[{"page":"91 - 95","abstract":[{"text":"Exposure of an isogenic bacterial population to a cidal antibiotic typically fails to eliminate a small fraction of refractory cells. Historically, fractional killing has been attributed to infrequently dividing or nondividing &quot;persisters.&quot; Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although persistence in these studies was characterized by stable numbers of cells, this apparent stability was actually a dynamic state of balanced division and death. Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic pulses that were negatively correlated with cell survival. These behaviors may reflect epigenetic effects, because KatG pulsing and death were correlated between sibling cells. Selection of lineages characterized by infrequent KatG pulsing could allow nonresponsive adaptation during prolonged drug exposure.","lang":"eng"}],"publication":"Science","issue":"6115","publist_id":"7321","status":"public","date_published":"2013-01-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"499","language":[{"iso":"eng"}],"intvolume":"       339","oa_version":"None","author":[{"full_name":"Wakamoto, Yurichi","last_name":"Wakamoto","first_name":"Yurichi"},{"full_name":"Dhar, Neraaj","first_name":"Neraaj","last_name":"Dhar"},{"orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P","last_name":"Chait"},{"last_name":"Schneider","first_name":"Katrin","full_name":"Schneider, Katrin"},{"first_name":"François","last_name":"Signorino Gelo","full_name":"Signorino Gelo, François"},{"last_name":"Leibler","first_name":"Stanislas","full_name":"Leibler, Stanislas"},{"full_name":"Mckinney, John","last_name":"Mckinney","first_name":"John"}],"month":"01","scopus_import":1,"citation":{"short":"Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler, J. Mckinney, Science 339 (2013) 91–95.","mla":"Wakamoto, Yurichi, et al. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” <i>Science</i>, vol. 339, no. 6115, American Association for the Advancement of Science, 2013, pp. 91–95, doi:<a href=\"https://doi.org/10.1126/science.1229858\">10.1126/science.1229858</a>.","ieee":"Y. Wakamoto <i>et al.</i>, “Dynamic persistence of antibiotic-stressed mycobacteria,” <i>Science</i>, vol. 339, no. 6115. American Association for the Advancement of Science, pp. 91–95, 2013.","chicago":"Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” <i>Science</i>. American Association for the Advancement of Science, 2013. <a href=\"https://doi.org/10.1126/science.1229858\">https://doi.org/10.1126/science.1229858</a>.","apa":"Wakamoto, Y., Dhar, N., Chait, R. P., Schneider, K., Signorino Gelo, F., Leibler, S., &#38; Mckinney, J. (2013). Dynamic persistence of antibiotic-stressed mycobacteria. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1229858\">https://doi.org/10.1126/science.1229858</a>","ista":"Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115), 91–95.","ama":"Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed mycobacteria. <i>Science</i>. 2013;339(6115):91-95. doi:<a href=\"https://doi.org/10.1126/science.1229858\">10.1126/science.1229858</a>"},"date_created":"2018-12-11T11:46:48Z","year":"2013","type":"journal_article","volume":339,"doi":"10.1126/science.1229858","title":"Dynamic persistence of antibiotic-stressed mycobacteria","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"quality_controlled":"1","day":"04","publication_status":"published","date_updated":"2021-01-12T08:01:06Z","publisher":"American Association for the Advancement of Science"},{"issue":"1","acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council, the Government of the Republic of Panama, the Interdisciplinary Centre for Human and Avian Influenza Research (www.ichair-flu.org) funded by the Scottish Funding Council, and the Institute for Science and Technology Austria.\r\nCC BY 2.0\r\n","_id":"500","language":[{"iso":"eng"}],"pubrep_id":"941","file_date_updated":"2020-07-14T12:46:36Z","month":"10","article_number":"222","author":[{"last_name":"Ward","first_name":"Melissa","full_name":"Ward, Melissa"},{"last_name":"Lycett","first_name":"Samantha","full_name":"Lycett, Samantha"},{"last_name":"Avila","first_name":"Dorita","full_name":"Avila, Dorita"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"},{"full_name":"Leigh Brown, Andrew","first_name":"Andrew","last_name":"Leigh Brown"}],"file":[{"file_size":1150052,"file_id":"4722","access_level":"open_access","date_updated":"2020-07-14T12:46:36Z","date_created":"2018-12-12T10:08:59Z","content_type":"application/pdf","relation":"main_file","file_name":"IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf","creator":"system","checksum":"52cf48a7c1794676ae8b0029573a84a9"}],"citation":{"short":"M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary Biology 13 (2013).","mla":"Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1, 222, BioMed Central, 2013, doi:<a href=\"https://doi.org/10.1186/1471-2148-13-222\">10.1186/1471-2148-13-222</a>.","chicago":"Ward, Melissa, Samantha Lycett, Dorita Avila, Jonathan P Bollback, and Andrew Leigh Brown. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2148-13-222\">https://doi.org/10.1186/1471-2148-13-222</a>.","ieee":"M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza,” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1. BioMed Central, 2013.","ista":"Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. 2013. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 13(1), 222.","apa":"Ward, M., Lycett, S., Avila, D., Bollback, J. P., &#38; Leigh Brown, A. (2013). Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-13-222\">https://doi.org/10.1186/1471-2148-13-222</a>","ama":"Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. <i>BMC Evolutionary Biology</i>. 2013;13(1). doi:<a href=\"https://doi.org/10.1186/1471-2148-13-222\">10.1186/1471-2148-13-222</a>"},"ddc":["576"],"has_accepted_license":"1","year":"2013","oa":1,"title":"Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza","doi":"10.1186/1471-2148-13-222","day":"09","date_updated":"2021-01-12T08:01:08Z","abstract":[{"lang":"eng","text":"Background: Reassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded the emergence of pandemic strains. It has been suggested that productive viral infection requires a balance in the level of functional activity of HA and NA, arising from their closely interacting roles in the viral life cycle, and that this functional balance could be mediated by genetic changes in the HA and NA. Here, we investigate how the selective pressure varies for H7 avian influenza HA on different NA subtype backgrounds. Results: By extending Bayesian stochastic mutational mapping methods to calculate the ratio of the rate of non-synonymous change to the rate of synonymous change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1 region to be significantly greater on an N2 NA subtype background than on an N1, N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different NA subtype backgrounds could not be attributed to underlying differences between avian host species or virus pathogenicity. Examination of d N/d S values for each subtype on a site-by-site basis indicated that the elevated d N/d S on the N2 NA background was a result of increased selection, rather than a relaxation of selective constraint. Conclusions: Our results are consistent with the hypothesis that reassortment exposes influenza HA to significant changes in selective pressure through genetic interactions with NA. Such epistatic effects might be explicitly accounted for in future models of influenza evolution."}],"date_published":"2013-10-09T00:00:00Z","status":"public","publication":"BMC Evolutionary Biology","publist_id":"7320","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"        13","oa_version":"Published Version","scopus_import":1,"date_created":"2018-12-11T11:46:49Z","volume":13,"type":"journal_article","department":[{"_id":"JoBo"}],"quality_controlled":"1","publication_status":"published","publisher":"BioMed Central"},{"date_created":"2018-12-11T11:46:49Z","scopus_import":1,"oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"intvolume":"        94","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7319","publication":"Journal of Mammalogy","date_published":"2013-12-01T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"All known species of extant tapirs are allopatric: 1 in southeastern Asia and 3 in Central and South America. The fossil record for tapirs, however, is much wider in geographical range, including Europe, Asia, and North and South America, going back to the late Oligocene, making the present distribution a relict of the original one. We here describe a new species of living Tapirus from the Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla in more than 100 years, from both morphological and molecular characters. It is shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque (Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia, where the biota faces increasing threats. Local peoples have long recognized our new species, suggesting a key role for traditional knowledge in understanding the biodiversity of the region."}],"publisher":"Oxford University Press","publication_status":"published","quality_controlled":"1","department":[{"_id":"JoBo"}],"type":"journal_article","volume":94,"ddc":["570"],"citation":{"ieee":"M. Cozzuol <i>et al.</i>, “A new species of tapir from the Amazon,” <i>Journal of Mammalogy</i>, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013.","chicago":"Cozzuol, Mario, Camila Clozato, Elizete Holanda, Flávio Rodrigues, Samuel Nienow, Benoit De Thoisy, Rodrigo A Fernandes Redondo, and Fabrício Santos. “A New Species of Tapir from the Amazon.” <i>Journal of Mammalogy</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">https://doi.org/10.1644/12-MAMM-A-169.1</a>.","mla":"Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” <i>Journal of Mammalogy</i>, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45, doi:<a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">10.1644/12-MAMM-A-169.1</a>.","short":"M. Cozzuol, C. Clozato, E. Holanda, F. Rodrigues, S. Nienow, B. De Thoisy, R.A. Fernandes Redondo, F. Santos, Journal of Mammalogy 94 (2013) 1331–1345.","ama":"Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon. <i>Journal of Mammalogy</i>. 