[{"publication_status":"published","day":"28","type":"journal_article","volume":459,"year":"2009","doi":"10.1038/nature07875","date_created":"2018-12-11T12:01:06Z","status":"public","publist_id":"3646","issue":"7246","title":"A regulated auxin minimum is required for seed dispersal in Arabidopsis","date_updated":"2021-01-12T07:40:44Z","month":"05","publisher":"Nature Publishing Group","quality_controlled":0,"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"}],"extern":1,"publication":"Nature","author":[{"full_name":"Sorefan, Karim","last_name":"Sorefan","first_name":"Karim"},{"full_name":"Girin, Thomas","last_name":"Girin","first_name":"Thomas"},{"last_name":"Liljegren","first_name":"Sarah","full_name":"Liljegren, Sarah J"},{"last_name":"Ljung","first_name":"Karin","full_name":"Ljung, Karin"},{"full_name":"Robles, Pedro","first_name":"Pedro","last_name":"Robles"},{"first_name":"Carlos","last_name":"Galván Ampudia","full_name":"Galván-Ampudia, Carlos S"},{"full_name":"Offringa, Remko","last_name":"Offringa","first_name":"Remko"},{"last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"},{"first_name":"Martin","last_name":"Yanofsky","full_name":"Yanofsky, Martin F"},{"first_name":"Lars","last_name":"Østergaard","full_name":"Østergaard, Lars"}],"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>.","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>","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>.","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.","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."},"date_published":"2009-05-28T00:00:00Z","page":"583 - 586","_id":"3056","intvolume":"       459"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":136,"year":"2009","publication_status":"published","date_updated":"2021-01-12T07:40:45Z","author":[{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml"}],"external_id":{"pmid":["    19633168"]},"extern":"1","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"}],"_id":"3057","oa_version":"Published Version","page":"2675 - 2688","oa":1,"status":"public","doi":"10.1242/dev.030353","date_created":"2018-12-11T12:01:07Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/19633168","open_access":"1"}],"day":"15","type":"journal_article","title":"Auxin transport routes in plant development","issue":"16","publist_id":"3644","publication":"Development","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Company of Biologists","pmid":1,"month":"08","intvolume":"       136","date_published":"2009-08-15T00:00:00Z","citation":{"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>.","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>","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>.","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.","short":"J. Petrášek, J. Friml, Development 136 (2009) 2675–2688.","ista":"Petrášek J, Friml J. 2009. Auxin transport routes in plant development. Development. 136(16), 2675–2688.","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>"}},{"author":[{"last_name":"Mravec","first_name":"Jozef","full_name":"Mravec, Jozef"},{"first_name":"Petr","last_name":"Skůpa","full_name":"Skůpa, Petr"},{"first_name":"Aurélien","last_name":"Bailly","full_name":"Bailly, Aurélien"},{"full_name":"Hoyerová, Klára","first_name":"Klára","last_name":"Hoyerová"},{"last_name":"Křeček","first_name":"Pavel","full_name":"Křeček, Pavel"},{"full_name":"Bielach, Agnieszka","last_name":"Bielach","first_name":"Agnieszka"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"full_name":"Zhang, Jing","first_name":"Jing","last_name":"Zhang"},{"full_name":"Gaykova, Vassilena","first_name":"Vassilena","last_name":"Gaykova"},{"last_name":"Stierhof","first_name":"York","full_name":"Stierhof, York-Dieter"},{"full_name":"Dobrev, Petre I","first_name":"Petre","last_name":"Dobrev"},{"full_name":"Schwarzerová, Kateřina","last_name":"Schwarzerová","first_name":"Kateřina"},{"full_name":"Rolčík, Jakub","first_name":"Jakub","last_name":"Rolčík"},{"full_name":"Seifertová, Daniela","first_name":"Daniela","last_name":"Seifertová"},{"full_name":"Luschnig, Christian","first_name":"Christian","last_name":"Luschnig"},{"full_name":"Eva Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"full_name":"Geisler, Markus","first_name":"Markus","last_name":"Geisler"},{"first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publication":"Nature","abstract":[{"lang":"eng","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."