[{"title":"Lifetime of turbulence in pipe flow","page":"556 - 558","_id":"2794","conference":{"name":"EETC11: European Turbulence Conference"},"publisher":"Springer","day":"01","status":"public","month":"06","author":[{"full_name":"Björn Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tax","first_name":"Wilco","full_name":"Tax, Wilco"},{"last_name":"Westerweel","full_name":"Westerweel, Jerry","first_name":"Jerry"}],"year":"2007","doi":"10.1007/978-3-540-72604-3_177","extern":1,"quality_controlled":0,"publist_id":"4095","type":"conference","alternative_title":["Springer Proceedings in Physics"],"date_published":"2007-06-01T00:00:00Z","date_updated":"2021-01-12T06:59:45Z","volume":117,"citation":{"chicago":"Hof, Björn, Wilco Tax, and Jerry Westerweel. “Lifetime of Turbulence in Pipe Flow,” 117:556–58. Springer, 2007. <a href=\"https://doi.org/10.1007/978-3-540-72604-3_177\">https://doi.org/10.1007/978-3-540-72604-3_177</a>.","short":"B. Hof, W. Tax, J. Westerweel, in:, Springer, 2007, pp. 556–558.","mla":"Hof, Björn, et al. <i>Lifetime of Turbulence in Pipe Flow</i>. Vol. 117, Springer, 2007, pp. 556–58, doi:<a href=\"https://doi.org/10.1007/978-3-540-72604-3_177\">10.1007/978-3-540-72604-3_177</a>.","apa":"Hof, B., Tax, W., &#38; Westerweel, J. (2007). Lifetime of turbulence in pipe flow (Vol. 117, pp. 556–558). Presented at the EETC11: European Turbulence Conference, Springer. <a href=\"https://doi.org/10.1007/978-3-540-72604-3_177\">https://doi.org/10.1007/978-3-540-72604-3_177</a>","ama":"Hof B, Tax W, Westerweel J. Lifetime of turbulence in pipe flow. In: Vol 117. Springer; 2007:556-558. doi:<a href=\"https://doi.org/10.1007/978-3-540-72604-3_177\">10.1007/978-3-540-72604-3_177</a>","ista":"Hof B, Tax W, Westerweel J. 2007. Lifetime of turbulence in pipe flow. EETC11: European Turbulence Conference, Springer Proceedings in Physics, vol. 117, 556–558.","ieee":"B. Hof, W. Tax, and J. Westerweel, “Lifetime of turbulence in pipe flow,” presented at the EETC11: European Turbulence Conference, 2007, vol. 117, pp. 556–558."},"date_created":"2018-12-11T11:59:38Z","intvolume":"       117","publication_status":"published"},{"type":"journal_article","date_published":"2007-01-01T00:00:00Z","date_updated":"2021-01-12T07:00:31Z","date_created":"2018-12-11T12:00:11Z","citation":{"ama":"Carneiro J, Leon K, Caramalho Í, et al. When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells. <i>Immunological Reviews</i>. 2007;216(1):48-68. doi:<a href=\"https://doi.org/10.1111/j.1600-065X.2007.00487.x\">10.1111/j.1600-065X.2007.00487.x</a>","ista":"Carneiro J, Leon K, Caramalho Í, Van Den Dool C, Gardner R, Oliveira V, Bergman M, Sepúlveda N, Paixao T, Faro J, Demengeot J. 2007. When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells. Immunological Reviews. 216(1), 48–68.","ieee":"J. Carneiro <i>et al.</i>, “When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells,” <i>Immunological Reviews</i>, vol. 216, no. 1. Wiley-Blackwell, pp. 48–68, 2007.","chicago":"Carneiro, Jorge, Kalet Leon, Íris Caramalho, Carline Van Den Dool, Rui Gardner, Vanessa Oliveira, Marie Bergman, et al. “When Three Is Not a Crowd a Crossregulation Model of the Dynamics and Repertoire Selection of Regulatory CD4 T Cells.” <i>Immunological Reviews</i>. Wiley-Blackwell, 2007. <a href=\"https://doi.org/10.1111/j.1600-065X.2007.00487.x\">https://doi.org/10.1111/j.1600-065X.2007.00487.x</a>.","short":"J. Carneiro, K. Leon, Í. Caramalho, C. Van Den Dool, R. Gardner, V. Oliveira, M. Bergman, N. Sepúlveda, T. Paixao, J. Faro, J. Demengeot, Immunological Reviews 216 (2007) 48–68.","mla":"Carneiro, Jorge, et al. “When Three Is Not a Crowd a Crossregulation Model of the Dynamics and Repertoire Selection of Regulatory CD4 T Cells.” <i>Immunological Reviews</i>, vol. 216, no. 1, Wiley-Blackwell, 2007, pp. 48–68, doi:<a href=\"https://doi.org/10.1111/j.1600-065X.2007.00487.x\">10.1111/j.1600-065X.2007.00487.x</a>.","apa":"Carneiro, J., Leon, K., Caramalho, Í., Van Den Dool, C., Gardner, R., Oliveira, V., … Demengeot, J. (2007). When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells. <i>Immunological Reviews</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1600-065X.2007.00487.x\">https://doi.org/10.1111/j.1600-065X.2007.00487.x</a>"},"volume":216,"intvolume":"       216","publication_status":"published","publication":"Immunological Reviews","year":"2007","doi":"10.1111/j.1600-065X.2007.00487.x","extern":1,"abstract":[{"text":"Summary: Regulatory CD4+ T cells, enriched in the CD25 pool of healthy individuals, mediate natural tolerance and prevent autoimmune diseases. Despite their fundamental and potential clinical significance, regulatory T (TR) cells have not yet been incorporated in a coherent theory of the immune system. This article reviews experimental evidence and theoretical arguments supporting a model of TR cell dynamics, uncovering some of its most relevant biological implications. According to this model, the persistence and expansion of TR cell populations depend strictly on specific interactions they make with antigen-presenting cells (APCs) and conventional effector T (TE) cells. This three-partner crossregulation imposes that TR cells feed on the specific autoimmune activities they suppress, with implications ranging from their interactions with other cells to their repertoire selection in the periphery and in the thymus, and to the relationship between these cells and the innate immune system. These implications stem from the basic prediction that the peripheral dynamics sort the CD4+ T-cell repertoire into two subsets: a less diverse set of small clones of autoreactive effector and regulatory cells that regulate each other’s growth, and a more diverse set of barely autoreactive TE cell clones, whose expansion is limited only by APC availability. It is argued that such partitioning of the repertoire sets the ground for self–non-self discrimination. ","lang":"eng"}],"quality_controlled":0,"publist_id":"3865","day":"01","status":"public","issue":"1","month":"01","author":[{"last_name":"Carneiro","full_name":"Carneiro, Jorge","first_name":"Jorge"},{"full_name":"Leon, Kalet","first_name":"Kalet","last_name":"Leon"},{"last_name":"Caramalho","first_name":"Íris","full_name":"Caramalho, Íris"},{"last_name":"Van Den Dool","full_name":"Van Den Dool, Carline","first_name":"Carline"},{"last_name":"Gardner","first_name":"Rui","full_name":"Gardner, Rui"},{"full_name":"Oliveira, Vanessa","first_name":"Vanessa","last_name":"Oliveira"},{"first_name":"Marie","full_name":"Bergman, Marie L","last_name":"Bergman"},{"first_name":"Nuno","full_name":"Sepúlveda, Nuno","last_name":"Sepúlveda"},{"first_name":"Tiago","full_name":"Tiago Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","last_name":"Paixao"},{"first_name":"Jose","full_name":"Faro, Jose","last_name":"Faro"},{"last_name":"Demengeot","first_name":"Jocelyne","full_name":"Demengeot, Jocelyne"}],"title":"When three is not a crowd a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4 T cells","_id":"2893","page":"48 - 68","publisher":"Wiley-Blackwell"},{"month":"01","author":[{"first_name":"Tiago","full_name":"Tiago Paixao","orcid":"0000-0003-2361-3953","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Carvalho","full_name":"Carvalho, Tiago P","first_name":"Tiago"},{"last_name":"Calado","full_name":"Calado, Dinis P","first_name":"Dinis"},{"last_name":"Carneiro","full_name":"Carneiro, Jorge","first_name":"Jorge"}],"day":"01","issue":"4","status":"public","title":"Quantitative insights into stochastic monoallelic expression of cytokine genes","publisher":"Nature Publishing Group","page":"315 - 322","_id":"2896","volume":85,"citation":{"apa":"Paixao, T., Carvalho, T., Calado, D., &#38; Carneiro, J. (2007). Quantitative insights into stochastic monoallelic expression of cytokine genes. <i>Immunology and Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/sj.icb.7100057\">https://doi.org/10.1038/sj.icb.7100057</a>","mla":"Paixao, Tiago, et al. “Quantitative Insights into Stochastic Monoallelic Expression of Cytokine Genes.” <i>Immunology and Cell Biology</i>, vol. 85, no. 4, Nature Publishing Group, 2007, pp. 315–22, doi:<a href=\"https://doi.org/10.1038/sj.icb.7100057\">10.1038/sj.icb.7100057</a>.","short":"T. Paixao, T. Carvalho, D. Calado, J. Carneiro, Immunology and Cell Biology 85 (2007) 315–322.","chicago":"Paixao, Tiago, Tiago Carvalho, Dinis Calado, and Jorge Carneiro. “Quantitative Insights into Stochastic Monoallelic Expression of Cytokine Genes.” <i>Immunology and Cell Biology</i>. Nature Publishing Group, 2007. <a href=\"https://doi.org/10.1038/sj.icb.7100057\">https://doi.org/10.1038/sj.icb.7100057</a>.","ieee":"T. Paixao, T. Carvalho, D. Calado, and J. Carneiro, “Quantitative insights into stochastic monoallelic expression of cytokine genes,” <i>Immunology and Cell Biology</i>, vol. 85, no. 4. Nature Publishing Group, pp. 315–322, 2007.","ista":"Paixao T, Carvalho T, Calado D, Carneiro J. 2007. Quantitative insights into stochastic monoallelic expression of cytokine genes. Immunology and Cell Biology. 85(4), 315–322.","ama":"Paixao T, Carvalho T, Calado D, Carneiro J. Quantitative insights into stochastic monoallelic expression of cytokine genes. <i>Immunology and Cell Biology</i>. 