2013;94(6):1331-1345. doi:<a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">10.1644/12-MAMM-A-169.1</a>","apa":"Cozzuol, M., Clozato, C., Holanda, E., Rodrigues, F., Nienow, S., De Thoisy, B., … Santos, F. (2013). A new species of tapir from the Amazon. <i>Journal of Mammalogy</i>. Oxford University Press. <a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">https://doi.org/10.1644/12-MAMM-A-169.1</a>","ista":"Cozzuol M, Clozato C, Holanda E, Rodrigues F, Nienow S, De Thoisy B, Fernandes Redondo RA, Santos F. 2013. A new species of tapir from the Amazon. Journal of Mammalogy. 94(6), 1331–1345."},"author":[{"full_name":"Cozzuol, Mario","first_name":"Mario","last_name":"Cozzuol"},{"first_name":"Camila","last_name":"Clozato","full_name":"Clozato, Camila"},{"first_name":"Elizete","last_name":"Holanda","full_name":"Holanda, Elizete"},{"full_name":"Rodrigues, Flávio","last_name":"Rodrigues","first_name":"Flávio"},{"first_name":"Samuel","last_name":"Nienow","full_name":"Nienow, Samuel"},{"first_name":"Benoit","last_name":"De Thoisy","full_name":"De Thoisy, Benoit"},{"orcid":"0000-0002-5837-2793","full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A","last_name":"Fernandes Redondo"},{"full_name":"Santos, Fabrício","last_name":"Santos","first_name":"Fabrício"}],"file":[{"file_name":"IST-2018-940-v1+1_2013_Redondo_A_new.pdf","relation":"main_file","checksum":"8007815078dccac21ecd1cf73a269dc6","creator":"system","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:36Z","date_created":"2018-12-12T10:12:59Z","file_size":1040765,"file_id":"4980"}],"file_date_updated":"2020-07-14T12:46:36Z","month":"12","_id":"501","language":[{"iso":"eng"}],"pubrep_id":"940","issue":"6","page":"1331 - 1345","date_updated":"2021-01-12T08:01:09Z","day":"01","doi":"10.1644/12-MAMM-A-169.1","title":"A new species of tapir from the Amazon","oa":1,"year":"2013","has_accepted_license":"1"},{"volume":21,"type":"journal_article","year":"2013","publisher":"IOS Press","date_updated":"2021-01-12T08:01:09Z","publication_status":"published","day":"22","quality_controlled":"1","department":[{"_id":"KrPi"}],"title":"Short blind signatures","doi":"10.3233/JCS-130477","_id":"502","intvolume":"        21","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2013-11-22T00:00:00Z","publication":"Journal of Computer Security","issue":"5","publist_id":"7318","abstract":[{"text":"Blind signatures allow users to obtain signatures on messages hidden from the signer; moreover, the signer cannot link the resulting message/signature pair to the signing session. This paper presents blind signature schemes, in which the number of interactions between the user and the signer is minimal and whose blind signatures are short. Our schemes are defined over bilinear groups and are proved secure in the common-reference-string model without random oracles and under standard assumptions: CDH and the decision-linear assumption. (We also give variants over asymmetric groups based on similar assumptions.) The blind signatures are Waters signatures, which consist of 2 group elements. Moreover, we instantiate partially blind signatures, where the message consists of a part hidden from the signer and a commonly known public part, and schemes achieving perfect blindness. We propose new variants of blind signatures, such as signer-friendly partially blind signatures, where the public part can be chosen by the signer without prior agreement, 3-party blind signatures, as well as blind signatures on multiple aggregated messages provided by independent sources. We also extend Waters signatures to non-binary alphabets by proving a new result on the underlying hash function. ","lang":"eng"}],"page":"627 - 661","citation":{"ista":"Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. 2013. Short blind signatures. Journal of Computer Security. 21(5), 627–661.","apa":"Blazy, O., Fuchsbauer, G., Pointcheval, D., &#38; Vergnaud, D. (2013). Short blind signatures. <i>Journal of Computer Security</i>. IOS Press. <a href=\"https://doi.org/10.3233/JCS-130477\">https://doi.org/10.3233/JCS-130477</a>","ama":"Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. Short blind signatures. <i>Journal of Computer Security</i>. 2013;21(5):627-661. doi:<a href=\"https://doi.org/10.3233/JCS-130477\">10.3233/JCS-130477</a>","short":"O. Blazy, G. Fuchsbauer, D. Pointcheval, D. Vergnaud, Journal of Computer Security 21 (2013) 627–661.","mla":"Blazy, Olivier, et al. “Short Blind Signatures.” <i>Journal of Computer Security</i>, vol. 21, no. 5, IOS Press, 2013, pp. 627–61, doi:<a href=\"https://doi.org/10.3233/JCS-130477\">10.3233/JCS-130477</a>.","chicago":"Blazy, Olivier, Georg Fuchsbauer, David Pointcheval, and Damien Vergnaud. “Short Blind Signatures.” <i>Journal of Computer Security</i>. IOS Press, 2013. <a href=\"https://doi.org/10.3233/JCS-130477\">https://doi.org/10.3233/JCS-130477</a>.","ieee":"O. Blazy, G. Fuchsbauer, D. Pointcheval, and D. Vergnaud, “Short blind signatures,” <i>Journal of Computer Security</i>, vol. 21, no. 5. IOS Press, pp. 627–661, 2013."},"date_created":"2018-12-11T11:46:50Z","scopus_import":1,"month":"11","oa_version":"None","author":[{"first_name":"Olivier","last_name":"Blazy","full_name":"Blazy, Olivier"},{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","first_name":"Georg","full_name":"Fuchsbauer, Georg"},{"full_name":"Pointcheval, David","last_name":"Pointcheval","first_name":"David"},{"full_name":"Vergnaud, Damien","first_name":"Damien","last_name":"Vergnaud"}]},{"scopus_import":1,"date_created":"2018-12-11T11:46:51Z","citation":{"chicago":"Greimel, Katrin, Veronika Perz, Klaus Koren, Roland Feola, Armin Temel, Christian Sohar, Enrique Herrero Acero, Ingo Klimant, and Georg Guebitz. “Banning Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.” <i>Green Chemistry</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c2gc36666e\">https://doi.org/10.1039/c2gc36666e</a>.","ieee":"K. Greimel <i>et al.</i>, “Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins,” <i>Green Chemistry</i>, vol. 15, no. 2. Royal Society of Chemistry, pp. 381–388, 2013.","short":"K. Greimel, V. Perz, K. Koren, R. Feola, A. Temel, C. Sohar, E. Herrero Acero, I. Klimant, G. Guebitz, Green Chemistry 15 (2013) 381–388.","mla":"Greimel, Katrin, et al. “Banning Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.” <i>Green Chemistry</i>, vol. 15, no. 2, Royal Society of Chemistry, 2013, pp. 381–88, doi:<a href=\"https://doi.org/10.1039/c2gc36666e\">10.1039/c2gc36666e</a>.","ama":"Greimel K, Perz V, Koren K, et al. Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. <i>Green Chemistry</i>. 2013;15(2):381-388. doi:<a href=\"https://doi.org/10.1039/c2gc36666e\">10.1039/c2gc36666e</a>","ista":"Greimel K, Perz V, Koren K, Feola R, Temel A, Sohar C, Herrero Acero E, Klimant I, Guebitz G. 2013. Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. 15(2), 381–388.","apa":"Greimel, K., Perz, V., Koren, K., Feola, R., Temel, A., Sohar, C., … Guebitz, G. (2013). Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. <i>Green Chemistry</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c2gc36666e\">https://doi.org/10.1039/c2gc36666e</a>"},"month":"02","oa_version":"None","author":[{"full_name":"Greimel, Katrin","first_name":"Katrin","last_name":"Greimel"},{"full_name":"Perz, Veronika","first_name":"Veronika","last_name":"Perz"},{"id":"382FBD6A-F248-11E8-B48F-1D18A9856A87","last_name":"Koren","first_name":"Klaus","full_name":"Koren, Klaus"},{"first_name":"Roland","last_name":"Feola","full_name":"Feola, Roland"},{"last_name":"Temel","first_name":"Armin","full_name":"Temel, Armin"},{"full_name":"Sohar, Christian","last_name":"Sohar","first_name":"Christian"},{"full_name":"Herrero Acero, Enrique","last_name":"Herrero Acero","first_name":"Enrique"},{"first_name":"Ingo","last_name":"Klimant","full_name":"Klimant, Ingo"},{"full_name":"Guebitz, Georg","first_name":"Georg","last_name":"Guebitz"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This study was performed within the Austrian Centre of Indus-\r\ntrial Biotechnology ACIB and the COST Action 868. This work\r\nhas been supported by the Federal Ministry of Economy,\r\nFamily and Youth (BMWFJ), the Federal Ministry of Tra\r\nffi\r\nc,\r\nInnovation and Technology (bmvit), the Styrian Business\r\nPromotion Agency SFG, the Standortagentur Tirol and ZIT\r\n–\r\nTechnology  Agency  of  the  City  of  Vienna  through  the\r\nCOMET-Funding Program managed by the Austrian Research\r\nPromotion Agency FFG. Dr Massimiliano Cardinale (Institute of\r\nEnvironmental Biotechnology, TU Graz) is gratefully acknowl-\r\nedged for technical support with the CLSM measurements.","language":[{"iso":"eng"}],"_id":"505","intvolume":"        15","abstract":[{"lang":"eng","text":"Alkyd resins are polyesters containing unsaturated fatty acids that are used as binding agents in paints and coatings. Chemical drying of these polyesters is based on heavy metal catalyzed cross-linking of the unsaturated fatty acid moieties. Among the heavy-metal catalysts, cobalt complexes are the most effective, yet they have been proven to be carcinogenic. Therefore, strategies to replace the cobalt-based catalyst by environmentally friendlier and less toxic alternatives are under development. Here, we demonstrate for the first time that a laccase-mediator system can effectively replace the heavy-metal catalyst and cross-link alkyd resins. Interestingly, the biocatalytic reaction does not only work in aqueous media, but also in a solid film, where enzyme diffusion is limited. Within the catalytic cycle, the mediator oxidizes the alkyd resin and is regenerated by the laccase, which is uniformly distributed within the drying film as evidenced by confocal laser scanning microscopy. During gradual build-up of molecular weight, there is a concomitant decrease of the oxygen content in the film. A new optical sensor to follow oxygen consumption during the cross-linking reaction was developed and validated with state of the art techniques. A remarkable feature is the low sample amount required, which allows faster screening of new catalysts."