[{"month":"11","issue":"11-12","language":[{"iso":"eng"}],"volume":91,"quality_controlled":"1","oa_version":"Submitted Version","author":[{"full_name":"Schachtner, Hannah","last_name":"Schachtner","first_name":"Hannah"},{"full_name":"Li, Ang","first_name":"Ang","last_name":"Li"},{"full_name":"Stevenson, David","first_name":"David","last_name":"Stevenson"},{"first_name":"Simon","last_name":"Calaminus","full_name":"Calaminus, Simon"},{"first_name":"Steven","last_name":"Thomas","full_name":"Thomas, Steven"},{"full_name":"Watson, Steve","first_name":"Steve","last_name":"Watson"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K"},{"first_name":"Roland","last_name":"Wedlich Söldner","full_name":"Wedlich Söldner, Roland"},{"last_name":"Strathdee","first_name":"Douglas","full_name":"Strathdee, Douglas"},{"full_name":"Machesky, Laura","first_name":"Laura","last_name":"Machesky"}],"date_created":"2018-12-11T12:01:44Z","_id":"3158","type":"journal_article","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930012/","open_access":"1"}],"status":"public","abstract":[{"text":"We describe here the development and characterization of a conditionally inducible mouse model expressing Lifeact-GFP, a peptide that reports the dynamics of filamentous actin. We have used this model to study platelets, megakaryocytes and melanoblasts and we provide evidence that Lifeact-GFP is a useful reporter in these cell types ex vivo. In the case of platelets and megakaryocytes, these cells are not transfectable by traditional methods, so conditional activation of Lifeact allows the study of actin dynamics in these cells live. We studied melanoblasts in native skin explants from embryos, allowing the visualization of live actin dynamics during cytokinesis and migration. Our study revealed that melanoblasts lacking the small GTPase Rac1 show a delay in the formation of new pseudopodia following cytokinesis that accounts for the previously reported cytokinesis delay in these cells. Thus, through use of this mouse model, we were able to gain insights into the actin dynamics of cells that could only previously be studied using fixed specimens or following isolation from their native tissue environment.","lang":"eng"}],"publication_status":"published","date_published":"2012-11-01T00:00:00Z","publisher":"Elsevier","pmid":1,"title":"Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo","date_updated":"2021-01-12T07:41:27Z","department":[{"_id":"MiSi"}],"citation":{"short":"H. Schachtner, A. Li, D. Stevenson, S. Calaminus, S. Thomas, S. Watson, M.K. Sixt, R. Wedlich Söldner, D. Strathdee, L. Machesky, European Journal of Cell Biology 91 (2012) 923–929.","mla":"Schachtner, Hannah, et al. “Tissue Inducible Lifeact Expression Allows Visualization of Actin Dynamics in Vivo and Ex Vivo.” <i>European Journal of Cell Biology</i>, vol. 91, no. 11–12, Elsevier, 2012, pp. 923–29, doi:<a href=\"https://doi.org/10.1016/j.ejcb.2012.04.002\">10.1016/j.ejcb.2012.04.002</a>.","ieee":"H. Schachtner <i>et al.</i>, “Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo,” <i>European Journal of Cell Biology</i>, vol. 91, no. 11–12. Elsevier, pp. 923–929, 2012.","apa":"Schachtner, H., Li, A., Stevenson, D., Calaminus, S., Thomas, S., Watson, S., … Machesky, L. (2012). Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. <i>European Journal of Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejcb.2012.04.002\">https://doi.org/10.1016/j.ejcb.2012.04.002</a>","ista":"Schachtner H, Li A, Stevenson D, Calaminus S, Thomas S, Watson S, Sixt MK, Wedlich Söldner R, Strathdee D, Machesky L. 2012. Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. European Journal of Cell Biology. 91(11–12), 923–929.","ama":"Schachtner H, Li A, Stevenson D, et al. Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. <i>European Journal of Cell Biology</i>. 2012;91(11-12):923-929. doi:<a href=\"https://doi.org/10.1016/j.ejcb.2012.04.002\">10.1016/j.ejcb.2012.04.002</a>","chicago":"Schachtner, Hannah, Ang Li, David Stevenson, Simon Calaminus, Steven Thomas, Steve Watson, Michael K Sixt, Roland Wedlich Söldner, Douglas Strathdee, and Laura Machesky. “Tissue Inducible Lifeact Expression Allows Visualization of Actin Dynamics in Vivo and Ex Vivo.” <i>European Journal of Cell Biology</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.ejcb.2012.04.002\">https://doi.org/10.1016/j.ejcb.2012.04.002</a>."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["22658956"]},"scopus_import":1,"intvolume":"        91","publist_id":"3534","publication":"European Journal of Cell Biology","oa":1,"page":"923 - 929","doi":"10.1016/j.ejcb.2012.04.002","day":"01","year":"2012"},{"citation":{"short":"Y. Mileyko, H. Edelsbrunner, C. Price, J. Weitz, PLoS One 7 (2012).","mla":"Mileyko, Yuriy, et al. “Hierarchical Ordering of Reticular Networks.” <i>PLoS One</i>, vol. 7, no. 6, e36715, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pone.0036715\">10.1371/journal.pone.0036715</a>.","apa":"Mileyko, Y., Edelsbrunner, H., Price, C., &#38; Weitz, J. (2012). Hierarchical ordering of reticular networks. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0036715\">https://doi.org/10.1371/journal.pone.0036715</a>","chicago":"Mileyko, Yuriy, Herbert Edelsbrunner, Charles Price, and Joshua Weitz. “Hierarchical Ordering of Reticular Networks.” <i>PLoS One</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pone.0036715\">https://doi.org/10.1371/journal.pone.0036715</a>.","ista":"Mileyko Y, Edelsbrunner H, Price C, Weitz J. 2012. Hierarchical ordering of reticular networks. PLoS One. 7(6), e36715.","ama":"Mileyko Y, Edelsbrunner H, Price C, Weitz J. Hierarchical ordering of reticular networks. <i>PLoS One</i>. 2012;7(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0036715\">10.1371/journal.pone.0036715</a>","ieee":"Y. Mileyko, H. Edelsbrunner, C. Price, and J. Weitz, “Hierarchical ordering of reticular networks,” <i>PLoS One</i>, vol. 7, no. 6. Public Library of Science, 2012."},"department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T07:41:28Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["510"],"publication_status":"published","abstract":[{"text":"The structure of hierarchical networks in biological and physical systems has long been characterized using the Horton-Strahler ordering scheme. The scheme assigns an integer order to each edge in the network based on the topology of branching such that the order increases from distal parts of the network (e.g., mountain streams or capillaries) to the &quot;root&quot; of the network (e.g., the river outlet or the aorta). However, Horton-Strahler ordering cannot be applied to networks with loops because they they create a contradiction in the edge ordering in terms of which edge precedes another in the hierarchy. Here, we present a generalization of the Horton-Strahler order to weighted planar reticular networks, where weights are assumed to correlate with the importance of network edges, e.g., weights estimated from edge widths may correlate to flow capacity. Our method assigns hierarchical levels not only to edges of the network, but also to its loops, and classifies the edges into reticular edges, which are responsible for loop formation, and tree edges. In addition, we perform a detailed and rigorous theoretical analysis of the sensitivity of the hierarchical levels to weight perturbations. In doing so, we show that the ordering of the reticular edges is more robust to noise in weight estimation than is the ordering of the tree edges. We discuss applications of this generalized Horton-Strahler ordering to the study of leaf venation and other biological networks.","lang":"eng"}],"title":"Hierarchical ordering of reticular networks","file_date_updated":"2020-07-14T12:46:01Z","date_published":"2012-06-06T00:00:00Z","publisher":"Public Library of Science","oa":1,"doi":"10.1371/journal.pone.0036715","day":"06","year":"2012","acknowledgement":"his work was supported by the National Science Foundation Plant Genome Research Program (grant 0820624 to H.E. and J.S.W.), the Defense Advanced Projects Research Agency (grant HR0011-09-1-0055 to H.E. and J.S.W.), and the European Science Foundation (under the Research Networking Programme on “Applied and Computational Algebraic Topology” run by H.E.). Joshua S. Weitz, Ph.D., holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund.