[{"abstract":[{"text":"ACAP-type ARF GTPase activating proteins (ARF-GAPs) regulate multiple cellular processes, including endocytosis, secretion, phagocytosis, cell adhesion and cell migration. However, the regulation of ACAP functions by other cellular proteins is poorly understood. We have reported previously that a plant ACAP, VAN3, plays a pivotal role in plant venation continuity. Here, we report on newly identified VAN3 regulators: the CVP2 (cotyledon vascular pattern 2) 5 PTase, which is considered to degrade IP3 and also to produce PtdIns(4)P from PtdIns(4,5)P2; and a PH domain-containing protein, VAB (VAN3 binding protein). Combinational mutations of both CVP2 and its closest homologue CVL1 (CVP2 like 1) phenocopied the strong allele of van3 mutants, showing severe vascular continuity. The phenotype of double mutants between van3, cvp2 and vab suggested that VAN3, CVP2 and VAB function in vascular pattern formation in the same pathway. Localization analysis revealed that both CVP2 and VAB colocalize with VAN3 in the trans- Golgi network (TGN), supporting their functions in the same pathway. The subcellular localization of VAN3 was dependent on its PH domain, and mislocalization of VAN3 was induced in cvp2 or vab mutants. These results suggest that CVP2 and VAB cooperatively regulate the subcellular localization of VAN3 through the interaction between its PH domain and phosphoinositides and/or inositol phosphates. In addition, PtdIns(4)P, to which VAN3 binds preferentially, enhanced the ARF-GAP activity of VAN3, whereas IP3 inhibited it. These results suggest the existence of PtdIns(4)P and/or IP3-dependent subcellular targeting and regulation of VAN3 ACAP activity that governs plant vascular tissue continuity.","lang":"eng"}],"issue":"9","date_updated":"2021-01-12T07:40:44Z","year":"2009","extern":1,"day":"01","author":[{"full_name":"Naramoto, Satoshi","last_name":"Naramoto","first_name":"Satoshi"},{"last_name":"Sawa","first_name":"Shinichiro","full_name":"Sawa, Shinichiro"},{"full_name":"Koizumi, Koji","first_name":"Koji","last_name":"Koizumi"},{"full_name":"Uemura, Tomohiro","first_name":"Tomohiro","last_name":"Uemura"},{"full_name":"Ueda, Takashi","first_name":"Takashi","last_name":"Ueda"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Jirí Friml"},{"full_name":"Nakano, Akihiko","last_name":"Nakano","first_name":"Akihiko"},{"full_name":"Fukuda, Hiroo","last_name":"Fukuda","first_name":"Hiroo"}],"_id":"3055","status":"public","publisher":"Company of Biologists","title":"Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants","month":"05","doi":"10.1242/dev.030098","publication_status":"published","publication":"Development","page":"1529 - 1538","date_created":"2018-12-11T12:01:06Z","type":"journal_article","date_published":"2009-05-01T00:00:00Z","publist_id":"3647","volume":136,"intvolume":"       136","quality_controlled":0,"citation":{"apa":"Naramoto, S., Sawa, S., Koizumi, K., Uemura, T., Ueda, T., Friml, J., … Fukuda, H. (2009). Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.030098\">https://doi.org/10.1242/dev.030098</a>","mla":"Naramoto, Satoshi, et al. “Phosphoinositide-Dependent Regulation of VAN3 ARF-GAP Localization and Activity Essential for Vascular Tissue Continuity in Plants.” <i>Development</i>, vol. 136, no. 9, Company of Biologists, 2009, pp. 1529–38, doi:<a href=\"https://doi.org/10.1242/dev.030098\">10.1242/dev.030098</a>.","ista":"Naramoto S, Sawa S, Koizumi K, Uemura T, Ueda T, Friml J, Nakano A, Fukuda H. 2009. Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants. Development. 136(9), 1529–1538.","chicago":"Naramoto, Satoshi, Shinichiro Sawa, Koji Koizumi, Tomohiro Uemura, Takashi Ueda, Jiří Friml, Akihiko Nakano, and Hiroo Fukuda. “Phosphoinositide-Dependent Regulation of VAN3 ARF-GAP Localization and Activity Essential for Vascular Tissue Continuity in Plants.” <i>Development</i>. Company of Biologists, 2009. <a href=\"https://doi.org/10.1242/dev.030098\">https://doi.org/10.1242/dev.030098</a>.","ieee":"S. Naramoto <i>et al.</i>, “Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants,” <i>Development</i>, vol. 136, no. 9. Company of Biologists, pp. 1529–1538, 2009.","ama":"Naramoto S, Sawa S, Koizumi K, et al. Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants. <i>Development</i>. 2009;136(9):1529-1538. doi:<a href=\"https://doi.org/10.1242/dev.030098\">10.1242/dev.030098</a>","short":"S. Naramoto, S. Sawa, K. Koizumi, T. Uemura, T. Ueda, J. Friml, A. Nakano, H. Fukuda, Development 136 (2009) 1529–1538."}},{"publist_id":"3646","volume":459,"citation":{"mla":"Sorefan, Karim, et al. “A Regulated Auxin Minimum Is Required for Seed Dispersal in Arabidopsis.” <i>Nature</i>, vol. 459, no. 7246, Nature Publishing Group, 2009, pp. 583–86, doi:<a href=\"https://doi.org/10.1038/nature07875\">10.1038/nature07875</a>.","apa":"Sorefan, K., Girin, T., Liljegren, S., Ljung, K., Robles, P., Galván Ampudia, C., … Østergaard, L. (2009). A regulated auxin minimum is required for seed dispersal in Arabidopsis. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature07875\">https://doi.org/10.1038/nature07875</a>","ista":"Sorefan K, Girin T, Liljegren S, Ljung K, Robles P, Galván Ampudia C, Offringa R, Friml J, Yanofsky M, Østergaard L. 2009. A regulated auxin minimum is required for seed dispersal in Arabidopsis. Nature. 459(7246), 583–586.","chicago":"Sorefan, Karim, Thomas Girin, Sarah Liljegren, Karin Ljung, Pedro Robles, Carlos Galván Ampudia, Remko Offringa, Jiří Friml, Martin Yanofsky, and Lars Østergaard. “A Regulated Auxin Minimum Is Required for Seed Dispersal in Arabidopsis.” <i>Nature</i>. Nature Publishing Group, 2009. <a href=\"https://doi.org/10.1038/nature07875\">https://doi.org/10.1038/nature07875</a>.","ama":"Sorefan K, Girin T, Liljegren S, et al. A regulated auxin minimum is required for seed dispersal in Arabidopsis. <i>Nature</i>. 2009;459(7246):583-586. doi:<a href=\"https://doi.org/10.1038/nature07875\">10.1038/nature07875</a>","ieee":"K. Sorefan <i>et al.</i>, “A regulated auxin minimum is required for seed dispersal in Arabidopsis,” <i>Nature</i>, vol. 459, no. 7246. Nature Publishing Group, pp. 583–586, 2009.","short":"K. Sorefan, T. Girin, S. Liljegren, K. Ljung, P. Robles, C. Galván Ampudia, R. Offringa, J. Friml, M. Yanofsky, L. Østergaard, Nature 459 (2009) 583–586."},"quality_controlled":0,"intvolume":"       459","publication_status":"published","doi":"10.1038/nature07875","page":"583 - 586","date_created":"2018-12-11T12:01:06Z","publication":"Nature","type":"journal_article","date_published":"2009-05-28T00:00:00Z","publisher":"Nature Publishing Group","status":"public","title":"A regulated auxin minimum is required for seed dispersal in Arabidopsis","month":"05","date_updated":"2021-01-12T07:40:44Z","issue":"7246","abstract":[{"text":"Local hormone maxima are essential for the development of multicellular structures and organs. For example, steroid hormones accumulate in specific cell types of the animal fetus to induce sexual differentiation and concentration peaks of the plant hormone auxin direct organ initiation and mediate tissue patterning. Here we provide an example of a regulated local hormone minimum required during organogenesis. Our results demonstrate that formation of a local auxin minimum is necessary for specification of the valve margin separation layer where Arabidopsis fruit opening takes place. Consequently, ectopic production of auxin, specifically in valve margin cells, leads to a complete loss of proper cell fate determination. The valve margin identity factor INDEHISCENT (IND) is responsible for forming the auxin minimum by coordinating auxin efflux in separation-layer cells. We propose that the simplicity of formation and maintenance make local hormone minima particularly well suited to specify a small number of cells such as the stripes at the valve margins.","lang":"eng"}],"day":"28","extern":1,"year":"2009","author":[{"full_name":"Sorefan, Karim","last_name":"Sorefan","first_name":"Karim"},{"full_name":"Girin, Thomas","last_name":"Girin","first_name":"Thomas"},{"first_name":"Sarah","last_name":"Liljegren","full_name":"Liljegren, Sarah J"},{"full_name":"Ljung, Karin","first_name":"Karin","last_name":"Ljung"},{"full_name":"Robles, Pedro","last_name":"Robles","first_name":"Pedro"},{"full_name":"Galván-Ampudia, Carlos S","first_name":"Carlos","last_name":"Galván Ampudia"},{"full_name":"Offringa, Remko","first_name":"Remko","last_name":"Offringa"},{"full_name":"Jirí Friml","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí"},{"full_name":"Yanofsky, Martin F","last_name":"Yanofsky","first_name":"Martin"},{"full_name":"Østergaard, Lars","last_name":"Østergaard","first_name":"Lars"}],"_id":"3056"},{"status":"public","oa":1,"month":"08","abstract":[{"text":"The differential distribution of the plant signaling molecule auxin is required for many aspects of plant development. Local auxin maxima and gradients arise as a result of local auxin metabolism and, predominantly, from directional cell-to-cell transport. In this primer, we discuss how the coordinated activity of several auxin influx and efflux systems, which transport auxin across the plasma membrane, mediates directional auxin flow. This activity crucially contributes to the correct setting of developmental cues in embryogenesis, organogenesis, vascular tissue formation and directional growth in response to environmental stimuli.","lang":"eng"}],"issue":"16","date_updated":"2021-01-12T07:40:45Z","year":"2009","_id":"3057","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/19633168"}],"citation":{"ieee":"J. Petrášek and J. Friml, “Auxin transport routes in plant development,” <i>Development</i>, vol. 136, no. 16. Company of Biologists, pp. 2675–2688, 2009.","ama":"Petrášek J, Friml J. Auxin transport routes in plant development. <i>Development</i>. 