[{"status":"public","author":[{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"first_name":"Tomoko","full_name":"Dainobu, Tomoko","last_name":"Dainobu"},{"first_name":"Hirotomo","full_name":"Takatsuka, Hirotomo","last_name":"Takatsuka"},{"full_name":"Okada, Teruyo","last_name":"Okada","first_name":"Teruyo"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"full_name":"Fukuda, Hiroo","last_name":"Fukuda","first_name":"Hiroo"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:56:06Z","scopus_import":1,"abstract":[{"lang":"eng","text":"Leaf venation develops complex patterns in angiosperms, but the mechanism underlying this process is largely unknown. To elucidate the molecular mechanisms governing vein pattern formation, we previously isolated vascular network defective (van) mutants that displayed venation discontinuities. Here, we report the phenotypic analysis of van4 mutants, and we identify and characterize the VAN4 gene. Detailed phenotypic analysis shows that van4 mutants are defective in procambium cell differentiation and subsequent vascular cell differentiation. Reduced shoot and root cell growth is observed in van4 mutants, suggesting that VAN4 function is important for cell growth and the establishment of venation continuity. Consistent with these phenotypes, the VAN4 gene is strongly expressed in vascular and meristematic cells. VAN4 encodes a putative TRS120, which is a known guanine nucleotide exchange factor (GEF) for Rab GTPase involved in regulating vesicle transport, and a known tethering factor that determines the specificity of membrane fusion. VAN4 protein localizes at the trans-Golgi network/early endosome (TGN/EE). Aberrant recycling of the auxin efflux carrier PIN proteins is observed in van4 mutants. These results suggest that VAN4-mediated exocytosis at the TGN plays important roles in plant vascular development and cell growth in shoot and root. Our identification of VAN4 as a putative TRS120 shows that Rab GTPases are crucial (in addition to ARF GTPases) for continuous vascular development, and provides further evidence for the importance of vesicle transport in leaf vascular formation."}],"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"year":"2014","month":"04","publication_identifier":{"issn":["00320781"]},"department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","publication_status":"published","issue":"4","_id":"2222","oa_version":"None","type":"journal_article","doi":"10.1093/pcp/pcu012","ec_funded":1,"publication":"Plant and Cell Physiology","day":"01","volume":55,"date_published":"2014-04-01T00:00:00Z","intvolume":"        55","page":"750 - 763","publist_id":"4742","title":"VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis","quality_controlled":"1","date_created":"2018-12-11T11:56:24Z","citation":{"chicago":"Naramoto, Satoshi, Tomasz Nodzyński, Tomoko Dainobu, Hirotomo Takatsuka, Teruyo Okada, Jiří Friml, and Hiroo Fukuda. “VAN4 Encodes a Putative TRS120 That Is Required for Normal Cell Growth and Vein Development in Arabidopsis.” <i>Plant and Cell Physiology</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/pcp/pcu012\">https://doi.org/10.1093/pcp/pcu012</a>.","apa":"Naramoto, S., Nodzyński, T., Dainobu, T., Takatsuka, H., Okada, T., Friml, J., &#38; Fukuda, H. (2014). VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. <i>Plant and Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcu012\">https://doi.org/10.1093/pcp/pcu012</a>","mla":"Naramoto, Satoshi, et al. “VAN4 Encodes a Putative TRS120 That Is Required for Normal Cell Growth and Vein Development in Arabidopsis.” <i>Plant and Cell Physiology</i>, vol. 55, no. 4, Oxford University Press, 2014, pp. 750–63, doi:<a href=\"https://doi.org/10.1093/pcp/pcu012\">10.1093/pcp/pcu012</a>.","short":"S. Naramoto, T. Nodzyński, T. Dainobu, H. Takatsuka, T. Okada, J. Friml, H. Fukuda, Plant and Cell Physiology 55 (2014) 750–763.","ieee":"S. Naramoto <i>et al.</i>, “VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis,” <i>Plant and Cell Physiology</i>, vol. 55, no. 4. Oxford University Press, pp. 750–763, 2014.","ista":"Naramoto S, Nodzyński T, Dainobu T, Takatsuka H, Okada T, Friml J, Fukuda H. 2014. VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. Plant and Cell Physiology. 55(4), 750–763.","ama":"Naramoto S, Nodzyński T, Dainobu T, et al. VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. <i>Plant and Cell Physiology</i>. 2014;55(4):750-763. doi:<a href=\"https://doi.org/10.1093/pcp/pcu012\">10.1093/pcp/pcu012</a>"}},{"oa":1,"quality_controlled":"1","citation":{"ieee":"H. Tanaka <i>et al.</i>, “BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis,” <i>Plant and Cell Physiology</i>, vol. 55, no. 4. Oxford University Press, pp. 737–749, 2014.","ista":"Tanaka H, Nodzyński T, Kitakura S, Feraru M, Sasabe M, Ishikawa T, Kleine Vehn J, Kakimoto T, Friml J. 2014. BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. Plant and Cell Physiology. 55(4), 737–749.","short":"H. Tanaka, T. Nodzyński, S. Kitakura, M. Feraru, M. Sasabe, T. Ishikawa, J. Kleine Vehn, T. Kakimoto, J. Friml, Plant and Cell Physiology 55 (2014) 737–749.","ama":"Tanaka H, Nodzyński T, Kitakura S, et al. BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. <i>Plant and Cell Physiology</i>. 2014;55(4):737-749. doi:<a href=\"https://doi.org/10.1093/pcp/pct196\">10.1093/pcp/pct196</a>","mla":"Tanaka, Hirokazu, et al. “BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling of PIN Auxin Transporters and Auxin-Mediated Development in Arabidopsis.” <i>Plant and Cell Physiology</i>, vol. 55, no. 4, Oxford University Press, 2014, pp. 737–49, doi:<a href=\"https://doi.org/10.1093/pcp/pct196\">10.1093/pcp/pct196</a>.","chicago":"Tanaka, Hirokazu, Tomasz Nodzyński, Saeko Kitakura, Mugurel Feraru, Michiko Sasabe, Tomomi Ishikawa, Jürgen Kleine Vehn, Tatsuo Kakimoto, and Jiří Friml. “BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling of PIN Auxin Transporters and Auxin-Mediated Development in Arabidopsis.” <i>Plant and Cell Physiology</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/pcp/pct196\">https://doi.org/10.1093/pcp/pct196</a>.","apa":"Tanaka, H., Nodzyński, T., Kitakura, S., Feraru, M., Sasabe, M., Ishikawa, T., … Friml, J. (2014). BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. <i>Plant and Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pct196\">https://doi.org/10.1093/pcp/pct196</a>"},"date_created":"2018-12-11T11:56:25Z","page":"737 - 749","publist_id":"4741","title":"BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis","volume":55,"publication":"Plant and Cell Physiology","day":"01","date_published":"2014-04-01T00:00:00Z","intvolume":"        55","has_accepted_license":"1","file_date_updated":"2020-07-14T12:45:34Z","doi":"10.1093/pcp/pct196","ec_funded":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"pubrep_id":"431","publisher":"Oxford University Press","issue":"4","_id":"2223","publication_status":"published","oa_version":"Published Version","type":"journal_article","file":[{"date_updated":"2020-07-14T12:45:34Z","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:14:25Z","checksum":"b781a76b32ac35a520256453c3ba9433","file_size":2028111,"file_name":"IST-2016-431-v1+1_Plant_Cell_Physiol-2014-Tanaka-737-49.pdf","relation":"main_file","file_id":"5076","creator":"system"}],"ddc":["570"],"month":"04","year":"2014","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"},{"_id":"256BDAB0-B435-11E9-9278-68D0E5697425","name":"Innovationsförderung in der Grenzregion Österreich – Tschechische Republik durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur"}],"publication_identifier":{"issn":["00320781"]},"department":[{"_id":"JiFr"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:56:07Z","scopus_import":1,"abstract":[{"lang":"eng","text":"Correct positioning of membrane proteins is an essential process in eukaryotic organisms. The plant hormone auxin is distributed through intercellular transport and triggers various cellular responses. Auxin transporters of the PIN-FORMED (PIN) family localize asymmetrically at the plasma membrane (PM) and mediate the directional transport of auxin between cells. A fungal toxin, brefeldin A (BFA), inhibits a subset of guanine nucleotide exchange factors for ADP-ribosylation factor small GTPases (ARF GEFs) including GNOM, which plays a major role in localization of PIN1 predominantly to the basal side of the PM. The Arabidopsis genome encodes 19 ARF-related putative GTPases. However, ARF components involved in PIN1 localization have been genetically poorly defined. Using a fluorescence imaging-based forward genetic approach, we identified an Arabidopsis mutant, bfa-visualized exocytic trafficking defective1 (bex1), in which PM localization of PIN1-green fluorescent protein (GFP) as well as development is hypersensitive to BFA. We found that in bex1 a member of the ARF1 gene family, ARF1A1C, was mutated. ARF1A1C localizes to the trans-Golgi network/early endosome and Golgi apparatus, acts synergistically to BEN1/MIN7 ARF GEF and is important for PIN recycling to the PM. Consistent with the developmental importance of PIN proteins, functional interference with ARF1 resulted in an impaired auxin response gradient and various developmental defects including embryonic patterning defects and growth arrest. Our results show that ARF1A1C is essential for recycling of PIN auxin transporters and for various auxin-dependent developmental processes."