\r\n\r\n\r\n\r\nDuring preparation of this manuscript the authors became aware of a related work by Katifori and Magnasco (arXiv:1110.1412v1), concurrently submitted and accepted for publication in PLoS ONE.","scopus_import":1,"publication":"PLoS One","publist_id":"3530","intvolume":"         7","oa_version":"Published Version","quality_controlled":"1","author":[{"full_name":"Mileyko, Yuriy","last_name":"Mileyko","first_name":"Yuriy"},{"first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"full_name":"Price, Charles","first_name":"Charles","last_name":"Price"},{"full_name":"Weitz, Joshua","last_name":"Weitz","first_name":"Joshua"}],"file":[{"relation":"main_file","file_size":541583,"access_level":"open_access","creator":"kschuh","file_id":"5922","checksum":"515a98ad72e470752f03f13663dcaff8","date_updated":"2020-07-14T12:46:01Z","date_created":"2019-02-05T12:38:43Z","content_type":"application/pdf","file_name":"2012_PLoS_Mileyko.PDF"}],"article_number":"e36715","issue":"6","month":"06","has_accepted_license":"1","volume":7,"language":[{"iso":"eng"}],"type":"journal_article","_id":"3159","date_created":"2018-12-11T12:01:44Z","status":"public","pubrep_id":"385"},{"publication":"Cell Cycle","intvolume":"        11","publist_id":"3531","scopus_import":1,"page":"2055 - 2058","year":"2012","day":"01","status":"public","doi":"10.4161/cc.20118","type":"journal_article","_id":"3160","date_created":"2018-12-11T12:01:44Z","title":"Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo","volume":11,"date_published":"2012-06-01T00:00:00Z","language":[{"iso":"eng"}],"publisher":"Taylor and Francis","issue":"11","abstract":[{"text":"There is a long-running controversy about how early cell fate decisions are made in the developing mammalian embryo. 1,2 In particular, it is controversial when the first events that can predict the establishment of the pluripotent and extra-embryonic lineages in the blastocyst of the pre-implantation embryo occur. It has long been proposed that the position and polarity of cells at the 16- to 32-cell stage embryo influence their decision to either give rise to the pluripotent cell lineage that eventually contributes to the inner cell mass (ICM), comprising the primitive endoderm (PE) and the epiblast (EPI), or the extra-embryonic trophectoderm (TE) surrounding the blastocoel. The positioning of cells in the embryo at this developmental stage could largely be the result of random events, making this a stochastic model of cell lineage allocation. Contrary to such a stochastic model, some studies have detected putative differences in the lineage potential of individual blastomeres before compaction, indicating that the first cell fate decisions may occur as early as at the 4-cell stage. Using a non-invasive, quantitative in vivo imaging assay to study the kinetic behavior of Oct4 (also known as POU5F1), a key transcription factor (TF) controlling pre-implantation development in the mouse embryo, 3-5 a recent study identifies Oct4 kinetics as a predictive measure of cell lineage patterning in the early mouse embryo. 6 Here, we discuss the implications of such molecular heterogeneities in early development and offer potential avenues toward a mechanistic understanding of these observations, contributing to the resolution of the controversy of developmental cell lineage allocation.","lang":"eng"}],"publication_status":"published","month":"06","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Pantazis, Periklis","first_name":"Periklis","last_name":"Pantazis"},{"last_name":"Bollenbach","first_name":"Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias"}],"citation":{"ieee":"P. Pantazis and M. T. Bollenbach, “Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo,” <i>Cell Cycle</i>, vol. 11, no. 11. Taylor and Francis, pp. 2055–2058, 2012.","apa":"Pantazis, P., &#38; Bollenbach, M. T. (2012). Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. <i>Cell Cycle</i>. Taylor and Francis. <a href=\"https://doi.org/10.4161/cc.20118\">https://doi.org/10.4161/cc.20118</a>","chicago":"Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics and the Emerging Asymmetry in the Early Mammalian Embryo.” <i>Cell Cycle</i>. Taylor and Francis, 2012. <a href=\"https://doi.org/10.4161/cc.20118\">https://doi.org/10.4161/cc.20118</a>.","ama":"Pantazis P, Bollenbach MT. Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. <i>Cell Cycle</i>. 2012;11(11):2055-2058. doi:<a href=\"https://doi.org/10.4161/cc.20118\">10.4161/cc.20118</a>","ista":"Pantazis P, Bollenbach MT. 2012. Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. 11(11), 2055–2058.","mla":"Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics and the Emerging Asymmetry in the Early Mammalian Embryo.” <i>Cell Cycle</i>, vol. 11, no. 11, Taylor and Francis, 2012, pp. 2055–58, doi:<a href=\"https://doi.org/10.4161/cc.20118\">10.4161/cc.20118</a>.","short":"P. Pantazis, M.T. Bollenbach, Cell Cycle 11 (2012) 2055–2058."},"oa_version":"None","date_updated":"2021-01-12T07:41:28Z","quality_controlled":"1","department":[{"_id":"ToBo"}]},{"oa":1,"year":"2012","doi":"10.1371/journal.pone.0036044","day":"14","acknowledgement":"Supported by National Institutes of Health grants GM071338 (ML) and AI059355 (BM).\r\nWe acknowledge the expertise of Dr. Martina Ralle in Department of Biochemistry and Molecular Biology at OHSU for measurements of potassium using inductively coupled plasma mass spectrometry.","scopus_import":1,"publication":"PLoS One","publist_id":"3526","intvolume":"         7","citation":{"mla":"Vyleta, Meghan, et al. “Suppression of Ribosomal Function Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.” <i>PLoS One</i>, vol. 7, no. 5, e36044, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pone.0036044\">10.1371/journal.pone.0036044</a>.","short":"M. Vyleta, J. Wong, B. Magun, PLoS One 7 (2012).","ista":"Vyleta M, Wong J, Magun B. 2012. Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. 7(5), e36044.","chicago":"Vyleta, Meghan, John Wong, and Bruce Magun. “Suppression of Ribosomal Function Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.” <i>PLoS One</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pone.0036044\">https://doi.org/10.1371/journal.pone.0036044</a>.","ama":"Vyleta M, Wong J, Magun B. Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. <i>PLoS One</i>. 2012;7(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0036044\">10.1371/journal.pone.0036044</a>","apa":"Vyleta, M., Wong, J., &#38; Magun, B. (2012). Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0036044\">https://doi.org/10.1371/journal.pone.0036044</a>","ieee":"M. Vyleta, J. Wong, and B. Magun, “Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome,” <i>PLoS One</i>, vol. 7, no. 5. Public Library of Science, 2012."},"department":[{"_id":"SyCr"}],"date_updated":"2021-01-12T07:41:29Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["610"],"publication_status":"published","abstract":[{"lang":"eng","text":"Some inflammatory stimuli trigger activation of the NLRP3 inflammasome by inducing efflux of cellular potassium. Loss of cellular potassium is known to potently suppress protein synthesis, leading us to test whether the inhibition of protein synthesis itself serves as an activating signal for the NLRP3 inflammasome. Murine bone marrow-derived macrophages, either primed by LPS or unprimed, were exposed to a panel of inhibitors of ribosomal function: ricin, cycloheximide, puromycin, pactamycin, and anisomycin. Macrophages were also exposed to nigericin, ATP, monosodium urate (MSU), and poly I:C. Synthesis of pro-IL-ß and release of IL-1ß from cells in response to these agents was detected by immunoblotting and ELISA. Release of intracellular potassium was measured by mass spectrometry. Inhibition of translation by each of the tested translation inhibitors led to processing of IL-1ß, which was released from cells. Processing and release of IL-1ß was reduced or absent from cells deficient in NLRP3, ASC, or caspase-1, demonstrating the role of the NLRP3 inflammasome. Despite the inability of these inhibitors to trigger efflux of intracellular potassium, the addition of high extracellular potassium suppressed activation of the NLRP3 inflammasome. MSU and double-stranded RNA, which are known to activate the NLRP3 inflammasome, also substantially inhibited protein translation, supporting a close association between inhibition of translation and inflammasome activation. These data demonstrate that translational inhibition itself constitutes a heretofore-unrecognized mechanism underlying IL-1ß dependent inflammatory signaling and that other physical, chemical, or pathogen-associated agents that impair translation may lead to IL-1ß-dependent inflammation through activation of the NLRP3 inflammasome. For agents that inhibit translation through decreased cellular potassium, the application of high extracellular potassium restores protein translation and suppresses activation of the NLRP inflammasome. For agents that inhibit translation through mechanisms that do not involve loss of potassium, high extracellular potassium suppresses IL-1ß processing through a mechanism that remains undefined."}],"title":"Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome","date_published":"2012-05-14T00:00:00Z","file_date_updated":"2020-07-14T12:46:01Z","publisher":"Public Library of Science","_id":"3161","type":"journal_article","date_created":"2018-12-11T12:01:45Z","status":"public","pubrep_id":"97","oa_version":"Published Version","quality_controlled":"1","author":[{"id":"418901AA-F248-11E8-B48F-1D18A9856A87","full_name":"Vyleta, Meghan","last_name":"Vyleta","first_name":"Meghan"},{"first_name":"John","last_name":"Wong","full_name":"Wong, John"},{"last_name":"Magun","first_name":"Bruce","full_name":"Magun, Bruce"}],"file":[{"creator":"system","checksum":"30cef37e27eaa467f6571b3640282010","file_id":"5082","file_size":2984012,"access_level":"open_access","relation":"main_file","file_name":"IST-2012-97-v1+1_journal.pone.0036044.