[{"publist_id":"7321","page":"91 - 95","year":"2013","month":"01","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"title":"Dynamic persistence of antibiotic-stressed mycobacteria","publisher":"American Association for the Advancement of Science","publication_status":"published","quality_controlled":"1","_id":"499","issue":"6115","type":"journal_article","oa_version":"None","citation":{"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>","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>.","short":"Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler, J. Mckinney, Science 339 (2013) 91–95.","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.","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.","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","doi":"10.1126/science.1229858","status":"public","author":[{"first_name":"Yurichi","full_name":"Wakamoto, Yurichi","last_name":"Wakamoto"},{"last_name":"Dhar","full_name":"Dhar, Neraaj","first_name":"Neraaj"},{"id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P","last_name":"Chait","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187"},{"full_name":"Schneider, Katrin","last_name":"Schneider","first_name":"Katrin"},{"full_name":"Signorino Gelo, François","last_name":"Signorino Gelo","first_name":"François"},{"first_name":"Stanislas","last_name":"Leibler","full_name":"Leibler, Stanislas"},{"last_name":"Mckinney","full_name":"Mckinney, John","first_name":"John"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"day":"04","publication":"Science","volume":339,"date_updated":"2021-01-12T08:01:06Z","scopus_import":1,"date_published":"2013-01-04T00:00:00Z","intvolume":"       339","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"}]},{"scopus_import":1,"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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:01:08Z","status":"public","author":[{"last_name":"Ward","full_name":"Ward, Melissa","first_name":"Melissa"},{"full_name":"Lycett, Samantha","last_name":"Lycett","first_name":"Samantha"},{"first_name":"Dorita","last_name":"Avila","full_name":"Avila, Dorita"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrew","last_name":"Leigh Brown","full_name":"Leigh Brown, Andrew"}],"publication_status":"published","issue":"1","_id":"500","file":[{"file_name":"IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf","creator":"system","file_id":"4722","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:36Z","checksum":"52cf48a7c1794676ae8b0029573a84a9","file_size":1150052,"date_created":"2018-12-12T10:08:59Z"}],"type":"journal_article","ddc":["576"],"oa_version":"Published Version","publisher":"BioMed Central","pubrep_id":"941","department":[{"_id":"JoBo"}],"year":"2013","month":"10","date_published":"2013-10-09T00:00:00Z","has_accepted_license":"1","intvolume":"        13","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","day":"09","publication":"BMC Evolutionary Biology","volume":13,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:46:36Z","doi":"10.1186/1471-2148-13-222","quality_controlled":"1","citation":{"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>.","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>","short":"M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary Biology 13 (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.","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.","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>"},"date_created":"2018-12-11T11:46:49Z","oa":1,"article_number":"222","title":"Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza","publist_id":"7320"},{"quality_controlled":"1","citation":{"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>.","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>","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>.","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>","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.","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.","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."},"date_created":"2018-12-11T11:46:49Z","oa":1,"title":"A new species of tapir from the Amazon","page":"1331 - 1345","publist_id":"7319","date_published":"2013-12-01T00:00:00Z","intvolume":"        94","has_accepted_license":"1","publication":"Journal of Mammalogy","day":"01","volume":94,"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"file_date_updated":"2020-07-14T12:46:36Z","doi":"10.1644/12-MAMM-A-169.1","publication_status":"published","_id":"501","issue":"6","file":[{"relation":"main_file","file_id":"4980","creator":"system","file_name":"IST-2018-940-v1+1_2013_Redondo_A_new.pdf","date_created":"2018-12-12T10:12:59Z","file_size":1040765,"checksum":"8007815078dccac21ecd1cf73a269dc6","date_updated":"2020-07-14T12:46:36Z","access_level":"open_access","content_type":"application/pdf"}],"type":"journal_article","oa_version":"Published Version","ddc":["570"],"publisher":"Oxford University Press","pubrep_id":"940","department":[{"_id":"JoBo"}],"year":"2013","month":"12","scopus_import":1,"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."}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:01:09Z","status":"public","author":[{"first_name":"Mario","full_name":"Cozzuol, Mario","last_name":"Cozzuol"},{"first_name":"Camila","last_name":"Clozato","full_name":"Clozato, Camila"},{"first_name":"Elizete","full_name":"Holanda, Elizete","last_name":"Holanda"},{"first_name":"Flávio","last_name":"Rodrigues","full_name":"Rodrigues, Flávio"},{"first_name":"Samuel","last_name":"Nienow","full_name":"Nienow, Samuel"},{"first_name":"Benoit","full_name":"De Thoisy, Benoit","last_name":"De Thoisy"},{"first_name":"Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793"},{"first_name":"Fabrício","last_name":"Santos","full_name":"Santos, Fabrício"}]},{"department":[{"_id":"KrPi"}],"title":"Short blind signatures","page":"627 - 661","publist_id":"7318","month":"11","year":"2013","type":"journal_article","oa_version":"None","citation":{"ista":"Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. 2013. Short blind signatures. Journal of Computer Security. 