}],"main_file_link":[{"url":"http://repository.ist.ac.at/id/eprint/431","open_access":"1"}],"author":[{"first_name":"Hirokazu","last_name":"Tanaka","full_name":"Tanaka, Hirokazu"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"full_name":"Kitakura, Saeko","last_name":"Kitakura","first_name":"Saeko"},{"last_name":"Feraru","full_name":"Feraru, Mugurel","first_name":"Mugurel"},{"full_name":"Sasabe, Michiko","last_name":"Sasabe","first_name":"Michiko"},{"last_name":"Ishikawa","full_name":"Ishikawa, Tomomi","first_name":"Tomomi"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen"},{"first_name":"Tatsuo","full_name":"Kakimoto, Tatsuo","last_name":"Kakimoto"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí"}],"status":"public"},{"intvolume":"        46","abstract":[{"lang":"eng","text":"This work investigates the transition between different traveling helical waves (spirals, SPIs) in the setup of differentially independent rotating cylinders. We use direct numerical simulations to consider an infinite long and periodic Taylor-Couette apparatus with fixed axial periodicity length. We find so-called mixed-cross-spirals (MCSs), that can be seen as nonlinear superpositions of SPIs, to establish stable footbridges connecting SPI states. While bridging the bifurcation branches of SPIs, the corresponding contributions within the MCS vary continuously with the control parameters. Here discussed MCSs presenting footbridge solutions start and end in different SPI branches. Therefore they differ significantly from the already known MCSs that present bypass solutions (Altmeyer and Hoffmann 2010 New J. Phys. 12 113035). The latter start and end in the same SPI branch, while they always bifurcate out of those SPI branches with the larger mode amplitude. Meanwhile, these only appear within the coexisting region of both SPIs. In contrast, the footbridge solutions can also bifurcate out of the minor SPI contribution. We also find they exist in regions where only one of the SPIs contributions exists. In addition, MCS as footbridge solution can appear either stable or unstable. The latter detected transient solutions offer similar spatio-temporal characteristics to the flow establishing stable footbridges. Such transition processes are interesting for pattern-forming systems in general because they accomplish transitions between traveling waves of different azimuthal wave numbers and have not been described in the literature yet."}],"scopus_import":1,"date_published":"2014-04-01T00:00:00Z","day":"01","publication":"Fluid Dynamics Research","date_updated":"2021-01-12T06:56:07Z","volume":46,"language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","author":[{"orcid":"0000-0001-5964-0203","last_name":"Altmeyer","full_name":"Altmeyer, Sebastian","first_name":"Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1088/0169-5983/46/2/025503","type":"journal_article","oa_version":"None","date_created":"2018-12-11T11:56:25Z","citation":{"ama":"Altmeyer S. On secondary instabilities generating footbridges between spiral vortex flow. <i>Fluid Dynamics Research</i>. 2014;46(2). doi:<a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">10.1088/0169-5983/46/2/025503</a>","ieee":"S. Altmeyer, “On secondary instabilities generating footbridges between spiral vortex flow,” <i>Fluid Dynamics Research</i>, vol. 46, no. 2. IOP Publishing Ltd., 2014.","short":"S. Altmeyer, Fluid Dynamics Research 46 (2014).","ista":"Altmeyer S. 2014. On secondary instabilities generating footbridges between spiral vortex flow. Fluid Dynamics Research. 46(2), 025503.","apa":"Altmeyer, S. (2014). On secondary instabilities generating footbridges between spiral vortex flow. <i>Fluid Dynamics Research</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">https://doi.org/10.1088/0169-5983/46/2/025503</a>","chicago":"Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between Spiral Vortex Flow.” <i>Fluid Dynamics Research</i>. IOP Publishing Ltd., 2014. <a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">https://doi.org/10.1088/0169-5983/46/2/025503</a>.","mla":"Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between Spiral Vortex Flow.” <i>Fluid Dynamics Research</i>, vol. 46, no. 2, 025503, IOP Publishing Ltd., 2014, doi:<a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">10.1088/0169-5983/46/2/025503</a>."},"quality_controlled":"1","publication_status":"published","_id":"2224","issue":"2","publisher":"IOP Publishing Ltd.","article_number":"025503","department":[{"_id":"BjHo"}],"title":"On secondary instabilities generating footbridges between spiral vortex flow","publication_identifier":{"issn":["01695983"]},"publist_id":"4740","year":"2014","month":"04"},{"title":"Isotropic local laws for sample covariance and generalized Wigner matrices","publist_id":"4739","citation":{"mla":"Bloemendal, Alex, et al. “Isotropic Local Laws for Sample Covariance and Generalized Wigner Matrices.” <i>Electronic Journal of Probability</i>, vol. 19, 33, Institute of Mathematical Statistics, 2014, doi:<a href=\"https://doi.org/10.1214/EJP.v19-3054\">10.1214/EJP.v19-3054</a>.","apa":"Bloemendal, A., Erdös, L., Knowles, A., Yau, H., &#38; Yin, J. (2014). Isotropic local laws for sample covariance and generalized Wigner matrices. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/EJP.v19-3054\">https://doi.org/10.1214/EJP.v19-3054</a>","chicago":"Bloemendal, Alex, László Erdös, Antti Knowles, Horng Yau, and Jun Yin. “Isotropic Local Laws for Sample Covariance and Generalized Wigner Matrices.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2014. <a href=\"https://doi.org/10.1214/EJP.v19-3054\">https://doi.org/10.1214/EJP.v19-3054</a>.","ama":"Bloemendal A, Erdös L, Knowles A, Yau H, Yin J. Isotropic local laws for sample covariance and generalized Wigner matrices. <i>Electronic Journal of Probability</i>. 2014;19. doi:<a href=\"https://doi.org/10.1214/EJP.v19-3054\">10.1214/EJP.v19-3054</a>","ieee":"A. Bloemendal, L. Erdös, A. Knowles, H. Yau, and J. Yin, “Isotropic local laws for sample covariance and generalized Wigner matrices,” <i>Electronic Journal of Probability</i>, vol. 19. Institute of Mathematical Statistics, 2014.","short":"A. Bloemendal, L. Erdös, A. Knowles, H. Yau, J. Yin, Electronic Journal of Probability 19 (2014).","ista":"Bloemendal A, Erdös L, Knowles A, Yau H, Yin J. 2014. Isotropic local laws for sample covariance and generalized Wigner matrices. Electronic Journal of Probability. 19, 33."},"date_created":"2018-12-11T11:56:25Z","quality_controlled":"1","article_number":"33","oa":1,"ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1214/EJP.v19-3054","file_date_updated":"2020-07-14T12:45:34Z","intvolume":"        19","has_accepted_license":"1","date_published":"2014-03-15T00:00:00Z","volume":19,"day":"15","publication":"Electronic Journal of Probability","department":[{"_id":"LaEr"}],"publication_identifier":{"issn":["10836489"]},"month":"03","year":"2014","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"oa_version":"Published Version","ddc":["510"],"file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:34Z","file_size":810150,"checksum":"7eb297ff367a2ee73b21b6dd1e1948e4","date_created":"2018-12-12T10:14:06Z","file_name":"IST-2016-427-v1+1_3054-16624-4-PB.pdf","creator":"system","file_id":"5055","relation":"main_file"}],"type":"journal_article","_id":"2225","publication_status":"published","pubrep_id":"427","publisher":"Institute of Mathematical Statistics","author":[{"last_name":"Bloemendal","full_name":"Bloemendal, Alex","first_name":"Alex"},{"orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Antti","full_name":"Knowles, Antti","last_name":"Knowles"},{"last_name":"Yau","full_name":"Yau, Horng","first_name":"Horng"},{"last_name":"Yin","full_name":"Yin, Jun","first_name":"Jun"}],"status":"public","abstract":[{"lang":"eng","text":"We consider sample covariance matrices of the form X∗X, where X is an M×N matrix with independent random entries.  We prove the isotropic local Marchenko-Pastur law, i.e. we prove that the resolvent (X∗X−z)−1 converges to a multiple of the identity in the sense of quadratic forms. More precisely, we establish sharp high-probability bounds on the quantity ⟨v,(X∗X−z)−1w⟩−⟨v,w⟩m(z), where m is the Stieltjes transform of the Marchenko-Pastur law and v,w∈CN. We require the logarithms of the dimensions M and N to be comparable. Our result holds down to scales Iz≥N−1+ε and throughout the entire spectrum away from 0. We also prove analogous results for generalized Wigner matrices.\r\n"}],"date_updated":"2021-01-12T06:56:07Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"Transient growth of Ekman-Couette flow","publist_id":"4737","quality_controlled":"1","citation":{"chicago":"Shi, Liang, Björn Hof, and Andreas Tilgner. “Transient Growth of Ekman-Couette Flow.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2014. <a href=\"https://doi.org/10.1103/PhysRevE.89.013001\">https://doi.org/10.1103/PhysRevE.89.013001</a>.","apa":"Shi, L., Hof, B., &#38; Tilgner, A. (2014). Transient growth of Ekman-Couette flow. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.89.013001\">https://doi.org/10.1103/PhysRevE.89.013001</a>","mla":"Shi, Liang, et al. “Transient Growth of Ekman-Couette Flow.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 89, no. 1, 013001, American Institute of Physics, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevE.89.013001\">10.1103/PhysRevE.89.013001</a>.","ieee":"L. Shi, B. Hof, and A. Tilgner, “Transient growth of Ekman-Couette flow,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 89, no. 1. American Institute of Physics, 2014.","ista":"Shi L, Hof B, Tilgner A. 2014. Transient growth of Ekman-Couette flow. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(1), 013001.","short":"L. Shi, B. Hof, A. Tilgner, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","ama":"Shi L, Hof B, Tilgner A. Transient growth of Ekman-Couette flow. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2014;89(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.89.013001\">10.1103/PhysRevE.89.013001</a>"},"date_created":"2018-12-11T11:56:26Z","oa":1,"article_number":"013001","doi":"10.1103/PhysRevE.89.013001","date_published":"2014-01-06T00:00:00Z","intvolume":"        89","day":"06","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","volume":89,"department":[{"_id":"BjHo"}],"project":[{"grant_number":"SFB-TR3-TP10B","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen"}],"month":"01","year":"2014","publication_identifier":{"issn":["15393755"]},"publication_status":"published","_id":"2226","issue":"1","type":"journal_article","oa_version":"Submitted Version","publisher":"American Institute of Physics","status":"public","author":[{"first_name":"Liang","full_name":"Shi, Liang","last_name":"Shi"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn"},{"last_name":"Tilgner","full_name":"Tilgner, Andreas","first_name":"Andreas"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1312.5095"}],"abstract":[{"text":"Coriolis force effects on shear flows are important in geophysical and astrophysical contexts. We report a study on the linear stability and the transient energy growth of the plane Couette flow with system rotation perpendicular to the shear direction. External rotation causes linear instability. At small rotation rates, the onset of linear instability scales inversely with the rotation rate and the optimal transient growth in the linearly stable region is slightly enhanced ∼Re2. The corresponding optimal initial perturbations are characterized by roll structures inclined in the streamwise direction and are twisted under external rotation. At large rotation rates, the transient growth is significantly inhibited and hence linear stability analysis is a reliable indicator for instability.","lang":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:56:08Z"},{"_id":"2227","issue":"1","publication_status":"published","quality_controlled":"1","citation":{"short":"E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, J. Prieto, Organisms Diversity and Evolution 14 (2014) 1–10.","ista":"Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. 