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:01Z","date_created":"2018-12-12T10:14:30Z"}],"article_number":"e36044","issue":"5","month":"05","has_accepted_license":"1","volume":7,"language":[{"iso":"eng"}]},{"publist_id":"3525","intvolume":"      7186","scopus_import":1,"year":"2012","day":"01","page":"147 - 160","doi":"10.1007/978-3-642-29860-8_12","oa":1,"publisher":"Springer","file_date_updated":"2020-07-14T12:46:01Z","date_published":"2012-01-01T00:00:00Z","title":"Parametric identification of temporal properties","publication_status":"published","abstract":[{"text":"Given a dense-time real-valued signal and a parameterized temporal logic formula with both magnitude and timing parameters, we compute the subset of the parameter space that renders the formula satisfied by the trace. We provide two preliminary implementations, one which follows the exact semantics and attempts to compute the validity domain by quantifier elimination in linear arithmetics and one which conducts adaptive search in the parameter space.","lang":"eng"}],"ddc":["000"],"alternative_title":["LNCS"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T07:41:29Z","citation":{"apa":"Asarin, E., Donzé, A., Maler, O., &#38; Nickovic, D. (2012). Parametric identification of temporal properties (Vol. 7186, pp. 147–160). Presented at the RV: Runtime Verification, San Francisco, CA, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-642-29860-8_12\">https://doi.org/10.1007/978-3-642-29860-8_12</a>","ista":"Asarin E, Donzé A, Maler O, Nickovic D. 2012. Parametric identification of temporal properties. RV: Runtime Verification, LNCS, vol. 7186, 147–160.","chicago":"Asarin, Eugene, Alexandre Donzé, Oded Maler, and Dejan Nickovic. “Parametric Identification of Temporal Properties,” 7186:147–60. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-29860-8_12\">https://doi.org/10.1007/978-3-642-29860-8_12</a>.","ama":"Asarin E, Donzé A, Maler O, Nickovic D. Parametric identification of temporal properties. In: Vol 7186. Springer; 2012:147-160. doi:<a href=\"https://doi.org/10.1007/978-3-642-29860-8_12\">10.1007/978-3-642-29860-8_12</a>","ieee":"E. Asarin, A. Donzé, O. Maler, and D. Nickovic, “Parametric identification of temporal properties,” presented at the RV: Runtime Verification, San Francisco, CA, United States, 2012, vol. 7186, pp. 147–160.","short":"E. Asarin, A. Donzé, O. Maler, D. Nickovic, in:, Springer, 2012, pp. 147–160.","mla":"Asarin, Eugene, et al. <i>Parametric Identification of Temporal Properties</i>. Vol. 7186, Springer, 2012, pp. 147–60, doi:<a href=\"https://doi.org/10.1007/978-3-642-29860-8_12\">10.1007/978-3-642-29860-8_12</a>."},"conference":{"name":"RV: Runtime Verification","location":"San Francisco, CA, United States","start_date":"2011-09-27","end_date":"2011-09-30"},"status":"public","date_created":"2018-12-11T12:01:45Z","_id":"3162","type":"conference","language":[{"iso":"eng"}],"volume":7186,"article_processing_charge":"No","has_accepted_license":"1","month":"01","file":[{"file_name":"2012_RV_Asarin.pdf","content_type":"application/pdf","date_created":"2020-05-15T12:50:15Z","date_updated":"2020-07-14T12:46:01Z","file_id":"7862","checksum":"ba4a75287008fc64b8fbf78a7476ec32","creator":"dernst","access_level":"open_access","file_size":374726,"relation":"main_file"}],"author":[{"last_name":"Asarin","first_name":"Eugene","full_name":"Asarin, Eugene"},{"full_name":"Donzé, Alexandre","first_name":"Alexandre","last_name":"Donzé"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","oa_version":"Submitted Version"},{"type":"journal_article","_id":"3164","date_created":"2018-12-11T12:01:46Z","year":"2012","status":"public","day":"01","page":"257 - 258","doi":"10.1007/s11263-012-0530-y","scopus_import":1,"publication":"International Journal of Computer Vision","intvolume":"        99","publist_id":"3521","oa_version":"None","citation":{"short":"M. Blaschko, C. Lampert, International Journal of Computer Vision 99 (2012) 257–258.","mla":"Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue on Structured Prediction and Inference.” <i>International Journal of Computer Vision</i>, vol. 99, no. 3, Springer, 2012, pp. 257–58, doi:<a href=\"https://doi.org/10.1007/s11263-012-0530-y\">10.1007/s11263-012-0530-y</a>.","apa":"Blaschko, M., &#38; Lampert, C. (2012). Guest editorial: Special issue on structured prediction and inference. <i>International Journal of Computer Vision</i>. Springer. <a href=\"https://doi.org/10.1007/s11263-012-0530-y\">https://doi.org/10.1007/s11263-012-0530-y</a>","chicago":"Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue on Structured Prediction and Inference.” <i>International Journal of Computer Vision</i>. Springer, 2012. <a href=\"https://doi.org/10.1007/s11263-012-0530-y\">https://doi.org/10.1007/s11263-012-0530-y</a>.","ista":"Blaschko M, Lampert C. 2012. Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. 99(3), 257–258.","ama":"Blaschko M, Lampert C. Guest editorial: Special issue on structured prediction and inference. <i>International Journal of Computer Vision</i>. 2012;99(3):257-258. doi:<a href=\"https://doi.org/10.1007/s11263-012-0530-y\">10.1007/s11263-012-0530-y</a>","ieee":"M. Blaschko and C. Lampert, “Guest editorial: Special issue on structured prediction and inference,” <i>International Journal of Computer Vision</i>, vol. 99, no. 3. Springer, pp. 257–258, 2012."},"date_updated":"2021-01-12T07:41:30Z","quality_controlled":"1","department":[{"_id":"ChLa"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Blaschko","first_name":"Matthew","full_name":"Blaschko, Matthew"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"issue":"3","abstract":[{"lang":"eng","text":"Overview of the Special Issue on structured prediction and inference."}],"publication_status":"published","month":"09","volume":99,"title":"Guest editorial: Special issue on structured prediction and inference","language":[{"iso":"eng"}],"publisher":"Springer","date_published":"2012-09-01T00:00:00Z"},{"pubrep_id":"15","ec_funded":1,"conference":{"name":"SODA: Symposium on Discrete Algorithms","location":"Kyoto, Japan","end_date":"2012-01-19","start_date":"2012-01-17"},"_id":"3165","type":"conference","date_created":"2018-12-11T12:01:46Z","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1109.5018"}],"month":"01","article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"None","quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"related_material":{"record":[{"id":"5379","relation":"earlier_version","status":"public"},{"relation":"later_version","id":"2141","status":"public"}]},"publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","publist_id":"3519","arxiv":1,"oa":1,"page":"1386 - 1399","doi":"10.1137/1.9781611973099.109","year":"2012","day":"01","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification, Vienna Science and Technology Fund (WWTF) Grant ICT10-002, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","abstract":[{"text":"Computing the winning set for Büchi objectives in alternating games on graphs is a central problem in computer aided verification with a large number of applications. The long standing best known upper bound for solving the problem is Õ(n·m), where n is the number of vertices and m is the number of edges in the graph. We are the first to break the Õ(n·m) boundary by presenting a new technique that reduces the running time to O(n 2). This bound also leads to O(n 2) time algorithms for computing the set of almost-sure winning vertices for Büchi objectives (1) in alternating games with probabilistic transitions (improving an earlier bound of Õ(n·m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n 3)), and (3) in Markov decision processes (improving for m &gt; n 4/3 an earlier bound of O(min(m 1.5, m·n 2/3)). We also show that the same technique can be used to compute the maximal end-component decomposition of a graph in time O(n 2), which is an improvement over earlier bounds for m &gt; n 4/3. Finally, we show how to maintain the winning set for Büchi objectives in alternating games under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per operation. This is the first dynamic algorithm for this problem.","lang":"eng"}],"publication_status":"published","title":"An O(n2) time algorithm for alternating Büchi games","publisher":"SIAM","date_published":"2012-01-01T00:00:00Z","citation":{"mla":"Chatterjee, Krishnendu, and Monika H. Henzinger. “An O(N2) Time Algorithm for Alternating Büchi Games.” <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, SIAM, 2012, pp. 1386–99, doi:<a href=\"https://doi.org/10.1137/1.9781611973099.109\">10.1137/1.9781611973099.109</a>.","short":"K. Chatterjee, M.H. Henzinger, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2012, pp. 1386–1399.","ista":"Chatterjee K, Henzinger MH. 2012. An O(n2) time algorithm for alternating Büchi games. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1386–1399.","ama":"Chatterjee K, Henzinger MH. An O(n2) time algorithm for alternating Büchi games. In: <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>. SIAM; 2012:1386-1399. doi:<a href=\"https://doi.org/10.1137/1.9781611973099.109\">10.1137/1.9781611973099.109</a>","chicago":"Chatterjee, Krishnendu, and Monika H Henzinger. “An O(N2) Time Algorithm for Alternating Büchi Games.” In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 1386–99. SIAM, 2012. <a href=\"https://doi.org/10.1137/1.9781611973099.109\">https://doi.org/10.1137/1.9781611973099.109</a>.","apa":"Chatterjee, K., &#38; Henzinger, M. H. (2012). An O(n2) time algorithm for alternating Büchi games. In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 1386–1399). Kyoto, Japan: SIAM. <a href=\"https://doi.org/10.1137/1.9781611973099.109\">https://doi.org/10.1137/1.9781611973099.109</a>","ieee":"K. Chatterjee and M. H. Henzinger, “An O(n2) time algorithm for alternating Büchi games,” in <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Kyoto, Japan, 2012, pp. 1386–1399."},"date_updated":"2025-06-02T08:53:48Z","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1109.5018"]}},{"date_created":"2018-12-11T12:01:46Z","_id":"3166","type":"journal_article","status":"public","pubrep_id":"99","ec_funded":1,"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa_version":"Published Version","author":[{"orcid":"0000-0002-5985-7653","first_name":"Harold","last_name":"Vladar","full_name":"Vladar, Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87"}],"month":"02","has_accepted_license":"1","article_number":"6","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:46:02Z","date_created":"2018-12-12T10:15:44Z","file_name":"IST-2012-99-v1+1_1745-6150-7-6.pdf","relation":"main_file","creator":"system","file_id":"5166","checksum":"e511e401e239ef608a7fd79b21a06d78","file_size":4099536,"access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":7,"oa":1,"acknowledgement":"The author was supported by the ERC-2009-AdG Grant for project 250152 SELECTIONINFORMATION. ","doi":"10.1186/1745-6150-7-6","year":"2012","day":"10","intvolume":"         7","publist_id":"3518","publication":"Biology Direct","date_updated":"2021-01-12T07:41:31Z","department":[{"_id":"NiBa"}],"citation":{"short":"H. de Vladar, Biology Direct 7 (2012).","mla":"de Vladar, Harold. “Amino Acid Fermentation at the Origin of the Genetic Code.” <i>Biology Direct</i>, vol. 7, 6, BioMed Central, 2012, doi:<a href=\"https://doi.org/10.1186/1745-6150-7-6\">10.1186/1745-6150-7-6</a>.","ieee":"H. de Vladar, “Amino acid fermentation at the origin of the genetic code,” <i>Biology Direct</i>, vol. 7. BioMed Central, 2012.","apa":"de Vladar, H. (2012). Amino acid fermentation at the origin of the genetic code. <i>Biology Direct</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1745-6150-7-6\">https://doi.org/10.1186/1745-6150-7-6</a>","ama":"de Vladar H. Amino acid fermentation at the origin of the genetic code. <i>Biology Direct</i>. 2012;7. doi:<a href=\"https://doi.org/10.1186/1745-6150-7-6\">10.1186/1745-6150-7-6</a>","ista":"de Vladar H. 2012. Amino acid fermentation at the origin of the genetic code. Biology Direct. 7, 6.","chicago":"Vladar, Harold de. “Amino Acid Fermentation at the Origin of the Genetic Code.” <i>Biology Direct</i>. BioMed Central, 2012. <a href=\"https://doi.org/10.1186/1745-6150-7-6\">https://doi.org/10.1186/1745-6150-7-6</a>."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"abstract":[{"lang":"eng","text":"There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eors Szathmary (nominated by Dr. Gaspar Jekely) and Dr. Adam Kun (nominated by Dr. Sandor Pongor)"}],"publication_status":"published","ddc":["570","576"],"file_date_updated":"2020-07-14T12:46:02Z","publisher":"BioMed Central","date_published":"2012-02-10T00:00:00Z","title":"Amino acid fermentation at the origin of the genetic code"},{"publist_id":"3516","intvolume":"       336","publication":"Science","page":"32-34","doi":"10.1126/science.336.6077.32","status":"public","year":"2012","day":"06","date_created":"2018-12-11T12:01:47Z","article_type":"letter_note","type":"journal_article","_id":"3167","pmid":1,"language":[{"iso":"eng"}],"date_published":"2012-04-06T00:00:00Z","publisher":"American Association for the Advancement of Science","volume":336,"title":"NextGen speaks 13 ","month":"04","publication_status":"published","issue":"6077","author":[{"first_name":"Michele","last_name":"Weber","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","full_name":"Weber, Michele"}],"external_id":{"pmid":["22491839"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","popular_science":"1","department":[{"_id":"MiSi"}],"date_updated":"2021-01-12T07:41:32Z","oa_version":"None","citation":{"ieee":"M. Weber, “NextGen speaks 13 ,” <i>Science</i>, vol. 336, no. 6077. American Association for the Advancement of Science, pp. 32–34, 2012.","apa":"Weber, M. (2012). NextGen speaks 13 . <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.336.6077.32\">https://doi.org/10.1126/science.336.6077.32</a>","ista":"Weber M. 2012. NextGen speaks 13 . Science. 336(6077), 32–34.","chicago":"Weber, Michele. “NextGen Speaks 13 .” <i>Science</i>. American Association for the Advancement of Science, 2012. <a href=\"https://doi.org/10.1126/science.336.6077.32\">https://doi.org/10.1126/science.336.6077.32</a>.","ama":"Weber M. NextGen speaks 13 . <i>Science</i>. 2012;336(6077):32-34. doi:<a href=\"https://doi.org/10.1126/science.336.6077.32\">10.1126/science.336.6077.32</a>","short":"M. Weber, Science 336 (2012) 32–34.","mla":"Weber, Michele. “NextGen Speaks 13 .” <i>Science</i>, vol. 336, no. 6077, American Association for the Advancement of Science, 2012, pp. 32–34, doi:<a href=\"https://doi.org/10.1126/science.336.6077.32\">10.1126/science.336.6077.32</a>."}},{"_id":"3168","type":"journal_article","date_created":"2018-12-11T12:01:47Z","doi":"10.1016/j.tcs.2011.12.059","status":"public","page":"137 - 164","day":"04","year":"2012","acknowledgement":"We would like to thank the anonymous reviewers for their comments on the different versions of the paper. We would also like to thank Ferdinanda Camporesi for her careful reading and the useful insights that she gave us about the paper.\r\nJérôme Feret’s contribution was partially supported by the AbstractCell ANR-Chair of Excellence. Heinz Koeppl’s research is supported by the Swiss National Science Foundation, grant no. 200020-117975/1. Tatjana Petrov’s research is supported by SystemsX.ch (the Swiss Initiative in Systems Biology).","scopus_import":1,"pubrep_id":"73","related_material":{"record":[{"status":"public","id":"3719","relation":"earlier_version"}]},"publication":"Theoretical Computer Science","publist_id":"3515","intvolume":"       431","citation":{"mla":"Feret, Jérôme, et al. “Lumpability Abstractions of Rule Based Systems.” <i>Theoretical Computer Science</i>, vol. 431, Elsevier, 2012, pp. 137–64, doi:<a href=\"https://doi.org/10.1016/j.tcs.2011.12.059\">10.1016/j.tcs.2011.12.059</a>.","short":"J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, Theoretical Computer Science 431 (2012) 137–164.","apa":"Feret, J., Henzinger, T. A., Koeppl, H., &#38; Petrov, T. (2012). Lumpability abstractions of rule based systems. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2011.12.059\">https://doi.org/10.1016/j.tcs.2011.12.059</a>","ama":"Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule based systems. <i>Theoretical Computer Science</i>. 2012;431:137-164. doi:<a href=\"https://doi.org/10.1016/j.tcs.2011.12.059\">10.1016/j.tcs.2011.12.059</a>","ista":"Feret J, Henzinger TA, Koeppl H, Petrov T. 2012. Lumpability abstractions of rule based systems. Theoretical Computer Science. 431, 137–164.","chicago":"Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability Abstractions of Rule Based Systems.” <i>Theoretical Computer Science</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.tcs.2011.12.059\">https://doi.org/10.1016/j.tcs.2011.12.059</a>.","ieee":"J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions of rule based systems,” <i>Theoretical Computer Science</i>, vol. 431. Elsevier, pp. 137–164, 2012."