21(5), 627–661.","short":"O. Blazy, G. Fuchsbauer, D. Pointcheval, D. Vergnaud, Journal of Computer Security 21 (2013) 627–661.","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.","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>","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>.","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>","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>."},"date_created":"2018-12-11T11:46:50Z","quality_controlled":"1","publication_status":"published","issue":"5","_id":"502","publisher":"IOS Press","status":"public","author":[{"full_name":"Blazy, Olivier","last_name":"Blazy","first_name":"Olivier"},{"first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg"},{"first_name":"David","full_name":"Pointcheval, David","last_name":"Pointcheval"},{"last_name":"Vergnaud","full_name":"Vergnaud, Damien","first_name":"Damien"}],"doi":"10.3233/JCS-130477","intvolume":"        21","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"}],"date_published":"2013-11-22T00:00:00Z","scopus_import":1,"publication":"Journal of Computer Security","day":"22","volume":21,"date_updated":"2021-01-12T08:01:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}]},{"status":"public","author":[{"last_name":"Greimel","full_name":"Greimel, Katrin","first_name":"Katrin"},{"first_name":"Veronika","last_name":"Perz","full_name":"Perz, Veronika"},{"last_name":"Koren","full_name":"Koren, Klaus","first_name":"Klaus","id":"382FBD6A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Feola","full_name":"Feola, Roland","first_name":"Roland"},{"first_name":"Armin","last_name":"Temel","full_name":"Temel, Armin"},{"last_name":"Sohar","full_name":"Sohar, Christian","first_name":"Christian"},{"last_name":"Herrero Acero","full_name":"Herrero Acero, Enrique","first_name":"Enrique"},{"last_name":"Klimant","full_name":"Klimant, Ingo","first_name":"Ingo"},{"first_name":"Georg","last_name":"Guebitz","full_name":"Guebitz, Georg"}],"doi":"10.1039/c2gc36666e","scopus_import":1,"date_published":"2013-02-01T00:00:00Z","intvolume":"        15","abstract":[{"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.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"day":"01","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.","publication":"Green Chemistry","date_updated":"2021-01-12T08:01:11Z","volume":15,"department":[{"_id":"HaJa"}],"title":"Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins","page":"381 - 388","publist_id":"7313","year":"2013","month":"02","quality_controlled":"1","publication_status":"published","_id":"505","issue":"2","type":"journal_article","oa_version":"None","citation":{"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>.","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>","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>.","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.","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.","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."},"date_created":"2018-12-11T11:46:51Z","publisher":"Royal Society of Chemistry"},{"publisher":"American Society of Plant Biologists","_id":"507","issue":"8","external_id":{"pmid":["23975898"]},"publication_status":"published","oa_version":"Submitted Version","type":"journal_article","month":"08","year":"2013","department":[{"_id":"JiFr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:01:12Z","scopus_import":1,"abstract":[{"lang":"eng","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."}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784592/"}],"author":[{"first_name":"Soo","last_name":"Kim","full_name":"Kim, Soo"},{"full_name":"Xu, Zheng","last_name":"Xu","first_name":"Zheng"},{"full_name":"Song, Kyungyoung","last_name":"Song","first_name":"Kyungyoung"},{"first_name":"Dae","last_name":"Kim","full_name":"Kim, Dae"},{"full_name":"Kang, Hyangju","last_name":"Kang","first_name":"Hyangju"},{"first_name":"Ilka","full_name":"Reichardt, Ilka","last_name":"Reichardt"},{"last_name":"Sohn","full_name":"Sohn, Eun","first_name":"Eun"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Juergens","full_name":"Juergens, Gerd","first_name":"Gerd"},{"last_name":"Hwang","full_name":"Hwang, Inhwan","first_name":"Inhwan"}],"status":"public","oa":1,"quality_controlled":"1","date_created":"2018-12-11T11:46:52Z","citation":{"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>","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>.","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>","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.","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.","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."},"publist_id":"7312","page":"2970 - 2985","title":"Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis","pmid":1,"volume":25,"publication":"Plant Cell","day":"01","date_published":"2013-08-01T00:00:00Z","intvolume":"        25","doi":"10.1105/tpc.113.114264"},{"external_id":{"pmid":["23821607"]},"publication_status":"published","_id":"508","issue":"9","type":"journal_article","oa_version":"Submitted Version","publisher":"Oxford University Press","department":[{"_id":"JoBo"}],"year":"2013","month":"09","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/"}],"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"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:01:12Z","status":"public","author":[{"first_name":"Eduardo","last_name":"Tarazona Santos","full_name":"Tarazona Santos, Eduardo"},{"first_name":"Moara","full_name":"Machado, Moara","last_name":"Machado"},{"first_name":"Wagner","last_name":"Magalhães","full_name":"Magalhães, Wagner"},{"last_name":"Chen","full_name":"Chen, Renee","first_name":"Renee"},{"full_name":"Lyon, Fernanda","last_name":"Lyon","first_name":"Fernanda"},{"last_name":"Burdett","full_name":"Burdett, Laurie","first_name":"Laurie"},{"first_name":"Andrew","full_name":"Crenshaw, Andrew","last_name":"Crenshaw"},{"full_name":"Fabbri, Cristina","last_name":"Fabbri","first_name":"Cristina"},{"full_name":"Pereira, Latife","last_name":"Pereira","first_name":"Latife"},{"first_name":"Laelia","full_name":"Pinto, Laelia","last_name":"Pinto"},{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793"},{"first_name":"Ben","last_name":"Sestanovich","full_name":"Sestanovich, Ben"},{"first_name":"Meredith","full_name":"Yeager, Meredith","last_name":"Yeager"},{"first_name":"Stephen","full_name":"Chanock, Stephen","last_name":"Chanock"}],"quality_controlled":"1","citation":{"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>","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.","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.","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.","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>.","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>","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>."