}],"extern":1,"quality_controlled":0,"publisher":"Nature Publishing Group","month":"06","intvolume":"       459","_id":"3058","page":"1136 - 1140","date_published":"2009-06-25T00:00:00Z","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>.","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>.","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>","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.","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>"},"status":"public","doi":"10.1038/nature08066","date_created":"2018-12-11T12:01:07Z","volume":459,"year":"2009","day":"25","type":"journal_article","publication_status":"published","date_updated":"2021-01-12T07:40:45Z","issue":"7250","title":"Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter","publist_id":"3645"},{"date_published":"2009-12-01T00:00:00Z","citation":{"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>.","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.","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>.","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>","short":"J. Kleine Vehn, F. Huang, S. Naramoto, J. Zhang, M. Michniewicz, R. Offringa, J. Friml, Plant Cell 21 (2009) 3839–3849.","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.","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>"},"page":"3839 - 3849","intvolume":"        21","_id":"3059","month":"12","publisher":"American Society of Plant Biologists","extern":1,"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"}],"quality_controlled":0,"author":[{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"last_name":"Huang","first_name":"Fang","full_name":"Huang, Fang"},{"full_name":"Naramoto, Satoshi","last_name":"Naramoto","first_name":"Satoshi"},{"first_name":"Jing","last_name":"Zhang","full_name":"Zhang, Jing"},{"first_name":"Marta","last_name":"Michniewicz","full_name":"Michniewicz, Marta"},{"full_name":"Offringa, Remko","last_name":"Offringa","first_name":"Remko"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml"}],"publication":"Plant Cell","publist_id":"3643","title":"PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis","issue":"12","date_updated":"2021-01-12T07:40:45Z","type":"journal_article","day":"01","publication_status":"published","volume":21,"year":"2009","date_created":"2018-12-11T12:01:07Z","doi":"10.1105/tpc.109.071639","status":"public"},{"oa_version":"None","_id":"3060","intvolume":"        12","date_published":"2009-12-01T00:00:00Z","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.","short":"K. Schumacher, J. Friml, Current Opinion in Plant Biology 12 (2009) 651–652.","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>","ieee":"K. Schumacher and J. Friml, “Cell biology,” <i>Current Opinion in Plant Biology</i>, vol. 12, no. 6. Elsevier, pp. 651–652, 2009.","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>.","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>."},"article_type":"letter_note","page":"651 - 652","extern":"1","quality_controlled":"1","author":[{"full_name":"Schumacher, Karin","first_name":"Karin","last_name":"Schumacher"},{"first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publication":"Current Opinion in Plant Biology","month":"12","language":[{"iso":"eng"}],"publisher":"Elsevier","title":"Cell biology","issue":"6","date_updated":"2021-01-12T07:40:46Z","publist_id":"3641","doi":"10.1016/j.pbi.2009.10.009","date_created":"2018-12-11T12:01:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","type":"journal_article","day":"01","publication_status":"published","volume":12,"year":"2009"},{"date_created":"2018-12-11T12:01:08Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812941/","open_access":"1"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1186/gb-2009-10-12-249","status":"public","type":"journal_article","day":"29","publication_status":"published","volume":10,"year":"2009","title":"The PIN-FORMED (PIN) protein family of auxin transporters","issue":"12","date_updated":"2021-01-12T07:40:46Z","publist_id":"3640","abstract":[{"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.","lang":"eng"}],"extern":"1","quality_controlled":"1","author":[{"full_name":"Křeček, Pavel","last_name":"Křeček","first_name":"Pavel"},{"last_name":"Skůpa","first_name":"Petr","full_name":"Skůpa, Petr"},{"last_name":"Libus","first_name":"Jiří","full_name":"Libus, Jiří"},{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"last_name":"Zažímalová","first_name":"Eva","full_name":"Zažímalová, Eva"}],"publication":"Genome