, Paciorek T, Benková E, Friml J. Immunocytochemical techniques for whole mount in situ protein localization in plants. Nature Protocols. 2006;1(1):98-103. doi:10.1038/nprot.2006.15 apa: Sauer, M., Paciorek, T., Benková, E., & Friml, J. (2006). Immunocytochemical techniques for whole mount in situ protein localization in plants. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.15 chicago: Sauer, Michael, Tomasz Paciorek, Eva Benková, and Jiří Friml. “Immunocytochemical Techniques for Whole Mount in Situ Protein Localization in Plants.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.15. ieee: M. Sauer, T. Paciorek, E. Benková, and J. Friml, “Immunocytochemical techniques for whole mount in situ protein localization in plants,” Nature Protocols, vol. 1, no. 1. Nature Publishing Group, pp. 98–103, 2006. ista: Sauer M, Paciorek T, Benková E, Friml J. 2006. Immunocytochemical techniques for whole mount in situ protein localization in plants. Nature Protocols. 1(1), 98–103. mla: Sauer, Michael, et al. “Immunocytochemical Techniques for Whole Mount in Situ Protein Localization in Plants.” Nature Protocols, vol. 1, no. 1, Nature Publishing Group, 2006, pp. 98–103, doi:10.1038/nprot.2006.15. short: M. Sauer, T. Paciorek, E. Benková, J. Friml, Nature Protocols 1 (2006) 98–103. date_created: 2018-12-11T12:00:52Z date_published: 2006-06-01T00:00:00Z date_updated: 2021-01-12T07:40:28Z day: '01' doi: 10.1038/nprot.2006.15 extern: 1 intvolume: ' 1' issue: '1' month: '06' page: 98 - 103 publication: Nature Protocols publication_status: published publisher: Nature Publishing Group publist_id: '3688' quality_controlled: 0 status: public title: Immunocytochemical techniques for whole mount in situ protein localization in plants type: journal_article volume: 1 year: '2006' ... --- _id: '3013' abstract: - lang: eng text: 'There is a growing demand for methods that allow rapid and reliable in situ localization of proteins in plant cells. The immunocytochemistry protocol presented here can be used routinely to observe protein localization patterns in tissue sections of various plant species. This protocol is especially suitable for plant species with more-complex tissue architecture (such as maize, Zea mays), which makes it difficult to use an easier whole-mount procedure for protein localization. To facilitate the antibody-antigen reaction, it is necessary to include a wax-embedding and tissue-sectioning step. The protocol consists of the following procedures: chemical fixation of tissue, dehydration, wax embedding, sectioning, dewaxing, rehydration, blocking and antibody incubation. The detailed protocol, recommended controls and troubleshooting are presented here, along with examples of applications.' author: - first_name: Tomasz full_name: Paciorek, Tomasz last_name: Paciorek - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jozef full_name: Balla, Jozef last_name: Balla - first_name: Justyna full_name: Wiśniewska, Justyna last_name: Wiśniewska - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Paciorek T, Sauer M, Balla J, Wiśniewska J, Friml J. Immunocytochemical technique for protein localization in sections of plant tissues. Nature Protocols. 2006;1(1):104-107. doi:10.1038/nprot.2006.16 apa: Paciorek, T., Sauer, M., Balla, J., Wiśniewska, J., & Friml, J. (2006). Immunocytochemical technique for protein localization in sections of plant tissues. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.16 chicago: Paciorek, Tomasz, Michael Sauer, Jozef Balla, Justyna Wiśniewska, and Jiří Friml. “Immunocytochemical Technique for Protein Localization in Sections of Plant Tissues.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.16. ieee: T. Paciorek, M. Sauer, J. Balla, J. Wiśniewska, and J. Friml, “Immunocytochemical technique for protein localization in sections of plant tissues,” Nature Protocols, vol. 1, no. 1. Nature Publishing Group, pp. 104–107, 2006. ista: Paciorek T, Sauer M, Balla J, Wiśniewska J, Friml J. 2006. Immunocytochemical technique for protein localization in sections of plant tissues. Nature Protocols. 1(1), 104–107. mla: Paciorek, Tomasz, et al. “Immunocytochemical Technique for Protein Localization in Sections of Plant Tissues.” Nature Protocols, vol. 1, no. 1, Nature Publishing Group, 2006, pp. 104–07, doi:10.1038/nprot.2006.16. short: T. Paciorek, M. Sauer, J. Balla, J. Wiśniewska, J. Friml, Nature Protocols 1 (2006) 104–107. date_created: 2018-12-11T12:00:52Z date_published: 2006-06-01T00:00:00Z date_updated: 2021-01-12T07:40:27Z day: '01' doi: 10.1038/nprot.2006.16 extern: 1 intvolume: ' 1' issue: '1' month: '06' page: 104 - 107 publication: Nature Protocols publication_status: published publisher: Nature Publishing Group publist_id: '3689' quality_controlled: 0 status: public title: Immunocytochemical technique