},"date_created":"2018-12-11T11:46:52Z","oa":1,"title":"Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications","publist_id":"7310","page":"2157 - 2167","date_published":"2013-09-01T00:00:00Z","intvolume":"        30","pmid":1,"publication":"Molecular Biology and Evolution","day":"01","volume":30,"doi":"10.1093/molbev/mst119"},{"abstract":[{"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. ","lang":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784593/","open_access":"1"}],"scopus_import":1,"date_updated":"2021-01-12T08:01:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"author":[{"first_name":"Simone","full_name":"Di Rubbo, Simone","last_name":"Di Rubbo"},{"first_name":"Niloufer","last_name":"Irani","full_name":"Irani, Niloufer"},{"last_name":"Kim","full_name":"Kim, Soo","first_name":"Soo"},{"first_name":"Zheng","full_name":"Xu, Zheng","last_name":"Xu"},{"last_name":"Gadeyne","full_name":"Gadeyne, Astrid","first_name":"Astrid"},{"first_name":"Wim","full_name":"Dejonghe, Wim","last_name":"Dejonghe"},{"first_name":"Isabelle","full_name":"Vanhoutte, Isabelle","last_name":"Vanhoutte"},{"first_name":"Geert","full_name":"Persiau, Geert","last_name":"Persiau"},{"full_name":"Eeckhout, Dominique","last_name":"Eeckhout","first_name":"Dominique"},{"first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","last_name":"Simon"},{"full_name":"Song, Kyungyoung","last_name":"Song","first_name":"Kyungyoung"},{"first_name":"Jürgen","full_name":"Kleine Vehn, Jürgen","last_name":"Kleine Vehn"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Geert","last_name":"De Jaeger","full_name":"De Jaeger, Geert"},{"first_name":"Daniël","last_name":"Van Damme","full_name":"Van Damme, Daniël"},{"last_name":"Hwang","full_name":"Hwang, Inhwan","first_name":"Inhwan"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"}],"status":"public","oa_version":"Submitted Version","type":"journal_article","_id":"509","issue":"8","external_id":{"pmid":["23975899"]},"publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"month":"08","year":"2013","intvolume":"        25","date_published":"2013-08-01T00:00:00Z","volume":25,"day":"01","publication":"Plant Cell","pmid":1,"doi":"10.1105/tpc.113.114058","date_created":"2018-12-11T11:46:52Z","citation":{"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.","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.","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.","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>","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>.","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>.","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>"},"quality_controlled":"1","oa":1,"title":"The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis","page":"2986 - 2997","publist_id":"7311"},{"citation":{"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>","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.","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.","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>","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>.","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>."},"date_created":"2018-12-11T11:46:53Z","quality_controlled":"1","oa":1,"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","publist_id":"7309","page":"3858 - 3870","intvolume":"        25","date_published":"2013-10-01T00:00:00Z","volume":25,"day":"01","publication":"Plant Cell","pmid":1,"doi":"10.1105/tpc.113.114421","type":"journal_article","oa_version":"Published Version","issue":"10","_id":"511","external_id":{"pmid":["24163311"]},"publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"year":"2013","month":"10","abstract":[{"lang":"eng","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."}],"main_file_link":[{"open_access":"1","url":"www.doi.org/10.1105/tpc.113.114421"}],"scopus_import":1,"date_updated":"2021-01-12T08:01:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"author":[{"first_name":"Aleš","full_name":"Pěnčík, 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"},{"orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","last_name":"Simon","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kathleen","full_name":"Greenham, Kathleen","last_name":"Greenham"},{"first_name":"Yi","last_name":"Zhang","full_name":"Zhang, Yi"},{"full_name":"Kowalczyk, Mariusz","last_name":"Kowalczyk","first_name":"Mariusz"},{"full_name":"Estelle, Mark","last_name":"Estelle","first_name":"Mark"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"first_name":"Göran","full_name":"Sandberg, Göran","last_name":"Sandberg"},{"first_name":"Karin","last_name":"Ljung","full_name":"Ljung, Karin"}],"status":"public"},{"article_processing_charge":"No","tmp":{"short":"CC BY-NC-SA (4.0)","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"},"doi":"10.1038/msb.2013.40","file_date_updated":"2020-07-14T12:46:36Z","has_accepted_license":"1","intvolume":"         9","date_published":"2013-09-10T00:00:00Z","volume":9,"day":"10","publication":"Molecular Systems Biology","title":"A map of cell type‐specific auxin responses","publist_id":"7303","citation":{"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>","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>.","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>","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.","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)."