Biology","external_id":{"pmid":["20053306"]},"month":"12","pmid":1,"language":[{"iso":"eng"}],"publisher":"BioMed Central","oa_version":"Published Version","intvolume":"        10","_id":"3061","date_published":"2009-12-29T00:00:00Z","citation":{"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>","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).","short":"P. Křeček, P. Skůpa, J. Libus, S. Naramoto, R. Tejos, J. Friml, E. Zažímalová, Genome Biology 10 (2009).","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.","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>."},"oa":1},{"publication":"Journal of Machine Learning Research","author":[{"full_name":"Kumar, M Pawan","first_name":"M Pawan","last_name":"Kumar"},{"first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Torr, Philip H","first_name":"Philip","last_name":"Torr"}],"quality_controlled":0,"extern":1,"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"}],"publisher":"Microtome Publishing","month":"01","intvolume":"        10","_id":"3197","page":"71 - 106","oa":1,"citation":{"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.","short":"M.P. Kumar, V. Kolmogorov, P. Torr, Journal of Machine Learning Research 10 (2009) 71–106.","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.","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.","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."},"date_published":"2009-01-01T00:00:00Z","status":"public","date_created":"2018-12-11T12:01:57Z","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-00773608"}],"volume":10,"year":"2009","publication_status":"published","type":"journal_article","day":"01","date_updated":"2021-01-12T07:41:44Z","title":"An analysis of convex relaxations for MAP estimation of discrete MRFs","publist_id":"3484"},{"publist_id":"3482","date_updated":"2021-01-12T07:41:44Z","title":"Joint optimization of segmentation and appearance models","year":"2009","day":"01","type":"conference","publication_status":"published","status":"public","main_file_link":[{"open_access":"0","url":"http://www.robots.ox.ac.uk/~vgg/rg/papers/segmentationappearance.pdf"}],"doi":"10.1109/ICCV.2009.5459287","date_created":"2018-12-11T12:01:58Z","conference":{"name":"ICCV: International Conference on Computer Vision"},"page":"755 - 762","date_published":"2009-05-01T00:00:00Z","citation":{"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>.","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>","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>.","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>","ista":"Vicente S, Kolmogorov V, Rother C. 2009. Joint optimization of segmentation and appearance models. ICCV: International Conference on Computer Vision, 755–762.","short":"S. Vicente, V. Kolmogorov, C. Rother, in:, IEEE, 2009, pp. 755–762."},"_id":"3199","publisher":"IEEE","month":"05","author":[{"last_name":"Vicente","first_name":"Sara","full_name":"Vicente, Sara"},{"first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"}],"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"}],"extern":1,"quality_controlled":0},{"publication_status":"published","type":"journal_article","day":"01","year":"2009","volume":6,"doi":"10.1016/j.disopt.2009.04.006","date_created":"2018-12-11T12:01:58Z","status":"public","publist_id":"3483","issue":"4","title":"New algorithms for convex cost tension problem with application to computer vision","date_updated":"2021-01-12T07:41:45Z","month":"11","publisher":"Elsevier","quality_controlled":0,"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."}],"extern":1,"publication":"Discrete Optimization","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov","first_name":"Vladimir"},{"full_name":"Shioura, Akiyoshi","last_name":"Shioura","first_name":"Akiyoshi"}],"citation":{"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>.","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.","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>.","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.","short":"V. Kolmogorov, A. Shioura, Discrete Optimization 6 (2009) 378–393."