2014. Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. Organisms Diversity and Evolution. 14(1), 1–10.","ieee":"E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, and J. Prieto, “Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences,” <i>Organisms Diversity and Evolution</i>, vol. 14, no. 1. Springer, pp. 1–10, 2014.","ama":"Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. <i>Organisms Diversity and Evolution</i>. 2014;14(1):1-10. doi:<a href=\"https://doi.org/10.1007/s13127-013-0150-6\">10.1007/s13127-013-0150-6</a>","chicago":"Cires Rodriguez, Eduardo, Matthias Baltisberger, Candela Cuesta, Pablo Vargas, and José Prieto. “Allopolyploid Origin of the Balkan Endemic Ranunculus Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.” <i>Organisms Diversity and Evolution</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s13127-013-0150-6\">https://doi.org/10.1007/s13127-013-0150-6</a>.","apa":"Cires Rodriguez, E., Baltisberger, M., Cuesta, C., Vargas, P., &#38; Prieto, J. (2014). Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. <i>Organisms Diversity and Evolution</i>. Springer. <a href=\"https://doi.org/10.1007/s13127-013-0150-6\">https://doi.org/10.1007/s13127-013-0150-6</a>","mla":"Cires Rodriguez, Eduardo, et al. “Allopolyploid Origin of the Balkan Endemic Ranunculus Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.” <i>Organisms Diversity and Evolution</i>, vol. 14, no. 1, Springer, 2014, pp. 1–10, doi:<a href=\"https://doi.org/10.1007/s13127-013-0150-6\">10.1007/s13127-013-0150-6</a>."},"date_created":"2018-12-11T11:56:26Z","oa_version":"None","type":"journal_article","publisher":"Springer","title":"Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"year":"2014","month":"03","page":"1 - 10","publist_id":"4734","publication_identifier":{"issn":["14396092"]},"date_published":"2014-03-01T00:00:00Z","scopus_import":"1","abstract":[{"text":"The Balkan Peninsula, characterized by high rates of endemism, is recognised as one of the most diverse and species-rich areas of Europe. However, little is known about the origin of Balkan endemics. The present study addresses the phylogenetic position of the Balkan endemic Ranunculus wettsteinii, as well as its taxonomic status and relationship with the widespread R. parnassiifolius, based on nuclear DNA (internal transcribed spacer, ITS) and plastid regions (rpl32-trnL, rps16-trnQ, trnK-matK and ycf6-psbM). Maximum parsimony and Bayesian inference analyses revealed a well-supported clade formed by accessions of R. wettsteinii. Furthermore, our phylogenetic and network analyses supported previous hypotheses of a likely allopolyploid origin for R. wettsteinii between R. montenegrinus and R. parnassiifolius, with the latter as the maternal parent.","lang":"eng"}],"intvolume":"        14","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":14,"date_updated":"2022-08-25T14:42:46Z","day":"01","publication":"Organisms Diversity and Evolution","article_processing_charge":"No","author":[{"last_name":"Cires Rodriguez","full_name":"Cires Rodriguez, Eduardo","id":"2AD56A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Eduardo"},{"first_name":"Matthias","full_name":"Baltisberger, Matthias","last_name":"Baltisberger"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","first_name":"Candela","orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela","last_name":"Cuesta"},{"first_name":"Pablo","full_name":"Vargas, Pablo","last_name":"Vargas"},{"last_name":"Prieto","full_name":"Prieto, José","first_name":"José"}],"status":"public","doi":"10.1007/s13127-013-0150-6"},{"department":[{"_id":"PeJo"}],"month":"03","year":"2014","project":[{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548"},{"_id":"25C26B1E-B435-11E9-9278-68D0E5697425","name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF","grant_number":"P24909-B24"}],"publication_identifier":{"issn":["10976256"]},"issue":"5","_id":"2228","publication_status":"published","oa_version":"Submitted Version","type":"journal_article","publisher":"Nature Publishing Group","author":[{"first_name":"Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","full_name":"Hu, Hua","last_name":"Hu"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M"}],"status":"public","scopus_import":1,"abstract":[{"lang":"eng","text":"Fast-spiking, parvalbumin-expressing GABAergic interneurons, a large proportion of which are basket cells (BCs), have a key role in feedforward and feedback inhibition, gamma oscillations and complex information processing. For these functions, fast propagation of action potentials (APs) from the soma to the presynaptic terminals is important. However, the functional properties of interneuron axons remain elusive. We examined interneuron axons by confocally targeted subcellular patch-clamp recording in rat hippocampal slices. APs were initiated in the proximal axon ∼20 μm from the soma and propagated to the distal axon with high reliability and speed. Subcellular mapping revealed a stepwise increase of Na^+ conductance density from the soma to the proximal axon, followed by a further gradual increase in the distal axon. Active cable modeling and experiments with partial channel block revealed that low axonal Na^+ conductance density was sufficient for reliability, but high Na^+ density was necessary for both speed of propagation and fast-spiking AP phenotype. Our results suggest that a supercritical density of Na^+ channels compensates for the morphological properties of interneuron axons (small segmental diameter, extensive branching and high bouton density), ensuring fast AP propagation and high-frequency repetitive firing."}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286295/","open_access":"1"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:56:08Z","title":"A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons","page":"686-693","publist_id":"4733","quality_controlled":"1","date_created":"2018-12-11T11:56:26Z","citation":{"chicago":"Hu, Hua, and Peter M Jonas. “A Supercritical Density of Na^+ Channels Ensures Fast Signaling in GABAergic Interneuron Axons.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nn.3678\">https://doi.org/10.1038/nn.3678</a>.","apa":"Hu, H., &#38; Jonas, P. M. (2014). A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.3678\">https://doi.org/10.1038/nn.3678</a>","mla":"Hu, Hua, and Peter M. Jonas. “A Supercritical Density of Na^+ Channels Ensures Fast Signaling in GABAergic Interneuron Axons.” <i>Nature Neuroscience</i>, vol. 17, no. 5, Nature Publishing Group, 2014, pp. 686–93, doi:<a href=\"https://doi.org/10.1038/nn.3678\">10.1038/nn.3678</a>.","short":"H. Hu, P.M. Jonas, Nature Neuroscience 17 (2014) 686–693.","ista":"Hu H, Jonas PM. 2014. A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. Nature Neuroscience. 17(5), 686–693.","ieee":"H. Hu and P. M. Jonas, “A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons,” <i>Nature Neuroscience</i>, vol. 17, no. 5. Nature Publishing Group, pp. 686–693, 2014.","ama":"Hu H, Jonas PM. A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. <i>Nature Neuroscience</i>. 2014;17(5):686-693. doi:<a href=\"https://doi.org/10.1038/nn.3678\">10.1038/nn.3678</a>"},"oa":1,"ec_funded":1,"doi":"10.1038/nn.3678","date_published":"2014-03-23T00:00:00Z","intvolume":"        17","volume":17,"day":"23","publication":"Nature Neuroscience"},{"volume":343,"day":"01","publication":"Science","date_published":"2014-02-01T00:00:00Z","intvolume":"       343","doi":"10.1126/science.1244811","ec_funded":1,"oa":1,"quality_controlled":"1","citation":{"apa":"Vyleta, N., &#38; Jonas, P. M. (2014). Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1244811\">https://doi.org/10.1126/science.1244811</a>","chicago":"Vyleta, Nicholas, and Peter M Jonas. “Loose Coupling between Ca^2+ Channels and Release Sensors at a Plastic Hippocampal Synapse.” <i>Science</i>. American Association for the Advancement of Science, 2014. <a href=\"https://doi.org/10.1126/science.1244811\">https://doi.org/10.1126/science.1244811</a>.","mla":"Vyleta, Nicholas, and Peter M. Jonas. “Loose Coupling between Ca^2+ Channels and Release Sensors at a Plastic Hippocampal Synapse.” <i>Science</i>, vol. 343, no. 6171, American Association for the Advancement of Science, 2014, pp. 665–70, doi:<a href=\"https://doi.org/10.1126/science.1244811\">10.1126/science.1244811</a>.","ama":"Vyleta N, Jonas PM. Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. <i>Science</i>. 2014;343(6171):665-670. doi:<a href=\"https://doi.org/10.1126/science.1244811\">10.1126/science.1244811</a>","ista":"Vyleta N, Jonas PM. 2014. Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. Science. 343(6171), 665–670.","short":"N. Vyleta, P.M. Jonas, Science 343 (2014) 665–670.","ieee":"N. Vyleta and P. M. Jonas, “Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse,” <i>Science</i>, vol. 343, no. 6171. American Association for the Advancement of Science, pp. 665–670, 2014."},"date_created":"2018-12-11T11:56:27Z","publist_id":"4732","page":"665 - 670","title":"Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:56:09Z","scopus_import":1,"abstract":[{"lang":"eng","text":"The distance between Ca^2+ channels and release sensors determines the speed and efficacy of synaptic transmission. Tight &quot;nanodomain&quot; channel-sensor coupling initiates transmitter release at synapses in the mature brain, whereas loose &quot;microdomain&quot; coupling appears restricted to early developmental stages. To probe the coupling configuration at a plastic synapse in the mature central nervous system, we performed paired recordings between mossy fiber terminals and CA3 pyramidal neurons in rat hippocampus. Millimolar concentrations of both the fast Ca^2+ chelator BAPTA [1,2-bis(2-aminophenoxy)ethane- N,N, N′,N′-tetraacetic acid] and the slow chelator EGTA efficiently suppressed transmitter release, indicating loose coupling between Ca^2+ channels and release sensors. Loose coupling enabled the control of initial release probability by fast endogenous Ca^2+ buffers and the generation of facilitation by buffer saturation. Thus, loose coupling provides the molecular framework for presynaptic plasticity."