},"date_created":"2018-12-11T11:46:55Z","quality_controlled":"1","article_number":"688","oa":1,"author":[{"full_name":"Bargmann, Bastiaan","last_name":"Bargmann","first_name":"Bastiaan"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"first_name":"Gabriel","last_name":"Krouk","full_name":"Krouk, Gabriel"},{"last_name":"Nawy","full_name":"Nawy, Tal","first_name":"Tal"},{"first_name":"Idan","last_name":"Efroni","full_name":"Efroni, Idan"},{"last_name":"Shani","full_name":"Shani, Eilon","first_name":"Eilon"},{"full_name":"Choe, Goh","last_name":"Choe","first_name":"Goh"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Dominique","full_name":"Bergmann, Dominique","last_name":"Bergmann"},{"full_name":"Estelle, Mark","last_name":"Estelle","first_name":"Mark"},{"first_name":"Kenneth","full_name":"Birnbaum, Kenneth","last_name":"Birnbaum"}],"status":"public","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","abstract":[{"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.","lang":"eng"}],"scopus_import":1,"date_updated":"2021-01-12T08:01:17Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"year":"2013","month":"09","type":"journal_article","file":[{"creator":"system","file_id":"4644","relation":"main_file","file_name":"IST-2018-936-v1+1_2008_Barton_A_map.pdf","checksum":"9c4fbe793af4bb22b3fe50cc677a39bf","file_size":3257692,"date_created":"2018-12-12T10:07:46Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:36Z"}],"ddc":["581"],"oa_version":"Published Version","_id":"516","issue":"1","publication_status":"published","pubrep_id":"936","publisher":"Nature Publishing Group"},{"scopus_import":1,"date_published":"2013-07-01T00:00:00Z","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."}],"intvolume":"       154","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"volume":154,"date_updated":"2021-01-12T08:01:22Z","publication":"Immunology Letters","day":"01","author":[{"first_name":"Elke","last_name":"Fuertbauer","full_name":"Fuertbauer, Elke"},{"first_name":"Jan","last_name":"Zaujec","full_name":"Zaujec, Jan"},{"last_name":"Uhrin","full_name":"Uhrin, Pavel","first_name":"Pavel"},{"full_name":"Raab, Ingrid","last_name":"Raab","first_name":"Ingrid"},{"id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","first_name":"Michele","full_name":"Weber, Michele","last_name":"Weber"},{"full_name":"Schachner, Helga","last_name":"Schachner","first_name":"Helga"},{"last_name":"Bauer","full_name":"Bauer, Miroslav","first_name":"Miroslav"},{"first_name":"Gerhard","last_name":"Schütz","full_name":"Schütz, Gerhard"},{"first_name":"Bernd","last_name":"Binder","full_name":"Binder, Bernd"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"},{"first_name":"Dontscho","full_name":"Kerjaschki, Dontscho","last_name":"Kerjaschki"},{"first_name":"Hannes","last_name":"Stockinger","full_name":"Stockinger, Hannes"}],"status":"public","doi":"10.1016/j.imlet.2013.07.007","_id":"522","issue":"1-2","publication_status":"published","quality_controlled":"1","citation":{"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.","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.","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>","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>.","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>.","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>"},"date_created":"2018-12-11T11:46:57Z","oa_version":"None","type":"journal_article","publisher":"Elsevier","title":"Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells","department":[{"_id":"MiSi"}],"month":"07","year":"2013","publist_id":"7300","page":"31 - 41"},{"scopus_import":1,"date_published":"2013-12-16T00:00:00Z","intvolume":"        23","abstract":[{"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.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"day":"16","publication":"Current Biology","date_updated":"2021-01-12T08:01:24Z","volume":23,"status":"public","ec_funded":1,"author":[{"first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560"},{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène"},{"first_name":"Richard","full_name":"Smith, Richard","last_name":"Smith"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1016/j.cub.2013.10.038","publication_status":"published","quality_controlled":"1","_id":"527","issue":"24","oa_version":"None","type":"journal_article","date_created":"2018-12-11T11:46:58Z","citation":{"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>","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.","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>"},"publisher":"Cell Press","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"title":"Modeling framework for the establishment of the apical-basal embryonic axis in plants","page":"2513 - 2518","publist_id":"7292","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300"}],"month":"12","year":"2013"},{"doi":"10.1016/j.cub.2013.09.039","status":"public","ec_funded":1,"author":[{"first_name":"Hélène","full_name":"Robert, Hélène","last_name":"Robert"},{"last_name":"Grones","full_name":"Grones, Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"full_name":"Stepanova, Anna","last_name":"Stepanova","first_name":"Anna"},{"full_name":"Robles, Linda","last_name":"Robles","first_name":"Linda"},{"first_name":"Annemarie","last_name":"Lokerse","full_name":"Lokerse, Annemarie"},{"first_name":"Jose","last_name":"Alonso","full_name":"Alonso, Jose"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"day":"16","publication":"Current Biology","volume":23,"date_updated":"2021-01-12T08:01:25Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        23","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]."