for protein localization in sections of plant tissues type: journal_article volume: 1 year: '2006' ... --- _id: '3014' abstract: - lang: eng text: Plant biology is currently confronted with an overflow of expression profile data provided by high-throughput microarray transcription analyses. However, the tissue and cellular resolution of these techniques is limited. Thus, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here we present an in situ mRNA hybridization method that is routinely used in the analysis of gene expression patterns. The protocol is optimized for mRNA localizations in sectioned tissue of Arabidopsis seedlings including embryos, roots, hypocotyls, young primary leaves and flowers. The detailed protocol, recommended controls and troubleshooting are presented along with examples of application. The total time for the process is 10 days. author: - first_name: Philip full_name: Brewer, Philip B last_name: Brewer - first_name: Marcus full_name: Heisler, Marcus G last_name: Heisler - first_name: Jan full_name: Hejátko, Jan last_name: Hejátko - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Brewer P, Heisler M, Hejátko J, Friml J, Benková E. In situ hybridization for mRNA detection in Arabidopsis tissue sections. Nature Protocols. 2006;1(3):1462-1467. doi:10.1038/nprot.2006.226 apa: Brewer, P., Heisler, M., Hejátko, J., Friml, J., & Benková, E. (2006). In situ hybridization for mRNA detection in Arabidopsis tissue sections. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.226 chicago: Brewer, Philip, Marcus Heisler, Jan Hejátko, Jiří Friml, and Eva Benková. “In Situ Hybridization for MRNA Detection in Arabidopsis Tissue Sections.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.226. ieee: P. Brewer, M. Heisler, J. Hejátko, J. Friml, and E. Benková, “In situ hybridization for mRNA detection in Arabidopsis tissue sections,” Nature Protocols, vol. 1, no. 3. Nature Publishing Group, pp. 1462–1467, 2006. ista: Brewer P, Heisler M, Hejátko J, Friml J, Benková E. 2006. In situ hybridization for mRNA detection in Arabidopsis tissue sections. Nature Protocols. 1(3), 1462–1467. mla: Brewer, Philip, et al. “In Situ Hybridization for MRNA Detection in Arabidopsis Tissue Sections.” Nature Protocols, vol. 1, no. 3, Nature Publishing Group, 2006, pp. 1462–67, doi:10.1038/nprot.2006.226. short: P. Brewer, M. Heisler, J. Hejátko, J. Friml, E. Benková, Nature Protocols 1 (2006) 1462–1467. date_created: 2018-12-11T12:00:52Z date_published: 2006-08-01T00:00:00Z date_updated: 2021-01-12T07:40:28Z day: '01' doi: 10.1038/nprot.2006.226 extern: 1 intvolume: ' 1' issue: '3' month: '08' page: 1462 - 1467 publication: Nature Protocols publication_status: published publisher: Nature Publishing Group publist_id: '3687' quality_controlled: 0 status: public title: In situ hybridization for mRNA detection in Arabidopsis tissue sections type: journal_article volume: 1 year: '2006' ... --- _id: '3152' abstract: - lang: eng text: The basic concepts of the molecular machinery that mediates cell migration have been gleaned from cell culture systems. However, the three-dimensional environment within an organism presents migrating cells with a much greater challenge. They must move between and among other cells while interpreting multiple attractive and repulsive cues to choose their proper path. They must coordinate their cell adhesion with their surroundings and know when to start and stop moving. New insights into the control of these remaining mysteries have emerged from genetic dissection and live imaging of germ cell migration in Drosophila, zebrafish, and mouse embryos. In this review, we first describe germ cell migration in cellular and mechanistic detail in these different model systems. We then compare these systems to highlight the emerging principles. Finally, we contrast the migration of germ cells with that of immune and cancer cells to outline the conserved and different mechanisms. author: - first_name: Prabhat full_name: Kunwar, Prabhat S last_name: Kunwar - first_name: Daria E full_name: Daria Siekhaus id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Ruth full_name: Lehmann, Ruth last_name: Lehmann citation: ama: Kunwar P, Siekhaus DE, Lehmann R. In vivo migration A germ cell perspective. Annual Review of Cell and Developmental Biology. 2006;22:237-265. doi:10.1146/annurev.cellbio.22.010305.103337 apa: Kunwar, P., Siekhaus, D. E., & Lehmann, R. (2006). In vivo migration A germ cell perspective. Annual Review of Cell and Developmental Biology. Annual Reviews. https://doi.org/10.1146/annurev.cellbio.22.010305.103337 chicago: Kunwar, Prabhat, Daria E Siekhaus, and Ruth Lehmann. “In Vivo Migration A Germ Cell Perspective.” Annual Review of Cell and Developmental Biology. Annual Reviews, 2006. https://doi.org/10.1146/annurev.cellbio.22.010305.103337. ieee: P. Kunwar, D. E. Siekhaus, and R. Lehmann, “In vivo migration A germ cell perspective,” Annual Review of Cell and Developmental Biology, vol. 22. Annual Reviews, pp. 237–265, 2006. ista: Kunwar P, Siekhaus DE, Lehmann R. 2006. In vivo migration A germ cell perspective. Annual Review of Cell and Developmental Biology. 