}],"page":"381 - 388","date_published":"2013-02-01T00:00:00Z","status":"public","issue":"2","publist_id":"7313","publication":"Green Chemistry","publication_status":"published","day":"01","publisher":"Royal Society of Chemistry","date_updated":"2021-01-12T08:01:11Z","department":[{"_id":"HaJa"}],"title":"Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins","doi":"10.1039/c2gc36666e","quality_controlled":"1","volume":15,"type":"journal_article","year":"2013"},{"volume":25,"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784592/"}],"publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"pmid":1,"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        25","abstract":[{"text":"Fertilization in flowering plants requires the temporal and spatial coordination of many developmental processes, including pollen production, anther dehiscence, ovule production, and pollen tube elongation. However, it remains elusive as to how this coordination occurs during reproduction. Here, we present evidence that endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays multiple defects in pollen production and viability, as well as elongation of staminal filaments and pollen tubes, all of which are pivotal processes needed for fertilization. Of these abnormalities, the defects in elongation of staminal filaments and pollen tubes were partially rescued by exogenous auxin. Moreover, DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed defects in both endocytosis of N-(3-triethylammonium-propyl)-4- (4-diethylaminophenylhexatrienyl) pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments. Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent endocytosis plays a crucial role in coordinating the multiple developmental aspects of male reproductive organs by modulating cellular auxin level through the regulation of the amount and polarity of PINs.","lang":"eng"}],"status":"public","date_published":"2013-08-01T00:00:00Z","publication":"Plant Cell","publist_id":"7312","scopus_import":1,"date_created":"2018-12-11T11:46:52Z","oa_version":"Submitted Version","oa":1,"year":"2013","day":"01","date_updated":"2021-01-12T08:01:12Z","title":"Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis","doi":"10.1105/tpc.113.114264","external_id":{"pmid":["23975898"]},"_id":"507","language":[{"iso":"eng"}],"page":"2970 - 2985","issue":"8","citation":{"ieee":"S. Kim <i>et al.</i>, “Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis,” <i>Plant Cell</i>, vol. 25, no. 8. American Society of Plant Biologists, pp. 2970–2985, 2013.","chicago":"Kim, Soo, Zheng Xu, Kyungyoung Song, Dae Kim, Hyangju Kang, Ilka Reichardt, Eun Sohn, Jiří Friml, Gerd Juergens, and Inhwan Hwang. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.114264\">https://doi.org/10.1105/tpc.113.114264</a>.","short":"S. Kim, Z. Xu, K. Song, D. Kim, H. Kang, I. Reichardt, E. Sohn, J. Friml, G. Juergens, I. Hwang, Plant Cell 25 (2013) 2970–2985.","mla":"Kim, Soo, et al. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” <i>Plant Cell</i>, vol. 25, no. 8, American Society of Plant Biologists, 2013, pp. 2970–85, doi:<a href=\"https://doi.org/10.1105/tpc.113.114264\">10.1105/tpc.113.114264</a>.","ama":"Kim S, Xu Z, Song K, et al. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. <i>Plant Cell</i>. 2013;25(8):2970-2985. doi:<a href=\"https://doi.org/10.1105/tpc.113.114264\">10.1105/tpc.113.114264</a>","apa":"Kim, S., Xu, Z., Song, K., Kim, D., Kang, H., Reichardt, I., … Hwang, I. (2013). Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.114264\">https://doi.org/10.1105/tpc.113.114264</a>","ista":"Kim S, Xu Z, Song K, Kim D, Kang H, Reichardt I, Sohn E, Friml J, Juergens G, Hwang I. 2013. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. Plant Cell. 25(8), 2970–2985."},"month":"08","author":[{"full_name":"Kim, Soo","last_name":"Kim","first_name":"Soo"},{"full_name":"Xu, Zheng","first_name":"Zheng","last_name":"Xu"},{"full_name":"Song, Kyungyoung","first_name":"Kyungyoung","last_name":"Song"},{"last_name":"Kim","first_name":"Dae","full_name":"Kim, Dae"},{"first_name":"Hyangju","last_name":"Kang","full_name":"Kang, Hyangju"},{"first_name":"Ilka","last_name":"Reichardt","full_name":"Reichardt, Ilka"},{"first_name":"Eun","last_name":"Sohn","full_name":"Sohn, Eun"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"full_name":"Juergens, Gerd","last_name":"Juergens","first_name":"Gerd"},{"last_name":"Hwang","first_name":"Inhwan","full_name":"Hwang, Inhwan"}]},{"month":"09","author":[{"last_name":"Tarazona Santos","first_name":"Eduardo","full_name":"Tarazona Santos, Eduardo"},{"first_name":"Moara","last_name":"Machado","full_name":"Machado, Moara"},{"full_name":"Magalhães, Wagner","last_name":"Magalhães","first_name":"Wagner"},{"first_name":"Renee","last_name":"Chen","full_name":"Chen, Renee"},{"full_name":"Lyon, Fernanda","first_name":"Fernanda","last_name":"Lyon"},{"full_name":"Burdett, Laurie","last_name":"Burdett","first_name":"Laurie"},{"full_name":"Crenshaw, Andrew","last_name":"Crenshaw","first_name":"Andrew"},{"full_name":"Fabbri, Cristina","last_name":"Fabbri","first_name":"Cristina"},{"full_name":"Pereira, Latife","last_name":"Pereira","first_name":"Latife"},{"first_name":"Laelia","last_name":"Pinto","full_name":"Pinto, Laelia"},{"full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A","last_name":"Fernandes Redondo"},{"full_name":"Sestanovich, Ben","last_name":"Sestanovich","first_name":"Ben"},{"full_name":"Yeager, Meredith","first_name":"Meredith","last_name":"Yeager"},{"full_name":"Chanock, Stephen","first_name":"Stephen","last_name":"Chanock"}],"citation":{"ista":"Tarazona Santos E, Machado M, Magalhães W, Chen R, Lyon F, Burdett L, Crenshaw A, Fabbri C, Pereira L, Pinto L, Fernandes Redondo RA, Sestanovich B, Yeager M, Chanock S. 2013. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. 30(9), 2157–2167.","apa":"Tarazona Santos, E., Machado, M., Magalhães, W., Chen, R., Lyon, F., Burdett, L., … Chanock, S. (2013). Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/mst119\">https://doi.org/10.1093/molbev/mst119</a>","ama":"Tarazona Santos E, Machado M, Magalhães W, et al. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. <i>Molecular Biology and Evolution</i>. 2013;30(9):2157-2167. doi:<a href=\"https://doi.org/10.1093/molbev/mst119\">10.1093/molbev/mst119</a>","mla":"Tarazona Santos, Eduardo, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” <i>Molecular Biology and Evolution</i>, vol. 30, no. 9, Oxford University Press, 2013, pp. 2157–67, doi:<a href=\"https://doi.org/10.1093/molbev/mst119\">10.1093/molbev/mst119</a>.","short":"E. Tarazona Santos, M. Machado, W. Magalhães, R. Chen, F. Lyon, L. Burdett, A. Crenshaw, C. Fabbri, L. Pereira, L. Pinto, R.A. Fernandes Redondo, B. Sestanovich, M. Yeager, S. Chanock, Molecular Biology and Evolution 30 (2013) 2157–2167.","chicago":"Tarazona Santos, Eduardo, Moara Machado, Wagner Magalhães, Renee Chen, Fernanda Lyon, Laurie Burdett, Andrew Crenshaw, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/molbev/mst119\">https://doi.org/10.1093/molbev/mst119</a>.","ieee":"E. Tarazona Santos <i>et al.</i>, “Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications,” <i>Molecular Biology and Evolution</i>, vol. 30, no. 9. Oxford University Press, pp. 2157–2167, 2013."},"page":"2157 - 2167","issue":"9","language":[{"iso":"eng"}],"_id":"508","title":"Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications","doi":"10.1093/molbev/mst119","external_id":{"pmid":["23821607"]},"day":"01","date_updated":"2021-01-12T08:01:12Z","year":"2013","oa":1,"oa_version":"Submitted Version","scopus_import":1,"date_created":"2018-12-11T11:46:52Z","abstract":[{"text":"The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen species with microbicidal activity. It is composed of two membrane-spanning subunits, gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively). Mutations in any of these genes can result in chronic granulomatous disease, a primary immunodeficiency characterized by recurrent infections. Using evolutionary mapping, we determined that episodes of adaptive natural selection have shaped the extracellular portion of gp91-phox during the evolution of mammals, which suggests that this region may have a function in host-pathogen interactions. On the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2, and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the pattern of CYBA diversity is compatible with balancing natural selection, perhaps mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern of diversity characterized by a differentiated haplotype structure. Our study provides insight into the role of pathogen-driven natural selection in an innate immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other complex diseases.","lang":"eng"}],"status":"public","date_published":"2013-09-01T00:00:00Z","publication":"Molecular Biology and Evolution","publist_id":"7310","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        30","department":[{"_id":"JoBo"}],"pmid":1,"quality_controlled":"1","publication_status":"published","publisher":"Oxford University Press","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/","open_access":"1"}],"volume":30,"type":"journal_article"},{"publication":"Plant Cell","publist_id":"7311","status":"public","date_published":"2013-08-01T00:00:00Z","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) regulates many aspects of plant development, including hormone signaling and responses to environmental stresses. Despite the importance of this process, the machinery that regulates CME in plants is largely unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is required for the formation of clathrin-coated vesicles at the plasma membrane (PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana, the biochemistry and functionality of the complex is still uncharacterized. Here, we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification and found that one of the large AP-2 subunits, AP2A1, localized at the PM and interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2. Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis is evolutionarily conserved and that AP-2 functions in receptormediated endocytosis. "}],"intvolume":"        25","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","date_created":"2018-12-11T11:46:52Z","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784593/","open_access":"1"}],"type":"journal_article","volume":25,"quality_controlled":"1","pmid":1,"department":[{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","publication_status":"published","issue":"8","page":"2986 - 2997","language":[{"iso":"eng"}],"_id":"509","author":[{"last_name":"Di Rubbo","first_name":"Simone","full_name":"Di Rubbo, Simone"},{"full_name":"Irani, Niloufer","first_name":"Niloufer","last_name":"Irani"},{"full_name":"Kim, Soo","last_name":"Kim","first_name":"Soo"},{"full_name":"Xu, Zheng","first_name":"Zheng","last_name":"Xu"},{"last_name":"Gadeyne","first_name":"Astrid","full_name":"Gadeyne, Astrid"},{"full_name":"Dejonghe, Wim","last_name":"Dejonghe","first_name":"Wim"},{"first_name":"Isabelle","last_name":"Vanhoutte","full_name":"Vanhoutte, Isabelle"},{"full_name":"Persiau, Geert","first_name":"Geert","last_name":"Persiau"},{"full_name":"Eeckhout, Dominique","last_name":"Eeckhout","first_name":"Dominique"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu","last_name":"Simon","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu"},{"last_name":"Song","first_name":"Kyungyoung","full_name":"Song, Kyungyoung"},{"full_name":"Kleine Vehn, Jürgen","first_name":"Jürgen","last_name":"Kleine Vehn"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"last_name":"De Jaeger","first_name":"Geert","full_name":"De Jaeger, Geert"},{"full_name":"Van Damme, Daniël","first_name":"Daniël","last_name":"Van Damme"},{"full_name":"Hwang, Inhwan","first_name":"Inhwan","last_name":"Hwang"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"}],"month":"08","citation":{"ama":"Di Rubbo S, Irani N, Kim S, et al. The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. <i>Plant Cell</i>. 