}],"scopus_import":1,"date_published":"2013-12-16T00:00:00Z","publist_id":"7291","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300"}],"page":"2506 - 2512","year":"2013","month":"12","department":[{"_id":"JiFr"}],"title":"Local auxin sources orient the apical basal axis in arabidopsis embryos","publisher":"Cell Press","oa_version":"None","type":"journal_article","citation":{"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>.","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>.","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>","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.","short":"H. Robert, P. Grones, A. Stepanova, L. Robles, A. Lokerse, J. Alonso, D. Weijers, J. Friml, Current Biology 23 (2013) 2506–2512.","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>"},"date_created":"2018-12-11T11:46:59Z","publication_status":"published","quality_controlled":"1","issue":"24","_id":"528"},{"department":[{"_id":"KrCh"}],"title":"TTP: Tool for Tumor Progression","publication_identifier":{"issn":["2664-1690"]},"page":"17","year":"2013","month":"01","file":[{"file_name":"IST-2013-104-v1+1_tumortool.pdf","file_id":"5542","creator":"system","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:46:44Z","checksum":"2cc8c6e157eca1271128db80bb3dec80","file_size":1471954,"date_created":"2018-12-12T11:54:20Z"}],"type":"technical_report","oa_version":"Published Version","ddc":["000"],"citation":{"mla":"Reiter, Johannes, et al. <i>TTP: Tool for Tumor Progression</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-104-v1-1\">10.15479/AT:IST-2013-104-v1-1</a>.","chicago":"Reiter, Johannes, Ivana Bozic, Krishnendu Chatterjee, and Martin Nowak. <i>TTP: Tool for Tumor Progression</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-104-v1-1\">https://doi.org/10.15479/AT:IST-2013-104-v1-1</a>.","apa":"Reiter, J., Bozic, I., Chatterjee, K., &#38; Nowak, M. (2013). <i>TTP: Tool for Tumor Progression</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-104-v1-1\">https://doi.org/10.15479/AT:IST-2013-104-v1-1</a>","ista":"Reiter J, Bozic I, Chatterjee K, Nowak M. 2013. TTP: Tool for Tumor Progression, IST Austria, 17p.","short":"J. Reiter, I. Bozic, K. Chatterjee, M. Nowak, TTP: Tool for Tumor Progression, IST Austria, 2013.","ieee":"J. Reiter, I. Bozic, K. Chatterjee, and M. Nowak, <i>TTP: Tool for Tumor Progression</i>. IST Austria, 2013.","ama":"Reiter J, Bozic I, Chatterjee K, Nowak M. <i>TTP: Tool for Tumor Progression</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-104-v1-1\">10.15479/AT:IST-2013-104-v1-1</a>"},"date_created":"2018-12-12T11:39:07Z","alternative_title":["IST Austria Technical Report"],"publication_status":"published","_id":"5399","publisher":"IST Austria","pubrep_id":"104","oa":1,"status":"public","author":[{"orcid":"0000-0002-0170-7353","last_name":"Reiter","full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"},{"full_name":"Bozic, Ivana","last_name":"Bozic","first_name":"Ivana"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"doi":"10.15479/AT:IST-2013-104-v1-1","file_date_updated":"2020-07-14T12:46:44Z","has_accepted_license":"1","related_material":{"record":[{"id":"2000","status":"public","relation":"later_version"}]},"abstract":[{"text":"In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics.","lang":"eng"}],"date_published":"2013-01-11T00:00:00Z","day":"11","date_updated":"2023-02-23T10:23:57Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}]},{"file_date_updated":"2020-07-14T12:46:44Z","doi":"10.15479/AT:IST-2013-109-v1-1","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"last_name":"Tracol","full_name":"Tracol, Mathieu","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","first_name":"Mathieu"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-02-23T10:36:45Z","day":"20","date_published":"2013-02-20T00:00:00Z","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages extends regular languages to infinite strings and provides a robust specification language to express all properties used in verification, and parity objectives are canonical forms to express ω-regular conditions. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satis- fied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, we establish decidability (with optimal complexity) of the qualitative analysis problems for POMDPs with all parity objectives under finite- memory strategies. We establish asymptotically optimal (exponential) memory bounds and EXPTIME- completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives."}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"1477"},{"id":"2295","relation":"later_version","status":"public"}]},"has_accepted_license":"1","month":"02","year":"2013","page":"41","publication_identifier":{"issn":["2664-1690"]},"title":"What is decidable about partially observable Markov decision processes with ω-regular objectives","department":[{"_id":"KrCh"}],"oa":1,"pubrep_id":"109","publisher":"IST Austria","_id":"5400","publication_status":"published","alternative_title":["IST Austria Technical Report"],"date_created":"2018-12-12T11:39:07Z","citation":{"ama":"Chatterjee K, Chmelik M, Tracol M. <i>What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-109-v1-1\">10.15479/AT:IST-2013-109-v1-1</a>","ista":"Chatterjee K, Chmelik M, Tracol M. 2013. What is decidable about partially observable Markov decision processes with ω-regular objectives, IST Austria, 41p.","short":"K. Chatterjee, M. Chmelik, M. Tracol, What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives, IST Austria, 2013.","ieee":"K. Chatterjee, M. Chmelik, and M. Tracol, <i>What is decidable about partially observable Markov decision processes with ω-regular objectives</i>. IST Austria, 2013.","mla":"Chatterjee, Krishnendu, et al. <i>What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-109-v1-1\">10.15479/AT:IST-2013-109-v1-1</a>.","apa":"Chatterjee, K., Chmelik, M., &#38; Tracol, M. (2013). <i>What is decidable about partially observable Markov decision processes with ω-regular objectives</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-109-v1-1\">https://doi.org/10.15479/AT:IST-2013-109-v1-1</a>","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. <i>What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-109-v1-1\">https://doi.org/10.15479/AT:IST-2013-109-v1-1</a>."