},"oa_version":"None","quality_controlled":"1","department":[{"_id":"ToHe"}],"date_updated":"2023-02-23T11:39:40Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Feret, Jérôme","last_name":"Feret","first_name":"Jérôme"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"first_name":"Heinz","last_name":"Koeppl","full_name":"Koeppl, Heinz"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana","first_name":"Tatjana","last_name":"Petrov","orcid":"0000-0002-9041-0905"}],"publication_status":"published","month":"05","abstract":[{"text":"The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a mathematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the combinatorial complexity by quotienting the reachable set of molecular species into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently, we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper, we prove that this quotienting yields a sufficient condition for weak lumpability (that is to say that the quotient system is still Markovian for a given set of initial distributions) and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system (which means that the conditional probability of being in a given state in the original system knowing that we are in its equivalence class is an invariant of the system). We illustrate the framework on a case study of the epidermal growth factor (EGF)/insulin receptor crosstalk.","lang":"eng"}],"volume":431,"title":"Lumpability abstractions of rule based systems","publisher":"Elsevier","date_published":"2012-05-04T00:00:00Z","language":[{"iso":"eng"}]},{"volume":10,"language":[{"iso":"eng"}],"issue":"4","article_number":"e1001300","file":[{"file_id":"4689","checksum":"4ebacefd9fbab5c68adf829124115fd1","creator":"system","access_level":"open_access","file_size":674228,"relation":"main_file","file_name":"IST-2012-96-v1+1_journal.pbio.1001300.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:08:28Z","date_updated":"2020-07-14T12:46:04Z"}],"month":"04","has_accepted_license":"1","author":[{"id":"46528076-F248-11E8-B48F-1D18A9856A87","full_name":"Konrad, Matthias","first_name":"Matthias","last_name":"Konrad"},{"id":"418901AA-F248-11E8-B48F-1D18A9856A87","full_name":"Vyleta, Meghan","last_name":"Vyleta","first_name":"Meghan"},{"full_name":"Theis, Fabian","last_name":"Theis","first_name":"Fabian"},{"full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam","last_name":"Stock"},{"first_name":"Simon","last_name":"Tragust","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","full_name":"Tragust, Simon"},{"first_name":"Martina","last_name":"Klatt","id":"E60F29C6-E9AE-11E9-AF6E-D190C7302F38","full_name":"Klatt, Martina"},{"full_name":"Drescher, Verena","last_name":"Drescher","first_name":"Verena"},{"full_name":"Marr, Carsten","first_name":"Carsten","last_name":"Marr"},{"first_name":"Line V","last_name":"Ugelvig","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","full_name":"Ugelvig, Line V"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"oa_version":"Published Version","quality_controlled":"1","project":[{"name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425"},{"name":"Antnet","_id":"25E0E184-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"pubrep_id":"96","status":"public","type":"journal_article","_id":"3242","date_created":"2018-12-11T12:02:13Z","title":"Social transfer of pathogenic fungus promotes active immunisation in ant colonies","publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:46:04Z","date_published":"2012-04-03T00:00:00Z","ddc":["570","579"],"abstract":[{"text":"Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”).","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"mla":"Konrad, Matthias, et al. “Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” <i>PLoS Biology</i>, vol. 10, no. 4, e1001300, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001300\">10.1371/journal.pbio.1001300</a>.","short":"M. Konrad, M. Vyleta, F. Theis, M. Stock, S. Tragust, M. Klatt, V. Drescher, C. Marr, L.V. Ugelvig, S. Cremer, PLoS Biology 10 (2012).","chicago":"Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Simon Tragust, Martina Klatt, Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer. “Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” <i>PLoS Biology</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pbio.1001300\">https://doi.org/10.1371/journal.pbio.1001300</a>.","ama":"Konrad M, Vyleta M, Theis F, et al. Social transfer of pathogenic fungus promotes active immunisation in ant colonies. <i>PLoS Biology</i>. 2012;10(4). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001300\">10.1371/journal.pbio.1001300</a>","ista":"Konrad M, Vyleta M, Theis F, Stock M, Tragust S, Klatt M, Drescher V, Marr C, Ugelvig LV, Cremer S. 2012. Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biology. 10(4), e1001300.","apa":"Konrad, M., Vyleta, M., Theis, F., Stock, M., Tragust, S., Klatt, M., … Cremer, S. (2012). Social transfer of pathogenic fungus promotes active immunisation in ant colonies. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1001300\">https://doi.org/10.1371/journal.pbio.1001300</a>","ieee":"M. Konrad <i>et al.</i>, “Social transfer of pathogenic fungus promotes active immunisation in ant colonies,” <i>PLoS Biology</i>, vol. 10, no. 4. Public Library of Science, 2012."},"date_updated":"2023-02-23T14:07:11Z","department":[{"_id":"SyCr"}],"publication":"PLoS Biology","intvolume":"        10","publist_id":"3434","related_material":{"record":[{"status":"public","relation":"research_data","id":"9755"}]},"scopus_import":1,"year":"2012","doi":"10.1371/journal.pbio.1001300","day":"03","acknowledgement":"Funding for this project was obtained by the German Research Foundation DFG (http://www.dfg.de/en/index.jsp) as an Individual Research Grant (CR118/2-1 to SC) and the European Research Council (http://erc.europa.eu/) in form of two ERC Starting Grants (ERC-2009-StG240371-SocialVaccines to SC and ERC-2010-StG259294-LatentCauses to FJT). In addition, the Junge Akademie (Young Academy of the Berlin-Brandenburg Academy of Sciences and Humanities and the National Academy of Sciences Leopoldina (http://www.diejungeakademie.de/english/i​ndex.html) funded this joint Antnet project of SC and FJT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","oa":1},{"citation":{"mla":"Danowski, Patrick. “Zwischen Technologie und Information.” <i>Büchereiperspektiven</i>, vol. 2012, no. 1, Büchereiverband Österreichs, 2012, p. 11.","short":"P. Danowski, Büchereiperspektiven 2012 (2012) 11.","ieee":"P. Danowski, “Zwischen Technologie und Information,” <i>Büchereiperspektiven</i>, vol. 2012, no. 1. Büchereiverband Österreichs, p. 11, 2012.","ista":"Danowski P. 2012. Zwischen Technologie und Information. Büchereiperspektiven. 2012(1), 11.","chicago":"Danowski, Patrick. “Zwischen Technologie und Information.” <i>Büchereiperspektiven</i>. Büchereiverband Österreichs, 2012.","ama":"Danowski P. Zwischen Technologie und Information. <i>Büchereiperspektiven</i>. 2012;2012(1):11.","apa":"Danowski, P. (2012). Zwischen Technologie und Information. <i>Büchereiperspektiven</i>. Büchereiverband Österreichs."},"department":[{"_id":"E-Lib"}],"date_updated":"2023-10-16T10:40:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"text":"Wie wandelt sich das Berufsbild in Wissenschaftlichen Bibliotheken? Patrick Danowski gibt seine Einschätzung ab. ","lang":"eng"}],"title":"Zwischen Technologie und Information","date_published":"2012-03-01T00:00:00Z","publisher":"Büchereiverband Österreichs","oa":1,"day":"01","page":"11","year":"2012","publication":"Büchereiperspektiven","publist_id":"3433","intvolume":"      2012","oa_version":"Published Version","popular_science":"1","author":[{"full_name":"Danowski, Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6026-4409","last_name":"Danowski","first_name":"Patrick"}],"issue":"1","month":"03","volume":2012,"article_processing_charge":"No","language":[{"iso":"ger"}],"article_type":"letter_note","type":"journal_article","_id":"3243","date_created":"2018-12-11T12:02:13Z","main_file_link":[{"open_access":"1","url":"https://www.bvoe.at/sites/default/files/2022-07/BP_1_12.pdf"}],"publication_identifier":{"issn":["1607-7172"]},"status":"public"},{"title":"Die Zeit des Abwartens ist vorbei!","date_published":"2012-04-15T00:00:00Z","publisher":"Fachzeitschrift des BIB – Berufsverband Information Bibliothek","publication_status":"published","abstract":[{"text":"Bibliothekare haben die Aufgabe, sich mit neuen Medienformen auseinanderzusetzen.\r\n","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"P. Danowski, BuB - Forum Bibliothek und Information 64 (2012) 284.","mla":"Danowski, Patrick. “Die Zeit des Abwartens ist vorbei!” <i>BuB - Forum Bibliothek und Information</i>, vol. 64, no. 4, Fachzeitschrift des BIB – Berufsverband Information Bibliothek, 2012, p. 284.","ista":"Danowski P. 2012. Die Zeit des Abwartens ist vorbei! BuB - Forum Bibliothek und Information. 64(4), 284.","ama":"Danowski P. Die Zeit des Abwartens ist vorbei! <i>BuB - Forum Bibliothek und Information</i>. 2012;64(4):284.","chicago":"Danowski, Patrick. “Die Zeit des Abwartens ist vorbei!” <i>BuB - Forum Bibliothek und Information</i>. Fachzeitschrift des BIB – Berufsverband Information Bibliothek, 2012.","apa":"Danowski, P. (2012). Die Zeit des Abwartens ist vorbei! <i>BuB - Forum Bibliothek und Information</i>. Fachzeitschrift des BIB – Berufsverband Information Bibliothek.","ieee":"P. Danowski, “Die Zeit des Abwartens ist vorbei!,” <i>BuB - Forum Bibliothek und Information</i>, vol. 64, no. 4. Fachzeitschrift des BIB – Berufsverband Information Bibliothek, p. 284, 2012."