[{"publist_id":"3818","publisher":"Wiley-Blackwell","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553380/","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2919","pmid":1,"abstract":[{"text":"The distribution of the phytohormone auxin regulates many aspects of plant development including growth response to gravity. Gravitropic root curvature involves coordinated and asymmetric cell elongation between the lower and upper side of the root, mediated by differential cellular auxin levels. The asymmetry in the auxin distribution is established and maintained by a spatio-temporal regulation of the PIN-FORMED (PIN) auxin transporter activity. We provide novel insights into the complex regulation of PIN abundance and activity during root gravitropism. We show that PIN2 turnover is differentially regulated on the upper and lower side of gravistimulated roots by distinct but partially overlapping auxin feedback mechanisms. In addition to regulating transcription and clathrin-mediated internalization, auxin also controls PIN abundance at the plasma membrane by promoting their vacuolar targeting and degradation. This effect of elevated auxin levels requires the activity of SKP-Cullin-F-box TIR1/AFB (SCF TIR1/AFB)-dependent pathway. Importantly, also suboptimal auxin levels mediate PIN degradation utilizing the same signalling pathway. These feedback mechanisms are functionally important during gravitropic response and ensure fine-tuning of auxin fluxes for maintaining as well as terminating asymmetric growth.","lang":"eng"}],"scopus_import":1,"publication":"EMBO Journal","language":[{"iso":"eng"}],"author":[{"id":"3028BD74-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","full_name":"Baster, Pawel","last_name":"Baster"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen","first_name":"Jürgen"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"first_name":"Urszula","full_name":"Kania, Urszula","last_name":"Kania","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grunewald, Wim","first_name":"Wim","last_name":"Grunewald"},{"first_name":"Bert","full_name":"De Rybel, Bert","last_name":"De Rybel"},{"first_name":"Tom","full_name":"Beeckman, Tom","last_name":"Beeckman"},{"last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"month":"01","type":"journal_article","date_created":"2018-12-11T12:00:20Z","page":"260 - 274","volume":32,"date_published":"2013-01-23T00:00:00Z","oa_version":"Submitted Version","department":[{"_id":"JiFr"}],"quality_controlled":"1","publication_status":"published","citation":{"ista":"Baster P, Robert S, Kleine Vehn J, Vanneste S, Kania U, Grunewald W, De Rybel B, Beeckman T, Friml J. 2013. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. EMBO Journal. 32(2), 260–274.","ieee":"P. Baster <i>et al.</i>, “SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism,” <i>EMBO Journal</i>, vol. 32, no. 2. Wiley-Blackwell, pp. 260–274, 2013.","short":"P. Baster, S. Robert, J. Kleine Vehn, S. Vanneste, U. Kania, W. Grunewald, B. De Rybel, T. Beeckman, J. Friml, EMBO Journal 32 (2013) 260–274.","mla":"Baster, Pawel, et al. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” <i>EMBO Journal</i>, vol. 32, no. 2, Wiley-Blackwell, 2013, pp. 260–74, doi:<a href=\"https://doi.org/10.1038/emboj.2012.310\">10.1038/emboj.2012.310</a>.","chicago":"Baster, Pawel, Stéphanie Robert, Jürgen Kleine Vehn, Steffen Vanneste, Urszula Kania, Wim Grunewald, Bert De Rybel, Tom Beeckman, and Jiří Friml. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2012.310\">https://doi.org/10.1038/emboj.2012.310</a>.","ama":"Baster P, Robert S, Kleine Vehn J, et al. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. <i>EMBO Journal</i>. 2013;32(2):260-274. doi:<a href=\"https://doi.org/10.1038/emboj.2012.310\">10.1038/emboj.2012.310</a>","apa":"Baster, P., Robert, S., Kleine Vehn, J., Vanneste, S., Kania, U., Grunewald, W., … Friml, J. (2013). SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2012.310\">https://doi.org/10.1038/emboj.2012.310</a>"},"status":"public","intvolume":"        32","date_updated":"2021-01-12T07:00:41Z","external_id":{"pmid":["23211744"]},"oa":1,"year":"2013","day":"23","doi":"10.1038/emboj.2012.310","issue":"2","title":"SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism"},{"quality_controlled":"1","citation":{"chicago":"Compagnon, Julien, and Carl-Philipp J Heisenberg. “Neurulation Coordinating Cell Polarisation and Lumen Formation.