},"date_published":"2009-11-01T00:00:00Z","page":"378 - 393","intvolume":"         6","_id":"3200"},{"publist_id":"3481","title":"A global perspective on MAP inference for low level vision","date_updated":"2021-01-12T07:41:46Z","type":"conference","day":"01","publication_status":"published","year":"2009","doi":"10.1109/ICCV.2009.5459434","date_created":"2018-12-11T12:01:59Z","status":"public","date_published":"2009-05-01T00:00:00Z","citation":{"short":"O. Woodford, C. Rother, V. Kolmogorov, in:, IEEE, 2009, pp. 2319–2326.","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.","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>","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>.","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.","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>.","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>"},"conference":{"name":"ICCV: International Conference on Computer Vision"},"page":"2319 - 2326","_id":"3203","month":"05","publisher":"IEEE","extern":1,"abstract":[{"lang":"eng","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."}],"quality_controlled":0,"author":[{"first_name":"Oliver","last_name":"Woodford","full_name":"Woodford, Oliver J"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"},{"full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"}]},{"year":"2009","volume":5479,"publication_status":"published","type":"conference","day":"28","status":"public","date_created":"2018-12-11T12:02:09Z","doi":"10.1007/978-3-642-01001-9_34","alternative_title":["LNCS"],"publist_id":"3449","date_updated":"2021-01-12T07:41:58Z","title":"A new randomness extraction paradigm for hybrid encryption","publisher":"Springer","month":"05","author":[{"full_name":"Kiltz, Eike","first_name":"Eike","last_name":"Kiltz"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Krzysztof Pietrzak"},{"last_name":"Stam","first_name":"Martijn","full_name":"Stam, Martijn"},{"full_name":"Yung, Moti","last_name":"Yung","first_name":"Moti"}],"quality_controlled":0,"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"}],"extern":1,"page":"590 - 609","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"citation":{"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>.","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>","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>.","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.","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>","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."},"date_published":"2009-05-28T00:00:00Z","intvolume":"      5479","_id":"3230"},{"doi":"10.1007/978-3-642-01001-9_23","date_created":"2018-12-11T12:02:09Z","status":"public","day":"28","type":"conference","publication_status":"published","year":"2009","volume":5479,"title":"On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model","date_updated":"2021-01-12T07:41:58Z","publist_id":"3450","alternative_title":["LNCS"],"abstract":[{"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. ","lang":"eng"}],"extern":1,"quality_controlled":0,"author":[{"last_name":"Kiltz","first_name":"Eike","full_name":"Kiltz, Eike"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Krzysztof Pietrzak","orcid":"0000-0002-9139-1654"}],"month":"05","publisher":"Springer","_id":"3231","intvolume":"      5479","date_published":"2009-05-28T00:00:00Z","citation":{"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.","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>","short":"E. Kiltz, K.Z. Pietrzak, in:, Springer, 2009, pp. 389–406.","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.","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>.","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>."},"conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"page":"389 - 406"},{"doi":"10.1007/978-3-642-01001-9_27","date_created":"2018-12-11T12:02:09Z","status":"public","publication_status":"published","day":"28","type":"conference","volume":5479,"year":"2009","title":"A leakage resilient mode of operation","date_updated":"2021-01-12T07:41:59Z","publist_id":"3448","alternative_title":["LNCS"],"quality_controlled":0,"extern":1,"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. "}],"author":[{"last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Krzysztof Pietrzak","orcid":"0000-0002-9139-1654"}],"month":"05","publisher":"Springer","intvolume":"      5479","_id":"3232","citation":{"ieee":"K. Z. Pietrzak, “A leakage resilient mode of operation,” presented at the CRYPTO: International Cryptology Conference, 2009, vol. 5479, pp. 462–482.","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>.","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>","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>.","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>","ista":"Pietrzak KZ. 2009. A leakage resilient mode of operation. CRYPTO: International Cryptology Conference, LNCS, vol. 5479, 462–482.","short":"K.Z. Pietrzak, in:, Springer, 2009, pp. 462–482."