2009;136(16):2675-2688. doi:<a href=\"https://doi.org/10.1242/dev.030353\">10.1242/dev.030353</a>","short":"J. Petrášek, J. Friml, Development 136 (2009) 2675–2688.","chicago":"Petrášek, Jan, and Jiří Friml. “Auxin Transport Routes in Plant Development.” <i>Development</i>. Company of Biologists, 2009. <a href=\"https://doi.org/10.1242/dev.030353\">https://doi.org/10.1242/dev.030353</a>.","ista":"Petrášek J, Friml J. 2009. Auxin transport routes in plant development. Development. 136(16), 2675–2688.","mla":"Petrášek, Jan, and Jiří Friml. “Auxin Transport Routes in Plant Development.” <i>Development</i>, vol. 136, no. 16, Company of Biologists, 2009, pp. 2675–88, doi:<a href=\"https://doi.org/10.1242/dev.030353\">10.1242/dev.030353</a>.","apa":"Petrášek, J., &#38; Friml, J. (2009). Auxin transport routes in plant development. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.030353\">https://doi.org/10.1242/dev.030353</a>"},"intvolume":"       136","doi":"10.1242/dev.030353","publication_status":"published","oa_version":"Published Version","date_published":"2009-08-15T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Company of Biologists","title":"Auxin transport routes in plant development","pmid":1,"extern":"1","day":"15","author":[{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí"}],"publist_id":"3644","quality_controlled":"1","volume":136,"external_id":{"pmid":["    19633168"]},"publication":"Development","date_created":"2018-12-11T12:01:07Z","page":"2675 - 2688","type":"journal_article","language":[{"iso":"eng"}]},{"title":"Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter","status":"public","publisher":"Nature Publishing Group","month":"06","extern":1,"year":"2009","day":"25","abstract":[{"text":"The plant signalling molecule auxin provides positional informa-tion in a variety of developmental processes by means of its differential distribution (gradients) within plant tissues. Thus, cellular auxin levels often determine the developmental output of auxin signalling. Conceptually, transmembrane transport and metabolic processes regulate the steady-state levels of auxin in any given cell2,3. In particular, PIN auxin-efflux-carrier-mediated, directional transport between cells is crucial for generating auxin gradients2,4,5. Here we show that Arabidopsis thaliana PIN5, an atypical member of the PIN gene family, encodes a functional auxin transporter that is required for auxin-mediated develop-ment. PIN5 does not have a direct role in cell-to-cell transport but regulates intracellular auxin homeostasis and metabolism. PIN5 localizes, unlike other characterized plasma membrane PIN proteins, to endoplasmic reticulum (ER), presumably medi-ating auxin flow from the cytosol to the lumen of the ER. The ER localization of other PIN5-like transporters (including the moss PIN) indicates that the diversification of PIN protein functions in mediating auxin homeostasis at the ER, and cell-to-cell auxin transport at the plasma membrane, represent an ancient event during the evolution of land plants.","lang":"eng"}],"issue":"7250","date_updated":"2021-01-12T07:40:45Z","_id":"3058","author":[{"full_name":"Mravec, Jozef","last_name":"Mravec","first_name":"Jozef"},{"first_name":"Petr","last_name":"Skůpa","full_name":"Skůpa, Petr"},{"full_name":"Bailly, Aurélien","first_name":"Aurélien","last_name":"Bailly"},{"full_name":"Hoyerová, Klára","last_name":"Hoyerová","first_name":"Klára"},{"full_name":"Křeček, Pavel","first_name":"Pavel","last_name":"Křeček"},{"last_name":"Bielach","first_name":"Agnieszka","full_name":"Bielach, Agnieszka"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"full_name":"Zhang, Jing","first_name":"Jing","last_name":"Zhang"},{"full_name":"Gaykova, Vassilena","last_name":"Gaykova","first_name":"Vassilena"},{"last_name":"Stierhof","first_name":"York","full_name":"Stierhof, York-Dieter"},{"first_name":"Petre","last_name":"Dobrev","full_name":"Dobrev, Petre I"},{"full_name":"Schwarzerová, Kateřina","last_name":"Schwarzerová","first_name":"Kateřina"},{"first_name":"Jakub","last_name":"Rolčík","full_name":"Rolčík, Jakub"},{"last_name":"Seifertová","first_name":"Daniela","full_name":"Seifertová, Daniela"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"},{"full_name":"Eva Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"},{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"},{"first_name":"Markus","last_name":"Geisler","full_name":"Geisler, Markus"},{"full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596"}],"publist_id":"3645","citation":{"mla":"Mravec, Jozef, et al. “Subcellular Homeostasis of Phytohormone Auxin Is Mediated by the ER Localized PIN5 Transporter.” <i>Nature</i>, vol. 459, no. 7250, Nature Publishing Group, 2009, pp. 1136–40, doi:<a href=\"https://doi.org/10.1038/nature08066\">10.1038/nature08066</a>.","ista":"Mravec J, Skůpa P, Bailly A, Hoyerová K, Křeček P, Bielach A, Petrášek J, Zhang J, Gaykova V, Stierhof Y, Dobrev P, Schwarzerová K, Rolčík J, Seifertová D, Luschnig C, Benková E, Zažímalová E, Geisler M, Friml J. 2009. Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter. Nature. 459(7250), 1136–1140.","apa":"Mravec, J., Skůpa, P., Bailly, A., Hoyerová, K., Křeček, P., Bielach, A., … Friml, J. (2009). Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature08066\">https://doi.org/10.1038/nature08066</a>","chicago":"Mravec, Jozef, Petr Skůpa, Aurélien Bailly, Klára Hoyerová, Pavel Křeček, Agnieszka Bielach, Jan Petrášek, et al. “Subcellular Homeostasis of Phytohormone Auxin Is Mediated by the ER Localized PIN5 Transporter.” <i>Nature</i>. Nature Publishing Group, 2009. <a href=\"https://doi.org/10.1038/nature08066\">https://doi.org/10.1038/nature08066</a>.","short":"J. Mravec, P. Skůpa, A. Bailly, K. Hoyerová, P. Křeček, A. Bielach, J. Petrášek, J. Zhang, V. Gaykova, Y. Stierhof, P. Dobrev, K. Schwarzerová, J. Rolčík, D. Seifertová, C. Luschnig, E. Benková, E. Zažímalová, M. Geisler, J. Friml, Nature 459 (2009) 1136–1140.","ieee":"J. Mravec <i>et al.</i>, “Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter,” <i>Nature</i>, vol. 459, no. 7250. Nature Publishing Group, pp. 1136–1140, 2009.","ama":"Mravec J, Skůpa P, Bailly A, et al. Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter. <i>Nature</i>. 2009;459(7250):1136-1140. doi:<a href=\"https://doi.org/10.1038/nature08066\">10.1038/nature08066</a>"},"quality_controlled":0,"volume":459,"intvolume":"       459","publication":"Nature","page":"1136 - 1140","date_created":"2018-12-11T12:01:07Z","doi":"10.1038/nature08066","publication_status":"published","date_published":"2009-06-25T00:00:00Z","type":"journal_article"},{"publist_id":"3643","intvolume":"        21","quality_controlled":0,"citation":{"ama":"Kleine Vehn J, Huang F, Naramoto S, et al. PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis. <i>Plant Cell</i>. 2009;21(12):3839-3849. doi:<a href=\"https://doi.org/10.1105/tpc.109.071639\">10.1105/tpc.109.071639</a>","ieee":"J. Kleine Vehn <i>et al.</i>, “PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis,” <i>Plant Cell</i>, vol. 21, no. 12. American Society of Plant Biologists, pp. 3839–3849, 2009.","short":"J. Kleine Vehn, F. Huang, S. Naramoto, J. Zhang, M. Michniewicz, R. Offringa, J. Friml, Plant Cell 21 (2009) 3839–3849.","apa":"Kleine Vehn, J., Huang, F., Naramoto, S., Zhang, J., Michniewicz, M., Offringa, R., &#38; Friml, J. (2009). PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.109.071639\">https://doi.org/10.1105/tpc.109.071639</a>","ista":"Kleine Vehn J, Huang F, Naramoto S, Zhang J, Michniewicz M, Offringa R, Friml J. 2009. PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis. Plant Cell. 21(12), 3839–3849.","mla":"Kleine Vehn, Jürgen, et al. “PIN Auxin Efflux Carrier Polarity Is Regulated by PINOID Kinase Mediated Recruitment into GNOM Independent Trafficking in Arabidopsis.” <i>Plant Cell</i>, vol. 21, no. 12, American Society of Plant Biologists, 2009, pp. 3839–49, doi:<a href=\"https://doi.org/10.1105/tpc.109.071639\">10.1105/tpc.109.071639</a>.","chicago":"Kleine Vehn, Jürgen, Fang Huang, Satoshi Naramoto, Jing Zhang, Marta Michniewicz, Remko Offringa, and Jiří Friml. “PIN Auxin Efflux Carrier Polarity Is Regulated by PINOID Kinase Mediated Recruitment into GNOM Independent Trafficking in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2009. <a href=\"https://doi.org/10.1105/tpc.109.071639\">https://doi.org/10.1105/tpc.109.071639</a>."