2013;25(8):2986-2997. doi:<a href=\"https://doi.org/10.1105/tpc.113.114058\">10.1105/tpc.113.114058</a>","apa":"Di Rubbo, S., Irani, N., Kim, S., Xu, Z., Gadeyne, A., Dejonghe, W., … Russinova, E. (2013). The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.114058\">https://doi.org/10.1105/tpc.113.114058</a>","ista":"Di Rubbo S, Irani N, Kim S, Xu Z, Gadeyne A, Dejonghe W, Vanhoutte I, Persiau G, Eeckhout D, Simon S, Song K, Kleine Vehn J, Friml J, De Jaeger G, Van Damme D, Hwang I, Russinova E. 2013. The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. 25(8), 2986–2997.","ieee":"S. Di Rubbo <i>et al.</i>, “The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis,” <i>Plant Cell</i>, vol. 25, no. 8. American Society of Plant Biologists, pp. 2986–2997, 2013.","chicago":"Di Rubbo, Simone, Niloufer Irani, Soo Kim, Zheng Xu, Astrid Gadeyne, Wim Dejonghe, Isabelle Vanhoutte, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.114058\">https://doi.org/10.1105/tpc.113.114058</a>.","short":"S. Di Rubbo, N. Irani, S. Kim, Z. Xu, A. Gadeyne, W. Dejonghe, I. Vanhoutte, G. Persiau, D. Eeckhout, S. Simon, K. Song, J. Kleine Vehn, J. Friml, G. De Jaeger, D. Van Damme, I. Hwang, E. Russinova, Plant Cell 25 (2013) 2986–2997.","mla":"Di Rubbo, Simone, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” <i>Plant Cell</i>, vol. 25, no. 8, American Society of Plant Biologists, 2013, pp. 2986–97, doi:<a href=\"https://doi.org/10.1105/tpc.113.114058\">10.1105/tpc.113.114058</a>."},"year":"2013","oa":1,"external_id":{"pmid":["23975899"]},"doi":"10.1105/tpc.113.114058","title":"The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis","date_updated":"2021-01-12T08:01:13Z","day":"01"},{"day":"01","date_updated":"2021-01-12T08:01:15Z","doi":"10.1105/tpc.113.114421","title":"Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid","external_id":{"pmid":["24163311"]},"oa":1,"year":"2013","citation":{"mla":"Pěnčík, Aleš, et al. “Regulation of Auxin Homeostasis and Gradients in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic Acid.” <i>Plant Cell</i>, vol. 25, no. 10, American Society of Plant Biologists, 2013, pp. 3858–70, doi:<a href=\"https://doi.org/10.1105/tpc.113.114421\">10.1105/tpc.113.114421</a>.","short":"A. Pěnčík, B. Simonovik, S. Petersson, E. Henyková, S. Simon, K. Greenham, Y. Zhang, M. Kowalczyk, M. Estelle, E. Zažímalová, O. Novák, G. Sandberg, K. Ljung, Plant Cell 25 (2013) 3858–3870.","ieee":"A. Pěnčík <i>et al.</i>, “Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid,” <i>Plant Cell</i>, vol. 25, no. 10. American Society of Plant Biologists, pp. 3858–3870, 2013.","chicago":"Pěnčík, Aleš, Biljana Simonovik, Sara Petersson, Eva Henyková, Sibu Simon, Kathleen Greenham, Yi Zhang, et al. “Regulation of Auxin Homeostasis and Gradients in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic Acid.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.114421\">https://doi.org/10.1105/tpc.113.114421</a>.","apa":"Pěnčík, A., Simonovik, B., Petersson, S., Henyková, E., Simon, S., Greenham, K., … Ljung, K. (2013). Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.114421\">https://doi.org/10.1105/tpc.113.114421</a>","ista":"Pěnčík A, Simonovik B, Petersson S, Henyková E, Simon S, Greenham K, Zhang Y, Kowalczyk M, Estelle M, Zažímalová E, Novák O, Sandberg G, Ljung K. 2013. Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell. 25(10), 3858–3870.","ama":"Pěnčík A, Simonovik B, Petersson S, et al. Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. <i>Plant Cell</i>. 2013;25(10):3858-3870. doi:<a href=\"https://doi.org/10.1105/tpc.113.114421\">10.1105/tpc.113.114421</a>"},"author":[{"full_name":"Pěnčík, Aleš","first_name":"Aleš","last_name":"Pěnčík"},{"first_name":"Biljana","last_name":"Simonovik","full_name":"Simonovik, Biljana"},{"first_name":"Sara","last_name":"Petersson","full_name":"Petersson, Sara"},{"first_name":"Eva","last_name":"Henyková","full_name":"Henyková, Eva"},{"full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","first_name":"Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Greenham, Kathleen","last_name":"Greenham","first_name":"Kathleen"},{"last_name":"Zhang","first_name":"Yi","full_name":"Zhang, Yi"},{"first_name":"Mariusz","last_name":"Kowalczyk","full_name":"Kowalczyk, Mariusz"},{"first_name":"Mark","last_name":"Estelle","full_name":"Estelle, Mark"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"first_name":"Göran","last_name":"Sandberg","full_name":"Sandberg, Göran"},{"full_name":"Ljung, Karin","last_name":"Ljung","first_name":"Karin"}],"month":"10","_id":"511","language":[{"iso":"eng"}],"page":"3858 - 3870","issue":"10","publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"quality_controlled":"1","pmid":1,"type":"journal_article","volume":25,"main_file_link":[{"open_access":"1","url":"www.doi.org/10.1105/tpc.113.114421"}],"scopus_import":1,"date_created":"2018-12-11T11:46:53Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        25","abstract":[{"text":"The native auxin, indole-3-acetic acid (IAA), is a major regulator of plant growth and development. Its nonuniform distribution between cells and tissues underlies the spatiotemporal coordination of many developmental events and responses to environmental stimuli. The regulation of auxin gradients and the formation of auxin maxima/minima most likely involve the regulation of both metabolic and transport processes. In this article, we have demonstrated that 2-oxindole-3-acetic acid (oxIAA) is a major primary IAA catabolite formed in Arabidopsis thaliana root tissues. OxIAA had little biological activity and was formed rapidly and irreversibly in response to increases in auxin levels. We further showed that there is cell type-specific regulation of oxIAA levels in the Arabidopsis root apex. We propose that oxIAA is an important element in the regulation of output from auxin gradients and, therefore, in the regulation of auxin homeostasis and response mechanisms.","lang":"eng"}],"publist_id":"7309","publication":"Plant Cell","date_published":"2013-10-01T00:00:00Z","status":"public"},{"oa_version":"Published Version","date_created":"2018-12-11T11:46:55Z","scopus_import":1,"status":"public","date_published":"2013-09-10T00:00:00Z","publist_id":"7303","publication":"Molecular Systems Biology","abstract":[{"lang":"eng","text":"In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin‐responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue‐specific transcriptional regulation of cell‐identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin‐response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome‐level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development."}],"intvolume":"         9","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","publication_status":"published","volume":9,"type":"journal_article","month":"09","file_date_updated":"2020-07-14T12:46:36Z","article_number":"688","author":[{"last_name":"Bargmann","first_name":"Bastiaan","full_name":"Bargmann, Bastiaan"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"full_name":"Krouk, Gabriel","first_name":"Gabriel","last_name":"Krouk"},{"first_name":"Tal","last_name":"Nawy","full_name":"Nawy, Tal"},{"full_name":"Efroni, Idan","last_name":"Efroni","first_name":"Idan"},{"last_name":"Shani","first_name":"Eilon","full_name":"Shani, Eilon"},{"first_name":"Goh","last_name":"Choe","full_name":"Choe, Goh"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"last_name":"Bergmann","first_name":"Dominique","full_name":"Bergmann, Dominique"},{"first_name":"Mark","last_name":"Estelle","full_name":"Estelle, Mark"},{"full_name":"Birnbaum, Kenneth","first_name":"Kenneth","last_name":"Birnbaum"}],"file":[{"access_level":"open_access","date_created":"2018-12-12T10:07:46Z","date_updated":"2020-07-14T12:46:36Z","file_size":3257692,"file_id":"4644","relation":"main_file","file_name":"IST-2018-936-v1+1_2008_Barton_A_map.pdf","creator":"system","checksum":"9c4fbe793af4bb22b3fe50cc677a39bf","content_type":"application/pdf"}],"citation":{"ama":"Bargmann B, Vanneste S, Krouk G, et al. A map of cell type‐specific auxin responses. <i>Molecular Systems Biology</i>. 2013;9(1). doi:<a href=\"https://doi.org/10.1038/msb.2013.40\">10.1038/msb.2013.40</a>","apa":"Bargmann, B., Vanneste, S., Krouk, G., Nawy, T., Efroni, I., Shani, E., … Birnbaum, K. (2013). A map of cell type‐specific auxin responses. <i>Molecular Systems Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/msb.2013.40\">https://doi.org/10.1038/msb.2013.40</a>","ista":"Bargmann B, Vanneste S, Krouk G, Nawy T, Efroni I, Shani E, Choe G, Friml J, Bergmann D, Estelle M, Birnbaum K. 2013. A map of cell type‐specific auxin responses. Molecular Systems Biology. 9(1), 688.","ieee":"B. Bargmann <i>et al.</i>, “A map of cell type‐specific auxin responses,” <i>Molecular Systems Biology</i>, vol. 9, no. 1. Nature Publishing Group, 2013.","chicago":"Bargmann, Bastiaan, Steffen Vanneste, Gabriel Krouk, Tal Nawy, Idan Efroni, Eilon Shani, Goh Choe, et al. “A Map of Cell Type‐specific Auxin Responses.” <i>Molecular Systems Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/msb.2013.40\">https://doi.org/10.1038/msb.2013.40</a>.","mla":"Bargmann, Bastiaan, et al. “A Map of Cell Type‐specific Auxin Responses.” <i>Molecular Systems Biology</i>, vol. 9, no. 1, 688, Nature Publishing Group, 2013, doi:<a href=\"https://doi.org/10.1038/msb.2013.40\">10.1038/msb.2013.40</a>.","short":"B. Bargmann, S. Vanneste, G. Krouk, T. Nawy, I. Efroni, E. Shani, G. Choe, J. Friml, D. Bergmann, M. Estelle, K. Birnbaum, Molecular Systems Biology 9 (2013)."