},"date_published":"2009-05-28T00:00:00Z","page":"462 - 482","conference":{"name":"CRYPTO: International Cryptology Conference"}},{"oa_version":"None","_id":"3292","intvolume":"       284","citation":{"short":"J. Engel, P.S. Schmalhorst, T. Dörk Bousset, V. Ferrières, F. Routier, Journal of Biological Chemistry 284 (2009) 33859–33868.","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>","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>.","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.","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>"},"date_published":"2009-12-04T00:00:00Z","page":"33859 - 33868","quality_controlled":"1","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"}],"extern":"1","publication":"Journal of Biological Chemistry","author":[{"first_name":"Jakob","last_name":"Engel","full_name":"Engel, Jakob"},{"first_name":"Philipp S","last_name":"Schmalhorst","full_name":"Schmalhorst, Philipp S","orcid":"0000-0002-5795-0133","id":"309D50DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dörk Bousset, Thilo","last_name":"Dörk Bousset","first_name":"Thilo"},{"full_name":"Ferrières, Vincent","first_name":"Vincent","last_name":"Ferrières"},{"first_name":"Françoise","last_name":"Routier","full_name":"Routier, Françoise"}],"month":"12","publisher":"American Society for Biochemistry and Molecular Biology","language":[{"iso":"eng"}],"issue":"49","title":"A single UDP galactofuranose transporter is required for galactofuranosylation in Aspergillus fumigatus","date_updated":"2021-01-12T07:42:26Z","publist_id":"3353","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1074/jbc.M109.070219 ","date_created":"2018-12-11T12:02:30Z","status":"public","publication_status":"published","day":"04","type":"journal_article","volume":284,"year":"2009"},{"volume":23,"year":"2009","type":"journal_article","day":"01","publication_status":"published","status":"public","date_created":"2018-12-11T12:02:30Z","doi":"10.1080/01677060802491559 ","publist_id":"3348","date_updated":"2021-01-12T07:42:27Z","title":"Sensory correlates of imaginal conditioning in Drosophila melanogaster","issue":"1-2","publisher":"Informa Healthcare","month":"01","author":[{"full_name":"Chakraborty Tuhin, Subhra","first_name":"Subhra","last_name":"Chakraborty Tuhin"},{"last_name":"Goswami","first_name":"Sarit","id":"3A578F32-F248-11E8-B48F-1D18A9856A87","full_name":"Sarit Goswami"},{"last_name":"Siddiqi","first_name":"Obaid","full_name":"Siddiqi, Obaid"}],"publication":"Journal of Neurogenetics","extern":1,"abstract":[{"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.","lang":"eng"}],"quality_controlled":0,"page":"210 - 9","date_published":"2009-01-01T00:00:00Z","citation":{"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>.","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>","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>.","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.","short":"S. Chakraborty Tuhin, S. Goswami, O. Siddiqi, Journal of Neurogenetics 23 (2009) 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>","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."},"intvolume":"        23","_id":"3293"},{"publication_status":"published","type":"journal_article","day":"01","year":"2009","volume":75,"date_created":"2018-12-11T12:02:34Z","doi":"10.1016/j.tpb.2009.02.006","status":"public","publist_id":"3336","title":"The rate at which asexual populations cross fitness valleys","issue":"4","date_updated":"2021-01-12T07:42:31Z","month":"06","publisher":"Academic Press","quality_controlled":0,"extern":1,"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."