},"volume":21,"page":"3839 - 3849","date_created":"2018-12-11T12:01:07Z","publication":"Plant Cell","publication_status":"published","doi":"10.1105/tpc.109.071639","date_published":"2009-12-01T00:00:00Z","type":"journal_article","title":"PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis","status":"public","publisher":"American Society of Plant Biologists","month":"12","day":"01","extern":1,"year":"2009","date_updated":"2021-01-12T07:40:45Z","issue":"12","abstract":[{"text":"The phytohormone auxin plays a major role in embryonic and postembryonic plant development. The temporal and spatial distribution of auxin largely depends on the subcellular polar localization of members of the PIN-FORMED (PIN) auxin efflux carrier family. The Ser/Thr protein kinase PINOID (PID) catalyzes PIN phosphorylation and crucially contributes to the regulation of apical-basal PIN polarity. The GTP exchange factor on ADP-ribosylation factors (ARF-GEF), GNOM preferentially mediates PIN recycling at the basal side of the cell. Interference with GNOM activity leads to dynamic PIN transcytosis between different sides of the cell. Our genetic, pharmacological, and cell biological approaches illustrate that PID and GNOM influence PIN polarity and plant development in an antagonistic manner and that the PID-dependent PIN phosphorylation results in GNOM-independent polar PIN targeting. The data suggest that PID and the protein phosphatase 2A not only regulate the static PIN polarity, but also act antagonistically on the rate of GNOM-dependent polar PIN transcytosis. We propose a model that includes PID-dependent PIN phosphorylation at the plasma membrane and the subsequent sorting of PIN proteins to a GNOM-independent pathway for polarity alterations during developmental processes, such as lateral root formation and leaf vasculature development.","lang":"eng"}],"_id":"3059","author":[{"full_name":"Kleine-Vehn, Jürgen","first_name":"Jürgen","last_name":"Kleine Vehn"},{"last_name":"Huang","first_name":"Fang","full_name":"Huang, Fang"},{"full_name":"Naramoto, Satoshi","last_name":"Naramoto","first_name":"Satoshi"},{"last_name":"Zhang","first_name":"Jing","full_name":"Zhang, Jing"},{"last_name":"Michniewicz","first_name":"Marta","full_name":"Michniewicz, Marta"},{"first_name":"Remko","last_name":"Offringa","full_name":"Offringa, Remko"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Jirí Friml"}]},{"_id":"3060","author":[{"full_name":"Schumacher, Karin","first_name":"Karin","last_name":"Schumacher"},{"full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596"}],"year":"2009","extern":"1","day":"01","issue":"6","date_updated":"2021-01-12T07:40:46Z","month":"12","title":"Cell biology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Elsevier","date_published":"2009-12-01T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"None","publication":"Current Opinion in Plant Biology","page":"651 - 652","date_created":"2018-12-11T12:01:08Z","doi":"10.1016/j.pbi.2009.10.009","publication_status":"published","volume":12,"citation":{"apa":"Schumacher, K., &#38; Friml, J. (2009). Cell biology. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2009.10.009\">https://doi.org/10.1016/j.pbi.2009.10.009</a>","ista":"Schumacher K, Friml J. 2009. Cell biology. Current Opinion in Plant Biology. 12(6), 651–652.","mla":"Schumacher, Karin, and Jiří Friml. “Cell Biology.” <i>Current Opinion in Plant Biology</i>, vol. 12, no. 6, Elsevier, 2009, pp. 651–52, doi:<a href=\"https://doi.org/10.1016/j.pbi.2009.10.009\">10.1016/j.pbi.2009.10.009</a>.","chicago":"Schumacher, Karin, and Jiří Friml. “Cell Biology.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.pbi.2009.10.009\">https://doi.org/10.1016/j.pbi.2009.10.009</a>.","ieee":"K. Schumacher and J. Friml, “Cell biology,” <i>Current Opinion in Plant Biology</i>, vol. 12, no. 6. Elsevier, pp. 651–652, 2009.","ama":"Schumacher K, Friml J. Cell biology. <i>Current Opinion in Plant Biology</i>. 2009;12(6):651-652. doi:<a href=\"https://doi.org/10.1016/j.pbi.2009.10.009\">10.1016/j.pbi.2009.10.009</a>","short":"K. Schumacher, J. Friml, Current Opinion in Plant Biology 12 (2009) 651–652."},"intvolume":"        12","quality_controlled":"1","article_type":"letter_note","publist_id":"3641"},{"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812941/","open_access":"1"}],"publist_id":"3640","external_id":{"pmid":["20053306"]},"citation":{"chicago":"Křeček, Pavel, Petr Skůpa, Jiří Libus, Satoshi Naramoto, Ricardo Tejos, Jiří Friml, and Eva Zažímalová. “The PIN-FORMED (PIN) Protein Family of Auxin Transporters.” <i>Genome Biology</i>. BioMed Central, 2009. <a href=\"https://doi.org/10.1186/gb-2009-10-12-249\">https://doi.org/10.1186/gb-2009-10-12-249</a>.","mla":"Křeček, Pavel, et al. “The PIN-FORMED (PIN) Protein Family of Auxin Transporters.” <i>Genome Biology</i>, vol. 10, no. 12, BioMed Central, 2009, doi:<a href=\"https://doi.org/10.1186/gb-2009-10-12-249\">10.1186/gb-2009-10-12-249</a>.","ista":"Křeček P, Skůpa P, Libus J, Naramoto S, Tejos R, Friml J, Zažímalová E. 2009. The PIN-FORMED (PIN) protein family of auxin transporters. Genome Biology. 10(12).","apa":"Křeček, P., Skůpa, P., Libus, J., Naramoto, S., Tejos, R., Friml, J., &#38; Zažímalová, E. (2009). The PIN-FORMED (PIN) protein family of auxin transporters. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/gb-2009-10-12-249\">https://doi.org/10.1186/gb-2009-10-12-249</a>","ama":"Křeček P, Skůpa P, Libus J, et al. The PIN-FORMED (PIN) protein family of auxin transporters. <i>Genome Biology</i>. 2009;10(12). doi:<a href=\"https://doi.org/10.1186/gb-2009-10-12-249\">10.1186/gb-2009-10-12-249</a>","ieee":"P. Křeček <i>et al.</i>, “The PIN-FORMED (PIN) protein family of auxin transporters,” <i>Genome Biology</i>, vol. 10, no. 12. BioMed Central, 2009.","short":"P. Křeček, P. Skůpa, J. Libus, S. Naramoto, R. Tejos, J. Friml, E. Zažímalová, Genome Biology 10 (2009)."},"intvolume":"        10","volume":10,"quality_controlled":"1","date_created":"2018-12-11T12:01:08Z","publication":"Genome Biology","publication_status":"published","doi":"10.1186/gb-2009-10-12-249","language":[{"iso":"eng"}],"date_published":"2009-12-29T00:00:00Z","oa_version":"Published Version","type":"journal_article","title":"The PIN-FORMED (PIN) protein family of auxin transporters","oa":1,"publisher":"BioMed Central","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"12","day":"29","extern":"1","year":"2009","date_updated":"2021-01-12T07:40:46Z","pmid":1,"issue":"12","abstract":[{"lang":"eng","text":"The PIN-FORMED (PIN) proteins are secondary transporters acting in the efflux of the plant signal molecule auxin from cells. They are asymmetrically localized within cells and their polarity determines the directionality of intercellular auxin flow. PIN genes are found exclusively in the genomes of multicellular plants and play an important role in regulating asymmetric auxin distribution in multiple developmental processes, including embryogenesis, organogenesis, tissue differentiation and tropic responses. All PIN proteins have a similar structure with amino- and carboxy-terminal hydrophobic, membrane-spanning domains separated by a central hydrophilic domain. The structure of the hydrophobic domains is well conserved. The hydrophilic domain is more divergent and it determines eight groups within the protein family. The activity of PIN proteins is regulated at multiple levels, including transcription, protein stability, subcellular localization and transport activity. Different endogenous and environmental signals can modulate PIN activity and thus modulate auxin-distribution-dependent development. A large group of PIN proteins, including the most ancient members known from mosses, localize to the endoplasmic reticulum and they regulate the subcellular compartmentalization of auxin and thus auxin metabolism. Further work is needed to establish the physiological importance of this unexpected mode of auxin homeostasis regulation. Furthermore, the evolution of PIN-based transport, PIN protein structure and more detailed biochemical characterization of the transport function are important topics for further studies."}],"_id":"3061","author":[{"full_name":"Křeček, Pavel","last_name":"Křeček","first_name":"Pavel"},{"full_name":"Skůpa, Petr","last_name":"Skůpa","first_name":"Petr"},{"full_name":"Libus, Jiří","first_name":"Jiří","last_name":"Libus"},{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"first_name":"Ricardo","last_name":"Tejos","full_name":"Tejos, Ricardo"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596"},{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"}]},{"_id":"3197","author":[{"full_name":"Kumar, M Pawan","first_name":"M Pawan","last_name":"Kumar"},{"full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"},{"first_name":"Philip","last_name":"Torr","full_name":"Torr, Philip H"}],"day":"01","year":"2009","extern":1,"date_updated":"2021-01-12T07:41:44Z","abstract":[{"text":"The problem of obtaining the maximum a posteriori estimate of a general discrete Markov random field (i.e., a Markov random field defined using a discrete set of labels) is known to be NP-hard. However, due to its central importance in many applications, several approximation algorithms have been proposed in the literature. In this paper, we present an analysis of three such algorithms based on convex relaxations: (i) LP-S: the linear programming (LP) relaxation proposed by Schlesinger (1976) for a special case and independently in Chekuri et al. (2001), Koster et al. (1998), and Wainwright et al. (2005) for the general case; (ii) QP-RL: the quadratic programming (QP) relaxation of Ravikumar and Lafferty (2006); and (iii) SOCP-MS: the second order cone programming (SOCP) relaxation first proposed by Muramatsu and Suzuki (2003) for two label problems and later extended by Kumar et al. (2006) for a general label set.