2007;85(4):315-322. doi:<a href=\"https://doi.org/10.1038/sj.icb.7100057\">10.1038/sj.icb.7100057</a>"},"date_created":"2018-12-11T12:00:12Z","date_updated":"2021-01-12T07:00:32Z","date_published":"2007-01-01T00:00:00Z","publication_status":"published","intvolume":"        85","acknowledgement":"Calado and Paixão acknowledge the financial support of Fundação para a Ciência e a Tecnologia (fellowships SFRH/BD/2973/2000 and SFRH/BD/10550/2002, respectively).","type":"journal_article","doi":"10.1038/sj.icb.7100057","publist_id":"3862","abstract":[{"text":"Gene expression from both parental alleles is beneficial by masking the effects of deleterious recessive mutations and by reducing the noise in gene expression in diploid organisms. However, a class of genes are expressed preferentially or strictly from a single allele. The selective advantage of avoiding biallelic expression is clear for allelic-excluded antigen receptor and odorant receptor genes, genes undergoing X-chromosome inactivation in females and parental genomic imprinted genes. In contrast, there is no clear biological rationale for the predominant and stochastic monoallelic expression of cytokine genes in the immune system, and the underlying mechanism is elusive and controversial. A clarification of the mechanism of predominant monoallelic expression would be instrumental in better understanding its eventual biological functional. This prompted the development of a quantitative framework that could describe the dynamics of the pattern of allele expression of the IL-10 gene, from which general quantitative insights could be gained. We report that the experimental observations on these patterns of allelic expression cannot be easily reconciled with a simple model of stochastic transcriptional activation, in which the two alleles are, at any time, equally competent for transcription. Instead, these observations call into action a general model of eukaryotic transcriptional regulation according to which the locus competence for transcription is dynamic, involving multiple, cooperative and stochastic modification steps. In this model, the probability that an allele becomes transcriptionally active is a function of the number of chromatin modifications that it accumulated. On the basis of the properties of this model, we argue that predominant monoallelic expression might have had no adaptive role, and may have evolved under indirect selection for low frequency of expressing cells.","lang":"eng"}],"quality_controlled":0,"extern":1,"publication":"Immunology and Cell Biology","year":"2007"},{"year":"2007","quality_controlled":0,"publist_id":"3803","extern":1,"type":"conference","date_created":"2018-12-11T12:00:25Z","citation":{"ama":"Kumar MP, Kolmogorov V, Torr P. An Analysis of Convex Relaxations for MAP Estimation. In: Neural Information Processing Systems; 2007.","ista":"Kumar MP, Kolmogorov V, Torr P. 2007. An Analysis of Convex Relaxations for MAP Estimation. Neural Information Processing Systems.","ieee":"M. P. Kumar, V. Kolmogorov, and P. Torr, “An Analysis of Convex Relaxations for MAP Estimation,” presented at the Neural Information Processing Systems, 2007.","chicago":"Kumar, M Pawan, Vladimir Kolmogorov, and Philip Torr. “An Analysis of Convex Relaxations for MAP Estimation.” Neural Information Processing Systems, 2007.","short":"M.P. Kumar, V. Kolmogorov, P. Torr, in:, Neural Information Processing Systems, 2007.","mla":"Kumar, M. Pawan, et al. <i>An Analysis of Convex Relaxations for MAP Estimation</i>. Neural Information Processing Systems, 2007.","apa":"Kumar, M. P., Kolmogorov, V., &#38; Torr, P. (2007). An Analysis of Convex Relaxations for MAP Estimation. Presented at the Neural Information Processing Systems, Neural Information Processing Systems."},"date_updated":"2021-01-12T07:39:52Z","date_published":"2007-12-01T00:00:00Z","publication_status":"published","title":"An Analysis of Convex Relaxations for MAP Estimation","conference":{"name":"Neural Information Processing Systems"},"publisher":"Neural Information Processing Systems","_id":"2933","day":"01","status":"public","month":"12","author":[{"full_name":"Kumar, M Pawan","first_name":"M Pawan","last_name":"Kumar"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Vladimir Kolmogorov"},{"full_name":"Torr, Philip H","first_name":"Philip","last_name":"Torr"}]},{"month":"01","author":[{"full_name":"Blakeslee, Joshua","first_name":"Joshua","last_name":"Blakeslee"},{"last_name":"Bandyopadhyay","full_name":"Bandyopadhyay, Anindita","first_name":"Anindita"},{"full_name":"Ok, Ran Lee","first_name":"Ran","last_name":"Ok"},{"last_name":"Mravec","full_name":"Mravec, Jozef","first_name":"Jozef"},{"last_name":"Titapiwatanakun","full_name":"Titapiwatanakun, Boosaree","first_name":"Boosaree"},{"full_name":"Sauer, Michael","first_name":"Michael","last_name":"Sauer"},{"last_name":"Makam","first_name":"Srinivas","full_name":"Makam, Srinivas N"},{"full_name":"Cheng, Yan","first_name":"Yan","last_name":"Cheng"},{"full_name":"Bouchard, Rodolphe","first_name":"Rodolphe","last_name":"Bouchard"},{"full_name":"Adamec, Jiří","first_name":"Jiří","last_name":"Adamec"},{"last_name":"Geisler","full_name":"Geisler, Markus","first_name":"Markus"},{"full_name":"Nagashima, Akitomo","first_name":"Akitomo","last_name":"Nagashima"},{"full_name":"Sakai, Tatsuya","first_name":"Tatsuya","last_name":"Sakai"},{"full_name":"Martinoia, Enrico","first_name":"Enrico","last_name":"Martinoia"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml"},{"last_name":"Peer","first_name":"Wendy","full_name":"Peer, Wendy A"},{"full_name":"Murphy, Angus S","first_name":"Angus","last_name":"Murphy"}],"day":"01","status":"public","issue":"1","title":"Interactions among PIN FORMED and P glycoprotein auxin transporters in Arabidopsis","page":"131 - 147","_id":"3019","publisher":"American Society of Plant Biologists","date_updated":"2021-01-12T07:40:29Z","date_published":"2007-01-01T00:00:00Z","volume":19,"citation":{"ama":"Blakeslee J, Bandyopadhyay A, Ok R, et al. Interactions among PIN FORMED and P glycoprotein auxin transporters in Arabidopsis. <i>Plant Cell</i>. 2007;19(1):131-147. doi:<a href=\"https://doi.org/10.1105/tpc.106.040782\">10.1105/tpc.106.040782</a>","ista":"Blakeslee J, Bandyopadhyay A, Ok R, Mravec J, Titapiwatanakun B, Sauer M, Makam S, Cheng Y, Bouchard R, Adamec J, Geisler M, Nagashima A, Sakai T, Martinoia E, Friml J, Peer W, Murphy A. 2007. Interactions among PIN FORMED and P glycoprotein auxin transporters in Arabidopsis. Plant Cell. 19(1), 131–147.","ieee":"J. Blakeslee <i>et al.</i>, “Interactions among PIN FORMED and P glycoprotein auxin transporters in Arabidopsis,” <i>Plant Cell</i>, vol. 19, no. 1. American Society of Plant Biologists, pp. 131–147, 2007.","chicago":"Blakeslee, Joshua, Anindita Bandyopadhyay, Ran Ok, Jozef Mravec, Boosaree Titapiwatanakun, Michael Sauer, Srinivas Makam, et al. “Interactions among PIN FORMED and P Glycoprotein Auxin Transporters in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2007. <a href=\"https://doi.org/10.1105/tpc.106.040782\">https://doi.org/10.1105/tpc.106.040782</a>.","short":"J. Blakeslee, A. Bandyopadhyay, R. Ok, J. Mravec, B. Titapiwatanakun, M. Sauer, S. Makam, Y. Cheng, R. Bouchard, J. Adamec, M. Geisler, A. Nagashima, T. Sakai, E. Martinoia, J. Friml, W. Peer, A. Murphy, Plant Cell 19 (2007) 131–147.","mla":"Blakeslee, Joshua, et al. “Interactions among PIN FORMED and P Glycoprotein Auxin Transporters in Arabidopsis.” <i>Plant Cell</i>, vol. 19, no. 1, American Society of Plant Biologists, 2007, pp. 131–47, doi:<a href=\"https://doi.org/10.1105/tpc.106.040782\">10.1105/tpc.106.040782</a>.","apa":"Blakeslee, J., Bandyopadhyay, A., Ok, R., Mravec, J., Titapiwatanakun, B., Sauer, M., … Murphy, A. (2007). Interactions among PIN FORMED and P glycoprotein auxin transporters in Arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.106.040782\">https://doi.org/10.1105/tpc.106.040782</a>"},"date_created":"2018-12-11T12:00:54Z","intvolume":"        19","publication_status":"published","type":"journal_article","doi":"10.1105/tpc.106.040782","extern":1,"abstract":[{"lang":"eng","text":"\nDirectional transport of the phytohormone auxin is established primarily at the point of cellular afflux and is required for the establishment and maintenance of plant polarity. Studies in whole plants and heterologous systems indicate that PIN-FORMED (PIN) and P-glycoprotein (PGP) transport proteins mediate the cellular efflux of natural and synthetic auxins. However, aromatic anion transport resulting from PGP and PIN expression in nonplant systems was also found to lack tha high level of substrate specificity seen in planta. Furthermore, previous reports that PGP19 stabilizes PIN1 on the plasma membrane suggested that PIN-PGP interactions might regulate polar auxin efflux. Hare, we show that PGP1 and PGP19 colocalized with PIN1 in the shoot apax in Arabidopsis thaliana and with PIN1 and PIN2 in root tissues. Specific PGP-PIN interactions were seen in yeast two-hybrid and colmmunoprecipitation assays. PIN-PGP interactions appeared to enhance transport activity and, to a greater extent, substrate/inhibitor specificities when coexpressed in heterologous systems. By contrast, no interactions between PGPs and the AUXIN1 influx carrier were observed. Phenotypes of pin and pgp mutants suggest discrete functional roles in auxin transport, but pin pgp mutants exhibited phenotypes that are both additive and synergistic. These results suggest that PINs and PGPs characterize coordinated, Independent auxin transport mechanisms but also function interactively in a tissue-specific manner."