}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617475/","open_access":"1"}],"author":[{"last_name":"Vyleta","full_name":"Vyleta, Nicholas","id":"36C4978E-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"status":"public","publisher":"American Association for the Advancement of Science","issue":"6171","_id":"2229","publication_status":"published","oa_version":"Submitted Version","type":"journal_article","year":"2014","month":"02","project":[{"grant_number":"P24909-B24","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548"}],"publication_identifier":{"issn":["00368075"]},"department":[{"_id":"PeJo"}]},{"pubrep_id":"425","publisher":"Frontiers Research Foundation","file":[{"file_name":"IST-2016-425-v1+1_fninf-08-00016.pdf","relation":"main_file","creator":"system","file_id":"4935","date_updated":"2020-07-14T12:45:34Z","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:12:17Z","checksum":"eeca00bba7232ff7d27db83321f6ea30","file_size":2883372}],"type":"journal_article","oa_version":"Published Version","ddc":["570"],"issue":"FEB","_id":"2230","publication_status":"published","publication_identifier":{"issn":["16625196"]},"year":"2014","month":"02","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"date_updated":"2021-01-12T06:56:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"Intracellular electrophysiological recordings provide crucial insights into elementary neuronal signals such as action potentials and synaptic currents. Analyzing and interpreting these signals is essential for a quantitative understanding of neuronal information processing, and requires both fast data visualization and ready access to complex analysis routines. To achieve this goal, we have developed Stimfit, a free software package for cellular neurophysiology with a Python scripting interface and a built-in Python shell. The program supports most standard file formats for cellular neurophysiology and other biomedical signals through the Biosig library. To quantify and interpret the activity of single neurons and communication between neurons, the program includes algorithms to characterize the kinetics of presynaptic action potentials and postsynaptic currents, estimate latencies between pre- and postsynaptic events, and detect spontaneously occurring events. We validate and benchmark these algorithms, give estimation errors, and provide sample use cases, showing that Stimfit represents an efficient, accessible and extensible way to accurately analyze and interpret neuronal signals.","lang":"eng"}],"scopus_import":1,"author":[{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José","last_name":"Guzmán","full_name":"Guzmán, José"},{"full_name":"Schlögl, Alois","last_name":"Schlögl","orcid":"0000-0002-5621-8100","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph","full_name":"Schmidt Hieber, Christoph","last_name":"Schmidt Hieber"}],"status":"public","article_number":"16","oa":1,"citation":{"ieee":"J. Guzmán, A. Schlögl, and C. Schmidt Hieber, “Stimfit: Quantifying electrophysiological data with Python,” <i>Frontiers in Neuroinformatics</i>, vol. 8, no. FEB. Frontiers Research Foundation, 2014.","short":"J. Guzmán, A. Schlögl, C. Schmidt Hieber, Frontiers in Neuroinformatics 8 (2014).","ista":"Guzmán J, Schlögl A, Schmidt Hieber C. 2014. Stimfit: Quantifying electrophysiological data with Python. Frontiers in Neuroinformatics. 8(FEB), 16.","ama":"Guzmán J, Schlögl A, Schmidt Hieber C. Stimfit: Quantifying electrophysiological data with Python. <i>Frontiers in Neuroinformatics</i>. 2014;8(FEB). doi:<a href=\"https://doi.org/10.3389/fninf.2014.00016\">10.3389/fninf.2014.00016</a>","mla":"Guzmán, José, et al. “Stimfit: Quantifying Electrophysiological Data with Python.” <i>Frontiers in Neuroinformatics</i>, vol. 8, no. FEB, 16, Frontiers Research Foundation, 2014, doi:<a href=\"https://doi.org/10.3389/fninf.2014.00016\">10.3389/fninf.2014.00016</a>.","chicago":"Guzmán, José, Alois Schlögl, and Christoph Schmidt Hieber. “Stimfit: Quantifying Electrophysiological Data with Python.” <i>Frontiers in Neuroinformatics</i>. Frontiers Research Foundation, 2014. <a href=\"https://doi.org/10.3389/fninf.2014.00016\">https://doi.org/10.3389/fninf.2014.00016</a>.","apa":"Guzmán, J., Schlögl, A., &#38; Schmidt Hieber, C. (2014). Stimfit: Quantifying electrophysiological data with Python. <i>Frontiers in Neuroinformatics</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fninf.2014.00016\">https://doi.org/10.3389/fninf.2014.00016</a>"},"date_created":"2018-12-11T11:56:27Z","quality_controlled":"1","publist_id":"4731","title":"Stimfit: Quantifying electrophysiological data with Python","volume":8,"day":"21","publication":"Frontiers in Neuroinformatics","intvolume":"         8","has_accepted_license":"1","date_published":"2014-02-21T00:00:00Z","doi":"10.3389/fninf.2014.00016","file_date_updated":"2020-07-14T12:45:34Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"doi":"10.1016/j.bpj.2014.01.014","intvolume":"       106","date_published":"2014-03-04T00:00:00Z","day":"04","publication":"Biophysical Journal","volume":106,"pmid":1,"title":"Noise and information transmission in promoters with multiple internal states","publist_id":"4730","page":"1194 - 1204","date_created":"2018-12-11T11:56:28Z","citation":{"apa":"Rieckh, G., &#38; Tkačik, G. (2014). Noise and information transmission in promoters with multiple internal states. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">https://doi.org/10.1016/j.bpj.2014.01.014</a>","chicago":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” <i>Biophysical Journal</i>. Biophysical Society, 2014. <a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">https://doi.org/10.1016/j.bpj.2014.01.014</a>.","mla":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” <i>Biophysical Journal</i>, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:<a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">10.1016/j.bpj.2014.01.014</a>.","ama":"Rieckh G, Tkačik G. Noise and information transmission in promoters with multiple internal states. <i>Biophysical Journal</i>. 2014;106(5):1194-1204. doi:<a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">10.1016/j.bpj.2014.01.014</a>","ieee":"G. Rieckh and G. Tkačik, “Noise and information transmission in promoters with multiple internal states,” <i>Biophysical Journal</i>, vol. 106, no. 5. Biophysical Society, pp. 1194–1204, 2014.","short":"G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204.","ista":"Rieckh G, Tkačik G. 2014. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 106(5), 1194–1204."},"quality_controlled":"1","oa":1,"status":"public","author":[{"first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","full_name":"Rieckh, Georg","last_name":"Rieckh"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026790/","open_access":"1"}],"abstract":[{"text":"Based on the measurements of noise in gene expression performed during the past decade, it has become customary to think of gene regulation in terms of a two-state model, where the promoter of a gene can stochastically switch between an ON and an OFF state. As experiments are becoming increasingly precise and the deviations from the two-state model start to be observable, we ask about the experimental signatures of complex multistate promoters, as well as the functional consequences of this additional complexity. In detail, we i), extend the calculations for noise in gene expression to promoters described by state transition diagrams with multiple states, ii), systematically compute the experimentally accessible noise characteristics for these complex promoters, and iii), use information theory to evaluate the channel capacities of complex promoter architectures and compare them with the baseline provided by the two-state model. We find that adding internal states to the promoter generically decreases channel capacity, except in certain cases, three of which (cooperativity, dual-role regulation, promoter cycling) we analyze in detail.","lang":"eng"}],"scopus_import":1,"date_updated":"2021-01-12T06:56:10Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"}],"publication_identifier":{"issn":["00063495"]},"month":"03","year":"2014","type":"journal_article","oa_version":"Submitted Version","external_id":{"pmid":["24606943"]},"publication_status":"published","_id":"2231","issue":"5","publisher":"Biophysical Society"},{"abstract":[{"text":"The purpose of this contribution is to summarize and discuss recent advances regarding the onset of turbulence in shear flows. The absence of a clear-cut instability mechanism, the spatio-temporal intermittent character and extremely long lived transients are some of the major difficulties encountered in these flows and have hindered progress towards understanding the transition process. We will show for the case of pipe flow that concepts from nonlinear dynamics and statistical physics can help to explain the onset of turbulence. In particular, the turbulent structures (puffs) observed close to onset are spatially localized chaotic transients and their lifetimes increase super-exponentially with Reynolds number. At the same time fluctuations of individual turbulent puffs can (although very rarely) lead to the nucleation of new puffs. The competition between these two stochastic processes gives rise to a non-equilibrium phase transition where turbulence changes from a super-transient to a sustained state.