\n\nWe show that the SOCP-MS and the QP-RL relaxations are equivalent. Furthermore, we prove that despite the flexibility in the form of the constraints/objective function offered by QP and SOCP, the LP-S relaxation strictly dominates (i.e., provides a better approximation than) QP-RL and SOCP-MS. We generalize these results by defining a large class of SOCP (and equivalent QP) relaxations which is dominated by the LP-S relaxation. Based on these results we propose some novel SOCP relaxations which define constraints using random variables that form cycles or cliques in the graphical model representation of the random field. Using some examples we show that the new SOCP relaxations strictly dominate the previous approaches.","lang":"eng"}],"month":"01","title":"An analysis of convex relaxations for MAP estimation of discrete MRFs","oa":1,"publisher":"Microtome Publishing","status":"public","date_published":"2009-01-01T00:00:00Z","type":"journal_article","page":"71 - 106","date_created":"2018-12-11T12:01:57Z","publication":"Journal of Machine Learning Research","publication_status":"published","intvolume":"        10","volume":10,"quality_controlled":0,"citation":{"chicago":"Kumar, M Pawan, Vladimir Kolmogorov, and Philip Torr. “An Analysis of Convex Relaxations for MAP Estimation of Discrete MRFs.” <i>Journal of Machine Learning Research</i>. Microtome Publishing, 2009.","apa":"Kumar, M. P., Kolmogorov, V., &#38; Torr, P. (2009). An analysis of convex relaxations for MAP estimation of discrete MRFs. <i>Journal of Machine Learning Research</i>. Microtome Publishing.","ista":"Kumar MP, Kolmogorov V, Torr P. 2009. An analysis of convex relaxations for MAP estimation of discrete MRFs. Journal of Machine Learning Research. 10, 71–106.","mla":"Kumar, M. Pawan, et al. “An Analysis of Convex Relaxations for MAP Estimation of Discrete MRFs.” <i>Journal of Machine Learning Research</i>, vol. 10, Microtome Publishing, 2009, pp. 71–106.","ieee":"M. P. Kumar, V. Kolmogorov, and P. Torr, “An analysis of convex relaxations for MAP estimation of discrete MRFs,” <i>Journal of Machine Learning Research</i>, vol. 10. Microtome Publishing, pp. 71–106, 2009.","ama":"Kumar MP, Kolmogorov V, Torr P. An analysis of convex relaxations for MAP estimation of discrete MRFs. <i>Journal of Machine Learning Research</i>. 2009;10:71-106.","short":"M.P. Kumar, V. Kolmogorov, P. Torr, Journal of Machine Learning Research 10 (2009) 71–106."},"main_file_link":[{"url":"https://hal.inria.fr/hal-00773608","open_access":"1"}],"publist_id":"3484"},{"citation":{"short":"S. Vicente, V. Kolmogorov, C. Rother, in:, IEEE, 2009, pp. 755–762.","ama":"Vicente S, Kolmogorov V, Rother C. Joint optimization of segmentation and appearance models. In: IEEE; 2009:755-762. doi:<a href=\"https://doi.org/10.1109/ICCV.2009.5459287\">10.1109/ICCV.2009.5459287</a>","ieee":"S. Vicente, V. Kolmogorov, and C. Rother, “Joint optimization of segmentation and appearance models,” presented at the ICCV: International Conference on Computer Vision, 2009, pp. 755–762.","chicago":"Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Joint Optimization of Segmentation and Appearance Models,” 755–62. IEEE, 2009. <a href=\"https://doi.org/10.1109/ICCV.2009.5459287\">https://doi.org/10.1109/ICCV.2009.5459287</a>.","mla":"Vicente, Sara, et al. <i>Joint Optimization of Segmentation and Appearance Models</i>. IEEE, 2009, pp. 755–62, doi:<a href=\"https://doi.org/10.1109/ICCV.2009.5459287\">10.1109/ICCV.2009.5459287</a>.","ista":"Vicente S, Kolmogorov V, Rother C. 2009. Joint optimization of segmentation and appearance models. ICCV: International Conference on Computer Vision, 755–762.","apa":"Vicente, S., Kolmogorov, V., &#38; Rother, C. (2009). Joint optimization of segmentation and appearance models (pp. 755–762). Presented at the ICCV: International Conference on Computer Vision, IEEE. <a href=\"https://doi.org/10.1109/ICCV.2009.5459287\">https://doi.org/10.1109/ICCV.2009.5459287</a>"},"quality_controlled":0,"main_file_link":[{"url":"http://www.robots.ox.ac.uk/~vgg/rg/papers/segmentationappearance.pdf","open_access":"0"}],"publist_id":"3482","type":"conference","date_published":"2009-05-01T00:00:00Z","doi":"10.1109/ICCV.2009.5459287","conference":{"name":"ICCV: International Conference on Computer Vision"},"publication_status":"published","date_created":"2018-12-11T12:01:58Z","page":"755 - 762","month":"05","publisher":"IEEE","status":"public","title":"Joint optimization of segmentation and appearance models","author":[{"full_name":"Vicente, Sara","first_name":"Sara","last_name":"Vicente"},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov"},{"full_name":"Rother, Carsten","first_name":"Carsten","last_name":"Rother"}],"_id":"3199","abstract":[{"text":"Many interactive image segmentation approaches use an objective function which includes appearance models as an unknown variable. Since the resulting optimization problem is NP-hard the segmentation and appearance are typically optimized separately, in an EM-style fashion. One contribution of this paper is to express the objective function purely in terms of the unknown segmentation, using higher-order cliques. This formulation reveals an interesting bias of the model towards balanced segmentations. Furthermore, it enables us to develop a new dual decomposition optimization procedure, which provides additionally a lower bound. Hence, we are able to improve on existing optimizers, and verify that for a considerable number of real world examples we even achieve global optimality. This is important since we are able, for the first time, to analyze the deficiencies of the model. Another contribution is to establish a property of a particular dual decomposition approach which involves convex functions depending on foreground area. As a consequence, we show that the optimal decomposition for our problem can be computed efficiently via a parametric maxflow algorithm.","lang":"eng"}],"date_updated":"2021-01-12T07:41:44Z","year":"2009","extern":1,"day":"01"},{"author":[{"full_name":"Vladimir Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"},{"full_name":"Shioura, Akiyoshi","last_name":"Shioura","first_name":"Akiyoshi"}],"_id":"3200","date_updated":"2021-01-12T07:41:45Z","issue":"4","abstract":[{"lang":"eng","text":"Motivated by various applications to computer vision, we consider the convex cost tension problem, which is the dual of the convex cost flow problem. In this paper, we first propose a primal algorithm for computing an optimal solution of the problem. Our primal algorithm iteratively updates primal variables by solving associated minimum cut problems. We show that the time complexity of the primal algorithm is O (K {dot operator} T (n, m)), where K is the range of primal variables and T (n, m) is the time needed to compute a minimum cut in a graph with n nodes and m edges. We then develop an improved version of the primal algorithm, called the primal-dual algorithm, by making good use of dual variables in addition to primal variables. Although its time complexity is the same as that of the primal algorithm, we can expect a better performance in practice. We finally consider an application to a computer vision problem called the panoramic image stitching."}],"day":"01","extern":1,"year":"2009","month":"11","publisher":"Elsevier","status":"public","title":"New algorithms for convex cost tension problem with application to computer vision","type":"journal_article","date_published":"2009-11-01T00:00:00Z","publication_status":"published","doi":"10.1016/j.disopt.2009.04.006","page":"378 - 393","date_created":"2018-12-11T12:01:58Z","publication":"Discrete Optimization","citation":{"short":"V. Kolmogorov, A. Shioura, Discrete Optimization 6 (2009) 378–393.","ieee":"V. Kolmogorov and A. Shioura, “New algorithms for convex cost tension problem with application to computer vision,” <i>Discrete Optimization</i>, vol. 6, no. 4. Elsevier, pp. 378–393, 2009.","ama":"Kolmogorov V, Shioura A. New algorithms for convex cost tension problem with application to computer vision. <i>Discrete Optimization</i>. 2009;6(4):378-393. doi:<a href=\"https://doi.org/10.1016/j.disopt.2009.04.006\">10.1016/j.disopt.2009.04.006</a>","chicago":"Kolmogorov, Vladimir, and Akiyoshi Shioura. “New Algorithms for Convex Cost Tension Problem with Application to Computer Vision.” <i>Discrete Optimization</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.disopt.2009.04.006\">https://doi.org/10.1016/j.disopt.2009.04.006</a>.","apa":"Kolmogorov, V., &#38; Shioura, A. (2009). New algorithms for convex cost tension problem with application to computer vision. <i>Discrete Optimization</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.disopt.2009.04.006\">https://doi.org/10.1016/j.disopt.2009.04.006</a>","ista":"Kolmogorov V, Shioura A. 2009. New algorithms for convex cost tension problem with application to computer vision. Discrete Optimization. 