}],"publist_id":"3682","quality_controlled":0,"publication":"Plant Cell","year":"2007"},{"title":"Interactions of PIN and PGP auxin transport mechanisms","conference":{"name":"Intercellular Signalling in Plants"},"publisher":"Portland Press","_id":"3021","page":"137 - 141","day":"01","issue":"1","status":"public","month":"02","author":[{"last_name":"Bandyopadhyay","full_name":"Bandyopadhyay, Anindita","first_name":"Anindita"},{"last_name":"Blakeslee","first_name":"Joshua","full_name":"Blakeslee, Joshua"},{"last_name":"Lee","first_name":"Ok","full_name":"Lee, Ok Ran"},{"last_name":"Mravec","full_name":"Mravec, Jozef","first_name":"Jozef"},{"last_name":"Sauer","first_name":"Michael","full_name":"Sauer, Michael"},{"last_name":"Titapiwatanakun","first_name":"Boosaree","full_name":"Titapiwatanakun, Boosaree"},{"last_name":"Makam","first_name":"Srinivas","full_name":"Makam, Srinivas N"},{"first_name":"Rodolphe","full_name":"Bouchard, Rodolphe","last_name":"Bouchard"},{"full_name":"Geisler, Markus","first_name":"Markus","last_name":"Geisler"},{"last_name":"Martinoia","full_name":"Martinoia, Enrico","first_name":"Enrico"},{"first_name":"Jirí","full_name":"Jirí Friml","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Peer, Wendy A","first_name":"Wendy","last_name":"Peer"},{"last_name":"Murphy","first_name":"Angus","full_name":"Murphy, Angus S"}],"year":"2007","doi":"10.1042/BST0350137","quality_controlled":0,"publist_id":"3681","abstract":[{"lang":"eng","text":"Polarized transport of the plant hormone auxin influences multiple growth processes in plants and is regulated by plasma-membrane-localized efflux and uptake carriers. The PGP (P-glycoprotein) ABC transporters (ATP-binding-cassette transporters), PIN (pin-formed) subfamily of major facilitator proteins and members of AUX/LAX families have been shown to independently transport auxin both in planta and in heterologous systems. However, PIN- and PGP-mediated transport in heterologous systems exhibits decreased substrate specificity and inhibitor-sensitivity compared with what is seen in plants and plant cells. To determine whether PIN-PGP interactions enhance transport specificity, we analysed interactions of the representative auxin-transporting PGPs with PIN1 and AUX1 in planta and in heterologous systems. Here, we provide evidence that PINs and PGPs interact and function both independently and co-ordinately to control polar auxin transport and impart transport specificity and directionality. These interactions take place in protein complexes stabilized by PGPs in detergent-resistant microdomains."}],"extern":1,"alternative_title":["Biochemical Society Transactions"],"type":"conference","date_created":"2018-12-11T12:00:54Z","volume":35,"citation":{"short":"A. Bandyopadhyay, J. Blakeslee, O. Lee, J. Mravec, M. Sauer, B. Titapiwatanakun, S. Makam, R. Bouchard, M. Geisler, E. Martinoia, J. Friml, W. Peer, A. Murphy, in:, Portland Press, 2007, pp. 137–141.","chicago":"Bandyopadhyay, Anindita, Joshua Blakeslee, Ok Lee, Jozef Mravec, Michael Sauer, Boosaree Titapiwatanakun, Srinivas Makam, et al. “Interactions of PIN and PGP Auxin Transport Mechanisms,” 35:137–41. Portland Press, 2007. <a href=\"https://doi.org/10.1042/BST0350137\">https://doi.org/10.1042/BST0350137</a>.","apa":"Bandyopadhyay, A., Blakeslee, J., Lee, O., Mravec, J., Sauer, M., Titapiwatanakun, B., … Murphy, A. (2007). Interactions of PIN and PGP auxin transport mechanisms (Vol. 35, pp. 137–141). Presented at the Intercellular Signalling in Plants, Portland Press. <a href=\"https://doi.org/10.1042/BST0350137\">https://doi.org/10.1042/BST0350137</a>","mla":"Bandyopadhyay, Anindita, et al. <i>Interactions of PIN and PGP Auxin Transport Mechanisms</i>. Vol. 35, no. 1, Portland Press, 2007, pp. 137–41, doi:<a href=\"https://doi.org/10.1042/BST0350137\">10.1042/BST0350137</a>.","ista":"Bandyopadhyay A, Blakeslee J, Lee O, Mravec J, Sauer M, Titapiwatanakun B, Makam S, Bouchard R, Geisler M, Martinoia E, Friml J, Peer W, Murphy A. 2007. Interactions of PIN and PGP auxin transport mechanisms. Intercellular Signalling in Plants, Biochemical Society Transactions, vol. 35, 137–141.","ama":"Bandyopadhyay A, Blakeslee J, Lee O, et al. Interactions of PIN and PGP auxin transport mechanisms. In: Vol 35. Portland Press; 2007:137-141. doi:<a href=\"https://doi.org/10.1042/BST0350137\">10.1042/BST0350137</a>","ieee":"A. Bandyopadhyay <i>et al.</i>, “Interactions of PIN and PGP auxin transport mechanisms,” presented at the Intercellular Signalling in Plants, 2007, vol. 35, no. 1, pp. 137–141."},"date_updated":"2021-01-12T07:40:30Z","date_published":"2007-02-01T00:00:00Z","publication_status":"published","intvolume":"        35"},{"publisher":"Cell Press","page":"520 - 527","_id":"3022","title":"Clathrin-mediated constitutive endocytosis of PIN auxin efflux carriers in Arabidopsis","issue":"6","status":"public","day":"24","author":[{"first_name":"Pankaj","full_name":"Dhonukshe, Pankaj","last_name":"Dhonukshe"},{"full_name":"Aniento, Fernando","first_name":"Fernando","last_name":"Aniento"},{"last_name":"Hwang","first_name":"Inhwan","full_name":"Hwang, Inhwan"},{"last_name":"Robinson","first_name":"David","full_name":"Robinson, David G"},{"last_name":"Mravec","first_name":"Jozef","full_name":"Mravec, Jozef"},{"first_name":"York","full_name":"Stierhof, York-Dieter","last_name":"Stierhof"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","first_name":"Jirí"}],"month":"03","year":"2007","publication":"Current Biology","abstract":[{"lang":"eng","text":"Endocytosis is an essential process by which eukaryotic cells internalize exogenous material or regulate signaling at the cell surface [1]. Different endocytic pathways are well established in yeast and animals; prominent among them is clathrin-dependent endocytosis [2, 3]. In plants, endocytosis is poorly defined, and no molecular mechanism for cargo internalization has been demonstrated so far [4, 5], although the internalization of receptor-ligand complexes at the plant plasma membrane has recently been shown [6]. Here we demonstrate by means of a green-to-red photoconvertible fluorescent reporter, EosFP [7], the constitutive endocytosis of PIN auxin efflux carriers [8] and their recycling to the plasma membrane. Using a plant clathrin-specific antibody, we show the presence of clathrin at different stages of coated-vesicle formation at the plasma membrane in Arabidopsis. Genetic interference with clathrin function inhibits PIN internalization and endocytosis in general. Furthermore, pharmacological interference with cargo recruitment into the clathrin pathway blocks internalization of PINs and other plasma-membrane proteins. Our data demonstrate that clathrin-dependent endocytosis is operational in plants and constitutes the predominant pathway for the internalization of numerous plasma-membrane-resident proteins including PIN auxin efflux carriers."}],"quality_controlled":0,"publist_id":"3680","extern":1,"doi":"10.1016/j.cub.2007.01.052","type":"journal_article","publication_status":"published","intvolume":"        17","volume":17,"date_created":"2018-12-11T12:00:55Z","citation":{"short":"P. Dhonukshe, F. Aniento, I. Hwang, D. Robinson, J. Mravec, Y. Stierhof, J. Friml, Current Biology 17 (2007) 520–527.","chicago":"Dhonukshe, Pankaj, Fernando Aniento, Inhwan Hwang, David Robinson, Jozef Mravec, York Stierhof, and Jiří Friml. “Clathrin-Mediated Constitutive Endocytosis of PIN Auxin Efflux Carriers in Arabidopsis.” <i>Current Biology</i>. Cell Press, 2007. <a href=\"https://doi.org/10.1016/j.cub.2007.01.052\">https://doi.org/10.1016/j.cub.2007.01.052</a>.","apa":"Dhonukshe, P., Aniento, F., Hwang, I., Robinson, D., Mravec, J., Stierhof, Y., &#38; Friml, J. (2007). Clathrin-mediated constitutive endocytosis of PIN auxin efflux carriers in Arabidopsis. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2007.01.052\">https://doi.org/10.1016/j.cub.2007.01.052</a>","mla":"Dhonukshe, Pankaj, et al. “Clathrin-Mediated Constitutive Endocytosis of PIN Auxin Efflux Carriers in Arabidopsis.” <i>Current Biology</i>, vol. 17, no. 6, Cell Press, 2007, pp. 520–27, doi:<a href=\"https://doi.org/10.1016/j.cub.2007.01.052\">10.1016/j.cub.2007.01.052</a>.","ista":"Dhonukshe P, Aniento F, Hwang I, Robinson D, Mravec J, Stierhof Y, Friml J. 2007. Clathrin-mediated constitutive endocytosis of PIN auxin efflux carriers in Arabidopsis. Current Biology. 17(6), 520–527.","ama":"Dhonukshe P, Aniento F, Hwang I, et al. Clathrin-mediated constitutive endocytosis of PIN auxin efflux carriers in Arabidopsis. <i>Current Biology</i>. 2007;17(6):520-527. doi:<a href=\"https://doi.org/10.1016/j.cub.2007.01.052\">10.1016/j.cub.2007.01.052</a>","ieee":"P. Dhonukshe <i>et al.</i>, “Clathrin-mediated constitutive endocytosis of PIN auxin efflux carriers in Arabidopsis,” <i>Current Biology</i>, vol. 17, no. 6. Cell Press, pp. 520–527, 2007."},"date_updated":"2021-01-12T07:40:31Z","date_published":"2007-03-24T00:00:00Z"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Pankaj","full_name":"Dhonukshe, Pankaj","last_name":"Dhonukshe"},{"full_name":"Šamaj, Jozef","first_name":"Jozef","last_name":"Šamaj"},{"full_name":"Baluška, František","first_name":"František","last_name":"Baluška"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí"}],"month":"04","issue":"4","status":"public","day":"01","oa_version":"None","publisher":"Wiley-Blackwell","_id":"3023","page":"371 - 381","title":"A unifying new model of cytokinesis for the dividing plant and animal cells","publication_status":"published","intvolume":"        29","date_created":"2018-12-11T12:00:55Z","volume":29,"citation":{"ieee":"P. Dhonukshe, J. Šamaj, F. Baluška, and J. Friml, “A unifying new model of cytokinesis for the dividing plant and animal cells,” <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>, vol. 29, no. 4. Wiley-Blackwell, pp. 371–381, 2007.","ama":"Dhonukshe P, Šamaj J, Baluška F, Friml J. A unifying new model of cytokinesis for the dividing plant and animal cells. <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>. 