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1403.4516"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2022-06-10T10:13:15Z","author":[{"id":"a79e57f5-e8a5-11ec-9dc9-83fb8c81cf72","first_name":"Baofang","last_name":"Song","full_name":"Song, Baofang"},{"orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"status":"public","issue":"2","_id":"2232","publication_status":"published","external_id":{"arxiv":["1403.4516"]},"oa_version":"Submitted Version","type":"journal_article","publisher":"IOP Publishing","article_type":"original","department":[{"_id":"BjHo"}],"month":"02","year":"2014","publication_identifier":{"issn":["17425468"]},"date_published":"2014-02-01T00:00:00Z","intvolume":"      2014","volume":2014,"publication":"Journal of Statistical Mechanics Theory and Experiment","day":"01","article_processing_charge":"No","doi":"10.1088/1742-5468/2014/02/P02001","arxiv":1,"quality_controlled":"1","date_created":"2018-12-11T11:56:28Z","citation":{"mla":"Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of the Transition to Turbulence.” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2014, no. 2, P02001, IOP Publishing, 2014, doi:<a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">10.1088/1742-5468/2014/02/P02001</a>.","chicago":"Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of the Transition to Turbulence.” <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing, 2014. <a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">https://doi.org/10.1088/1742-5468/2014/02/P02001</a>.","apa":"Song, B., &#38; Hof, B. (2014). Deterministic and stochastic aspects of the transition to turbulence. <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">https://doi.org/10.1088/1742-5468/2014/02/P02001</a>","ieee":"B. Song and B. Hof, “Deterministic and stochastic aspects of the transition to turbulence,” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2014, no. 2. IOP Publishing, 2014.","ista":"Song B, Hof B. 2014. Deterministic and stochastic aspects of the transition to turbulence. Journal of Statistical Mechanics Theory and Experiment. 2014(2), P02001.","short":"B. Song, B. Hof, Journal of Statistical Mechanics Theory and Experiment 2014 (2014).","ama":"Song B, Hof B. Deterministic and stochastic aspects of the transition to turbulence. <i>Journal of Statistical Mechanics Theory and Experiment</i>. 2014;2014(2). doi:<a href=\"https://doi.org/10.1088/1742-5468/2014/02/P02001\">10.1088/1742-5468/2014/02/P02001</a>"},"article_number":"P02001","oa":1,"title":"Deterministic and stochastic aspects of the transition to turbulence","publist_id":"4729"},{"doi":"10.2168/LMCS-10(1:10)2014","file_date_updated":"2020-07-14T12:45:34Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"publication":"Logical Methods in Computer Science","day":"13","volume":10,"has_accepted_license":"1","intvolume":"        10","date_published":"2014-02-13T00:00:00Z","publist_id":"4728","title":"Exact and approximate determinization of discounted-sum automata","oa":1,"citation":{"mla":"Boker, Udi, and Thomas A. Henzinger. “Exact and Approximate Determinization of Discounted-Sum Automata.” <i>Logical Methods in Computer Science</i>, vol. 10, no. 1, International Federation of Computational Logic, 2014, doi:<a href=\"https://doi.org/10.2168/LMCS-10(1:10)2014\">10.2168/LMCS-10(1:10)2014</a>.","apa":"Boker, U., &#38; Henzinger, T. A. (2014). Exact and approximate determinization of discounted-sum automata. <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic. <a href=\"https://doi.org/10.2168/LMCS-10(1:10)2014\">https://doi.org/10.2168/LMCS-10(1:10)2014</a>","chicago":"Boker, Udi, and Thomas A Henzinger. “Exact and Approximate Determinization of Discounted-Sum Automata.” <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic, 2014. <a href=\"https://doi.org/10.2168/LMCS-10(1:10)2014\">https://doi.org/10.2168/LMCS-10(1:10)2014</a>.","ama":"Boker U, Henzinger TA. Exact and approximate determinization of discounted-sum automata. <i>Logical Methods in Computer Science</i>. 2014;10(1). doi:<a href=\"https://doi.org/10.2168/LMCS-10(1:10)2014\">10.2168/LMCS-10(1:10)2014</a>","ista":"Boker U, Henzinger TA. 2014. Exact and approximate determinization of discounted-sum automata. Logical Methods in Computer Science. 10(1).","ieee":"U. Boker and T. A. Henzinger, “Exact and approximate determinization of discounted-sum automata,” <i>Logical Methods in Computer Science</i>, vol. 10, no. 1. International Federation of Computational Logic, 2014.","short":"U. Boker, T.A. Henzinger, Logical Methods in Computer Science 10 (2014)."},"date_created":"2018-12-11T11:56:28Z","quality_controlled":"1","status":"public","author":[{"first_name":"Udi","full_name":"Boker, Udi","last_name":"Boker"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"date_updated":"2021-01-12T06:56:11Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":" A discounted-sum automaton (NDA) is a nondeterministic finite automaton with edge weights, valuing a run by the discounted sum of visited edge weights. More precisely, the weight in the i-th position of the run is divided by λi, where the discount factor λ is a fixed rational number greater than 1. The value of a word is the minimal value of the automaton runs on it. Discounted summation is a common and useful measuring scheme, especially for infinite sequences, reflecting the assumption that earlier weights are more important than later weights. Unfortunately, determinization of NDAs, which is often essential in formal verification, is, in general, not possible. We provide positive news, showing that every NDA with an integral discount factor is determinizable. We complete the picture by proving that the integers characterize exactly the discount factors that guarantee determinizability: for every nonintegral rational discount factor λ, there is a nondeterminizable λ-NDA. We also prove that the class of NDAs with integral discount factors enjoys closure under the algebraic operations min, max, addition, and subtraction, which is not the case for general NDAs nor for deterministic NDAs. For general NDAs, we look into approximate determinization, which is always possible as the influence of a word's suffix decays. We show that the naive approach, of unfolding the automaton computations up to a sufficient level, is doubly exponential in the discount factor. We provide an alternative construction for approximate determinization, which is singly exponential in the discount factor, in the precision, and in the number of states. We also prove matching lower bounds, showing that the exponential dependency on each of these three parameters cannot be avoided. All our results hold equally for automata over finite words and for automata over infinite words. ","lang":"eng"}],"scopus_import":1,"publication_identifier":{"issn":["18605974"]},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"}],"year":"2014","month":"02","department":[{"_id":"ToHe"}],"publisher":"International Federation of Computational Logic","pubrep_id":"389","type":"journal_article","ddc":["000"],"oa_version":"Published Version","file":[{"checksum":"9f6ea2e2d8d4a32ff0becc29d835bbf8","file_size":550936,"date_created":"2018-12-12T10:07:45Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:34Z","file_id":"4643","creator":"system","relation":"main_file","file_name":"IST-2015-389-v1+1_1401.3957.pdf"}],"publication_status":"published","issue":"1","_id":"2233"},{"publist_id":"4727","title":"Markov decision processes with multiple long-run average objectives","oa":1,"citation":{"chicago":"Brázdil, Tomáš, Václav Brožek, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Markov Decision Processes with Multiple Long-Run Average Objectives.” <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic, 2014. <a href=\"https://doi.org/10.2168/LMCS-10(1:13)2014\">https://doi.org/10.2168/LMCS-10(1:13)2014</a>.","apa":"Brázdil, T., Brožek, V., Chatterjee, K., Forejt, V., &#38; Kučera, A. (2014). Markov decision processes with multiple long-run average objectives. <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic. <a href=\"https://doi.org/10.2168/LMCS-10(1:13)2014\">https://doi.org/10.2168/LMCS-10(1:13)2014</a>","mla":"Brázdil, Tomáš, et al. “Markov Decision Processes with Multiple Long-Run Average Objectives.” <i>Logical Methods in Computer Science</i>, vol. 10, no. 1, International Federation of Computational Logic, 2014, doi:<a href=\"https://doi.org/10.2168/LMCS-10(1:13)2014\">10.2168/LMCS-10(1:13)2014</a>.","ista":"Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. 2014. Markov decision processes with multiple long-run average objectives. Logical Methods in Computer Science. 10(1).","short":"T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, A. Kučera, Logical Methods in Computer Science 10 (2014).","ieee":"T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, and A. Kučera, “Markov decision processes with multiple long-run average objectives,” <i>Logical Methods in Computer Science</i>, vol. 10, no. 1. International Federation of Computational Logic, 2014.","ama":"Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. Markov decision processes with multiple long-run average objectives. <i>Logical Methods in Computer Science</i>. 