},"ddc":["581"],"issue":"1","pubrep_id":"936","_id":"516","language":[{"iso":"eng"}],"title":"A map of cell type‐specific auxin responses","doi":"10.1038/msb.2013.40","date_updated":"2021-01-12T08:01:17Z","day":"10","year":"2013","has_accepted_license":"1","article_processing_charge":"No","oa":1},{"volume":154,"type":"journal_article","year":"2013","publisher":"Elsevier","date_updated":"2021-01-12T08:01:22Z","publication_status":"published","day":"01","quality_controlled":"1","title":"Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells","department":[{"_id":"MiSi"}],"doi":"10.1016/j.imlet.2013.07.007","_id":"522","intvolume":"       154","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2013-07-01T00:00:00Z","status":"public","issue":"1-2","publist_id":"7300","publication":"Immunology Letters","abstract":[{"lang":"eng","text":"Podoplanin, a mucin-like plasma membrane protein, is expressed by lymphatic endothelial cells and responsible for separation of blood and lymphatic circulation through activation of platelets. Here we show that podoplanin is also expressed by thymic fibroblastic reticular cells (tFRC), a novel thymic medulla stroma cell type associated with thymic conduits, and involved in development of natural regulatory T cells (nTreg). Young mice deficient in podoplanin lack nTreg owing to retardation of CD4+CD25+ thymocytes in the cortex and missing differentiation of Foxp3+ thymocytes in the medulla. This might be due to CCL21 that delocalizes upon deletion of the CCL21-binding podoplanin from medullar tFRC to cortex areas. The animals do not remain devoid of nTreg but generate them delayed within the first month resulting in Th2-biased hypergammaglobulinemia but not in the death-causing autoimmune phenotype of Foxp3-deficient Scurfy mice."}],"page":"31 - 41","date_created":"2018-12-11T11:46:57Z","citation":{"mla":"Fuertbauer, Elke, et al. “Thymic Medullar Conduits-Associated Podoplanin Promotes Natural Regulatory T Cells.” <i>Immunology Letters</i>, vol. 154, no. 1–2, Elsevier, 2013, pp. 31–41, doi:<a href=\"https://doi.org/10.1016/j.imlet.2013.07.007\">10.1016/j.imlet.2013.07.007</a>.","short":"E. Fuertbauer, J. Zaujec, P. Uhrin, I. Raab, M. Weber, H. Schachner, M. Bauer, G. Schütz, B. Binder, M.K. Sixt, D. Kerjaschki, H. Stockinger, Immunology Letters 154 (2013) 31–41.","chicago":"Fuertbauer, Elke, Jan Zaujec, Pavel Uhrin, Ingrid Raab, Michele Weber, Helga Schachner, Miroslav Bauer, et al. “Thymic Medullar Conduits-Associated Podoplanin Promotes Natural Regulatory T Cells.” <i>Immunology Letters</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.imlet.2013.07.007\">https://doi.org/10.1016/j.imlet.2013.07.007</a>.","ieee":"E. Fuertbauer <i>et al.</i>, “Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells,” <i>Immunology Letters</i>, vol. 154, no. 1–2. Elsevier, pp. 31–41, 2013.","ista":"Fuertbauer E, Zaujec J, Uhrin P, Raab I, Weber M, Schachner H, Bauer M, Schütz G, Binder B, Sixt MK, Kerjaschki D, Stockinger H. 2013. Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells. Immunology Letters. 154(1–2), 31–41.","apa":"Fuertbauer, E., Zaujec, J., Uhrin, P., Raab, I., Weber, M., Schachner, H., … Stockinger, H. (2013). Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells. <i>Immunology Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.imlet.2013.07.007\">https://doi.org/10.1016/j.imlet.2013.07.007</a>","ama":"Fuertbauer E, Zaujec J, Uhrin P, et al. Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells. <i>Immunology Letters</i>. 2013;154(1-2):31-41. doi:<a href=\"https://doi.org/10.1016/j.imlet.2013.07.007\">10.1016/j.imlet.2013.07.007</a>"},"scopus_import":1,"month":"07","author":[{"full_name":"Fuertbauer, Elke","first_name":"Elke","last_name":"Fuertbauer"},{"full_name":"Zaujec, Jan","first_name":"Jan","last_name":"Zaujec"},{"full_name":"Uhrin, Pavel","last_name":"Uhrin","first_name":"Pavel"},{"last_name":"Raab","first_name":"Ingrid","full_name":"Raab, Ingrid"},{"full_name":"Weber, Michele","last_name":"Weber","first_name":"Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schachner","first_name":"Helga","full_name":"Schachner, Helga"},{"first_name":"Miroslav","last_name":"Bauer","full_name":"Bauer, Miroslav"},{"first_name":"Gerhard","last_name":"Schütz","full_name":"Schütz, Gerhard"},{"first_name":"Bernd","last_name":"Binder","full_name":"Binder, Bernd"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Kerjaschki, Dontscho","last_name":"Kerjaschki","first_name":"Dontscho"},{"first_name":"Hannes","last_name":"Stockinger","full_name":"Stockinger, Hannes"}],"oa_version":"None"},{"type":"journal_article","volume":23,"ec_funded":1,"year":"2013","day":"16","publication_status":"published","date_updated":"2021-01-12T08:01:24Z","publisher":"Cell Press","doi":"10.1016/j.cub.2013.10.038","title":"Modeling framework for the establishment of the apical-basal embryonic axis in plants","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"quality_controlled":"1","project":[{"name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"527","intvolume":"        23","language":[{"iso":"eng"}],"page":"2513 - 2518","abstract":[{"lang":"eng","text":"The apical-basal axis of the early plant embryo determines the body plan of the adult organism. To establish a polarized embryonic axis, plants evolved a unique mechanism that involves directional, cell-to-cell transport of the growth regulator auxin. Auxin transport relies on PIN auxin transporters [1], whose polar subcellular localization determines the flow directionality. PIN-mediated auxin transport mediates the spatial and temporal activity of the auxin response machinery [2-7] that contributes to embryo patterning processes, including establishment of the apical (shoot) and basal (root) embryo poles [8]. However, little is known of upstream mechanisms guiding the (re)polarization of auxin fluxes during embryogenesis [9]. Here, we developed a model of plant embryogenesis that correctly generates emergent cell polarities and auxin-mediated sequential initiation of apical-basal axis of plant embryo. The model relies on two precisely localized auxin sources and a feedback between auxin and the polar, subcellular PIN transporter localization. Simulations reproduced PIN polarity and auxin distribution, as well as previously unknown polarization events during early embryogenesis. The spectrum of validated model predictions suggests that our model corresponds to a minimal mechanistic framework for initiation and orientation of the apical-basal axis to guide both embryonic and postembryonic plant development."}],"publist_id":"7292","issue":"24","publication":"Current Biology","date_published":"2013-12-16T00:00:00Z","status":"public","scopus_import":1,"citation":{"mla":"Wabnik, Krzysztof T., et al. “Modeling Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants.” <i>Current Biology</i>, vol. 23, no. 24, Cell Press, 2013, pp. 2513–18, doi:<a href=\"https://doi.org/10.1016/j.cub.2013.10.038\">10.1016/j.cub.2013.10.038</a>.","short":"K.T. Wabnik, H. Robert, R. Smith, J. Friml, Current Biology 23 (2013) 2513–2518.","ieee":"K. T. Wabnik, H. Robert, R. Smith, and J. Friml, “Modeling framework for the establishment of the apical-basal embryonic axis in plants,” <i>Current Biology</i>, vol. 23, no. 24. Cell Press, pp. 2513–2518, 2013.","chicago":"Wabnik, Krzysztof T, Hélène Robert, Richard Smith, and Jiří Friml. “Modeling Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2013.10.038\">https://doi.org/10.1016/j.cub.2013.10.038</a>.","apa":"Wabnik, K. T., Robert, H., Smith, R., &#38; Friml, J. (2013). Modeling framework for the establishment of the apical-basal embryonic axis in plants. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2013.10.038\">https://doi.org/10.1016/j.cub.2013.10.038</a>","ista":"Wabnik KT, Robert H, Smith R, Friml J. 2013. Modeling framework for the establishment of the apical-basal embryonic axis in plants. Current Biology. 23(24), 2513–2518.","ama":"Wabnik KT, Robert H, Smith R, Friml J. Modeling framework for the establishment of the apical-basal embryonic axis in plants. <i>Current Biology</i>. 2013;23(24):2513-2518. doi:<a href=\"https://doi.org/10.1016/j.cub.2013.10.038\">10.1016/j.cub.2013.10.038</a>"},"date_created":"2018-12-11T11:46:58Z","author":[{"orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T","last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Robert","first_name":"Hélène","full_name":"Robert, Hélène"},{"full_name":"Smith, Richard","last_name":"Smith","first_name":"Richard"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"oa_version":"None","month":"12"},{"scopus_import":1,"date_created":"2018-12-11T11:46:59Z","citation":{"apa":"Robert, H., Grones, P., Stepanova, A., Robles, L., Lokerse, A., Alonso, J., … Friml, J. (2013). Local auxin sources orient the apical basal axis in arabidopsis embryos. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2013.09.039\">https://doi.org/10.1016/j.cub.2013.09.039</a>","ista":"Robert H, Grones P, Stepanova A, Robles L, Lokerse A, Alonso J, Weijers D, Friml J. 2013. Local auxin sources orient the apical basal axis in arabidopsis embryos. Current Biology. 23(24), 2506–2512.","ama":"Robert H, Grones P, Stepanova A, et al. Local auxin sources orient the apical basal axis in arabidopsis embryos. <i>Current Biology</i>. 2013;23(24):2506-2512. doi:<a href=\"https://doi.org/10.1016/j.cub.2013.09.039\">10.1016/j.cub.2013.09.039</a>","mla":"Robert, Hélène, et al. “Local Auxin Sources Orient the Apical Basal Axis in Arabidopsis Embryos.” <i>Current Biology</i>, vol. 23, no. 24, Cell Press, 2013, pp. 2506–12, doi:<a href=\"https://doi.org/10.1016/j.cub.2013.09.039\">10.1016/j.cub.2013.09.039</a>.","short":"H. Robert, P. Grones, A. Stepanova, L. Robles, A. Lokerse, J. Alonso, D. Weijers, J. Friml, Current Biology 23 (2013) 2506–2512.","ieee":"H. Robert <i>et al.</i>, “Local auxin sources orient the apical basal axis in arabidopsis embryos,” <i>Current Biology</i>, vol. 23, no. 24. Cell Press, pp. 2506–2512, 2013.","chicago":"Robert, Hélène, Peter Grones, Anna Stepanova, Linda Robles, Annemarie Lokerse, Jose Alonso, Dolf Weijers, and Jiří Friml. “Local Auxin Sources Orient the Apical Basal Axis in Arabidopsis Embryos.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2013.09.039\">https://doi.org/10.1016/j.cub.2013.09.039</a>."