2007;29(4):371-381. doi:<a href=\"https://doi.org/10.1002/bies.20559\">10.1002/bies.20559</a>","ista":"Dhonukshe P, Šamaj J, Baluška F, Friml J. 2007. A unifying new model of cytokinesis for the dividing plant and animal cells. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 29(4), 371–381.","mla":"Dhonukshe, Pankaj, et al. “A Unifying New Model of Cytokinesis for the Dividing Plant and Animal Cells.” <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>, vol. 29, no. 4, Wiley-Blackwell, 2007, pp. 371–81, doi:<a href=\"https://doi.org/10.1002/bies.20559\">10.1002/bies.20559</a>.","apa":"Dhonukshe, P., Šamaj, J., Baluška, F., &#38; Friml, J. (2007). A unifying new model of cytokinesis for the dividing plant and animal cells. <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/bies.20559\">https://doi.org/10.1002/bies.20559</a>","chicago":"Dhonukshe, Pankaj, Jozef Šamaj, František Baluška, and Jiří Friml. “A Unifying New Model of Cytokinesis for the Dividing Plant and Animal Cells.” <i>Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology</i>. Wiley-Blackwell, 2007. <a href=\"https://doi.org/10.1002/bies.20559\">https://doi.org/10.1002/bies.20559</a>.","short":"P. Dhonukshe, J. Šamaj, F. Baluška, J. Friml, Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology 29 (2007) 371–381."},"date_published":"2007-04-01T00:00:00Z","date_updated":"2021-01-12T07:40:31Z","external_id":{"pmid":["    17373659"]},"type":"journal_article","publist_id":"3678","quality_controlled":"1","abstract":[{"text":"Cytokinesis ensures proper partitioning of the nucleocytoplasmic contents into two daughter cells. It has generally been thought that cytokinesis is accomplished differently in animals and plants because of the differences in the preparatory phases, into the centrosomal or acentrosomal nature of the process, the presence or absence of rigid cell walls, and on the basis of ‘outside‐in’ or ‘inside‐out’ mechanism. However, this long‐standing paradigm needs further reevaluation based on new findings. Recent advances reveal that plant cells, similarly to animal cells, possess astral microtubules that regulate the cell division plane. Furthermore, endocytosis has been found to be important for cytokinesis in animal and plant cells: vesicles containing endocytosed cargo provide material for the cell plate formation in plants and for closure of the midbody channel in animals. Thus, although the preparatory phases of the cell division process differ between plant and animal cells, the later phases show similarities. We unify these findings in a model that suggests a conserved mode of cytokinesis.","lang":"eng"}],"language":[{"iso":"eng"}],"extern":"1","doi":"10.1002/bies.20559","year":"2007","publication":"Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology","pmid":1},{"oa_version":"None","title":"Molecular and cellular aspects of auxin-transport-mediated development","page":"160 - 168","_id":"3024","publisher":"Cell Press","month":"04","author":[{"last_name":"Vieten","first_name":"Anne","full_name":"Vieten, Anne"},{"last_name":"Sauer","full_name":"Sauer, Michael","first_name":"Michael"},{"last_name":"Brewer","first_name":"Philip","full_name":"Brewer, Philip"},{"full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","status":"public","issue":"4","doi":"10.1016/j.tplants.2007.03.006","language":[{"iso":"eng"}],"extern":"1","publist_id":"3679","quality_controlled":"1","abstract":[{"lang":"eng","text":"The plant hormone auxin is frequently observed to be asymmetrically distributed across adjacent cells during crucial stages of growth and development. These auxin gradients depend on polar transport and regulate a wide variety of processes, including embryogenesis, organogenesis, vascular tissue differentiation, root meristem maintenance and tropic growth. Auxin can mediate such a perplexing array of developmental processes by acting as a general trigger for the change in developmental program in cells where it accumulates and by providing vectorial information to the tissues by its polar intercellular flow. In recent years, a wealth of molecular data on the mechanism of auxin transport and its regulation has been generated, providing significant insights into the action of this versatile coordinative signal."}],"pmid":1,"publication":"Trends in Plant Science","year":"2007","date_updated":"2021-01-12T07:40:31Z","date_published":"2007-04-01T00:00:00Z","volume":12,"date_created":"2018-12-11T12:00:55Z","citation":{"ieee":"A. Vieten, M. Sauer, P. Brewer, and J. Friml, “Molecular and cellular aspects of auxin-transport-mediated development,” <i>Trends in Plant Science</i>, vol. 12, no. 4. Cell Press, pp. 160–168, 2007.","ista":"Vieten A, Sauer M, Brewer P, Friml J. 2007. Molecular and cellular aspects of auxin-transport-mediated development. Trends in Plant Science. 12(4), 160–168.","ama":"Vieten A, Sauer M, Brewer P, Friml J. Molecular and cellular aspects of auxin-transport-mediated development. <i>Trends in Plant Science</i>. 2007;12(4):160-168. doi:<a href=\"https://doi.org/10.1016/j.tplants.2007.03.006\">10.1016/j.tplants.2007.03.006</a>","apa":"Vieten, A., Sauer, M., Brewer, P., &#38; Friml, J. (2007). Molecular and cellular aspects of auxin-transport-mediated development. <i>Trends in Plant Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tplants.2007.03.006\">https://doi.org/10.1016/j.tplants.2007.03.006</a>","mla":"Vieten, Anne, et al. “Molecular and Cellular Aspects of Auxin-Transport-Mediated Development.” <i>Trends in Plant Science</i>, vol. 12, no. 4, Cell Press, 2007, pp. 160–68, doi:<a href=\"https://doi.org/10.1016/j.tplants.2007.03.006\">10.1016/j.tplants.2007.03.006</a>.","short":"A. Vieten, M. Sauer, P. Brewer, J. Friml, Trends in Plant Science 12 (2007) 160–168.","chicago":"Vieten, Anne, Michael Sauer, Philip Brewer, and Jiří Friml. “Molecular and Cellular Aspects of Auxin-Transport-Mediated Development.” <i>Trends in Plant Science</i>. Cell Press, 2007. <a href=\"https://doi.org/10.1016/j.tplants.2007.03.006\">https://doi.org/10.1016/j.tplants.2007.03.006</a>."},"intvolume":"        12","publication_status":"published","type":"journal_article","external_id":{"pmid":["    17369077"]}},{"publication":"Plant Cell","year":"2007","doi":"10.1105/tpc.107.052126","abstract":[{"lang":"eng","text":"In plants, each developmental process integrates a network of signaling events that are regulated by different phytohormones, and interactions among hormonal pathways are essential to modulate their effect. Continuous growth of roots results from the postembryonic activity of cells within the root meristem that is controlled by the coordinated action of several phytohormones, including auxin and ethylene. Although their interaction has been studied intensively, the molecular and cellular mechanisms underlying this interplay are unknown. We show that the effect of ethylene on root growth is largely mediated by the regulation of the auxin biosynthesis and transport-dependent local auxin distribution. Ethylene stimulates auxin biosynthesis and basipetal auxin transport toward the elongation zone, where it activates a local auxin response leading to inhibition of cell elongation. Consistently, in mutants affected in auxin perception or basipetal auxin transport, ethylene cannot activate the auxin response nor regulate the root growth. In addition, ethylene modulates the transcription of several components of the auxin transport machinery. Thus, ethylene achieves a local activation of the auxin signaling pathway and regulates root growth by both stimulating the auxin biosynthesis and by modulating the auxin transport machinery."}],"quality_controlled":0,"publist_id":"3676","extern":1,"type":"journal_article","date_created":"2018-12-11T12:00:56Z","volume":19,"citation":{"chicago":"Růžička, Kamil, Karin Ljung, Steffen Vanneste, Radka Podhorská, Tom Beeckman, Jiří Friml, and Eva Benková. “Ethylene Regulates Root Growth through Effects on Auxin Biosynthesis and Transport Dependent Auxin Distribution.” <i>Plant Cell</i>. American Society of Plant Biologists, 2007. <a href=\"https://doi.org/10.1105/tpc.107.052126\">https://doi.org/10.1105/tpc.107.052126</a>.","short":"K. Růžička, K. Ljung, S. Vanneste, R. Podhorská, T. Beeckman, J. Friml, E. Benková, Plant Cell 19 (2007) 2197–2212.","mla":"Růžička, Kamil, et al. “Ethylene Regulates Root Growth through Effects on Auxin Biosynthesis and Transport Dependent Auxin Distribution.” <i>Plant Cell</i>, vol. 19, no. 7, American Society of Plant Biologists, 2007, pp. 2197–212, doi:<a href=\"https://doi.org/10.1105/tpc.107.052126\">10.1105/tpc.107.052126</a>.","apa":"Růžička, K., Ljung, K., Vanneste, S., Podhorská, R., Beeckman, T., Friml, J., &#38; Benková, E. (2007). Ethylene regulates root growth through effects on auxin biosynthesis and transport dependent auxin distribution. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.107.052126\">https://doi.org/10.1105/tpc.107.052126</a>","ama":"Růžička K, Ljung K, Vanneste S, et al. Ethylene regulates root growth through effects on auxin biosynthesis and transport dependent auxin distribution. <i>Plant Cell</i>. 2007;19(7):2197-2212. doi:<a href=\"https://doi.org/10.1105/tpc.107.052126\">10.1105/tpc.107.052126</a>","ista":"Růžička K, Ljung K, Vanneste S, Podhorská R, Beeckman T, Friml J, Benková E. 2007. Ethylene regulates root growth through effects on auxin biosynthesis and transport dependent auxin distribution. Plant Cell. 19(7), 2197–2212.","ieee":"K. Růžička <i>et al.