2014;10(1). doi:<a href=\"https://doi.org/10.2168/LMCS-10(1:13)2014\">10.2168/LMCS-10(1:13)2014</a>"},"date_created":"2018-12-11T11:56:29Z","quality_controlled":"1","doi":"10.2168/LMCS-10(1:13)2014","file_date_updated":"2020-07-14T12:45:34Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"day":"14","publication":"Logical Methods in Computer Science","volume":10,"intvolume":"        10","has_accepted_license":"1","date_published":"2014-02-14T00:00:00Z","publication_identifier":{"issn":["18605974"]},"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"month":"02","year":"2014","department":[{"_id":"KrCh"}],"publisher":"International Federation of Computational Logic","pubrep_id":"428","ddc":["000"],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"IST-2016-428-v1+1_1104.3489.pdf","file_id":"4656","creator":"system","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:34Z","checksum":"803edcc2d8c1acfba44a9ec43a5eb9f0","file_size":375388,"date_created":"2018-12-12T10:07:57Z"}],"publication_status":"published","_id":"2234","issue":"1","status":"public","author":[{"first_name":"Tomáš","full_name":"Brázdil, Tomáš","last_name":"Brázdil"},{"full_name":"Brožek, Václav","last_name":"Brožek","first_name":"Václav"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Forejt","full_name":"Forejt, Vojtěch","first_name":"Vojtěch"},{"first_name":"Antonín","full_name":"Kučera, Antonín","last_name":"Kučera"}],"date_updated":"2021-01-12T06:56:11Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://repository.ist.ac.at/id/eprint/428","open_access":"1"}],"abstract":[{"lang":"eng","text":"We study Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) functions. We consider two different objectives, namely, expectation and satisfaction objectives. Given an MDP with κ limit-average functions, in the expectation objective the goal is to maximize the expected limit-average value, and in the satisfaction objective the goal is to maximize the probability of runs such that the limit-average value stays above a given vector. We show that under the expectation objective, in contrast to the case of one limit-average function, both randomization and memory are necessary for strategies even for ε-approximation, and that finite-memory randomized strategies are sufficient for achieving Pareto optimal values. Under the satisfaction objective, in contrast to the case of one limit-average function, infinite memory is necessary for strategies achieving a specific value (i.e. randomized finite-memory strategies are not sufficient), whereas memoryless randomized strategies are sufficient for ε-approximation, for all ε &gt; 0. We further prove that the decision problems for both expectation and satisfaction objectives can be solved in polynomial time and the trade-off curve (Pareto curve) can be ε-approximated in time polynomial in the size of the MDP and 1/ε, and exponential in the number of limit-average functions, for all ε &gt; 0. Our analysis also reveals flaws in previous work for MDPs with multiple mean-payoff functions under the expectation objective, corrects the flaws, and allows us to obtain improved results."}],"scopus_import":1},{"quality_controlled":"1","date_created":"2018-12-11T11:56:29Z","citation":{"apa":"Fürst, M., Mcmahon, D., Osborne, J., Paxton, R., &#38; Brown, M. (2014). Disease associations between honeybees and bumblebees as a threat to wild pollinators. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature12977\">https://doi.org/10.1038/nature12977</a>","chicago":"Fürst, Matthias, Dino Mcmahon, Juliet Osborne, Robert Paxton, and Mark Brown. “Disease Associations between Honeybees and Bumblebees as a Threat to Wild Pollinators.” <i>Nature</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nature12977\">https://doi.org/10.1038/nature12977</a>.","mla":"Fürst, Matthias, et al. “Disease Associations between Honeybees and Bumblebees as a Threat to Wild Pollinators.” <i>Nature</i>, vol. 506, no. 7488, Nature Publishing Group, 2014, pp. 364–66, doi:<a href=\"https://doi.org/10.1038/nature12977\">10.1038/nature12977</a>.","ama":"Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. Disease associations between honeybees and bumblebees as a threat to wild pollinators. <i>Nature</i>. 2014;506(7488):364-366. doi:<a href=\"https://doi.org/10.1038/nature12977\">10.1038/nature12977</a>","ista":"Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. 2014. Disease associations between honeybees and bumblebees as a threat to wild pollinators. Nature. 506(7488), 364–366.","ieee":"M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, and M. Brown, “Disease associations between honeybees and bumblebees as a threat to wild pollinators,” <i>Nature</i>, vol. 506, no. 7488. Nature Publishing Group, pp. 364–366, 2014.","short":"M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, M. Brown, Nature 506 (2014) 364–366."},"oa":1,"title":"Disease associations between honeybees and bumblebees as a threat to wild pollinators","publist_id":"4726","page":"364 - 366","date_published":"2014-02-20T00:00:00Z","intvolume":"       506","volume":506,"day":"20","publication":"Nature","doi":"10.1038/nature12977","issue":"7488","_id":"2235","publication_status":"published","type":"journal_article","oa_version":"Submitted Version","publisher":"Nature Publishing Group","department":[{"_id":"SyCr"}],"year":"2014","month":"02","publication_identifier":{"issn":["00280836"]},"scopus_import":1,"abstract":[{"text":"Emerging infectious diseases (EIDs) pose a risk to human welfare, both directly and indirectly, by affecting managed livestock and wildlife that provide valuable resources and ecosystem services, such as the pollination of crops. Honeybees (Apis mellifera), the prevailing managed insect crop pollinator, suffer from a range of emerging and exotic high-impact pathogens, and population maintenance requires active management by beekeepers to control them. Wild pollinators such as bumblebees (Bombus spp.) are in global decline, one cause of which may be pathogen spillover from managed pollinators like honeybees or commercial colonies of bumblebees. Here we use a combination of infection experiments and landscape-scale field data to show that honeybee EIDs are indeed widespread infectious agents within the pollinator assemblage. The prevalence of deformed wing virus (DWV) and the exotic parasite Nosema ceranae in honeybees and bumblebees is linked; as honeybees have higher DWV prevalence, and sympatric bumblebees and honeybees are infected by the same DWV strains, Apis is the likely source of at least one major EID in wild pollinators. Lessons learned from vertebrates highlight the need for increased pathogen control in managed bee species to maintain wild pollinators, as declines in native pollinators may be caused by interspecies pathogen transmission originating from managed pollinators.","lang":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985068/","open_access":"1"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:56:11Z","author":[{"last_name":"Fürst","full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X","first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dino","full_name":"Mcmahon, Dino","last_name":"Mcmahon"},{"first_name":"Juliet","last_name":"Osborne","full_name":"Osborne, Juliet"},{"last_name":"Paxton","full_name":"Paxton, Robert","first_name":"Robert"},{"first_name":"Mark","full_name":"Brown, Mark","last_name":"Brown"}],"status":"public"},{"oa":1,"date_created":"2018-12-11T11:56:29Z","citation":{"mla":"Jetchev, Dimitar, and Krzysztof Z. Pietrzak. <i>How to Fake Auxiliary Input</i>. Edited by Yehuda Lindell, vol. 8349, Springer, 2014, pp. 566–90, doi:<a href=\"https://doi.org/10.1007/978-3-642-54242-8_24\">10.1007/978-3-642-54242-8_24</a>.","chicago":"Jetchev, Dimitar, and Krzysztof Z Pietrzak. “How to Fake Auxiliary Input.” edited by Yehuda Lindell, 8349:566–90. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54242-8_24\">https://doi.org/10.1007/978-3-642-54242-8_24</a>.","apa":"Jetchev, D., &#38; Pietrzak, K. Z. (2014). How to fake auxiliary input. In Y. Lindell (Ed.) (Vol. 8349, pp. 566–590). Presented at the TCC: Theory of Cryptography Conference, San Diego, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-54242-8_24\">https://doi.org/10.1007/978-3-642-54242-8_24</a>","ieee":"D. Jetchev and K. Z. Pietrzak, “How to fake auxiliary input,” presented at the TCC: Theory of Cryptography Conference, San Diego, USA, 2014, vol. 8349, pp. 566–590.","short":"D. Jetchev, K.Z. Pietrzak, in:, Y. Lindell (Ed.), Springer, 2014, pp. 566–590.","ista":"Jetchev D, Pietrzak KZ. 2014. How to fake auxiliary input. TCC: Theory of Cryptography Conference, LNCS, vol. 8349, 566–590.","ama":"Jetchev D, Pietrzak KZ. How to fake auxiliary input. In: Lindell Y, ed. Vol 8349. Springer; 2014:566-590. doi:<a href=\"https://doi.org/10.1007/978-3-642-54242-8_24\">10.1007/978-3-642-54242-8_24</a>"},"conference":{"end_date":"2014-02-26","location":"San Diego, USA","start_date":"2014-02-24","name":"TCC: Theory of Cryptography Conference"},"quality_controlled":"1","page":"566 - 590","publist_id":"4725","title":"How to fake auxiliary input","volume":8349,"day":"01","has_accepted_license":"1","intvolume":"      8349","editor":[{"first_name":"Yehuda","last_name":"Lindell","full_name":"Lindell, Yehuda"}],"date_published":"2014-02-01T00:00:00Z","doi":"10.1007/978-3-642-54242-8_24","file_date_updated":"2020-07-14T12:45:34Z","ec_funded":1,"pubrep_id":"681","publisher":"Springer","ddc":["004"],"type":"conference","oa_version":"Submitted Version","file":[{"file_name":"IST-2016-681-v1+1_869_1_.pdf","relation":"main_file","file_id":"5275","creator":"system","date_updated":"2020-07-14T12:45:34Z","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:17:21Z","file_size":313528,"checksum":"42960325c29dcd8d832edadcc3ce0045"}],"_id":"2236","publication_status":"published","alternative_title":["LNCS"],"publication_identifier":{"isbn":["978-364254241-1"]},"year":"2014","month":"02","project":[{"grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T06:56:12Z","language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Consider a joint distribution (X,A) on a set. We show that for any family of distinguishers, there exists a simulator such that 1 no function in can distinguish (X,A) from (X,h(X)) with advantage ε, 2 h is only O(2 3ℓ ε -2) times less efficient than the functions in. For the most interesting settings of the parameters (in particular, the cryptographic case where X has superlogarithmic min-entropy, ε &gt; 0 is negligible and consists of circuits of polynomial size), we can make the simulator h deterministic. As an illustrative application of our theorem, we give a new security proof for the leakage-resilient stream-cipher from Eurocrypt'09. Our proof is simpler and quantitatively much better than the original proof using the dense model theorem, giving meaningful security guarantees if instantiated with a standard blockcipher like AES. Subsequent to this work, Chung, Lui and Pass gave an interactive variant of our main theorem, and used it to investigate weak notions of Zero-Knowledge. Vadhan and Zheng give a more constructive version of our theorem using their new uniform min-max theorem."