}],"publication":"Theoretical Population Biology","author":[{"first_name":"Daniel","last_name":"Weissman","full_name":"Daniel Weissman","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","last_name":"Desai","full_name":"Desai, Michael M"},{"full_name":"Fisher, Daniel S","last_name":"Fisher","first_name":"Daniel"},{"first_name":"Marcus","last_name":"Feldman","full_name":"Feldman, Marcus W"}],"citation":{"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.","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>","short":"D. Weissman, M. Desai, D. Fisher, M. Feldman, Theoretical Population Biology 75 (2009) 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>.","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.","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>","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>."},"date_published":"2009-06-01T00:00:00Z","page":"286 - 300","intvolume":"        75","_id":"3304"},{"author":[{"last_name":"Uhler","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Caroline Uhler","orcid":"0000-0002-7008-0216"}],"publication":"Journal of Agricultural Biological and Environmental Statistics","extern":1,"abstract":[{"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.","lang":"eng"}],"quality_controlled":0,"publisher":"Springer","month":"03","_id":"3309","intvolume":"        14","page":"79 - 98","date_published":"2009-03-01T00:00:00Z","citation":{"short":"C. Uhler, Journal of Agricultural Biological and Environmental Statistics 14 (2009) 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>","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.","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>.","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.","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>.","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>"},"status":"public","date_created":"2018-12-11T12:02:35Z","doi":"10.1198/jabes.2009.0005","volume":14,"year":"2009","day":"01","type":"journal_article","publication_status":"published","date_updated":"2021-01-12T07:42:33Z","issue":"1","title":"Mastitis in dairy production: Estimation of sensitivity, specificity and disease prevalence in the absence of a gold standard","publist_id":"3331"},{"date_updated":"2021-01-12T07:43:00Z","title":"Reaction regimes on the synthesis of hollow particles by the Kirkendall effect","issue":"32","publist_id":"7494","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1021/ja903751p","date_created":"2018-12-11T11:45:53Z","year":"2009","volume":131,"publication_status":"published","type":"journal_article","day":"01","intvolume":"       131","_id":"337","oa_version":"None","page":"11326 - 11328","article_type":"original","citation":{"short":"A. Cabot, M. Ibáñez, P. Guardia, P. Alivisatos, Journal of the American Chemical Society 131 (2009) 11326–11328.","ista":"Cabot A, Ibáñez M, Guardia P, Alivisatos P. 2009. Reaction regimes on the synthesis of hollow particles by the Kirkendall effect. Journal of the American Chemical Society. 131(32), 11326–11328.","apa":"Cabot, A., Ibáñez, M., Guardia, P., &#38; Alivisatos, P. (2009). Reaction regimes on the synthesis of hollow particles by the Kirkendall effect. <i>Journal of the American Chemical Society</i>. ACS. <a href=\"https://doi.org/10.1021/ja903751p\">https://doi.org/10.1021/ja903751p</a>","mla":"Cabot, Andreu, et al. “Reaction Regimes on the Synthesis of Hollow Particles by the Kirkendall Effect.” <i>Journal of the American Chemical Society</i>, vol. 131, no. 32, ACS, 2009, pp. 11326–28, doi:<a href=\"https://doi.org/10.1021/ja903751p\">10.1021/ja903751p</a>.","ama":"Cabot A, Ibáñez M, Guardia P, Alivisatos P. Reaction regimes on the synthesis of hollow particles by the Kirkendall effect. <i>Journal of the American Chemical Society</i>. 2009;131(32):11326-11328. doi:<a href=\"https://doi.org/10.1021/ja903751p\">10.1021/ja903751p</a>","ieee":"A. Cabot, M. Ibáñez, P. Guardia, and P. Alivisatos, “Reaction regimes on the synthesis of hollow particles by the Kirkendall effect,” <i>Journal of the American Chemical Society</i>, vol. 131, no. 32. ACS, pp. 11326–11328, 2009.","chicago":"Cabot, Andreu, Maria Ibáñez, Pablo Guardia, and Paul Alivisatos. “Reaction Regimes on the Synthesis of Hollow Particles by the Kirkendall Effect.” <i>Journal of the American Chemical Society</i>. ACS, 2009. <a href=\"https://doi.org/10.1021/ja903751p\">https://doi.org/10.1021/ja903751p</a>."