</i>, “Ethylene regulates root growth through effects on auxin biosynthesis and transport dependent auxin distribution,” <i>Plant Cell</i>, vol. 19, no. 7. American Society of Plant Biologists, pp. 2197–2212, 2007."},"date_published":"2007-07-01T00:00:00Z","date_updated":"2021-01-12T07:40:32Z","publication_status":"published","intvolume":"        19","title":"Ethylene regulates root growth through effects on auxin biosynthesis and transport dependent auxin distribution","publisher":"American Society of Plant Biologists","page":"2197 - 2212","_id":"3026","day":"01","issue":"7","status":"public","month":"07","author":[{"last_name":"Růžička","first_name":"Kamil","full_name":"Růžička, Kamil"},{"last_name":"Ljung","first_name":"Karin","full_name":"Ljung, Karin"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"last_name":"Podhorská","first_name":"Radka","full_name":"Podhorská, Radka"},{"first_name":"Tom","full_name":"Beeckman, Tom","last_name":"Beeckman"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","first_name":"Jirí"},{"first_name":"Eva","full_name":"Eva Benková","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}]},{"issue":"4","status":"public","day":"01","author":[{"last_name":"Malenica","full_name":"Malenica, Nenad","first_name":"Nenad"},{"last_name":"Abas","first_name":"Lindy","full_name":"Abas, Lindy"},{"last_name":"Benjamins","full_name":"Benjamins, René","first_name":"René"},{"first_name":"Saeko","full_name":"Kitakura, Saeko","last_name":"Kitakura"},{"first_name":"Harald","full_name":"Sigmund, Harald F","last_name":"Sigmund"},{"full_name":"Jun, Kim S","first_name":"Kim","last_name":"Jun"},{"first_name":"Marie","full_name":"Hauser, Marie-Theres","last_name":"Hauser"},{"full_name":"Jirí Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"full_name":"Luschnig, Christian","first_name":"Christian","last_name":"Luschnig"}],"month":"08","publisher":"Wiley-Blackwell","_id":"3027","page":"537 - 550","title":"MODULATOR of PIN genes control steady state levels of Arabidopsis PIN proteins","type":"journal_article","publication_status":"published","intvolume":"        51","volume":51,"date_created":"2018-12-11T12:00:56Z","citation":{"ista":"Malenica N, Abas L, Benjamins R, Kitakura S, Sigmund H, Jun K, Hauser M, Friml J, Luschnig C. 2007. MODULATOR of PIN genes control steady state levels of Arabidopsis PIN proteins. Plant Journal. 51(4), 537–550.","ama":"Malenica N, Abas L, Benjamins R, et al. MODULATOR of PIN genes control steady state levels of Arabidopsis PIN proteins. <i>Plant Journal</i>. 2007;51(4):537-550. doi:<a href=\"https://doi.org/10.1111/j.1365-313X.2007.03158.x\">10.1111/j.1365-313X.2007.03158.x</a>","ieee":"N. Malenica <i>et al.</i>, “MODULATOR of PIN genes control steady state levels of Arabidopsis PIN proteins,” <i>Plant Journal</i>, vol. 51, no. 4. Wiley-Blackwell, pp. 537–550, 2007.","short":"N. Malenica, L. Abas, R. Benjamins, S. Kitakura, H. Sigmund, K. Jun, M. Hauser, J. Friml, C. Luschnig, Plant Journal 51 (2007) 537–550.","chicago":"Malenica, Nenad, Lindy Abas, René Benjamins, Saeko Kitakura, Harald Sigmund, Kim Jun, Marie Hauser, Jiří Friml, and Christian Luschnig. “MODULATOR of PIN Genes Control Steady State Levels of Arabidopsis PIN Proteins.” <i>Plant Journal</i>. Wiley-Blackwell, 2007. <a href=\"https://doi.org/10.1111/j.1365-313X.2007.03158.x\">https://doi.org/10.1111/j.1365-313X.2007.03158.x</a>.","apa":"Malenica, N., Abas, L., Benjamins, R., Kitakura, S., Sigmund, H., Jun, K., … Luschnig, C. (2007). MODULATOR of PIN genes control steady state levels of Arabidopsis PIN proteins. <i>Plant Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-313X.2007.03158.x\">https://doi.org/10.1111/j.1365-313X.2007.03158.x</a>","mla":"Malenica, Nenad, et al. “MODULATOR of PIN Genes Control Steady State Levels of Arabidopsis PIN Proteins.” <i>Plant Journal</i>, vol. 51, no. 4, Wiley-Blackwell, 2007, pp. 537–50, doi:<a href=\"https://doi.org/10.1111/j.1365-313X.2007.03158.x\">10.1111/j.1365-313X.2007.03158.x</a>."},"date_updated":"2021-01-12T07:40:32Z","date_published":"2007-08-01T00:00:00Z","year":"2007","publication":"Plant Journal","publist_id":"3675","quality_controlled":0,"abstract":[{"lang":"eng","text":"Polar transport of the phytohormone auxin controls numerous growth responses in plants. Molecular characterization of auxin transport in Arabidopsis thaliana has provided important insights into the mechanisms underlying the regulation of auxin distribution. In particular, the control of subcellular localization and expression of PIN-type auxin efflux components appears to be fundamental for orchestrated distribution of the growth regulator throughout the entire plant body. Here we describe the identification of two Arabidopsis loci, MOP2 and MOP3 (for MODULATOR OF PIN), that are involved in control of the steady-state levels of PIN protein. Mutations in both loci result in defects in auxin distribution and polar auxin transport, and cause phenotypes consistent with a reduction of PIN protein levels. Genetic interaction between PIN2 and both MOP loci is suggestive of functional cross-talk, which is further substantiated by findings demonstrating that ectopic PIN up-regulation is compensated in the mop background. Thus, in addition to pathways that control PIN localization and transcription, MOP2 and MOP3 appear to be involved in fine-tuning of auxin distribution via post-transcriptional regulation of PIN expression."}],"extern":1,"doi":"10.1111/j.1365-313X.2007.03158.x"},{"extern":1,"publist_id":"3674","abstract":[{"text":"In plants, cell polarity and tissue patterning are connected by intercellular flow of the phytohormone auxin, whose directional signaling depends on polar subcellular localization of PIN auxin transport proteins. The mechanism of polar targeting of PINs or other cargos in plants is largely unidentified, with the PINOID kinase being the only known molecular component. Here, we identify PP2A phosphatase as an important regulator of PIN apical-basal targeting and auxin distribution. Genetic analysis, localization, and phosphorylation studies demonstrate that PP2A and PINOID both partially colocalize with PINs and act antagonistically on the phosphorylation state of their central hydrophilic loop, hence mediating PIN apical-basal polar targeting. Thus, in plants, polar sorting by the reversible phosphorylation of cargos allows for their conditional delivery to specific intracellular destinations. In the case of PIN proteins, this mechanism enables switches in the direction of intercellular auxin fluxes, which mediate differential growth, tissue patterning, and organogenesis.","lang":"eng"}],"quality_controlled":0,"doi":"10.1016/j.cell.2007.07.033","year":"2007","publication":"Cell","intvolume":"       130","publication_status":"published","date_published":"2007-09-21T00:00:00Z","date_updated":"2021-01-12T07:40:33Z","date_created":"2018-12-11T12:00:57Z","volume":130,"citation":{"mla":"Michniewicz, Marta, et al. “Antagonistic Regulation of PIN Phosphorylation by PP2A and PINOID Directs Auxin Flux.” <i>Cell</i>, vol. 130, no. 6, Cell Press, 2007, pp. 1044–56, doi:<a href=\"https://doi.org/10.1016/j.cell.2007.07.033\">10.1016/j.cell.2007.07.033</a>.","apa":"Michniewicz, M., Zago, M., Abas, L., Weijers, D., Schweighofer, A., Meskiene, I., … Friml, J. (2007). Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2007.07.033\">https://doi.org/10.1016/j.cell.2007.07.033</a>","chicago":"Michniewicz, Marta, Marcelo Zago, Lindy Abas, Dolf Weijers, Alois Schweighofer, Irute Meskiene, Marcus Heisler, et al. “Antagonistic Regulation of PIN Phosphorylation by PP2A and PINOID Directs Auxin Flux.” <i>Cell</i>. Cell Press, 2007. <a href=\"https://doi.org/10.1016/j.cell.2007.07.033\">https://doi.org/10.1016/j.cell.2007.07.033</a>.","short":"M. Michniewicz, M. Zago, L. Abas, D. Weijers, A. Schweighofer, I. Meskiene, M. Heisler, C. Ohno, J. Zhang, F. Huang, R. Schwab, D. Weigel, E. Meyerowitz, C. Luschnig, R. Offringa, J. Friml, Cell 130 (2007) 1044–1056.","ieee":"M. Michniewicz <i>et al.</i>, “Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux,” <i>Cell</i>, vol. 130, no. 6. Cell Press, pp. 1044–1056, 2007.","ama":"Michniewicz M, Zago M, Abas L, et al. Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux. <i>Cell</i>. 2007;130(6):1044-1056. doi:<a href=\"https://doi.org/10.1016/j.cell.2007.07.033\">10.1016/j.cell.2007.07.033</a>","ista":"Michniewicz M, Zago M, Abas L, Weijers D, Schweighofer A, Meskiene I, Heisler M, Ohno C, Zhang J, Huang F, Schwab R, Weigel D, Meyerowitz E, Luschnig C, Offringa R, Friml J. 2007. Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux. Cell. 130(6), 1044–1056."},"type":"journal_article","_id":"3028","page":"1044 - 1056","publisher":"Cell Press","title":"Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux","author":[{"first_name":"Marta","full_name":"Michniewicz, Marta","last_name":"Michniewicz"},{"last_name":"Zago","full_name":"Zago, Marcelo K","first_name":"Marcelo"},{"last_name":"Abas","full_name":"Abas, Lindy","first_name":"Lindy"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"full_name":"Schweighofer, Alois","first_name":"Alois","last_name":"Schweighofer"},{"last_name":"Meskiene","first_name":"Irute","full_name":"Meskiene, Irute"},{"last_name":"Heisler","first_name":"Marcus","full_name":"Heisler, Marcus G"},{"first_name":"Carolyn","full_name":"Ohno, Carolyn","last_name":"Ohno"},{"last_name":"Zhang","full_name":"Zhang, Jing","first_name":"Jing"},{"first_name":"Fang","full_name":"Huang, Fang","last_name":"Huang"},{"full_name":"Schwab, Rebecca","first_name":"Rebecca","last_name":"Schwab"},{"full_name":"Weigel, Detlef","first_name":"Detlef","last_name":"Weigel"},{"full_name":"Meyerowitz, Elliot M","first_name":"Elliot","last_name":"Meyerowitz"},{"last_name":"Luschnig","first_name":"Christian","full_name":"Luschnig, Christian"},{"last_name":"Offringa","full_name":"Offringa, Remko","first_name":"Remko"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml"}],"month":"09","status":"public","issue":"6","day":"21"},{"type":"journal_article","intvolume":"        19","publication_status":"published","date_updated":"2021-01-12T07:40:33Z","date_published":"2007-12-01T00:00:00Z","date_created":"2018-12-11T12:00:57Z","citation":{"apa":"Laplaze, L., Benková, E., Casimiro, I., Maes, L., Vanneste, S., Swarup, R., … Bennett, M. (2007). Cytokinins act directly on lateral root founder cells to inhibit root initiation. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.107.055863\">https://doi.org/10.1105/tpc.107.055863</a>","mla":"Laplaze, Laurent, et al. “Cytokinins Act Directly on Lateral Root Founder Cells to Inhibit Root Initiation.” <i>Plant Cell</i>, vol. 19, no. 12, American Society of Plant Biologists, 2007, pp. 3889–900, doi:<a href=\"https://doi.org/10.1105/tpc.107.055863\">10.1105/tpc.107.055863</a>.","short":"L. Laplaze, E. Benková, I. Casimiro, L. Maes, S. Vanneste, R. Swarup, D. Weijers, V. Calvo, B. Parizot, M. Herrera Rodriguez, R. Offringa, N. Graham, P. Doumas, J. Friml, D. Bogusz, T. Beeckman, M. Bennett, Plant Cell 19 (2007) 3889–3900.","chicago":"Laplaze, Laurent, Eva Benková, Ilda Casimiro, Lies Maes, Steffen Vanneste, Ranjan Swarup, Dolf Weijers, et al. “Cytokinins Act Directly on Lateral Root Founder Cells to Inhibit Root Initiation.” <i>Plant Cell</i>. American Society of Plant Biologists, 2007. <a href=\"https://doi.org/10.1105/tpc.107.055863\">https://doi.org/10.1105/tpc.107.055863</a>.","ieee":"L. Laplaze <i>et al.</i>, “Cytokinins act directly on lateral root founder cells to inhibit root initiation,” <i>Plant Cell</i>, vol. 19, no. 12. American Society of Plant Biologists, pp. 3889–3900, 2007.","ista":"Laplaze L, Benková E, Casimiro I, Maes L, Vanneste S, Swarup R, Weijers D, Calvo V, Parizot B, Herrera Rodriguez M, Offringa R, Graham N, Doumas P, Friml J, Bogusz D, Beeckman T, Bennett M. 2007. Cytokinins act directly on lateral root founder cells to inhibit root initiation. Plant Cell. 19(12), 3889–3900.","ama":"Laplaze L, Benková E, Casimiro I, et al. Cytokinins act directly on lateral root founder cells to inhibit root initiation. <i>Plant Cell</i>. 2007;19(12):3889-3900. doi:<a href=\"https://doi.org/10.1105/tpc.107.055863\">10.1105/tpc.107.055863</a>"},"volume":19,"year":"2007","publication":"Plant Cell","extern":1,"quality_controlled":0,"abstract":[{"text":"In Arabidopsis thaliana, lateral roots are formed from root pericycle cells adjacent to the xylem poles. Lateral root development is regulated antagonistically by the plant hormones auxin and cytokinin. While a great deal is known about how auxin promotes lateral root development, the mechanism of cytokinin repression is still unclear. Elevating cytokinin levels was observed to disrupt lateral root initiation and the regular pattern of divisions that characterizes lateral root development in Arabidopsis. To identify the stage of lateral root development that is sensitive to cytokinins, we targeted the expression of the Agrobacterium tumefaciens cytokinin biosynthesis enzyme isopentenyltransferase to either xylem-pole pericycle cells or young lateral root primordia using GAL4-GFP enhancer trap lines. Transactivation experiments revealed that xylem-pole pericycle cells are sensitive to cytokinins, whereas young lateral root primordia are not. This effect is physiologically significant because transactivation of the Arabidopsis cytokinin degrading enzyme cytokinin oxidase 1 in lateral root founder cells results in increased lateral root formation. We observed that cytokinins perturb the expression of PIN genes in lateral root founder cells and prevent the formation of an auxin gradient that is required to pattern lateral root primordia.","lang":"eng"}],"publist_id":"3673","doi":"10.1105/tpc.107.055863","status":"public","issue":"12","day":"01","author":[{"last_name":"Laplaze","first_name":"Laurent","full_name":"Laplaze, Laurent"},{"full_name":"Eva Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739"},{"last_name":"Casimiro","first_name":"Ilda","full_name":"Casimiro, Ilda"},{"first_name":"Lies","full_name":"Maes, Lies","last_name":"Maes"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"first_name":"Ranjan","full_name":"Swarup, Ranjan","last_name":"Swarup"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"},{"last_name":"Calvo","full_name":"Calvo, Vanessa","first_name":"Vanessa"},{"full_name":"Parizot, Boris","first_name":"Boris","last_name":"Parizot"},{"first_name":"Maria","full_name":"Herrera-Rodriguez, Maria Begoña","last_name":"Herrera Rodriguez"},{"last_name":"Offringa","first_name":"Remko","full_name":"Offringa, Remko"},{"last_name":"Graham","first_name":"Neil","full_name":"Graham, Neil"},{"first_name":"Patrick","full_name":"Doumas, Patrick","last_name":"Doumas"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml"},{"last_name":"Bogusz","full_name":"Bogusz, Didier","first_name":"Didier"},{"first_name":"Tom","full_name":"Beeckman, Tom","last_name":"Beeckman"},{"last_name":"Bennett","first_name":"Malcolm","full_name":"Bennett, Malcolm"}],"month":"12","page":"3889 - 3900","_id":"3029","publisher":"American Society of Plant Biologists","title":"Cytokinins act directly on lateral root founder cells to inhibit root initiation"},{"title":"ETS transcription factor Erm controls subsynaptic gene expression in skeletal muscles","page":"726 - 740","_id":"3144","publisher":"Elsevier","day":"06","status":"public","issue":"5","month":"09","author":[{"full_name":"Simon Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roland","full_name":"Huber, Roland M","last_name":"Huber"},{"first_name":"David","full_name":"Ladle, David R","last_name":"Ladle"},{"last_name":"Murphy","first_name":"Kenneth","full_name":"Murphy, Kenneth"},{"first_name":"Silvia","full_name":"Arber, Silvia","last_name":"Arber"}],"publication":"Neuron","year":"2007","doi":"10.1016/j.neuron.2007.07.028","extern":1,"quality_controlled":0,"abstract":[{"lang":"eng","text":"Accumulation of specific proteins at synaptic structures is essential for synapse assembly and function, but mechanisms regulating local protein enrichment remain poorly understood. At the neuromuscular junction (NMJ), subsynaptic nuclei underlie motor axon terminals within extrafusal muscle fibers and are transcriptionally distinct from neighboring nuclei. In this study, we show that expression of the ETS transcription factor Erm is highly concentrated at subsynaptic nuclei, and its mutation in mice leads to severe downregulation of many genes with normally enriched subsynaptic expression. Erm mutant mice display an expansion of the muscle central domain in which acetylcholine receptor (AChR) clusters accumulate, show gradual fragmentation of AChR clusters, and exhibit symptoms of muscle weakness mimicking congenital myasthenic syndrome (CMS). Together, our findings define Erm as an upstream regulator of a transcriptional program selective to subsynaptic nuclei at the NMJ and underscore the importance of transcriptional control of local synaptic protein accumulation."}],"publist_id":"3551","type":"journal_article","date_updated":"2021-01-12T07:41:22Z","date_published":"2007-09-06T00:00:00Z","citation":{"ista":"Hippenmeyer S, Huber R, Ladle D, Murphy K, Arber S. 2007. ETS transcription factor Erm controls subsynaptic gene expression in skeletal muscles. Neuron. 55(5), 726–740.","ama":"Hippenmeyer S, Huber R, Ladle D, Murphy K, Arber S. ETS transcription factor Erm controls subsynaptic gene expression in skeletal muscles. <i>Neuron</i>. 2007;55(5):726-740. doi:<a href=\"https://doi.org/10.1016/j.neuron.2007.07.028\">10.1016/j.neuron.2007.07.028</a>","ieee":"S. Hippenmeyer, R. Huber, D. Ladle, K. Murphy, and S. Arber, “ETS transcription factor Erm controls subsynaptic gene expression in skeletal muscles,” <i>Neuron</i>, vol. 55, no. 5. Elsevier, pp. 726–740, 2007.","short":"S. Hippenmeyer, R. Huber, D. Ladle, K. Murphy, S. Arber, Neuron 55 (2007) 726–740.","chicago":"Hippenmeyer, Simon, Roland Huber, David Ladle, Kenneth Murphy, and Silvia Arber. “ETS Transcription Factor Erm Controls Subsynaptic Gene Expression in Skeletal Muscles.” <i>Neuron</i>. Elsevier, 2007. <a href=\"https://doi.org/10.1016/j.neuron.2007.07.028\">https://doi.org/10.1016/j.neuron.2007.07.028</a>.","apa":"Hippenmeyer, S., Huber, R., Ladle, D., Murphy, K., &#38; Arber, S. (2007). ETS transcription factor Erm controls subsynaptic gene expression in skeletal muscles. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2007.07.028\">https://doi.org/10.1016/j.neuron.2007.07.028</a>","mla":"Hippenmeyer, Simon, et al. “ETS Transcription Factor Erm Controls Subsynaptic Gene Expression in Skeletal Muscles.” <i>Neuron</i>, vol. 55, no. 5, Elsevier, 2007, pp. 726–40, doi:<a href=\"https://doi.org/10.1016/j.neuron.2007.07.028\">10.1016/j.neuron.2007.07.028</a>."