}],"main_file_link":[{"url":"https://repository.ist.ac.at/id/eprint/681","open_access":"1"}],"author":[{"first_name":"Dimitar","last_name":"Jetchev","full_name":"Jetchev, Dimitar"},{"orcid":"0000-0002-9139-1654","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"status":"public"},{"date_published":"2014-01-13T00:00:00Z","intvolume":"        49","volume":49,"day":"13","ec_funded":1,"doi":"10.1145/2535838.2535875","conference":{"end_date":"2014-01-24","location":"San Diego, USA","start_date":"2014-01-22","name":"POPL: Principles of Programming Languages"},"quality_controlled":"1","citation":{"mla":"Boker, Udi, et al. <i>Battery Transition Systems</i>. Vol. 49, no. 1, ACM, 2014, pp. 595–606, doi:<a href=\"https://doi.org/10.1145/2535838.2535875\">10.1145/2535838.2535875</a>.","chicago":"Boker, Udi, Thomas A Henzinger, and Arjun Radhakrishna. “Battery Transition Systems,” 49:595–606. ACM, 2014. <a href=\"https://doi.org/10.1145/2535838.2535875\">https://doi.org/10.1145/2535838.2535875</a>.","apa":"Boker, U., Henzinger, T. A., &#38; Radhakrishna, A. (2014). Battery transition systems (Vol. 49, pp. 595–606). Presented at the POPL: Principles of Programming Languages, San Diego, USA: ACM. <a href=\"https://doi.org/10.1145/2535838.2535875\">https://doi.org/10.1145/2535838.2535875</a>","short":"U. Boker, T.A. Henzinger, A. Radhakrishna, in:, ACM, 2014, pp. 595–606.","ieee":"U. Boker, T. A. Henzinger, and A. Radhakrishna, “Battery transition systems,” presented at the POPL: Principles of Programming Languages, San Diego, USA, 2014, vol. 49, no. 1, pp. 595–606.","ista":"Boker U, Henzinger TA, Radhakrishna A. 2014. Battery transition systems. POPL: Principles of Programming Languages vol. 49, 595–606.","ama":"Boker U, Henzinger TA, Radhakrishna A. Battery transition systems. In: Vol 49. ACM; 2014:595-606. doi:<a href=\"https://doi.org/10.1145/2535838.2535875\">10.1145/2535838.2535875</a>"},"date_created":"2018-12-11T11:56:30Z","title":"Battery transition systems","publist_id":"4722","page":"595 - 606","scopus_import":1,"abstract":[{"lang":"eng","text":"The analysis of the energy consumption of software is an important goal for quantitative formal methods. Current methods, using weighted transition systems or energy games, model the energy source as an ideal resource whose status is characterized by one number, namely the amount of remaining energy. Real batteries, however, exhibit behaviors that can deviate substantially from an ideal energy resource. Based on a discretization of a standard continuous battery model, we introduce battery transition systems. In this model, a battery is viewed as consisting of two parts-the available-charge tank and the bound-charge tank. Any charge or discharge is applied to the available-charge tank. Over time, the energy from each tank diffuses to the other tank. Battery transition systems are infinite state systems that, being not well-structured, fall into no decidable class that is known to us. Nonetheless, we are able to prove that the !-regular modelchecking problem is decidable for battery transition systems. We also present a case study on the verification of control programs for energy-constrained semi-autonomous robots."}],"language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:56:13Z","author":[{"id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi","full_name":"Boker, Udi","last_name":"Boker"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun"}],"status":"public","_id":"2239","issue":"1","publication_status":"published","oa_version":"None","type":"conference","publisher":"ACM","department":[{"_id":"ToHe"}],"year":"2014","month":"01","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"publication_identifier":{"isbn":["978-145032544-8"]}},{"date_published":"2014-02-13T00:00:00Z","scopus_import":1,"intvolume":"       156","abstract":[{"text":"Clathrin-mediated endocytosis is the major mechanism for eukaryotic plasma membrane-based proteome turn-over. In plants, clathrin-mediated endocytosis is essential for physiology and development, but the identification and organization of the machinery operating this process remains largely obscure. Here, we identified an eight-core-component protein complex, the TPLATE complex, essential for plant growth via its role as major adaptor module for clathrin-mediated endocytosis. This complex consists of evolutionarily unique proteins that associate closely with core endocytic elements. The TPLATE complex is recruited as dynamic foci at the plasma membrane preceding recruitment of adaptor protein complex 2, clathrin, and dynamin-related proteins. Reduced function of different complex components severely impaired internalization of assorted endocytic cargoes, demonstrating its pivotal role in clathrin-mediated endocytosis. Taken together, the TPLATE complex is an early endocytic module representing a unique evolutionary plant adaptation of the canonical eukaryotic pathway for clathrin-mediated endocytosis.","lang":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"day":"13","publication":"Cell","date_updated":"2021-01-12T06:56:13Z","volume":156,"status":"public","author":[{"last_name":"Gadeyne","full_name":"Gadeyne, Astrid","first_name":"Astrid"},{"first_name":"Clara","full_name":"Sánchez Rodríguez, Clara","last_name":"Sánchez Rodríguez"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"first_name":"Simone","last_name":"Di Rubbo","full_name":"Di Rubbo, Simone"},{"first_name":"Henrik","full_name":"Zauber, Henrik","last_name":"Zauber"},{"first_name":"Kevin","last_name":"Vanneste","full_name":"Vanneste, Kevin"},{"first_name":"Jelle","last_name":"Van Leene","full_name":"Van Leene, Jelle"},{"last_name":"De Winne","full_name":"De Winne, Nancy","first_name":"Nancy"},{"first_name":"Dominique","full_name":"Eeckhout, Dominique","last_name":"Eeckhout"},{"first_name":"Geert","full_name":"Persiau, Geert","last_name":"Persiau"},{"first_name":"Eveline","full_name":"Van De Slijke, Eveline","last_name":"Van De Slijke"},{"last_name":"Cannoot","full_name":"Cannoot, Bernard","first_name":"Bernard"},{"first_name":"Leen","last_name":"Vercruysse","full_name":"Vercruysse, Leen"},{"first_name":"Jonathan","last_name":"Mayers","full_name":"Mayers, Jonathan"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","full_name":"Adamowski, Maciek","last_name":"Adamowski","orcid":"0000-0001-6463-5257"},{"last_name":"Kania","full_name":"Kania, Urszula","first_name":"Urszula","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ehrlich","full_name":"Ehrlich, Matthias","first_name":"Matthias"},{"last_name":"Schweighofer","full_name":"Schweighofer, Alois","first_name":"Alois"},{"first_name":"Tijs","full_name":"Ketelaar, Tijs","last_name":"Ketelaar"},{"first_name":"Steven","last_name":"Maere","full_name":"Maere, Steven"},{"first_name":"Sebastian","last_name":"Bednarek","full_name":"Bednarek, Sebastian"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"first_name":"Kris","last_name":"Gevaert","full_name":"Gevaert, Kris"},{"first_name":"Erwin","full_name":"Witters, Erwin","last_name":"Witters"},{"last_name":"Russinova","full_name":"Russinova, Eugenia","first_name":"Eugenia"},{"first_name":"Staffan","last_name":"Persson","full_name":"Persson, Staffan"},{"full_name":"De Jaeger, Geert","last_name":"De Jaeger","first_name":"Geert"},{"first_name":"Daniël","full_name":"Van Damme, Daniël","last_name":"Van Damme"}],"doi":"10.1016/j.cell.2014.01.039","publication_status":"published","quality_controlled":"1","issue":"4","_id":"2240","type":"journal_article","oa_version":"None","citation":{"apa":"Gadeyne, A., Sánchez Rodríguez, C., Vanneste, S., Di Rubbo, S., Zauber, H., Vanneste, K., … Van Damme, D. (2014). The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2014.01.039\">https://doi.org/10.1016/j.cell.2014.01.039</a>","chicago":"Gadeyne, Astrid, Clara Sánchez Rodríguez, Steffen Vanneste, Simone Di Rubbo, Henrik Zauber, Kevin Vanneste, Jelle Van Leene, et al. “The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants.” <i>Cell</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.039\">https://doi.org/10.1016/j.cell.2014.01.039</a>.","mla":"Gadeyne, Astrid, et al. “The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants.” <i>Cell</i>, vol. 156, no. 4, Cell Press, 2014, pp. 691–704, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.039\">10.1016/j.cell.2014.01.039</a>.","ama":"Gadeyne A, Sánchez Rodríguez C, Vanneste S, et al. The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. <i>Cell</i>. 2014;156(4):691-704. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.039\">10.1016/j.cell.2014.01.039</a>","ista":"Gadeyne A, Sánchez Rodríguez C, Vanneste S, Di Rubbo S, Zauber H, Vanneste K, Van Leene J, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Cannoot B, Vercruysse L, Mayers J, Adamowski M, Kania U, Ehrlich M, Schweighofer A, Ketelaar T, Maere S, Bednarek S, Friml J, Gevaert K, Witters E, Russinova E, Persson S, De Jaeger G, Van Damme D. 2014. The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. Cell. 156(4), 691–704.","short":"A. Gadeyne, C. Sánchez Rodríguez, S. Vanneste, S. Di Rubbo, H. Zauber, K. Vanneste, J. Van Leene, N. De Winne, D. Eeckhout, G. Persiau, E. Van De Slijke, B. Cannoot, L. Vercruysse, J. Mayers, M. Adamowski, U. Kania, M. Ehrlich, A. Schweighofer, T. Ketelaar, S. Maere, S. Bednarek, J. Friml, K. Gevaert, E. Witters, E. Russinova, S. Persson, G. De Jaeger, D. Van Damme, Cell 156 (2014) 691–704.","ieee":"A. Gadeyne <i>et al.</i>, “The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants,” <i>Cell</i>, vol. 156, no. 4. Cell Press, pp. 691–704, 2014."},"date_created":"2018-12-11T11:56:31Z","publisher":"Cell Press","department":[{"_id":"JiFr"}],"title":"The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants","publist_id":"4721","page":"691 - 704","year":"2014","month":"02","publication_identifier":{"issn":["00928674"]}},{"publisher":"Elsevier","_id":"2241","issue":"2","quality_controlled":"1","publication_status":"published","date_created":"2018-12-11T11:56:31Z","citation":{"chicago":"Beppu, Kaoru, Takuya Sasaki, Kenji Tanaka, Akihiro Yamanaka, Yugo Fukazawa, Ryuichi Shigemoto, and Ko Matsui. “Optogenetic Countering of Glial Acidosis Suppresses Glial Glutamate Release and Ischemic Brain Damage.” <i>Neuron</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">https://doi.org/10.1016/j.neuron.2013.11.011</a>.","apa":"Beppu, K., Sasaki, T., Tanaka, K., Yamanaka, A., Fukazawa, Y., Shigemoto, R., &#38; Matsui, K. (2014). Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">https://doi.org/10.1016/j.neuron.2013.11.011</a>","mla":"Beppu, Kaoru, et al. “Optogenetic Countering of Glial Acidosis Suppresses Glial Glutamate Release and Ischemic Brain Damage.” <i>Neuron</i>, vol. 81, no. 2, Elsevier, 2014, pp. 314–20, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">10.1016/j.neuron.2013.11.011</a>.","short":"K. Beppu, T. Sasaki, K. Tanaka, A. Yamanaka, Y. Fukazawa, R. Shigemoto, K. Matsui, Neuron 81 (2014) 314–320.","ieee":"K. Beppu <i>et al.