},"date_published":"2009-01-01T00:00:00Z","publication":"Journal of the American Chemical Society","author":[{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"},{"last_name":"Ibáñez","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"},{"full_name":"Guardia, Pablo","last_name":"Guardia","first_name":"Pablo"},{"last_name":"Alivisatos","first_name":"Paul","full_name":"Alivisatos, Paul"}],"quality_controlled":"1","article_processing_charge":"No","extern":"1","abstract":[{"text":"The formation of hollow vs solid particles by means of the oxidation reaction of solid metal particles depends on the differential self-diffusivities of the reactants through the composite shell, the reaction probabilities at each interface, and the concentration and diffusivity of the element in solution. By means of a kinetic model of the oxidation process, we determine the phase diagrams for the geometry of the oxidized particles and propose four shell growth regimes. We experimentally illustrate the different growth scenarios by changing the conditions of oxidation of cadmium spherical crystals using different chalcogen precursors. ","lang":"eng"}],"publisher":"ACS","language":[{"iso":"eng"}],"month":"01"},{"intvolume":"       139","_id":"3398","oa_version":"None","page":"460 - 461","date_published":"2009-10-30T00:00:00Z","citation":{"short":"M.T. Bollenbach, R. Kishony, Cell 139 (2009) 460–461.","ista":"Bollenbach MT, Kishony R. 2009. Quiet gene circuit more fragile than its noisy peer. Cell. 139(3), 460–461.","apa":"Bollenbach, M. T., &#38; Kishony, R. (2009). Quiet gene circuit more fragile than its noisy peer. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2009.10.005\">https://doi.org/10.1016/j.cell.2009.10.005</a>","mla":"Bollenbach, Mark Tobias, and Roy Kishony. “Quiet Gene Circuit More Fragile than Its Noisy Peer.” <i>Cell</i>, vol. 139, no. 3, Cell Press, 2009, pp. 460–61, doi:<a href=\"https://doi.org/10.1016/j.cell.2009.10.005\">10.1016/j.cell.2009.10.005</a>.","ama":"Bollenbach MT, Kishony R. Quiet gene circuit more fragile than its noisy peer. <i>Cell</i>. 2009;139(3):460-461. doi:<a href=\"https://doi.org/10.1016/j.cell.2009.10.005\">10.1016/j.cell.2009.10.005</a>","ieee":"M. T. Bollenbach and R. Kishony, “Quiet gene circuit more fragile than its noisy peer,” <i>Cell</i>, vol. 139, no. 3. Cell Press, pp. 460–461, 2009.","chicago":"Bollenbach, Mark Tobias, and Roy Kishony. “Quiet Gene Circuit More Fragile than Its Noisy Peer.” <i>Cell</i>. Cell Press, 2009. <a href=\"https://doi.org/10.1016/j.cell.2009.10.005\">https://doi.org/10.1016/j.cell.2009.10.005</a>."},"author":[{"first_name":"Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roy","last_name":"Kishony","full_name":"Kishony, Roy"}],"publication":"Cell","abstract":[{"lang":"eng","text":"Why is a particular architecture for a pathway chosen over seemingly equivalent alternatives? Çağatay et al. (2009) use a synthetic biology approach to show that fluctuations—or noise—in protein levels may play a key role in determining which network design is selected during evolution."}],"article_processing_charge":"No","extern":"1","language":[{"iso":"eng"}],"publisher":"Cell Press","month":"10","date_updated":"2021-01-12T07:43:12Z","title":"Quiet gene circuit more fragile than its noisy peer","issue":"3","publist_id":"3061","status":"public","doi":"10.1016/j.cell.2009.10.005","date_created":"2018-12-11T12:03:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":139,"year":"2009","type":"journal_article","day":"30","publication_status":"published"},{"publisher":"Gottfried Wilhelm Leibniz Universität Hannover","month":"08","author":[{"last_name":"Schmalhorst","first_name":"Philipp S","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","full_name":"Philipp Schmalhorst","orcid":"0000-0002-5795-0133"}],"quality_controlled":0,"extern":1,"abstract":[{"lang":"eng","text":"Invasive fungal infections pose a serious threat to immunocompromised people. Most of these infections are caused by either Candida or Aspergillus species, with A. fumigatus being the predominant causative agent of Invasive Aspergillosis. Affected people comprise mainly haematopoietic stem cell or solid organ transplant patients who receive either high-dose corticosteroids or immunosuppressants. These risk factors predispose to the development of Invasive\nAspergillosis which is lethal in 20 to 80 % of the cases, largely due to insufficient efficacy of current antifungal therapy. Thus one major aim in current mycological research is the identification of new drug targets.