},"date_created":"2018-12-11T12:01:39Z","volume":55,"intvolume":"        55","publication_status":"published"},{"main_file_link":[{"open_access":"0","url":"http://research.microsoft.com/pubs/67417/criminisi_isrr2005.pdf"}],"publisher":"Springer","page":"295 - 304","_id":"3187","title":"Fusion of stereo colour and contrast","author":[{"first_name":"Andrew","full_name":"Blake, Andrew","last_name":"Blake"},{"last_name":"Criminisi","first_name":"Antonio","full_name":"Criminisi, Antonio"},{"last_name":"Cross","first_name":"Geoffrey","full_name":"Cross, Geoffrey"},{"first_name":"Vladimir","full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"},{"last_name":"Rother","first_name":"Carsten","full_name":"Rother, Carsten"}],"month":"02","status":"public","day":"05","abstract":[{"text":"Stereo vision has numerous applications in robotics, graphics, inspection and other areas. A prime application, one which has driven work on stereo in our laboratory, is teleconferencing in which the use of a stereo webcam already makes possible various transformations of the video stream. These include digital camera control, insertion of virtual objects, background substitution, and eye-gaze correction [9, 8].","lang":"eng"}],"publist_id":"3492","quality_controlled":0,"extern":1,"doi":"10.1007/978-3-540-48113-3_27","year":"2007","publication":"Springer Tracts in Advanced Robotics","publication_status":"published","intvolume":"        28","date_created":"2018-12-11T12:01:54Z","citation":{"short":"A. Blake, A. Criminisi, G. Cross, V. Kolmogorov, C. Rother, Springer Tracts in Advanced Robotics 28 (2007) 295–304.","chicago":"Blake, Andrew, Antonio Criminisi, Geoffrey Cross, Vladimir Kolmogorov, and Carsten Rother. “Fusion of Stereo Colour and Contrast.” <i>Springer Tracts in Advanced Robotics</i>. Springer, 2007. <a href=\"https://doi.org/10.1007/978-3-540-48113-3_27\">https://doi.org/10.1007/978-3-540-48113-3_27</a>.","apa":"Blake, A., Criminisi, A., Cross, G., Kolmogorov, V., &#38; Rother, C. (2007). Fusion of stereo colour and contrast. <i>Springer Tracts in Advanced Robotics</i>. Springer. <a href=\"https://doi.org/10.1007/978-3-540-48113-3_27\">https://doi.org/10.1007/978-3-540-48113-3_27</a>","mla":"Blake, Andrew, et al. “Fusion of Stereo Colour and Contrast.” <i>Springer Tracts in Advanced Robotics</i>, vol. 28, Springer, 2007, pp. 295–304, doi:<a href=\"https://doi.org/10.1007/978-3-540-48113-3_27\">10.1007/978-3-540-48113-3_27</a>.","ista":"Blake A, Criminisi A, Cross G, Kolmogorov V, Rother C. 2007. Fusion of stereo colour and contrast. Springer Tracts in Advanced Robotics. 28, 295–304.","ama":"Blake A, Criminisi A, Cross G, Kolmogorov V, Rother C. Fusion of stereo colour and contrast. <i>Springer Tracts in Advanced Robotics</i>. 2007;28:295-304. doi:<a href=\"https://doi.org/10.1007/978-3-540-48113-3_27\">10.1007/978-3-540-48113-3_27</a>","ieee":"A. Blake, A. Criminisi, G. Cross, V. Kolmogorov, and C. Rother, “Fusion of stereo colour and contrast,” <i>Springer Tracts in Advanced Robotics</i>, vol. 28. Springer, pp. 295–304, 2007."},"volume":28,"date_updated":"2021-01-12T07:41:40Z","date_published":"2007-02-05T00:00:00Z","type":"journal_article"},{"status":"public","day":"26","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov","first_name":"Vladimir"},{"last_name":"Boykov","full_name":"Boykov, Yuri","first_name":"Yuri"},{"first_name":"Carsten","full_name":"Rother, Carsten","last_name":"Rother"}],"month":"12","conference":{"name":"ICCV: International Conference on Computer Vision"},"publisher":"IEEE","_id":"3191","title":"Applications of parametric maxflow in computer vision","main_file_link":[{"url":"http://research.microsoft.com/pubs/70474/iccv07-paramaxflow.pdf","open_access":"0"}],"type":"conference","publication_status":"published","citation":{"ista":"Kolmogorov V, Boykov Y, Rother C. 2007. Applications of parametric maxflow in computer vision. ICCV: International Conference on Computer Vision.","ama":"Kolmogorov V, Boykov Y, Rother C. Applications of parametric maxflow in computer vision. In: IEEE; 2007. doi:<a href=\"https://doi.org/10.1109/ICCV.2007.4408910\">10.1109/ICCV.2007.4408910</a>","ieee":"V. Kolmogorov, Y. Boykov, and C. Rother, “Applications of parametric maxflow in computer vision,” presented at the ICCV: International Conference on Computer Vision, 2007.","short":"V. Kolmogorov, Y. Boykov, C. Rother, in:, IEEE, 2007.","chicago":"Kolmogorov, Vladimir, Yuri Boykov, and Carsten Rother. “Applications of Parametric Maxflow in Computer Vision.” IEEE, 2007. <a href=\"https://doi.org/10.1109/ICCV.2007.4408910\">https://doi.org/10.1109/ICCV.2007.4408910</a>.","apa":"Kolmogorov, V., Boykov, Y., &#38; Rother, C. (2007). Applications of parametric maxflow in computer vision. Presented at the ICCV: International Conference on Computer Vision, IEEE. <a href=\"https://doi.org/10.1109/ICCV.2007.4408910\">https://doi.org/10.1109/ICCV.2007.4408910</a>","mla":"Kolmogorov, Vladimir, et al. <i>Applications of Parametric Maxflow in Computer Vision</i>. IEEE, 2007, doi:<a href=\"https://doi.org/10.1109/ICCV.2007.4408910\">10.1109/ICCV.2007.4408910</a>."},"date_created":"2018-12-11T12:01:55Z","date_published":"2007-12-26T00:00:00Z","date_updated":"2021-01-12T07:41:41Z","year":"2007","abstract":[{"lang":"eng","text":"The maximum flow algorithm for minimizing energy functions of binary variables has become a standard tool in computer vision. In many cases, unary costs of the energy depend linearly on parameter lambda. In this paper we study vision applications for which it is important to solve the maxflow problem for different lambda's. An example is a weighting between data and regularization terms in image segmentation or stereo: it is desirable to vary it both during training (to learn lambda from ground truth data) and testing (to select best lambda using high-knowledge constraints, e.g. user input). We review algorithmic aspects of this parametric maximum flow problem previously unknown in vision, such as the ability to compute all breakpoints of lambda and corresponding optimal configurations infinite time. These results allow, in particular, to minimize the ratio of some geometric functional, such as flux of a vector field over length (or area). Previously, such functional were tackled with shortest path techniques applicable only in 2D. We give theoretical improvements for &quot;PDE cuts&quot; [5]. We present experimental results for image segmentation, 3D reconstruction, and the cosegmentation problem."}],"quality_controlled":0,"publist_id":"3489","extern":1,"doi":"10.1109/ICCV.2007.4408910"},{"month":"07","author":[{"first_name":"Carsten","full_name":"Rother, Carsten","last_name":"Rother"},{"last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov","first_name":"Vladimir"},{"first_name":"Victor","full_name":"Lempitsky, Victor","last_name":"Lempitsky"},{"last_name":"Szummer","full_name":"Szummer, Martin","first_name":"Martin"}],"day":"16","status":"public","main_file_link":[{"open_access":"0","url":"http://www.robots.ox.ac.uk/~vilem/QPBOPI.pdf"}],"title":"Optimizing binary MRFs via extended roof duality","_id":"3192","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"publisher":"IEEE","date_published":"2007-07-16T00:00:00Z","date_updated":"2021-01-12T07:41:42Z","date_created":"2018-12-11T12:01:55Z","citation":{"chicago":"Rother, Carsten, Vladimir Kolmogorov, Victor Lempitsky, and Martin Szummer. “Optimizing Binary MRFs via Extended Roof Duality.” IEEE, 2007. <a href=\"https://doi.org/10.1109/CVPR.2007.383203\">https://doi.org/10.1109/CVPR.2007.383203</a>.","short":"C. Rother, V. Kolmogorov, V. Lempitsky, M. Szummer, in:, IEEE, 2007.","mla":"Rother, Carsten, et al. <i>Optimizing Binary MRFs via Extended Roof Duality</i>. IEEE, 2007, doi:<a href=\"https://doi.org/10.1109/CVPR.2007.383203\">10.1109/CVPR.2007.383203</a>.","apa":"Rother, C., Kolmogorov, V., Lempitsky, V., &#38; Szummer, M. (2007). Optimizing binary MRFs via extended roof duality. Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. <a href=\"https://doi.org/10.1109/CVPR.2007.383203\">https://doi.org/10.1109/CVPR.2007.383203</a>","ama":"Rother C, Kolmogorov V, Lempitsky V, Szummer M. Optimizing binary MRFs via extended roof duality. In: IEEE; 2007. doi:<a href=\"https://doi.org/10.1109/CVPR.2007.383203\">10.1109/CVPR.2007.383203</a>","ista":"Rother C, Kolmogorov V, Lempitsky V, Szummer M. 2007. Optimizing binary MRFs via extended roof duality. CVPR: Computer Vision and Pattern Recognition.","ieee":"C. Rother, V. Kolmogorov, V. Lempitsky, and M. Szummer, “Optimizing binary MRFs via extended roof duality,” presented at the CVPR: Computer Vision and Pattern Recognition, 2007."},"publication_status":"published","type":"conference","doi":"10.1109/CVPR.2007.383203","extern":1,"quality_controlled":0,"abstract":[{"text":"Many computer vision applications rely on the efficient optimization of challenging, so-called non-submodular, binary pairwise MRFs. A promising graph cut based approach for optimizing such MRFs known as &quot;roof duality&quot; was recently introduced into computer vision. We study two methods which extend this approach. First, we discuss an efficient implementation of the &quot;probing&quot; technique introduced recently by Boros et al. [5]. It simplifies the MRF while preserving the global optimum. Our code is 400-700 faster on some graphs than the implementation of [5]. Second, we present a new technique which takes an arbitrary input labeling and tries to improve its energy. We give theoretical characterizations of local minima of this procedure. We applied both techniques to many applications, including image segmentation, new view synthesis, superresolution, diagram recognition, parameter learning, texture restoration, and image deconvolution. For several applications we see that we are able to find the global minimum very efficiently, and considerably outperform the original roof duality approach. In comparison to existing techniques, such as graph cut, TRW, BP, ICM, and simulated annealing, we nearly always find a lower energy.","lang":"eng"}],"publist_id":"3490","year":"2007"},{"date_created":"2018-12-11T12:01:56Z","citation":{"ista":"Kolmogorov V, Rother C. 2007. Minimizing nonsubmodular functions with graph cuts - A review. IEEE Transactions on Pattern Analysis and Machine Intelligence. 