22, 237–265. mla: Kunwar, Prabhat, et al. “In Vivo Migration A Germ Cell Perspective.” Annual Review of Cell and Developmental Biology, vol. 22, Annual Reviews, 2006, pp. 237–65, doi:10.1146/annurev.cellbio.22.010305.103337. short: P. Kunwar, D.E. Siekhaus, R. Lehmann, Annual Review of Cell and Developmental Biology 22 (2006) 237–265. date_created: 2018-12-11T12:01:42Z date_published: 2006-06-14T00:00:00Z date_updated: 2021-01-12T07:41:25Z day: '14' doi: 10.1146/annurev.cellbio.22.010305.103337 extern: 1 intvolume: ' 22' month: '06' page: 237 - 265 publication: Annual Review of Cell and Developmental Biology publication_status: published publisher: Annual Reviews publist_id: '3543' quality_controlled: 0 status: public title: In vivo migration A germ cell perspective type: journal_article volume: 22 year: '2006' ... --- _id: '3189' abstract: - lang: eng text: This paper presents an algorithm capable of real-time separation of foreground from background in monocular video sequences. Automatic segmentation of layers from colour/contrast or from motion alone is known to be error-prone. Here motion, colour and contrast cues are probabilistically fused together with spatial and temporal priors to infer layers accurately and efficiently. Central to our algorithm is the fact that pixel velocities are not needed, thus removing the need for optical flow estimation, with its tendency to error and computational expense. Instead, an efficient motion vs non-motion classifier is trained to operate directly and jointly on intensity-change and contrast. Its output is then fused with colour information. The prior on segmentation is represented by a second order, temporal, Hidden Markov Model, together with a spatial MRF favouring coherence except where contrast is high. Finally, accurate layer segmentation and explicit occlusion detection are efficiently achieved by binary graph cut. The segmentation accuracy of the proposed algorithm is quantitatively evaluated with respect to existing ground-truth data and found to be comparable to the accuracy of a state of the art stereo segmentation algorithm. Fore-ground/background segmentation is demonstrated in the application of live background substitution and shown to generate convincingly good quality composite video. author: - first_name: Antonio full_name: Criminisi, Antonio last_name: Criminisi - first_name: Geoffrey full_name: Cross, Geoffrey last_name: Cross - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Criminisi A, Cross G, Blake A, Kolmogorov V. Bilayer segmentation of live video. In: Vol 1. IEEE; 2006:53-60. doi:10.1109/CVPR.2006.69' apa: 'Criminisi, A., Cross, G., Blake, A., & Kolmogorov, V. (2006). Bilayer segmentation of live video (Vol. 1, pp. 53–60). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2006.69' chicago: Criminisi, Antonio, Geoffrey Cross, Andrew Blake, and Vladimir Kolmogorov. “Bilayer Segmentation of Live Video,” 1:53–60. IEEE, 2006. https://doi.org/10.1109/CVPR.2006.69. ieee: 'A. Criminisi, G. Cross, A. Blake, and V. Kolmogorov, “Bilayer segmentation of live video,” presented at the CVPR: Computer Vision and Pattern Recognition, 2006, vol. 1, pp. 53–60.' ista: 'Criminisi A, Cross G, Blake A, Kolmogorov V. 2006. Bilayer segmentation of live video. CVPR: Computer Vision and Pattern Recognition vol. 1, 53–60.' mla: Criminisi, Antonio, et al. Bilayer Segmentation of Live Video. Vol. 1, IEEE, 2006, pp. 53–60, doi:10.1109/CVPR.2006.69. short: A. Criminisi, G. Cross, A. Blake, V. Kolmogorov, in:, IEEE, 2006, pp. 53–60. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:01:54Z date_published: 2006-07-05T00:00:00Z date_updated: 2021-01-12T07:41:40Z day: '05' doi: 10.1109/CVPR.2006.69 extern: 1 intvolume: ' 1' main_file_link: - open_access: '0' url: http://research.microsoft.com/en-us/um/people/ablake/papers/ablake/criminisi_cvpr06.pdf month: '07' page: 53 - 60 publication_status: published publisher: IEEE publist_id: '3494' quality_controlled: 0 status: public title: Bilayer segmentation of live video type: conference volume: 1 year: '2006' ... --- _id: '3190' abstract: - lang: eng text: Algorithms for discrete energy minimization are of fundamental importance in computer vision. In this paper, we focus on the recent technique proposed by Wainwright et al. (Nov. 2005)- tree-reweighted max-product message passing (TRW). It was inspired by the problem of maximizing a lower bound on the energy. However, the algorithm is not