\nThe polysaccharide-based fungal cell wall is both essential to fungi and absent from human cells which makes it appear an attractive new target. Notably, many components of the A. fumigatus cell wall, including the polysaccharide galactomannan, glycoproteins, and glycolipids, contain the unusual sugar galactofuranose (Galf). In contrast to the other cell wall monosaccharides, Galf does not occur on human cells but is known as component of cell surface molecules of many pathogenic bacteria and protozoa, such as Mycobacterium tuberculosis or Leishmania major. These molecules are often essential for virulence or viability of these organisms which suggested a possible role of Galf in the pathogenicity of A. fumigatus.\nTo address the importance of Galf in A. fumigatus, the key biosynthesis gene glfA, encoding UDPgalactopyranose mutase (UGM), was deleted. In different experimental approaches it was demonstrated that the absence of the glfA gene led to a complete loss of Galf-containing glycans.\nAnalysis of the DeltaglfA phenotype revealed growth and sporulation defects, reduced thermotolerance and an increased susceptibility to antifungal drugs. Electron Microscopy indicated a cell wall defect as a likely cause for the observed impairments. Furthermore, the virulence of the DeltaglfA mutant was found to be severely attenuated in a murine model of Invasive Aspergillosis.\nThe second focus of this study was laid on further elucidation of the galactofuranosylation pathway in A. fumigatus. In eukaryotes, a UDP-Galf transporter is likely required to transport UDP-Galf from the\ncytosol into the organelles of the secretory pathway, but no such activity had been described. Sixteen candidate genes were identified in the A. fumigatus genome of which one, glfB, was found in close proximity to the glfA gene. In vitro transport assays revealed specificity of GlfB for UDP-Galf suggesting that glfB encoded indeed a UDP-Galf transporter. The influence of glfB on\ngalactofuranosylation was determined by a DeltaglfB deletion mutant, which closely recapitulated the DeltaglfA phenotype and was likewise found to be completely devoid of Galf. It could be concluded that all galactofuranosylation processes in A. fumigatus occur in the secretory pathway, including the biosynthesis of the cell wall polysaccharide galactomannan whose subcellular origin was previously disputed.\n\nThus in the course of this study the first UDP-Galf specific nucleotide sugar transporter was identified and its requirement for galactofuranosylation in A. fumigatus demonstrated. Moreover, it was shown that blocking the galactofuranosylation pathway impaired virulence of A. fumigatus which suggests the UDP-Galf biosynthesis enzyme UGM as a target for new antifungal drugs."}],"page":"1 - 72","citation":{"mla":"Schmalhorst, Philipp S. <i>Biosynthesis of Galactofuranose Containing Glycans and Their Relevance for the Pathogenic Fungus Aspergillus Fumigatus</i>. Gottfried Wilhelm Leibniz Universität Hannover, 2009, pp. 1–72.","ama":"Schmalhorst PS. Biosynthesis of Galactofuranose Containing Glycans and Their Relevance for the Pathogenic Fungus Aspergillus fumigatus. 2009:1-72.","chicago":"Schmalhorst, Philipp S. “Biosynthesis of Galactofuranose Containing Glycans and Their Relevance for the Pathogenic Fungus Aspergillus Fumigatus.” Gottfried Wilhelm Leibniz Universität Hannover, 2009.","ieee":"P. S. Schmalhorst, “Biosynthesis of Galactofuranose Containing Glycans and Their Relevance for the Pathogenic Fungus Aspergillus fumigatus,” Gottfried Wilhelm Leibniz Universität Hannover, 2009.","short":"P.S. Schmalhorst, Biosynthesis of Galactofuranose Containing Glycans and Their Relevance for the Pathogenic Fungus Aspergillus Fumigatus, Gottfried Wilhelm Leibniz Universität Hannover, 2009.","apa":"Schmalhorst, P. S. (2009). <i>Biosynthesis of Galactofuranose Containing Glycans and Their Relevance for the Pathogenic Fungus Aspergillus fumigatus</i>. Gottfried Wilhelm Leibniz Universität Hannover.","ista":"Schmalhorst PS. 2009. Biosynthesis of Galactofuranose Containing Glycans and Their Relevance for the Pathogenic Fungus Aspergillus fumigatus. Gottfried Wilhelm Leibniz Universität Hannover."},"date_published":"2009-08-13T00:00:00Z","_id":"3400","year":"2009","publication_status":"published","day":"13","type":"dissertation","status":"public","main_file_link":[{"open_access":"0","url":"http://edok01.tib.uni-hannover.de/edoks/e01dh09/609861891.pdf"}],"date_created":"2018-12-11T12:03:07Z","publist_id":"3058","date_updated":"2021-01-12T07:43:13Z","title":"Biosynthesis of Galactofuranose Containing Glycans and Their Relevance for the Pathogenic Fungus Aspergillus fumigatus"}]