},"department":[{"_id":"E-Lib"}],"date_updated":"2023-10-16T10:19:14Z","publication":"BuB - Forum Bibliothek und Information","publist_id":"3432","intvolume":"        64","day":"15","page":"284","year":"2012","oa":1,"volume":64,"article_processing_charge":"No","language":[{"iso":"ger"}],"issue":"4","month":"04","author":[{"orcid":"0000-0002-6026-4409","first_name":"Patrick","last_name":"Danowski","full_name":"Danowski, Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","popular_science":"1","status":"public","main_file_link":[{"url":"https://www.b-u-b.de/fileadmin/archiv/imports/pdf_files/2012/bub_2012_04_284.pdf","open_access":"1"}],"publication_identifier":{"issn":["1869 -1137"]},"article_type":"letter_note","type":"journal_article","_id":"3244","date_created":"2018-12-11T12:02:13Z"},{"language":[{"iso":"eng"}],"publisher":"Cell Press","date_published":"2012-01-17T00:00:00Z","title":"Spurred by resistance mechanosensation in collective migration","volume":22,"publication_status":"published","month":"01","abstract":[{"lang":"eng","text":"How cells orchestrate their behavior during collective migration is a long-standing question. Using magnetic tweezers to apply mechanical stimuli to Xenopus mesendoderm cells, Weber etal. (2012) now reveal, in this issue of Developmental Cell, a cadherin-mediated mechanosensitive response that promotes cell polarization and movement persistence during the collective mesendoderm migration in gastrulation."}],"issue":"1","author":[{"first_name":"Martin","last_name":"Behrndt","full_name":"Behrndt, Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","department":[{"_id":"CaHe"}],"date_updated":"2021-01-12T07:42:05Z","oa_version":"None","citation":{"short":"M. Behrndt, C.-P.J. Heisenberg, Developmental Cell 22 (2012) 3–4.","mla":"Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Spurred by Resistance Mechanosensation in Collective Migration.” <i>Developmental Cell</i>, vol. 22, no. 1, Cell Press, 2012, pp. 3–4, doi:<a href=\"https://doi.org/10.1016/j.devcel.2011.12.018\">10.1016/j.devcel.2011.12.018</a>.","chicago":"Behrndt, Martin, and Carl-Philipp J Heisenberg. “Spurred by Resistance Mechanosensation in Collective Migration.” <i>Developmental Cell</i>. Cell Press, 2012. <a href=\"https://doi.org/10.1016/j.devcel.2011.12.018\">https://doi.org/10.1016/j.devcel.2011.12.018</a>.","ista":"Behrndt M, Heisenberg C-PJ. 2012. Spurred by resistance mechanosensation in collective migration. Developmental Cell. 22(1), 3–4.","ama":"Behrndt M, Heisenberg C-PJ. Spurred by resistance mechanosensation in collective migration. <i>Developmental Cell</i>. 2012;22(1):3-4. doi:<a href=\"https://doi.org/10.1016/j.devcel.2011.12.018\">10.1016/j.devcel.2011.12.018</a>","apa":"Behrndt, M., &#38; Heisenberg, C.-P. J. (2012). Spurred by resistance mechanosensation in collective migration. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2011.12.018\">https://doi.org/10.1016/j.devcel.2011.12.018</a>","ieee":"M. Behrndt and C.-P. J. Heisenberg, “Spurred by resistance mechanosensation in collective migration,” <i>Developmental Cell</i>, vol. 22, no. 1. Cell Press, pp. 3–4, 2012."},"publist_id":"3426","intvolume":"        22","publication":"Developmental Cell","scopus_import":1,"doi":"10.1016/j.devcel.2011.12.018","page":"3 - 4","status":"public","day":"17","year":"2012","date_created":"2018-12-11T12:02:14Z","_id":"3245","type":"journal_article"},{"abstract":[{"lang":"eng","text":"Visualizing and analyzing shape changes at various scales, ranging from single molecules to whole organisms, are essential for understanding complex morphogenetic processes, such as early embryonic development. Embryo morphogenesis relies on the interplay between different tissues, the properties of which are again determined by the interaction between their constituent cells. Cell interactions, on the other hand, are controlled by various molecules, such as signaling and adhesion molecules, which in order to exert their functions need to be spatiotemporally organized within and between the interacting cells. In this review, we will focus on the role of cell adhesion functioning at different scales to organize cell, tissue and embryo morphogenesis. We will specifically ask how the subcellular distribution of adhesion molecules controls the formation of cell-cell contacts, how cell-cell contacts determine tissue shape, and how tissue interactions regulate embryo morphogenesis."}],"month":"02","publication_status":"published","issue":"1","date_published":"2012-02-01T00:00:00Z","publisher":"Elsevier","language":[{"iso":"eng"}],"volume":24,"title":"Cell adhesion in embryo morphogenesis","date_updated":"2023-09-07T12:05:08Z","department":[{"_id":"CaHe"}],"quality_controlled":"1","oa_version":"None","citation":{"chicago":"Barone, Vanessa, and Carl-Philipp J Heisenberg. “Cell Adhesion in Embryo Morphogenesis.” <i>Current Opinion in Cell Biology</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.ceb.2011.11.006\">https://doi.org/10.1016/j.ceb.2011.11.006</a>.","ama":"Barone V, Heisenberg C-PJ. Cell adhesion in embryo morphogenesis. <i>Current Opinion in Cell Biology</i>. 2012;24(1):148-153. doi:<a href=\"https://doi.org/10.1016/j.ceb.2011.11.006\">10.1016/j.ceb.2011.11.006</a>","ista":"Barone V, Heisenberg C-PJ. 2012. Cell adhesion in embryo morphogenesis. Current Opinion in Cell Biology. 24(1), 148–153.","apa":"Barone, V., &#38; Heisenberg, C.-P. J. (2012). Cell adhesion in embryo morphogenesis. <i>Current Opinion in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ceb.2011.11.006\">https://doi.org/10.1016/j.ceb.2011.11.006</a>","ieee":"V. Barone and C.-P. J. Heisenberg, “Cell adhesion in embryo morphogenesis,” <i>Current Opinion in Cell Biology</i>, vol. 24, no. 1. Elsevier, pp. 148–153, 2012.","mla":"Barone, Vanessa, and Carl-Philipp J. Heisenberg. “Cell Adhesion in Embryo Morphogenesis.” <i>Current Opinion in Cell Biology</i>, vol. 24, no. 1, Elsevier, 2012, pp. 148–53, doi:<a href=\"https://doi.org/10.1016/j.ceb.2011.11.006\">10.1016/j.ceb.2011.11.006</a>.","short":"V. Barone, C.-P.J. Heisenberg, Current Opinion in Cell Biology 24 (2012) 148–153."},"author":[{"full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","first_name":"Vanessa","last_name":"Barone"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"961"}]},"scopus_import":1,"intvolume":"        24","publist_id":"3423","publication":"Current Opinion in Cell Biology","date_created":"2018-12-11T12:02:14Z","type":"journal_article","_id":"3246","acknowledgement":"This review comes from a themed issue on Cell structure and dynamics Edited by Jason Swedlow and Gaudenz Danuser","page":"148 - 153","doi":"10.1016/j.ceb.2011.11.006","status":"public","day":"01","year":"2012"},{"publication_status":"published","month":"02","abstract":[{"lang":"eng","text":"The Brazilian Merganser is a very rare and threatened species that nowadays inhabits only a few protected areas and their surroundings in the Brazilian territory. In order to estimate the remaining genetic diversity and population structure in this species, two mitochondrial genes were sequenced in 39 individuals belonging to two populations and in one individual collected in Argentina in 1950. We found a highly significant divergence between two major remaining populations of Mergus octosetaceus, which suggests a historical population structure in this species. Furthermore, two deeply divergent lineages were found in a single location, which could due to current or historical secondary contact. Based on the available genetic data, we point out future directions which would contribute to design strategies for conservation and management of this threatened species."}],"issue":"1","date_published":"2012-02-01T00:00:00Z","publisher":"Springer","language":[{"iso":"eng"}],"title":"Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus)","volume":13,"department":[{"_id":"JoBo"}],"quality_controlled":"1","date_updated":"2021-01-12T07:42:05Z","oa_version":"None","citation":{"short":"S. Vilaça, R.A. Fernandes Redondo, L. Lins, F. Santos, Conservation Genetics 13 (2012) 293–298.","mla":"Vilaça, Sibelle, et al. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” <i>Conservation Genetics</i>, vol. 13, no. 1, Springer, 2012, pp. 293–98, doi:<a href=\"https://doi.org/10.1007/s10592-011-0262-5\">10.1007/s10592-011-0262-5</a>.","ieee":"S. Vilaça, R. A. Fernandes Redondo, L. Lins, and F. Santos, “Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus),” <i>Conservation Genetics</i>, vol. 13, no. 1. Springer, pp. 293–298, 2012.","ama":"Vilaça S, Fernandes Redondo RA, Lins L, Santos F. Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). <i>Conservation Genetics</i>. 2012;13(1):293-298. doi:<a href=\"https://doi.org/10.1007/s10592-011-0262-5\">10.1007/s10592-011-0262-5</a>","chicago":"Vilaça, Sibelle, Rodrigo A Fernandes Redondo, Lívia Lins, and Fabrício Santos. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” <i>Conservation Genetics</i>. Springer, 2012. <a href=\"https://doi.org/10.1007/s10592-011-0262-5\">https://doi.org/10.1007/s10592-011-0262-5</a>.","ista":"Vilaça S, Fernandes Redondo RA, Lins L, Santos F. 2012. Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. 13(1), 293–298.","apa":"Vilaça, S., Fernandes Redondo, R. A., Lins, L., &#38; Santos, F. (2012). Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). <i>Conservation Genetics</i>. Springer. <a href=\"https://doi.org/10.1007/s10592-011-0262-5\">https://doi.org/10.1007/s10592-011-0262-5</a>"},"author":[{"full_name":"Vilaça, Sibelle","first_name":"Sibelle","last_name":"Vilaça"},{"first_name":"Rodrigo A","last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A"},{"first_name":"Lívia","last_name":"Lins","full_name":"Lins, Lívia"},{"last_name":"Santos","first_name":"Fabrício","full_name":"Santos, Fabrício"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publist_id":"3420","intvolume":"        13","publication":"Conservation Genetics","date_created":"2018-12-11T12:02:15Z","_id":"3247","type":"journal_article","acknowledgement":"The present study received grants from FAPEMIG, CNPq, Petrobras Ambiental and Fundação O Boticário de Conservação da Natureza, and followed all ethical guidelines and legal requirements of Brazil for sampling and studying an endangered species.\r\nWe thank the Specialist Work Group for the Conservation of Brazilian Merganser for valuable discussions and opinions on this manuscript. We also thank all the staff from Instituto Terra Brasilis and Funatura (Vivian S. Braz and Gislaine Disconzi) for collecting the samples at Serra da Canastra and Chapada dos Veadeiros, respectively; Dario A. Lijtmaerand and Pablo Tubaro for providing the samples from Argentina, Bradley C. Livezey for sending copies of his papers, and Geoff M. Hilton and Paulo de Tarso Z. Antas for useful suggestions that greatly improved this manuscript.","year":"2012","status":"public","day":"01","doi":"10.1007/s10592-011-0262-5","page":"293 - 298"},{"quality_controlled":"1","oa_version":"Submitted Version","author":[{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph"},{"full_name":"Peters, Jan","last_name":"Peters","first_name":"Jan"}],"has_accepted_license":"1","month":"03","issue":"1","file":[{"relation":"main_file","access_level":"open_access","file_size":2933187,"file_id":"5958","checksum":"241be47ea50e81a283bcf4c45b07e8cc","creator":"kschuh","date_created":"2019-02-12T10:52:25Z","date_updated":"2020-07-14T12:46:04Z","content_type":"application/pdf","file_name":"2012_Springer_Lampert.pdf"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","volume":7,"date_created":"2018-12-11T12:02:15Z","_id":"3248","type":"journal_article","article_type":"original","publication_identifier":{"issn":["1861-8200"],"eissn":["1861-8219"]},"status":"public","date_updated":"2022-05-24T08:05:40Z","department":[{"_id":"ChLa"}],"citation":{"mla":"Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects in Multiple Camera Streams with off-the-Shelf Hardware Components.” <i>Journal of Real-Time Image Processing</i>, vol. 7, no. 1, Springer, 2012, pp. 31–41, doi:<a href=\"https://doi.org/10.1007/s11554-010-0168-3\">10.1007/s11554-010-0168-3</a>.","short":"C. Lampert, J. Peters, Journal of Real-Time Image Processing 7 (2012) 31–41.","ieee":"C. Lampert and J. Peters, “Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components,” <i>Journal of Real-Time Image Processing</i>, vol. 7, no. 1. Springer, pp. 31–41, 2012.","apa":"Lampert, C., &#38; Peters, J. (2012). Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. <i>Journal of Real-Time Image Processing</i>. Springer. <a href=\"https://doi.org/10.1007/s11554-010-0168-3\">https://doi.org/10.1007/s11554-010-0168-3</a>","ama":"Lampert C, Peters J. Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. <i>Journal of Real-Time Image Processing</i>. 2012;7(1):31-41. doi:<a href=\"https://doi.org/10.1007/s11554-010-0168-3\">10.1007/s11554-010-0168-3</a>","chicago":"Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects in Multiple Camera Streams with off-the-Shelf Hardware Components.” <i>Journal of Real-Time Image Processing</i>. Springer, 2012. <a href=\"https://doi.org/10.1007/s11554-010-0168-3\">https://doi.org/10.1007/s11554-010-0168-3</a>.","ista":"Lampert C, Peters J. 2012. Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. Journal of Real-Time Image Processing. 7(1), 31–41."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We describe RTblob, a high speed vision system that detects objects in cluttered scenes based on their color and shape at a speed of over 800 frames/s. Because the system is available as open-source software and relies only on off-the-shelf PC hardware components, it can provide the basis for multiple application scenarios. As an illustrative example, we show how RTblob can be used in a robotic table tennis scenario to estimate ball trajectories through 3D space simultaneously from four cameras images at a speed of 200 Hz.","lang":"eng"}],"publication_status":"published","ddc":["000"],"publisher":"Springer","date_published":"2012-03-01T00:00:00Z","file_date_updated":"2020-07-14T12:46:04Z","title":"Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components","oa":1,"doi":"10.1007/s11554-010-0168-3","page":"31 - 41","year":"2012","day":"01","scopus_import":"1","intvolume":"         7","publist_id":"3417","publication":"Journal of Real-Time Image Processing"},{"department":[{"_id":"ToHe"}],"date_updated":"2023-02-23T12:24:04Z","citation":{"short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, Theoretical Computer Science 413 (2012) 21–35.","mla":"Cerny, Pavol, et al. “Simulation Distances.” <i>Theoretical Computer Science</i>, vol. 413, no. 1, Elsevier, 2012, pp. 21–35, doi:<a href=\"https://doi.org/10.1016/j.tcs.2011.08.002\">10.1016/j.tcs.2011.08.002</a>.","apa":"Cerny, P., Henzinger, T. A., &#38; Radhakrishna, A. (2012). Simulation distances. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2011.08.002\">https://doi.org/10.1016/j.tcs.2011.08.002</a>","ista":"Cerny P, Henzinger TA, Radhakrishna A. 2012. Simulation distances. Theoretical Computer Science. 413(1), 21–35.","ama":"Cerny P, Henzinger TA, Radhakrishna A. Simulation distances. <i>Theoretical Computer Science</i>. 2012;413(1):21-35. doi:<a href=\"https://doi.org/10.1016/j.tcs.2011.08.002\">10.1016/j.tcs.2011.08.002</a>","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Simulation Distances.” <i>Theoretical Computer Science</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.tcs.2011.08.002\">https://doi.org/10.1016/j.tcs.2011.08.002</a>.","ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Simulation distances,” <i>Theoretical Computer Science</i>, vol. 413, no. 1. Elsevier, pp. 21–35, 2012."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"text":"Boolean notions of correctness are formalized by preorders on systems. Quantitative measures of correctness can be formalized by real-valued distance functions between systems, where the distance between implementation and specification provides a measure of &quot;fit&quot; or &quot;desirability&quot;. We extend the simulation preorder to the quantitative setting by making each player of a simulation game pay a certain price for her choices. We use the resulting games with quantitative objectives to define three different simulation distances. The correctness distance measures how much the specification must be changed in order to be satisfied by the implementation. The coverage distance measures how much the implementation restricts the degrees of freedom offered by the specification. The robustness distance measures how much a system can deviate from the implementation description without violating the specification. We consider these distances for safety as well as liveness specifications. The distances can be computed in polynomial time for safety specifications, and for liveness specifications given by weak fairness constraints. We show that the distance functions satisfy the triangle inequality, that the distance between two systems does not increase under parallel composition with a third system, and that the distance between two systems can be bounded from above and below by distances between abstractions of the two systems. These properties suggest that our simulation distances provide an appropriate basis for a quantitative theory of discrete systems. We also demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes.","lang":"eng"}],"publisher":"Elsevier","date_published":"2012-01-06T00:00:00Z","title":"Simulation distances","acknowledgement":"This work was partially supported by the ERC Advanced Grant QUAREM, the FWF NFN Grant S11402-N23 (RiSE), the European Union project COMBEST and the European Network of Excellence Artist Design.","doi":"10.1016/j.tcs.2011.08.002","day":"06","year":"2012","page":"21 - 35","scopus_import":1,"related_material":{"record":[{"id":"4393","relation":"earlier_version","status":"public"},{"id":"5389","relation":"earlier_version","status":"public"}]},"publist_id":"3408","intvolume":"       413","publication":"Theoretical