guaranteed to increase this bound - it may actually go down. In addition, TRW does not always converge. We develop a modification of this algorithm which we call sequential tree-reweighted message passing. Its main property is that the bound is guaranteed not to decrease. We also give a weak tree agreement condition which characterizes local maxima of the bound with respect to TRW algorithms. We prove that our algorithm has a limit point that achieves weak tree agreement. Finally, we show that, our algorithm requires half as much memory as traditional message passing approaches. Experimental results demonstrate that on certain synthetic and real problems, our algorithm outperforms both the ordinary belief propagation and tree-reweighted algorithm in (M. J. Wainwright, et al., Nov. 2005). In addition, on stereo problems with Potts interactions, we obtain a lower energy than graph cuts. author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Kolmogorov V. Convergent tree reweighted message passing for energy minimization. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2006;28(10):1568-1583. doi:10.1109/TPAMI.2006.200 apa: Kolmogorov, V. (2006). Convergent tree reweighted message passing for energy minimization. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2006.200 chicago: Kolmogorov, Vladimir. “Convergent Tree Reweighted Message Passing for Energy Minimization.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2006. https://doi.org/10.1109/TPAMI.2006.200. ieee: V. Kolmogorov, “Convergent tree reweighted message passing for energy minimization,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 10. IEEE, pp. 1568–1583, 2006. ista: Kolmogorov V. 2006. Convergent tree reweighted message passing for energy minimization. IEEE Transactions on Pattern Analysis and Machine Intelligence. 28(10), 1568–1583. mla: Kolmogorov, Vladimir. “Convergent Tree Reweighted Message Passing for Energy Minimization.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 10, IEEE, 2006, pp. 1568–83, doi:10.1109/TPAMI.2006.200. short: V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine Intelligence 28 (2006) 1568–1583. date_created: 2018-12-11T12:01:55Z date_published: 2006-08-21T00:00:00Z date_updated: 2021-01-12T07:41:41Z day: '21' doi: 10.1109/TPAMI.2006.200 extern: 1 intvolume: ' 28' issue: '10' main_file_link: - open_access: '0' url: http://research.microsoft.com/pubs/67371/trw_maxproduct_aistats05.pdf month: '08' page: 1568 - 1583 publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_status: published publisher: IEEE publist_id: '3495' quality_controlled: 0 status: public title: Convergent tree reweighted message passing for energy minimization type: journal_article volume: 28 year: '2006' ... --- _id: '3188' abstract: - lang: eng text: 'We introduce the term cosegmentation which denotes the task of segmenting simultaneously the common parts of an image pair. A generative model for cosegmentation is presented. Inference in the model leads to minimizing an energy with an MRF term encoding spatial coherency and a global constraint which attempts to match the appearance histograms of the common parts. This energy has not been proposed previously and its optimization is challenging and NP-hard. For this problem a novel optimization scheme which we call trust region graph cuts is presented. We demonstrate that this framework has the potential to improve a wide range of research: Object driven image retrieval, video tracking and segmentation, and interactive image editing. The power of the framework lies in its generality, the common part can be a rigid/non-rigid object (or scene), observed from different viewpoints or even similar objects of the same class.' author: - first_name: Carsten full_name: Rother, Carsten last_name: Rother - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Thomas full_name: Minka, Thomas P last_name: Minka - first_name: Andrew full_name: Blake, Andrew last_name: Blake citation: ama: 'Rother C, Kolmogorov V, Minka T, Blake A. Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs. In: IEEE; 2006:993-1000. doi:10.1109/CVPR.2006.91' apa: 'Rother, C., Kolmogorov, V., Minka, T., & Blake, A. (2006). Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs (pp. 993–1000). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2006.91' chicago: Rother, Carsten, Vladimir Kolmogorov, Thomas Minka, and Andrew Blake. “Cosegmentation of Image Pairs by Histogram Matching - Incorporating a Global Constraint into MRFs,” 993–1000. IEEE, 2006. https://doi.org/10.1109/CVPR.2006.91. ieee: 'C. Rother, V. Kolmogorov, T. Minka, and A. Blake, “Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs,” presented at the CVPR: Computer Vision and Pattern Recognition, 2006, pp. 993–1000.' ista: 'Rother C, Kolmogorov V, Minka T, Blake A. 2006. Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs. CVPR: Computer Vision and Pattern Recognition, 993–1000.' mla: Rother, Carsten, et al. Cosegmentation of Image Pairs by Histogram Matching - Incorporating a Global Constraint into MRFs. IEEE, 2006, pp. 993–1000, doi:10.1109/CVPR.2006.91. short: C. Rother, V. Kolmogorov, T. Minka, A. Blake, in:, IEEE, 2006, pp. 993–1000. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:01:54Z date_published: 2006-07-05T00:00:00Z date_updated: 2021-01-12T07:41:40Z day: '05' doi: 10.1109/CVPR.2006.91 extern: 1 month: '07' page: 993 - 1000 publication_status: published publisher: IEEE publist_id: '3493' quality_controlled: 0 status: public title: Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs type: conference year: '2006' ... --- _id: '3214' abstract: - lang: eng text: |- The Feistel-network is a popular structure underlying many block-ciphers where the cipher is constructed from many simpler rounds, each defined by some function which is derived from the secret key. Luby and Rackoff showed that the three-round Feistel-network – each round instantiated with a pseudorandom function secure against adaptive chosen plaintext attacks (CPA) – is a CPA secure pseudorandom permutation, thus giving some confidence in the soundness of using a Feistel-network to design block-ciphers. But the round functions used in actual block-ciphers are – for efficiency reasons – far from being pseudorandom. We investigate the security of the Feistel-network against CPA distinguishers when the only security guarantee we have for the round functions is that they are secure against non-adaptive chosen plaintext attacks (nCPA). We show that in the information-theoretic setting, four rounds with nCPA secure round functions are sufficient (and necessary) to get a CPA secure permutation. Unfortunately, this result does not translate into the more interesting pseudorandom setting. In fact, under the so-called Inverse Decisional Diffie-Hellman assumption the Feistel-network with four rounds, each instantiated with a nCPA secure pseudorandom function, is in general not a CPA secure pseudorandom permutation. acknowledgement: Most of this work was done while the K. Pietrzak was a PhD student at ETH where he was supported by the Swiss National Science Foundation, project No. 200020- 103847/1. Currently he is partially supported by the Commission of the European Communities through the IST program under contract IST-2002-507932 ECRYPT. alternative_title: - LNCS author: - first_name: Ueli full_name: Maurer, Ueli M last_name: Maurer - first_name: Yvonne full_name: Oswald, Yvonne A last_name: Oswald - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Johan full_name: Sjödin, Johan last_name: Sjödin citation: ama: 'Maurer U, Oswald Y, Pietrzak KZ, Sjödin J. Luby Rackoff ciphers from weak round functions . In: Vol 4004. Springer; 2006:391-408. doi:10.1007/11761679_24' apa: 'Maurer, U., Oswald, Y., Pietrzak, K. Z., & Sjödin, J. (2006). Luby Rackoff ciphers from weak round functions (Vol. 4004, pp. 391–408). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/11761679_24' chicago: Maurer, Ueli, Yvonne Oswald, Krzysztof Z Pietrzak, and Johan Sjödin. “Luby Rackoff Ciphers from Weak Round Functions ,” 4004:391–408. Springer, 2006. https://doi.org/10.1007/11761679_24. ieee: 'U. Maurer, Y. Oswald, K. Z. Pietrzak, and J. Sjödin, “Luby Rackoff ciphers from weak round functions ,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2006, vol. 4004, pp. 391–408.' ista: 'Maurer U, Oswald Y, Pietrzak KZ, Sjödin J. 2006. Luby Rackoff ciphers from weak round functions . EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 4004, 391–408.' mla: Maurer, Ueli, et al. Luby Rackoff Ciphers from Weak Round Functions . Vol. 4004, Springer, 2006, pp. 391–408, doi:10.1007/11761679_24. short: U. Maurer, Y. Oswald, K.Z. Pietrzak, J. Sjödin, in:, Springer, 2006, pp. 391–408. conference: name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' date_created: 2018-12-11T12:02:03Z date_published: 2006-07-11T00:00:00Z date_updated: 2021-01-12T07:41:51Z day: '11' doi: 10.1007/11761679_24 extern: 1 intvolume: ' 4004' month: '07' page: 391 - 408 publication_status: published publisher: Springer publist_id: '3465' quality_controlled: 0 status: public title: 'Luby Rackoff ciphers from weak round functions ' type: conference volume: 4004 year: '2006' ... --- _id: '3215' abstract: - lang: eng text: 'Most cryptographic primitives such as encryption, authentication or secret sharing require randomness. Usually one assumes that perfect randomness is available, but those primitives might also be realized under weaker assumptions. In this work we continue the study of building secure cryptographic primitives from imperfect random sources initiated by Dodis and