},"oa_version":"Published Version","ddc":["000","005"],"file":[{"date_created":"2018-12-12T11:53:06Z","checksum":"cbba40210788a1b22c6cf06433b5ed6f","file_size":483407,"date_updated":"2020-07-14T12:46:44Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"system","file_id":"5467","file_name":"IST-2013-109-v1+1_What_is_Decidable_about_Partially_Observable_Markov_Decision_Processes_with_ω-Regular_Objectives.pdf"}],"type":"technical_report"},{"publication_status":"published","alternative_title":["IST Austria Technical Report"],"_id":"5402","ddc":["000","004"],"oa_version":"Published Version","type":"technical_report","file":[{"date_created":"2018-12-12T11:53:19Z","checksum":"ce580605ae9756a8c99d7b403ebb8eed","file_size":249790,"date_updated":"2020-07-14T12:46:45Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"5480","creator":"system","file_name":"IST-2013-123-v1+1_main-concur2013.pdf"}],"date_created":"2018-12-12T11:39:07Z","citation":{"ama":"Henzinger TA, Sezgin A. <i>How Free Is Your Linearizable Concurrent Data Structure?</i> IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">10.15479/AT:IST-2013-123-v1-1</a>","ieee":"T. A. Henzinger and A. Sezgin, <i>How free is your linearizable concurrent data structure?</i> IST Austria, 2013.","short":"T.A. Henzinger, A. Sezgin, How Free Is Your Linearizable Concurrent Data Structure?, IST Austria, 2013.","ista":"Henzinger TA, Sezgin A. 2013. How free is your linearizable concurrent data structure?, IST Austria, 16p.","mla":"Henzinger, Thomas A., and Ali Sezgin. <i>How Free Is Your Linearizable Concurrent Data Structure?</i> IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">10.15479/AT:IST-2013-123-v1-1</a>.","apa":"Henzinger, T. A., &#38; Sezgin, A. (2013). <i>How free is your linearizable concurrent data structure?</i> IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">https://doi.org/10.15479/AT:IST-2013-123-v1-1</a>","chicago":"Henzinger, Thomas A, and Ali Sezgin. <i>How Free Is Your Linearizable Concurrent Data Structure?</i> IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">https://doi.org/10.15479/AT:IST-2013-123-v1-1</a>."},"oa":1,"publisher":"IST Austria","pubrep_id":"123","department":[{"_id":"ToHe"}],"title":"How free is your linearizable concurrent data structure?","page":"16","month":"06","year":"2013","publication_identifier":{"issn":["2664-1690"]},"date_published":"2013-06-12T00:00:00Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Linearizability requires that the outcome of calls by competing threads to a concurrent data structure is the same as some sequential execution where each thread has exclusive access to the data structure. In an ordered data structure, such as a queue or a stack, linearizability is ensured by requiring threads commit in the order dictated by the sequential semantics of the data structure; e.g., in a concurrent queue implementation a dequeue can only remove the oldest element. \r\nIn this paper, we investigate the impact of this strict ordering, by comparing what linearizability allows to what existing implementations do. We first give an operational definition for linearizability which allows us to build the most general linearizable implementation as a transition system for any given sequential specification. We then use this operational definition to categorize linearizable implementations based on whether they are bound or free. In a bound implementation, whenever all threads observe the same logical state, the updates to the logical state and the temporal order of commits coincide. All existing queue implementations we know of are bound. We then proceed to present, to the best of our knowledge, the first ever free queue implementation. Our experiments show that free implementations have the potential for better performance by suffering less from contention."}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"12","date_updated":"2020-07-14T23:04:47Z","status":"public","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"last_name":"Sezgin","full_name":"Sezgin, Ali","first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:46:45Z","doi":"10.15479/AT:IST-2013-123-v1-1"},{"status":"public","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"}],"doi":"10.15479/AT:IST-2013-126-v1-1","file_date_updated":"2020-07-14T12:46:45Z","has_accepted_license":"1","related_material":{"record":[{"id":"524","relation":"later_version","status":"public"}]},"abstract":[{"text":"We consider concurrent games played by two-players on a finite state graph, where in every round the players simultaneously choose a move, and the current state along with the joint moves determine the successor state. We study the most fundamental objective for concurrent games, namely, mean-payoff or limit-average objective, where a reward is associated to every transition, and the goal of player 1 is to maximize the long-run average of the rewards, and the objective of player 2 is strictly the opposite (i.e., the games are zero-sum). The path constraint for player 1 could be qualitative, i.e., the mean-payoff is the maximal reward, or arbitrarily close to it; or quantitative, i.e., a given threshold between the minimal and maximal reward. We consider the computation of the almost-sure (resp. positive) winning sets, where player 1 can ensure that the path constraint is satisfied with probability 1 (resp. positive probability). Almost-sure winning with qualitative constraint exactly corresponds to the question whether there exists a strategy to ensure that the payoff is the maximal reward of the game. Our main results for qualitative path constraints are as follows: (1) we establish qualitative determinacy results that show for every state either player 1 has a strategy to ensure almost-sure (resp. positive) winning against all player-2 strategies or player 2 has a spoiling strategy to falsify almost-sure (resp. positive) winning against all player-1 strategies; (2) we present optimal strategy complexity results that precisely characterize the classes of strategies required for almost-sure and positive winning for both players; and (3) we present quadratic time algorithms to compute the almost-sure and the positive winning sets, matching the best known bound of the algorithms for much simpler problems (such as reachability objectives). For