6(4), 378–393.","mla":"Kolmogorov, Vladimir, and Akiyoshi Shioura. “New Algorithms for Convex Cost Tension Problem with Application to Computer Vision.” <i>Discrete Optimization</i>, vol. 6, no. 4, Elsevier, 2009, pp. 378–93, doi:<a href=\"https://doi.org/10.1016/j.disopt.2009.04.006\">10.1016/j.disopt.2009.04.006</a>."},"quality_controlled":0,"volume":6,"intvolume":"         6","publist_id":"3483"},{"status":"public","publisher":"IEEE","title":"A global perspective on MAP inference for low level vision","month":"05","date_updated":"2021-01-12T07:41:46Z","abstract":[{"text":"In recent years the Markov Random Field (MRF) has become the de facto probabilistic model for low-level vision applications. However, in a maximum a posteriori (MAP) framework, MRFs inherently encourage delta function marginal statistics. By contrast, many low-level vision problems have heavy tailed marginal statistics, making the MRF model unsuitable. In this paper we introduce a more general Marginal Probability Field (MPF), of which the MRF is a special, linear case, and show that convex energy MPFs can be used to encourage arbitrary marginal statistics. We introduce a flexible, extensible framework for effectively optimizing the resulting NP-hard MAP problem, based around dual-decomposition and a modified mincost flow algorithm, and which achieves global optimality in some instances. We use a range of applications, including image denoising and texture synthesis, to demonstrate the benefits of this class of MPF over MRFs.","lang":"eng"}],"day":"01","year":"2009","extern":1,"author":[{"full_name":"Woodford, Oliver J","first_name":"Oliver","last_name":"Woodford"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"},{"full_name":"Vladimir Kolmogorov","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"_id":"3203","publist_id":"3481","quality_controlled":0,"citation":{"apa":"Woodford, O., Rother, C., &#38; Kolmogorov, V. (2009). A global perspective on MAP inference for low level vision (pp. 2319–2326). Presented at the ICCV: International Conference on Computer Vision, IEEE. <a href=\"https://doi.org/10.1109/ICCV.2009.5459434\">https://doi.org/10.1109/ICCV.2009.5459434</a>","ista":"Woodford O, Rother C, Kolmogorov V. 2009. A global perspective on MAP inference for low level vision. ICCV: International Conference on Computer Vision, 2319–2326.","mla":"Woodford, Oliver, et al. <i>A Global Perspective on MAP Inference for Low Level Vision</i>. IEEE, 2009, pp. 2319–26, doi:<a href=\"https://doi.org/10.1109/ICCV.2009.5459434\">10.1109/ICCV.2009.5459434</a>.","chicago":"Woodford, Oliver, Carsten Rother, and Vladimir Kolmogorov. “A Global Perspective on MAP Inference for Low Level Vision,” 2319–26. IEEE, 2009. <a href=\"https://doi.org/10.1109/ICCV.2009.5459434\">https://doi.org/10.1109/ICCV.2009.5459434</a>.","short":"O. Woodford, C. Rother, V. Kolmogorov, in:, IEEE, 2009, pp. 2319–2326.","ieee":"O. Woodford, C. Rother, and V. Kolmogorov, “A global perspective on MAP inference for low level vision,” presented at the ICCV: International Conference on Computer Vision, 2009, pp. 2319–2326.","ama":"Woodford O, Rother C, Kolmogorov V. A global perspective on MAP inference for low level vision. In: IEEE; 2009:2319-2326. doi:<a href=\"https://doi.org/10.1109/ICCV.2009.5459434\">10.1109/ICCV.2009.5459434</a>"},"publication_status":"published","conference":{"name":"ICCV: International Conference on Computer Vision"},"doi":"10.1109/ICCV.2009.5459434","page":"2319 - 2326","date_created":"2018-12-11T12:01:59Z","type":"conference","date_published":"2009-05-01T00:00:00Z"},{"title":"A new randomness extraction paradigm for hybrid encryption","status":"public","publisher":"Springer","alternative_title":["LNCS"],"month":"05","year":"2009","extern":1,"day":"28","abstract":[{"text":"We present a new approach to the design of IND-CCA2 secure hybrid encryption schemes in the standard model. Our approach provides an efficient generic transformation from 1-universal to 2-universal hash proof systems. The transformation involves a randomness extractor based on a 4-wise independent hash function as the key derivation function. Our methodology can be instantiated with efficient schemes based on standard intractability assumptions such as Decisional Diffie-Hellman, Quadratic Residuosity, and Paillier's Decisional Composite Residuosity. Interestingly, our framework also allows to prove IND-CCA2 security of a hybrid version of 1991's Damgård's ElGamal public-key encryption scheme under the DDH assumption. ","lang":"eng"}],"date_updated":"2021-01-12T07:41:58Z","_id":"3230","author":[{"first_name":"Eike","last_name":"Kiltz","full_name":"Kiltz, Eike"},{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Krzysztof Pietrzak"},{"full_name":"Stam, Martijn","last_name":"Stam","first_name":"Martijn"},{"first_name":"Moti","last_name":"Yung","full_name":"Yung, Moti"}],"publist_id":"3449","intvolume":"      5479","citation":{"ama":"Kiltz E, Pietrzak KZ, Stam M, Yung M. A new randomness extraction paradigm for hybrid encryption. In: Vol 5479. Springer; 2009:590-609. doi:<a href=\"https://doi.org/10.1007/978-3-642-01001-9_34\">10.1007/978-3-642-01001-9_34</a>","ieee":"E. Kiltz, K. Z. Pietrzak, M. Stam, and M. Yung, “A new randomness extraction paradigm for hybrid encryption,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2009, vol. 5479, pp. 590–609.","short":"E. Kiltz, K.Z. Pietrzak, M. Stam, M. Yung, in:, Springer, 2009, pp. 590–609.","chicago":"Kiltz, Eike, Krzysztof Z Pietrzak, Martijn Stam, and Moti Yung. “A New Randomness Extraction Paradigm for Hybrid Encryption,” 5479:590–609. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-01001-9_34\">https://doi.org/10.1007/978-3-642-01001-9_34</a>.","apa":"Kiltz, E., Pietrzak, K. Z., Stam, M., &#38; Yung, M. (2009). A new randomness extraction paradigm for hybrid encryption (Vol. 5479, pp. 590–609). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. <a href=\"https://doi.org/10.1007/978-3-642-01001-9_34\">https://doi.org/10.1007/978-3-642-01001-9_34</a>","mla":"Kiltz, Eike, et al. <i>A New Randomness Extraction Paradigm for Hybrid Encryption</i>. Vol. 5479, Springer, 2009, pp. 590–609, doi:<a href=\"https://doi.org/10.1007/978-3-642-01001-9_34\">10.1007/978-3-642-01001-9_34</a>.","ista":"Kiltz E, Pietrzak KZ, Stam M, Yung M. 2009. A new randomness extraction paradigm for hybrid encryption. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 5479, 590–609."},"quality_controlled":0,"volume":5479,"date_created":"2018-12-11T12:02:09Z","page":"590 - 609","doi":"10.1007/978-3-642-01001-9_34","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"publication_status":"published","date_published":"2009-05-28T00:00:00Z","type":"conference"},{"alternative_title":["LNCS"],"month":"05","title":"On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model","publisher":"Springer","status":"public","_id":"3231","author":[{"full_name":"Kiltz, Eike","last_name":"Kiltz","first_name":"Eike"},{"full_name":"Krzysztof Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"year":"2009","extern":1,"day":"28","abstract":[{"lang":"eng","text":"We investigate the security of &quot;padding-based&quot; encryption schemes in the standard model. This class contains all public-key encryption schemes where the encryption algorithm first applies some invertible public transformation to the message (the &quot;padding&quot;), followed by a trapdoor permutation. In particular, this class contains OAEP and its variants. Our main result is a black-box impossibility result showing that one cannot prove any such padding-based scheme chosen-ciphertext secure even assuming the existence of ideal trapdoor permutations. The latter is a strong ideal abstraction of trapdoor permutations which inherits all security properties of uniform random permutations. "}],"date_updated":"2021-01-12T07:41:58Z","citation":{"ama":"Kiltz E, Pietrzak KZ. On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model. In: Vol 5479. Springer; 2009:389-406. doi:<a href=\"https://doi.org/10.1007/978-3-642-01001-9_23\">10.1007/978-3-642-01001-9_23</a>","ieee":"E. Kiltz and K. Z. Pietrzak, “On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2009, vol. 5479, pp. 389–406.","short":"E. Kiltz, K.Z. Pietrzak, in:, Springer, 2009, pp. 389–406.","ista":"Kiltz E, Pietrzak KZ. 2009. On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 5479, 389–406.","mla":"Kiltz, Eike, and Krzysztof Z. Pietrzak. <i>On the Security of Padding Based Encryption Schemes Why We Cannot Prove OAEP Secure in the Standard Model</i>. Vol. 5479, Springer, 2009, pp. 389–406, doi:<a href=\"https://doi.org/10.1007/978-3-642-01001-9_23\">10.1007/978-3-642-01001-9_23</a>.","apa":"Kiltz, E., &#38; Pietrzak, K. Z. (2009). On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model (Vol. 5479, pp. 389–406). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. <a href=\"https://doi.org/10.1007/978-3-642-01001-9_23\">https://doi.org/10.1007/978-3-642-01001-9_23</a>","chicago":"Kiltz, Eike, and Krzysztof Z Pietrzak. “On the Security of Padding Based Encryption Schemes Why We Cannot Prove OAEP Secure in the Standard Model,” 5479:389–406. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-01001-9_23\">https://doi.org/10.1007/978-3-642-01001-9_23</a>."},"intvolume":"      5479","quality_controlled":0,"volume":5479,"publist_id":"3450","date_published":"2009-05-28T00:00:00Z","type":"conference","page":"389 - 406","date_created":"2018-12-11T12:02:09Z","doi":"10.1007/978-3-642-01001-9_23","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"publication_status":"published"},{"publist_id":"3448","volume":5479,"citation":{"chicago":"Pietrzak, Krzysztof Z. “A Leakage Resilient Mode of Operation,” 5479:462–82. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-01001-9_27\">https://doi.org/10.1007/978-3-642-01001-9_27</a>.","ista":"Pietrzak KZ. 2009. A leakage resilient mode of operation. CRYPTO: International Cryptology Conference, LNCS, vol. 5479, 462–482.","apa":"Pietrzak, K. Z. (2009). A leakage resilient mode of operation (Vol. 5479, pp. 462–482). Presented at the CRYPTO: International Cryptology Conference, Springer. <a href=\"https://doi.org/10.1007/978-3-642-01001-9_27\">https://doi.org/10.1007/978-3-642-01001-9_27</a>","mla":"Pietrzak, Krzysztof Z. <i>A Leakage Resilient Mode of Operation</i>. Vol. 5479, Springer, 2009, pp. 462–82, doi:<a href=\"https://doi.org/10.1007/978-3-642-01001-9_27\">10.1007/978-3-642-01001-9_27</a>.","ama":"Pietrzak KZ. A leakage resilient mode of operation. In: Vol 5479. Springer; 2009:462-482. doi:<a href=\"https://doi.org/10.1007/978-3-642-01001-9_27\">10.1007/978-3-642-01001-9_27</a>","ieee":"K. Z. Pietrzak, “A leakage resilient mode of operation,” presented at the CRYPTO: International Cryptology Conference, 2009, vol. 5479, pp. 462–482.","short":"K.Z. Pietrzak, in:, Springer, 2009, pp. 462–482."},"quality_controlled":0,"intvolume":"      5479","publication_status":"published","conference":{"name":"CRYPTO: International Cryptology Conference"},"doi":"10.1007/978-3-642-01001-9_27","date_created":"2018-12-11T12:02:09Z","page":"462 - 482","type":"conference","date_published":"2009-05-28T00:00:00Z","publisher":"Springer","status":"public","title":"A leakage resilient mode of operation","month":"05","alternative_title":["LNCS"],"date_updated":"2021-01-12T07:41:59Z","abstract":[{"lang":"eng","text":"A weak pseudorandom function (wPRF) is a cryptographic primitive similar to - but weaker than - a pseudorandom function: for wPRFs one only requires that the output is pseudorandom when queried on random inputs.We show that unlike &quot;normal&quot; PRFs, wPRFs are seedincompressible, in the sense that the output of a wPRF is pseudorandom even if a bounded amount of information about the key is leaked. As an application of this result we construct a simple mode of operation which - when instantiated with any wPRF - gives a leakage-resilient stream-cipher. The implementation of such a cipher is secure against every side-channel attack, as long as the amount of information leaked per round is bounded, but overall can be arbitrary large. The construction is simpler than the previous one (Dziembowski-Pietrzak FOCS'08) as it only uses a single primitive (a wPRF) in a straight forward manner. "}],"day":"28","extern":1,"year":"2009","author":[{"last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","full_name":"Krzysztof Pietrzak"}],"_id":"3232"},{"month":"12","title":"A single UDP galactofuranose transporter is required for galactofuranosylation in Aspergillus fumigatus","status":"public","publisher":"American Society for Biochemistry and Molecular Biology","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3292","author":[{"last_name":"Engel","first_name":"Jakob","full_name":"Engel, Jakob"},{"orcid":"0000-0002-5795-0133","first_name":"Philipp S","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","last_name":"Schmalhorst","full_name":"Schmalhorst, Philipp S"},{"full_name":"Dörk Bousset, Thilo","first_name":"Thilo","last_name":"Dörk Bousset"},{"full_name":"Ferrières, Vincent","first_name":"Vincent","last_name":"Ferrières"},{"first_name":"Françoise","last_name":"Routier","full_name":"Routier, Françoise"}],"day":"04","extern":"1","year":"2009","date_updated":"2021-01-12T07:42:26Z","issue":"49","abstract":[{"text":"Galactofuranose (Galf) containing molecules have been described at the cell surface of several eukaryotes and shown to contribute to the virulence of the parasite Leishmania major and the fungus Aspergillus fumigatus. It is anticipated that a number of the surface glycoconjugates such as N-glycans or glycolipids are galactofuranosylated in the Golgi apparatus. This raises the question of how the substrate for galactofuranosylation reactions, UDP-Galf, which is synthesized in the cytosol, translocates into the organelles of the secretory pathway. Here we report the first identification of a Golgi-localized nucleotide sugar transporter, named GlfB, with specificity for a UDP-Galf. In vitro transport assays established binding of UDP-Galf to GlfB and excluded transport of several other nucleotide sugars. Furthermore, the implication of glfB in the galactofuranosylation of A. fumigatus glycoconjugates and galactomannan was demonstrated by a targeted gene deletion approach. Our data reveal a direct connection between galactomannan and the organelles of the secretory pathway that strongly suggests that the cell wall-bound polysaccharide originates from its glycosylphosphatidylinositol-anchored form.","lang":"eng"}],"citation":{"ista":"Engel J, Schmalhorst PS, Dörk Bousset T, Ferrières V, Routier F. 2009. A single UDP galactofuranose transporter is required for galactofuranosylation in Aspergillus fumigatus. Journal of Biological Chemistry. 284(49), 33859–33868.","mla":"Engel, Jakob, et al. “A Single UDP Galactofuranose Transporter Is Required for Galactofuranosylation in Aspergillus Fumigatus.” <i>Journal of Biological Chemistry</i>, vol. 284, no. 49, American Society for Biochemistry and Molecular Biology, 2009, pp. 33859–68, doi:<a href=\"https://doi.org/10.1074/jbc.M109.070219 \">10.1074/jbc.M109.070219 </a>.","apa":"Engel, J., Schmalhorst, P. S., Dörk Bousset, T., Ferrières, V., &#38; Routier, F. (2009). A single UDP galactofuranose transporter is required for galactofuranosylation in Aspergillus fumigatus. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.M109.070219 \">https://doi.org/10.1074/jbc.M109.070219 </a>","chicago":"Engel, Jakob, Philipp S Schmalhorst, Thilo Dörk Bousset, Vincent Ferrières, and Françoise Routier. “A Single UDP Galactofuranose Transporter Is Required for Galactofuranosylation in Aspergillus Fumigatus.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology, 2009. <a href=\"https://doi.org/10.1074/jbc.M109.070219 \">https://doi.org/10.1074/jbc.M109.070219 </a>.","ama":"Engel J, Schmalhorst PS, Dörk Bousset T, Ferrières V, Routier F. A single UDP galactofuranose transporter is required for galactofuranosylation in Aspergillus fumigatus. <i>Journal of Biological Chemistry</i>. 2009;284(49):33859-33868. doi:<a href=\"https://doi.org/10.1074/jbc.M109.070219 \">10.1074/jbc.M109.070219 </a>","ieee":"J. Engel, P. S. Schmalhorst, T. Dörk Bousset, V. Ferrières, and F. Routier, “A single UDP galactofuranose transporter is required for galactofuranosylation in Aspergillus fumigatus,” <i>Journal of Biological Chemistry</i>, vol. 284, no. 49. American Society for Biochemistry and Molecular Biology, pp. 33859–33868, 2009.","short":"J. Engel, P.S. Schmalhorst, T. Dörk Bousset, V. Ferrières, F. Routier, Journal of Biological Chemistry 284 (2009) 33859–33868."},"quality_controlled":"1","intvolume":"       284","volume":284,"publist_id":"3353","language":[{"iso":"eng"}],"date_published":"2009-12-04T00:00:00Z","oa_version":"None","type":"journal_article","page":"33859 - 33868","date_created":"2018-12-11T12:02:30Z","publication":"Journal of Biological Chemistry","publication_status":"published","doi":"10.1074/jbc.M109.070219 "},{"publist_id":"3348","quality_controlled":0,"volume":23,"citation":{"short":"S. Chakraborty Tuhin, S. Goswami, O. Siddiqi, Journal of Neurogenetics 23 (2009) 210–9.","ieee":"S. Chakraborty Tuhin, S. Goswami, and O. Siddiqi, “Sensory correlates of imaginal conditioning in Drosophila melanogaster,” <i>Journal of Neurogenetics</i>, vol. 23, no. 1–2. Informa Healthcare, pp. 210–9, 2009.","ama":"Chakraborty Tuhin S, Goswami S, Siddiqi O. Sensory correlates of imaginal conditioning in Drosophila melanogaster. <i>Journal of Neurogenetics</i>. 2009;23(1-2):210-219. doi:<a href=\"https://doi.org/10.1080/01677060802491559 \">10.1080/01677060802491559 </a>","mla":"Chakraborty Tuhin, Subhra, et al. “Sensory Correlates of Imaginal Conditioning in Drosophila Melanogaster.” <i>Journal of Neurogenetics</i>, vol. 23, no. 1–2, Informa Healthcare, 2009, pp. 210–19, doi:<a href=\"https://doi.org/10.1080/01677060802491559 \">10.1080/01677060802491559 </a>.","ista":"Chakraborty Tuhin S, Goswami S, Siddiqi O. 2009. Sensory correlates of imaginal conditioning in Drosophila melanogaster. Journal of Neurogenetics. 