Spencer (FOCS’02). Their main result shows that there exists a (high-entropy) source of randomness allowing for perfect encryption of a bit, and yet from which one cannot extract even a single weakly random bit, separating encryption from extraction. Our main result separates encryption from 2-out-2 secret sharing (both in the information-theoretic and in the computational settings): any source which can be used to achieve one-bit encryption also can be used for 2-out-2 secret sharing of one bit, but the converse is false, even for high-entropy sources. Therefore, possibility of extraction strictly implies encryption, which in turn strictly implies 2-out-2 secret sharing.' acknowledgement: Supported in part by NSF career award CCR-0133806 and NSF grant CCR-0311095. Supported by the Swiss National Science Foundation, project No. 200020-103847/1. alternative_title: - LNCS author: - first_name: Yevgeniy full_name: Dodis, Yevgeniy last_name: Dodis - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Bartosz full_name: Przydatek, Bartosz last_name: Przydatek citation: ama: 'Dodis Y, Pietrzak KZ, Przydatek B. Separating sources for encryption and secret sharing. In: Vol 3876. Springer; 2006:601-616. doi:10.1007/11681878_31' apa: 'Dodis, Y., Pietrzak, K. Z., & Przydatek, B. (2006). Separating sources for encryption and secret sharing (Vol. 3876, pp. 601–616). Presented at the TCC: Theory of Cryptography Conference, Springer. https://doi.org/10.1007/11681878_31' chicago: Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Bartosz Przydatek. “Separating Sources for Encryption and Secret Sharing,” 3876:601–16. Springer, 2006. https://doi.org/10.1007/11681878_31. ieee: 'Y. Dodis, K. Z. Pietrzak, and B. Przydatek, “Separating sources for encryption and secret sharing,” presented at the TCC: Theory of Cryptography Conference, 2006, vol. 3876, pp. 601–616.' ista: 'Dodis Y, Pietrzak KZ, Przydatek B. 2006. Separating sources for encryption and secret sharing. TCC: Theory of Cryptography Conference, LNCS, vol. 3876, 601–616.' mla: Dodis, Yevgeniy, et al. Separating Sources for Encryption and Secret Sharing. Vol. 3876, Springer, 2006, pp. 601–16, doi:10.1007/11681878_31. short: Y. Dodis, K.Z. Pietrzak, B. Przydatek, in:, Springer, 2006, pp. 601–616. conference: name: 'TCC: Theory of Cryptography Conference' date_created: 2018-12-11T12:02:04Z date_published: 2006-04-11T00:00:00Z date_updated: 2021-01-12T07:41:51Z day: '11' doi: 10.1007/11681878_31 extern: 1 intvolume: ' 3876' month: '04' page: 601 - 616 publication_status: published publisher: Springer publist_id: '3466' quality_controlled: 0 status: public title: Separating sources for encryption and secret sharing type: conference volume: 3876 year: '2006' ... --- _id: '3217' abstract: - lang: eng text: |- To prove that a secure key-agreement protocol exists one must at least show P ≠NP. Moreover any proof that the sequential composition of two non-adaptively secure pseudorandom functions is secure against at least two adaptive queries must falsify the decisional Diffie-Hellman assumption, a standard assumption from public-key cryptography. Hence proving any of this two seemingly unrelated statements would require a significant breakthrough. We show that at least one of the two statements is true. To our knowledge this gives the first positive cryptographic result (namely that composition implies some weak adaptive security) which holds in Minicrypt, but not in Cryptomania, i.e. under the assumption that one-way functions exist, but public-key cryptography does not. acknowledgement: Author was supported during the writing of this work by the Swiss National Science Foundation, project No. 200020-103847/1. Part of this work is supported by the Commission of the European Communities through the IST program under contract IST-2002-507932 alternative_title: - LNCS author: - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Pietrzak KZ. Composition implies adaptive security in minicrypt. In: Vol 4004. Springer; 2006:328-338. doi:10.1007/11761679_20' apa: 'Pietrzak, K. Z. (2006). Composition implies adaptive security in minicrypt (Vol. 4004, pp. 328–338). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/11761679_20' chicago: Pietrzak, Krzysztof Z. “Composition Implies Adaptive Security in Minicrypt,” 4004:328–38. Springer, 2006. https://doi.org/10.1007/11761679_20. ieee: 'K. Z. Pietrzak, “Composition implies adaptive security in minicrypt,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2006, vol. 4004, pp. 328–338.' ista: 'Pietrzak KZ. 2006. Composition implies adaptive security in minicrypt. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 4004, 328–338.' mla: Pietrzak, Krzysztof Z. Composition Implies Adaptive Security in Minicrypt. Vol. 4004, Springer, 2006, pp. 328–38, doi:10.1007/11761679_20. short: K.Z. Pietrzak, in:, Springer, 2006, pp. 328–338. conference: name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' date_created: 2018-12-11T12:02:04Z date_published: 2006-07-11T00:00:00Z date_updated: 2021-01-12T07:41:52Z day: '11' doi: 10.1007/11761679_20 extern: 1 intvolume: ' 4004' month: '07' page: 328 - 338 publication_status: published publisher: Springer publist_id: '3464' quality_controlled: 0 status: public title: Composition implies adaptive security in minicrypt type: conference volume: 4004 year: '2006' ... --- _id: '3216' abstract: - lang: eng text: |- We prove a new upper bound on the advantage of any adversary for distinguishing the encrypted CBC-MAC (EMAC) based on random permutations from a random function. Our proof uses techniques recently introduced in [BPR05], which again were inspired by [DGH + 04]. The bound we prove is tight — in the sense that it matches the advantage of known attacks up to a constant factor — for a wide range of the parameters: let n denote the block-size, q the number of queries the adversary is allowed to make and ℓ an upper bound on the length (i.e. number of blocks) of the messages, then for ℓ ≤ 2 n/8 and q≥ł2 the advantage is in the order of q 2/2 n (and in particular independent of ℓ). This improves on the previous bound of q 2ℓΘ(1/ln ln ℓ)/2 n from [BPR05] and matches the trivial attack (which thus is basically optimal) where one simply asks random queries until a collision is found. acknowledgement: Part of this work is supported by the Commission of the European Communities through the IST program under contract IST-2002-507932 ECRYPT. alternative_title: - LNCS author: - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Pietrzak KZ. A tight bound for EMAC. In: Vol 4052. Springer; 2006:168-179. doi:10.1007/11787006_15' apa: 'Pietrzak, K. Z. (2006). A tight bound for EMAC (Vol. 4052, pp. 168–179). Presented at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/11787006_15' chicago: Pietrzak, Krzysztof Z. “A Tight Bound for EMAC,” 4052:168–79. Springer, 2006. https://doi.org/10.1007/11787006_15. ieee: 'K. Z. Pietrzak, “A tight bound for EMAC,” presented at the ICALP: Automata, Languages and Programming, 2006, vol. 4052, pp. 168–179.' ista: 'Pietrzak KZ. 2006. A tight bound for EMAC. ICALP: Automata, Languages and Programming, LNCS, vol. 4052, 168–179.' mla: Pietrzak, Krzysztof Z. A Tight Bound for EMAC. Vol. 4052, Springer, 2006, pp. 168–79, doi:10.1007/11787006_15. short: K.Z. Pietrzak, in:, Springer, 2006, pp. 168–179. conference: name: 'ICALP: Automata, Languages and Programming' date_created: 2018-12-11T12:02:04Z date_published: 2006-07-28T00:00:00Z date_updated: 2021-01-12T07:41:52Z day: '28' doi: 10.1007/11787006_15 extern: 1 intvolume: ' 4052' month: '07' page: 168 - 179 publication_status: published publisher: Springer publist_id: '3463' quality_controlled: 0 status: public title: A tight bound for EMAC type: conference volume: 4052 year: '2006' ... --- _id: '3522' abstract: - lang: eng text: We observed sharp wave/ripples (SWR) during exploration within brief (< 2.4 s) interruptions of or during theta oscillations. CA1 network responses of SWRs occurring during exploration (eSWR) and SWRs detected in waking immobility or sleep were similar. However, neuronal activity during eSWR was location dependent, and eSWR-related firing was stronger inside the place field than outside. The eSPW-related firing increase was stronger than the baseline increase inside compared to outside, suggesting a “supralinear” summation of eSWR and place-selective inputs. Pairs of cells with similar place fields and/or correlated firing during exploration showed stronger coactivation during eSWRs and subsequent sleep-SWRs. Sequential activation of place cells was not required for the reactivation of waking co-firing patterns; cell pairs with symmetrical cross-correlations still showed reactivated waking co-firing patterns during sleep-SWRs. We suggest that place-selective firing during eSWRs facilitates initial associations between cells with similar place fields that enable place-related ensemble patterns to recur during subsequent sleep-SWRs. author: - first_name: Joseph full_name: Joseph O'Neill id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - first_name: Timothy full_name: Senior,Timothy last_name: Senior - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: O’Neill J, Senior T, Csicsvari JL. Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior. Neuron. 2006;49(1):143-155. doi:10.1016/j.neuron.2005.10.037 apa: O’Neill, J., Senior, T., & Csicsvari, J. L. (2006). Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2005.10.037 chicago: O’Neill, Joseph, Timothy Senior, and Jozsef L Csicsvari. “Place-Selective Firing of CA1 Pyramidal Cells during Sharp Wave/Ripple Network Patterns in Exploratory Behavior.” Neuron. Elsevier, 2006. https://doi.org/10.1016/j.neuron.2005.10.037. ieee: J. O’Neill, T. Senior, and J. L. Csicsvari, “Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior,” Neuron, vol. 49, no. 1. Elsevier, pp. 143–155, 2006. ista: O’Neill J, Senior T, Csicsvari JL. 2006. Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior. Neuron. 49(1), 143–155. mla: O’Neill, Joseph, et al. “Place-Selective Firing of CA1 Pyramidal Cells during Sharp Wave/Ripple Network Patterns in Exploratory Behavior.” Neuron, vol. 49, no. 1, Elsevier, 2006, pp. 143–55, doi:10.1016/j.neuron.2005.10.037. short: J. O’Neill, T. Senior, J.L. Csicsvari, Neuron 49 (2006) 143–155. date_created: 2018-12-11T12:03:46Z date_published: 2006-01-05T00:00:00Z date_updated: 2021-01-12T07:44:03Z day: '05' doi: 10.1016/j.neuron.2005.10.037 extern: 1 intvolume: ' 49' issue: '1' month: '01' page: 143 - 155 publication: Neuron publication_status: published publisher: Elsevier publist_id: '2863' quality_controlled: 0 status: public title: Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior type: journal_article volume: 49 year: '2006' ... --- _id: '3607' abstract: - lang: eng text: We apply new analytical methods to understand the consequences of population bottlenecks for expected additive genetic variance. We analyze essentially all models for multilocus epistasis that have been numerically simulated to demonstrate increased additive variance. We conclude that for biologically plausible models, large increases in expected additive variance–attributable to epistasis rather than dominance–are unlikely. Naciri-Graven and Goudet (2003) found that as the number of epistatically interacting loci increases, additive variance tends to be inflated more after a bottleneck. We argue that this result reflects biologically unrealistic aspects of their models. Specifically, as the number of loci increases, higher-order epistatic interactions become increasingly important in these models, with an increasing fraction of the genetic variance becoming nonadditive, contrary to empirical observations. As shown by Barton and Turelli (2004), without dominance, conversion of nonadditive to additive variance depends only on the variance components and not on the number of loci per se. Numerical results indicating that more inbreeding is needed to produce maximal release of additive variance with more loci follow directly from our analytical results, which show that high levels of inbreeding (F > 0.5) are needed for significant conversion of higher-order components. We discuss alternative approaches to modeling multilocus epistasis and understanding its consequences. author: - first_name: Michael full_name: Turelli, Michael last_name: Turelli - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Turelli M, Barton NH. Will population bottlenecks and multilocus epistasis increase additive genetic variance? Evolution; International Journal of Organic Evolution. 2006;60(9):1763-1776. doi:10.1111/j.0014-3820.2006.tb00521.x apa: Turelli, M., & Barton, N. H. (2006). Will population bottlenecks and multilocus epistasis increase additive genetic variance? Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2006.tb00521.x chicago: Turelli, Michael, and Nicholas H Barton. “Will Population Bottlenecks and Multilocus Epistasis Increase Additive Genetic Variance?” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.0014-3820.2006.tb00521.x. ieee: M. Turelli and N. H. Barton, “Will population bottlenecks and multilocus epistasis increase additive genetic variance?,” Evolution; International Journal of Organic Evolution, vol. 60, no. 9. Wiley-Blackwell, pp. 1763–1776, 2006. ista: Turelli M, Barton NH. 2006. Will population bottlenecks and multilocus epistasis increase additive genetic variance? Evolution; International Journal of Organic Evolution. 60(9), 1763–1776. mla: Turelli, Michael, and Nicholas H. Barton. “Will Population Bottlenecks and Multilocus Epistasis Increase Additive Genetic Variance?” Evolution; International Journal of Organic Evolution, vol. 60, no. 9, Wiley-Blackwell, 2006, pp. 1763–76, doi:10.1111/j.0014-3820.2006.tb00521.x. short: M. Turelli, N.H. Barton, Evolution; International Journal of Organic Evolution 60 (2006) 1763–1776. date_created: 2018-12-11T12:04:13Z date_published: 2006-09-01T00:00:00Z date_updated: 2021-01-12T07:44:37Z day: '01' doi: 10.1111/j.0014-3820.2006.tb00521.x extern: 1 intvolume: ' 60' issue: '9' month: '09' page: 1763 - 1776 publication: Evolution; International Journal of Organic Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '2776' quality_controlled: 0 status: public title: Will population bottlenecks and multilocus epistasis increase additive genetic variance? type: journal_article volume: 60 year: '2006' ...