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2012.325\">https://doi.org/10.1038/emboj.2012.325</a>.","apa":"Compagnon, J., &#38; Heisenberg, C.-P. J. (2013). Neurulation coordinating cell polarisation and lumen formation. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2012.325\">https://doi.org/10.1038/emboj.2012.325</a>","ama":"Compagnon J, Heisenberg C-PJ. Neurulation coordinating cell polarisation and lumen formation. <i>EMBO Journal</i>. 2013;32(1):1-3. doi:<a href=\"https://doi.org/10.1038/emboj.2012.325\">10.1038/emboj.2012.325</a>","ista":"Compagnon J, Heisenberg C-PJ. 2013. Neurulation coordinating cell polarisation and lumen formation. EMBO Journal. 32(1), 1–3.","mla":"Compagnon, Julien, and Carl-Philipp J. Heisenberg. “Neurulation Coordinating Cell Polarisation and Lumen Formation.” <i>EMBO Journal</i>, vol. 32, no. 1, Wiley-Blackwell, 2013, pp. 1–3, doi:<a href=\"https://doi.org/10.1038/emboj.2012.325\">10.1038/emboj.2012.325</a>.","short":"J. Compagnon, C.-P.J. Heisenberg, EMBO Journal 32 (2013) 1–3.","ieee":"J. Compagnon and C.-P. J. Heisenberg, “Neurulation coordinating cell polarisation and lumen formation,” <i>EMBO Journal</i>, vol. 32, no. 1. Wiley-Blackwell, pp. 1–3, 2013."},"publication_status":"published","date_published":"2013-01-09T00:00:00Z","department":[{"_id":"CaHe"}],"oa_version":"Submitted Version","year":"2013","issue":"1","title":"Neurulation coordinating cell polarisation and lumen formation","day":"09","doi":"10.1038/emboj.2012.325","date_updated":"2021-01-12T07:00:42Z","status":"public","intvolume":"        32","oa":1,"external_id":{"pmid":["23211745"]},"pmid":1,"_id":"2920","abstract":[{"lang":"eng","text":"Cell polarisation in development is a common and fundamental process underlying embryo patterning and morphogenesis, and has been extensively studied over the past years. Our current knowledge of cell polarisation in development is predominantly based on studies that have analysed polarisation of single cells, such as eggs, or cellular aggregates with a stable polarising interface, such as cultured epithelial cells (St Johnston and Ahringer, 2010). However, in embryonic development, particularly of vertebrates, cell polarisation processes often encompass large numbers of cells that are placed within moving and proliferating tissues, and undergo mesenchymal-to-epithelial transitions with a highly complex spatiotemporal choreography. How such intricate cell polarisation processes in embryonic development are achieved has only started to be analysed. By using live imaging of neurulation in the transparent zebrafish embryo, Buckley et al (2012) now describe a novel polarisation strategy by which cells assemble an apical domain in the part of their cell body that intersects with the midline of the forming neural rod. This mechanism, along with the previously described mirror-symmetric divisions (Tawk et al, 2007), is thought to trigger formation of both neural rod midline and lumen."}],"publist_id":"3817","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley-Blackwell","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545307/"}],"page":"1 - 3","date_created":"2018-12-11T12:00:20Z","volume":32,"publication":"EMBO Journal","scopus_import":1,"month":"01","author":[{"id":"2E3E0988-F248-11E8-B48F-1D18A9856A87","full_name":"Compagnon, Julien","first_name":"Julien","last_name":"Compagnon"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"type":"journal_article"},{"publist_id":"3811","ec_funded":1,"project":[{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1"},{"call_identifier":"FP7","grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425"},{"grant_number":"302004","call_identifier":"FP7","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","name":"Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach"}],"publisher":"Cell Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Funding for this project was obtained by the German Research Foundation (DFG, to S.C.) and the European Research Council (ERC, through an ERC-Starting Grant to S.C. and an Individual Marie Curie IEF fellowship to L.V.U.).