Computer Science","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7"},{"call_identifier":"FP7","grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems"}],"quality_controlled":"1","oa_version":"None","author":[{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","first_name":"Pavol","last_name":"Cerny"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","first_name":"Arjun"}],"month":"01","issue":"1","language":[{"iso":"eng"}],"volume":413,"date_created":"2018-12-11T12:02:15Z","type":"journal_article","_id":"3249","status":"public","pubrep_id":"42","ec_funded":1},{"scopus_import":1,"conference":{"name":"SOFSEM: Current Trends in Theory and Practice of Computer Science","location":"Špindlerův Mlýn, Czech Republic","start_date":"2012-01-21","end_date":"2012-01-27"},"publist_id":"3407","intvolume":"      7147","_id":"3250","type":"conference","date_created":"2018-12-11T12:02:15Z","status":"public","day":"19","year":"2012","doi":"10.1007/978-3-642-27660-6_9","page":"99 - 114","month":"02","publication_status":"published","abstract":[{"lang":"eng","text":"The Learning Parity with Noise (LPN) problem has recently found many applications in cryptography as the hardness assumption underlying the constructions of &quot;provably secure&quot; cryptographic schemes like encryption or authentication protocols. Being provably secure means that the scheme comes with a proof showing that the existence of an efficient adversary against the scheme implies that the underlying hardness assumption is wrong. LPN based schemes are appealing for theoretical and practical reasons. On the theoretical side, LPN based schemes offer a very strong security guarantee. The LPN problem is equivalent to the problem of decoding random linear codes, a problem that has been extensively studied in the last half century. The fastest known algorithms run in exponential time and unlike most number-theoretic problems used in cryptography, the LPN problem does not succumb to known quantum algorithms. On the practical side, LPN based schemes are often extremely simple and efficient in terms of code-size as well as time and space requirements. This makes them prime candidates for light-weight devices like RFID tags, which are too weak to implement standard cryptographic primitives like the AES block-cipher. This talk will be a gentle introduction to provable security using simple LPN based schemes as examples. Starting from pseudorandom generators and symmetric key encryption, over secret-key authentication protocols, and, if time admits, touching on recent constructions of public-key identification, commitments and zero-knowledge proofs."}],"title":"Cryptography from learning parity with noise","volume":7147,"language":[{"iso":"eng"}],"publisher":"Springer","date_published":"2012-02-19T00:00:00Z","citation":{"short":"K.Z. Pietrzak, in:, Springer, 2012, pp. 99–114.","mla":"Pietrzak, Krzysztof Z. <i>Cryptography from Learning Parity with Noise</i>. Vol. 7147, Springer, 2012, pp. 99–114, doi:<a href=\"https://doi.org/10.1007/978-3-642-27660-6_9\">10.1007/978-3-642-27660-6_9</a>.","chicago":"Pietrzak, Krzysztof Z. “Cryptography from Learning Parity with Noise,” 7147:99–114. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-27660-6_9\">https://doi.org/10.1007/978-3-642-27660-6_9</a>.","ama":"Pietrzak KZ. Cryptography from learning parity with noise. In: Vol 7147. Springer; 2012:99-114. doi:<a href=\"https://doi.org/10.1007/978-3-642-27660-6_9\">10.1007/978-3-642-27660-6_9</a>","ista":"Pietrzak KZ. 2012. Cryptography from learning parity with noise. SOFSEM: Current Trends in Theory and Practice of Computer Science, LNCS, vol. 7147, 99–114.","apa":"Pietrzak, K. Z. (2012). Cryptography from learning parity with noise (Vol. 7147, pp. 99–114). Presented at the SOFSEM: Current Trends in Theory and Practice of Computer Science, Špindlerův Mlýn, Czech Republic: Springer. <a href=\"https://doi.org/10.1007/978-3-642-27660-6_9\">https://doi.org/10.1007/978-3-642-27660-6_9</a>","ieee":"K. Z. Pietrzak, “Cryptography from learning parity with noise,” presented at the SOFSEM: Current Trends in Theory and Practice of Computer Science, Špindlerův Mlýn, Czech Republic, 2012, vol. 7147, pp. 99–114."},"oa_version":"None","quality_controlled":"1","department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T07:42:07Z","alternative_title":["LNCS"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}]},{"day":"01","doi":"10.1007/978-3-642-27940-9_29","page":"445 - 460","year":"2012","acknowledgement":"This research was supported in part by the European Research Council (ERC) Advanced Investigator Grant QUAREM and by the Austrian Science Fund (FWF) project S11402-N23.","oa":1,"publist_id":"3406","intvolume":"      7148","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1405"}]},"alternative_title":["LNCS"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"D. Zufferey, T. Wies, and T. A. Henzinger, “Ideal abstractions for well structured transition systems,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA, 2012, vol. 7148, pp. 445–460.","apa":"Zufferey, D., Wies, T., &#38; Henzinger, T. A. (2012). Ideal abstractions for well structured transition systems (Vol. 7148, pp. 445–460). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-27940-9_29\">https://doi.org/10.1007/978-3-642-27940-9_29</a>","chicago":"Zufferey, Damien, Thomas Wies, and Thomas A Henzinger. “Ideal Abstractions for Well Structured Transition Systems,” 7148:445–60. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-27940-9_29\">https://doi.org/10.1007/978-3-642-27940-9_29</a>.","ista":"Zufferey D, Wies T, Henzinger TA. 2012. Ideal abstractions for well structured transition systems. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 7148, 445–460.","ama":"Zufferey D, Wies T, Henzinger TA. Ideal abstractions for well structured transition systems. In: Vol 7148. Springer; 2012:445-460. doi:<a href=\"https://doi.org/10.1007/978-3-642-27940-9_29\">10.1007/978-3-642-27940-9_29</a>","short":"D. Zufferey, T. Wies, T.A. Henzinger, in:, Springer, 2012, pp. 445–460.","mla":"Zufferey, Damien, et al. <i>Ideal Abstractions for Well Structured Transition Systems</i>. Vol. 7148, Springer, 2012, pp. 445–60, doi:<a href=\"https://doi.org/10.1007/978-3-642-27940-9_29\">10.1007/978-3-642-27940-9_29</a>."},"department":[{"_id":"ToHe"}],"date_updated":"2023-09-07T11:36:36Z","title":"Ideal abstractions for well structured transition systems","file_date_updated":"2020-07-14T12:46:05Z","publisher":"Springer","date_published":"2012-01-01T00:00:00Z","ddc":["000","005"],"publication_status":"published","abstract":[{"lang":"eng","text":"Many infinite state systems can be seen as well-structured transition systems (WSTS), i.e., systems equipped with a well-quasi-ordering on states that is also a simulation relation. WSTS are an attractive target for formal analysis because there exist generic algorithms that decide interesting verification problems for this class. Among the most popular algorithms are acceleration-based forward analyses for computing the covering set. Termination of these algorithms can only be guaranteed for flattable WSTS. Yet, many WSTS of practical interest are not flattable and the question whether any given WSTS is flattable is itself undecidable. We therefore propose an analysis that computes the covering set and captures the essence of acceleration-based algorithms, but sacrifices precision for guaranteed termination. Our analysis is an abstract interpretation whose abstract domain builds on the ideal completion of the well-quasi-ordered state space, and a widening operator that mimics acceleration and controls the loss of precision of the analysis. We present instances of our framework for various classes of WSTS. Our experience with a prototype implementation indicates that, despite the inherent precision loss, our analysis often computes the precise covering set of the analyzed system."}],"status":"public","type":"conference","_id":"3251","date_created":"2018-12-11T12:02:16Z","conference":{"location":"Philadelphia, PA, USA","name":"VMCAI: Verification, Model Checking and Abstract Interpretation","start_date":"2012-01-22","end_date":"2012-01-24"},"ec_funded":1,"pubrep_id":"100","author":[{"first_name":"Damien","last_name":"Zufferey","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","full_name":"Zufferey, Damien"},{"full_name":"Wies, Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Wies"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Submitted Version","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","volume":7148,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2012-100-v1+1_Ideal_abstractions_for_well-structured_transition_systems.pdf","date_updated":"2020-07-14T12:46:05Z","date_created":"2018-12-12T10:09:35Z","content_type":"application/pdf","file_size":217104,"access_level":"open_access","creator":"system","file_id":"4759","checksum":"f2f0d55efa32309ad1fe65a5fcaad90c","relation":"main_file"}],"month":"01","has_accepted_license":"1"}]