},"author":[{"last_name":"Robert","first_name":"Hélène","full_name":"Robert, Hélène"},{"last_name":"Grones","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"first_name":"Anna","last_name":"Stepanova","full_name":"Stepanova, Anna"},{"full_name":"Robles, Linda","last_name":"Robles","first_name":"Linda"},{"full_name":"Lokerse, Annemarie","first_name":"Annemarie","last_name":"Lokerse"},{"full_name":"Alonso, Jose","first_name":"Jose","last_name":"Alonso"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"528","language":[{"iso":"eng"}],"intvolume":"        23","page":"2506 - 2512","abstract":[{"lang":"eng","text":"Establishment of the embryonic axis foreshadows the main body axis of adults both in plants and in animals, but underlying mechanisms are considered distinct. Plants utilize directional, cell-to-cell transport of the growth hormone auxin [1, 2] to generate an asymmetric auxin response that specifies the embryonic apical-basal axis [3-6]. The auxin flow directionality depends on the polarized subcellular localization of PIN-FORMED (PIN) auxin transporters [7, 8]. It remains unknown which mechanisms and spatial cues guide cell polarization and axis orientation in early embryos. Herein, we provide conceptually novel insights into the formation of embryonic axis in Arabidopsis by identifying a crucial role of localized tryptophan-dependent auxin biosynthesis [9-12]. Local auxin production at the base of young embryos and the accompanying PIN7-mediated auxin flow toward the proembryo are required for the apical auxin response maximum and the specification of apical embryonic structures. Later in embryogenesis, the precisely timed onset of localized apical auxin biosynthesis mediates PIN1 polarization, basal auxin response maximum, and specification of the root pole. Thus, the tight spatiotemporal control of distinct local auxin sources provides a necessary, non-cell-autonomous trigger for the coordinated cell polarization and subsequent apical-basal axis orientation during embryogenesis and, presumably, also for other polarization events during postembryonic plant life [13, 14]."}],"publication":"Current Biology","issue":"24","publist_id":"7291","date_published":"2013-12-16T00:00:00Z","status":"public","day":"16","publication_status":"published","date_updated":"2021-01-12T08:01:25Z","publisher":"Cell Press","doi":"10.1016/j.cub.2013.09.039","department":[{"_id":"JiFr"}],"title":"Local auxin sources orient the apical basal axis in arabidopsis embryos","quality_controlled":"1","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7"}],"type":"journal_article","volume":23,"ec_funded":1,"year":"2013"},{"publication_status":"published","publisher":"IEEE","department":[{"_id":"ChLa"}],"quality_controlled":"1","type":"journal_article","volume":36,"scopus_import":"1","date_created":"2018-12-11T11:58:08Z","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        36","abstract":[{"text":"We study the problem of object recognition for categories for which we have no training examples, a task also called zero-data or zero-shot learning. This situation has hardly been studied in computer vision research, even though it occurs frequently: the world contains tens of thousands of different object classes and for only few of them image collections have been formed and suitably annotated. To tackle the problem we introduce attribute-based classification: objects are identified based on a high-level description that is phrased in terms of semantic attributes, such as the object's color or shape. Because the identification of each such property transcends the specific learning task at hand, the attribute classifiers can be pre-learned independently, e.g. from existing image datasets unrelated to the current task. Afterwards, new classes can be detected based on their attribute representation, without the need for a new training phase. In this paper we also introduce a new dataset, Animals with Attributes, of over 30,000 images of 50 animal classes, annotated with 85 semantic attributes. Extensive experiments on this and two more datasets show that attribute-based classification indeed is able to categorize images without access to any training images of the target classes.","lang":"eng"}],"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","publist_id":"4385","status":"public","date_published":"2013-07-30T00:00:00Z","day":"30","date_updated":"2026-06-18T07:51:30Z","doi":"10.1109/TPAMI.2013.140","title":"Attribute-based classification for zero-shot learning of object categories","article_processing_charge":"No","year":"2013","das_tickbox":"1","ddc":["000"],"citation":{"ista":"Lampert C, Nickisch H, Harmeling S. 2013. Attribute-based classification for zero-shot learning of object categories. IEEE Transactions on Pattern Analysis and Machine Intelligence. 36(3), 453–465.","apa":"Lampert, C., Nickisch, H., &#38; Harmeling, S. (2013). Attribute-based classification for zero-shot learning of object categories. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/TPAMI.2013.140\">https://doi.org/10.1109/TPAMI.2013.140</a>","ama":"Lampert C, Nickisch H, Harmeling S. Attribute-based classification for zero-shot learning of object categories. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2013;36(3):453-465. doi:<a href=\"https://doi.org/10.1109/TPAMI.2013.140\">10.1109/TPAMI.2013.140</a>","short":"C. Lampert, H. Nickisch, S. Harmeling, IEEE Transactions on Pattern Analysis and Machine Intelligence 36 (2013) 453–465.","mla":"Lampert, Christoph, et al. “Attribute-Based Classification for Zero-Shot Learning of Object Categories.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 3, IEEE, 2013, pp. 453–65, doi:<a href=\"https://doi.org/10.1109/TPAMI.2013.140\">10.1109/TPAMI.2013.140</a>.","chicago":"Lampert, Christoph, Hannes Nickisch, and Stefan Harmeling. “Attribute-Based Classification for Zero-Shot Learning of Object Categories.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2013. <a href=\"https://doi.org/10.1109/TPAMI.2013.140\">https://doi.org/10.1109/TPAMI.2013.140</a>.","ieee":"C. Lampert, H. Nickisch, and S. Harmeling, “Attribute-based classification for zero-shot learning of object categories,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 3. IEEE, pp. 453–465, 2013."},"author":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hannes","last_name":"Nickisch","full_name":"Nickisch, Hannes"},{"last_name":"Harmeling","first_name":"Stefan","full_name":"Harmeling, Stefan"}],"month":"07","language":[{"iso":"eng"}],"_id":"2516","page":"453 - 465","issue":"3"},{"scopus_import":"1","date_created":"2023-01-16T09:21:24Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       337","abstract":[{"lang":"eng","text":"The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations."}],"publication":"Science","status":"public","date_published":"2012-09-14T00:00:00Z","publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"XiFe"}],"quality_controlled":"1","pmid":1,"type":"journal_article","volume":337,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/","open_access":"1"}],"article_type":"original","keyword":["Multidisciplinary"],"citation":{"ama":"Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. <i>Science</i>. 2012;337(6100):1360-1364. doi:<a href=\"https://doi.org/10.1126/science.1224839\">10.1126/science.1224839</a>","ista":"Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 337(6100), 1360–1364.","apa":"Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1224839\">https://doi.org/10.1126/science.1224839</a>","chicago":"Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” <i>Science</i>. American Association for the Advancement of Science, 2012. <a href=\"https://doi.org/10.1126/science.1224839\">https://doi.org/10.1126/science.1224839</a>.","ieee":"C. A. Ibarra <i>et al.</i>, “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes,” <i>Science</i>, vol. 337, no. 6100. American Association for the Advancement of Science, pp. 1360–1364, 2012.","mla":"Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” <i>Science</i>, vol. 337, no. 6100, American Association for the Advancement of Science, 2012, pp. 1360–64, doi:<a href=\"https://doi.org/10.1126/science.1224839\">10.1126/science.1224839</a>.","short":"C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H. Tamaru, D. Zilberman, Science 337 (2012) 1360–1364."},"author":[{"full_name":"Ibarra, Christian A.","last_name":"Ibarra","first_name":"Christian A."},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi"},{"last_name":"Schoft","first_name":"Vera K.","full_name":"Schoft, Vera K."},{"full_name":"Hsieh, Tzung-Fu","first_name":"Tzung-Fu","last_name":"Hsieh"},{"last_name":"Uzawa","first_name":"Rie","full_name":"Uzawa, Rie"},{"full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues","first_name":"Jessica A."},{"full_name":"Zemach, Assaf","first_name":"Assaf","last_name":"Zemach"},{"first_name":"Nina","last_name":"Chumak","full_name":"Chumak, Nina"},{"full_name":"Machlicova, Adriana","first_name":"Adriana","last_name":"Machlicova"},{"full_name":"Nishimura, Toshiro","first_name":"Toshiro","last_name":"Nishimura"},{"full_name":"Rojas, Denisse","first_name":"Denisse","last_name":"Rojas"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"last_name":"Tamaru","first_name":"Hisashi","full_name":"Tamaru, Hisashi"},{"last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel"}],"month":"09","_id":"12198","language":[{"iso":"eng"}],"acknowledgement":"We thank S. Harmer for assistance with the analysis of histone modifications, the BioOptics team at the Vienna Biocenter Campus for sorting sperm and vegetative cell nuclei, K. Slotkin for the LAT52p-amiRNA=GFP plasmid, and G. Drews for the DD45p-GFP transgenic line. This work was partially funded by an NIH grant (GM69415) to R.L.F., NSF grants (MCB-0918821 and IOS-1025890) to R.L.F. and D.Z., a Young Investigator Grant from the Arnold and Mabel Beckman Foundation to D.Z., an Austrian Science Fund (FWF) grant P21389-B03 to H.T., a Ruth L. Kirschstein NIH Predoctoral Fellowship (GM093633) to C.A.I., a Fulbright Scholarship to J.A.R., a fellowship from the Jane Coffin Childs Memorial Fund to A.Z., and a Robert and Colleen Haas Scholarship to D.R. Sequencing data are deposited in GEO (GSE38935).","page":"1360-1364","issue":"6100","day":"14","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"date_updated":"2023-10-16T09:27:26Z","doi":"10.1126/science.1224839","title":"Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes","external_id":{"pmid":["22984074"]},"oa":1,"article_processing_charge":"No","year":"2012"},{"intvolume":"        48","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Water Resources Research","status":"public","date_published":"2012-03-01T00:00:00Z","abstract":[{"text":"In the Dry Andes of central Chile, summer water resources originate mostly from snowmelt and ice melt. We use the physically based, spatially distributed