23(1–2), 210–9.","apa":"Chakraborty Tuhin, S., Goswami, S., &#38; Siddiqi, O. (2009). Sensory correlates of imaginal conditioning in Drosophila melanogaster. <i>Journal of Neurogenetics</i>. Informa Healthcare. <a href=\"https://doi.org/10.1080/01677060802491559 \">https://doi.org/10.1080/01677060802491559 </a>","chicago":"Chakraborty Tuhin, Subhra, Sarit Goswami, and Obaid Siddiqi. “Sensory Correlates of Imaginal Conditioning in Drosophila Melanogaster.” <i>Journal of Neurogenetics</i>. Informa Healthcare, 2009. <a href=\"https://doi.org/10.1080/01677060802491559 \">https://doi.org/10.1080/01677060802491559 </a>."},"intvolume":"        23","doi":"10.1080/01677060802491559 ","publication_status":"published","publication":"Journal of Neurogenetics","page":"210 - 9","date_created":"2018-12-11T12:02:30Z","type":"journal_article","date_published":"2009-01-01T00:00:00Z","publisher":"Informa Healthcare","status":"public","title":"Sensory correlates of imaginal conditioning in Drosophila melanogaster","month":"01","abstract":[{"lang":"eng","text":"Chemotactic responses of Drosophila to certain esters and alcohols are experience dependent. When the flies are exposed after eclosion to these chemicals, the odorants become strongly attractive. We show that behavioral conditioning is accompanied by an increase in the electrophysiological responses of single neurons in sensilla basiconica. Sensitization involves odorants that act on a common olfactory receptor. The possible mechanism of imaginal conditioning and its ecological and evolutionary significance are discussed."}],"issue":"1-2","date_updated":"2021-01-12T07:42:27Z","year":"2009","extern":1,"day":"01","author":[{"first_name":"Subhra","last_name":"Chakraborty Tuhin","full_name":"Chakraborty Tuhin, Subhra"},{"id":"3A578F32-F248-11E8-B48F-1D18A9856A87","last_name":"Goswami","first_name":"Sarit","full_name":"Sarit Goswami"},{"full_name":"Siddiqi, Obaid","first_name":"Obaid","last_name":"Siddiqi"}],"_id":"3293"},{"citation":{"apa":"Weissman, D., Desai, M., Fisher, D., &#38; Feldman, M. (2009). The rate at which asexual populations cross fitness valleys. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2009.02.006\">https://doi.org/10.1016/j.tpb.2009.02.006</a>","mla":"Weissman, Daniel, et al. “The Rate at Which Asexual Populations Cross Fitness Valleys.” <i>Theoretical Population Biology</i>, vol. 75, no. 4, Academic Press, 2009, pp. 286–300, doi:<a href=\"https://doi.org/10.1016/j.tpb.2009.02.006\">10.1016/j.tpb.2009.02.006</a>.","ista":"Weissman D, Desai M, Fisher D, Feldman M. 2009. The rate at which asexual populations cross fitness valleys. Theoretical Population Biology. 75(4), 286–300.","chicago":"Weissman, Daniel, Michael Desai, Daniel Fisher, and Marcus Feldman. “The Rate at Which Asexual Populations Cross Fitness Valleys.” <i>Theoretical Population Biology</i>. Academic Press, 2009. <a href=\"https://doi.org/10.1016/j.tpb.2009.02.006\">https://doi.org/10.1016/j.tpb.2009.02.006</a>.","ama":"Weissman D, Desai M, Fisher D, Feldman M. The rate at which asexual populations cross fitness valleys. <i>Theoretical Population Biology</i>. 2009;75(4):286-300. doi:<a href=\"https://doi.org/10.1016/j.tpb.2009.02.006\">10.1016/j.tpb.2009.02.006</a>","ieee":"D. Weissman, M. Desai, D. Fisher, and M. Feldman, “The rate at which asexual populations cross fitness valleys,” <i>Theoretical Population Biology</i>, vol. 75, no. 4. Academic Press, pp. 286–300, 2009.","short":"D. Weissman, M. Desai, D. Fisher, M. Feldman, Theoretical Population Biology 75 (2009) 286–300."},"quality_controlled":0,"intvolume":"        75","volume":75,"publist_id":"3336","date_published":"2009-06-01T00:00:00Z","type":"journal_article","publication":"Theoretical Population Biology","date_created":"2018-12-11T12:02:34Z","page":"286 - 300","doi":"10.1016/j.tpb.2009.02.006","publication_status":"published","month":"06","title":"The rate at which asexual populations cross fitness valleys","status":"public","publisher":"Academic Press","_id":"3304","author":[{"full_name":"Daniel Weissman","first_name":"Daniel","last_name":"Weissman","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Desai","first_name":"Michael","full_name":"Desai, Michael M"},{"full_name":"Fisher, Daniel S","first_name":"Daniel","last_name":"Fisher"},{"full_name":"Feldman, Marcus W","last_name":"Feldman","first_name":"Marcus"}],"extern":1,"year":"2009","day":"01","issue":"4","abstract":[{"lang":"eng","text":"Complex traits often involve interactions between different genetic loci. This can lead to sign epistasis, whereby mutations that are individually deleterious or neutral combine to confer a fitness benefit. In order to acquire the beneficial genotype, an asexual population must cross a fitness valley or plateau by first acquiring the deleterious or neutral intermediates. Here, we present a complete, intuitive theoretical description of the valley-crossing process across the full spectrum of possible parameter regimes. We calculate the rate at which a population crosses a fitness valley or plateau of arbitrary width, as a function of the mutation rates, the population size, and the fitnesses of the intermediates. We find that when intermediates are close to neutral, a large population can cross even wide fitness valleys remarkably quickly, so that valley-crossing dynamics may be common even when mutations that directly increase fitness are also possible. Thus the evolutionary dynamics of large populations can be sensitive to the structure of an extended region of the fitness landscape — the population may not take directly uphill paths in favor of paths across valleys and plateaus that lead eventually to fitter genotypes. In smaller populations, we find that below a threshold size, which depends on the width of the fitness valley and the strength of selection against intermediate genotypes, valley-crossing is much less likely and hence the evolutionary dynamics are less influenced by distant regions of the fitness landscape."}],"date_updated":"2021-01-12T07:42:31Z"},{"month":"03","publisher":"Springer","status":"public","title":"Mastitis in dairy production: Estimation of sensitivity, specificity and disease prevalence in the absence of a gold standard","author":[{"orcid":"0000-0002-7008-0216","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","full_name":"Caroline Uhler"}],"_id":"3309","date_updated":"2021-01-12T07:42:33Z","issue":"1","abstract":[{"lang":"eng","text":"\n\nMastitis, a worldwide endemic disease of dairy cows, is an important cause of decreased efficiency in milk production. Early medical treatment can reduce the nonreversible losses in milk production caused by this infection. Various diagnostic tests for mastitis are available, including a test measuring the electrical conductivity of milk (MEC test), the industry standard of somatic cell counting (SCC test), a bacteriological test, and a recently developed test measuring mammary associated amyloid A (MAA test). None of these tests is considered a gold standard, however. The aim of the present study was to determine which of these tests provides the best results, and at what cost, to improve the efficiency of milk production. For this study, 25 cows were tested at all four quarters of the udder with each of the aforementioned mastitis diagnostic tests. Based on the data, the disease prevalence as well as the sensitivity and the specificity of the four tests were estimated with a Bayesian approach by extending the Hui and Walter model with two independent tests and two populations to a model with four partially dependent tests and one population. This model was further combined with a receiver operating characteristics analysis to estimate the overall test accuracy."}],"day":"01","extern":1,"year":"2009","quality_controlled":0,"volume":14,"intvolume":"        14","citation":{"chicago":"Uhler, Caroline. “Mastitis in Dairy Production: Estimation of Sensitivity, Specificity and Disease Prevalence in the Absence of a Gold Standard.” <i>Journal of Agricultural Biological and Environmental Statistics</i>. Springer, 2009. <a href=\"https://doi.org/10.1198/jabes.2009.0005\">https://doi.org/10.1198/jabes.2009.0005</a>.","ista":"Uhler C. 2009. Mastitis in dairy production: Estimation of sensitivity, specificity and disease prevalence in the absence of a gold standard. Journal of Agricultural Biological and Environmental Statistics. 14(1), 79–98.","apa":"Uhler, C. (2009). Mastitis in dairy production: Estimation of sensitivity, specificity and disease prevalence in the absence of a gold standard. <i>Journal of Agricultural Biological and Environmental Statistics</i>. Springer. <a href=\"https://doi.org/10.1198/jabes.2009.0005\">https://doi.org/10.1198/jabes.2009.0005</a>","mla":"Uhler, Caroline. “Mastitis in Dairy Production: Estimation of Sensitivity, Specificity and Disease Prevalence in the Absence of a Gold Standard.” <i>Journal of Agricultural Biological and Environmental Statistics</i>, vol. 14, no. 1, Springer, 2009, pp. 79–98, doi:<a href=\"https://doi.org/10.1198/jabes.2009.0005\">10.1198/jabes.2009.0005</a>.","ama":"Uhler C. Mastitis in dairy production: Estimation of sensitivity, specificity and disease prevalence in the absence of a gold standard. <i>Journal of Agricultural Biological and Environmental Statistics</i>. 