29(7), 1274–1279.","ama":"Kolmogorov V, Rother C. Minimizing nonsubmodular functions with graph cuts - A review. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2007;29(7):1274-1279. doi:<a href=\"https://doi.org/10.1109/TPAMI.2007.1031\">10.1109/TPAMI.2007.1031</a>","ieee":"V. Kolmogorov and C. Rother, “Minimizing nonsubmodular functions with graph cuts - A review,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 29, no. 7. IEEE, pp. 1274–1279, 2007.","short":"V. Kolmogorov, C. Rother, IEEE Transactions on Pattern Analysis and Machine Intelligence 29 (2007) 1274–1279.","chicago":"Kolmogorov, Vladimir, and Carsten Rother. “Minimizing Nonsubmodular Functions with Graph Cuts - A Review.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2007. <a href=\"https://doi.org/10.1109/TPAMI.2007.1031\">https://doi.org/10.1109/TPAMI.2007.1031</a>.","apa":"Kolmogorov, V., &#38; Rother, C. (2007). Minimizing nonsubmodular functions with graph cuts - A review. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/TPAMI.2007.1031\">https://doi.org/10.1109/TPAMI.2007.1031</a>","mla":"Kolmogorov, Vladimir, and Carsten Rother. “Minimizing Nonsubmodular Functions with Graph Cuts - A Review.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 29, no. 7, IEEE, 2007, pp. 1274–79, doi:<a href=\"https://doi.org/10.1109/TPAMI.2007.1031\">10.1109/TPAMI.2007.1031</a>."},"volume":29,"date_updated":"2021-01-12T07:41:42Z","date_published":"2007-07-01T00:00:00Z","publication_status":"published","intvolume":"        29","type":"journal_article","doi":"10.1109/TPAMI.2007.1031","abstract":[{"lang":"eng","text":"Optimization techniques based on graph cuts have become a standard tool for many vision applications. These techniques allow to minimize efficiently certain energy functions corresponding to pairwise Markov Random Fields (MRFs). Currently, there is an accepted view within the computer vision community that graph cuts can only be used for optimizing a limited class of MRF energies (e.g., submodular functions). In this survey, we review some results that show that graph cuts can be applied to a much larger class of energy functions (in particular, nonsubmodular functions). While these results are well-known in the optimization community, to our knowledge they were not used in the context of computer vision and MRF optimization. We demonstrate the relevance of these results to vision on the problem of binary texture restoration. "}],"publist_id":"3491","quality_controlled":0,"extern":1,"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","year":"2007","month":"07","author":[{"full_name":"Vladimir Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"},{"full_name":"Rother, Carsten","first_name":"Carsten","last_name":"Rother"}],"day":"01","issue":"7","status":"public","title":"Minimizing nonsubmodular functions with graph cuts - A review","publisher":"IEEE","_id":"3193","page":"1274 - 1279"},{"_id":"3218","page":"23 - 33","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"publisher":"Springer","title":"Non-trivial black-box combiners for collision-resistant hash-functions don't exist","status":"public","day":"12","author":[{"first_name":"Krzysztof Z","full_name":"Krzysztof Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654"}],"month":"06","year":"2007","extern":1,"abstract":[{"text":"A (k, ℓ)-robust combiner for collision-resistant hash-functions is a construction which from ℓ hash-functions constructs a hash-function which is collision-resistant if at least k of the components are collision-resistant. One trivially gets a (k, ℓ)-robust combiner by concatenating the output of any ℓ - k + 1 of the components, unfortunately this is not very practical as the length of the output of the combiner is quite large. We show that this is unavoidable as no black-box (k, ℓ)-robust combiner whose output is significantly shorter than what can be achieved by concatenation exists. This answers a question of Boneh and Boyen (Crypto'06). ","lang":"eng"}],"publist_id":"3461","quality_controlled":0,"doi":"10.1007/978-3-540-72540-4_2","type":"conference","alternative_title":["LNCS"],"acknowledgement":"Supported by DIAMANT, the Dutch national mathematics cluster for discrete interactive and algorithmic algebra and number theory.","intvolume":"      4515","publication_status":"published","date_updated":"2021-01-12T07:41:52Z","date_published":"2007-06-12T00:00:00Z","volume":4515,"citation":{"ieee":"K. Z. Pietrzak, “Non-trivial black-box combiners for collision-resistant hash-functions don’t exist,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2007, vol. 4515, pp. 23–33.","ista":"Pietrzak KZ. 2007. Non-trivial black-box combiners for collision-resistant hash-functions don’t exist. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 4515, 23–33.","ama":"Pietrzak KZ. Non-trivial black-box combiners for collision-resistant hash-functions don’t exist. In: Vol 4515. Springer; 2007:23-33. doi:<a href=\"https://doi.org/10.1007/978-3-540-72540-4_2\">10.1007/978-3-540-72540-4_2</a>","apa":"Pietrzak, K. Z. (2007). Non-trivial black-box combiners for collision-resistant hash-functions don’t exist (Vol. 4515, pp. 23–33). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. <a href=\"https://doi.org/10.1007/978-3-540-72540-4_2\">https://doi.org/10.1007/978-3-540-72540-4_2</a>","mla":"Pietrzak, Krzysztof Z. <i>Non-Trivial Black-Box Combiners for Collision-Resistant Hash-Functions Don’t Exist</i>. Vol. 4515, Springer, 2007, pp. 23–33, doi:<a href=\"https://doi.org/10.1007/978-3-540-72540-4_2\">10.1007/978-3-540-72540-4_2</a>.","short":"K.Z. Pietrzak, in:, Springer, 2007, pp. 23–33.","chicago":"Pietrzak, Krzysztof Z. “Non-Trivial Black-Box Combiners for Collision-Resistant Hash-Functions Don’t Exist,” 4515:23–33. Springer, 2007. <a href=\"https://doi.org/10.1007/978-3-540-72540-4_2\">https://doi.org/10.1007/978-3-540-72540-4_2</a>."},"date_created":"2018-12-11T12:02:05Z"},{"doi":"10.1007/978-3-540-74143-5_8","extern":1,"quality_controlled":0,"abstract":[{"text":"Many aspects of cryptographic security proofs can be seen as the proof that a certain system (e.g. a block cipher) is indistinguishable from an ideal system (e.g. a random permutation), for different types of distinguishers. This paper presents a new generic approach to proving upper bounds on the information-theoretic distinguishing advantage (from an ideal system) for a combined system, assuming upper bounds of certain types for the component systems. For a general type of combination operation of systems, including the XOR of functions or the cascade of permutations, we prove two amplification theorems. The first is a product theorem, in the spirit of XOR-lemmas: The distinguishing advantage of the combination of two systems is at most twice the product of the individual distinguishing advantages. This bound is optimal. The second theorem states that the combination of systems is secure against some strong class of distinguishers, assuming only that the components are secure against some weaker class of distinguishers. A key technical tool of the paper is the proof of a tight two-way correspondence, previously only known to hold in one direction, between the distinguishing advantage of two systems and the probability of winning an appropriately defined game. © International Association for Cryptologic Research 2007.","lang":"eng"}],"publist_id":"3462","year":"2007","date_updated":"2021-01-12T07:41:53Z","date_published":"2007-10-03T00:00:00Z","citation":{"apa":"Maurer, U., Pietrzak, K. Z., &#38; Renner, R. (2007). Indistinguishability amplification (Vol. 4622, pp. 130–149). Presented at the CRYPTO: International Cryptology Conference, Springer. <a href=\"https://doi.org/10.1007/978-3-540-74143-5_8\">https://doi.org/10.1007/978-3-540-74143-5_8</a>","mla":"Maurer, Ueli, et al. <i>Indistinguishability Amplification</i>. Vol. 4622, Springer, 2007, pp. 130–49, doi:<a href=\"https://doi.org/10.1007/978-3-540-74143-5_8\">10.1007/978-3-540-74143-5_8</a>.","short":"U. Maurer, K.Z. Pietrzak, R. Renner, in:, Springer, 2007, pp. 130–149.","chicago":"Maurer, Ueli, Krzysztof Z Pietrzak, and Renato Renner. “Indistinguishability Amplification,” 4622:130–49. Springer, 2007. <a href=\"https://doi.org/10.1007/978-3-540-74143-5_8\">https://doi.org/10.1007/978-3-540-74143-5_8</a>.","ieee":"U. Maurer, K. Z. Pietrzak, and R. Renner, “Indistinguishability amplification,” presented at the CRYPTO: International Cryptology Conference, 2007, vol. 4622, pp. 130–149.","ista":"Maurer U, Pietrzak KZ, Renner R. 2007. Indistinguishability amplification. CRYPTO: International Cryptology Conference, LNCS, vol. 4622, 130–149.","ama":"Maurer U, Pietrzak KZ, Renner R. Indistinguishability amplification. In: Vol 4622. Springer; 2007:130-149. doi:<a href=\"https://doi.org/10.1007/978-3-540-74143-5_8\">10.1007/978-3-540-74143-5_8</a>"},"date_created":"2018-12-11T12:02:05Z","volume":4622,"intvolume":"      4622","publication_status":"published","type":"conference","alternative_title":["LNCS"],"title":"Indistinguishability amplification","page":"130 - 149","_id":"3219","publisher":"Springer","conference":{"name":"CRYPTO: International Cryptology Conference"},"month":"10","author":[{"last_name":"Maurer","full_name":"Maurer, Ueli M","first_name":"Ueli"},{"first_name":"Krzysztof Z","full_name":"Krzysztof Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654"},{"last_name":"Renner","full_name":"Renner, Renato","first_name":"Renato"}],"day":"03","status":"public"}]