hydrological model TOPKAPI to study the exchange between glaciers and climate in the upper Aconcagua River Basin during the summer season and identify the model parameters that are robust and transferable and those that are more dependent on calibration. TOPKAPI has recently been adapted to incorporate an enhanced temperature index approach for snow and ice melting. We suggest a calibration procedure that allows calibration of parameters in three steps by separating parameters governing distinct processes. We evaluate the parameters' transferability in time and in space by applying the model at two spatial scales. TOPKAPI's ability to simulate the relevant processes is tested against meteorological, ablation, and glacier runoff data measured on Juncal Norte Glacier during two glacier ablation seasons. The model was applied successfully to the climatic setting of the Dry Andes once its parameters were recalibrated. We found a clear distinction between parameters that are stable in time and those that need recalibration. The parameters of the melt model are transferable from one season to the other, while the parameters governing the extrapolation of meteorological input data and the routing of glacier meltwater need recalibration from one season to the other. Sensitivity analysis revealed that the model is most sensitive to the temperature lapse rate governing the extrapolation of air temperature from point measurements to the glacier scale and to the melt parameter that multiplies the shortwave radiation balance.","lang":"eng"}],"date_created":"2023-02-20T08:17:39Z","extern":"1","scopus_import":"1","oa_version":"Published Version","type":"journal_article","volume":48,"main_file_link":[{"url":"https://doi.org/10.1029/2011WR010559","open_access":"1"}],"publisher":"American Geophysical Union","publication_status":"published","quality_controlled":"1","_id":"12644","language":[{"iso":"eng"}],"issue":"3","citation":{"apa":"Ragettli, S., &#38; Pellicciotti, F. (2012). Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters. <i>Water Resources Research</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2011wr010559\">https://doi.org/10.1029/2011wr010559</a>","ista":"Ragettli S, Pellicciotti F. 2012. Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters. Water Resources Research. 48(3), W03509.","ama":"Ragettli S, Pellicciotti F. Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters. <i>Water Resources Research</i>. 2012;48(3). doi:<a href=\"https://doi.org/10.1029/2011wr010559\">10.1029/2011wr010559</a>","mla":"Ragettli, S., and Francesca Pellicciotti. “Calibration of a Physically Based, Spatially Distributed Hydrological Model in a Glacierized Basin: On the Use of Knowledge from Glaciometeorological Processes to Constrain Model Parameters.” <i>Water Resources Research</i>, vol. 48, no. 3, W03509, American Geophysical Union, 2012, doi:<a href=\"https://doi.org/10.1029/2011wr010559\">10.1029/2011wr010559</a>.","short":"S. Ragettli, F. Pellicciotti, Water Resources Research 48 (2012).","ieee":"S. Ragettli and F. Pellicciotti, “Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters,” <i>Water Resources Research</i>, vol. 48, no. 3. American Geophysical Union, 2012.","chicago":"Ragettli, S., and Francesca Pellicciotti. “Calibration of a Physically Based, Spatially Distributed Hydrological Model in a Glacierized Basin: On the Use of Knowledge from Glaciometeorological Processes to Constrain Model Parameters.” <i>Water Resources Research</i>. American Geophysical Union, 2012. <a href=\"https://doi.org/10.1029/2011wr010559\">https://doi.org/10.1029/2011wr010559</a>."},"article_type":"original","author":[{"full_name":"Ragettli, S.","last_name":"Ragettli","first_name":"S."},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"}],"article_number":"W03509","month":"03","article_processing_charge":"No","oa":1,"year":"2012","date_updated":"2023-02-21T09:38:36Z","day":"01","publication_identifier":{"issn":["0043-1397"]},"doi":"10.1029/2011wr010559","title":"Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters"},{"author":[{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"},{"full_name":"Buergi, Cyrill","first_name":"Cyrill","last_name":"Buergi"},{"full_name":"Immerzeel, Walter Willem","last_name":"Immerzeel","first_name":"Walter Willem"},{"last_name":"Konz","first_name":"Markus","full_name":"Konz, Markus"},{"full_name":"Shrestha, Arun B.","last_name":"Shrestha","first_name":"Arun B."}],"month":"02","citation":{"ista":"Pellicciotti F, Buergi C, Immerzeel WW, Konz M, Shrestha AB. 2012. Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies. Mountain Research and Development. 32(1), 39–50.","apa":"Pellicciotti, F., Buergi, C., Immerzeel, W. W., Konz, M., &#38; Shrestha, A. B. (2012). Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies. <i>Mountain Research and Development</i>. International Mountain Society. <a href=\"https://doi.org/10.1659/mrd-journal-d-11-00092.1\">https://doi.org/10.1659/mrd-journal-d-11-00092.1</a>","ama":"Pellicciotti F, Buergi C, Immerzeel WW, Konz M, Shrestha AB. Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies. <i>Mountain Research and Development</i>. 2012;32(1):39-50. doi:<a href=\"https://doi.org/10.1659/mrd-journal-d-11-00092.1\">10.1659/mrd-journal-d-11-00092.1</a>","short":"F. Pellicciotti, C. Buergi, W.W. Immerzeel, M. Konz, A.B. Shrestha, Mountain Research and Development 32 (2012) 39–50.","mla":"Pellicciotti, Francesca, et al. “Challenges and Uncertainties in Hydrological Modeling of Remote Hindu Kush–Karakoram–Himalayan (HKH) Basins: Suggestions for Calibration Strategies.” <i>Mountain Research and Development</i>, vol. 32, no. 1, International Mountain Society, 2012, pp. 39–50, doi:<a href=\"https://doi.org/10.1659/mrd-journal-d-11-00092.1\">10.1659/mrd-journal-d-11-00092.1</a>.","chicago":"Pellicciotti, Francesca, Cyrill Buergi, Walter Willem Immerzeel, Markus Konz, and Arun B. Shrestha. “Challenges and Uncertainties in Hydrological Modeling of Remote Hindu Kush–Karakoram–Himalayan (HKH) Basins: Suggestions for Calibration Strategies.” <i>Mountain Research and Development</i>. International Mountain Society, 2012. <a href=\"https://doi.org/10.1659/mrd-journal-d-11-00092.1\">https://doi.org/10.1659/mrd-journal-d-11-00092.1</a>.","ieee":"F. Pellicciotti, C. Buergi, W. W. Immerzeel, M. Konz, and A. B. Shrestha, “Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies,” <i>Mountain Research and Development</i>, vol. 32, no. 1. International Mountain Society, pp. 39–50, 2012."},"article_type":"original","issue":"1","page":"39-50","language":[{"iso":"eng"}],"_id":"12646","doi":"10.1659/mrd-journal-d-11-00092.1","title":"Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies","date_updated":"2023-02-21T09:31:54Z","day":"01","publication_identifier":{"eissn":["1994-7151"],"issn":["0276-4741"]},"year":"2012","oa":1,"article_processing_charge":"No","oa_version":"Published Version","date_created":"2023-02-20T08:17:47Z","scopus_import":"1","extern":"1","publication":"Mountain Research and Development","status":"public","date_published":"2012-02-01T00:00:00Z","abstract":[{"lang":"eng","text":"Assessment of water resources from remote mountainous catchments plays a crucial role for the development of rural areas in or in the vicinity of mountain ranges. The scarcity of data, however, prevents the application of standard approaches that are based on data-driven models. The Hindu Kush–Karakoram–Himalaya mountain range is a crucial area in terms of water resources, but our understanding of the response of its high-elevation catchments to a changing climate is hindered by lack of hydro-meteorological and cryospheric data. Hydrological modeling is challenging here because internal inconsistencies—such as an underestimation of precipitation input that can be compensated for by an overestimation of meltwater—might be hidden due to the complexity of feedback mechanisms that govern melt and runoff generation in such basins. Data scarcity adds to this difficulty by preventing the application of systematic calibration procedures that would allow identification of the parameter set that could guarantee internal consistency in the simulation of the single hydrological components. In this work, we use simulations from the Hunza River Basin in the Karakoram region obtained with the hydrological model TOPKAPI to quantify the predictive power of discharge and snow-cover data sets, as well as the combination of both. We also show that short-term measurements of meteorological variables such as radiative fluxes, wind speed, relative humidity, and air temperature from glacio-meteorological experiments are crucial for a correct parameterization of surface melt processes. They enable detailed simulations of the energy fluxes governing glacier–atmosphere interaction and the resulting ablation through energy-balance modeling. These simulations are used to derive calibrated parameters for the simplified snow and glacier routines in TOPKAPI. We demonstrate that such parameters are stable in space and time in similar climatic regions, thus reducing the number of parameters requiring calibration."