quantitative constraints we show that a polynomial time solution for the almost-sure or the positive winning set would imply a solution to a long-standing open problem (of solving the value problem of mean-payoff games) that is not known to be in polynomial time.","lang":"eng"}],"date_published":"2013-07-03T00:00:00Z","day":"03","date_updated":"2023-02-23T12:22:53Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"title":"Qualitative analysis of concurrent mean-payoff games","publication_identifier":{"issn":["2664-1690"]},"page":"33","year":"2013","month":"07","oa_version":"Published Version","ddc":["000","005"],"file":[{"file_id":"5510","creator":"system","relation":"main_file","file_name":"IST-2013-126-v1+1_soda_full.pdf","checksum":"063868c665beec37bf28160e2a695746","file_size":434523,"date_created":"2018-12-12T11:53:49Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:46:45Z"}],"type":"technical_report","date_created":"2018-12-12T11:39:08Z","citation":{"ama":"Chatterjee K, Ibsen-Jensen R. <i>Qualitative Analysis of Concurrent Mean-Payoff Games</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-126-v1-1\">10.15479/AT:IST-2013-126-v1-1</a>","ista":"Chatterjee K, Ibsen-Jensen R. 2013. Qualitative analysis of concurrent mean-payoff games, IST Austria, 33p.","ieee":"K. Chatterjee and R. Ibsen-Jensen, <i>Qualitative analysis of concurrent mean-payoff games</i>. IST Austria, 2013.","short":"K. Chatterjee, R. Ibsen-Jensen, Qualitative Analysis of Concurrent Mean-Payoff Games, IST Austria, 2013.","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. <i>Qualitative Analysis of Concurrent Mean-Payoff Games</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-126-v1-1\">10.15479/AT:IST-2013-126-v1-1</a>.","apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2013). <i>Qualitative analysis of concurrent mean-payoff games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-126-v1-1\">https://doi.org/10.15479/AT:IST-2013-126-v1-1</a>","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. <i>Qualitative Analysis of Concurrent Mean-Payoff Games</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-126-v1-1\">https://doi.org/10.15479/AT:IST-2013-126-v1-1</a>."},"publication_status":"published","alternative_title":["IST Austria Technical Report"],"_id":"5403","publisher":"IST Austria","pubrep_id":"126","oa":1},{"oa":1,"pubrep_id":"127","publisher":"IST Austria","_id":"5404","alternative_title":["IST Austria Technical Report"],"publication_status":"published","citation":{"apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2013). <i>The complexity of ergodic games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-127-v1-1\">https://doi.org/10.15479/AT:IST-2013-127-v1-1</a>","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. <i>The Complexity of Ergodic Games</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-127-v1-1\">https://doi.org/10.15479/AT:IST-2013-127-v1-1</a>.","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. <i>The Complexity of Ergodic Games</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-127-v1-1\">10.15479/AT:IST-2013-127-v1-1</a>.","ama":"Chatterjee K, Ibsen-Jensen R. <i>The Complexity of Ergodic Games</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-127-v1-1\">10.15479/AT:IST-2013-127-v1-1</a>","ista":"Chatterjee K, Ibsen-Jensen R. 2013. The complexity of ergodic games, IST Austria, 29p.","ieee":"K. Chatterjee and R. Ibsen-Jensen, <i>The complexity of ergodic games</i>. IST Austria, 2013.","short":"K. Chatterjee, R. Ibsen-Jensen, The Complexity of Ergodic Games, IST Austria, 2013."},"date_created":"2018-12-12T11:39:08Z","ddc":["000","005"],"type":"technical_report","oa_version":"Published Version","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:45Z","checksum":"79ee5e677a82611ce06e0360c69d494a","file_size":517275,"date_created":"2018-12-12T11:53:35Z","file_name":"IST-2013-127-v1+1_ergodic.pdf","creator":"system","file_id":"5496","relation":"main_file"}],"year":"2013","month":"07","page":"29","publication_identifier":{"issn":["2664-1690"]},"title":"The complexity of ergodic games","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-02-23T10:30:55Z","day":"03","date_published":"2013-07-03T00:00:00Z","abstract":[{"text":"We study finite-state two-player (zero-sum) concurrent mean-payoff games played on a graph. We focus on the important sub-class of ergodic games where all states are visited infinitely often with probability 1. The algorithmic study of ergodic games was initiated in a seminal work of Hoffman and Karp in 1966, but all basic complexity questions have remained unresolved. Our main results for ergodic games are as follows: We establish (1) an optimal exponential bound on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy); (2) the approximation problem lie in FNP; (3) the approximation problem is at least as hard as the decision problem for simple stochastic games (for which NP and coNP is the long-standing best known bound). We show that the exact value can be expressed in the existential theory of the reals, and also establish square-root sum hardness for a related class of games.","lang":"eng"}],"has_accepted_license":"1","related_material":{"record":[{"relation":"later_version","status":"public","id":"2162"}]},"file_date_updated":"2020-07-14T12:46:45Z","doi":"10.15479/AT:IST-2013-127-v1-1","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389"}],"status":"public"},{"file_date_updated":"2020-07-14T12:46:45Z","doi":"10.15479/AT:IST-2013-128-v1-1","status":"public","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"},{"full_name":"Gimbert, Hugo","last_name":"Gimbert","first_name":"Hugo"},{"full_name":"Oualhadj, Youssouf","last_name":"Oualhadj","first_name":"Youssouf"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"08","date_updated":"2023-02-23T10:33:08Z","date_published":"2013-07-08T00:00:00Z","has_accepted_license":"1","related_material":{"record":[{"id":"2212","status":"public","relation":"later_version"}]},"abstract":[{"text":"The theory of graph games is the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic processes, we