2009;14(1):79-98. doi:<a href=\"https://doi.org/10.1198/jabes.2009.0005\">10.1198/jabes.2009.0005</a>","ieee":"C. Uhler, “Mastitis in dairy production: Estimation of sensitivity, specificity and disease prevalence in the absence of a gold standard,” <i>Journal of Agricultural Biological and Environmental Statistics</i>, vol. 14, no. 1. Springer, pp. 79–98, 2009.","short":"C. Uhler, Journal of Agricultural Biological and Environmental Statistics 14 (2009) 79–98."},"publist_id":"3331","type":"journal_article","date_published":"2009-03-01T00:00:00Z","publication_status":"published","doi":"10.1198/jabes.2009.0005","date_created":"2018-12-11T12:02:35Z","page":"79 - 98","publication":"Journal of Agricultural Biological and Environmental Statistics"},{"month":"03","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"IOP Publishing Ltd.","status":"public","title":"Reconnection in three dimensions: The role of spines in three eruptive flares","author":[{"last_name":"Des Jardins","first_name":"Angela","full_name":"Des Jardins, Angela"},{"full_name":"Canfield, Richard","first_name":"Richard","last_name":"Canfield"},{"full_name":"Longcope, Dana","first_name":"Dana","last_name":"Longcope"},{"full_name":"Fordyce, Crystal","last_name":"Fordyce","first_name":"Crystal"},{"orcid":"0000-0002-2299-3176","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R"}],"_id":"110","issue":"2","acknowledgement":"This work was supported by RHESSI funds from the University of California at Berkeley through a contract, SA1868-26308PG, with Montana State University. Funding for our Research Experience for Undergraduates (REU) students was provided by NSF grant ATM-0243923.","abstract":[{"lang":"eng","text":"In order to better understand magnetic reconnection and particle acceleration in solar flares, we compare the RHESSI hard X-ray (HXR) footpoint motions of three flares with a detailed study of the corresponding topology given by a Magnetic Charge Topology model. We analyze the relationship between the footpoint motions and topological spine lines and find that the examined footpoint sources move along spine lines. We present a three-dimensional topological model in which this movement can be understood. As reconnection proceeds, flux is transferred between the reconnecting domains, causing the separator to move. The movement of the separator\\'s chromospheric ends, identified with the HXR footpoints, is along those spine lines on which the separator ends."}],"date_updated":"2021-01-12T06:48:16Z","year":"2009","extern":"1","day":"10","quality_controlled":"1","intvolume":"       693","volume":693,"citation":{"chicago":"Des Jardins, Angela, Richard Canfield, Dana Longcope, Crystal Fordyce, and Scott R Waitukaitis. “Reconnection in Three Dimensions: The Role of Spines in Three Eruptive Flares.” <i>The Astrophysical Journal</i>. IOP Publishing Ltd., 2009. <a href=\"https://doi.org/10.1088/0004-637X/693/2/1628\">https://doi.org/10.1088/0004-637X/693/2/1628</a>.","mla":"Des Jardins, Angela, et al. “Reconnection in Three Dimensions: The Role of Spines in Three Eruptive Flares.” <i>The Astrophysical Journal</i>, vol. 693, no. 2, IOP Publishing Ltd., 2009, pp. 1628–36, doi:<a href=\"https://doi.org/10.1088/0004-637X/693/2/1628\">10.1088/0004-637X/693/2/1628</a>.","ista":"Des Jardins A, Canfield R, Longcope D, Fordyce C, Waitukaitis SR. 2009. Reconnection in three dimensions: The role of spines in three eruptive flares. The Astrophysical Journal. 693(2), 1628–1636.","apa":"Des Jardins, A., Canfield, R., Longcope, D., Fordyce, C., &#38; Waitukaitis, S. R. (2009). Reconnection in three dimensions: The role of spines in three eruptive flares. <i>The Astrophysical Journal</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/0004-637X/693/2/1628\">https://doi.org/10.1088/0004-637X/693/2/1628</a>","short":"A. Des Jardins, R. Canfield, D. Longcope, C. Fordyce, S.R. Waitukaitis, The Astrophysical Journal 693 (2009) 1628–1636.","ama":"Des Jardins A, Canfield R, Longcope D, Fordyce C, Waitukaitis SR. Reconnection in three dimensions: The role of spines in three eruptive flares. <i>The Astrophysical Journal</i>. 2009;693(2):1628-1636. doi:<a href=\"https://doi.org/10.1088/0004-637X/693/2/1628\">10.1088/0004-637X/693/2/1628</a>","ieee":"A. Des Jardins, R. Canfield, D. Longcope, C. Fordyce, and S. R. Waitukaitis, “Reconnection in three dimensions: The role of spines in three eruptive flares,” <i>The Astrophysical Journal</i>, vol. 693, no. 2. IOP Publishing Ltd., pp. 1628–1636, 2009."},"publist_id":"7944","oa_version":"None","type":"journal_article","date_published":"2009-03-10T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1088/0004-637X/693/2/1628","publication_status":"published","publication":"The Astrophysical Journal","page":"1628 - 1636","date_created":"2018-12-11T11:44:41Z"},{"publist_id":"7943","citation":{"ista":"Royer J, Evans D, Oyarte L, Guo Q, Kapit E, Möbius M, Waitukaitis SR, Jaeger H. 2009. High-speed tracking of rupture and clustering in freely falling granular streams. Nature. 459(7250), 1110–1113.","mla":"Royer, John, et al. “High-Speed Tracking of Rupture and Clustering in Freely Falling Granular Streams.” <i>Nature</i>, vol. 459, no. 7250, Nature Publishing Group, 2009, pp. 1110–13, doi:<a href=\"https://doi.org/10.1038/nature08115\">10.1038/nature08115</a>.","apa":"Royer, J., Evans, D., Oyarte, L., Guo, Q., Kapit, E., Möbius, M., … Jaeger, H. (2009). High-speed tracking of rupture and clustering in freely falling granular streams. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature08115\">https://doi.org/10.1038/nature08115</a>","chicago":"Royer, John, Daniel Evans, Loreto Oyarte, Qiti Guo, Eliot Kapit, Matthias Möbius, Scott R Waitukaitis, and Heinrich Jaeger. “High-Speed Tracking of Rupture and Clustering in Freely Falling Granular Streams.” <i>Nature</i>. Nature Publishing Group, 2009. <a href=\"https://doi.org/10.1038/nature08115\">https://doi.org/10.1038/nature08115</a>.","ama":"Royer J, Evans D, Oyarte L, et al. High-speed tracking of rupture and clustering in freely falling granular streams. <i>Nature</i>. 2009;459(7250):1110-1113. doi:<a href=\"https://doi.org/10.1038/nature08115\">10.1038/nature08115</a>","ieee":"J. Royer <i>et al.</i>, “High-speed tracking of rupture and clustering in freely falling granular streams,” <i>Nature</i>, vol. 459, no. 7250. Nature Publishing Group, pp. 1110–1113, 2009.","short":"J. Royer, D. Evans, L. Oyarte, Q. Guo, E. Kapit, M. Möbius, S.R. Waitukaitis, H. Jaeger, Nature 459 (2009) 1110–1113."},"intvolume":"       459","volume":459,"quality_controlled":"1","publication_status":"published","doi":"10.1038/nature08115","date_created":"2018-12-11T11:44:41Z","page":"1110 - 1113","publication":"Nature","oa_version":"None","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2009-06-25T00:00:00Z","publisher":"Nature Publishing Group","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"High-speed tracking of rupture and clustering in freely falling granular streams","month":"06","date_updated":"2021-01-12T06:48:21Z","issue":"7250","abstract":[{"lang":"eng","text":"Thin streams of liquid commonly break up into characteristic droplet patterns owing to the surface-tension-driven PlateauRayleigh instability 1-3. Very similar patterns are observed when initially uniform streams of dry granular material break up into clusters of grains4-6, even though flows of macroscopic particles are considered to lack surface tension7,8. Recent studies on freely falling granular streams tracked fluctuations in the stream profile9, but the clustering mechanism remained unresolved because the full evolution of the instability could not be observed. Here we demonstrate that the cluster formation is driven by minute, nanoNewton cohesive forces that arise from a combination of van der Waals interactions and capillary bridges between nanometre-scale surface asperities. Our experiments involve high-speed video imaging of the granular stream in the co-moving frame, control over the properties of the grain surfaces and the use of atomic force microscopy to measure grain-grain interactions. The cohesive forces that we measure correspond to an equivalent surface tension five orders of magnitude below that, of ordinary liquids. We find that, the shapes of these weakly cohesive, non-thermal clusters of macroscopic particles closely resemble droplets resulting from thermally induced rupture of liquid nanojets 10-12."}],"acknowledgement":"This work was supported by NSF through its MRSEC programme and the Inter-American Materials Collaboration Chicago-Chile, and by the Keck Initiative for Ultrafast Imaging at the University of Chicago.","day":"25","extern":"1","year":"2009","author":[{"full_name":"Royer, John","last_name":"Royer","first_name":"John"},{"first_name":"Daniel","last_name":"Evans","full_name":"Evans, Daniel"},{"full_name":"Oyarte, Loreto","last_name":"Oyarte","first_name":"Loreto"},{"full_name":"Guo, Qiti","first_name":"Qiti","last_name":"Guo"},{"first_name":"Eliot","last_name":"Kapit","full_name":"Kapit, Eliot"},{"first_name":"Matthias","last_name":"Möbius","full_name":"Möbius, Matthias"},{"last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","first_name":"Scott R","full_name":"Waitukaitis, Scott R"},{"first_name":"Heinrich","last_name":"Jaeger","full_name":"Jaeger, Heinrich"}],"_id":"111"}]