}],"intvolume":"        32","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"International Mountain Society","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1659/MRD-JOURNAL-D-11-00092.1","open_access":"1"}],"type":"journal_article","volume":32},{"quality_controlled":"1","publisher":"International Mountain Society","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1659/MRD-JOURNAL-D-11-00097.1"}],"volume":32,"type":"journal_article","oa_version":"Published Version","date_created":"2023-02-20T08:17:52Z","scopus_import":"1","extern":"1","date_published":"2012-02-01T00:00:00Z","status":"public","publication":"Mountain Research and Development","abstract":[{"text":"Accurate quantification of the spatial distribution of precipitation in mountain regions is crucial for assessments of water resources and for the understanding of high-altitude hydrology, yet it is one of the largest unknowns due to the lack of high-altitude observations. The Hunza basin in Pakistan contains very large glacier systems, which, given the melt, cannot persist unless precipitation (snow input) is much higher than what is observed at the meteorological stations, mostly located in mountain valleys. Several studies, therefore, suggest strong positive vertical precipitation lapse rates; in the present study, we quantify this lapse rate by using glaciers as a proxy. We assume a neutral mass balance for the glaciers for the period from 2001 to 2003, and we inversely model the precipitation lapse by balancing the total accumulation in the catchment area and the ablation over the glacier area for the 50 largest glacier systems in the Hunza basin in the Karakoram. Our results reveal a vertical precipitation lapse rate that equals 0.21 ± 0.12% m−1, with a maximum precipitation at an elevation of 5500 masl. We showed that the total annual basin precipitation (828 mm) is 260% higher than what is estimated based on interpolated observations (319 mm); this has major consequences for hydrological modeling and water resource assessments in general. Our results were validated by using previously published studies on individual glaciers as well as the water balance of the Hunza basin. The approach is more widely applicable in mountain ranges where precipitation measurements at high altitude are lacking.","lang":"eng"}],"intvolume":"        32","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin","doi":"10.1659/mrd-journal-d-11-00097.1","date_updated":"2023-02-21T08:56:29Z","publication_identifier":{"eissn":["1994-7151"],"issn":["0276-4741"]},"day":"01","year":"2012","article_processing_charge":"No","oa":1,"month":"02","author":[{"last_name":"Immerzeel","first_name":"Walter Willem","full_name":"Immerzeel, Walter Willem"},{"full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti"},{"full_name":"Shrestha, Arun B.","first_name":"Arun B.","last_name":"Shrestha"}],"citation":{"ieee":"W. W. Immerzeel, F. Pellicciotti, and A. B. Shrestha, “Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin,” <i>Mountain Research and Development</i>, vol. 32, no. 1. International Mountain Society, pp. 30–38, 2012.","chicago":"Immerzeel, Walter Willem, Francesca Pellicciotti, and Arun B. Shrestha. “Glaciers as a Proxy to Quantify the Spatial Distribution of Precipitation in the Hunza Basin.” <i>Mountain Research and Development</i>. International Mountain Society, 2012. <a href=\"https://doi.org/10.1659/mrd-journal-d-11-00097.1\">https://doi.org/10.1659/mrd-journal-d-11-00097.1</a>.","mla":"Immerzeel, Walter Willem, et al. “Glaciers as a Proxy to Quantify the Spatial Distribution of Precipitation in the Hunza Basin.” <i>Mountain Research and Development</i>, vol. 32, no. 1, International Mountain Society, 2012, pp. 30–38, doi:<a href=\"https://doi.org/10.1659/mrd-journal-d-11-00097.1\">10.1659/mrd-journal-d-11-00097.1</a>.","short":"W.W. Immerzeel, F. Pellicciotti, A.B. Shrestha, Mountain Research and Development 32 (2012) 30–38.","ama":"Immerzeel WW, Pellicciotti F, Shrestha AB. Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin. <i>Mountain Research and Development</i>. 2012;32(1):30-38. doi:<a href=\"https://doi.org/10.1659/mrd-journal-d-11-00097.1\">10.1659/mrd-journal-d-11-00097.1</a>","apa":"Immerzeel, W. W., Pellicciotti, F., &#38; Shrestha, A. B. (2012). Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin. <i>Mountain Research and Development</i>. International Mountain Society. <a href=\"https://doi.org/10.1659/mrd-journal-d-11-00097.1\">https://doi.org/10.1659/mrd-journal-d-11-00097.1</a>","ista":"Immerzeel WW, Pellicciotti F, Shrestha AB. 2012. Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin. Mountain Research and Development. 32(1), 30–38."},"keyword":["General Environmental Science","Development","Environmental Chemistry"],"article_type":"original","issue":"1","page":"30-38","_id":"12647","language":[{"iso":"eng"}]},{"oa_version":"Published Version","date_created":"2023-02-20T08:17:57Z","scopus_import":"1","extern":"1","status":"public","date_published":"2012-09-27T00:00:00Z","publication":"Journal of Geophysical Research: Atmospheres","abstract":[{"lang":"eng","text":"Distributed glacier melt models generally assume that the glacier surface consists of bare exposed ice and snow. In reality, many glaciers are wholly or partially covered in layers of debris that tend to suppress ablation rates. In this paper, an existing physically based point model for the ablation of debris-covered ice is incorporated in a distributed melt model and applied to Haut Glacier d'Arolla, Switzerland, which has three large patches of debris cover on its surface. The model is based on a 10 m resolution digital elevation model (DEM) of the area; each glacier pixel in the DEM is defined as either bare or debris-covered ice, and may be covered in snow that must be melted off before ice ablation is assumed to occur. Each debris-covered pixel is assigned a debris thickness value using probability distributions based on over 1000 manual thickness measurements. Locally observed meteorological data are used to run energy balance calculations in every pixel, using an approach suitable for snow, bare ice or debris-covered ice as appropriate. The use of the debris model significantly reduces the total ablation in the debris-covered areas, however the precise reduction is sensitive to the temperature extrapolation used in the model distribution because air near the debris surface tends to be slightly warmer than over bare ice. Overall results suggest that the debris patches, which cover 10% of the glacierized area, reduce total runoff from the glacierized part of the basin by up to 7%."}],"intvolume":"       117","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"American Geophysical Union","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1029/2012JD017795"}],"volume":117,"type":"journal_article","month":"09","article_number":"D18105","author":[{"first_name":"T. D.","last_name":"Reid","full_name":"Reid, T. D."},{"last_name":"Carenzo","first_name":"M.","full_name":"Carenzo, M."},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"},{"first_name":"B. W.","last_name":"Brock","full_name":"Brock, B. W."}],"keyword":["Paleontology","Space and Planetary Science","Earth and Planetary Sciences (miscellaneous)","Atmospheric Science","Earth-Surface Processes","Geochemistry and Petrology","Soil Science","Water Science and Technology","Ecology","Aquatic Science","Forestry","Oceanography","Geophysics"],"citation":{"mla":"Reid, T. D., et al. “Including Debris Cover Effects in a Distributed Model of Glacier Ablation.” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 117, no. D18, D18105, American Geophysical Union, 2012, doi:<a href=\"https://doi.org/10.1029/2012jd017795\">10.1029/2012jd017795</a>.","short":"T.D. Reid, M. Carenzo, F. Pellicciotti, B.W. Brock, Journal of Geophysical Research: Atmospheres 117 (2012).","ieee":"T. D. Reid, M. Carenzo, F. Pellicciotti, and B. W. Brock, “Including debris cover effects in a distributed model of glacier ablation,” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 117, no. D18. American Geophysical Union, 2012.","chicago":"Reid, T. D., M. Carenzo, Francesca Pellicciotti, and B. W. Brock. “Including Debris Cover Effects in a Distributed Model of Glacier Ablation.” <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union, 2012. <a href=\"https://doi.org/10.1029/2012jd017795\">https://doi.org/10.1029/2012jd017795</a>.","apa":"Reid, T. D., Carenzo, M., Pellicciotti, F., &#38; Brock, B. W. (2012). Including debris cover effects in a distributed model of glacier ablation. <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2012jd017795\">https://doi.org/10.1029/2012jd017795</a>","ista":"Reid TD, Carenzo M, Pellicciotti F, Brock BW. 2012. Including debris cover effects in a distributed model of glacier ablation. Journal of Geophysical Research: Atmospheres. 117(D18), D18105.","ama":"Reid TD, Carenzo M, Pellicciotti F, Brock BW. Including debris cover effects in a distributed model of glacier ablation. <i>Journal of Geophysical Research: Atmospheres</i>. 2012;117(D18). doi:<a href=\"https://doi.org/10.1029/2012jd017795\">10.1029/2012jd017795</a>"},"article_type":"original","issue":"D18","language":[{"iso":"eng"}],"_id":"12648","title":"Including debris cover effects in a distributed model of glacier ablation","doi":"10.1029/2012jd017795","date_updated":"2023-02-20T10:57:31Z","publication_identifier":{"issn":["0148-0227"]},"day":"27","year":"2012","article_processing_charge":"No","oa":1},{"ddc":["570"],"date_created":"2023-05-23T17:01:02Z","citation":{"ama":"Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison of population histories in a parasitoid guild. 2012. doi:<a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">10.5061/DRYAD.0G0FS</a>","apa":"Lohse, K., Barton, N. H., Stone, G., &#38; Melika, G. (2012). Data from: A likelihood-based comparison of population histories in a parasitoid guild. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">https://doi.org/10.5061/DRYAD.0G0FS</a>","ista":"Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based comparison of population histories in a parasitoid guild, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">10.5061/DRYAD.0G0FS</a>.","ieee":"K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based comparison of population histories in a parasitoid guild.” Dryad, 2012.","chicago":"Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.” Dryad, 2012. <a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">https://doi.org/10.5061/DRYAD.0G0FS</a>.","mla":"Lohse, Konrad, et al. <i>Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild</i>. Dryad, 2012, doi:<a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">10.5061/DRYAD.0G0FS</a>.","short":"K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012)."},"author":[{"full_name":"Lohse, Konrad","last_name":"Lohse","first_name":"Konrad"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stone","first_name":"Graham","full_name":"Stone, Graham"},{"last_name":"Melika","first_name":"George","full_name":"Melika, George"}],"oa_version":"Published Version","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/publicdomain/zero/1.0/","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"_id":"13075","abstract":[{"lang":"eng","text":"Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and - using triplet alignments of intronic loci - quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times."}],"date_published":"2012-06-08T00:00:00Z","status":"public","day":"08","date_updated":"2025-05-28T11:56:58Z","publisher":"Dryad","doi":"10.5061/DRYAD.0G0FS","title":"Data from: A likelihood-based comparison of population histories in a parasitoid guild","department":[{"_id":"NiBa"}],"type":"research_data_reference","article_processing_charge":"No","oa":1,"related_material":{"record":[{"status":"public","id":"2968","relation":"used_in_publication"}]},"year":"2012","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0g0fs"}]}]