</i>, “Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage,” <i>Neuron</i>, vol. 81, no. 2. Elsevier, pp. 314–320, 2014.","ista":"Beppu K, Sasaki T, Tanaka K, Yamanaka A, Fukazawa Y, Shigemoto R, Matsui K. 2014. Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. Neuron. 81(2), 314–320.","ama":"Beppu K, Sasaki T, Tanaka K, et al. Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. <i>Neuron</i>. 2014;81(2):314-320. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">10.1016/j.neuron.2013.11.011</a>"},"type":"journal_article","oa_version":"None","month":"01","year":"2014","page":"314 - 320","publist_id":"4715","publication_identifier":{"issn":["08966273"]},"title":"Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage","department":[{"_id":"RySh"}],"language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","volume":81,"date_updated":"2021-01-12T06:56:14Z","day":"22","publication":"Neuron","scopus_import":1,"date_published":"2014-01-22T00:00:00Z","abstract":[{"text":"The brain demands high-energy supply and obstruction of blood flow causes rapid deterioration of the healthiness of brain cells. Two major events occur upon ischemia: acidosis and liberation of excess glutamate, which leads to excitotoxicity. However, cellular source of glutamate and its release mechanism upon ischemia remained unknown. Here we show a causal relationship between glial acidosis and neuronal excitotoxicity. As the major cation that flows through channelrhodopsin-2 (ChR2) is proton, this could be regarded as an optogenetic tool for instant intracellular acidification. Optical activation of ChR2 expressed in glial cells led to glial acidification and to release of glutamate. On the other hand, glial alkalization via optogenetic activation of a proton pump, archaerhodopsin (ArchT), led to cessation of glutamate release and to the relief of ischemic brain damage in vivo. Our results suggest that controlling glial pH may be an effective therapeutic strategy for intervention of ischemic brain damage.","lang":"eng"}],"intvolume":"        81","doi":"10.1016/j.neuron.2013.11.011","author":[{"last_name":"Beppu","full_name":"Beppu, Kaoru","first_name":"Kaoru"},{"full_name":"Sasaki, Takuya","last_name":"Sasaki","first_name":"Takuya"},{"last_name":"Tanaka","full_name":"Tanaka, Kenji","first_name":"Kenji"},{"full_name":"Yamanaka, Akihiro","last_name":"Yamanaka","first_name":"Akihiro"},{"first_name":"Yugo","full_name":"Fukazawa, Yugo","last_name":"Fukazawa"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"first_name":"Ko","full_name":"Matsui, Ko","last_name":"Matsui"}],"status":"public"},{"department":[{"_id":"MiSi"}],"title":"A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation","publication_identifier":{"issn":["00145793"]},"publist_id":"4714","page":"632 - 640","month":"02","year":"2014","oa_version":"None","type":"journal_article","citation":{"chicago":"Dueck, Anne, Alexander Eichner, Michael K Sixt, and Gunter Meister. “A MiR-155-Dependent MicroRNA Hierarchy in Dendritic Cell Maturation and Macrophage Activation.” <i>FEBS Letters</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.febslet.2014.01.009\">https://doi.org/10.1016/j.febslet.2014.01.009</a>.","apa":"Dueck, A., Eichner, A., Sixt, M. K., &#38; Meister, G. (2014). A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. <i>FEBS Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.febslet.2014.01.009\">https://doi.org/10.1016/j.febslet.2014.01.009</a>","mla":"Dueck, Anne, et al. “A MiR-155-Dependent MicroRNA Hierarchy in Dendritic Cell Maturation and Macrophage Activation.” <i>FEBS Letters</i>, vol. 588, no. 4, Elsevier, 2014, pp. 632–40, doi:<a href=\"https://doi.org/10.1016/j.febslet.2014.01.009\">10.1016/j.febslet.2014.01.009</a>.","short":"A. Dueck, A. Eichner, M.K. Sixt, G. Meister, FEBS Letters 588 (2014) 632–640.","ista":"Dueck A, Eichner A, Sixt MK, Meister G. 2014. A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. FEBS Letters. 588(4), 632–640.","ieee":"A. Dueck, A. Eichner, M. K. Sixt, and G. Meister, “A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation,” <i>FEBS Letters</i>, vol. 588, no. 4. Elsevier, pp. 632–640, 2014.","ama":"Dueck A, Eichner A, Sixt MK, Meister G. A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. <i>FEBS Letters</i>. 2014;588(4):632-640. doi:<a href=\"https://doi.org/10.1016/j.febslet.2014.01.009\">10.1016/j.febslet.2014.01.009</a>"},"date_created":"2018-12-11T11:56:31Z","quality_controlled":"1","publication_status":"published","_id":"2242","issue":"4","publisher":"Elsevier","status":"public","author":[{"full_name":"Dueck, Anne","last_name":"Dueck","first_name":"Anne"},{"first_name":"Alexander","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","full_name":"Eichner, Alexander","last_name":"Eichner"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K"},{"first_name":"Gunter","full_name":"Meister, Gunter","last_name":"Meister"}],"doi":"10.1016/j.febslet.2014.01.009","intvolume":"       588","abstract":[{"text":"MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in many cellular pathways. MiRNAs associate with members of the Argonaute protein family and bind to partially complementary sequences on mRNAs and induce translational repression or mRNA decay. Using deep sequencing and Northern blotting, we characterized miRNA expression in wild type and miR-155-deficient dendritic cells (DCs) and macrophages. Analysis of different stimuli (LPS, LDL, eLDL, oxLDL) reveals a direct influence of miR-155 on the expression levels of other miRNAs. For example, miR-455 is negatively regulated in miR-155-deficient cells possibly due to inhibition of the transcription factor C/EBPbeta by miR-155. Based on our comprehensive data sets, we propose a model of hierarchical miRNA expression dominated by miR-155 in DCs and macrophages.","lang":"eng"}],"scopus_import":1,"date_published":"2014-02-14T00:00:00Z","day":"14","publication":"FEBS Letters","volume":588,"date_updated":"2021-01-12T06:56:14Z","language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"year":"2014","month":"01","publication_identifier":{"issn":["10643745"]},"department":[{"_id":"JiFr"}],"publisher":"Springer","publication_status":"published","alternative_title":["Methods in Molecular Biology"],"_id":"2245","oa_version":"None","type":"book_chapter","status":"public","author":[{"orcid":"0000-0002-1998-6741","last_name":"Simon","full_name":"Simon, Sibu","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Skůpa","full_name":"Skůpa, Petr","first_name":"Petr"},{"first_name":"Petre","last_name":"Dobrev","full_name":"Dobrev, Petre"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"first_name":"Eva","full_name":"Zažímalová, Eva","last_name":"Zažímalová"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","series_title":"Methods in Molecular Biology","date_updated":"2021-01-12T06:56:15Z","scopus_import":1,"abstract":[{"text":"Exogenous application of biologically important molecules for plant growth promotion and/or regulation is very common both in plant research and horticulture. Plant hormones such as auxins and cytokinins are classes of compounds which are often applied exogenously. Nevertheless, plants possess a well-established machinery to regulate the active pool of exogenously applied compounds by converting them to metabolites and conjugates. Consequently, it is often very useful to know the in vivo status of applied compounds to connect them with some of the regulatory events in plant developmental processes. The in vivo status of applied compounds can be measured by incubating plants with radiolabeled compounds, followed by extraction, purification, and HPLC metabolic profiling of plant extracts. Recently we have used this method to characterize the intracellularly localized PIN protein, PIN5. Here we explain the method in detail, with a focus on general application. ","lang":"eng"}],"page":"255 - 264","publist_id":"4704","title":"Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters","quality_controlled":"1","citation":{"ama":"Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In: Hicks G, Robert S, eds. <i>Plant Chemical Genomics</i>. Vol 1056. Methods in Molecular Biology. Springer; 2014:255-264. doi:<a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">10.1007/978-1-62703-592-7_23</a>","ista":"Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. 2014.Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In: Plant Chemical Genomics. Methods in Molecular Biology, vol. 1056, 255–264.","short":"S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, J. Friml, in:, G. Hicks, S. Robert (Eds.), Plant Chemical Genomics, Springer, 2014, pp. 255–264.","ieee":"S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, and J. Friml, “Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters,” in <i>Plant Chemical Genomics</i>, vol. 1056, G. Hicks and S. Robert, Eds. Springer, 2014, pp. 255–264.","apa":"Simon, S., Skůpa, P., Dobrev, P., Petrášek, J., Zažímalová, E., &#38; Friml, J. (2014). Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters. In G. Hicks &#38; S. Robert (Eds.), <i>Plant Chemical Genomics</i> (Vol. 1056, pp. 255–264). Springer. <a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">https://doi.org/10.1007/978-1-62703-592-7_23</a>","chicago":"Simon, Sibu, Petr Skůpa, Petre Dobrev, Jan Petrášek, Eva Zažímalová, and Jiří Friml. “Analyzing the in Vivo Status of Exogenously Applied Auxins: A HPLC-Based Method to Characterize the Intracellularly Localized Auxin Transporters.” In <i>Plant Chemical Genomics</i>, edited by Glenn Hicks and Stéphanie Robert, 1056:255–64. Methods in Molecular Biology. Springer, 2014. <a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">https://doi.org/10.1007/978-1-62703-592-7_23</a>.","mla":"Simon, Sibu, et al. “Analyzing the in Vivo Status of Exogenously Applied Auxins: A HPLC-Based Method to Characterize the Intracellularly Localized Auxin Transporters.” <i>Plant Chemical Genomics</i>, edited by Glenn Hicks and Stéphanie Robert, vol. 1056, Springer, 2014, pp. 255–64, doi:<a href=\"https://doi.org/10.1007/978-1-62703-592-7_23\">10.1007/978-1-62703-592-7_23</a>."},"date_created":"2018-12-11T11:56:32Z","doi":"10.1007/978-1-62703-592-7_23","publication":"Plant Chemical Genomics","day":"01","volume":1056,"date_published":"2014-01-01T00:00:00Z","intvolume":"      1056","editor":[{"last_name":"Hicks","full_name":"Hicks, Glenn","first_name":"Glenn"},{"last_name":"Robert","full_name":"Robert, Stéphanie","first_name":"Stéphanie"}]}]