use 2-1/2-player games where some transitions of the game graph are controlled by two adversarial players, the System and the Environment, and the other transitions are determined probabilistically. We consider 2-1/2-player games where the objective of the System is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a mean-payoff condition). We establish that the problem of deciding whether the System can ensure that the probability to satisfy the mean-payoff parity objective is at least a given threshold is in NP ∩ coNP, matching the best known bound in the special case of 2-player games (where all transitions are deterministic) with only parity objectives, or with only mean-payoff objectives. We present an algorithm running\r\nin time O(d · n^{2d}·MeanGame) to compute the set of almost-sure winning states from which the objective\r\ncan be ensured with probability 1, where n is the number of states of the game, d the number of priorities\r\nof the parity objective, and MeanGame is the complexity to compute the set of almost-sure winning states\r\nin 2-1/2-player mean-payoff games. Our results are useful in the synthesis of stochastic reactive systems\r\nwith both functional requirement (given as a qualitative objective) and performance requirement (given\r\nas a quantitative objective).","lang":"eng"}],"page":"22","month":"07","year":"2013","publication_identifier":{"issn":["2664-1690"]},"department":[{"_id":"KrCh"}],"title":"Perfect-information stochastic mean-payoff parity games","oa":1,"publisher":"IST Austria","pubrep_id":"128","publication_status":"published","alternative_title":["IST Austria Technical Report"],"_id":"5405","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:46:45Z","file_size":387467,"checksum":"ede787a10e74e4f7db302fab8f12f3ca","date_created":"2018-12-12T11:53:54Z","file_name":"IST-2013-128-v1+1_full_stoch_mpp.pdf","file_id":"5516","creator":"system","relation":"main_file"}],"type":"technical_report","oa_version":"Published Version","ddc":["000","005","510"],"citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Perfect-Information Stochastic Mean-Payoff Parity Games</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-128-v1-1\">10.15479/AT:IST-2013-128-v1-1</a>.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Youssouf Oualhadj. <i>Perfect-Information Stochastic Mean-Payoff Parity Games</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-128-v1-1\">https://doi.org/10.15479/AT:IST-2013-128-v1-1</a>.","apa":"Chatterjee, K., Doyen, L., Gimbert, H., &#38; Oualhadj, Y. (2013). <i>Perfect-information stochastic mean-payoff parity games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-128-v1-1\">https://doi.org/10.15479/AT:IST-2013-128-v1-1</a>","ista":"Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. 2013. Perfect-information stochastic mean-payoff parity games, IST Austria, 22p.","ieee":"K. Chatterjee, L. Doyen, H. Gimbert, and Y. Oualhadj, <i>Perfect-information stochastic mean-payoff parity games</i>. IST Austria, 2013.","short":"K. Chatterjee, L. Doyen, H. Gimbert, Y. Oualhadj, Perfect-Information Stochastic Mean-Payoff Parity Games, IST Austria, 2013.","ama":"Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. <i>Perfect-Information Stochastic Mean-Payoff Parity Games</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-128-v1-1\">10.15479/AT:IST-2013-128-v1-1</a>"},"date_created":"2018-12-12T11:39:09Z"},{"date_updated":"2023-02-21T17:01:26Z","day":"08","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We consider the distributed synthesis problem fortemporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTLand our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3)Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition.","lang":"eng"}],"has_accepted_license":"1","related_material":{"record":[{"id":"1376","relation":"later_version","status":"public"}]},"date_published":"2013-07-08T00:00:00Z","doi":"10.15479/AT:IST-2013-130-v1-1","file_date_updated":"2020-07-14T12:46:45Z","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"last_name":"Otop","full_name":"Otop, Jan","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"}],"status":"public","pubrep_id":"130","publisher":"IST Austria","oa":1,"citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis. <i>Distributed Synthesis for LTL Fragments</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-130-v1-1\">https://doi.org/10.15479/AT:IST-2013-130-v1-1</a>.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Pavlogiannis, A. (2013). <i>Distributed synthesis for LTL Fragments</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-130-v1-1\">https://doi.org/10.15479/AT:IST-2013-130-v1-1</a>","mla":"Chatterjee, Krishnendu, et al. <i>Distributed Synthesis for LTL Fragments</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-130-v1-1\">10.15479/AT:IST-2013-130-v1-1</a>.","ista":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis for LTL Fragments, IST Austria, 11p.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, Distributed Synthesis for LTL Fragments, IST Austria, 2013.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, <i>Distributed synthesis for LTL Fragments</i>. IST Austria, 2013.","ama":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. <i>Distributed Synthesis for LTL Fragments</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-130-v1-1\">10.15479/AT:IST-2013-130-v1-1</a>"},"date_created":"2018-12-12T11:39:09Z","file":[{"relation":"main_file","file_id":"5540","creator":"system","file_name":"IST-2013-130-v1+1_Distributed_Synthesis.pdf","date_created":"2018-12-12T11:54:18Z","file_size":467895,"checksum":"855513ebaf6f72228800c5fdb522f93c","date_updated":"2020-07-14T12:46:45Z","access_level":"open_access","content_type":"application/pdf"}],"oa_version":"Published Version","type":"technical_report","ddc":["005"],"_id":"5406","publication_status":"published","alternative_title":["IST Austria Technical Report"],"publication_identifier":{"issn":["2664-1690"]},"month":"07","year":"2013","page":"11","title":"Distributed synthesis for LTL Fragments","department":[{"_id":"KrCh"},{"_id":"ToHe"}]}]