\r\nWe thank Jørgen Eilenberg, Bernhardt Steinwender, Miriam Stock, and Meghan L. Vyleta for the fungal strain and its characterization; Volker Witte for chemical information; Eva Sixt for ant drawings; and Robert Hauschild for help with image analysis. We further thank Martin Kaltenpoth, Michael Sixt, Jürgen Heinze, and Joachim Ruther for discussion and Daria Siekhaus, Sophie A.O. Armitage, and Leila Masri for comments on the manuscript. \r\n","_id":"2926","abstract":[{"text":"To fight infectious diseases, host immune defenses are employed at multiple levels. Sanitary behavior, such as pathogen avoidance and removal, acts as a first line of defense to prevent infection [1] before activation of the physiological immune system. Insect societies have evolved a wide range of collective hygiene measures and intensive health care toward pathogen-exposed group members [2]. One of the most common behaviors is allogrooming, in which nestmates remove infectious particles from the body surfaces of exposed individuals [3]. Here we show that, in invasive garden ants, grooming of fungus-exposed brood is effective beyond the sheer mechanical removal of fungal conidiospores; it also includes chemical disinfection through the application of poison produced by the ants themselves. Formic acid is the main active component of the poison. It inhibits fungal growth of conidiospores remaining on the brood surface after grooming and also those collected in the mouth of the grooming ant. This dual function is achieved by uptake of the poison droplet into the mouth through acidopore self-grooming and subsequent application onto the infectious brood via brood grooming. This extraordinary behavior extends the current understanding of grooming and the establishment of social immunity in insect societies.","lang":"eng"}],"scopus_import":1,"publication":"Current Biology","type":"journal_article","language":[{"iso":"eng"}],"month":"01","author":[{"last_name":"Tragust","first_name":"Simon","full_name":"Tragust, Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"id":"479DDAAC-E9CD-11E9-9B5F-82450873F7A1","full_name":"Mitteregger, Barbara","first_name":"Barbara","last_name":"Mitteregger"},{"last_name":"Barone","full_name":"Barone, Vanessa","first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367"},{"last_name":"Konrad","first_name":"Matthias","full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ugelvig, Line V","first_name":"Line V","last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T12:00:23Z","page":"76 - 82","related_material":{"record":[{"id":"9757","relation":"research_data","status":"public"},{"relation":"dissertation_contains","id":"961","status":"public"}]},"volume":23,"date_published":"2013-01-07T00:00:00Z","oa_version":"None","department":[{"_id":"SyCr"},{"_id":"CaHe"}],"quality_controlled":"1","publication_status":"published","citation":{"mla":"Tragust, Simon, et al. “Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” <i>Current Biology</i>, vol. 23, no. 1, Cell Press, 2013, pp. 76–82, doi:<a href=\"https://doi.org/10.1016/j.cub.2012.11.034\">10.1016/j.cub.2012.11.034</a>.","short":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer, Current Biology 23 (2013) 76–82.","ieee":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer, “Ants disinfect fungus-exposed brood by oral uptake and spread of their poison,” <i>Current Biology</i>, vol. 23, no. 1. Cell Press, pp. 76–82, 2013.","ista":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. 2013. Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Current Biology. 23(1), 76–82.","ama":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. <i>Current Biology</i>. 2013;23(1):76-82. doi:<a href=\"https://doi.org/10.1016/j.cub.2012.11.034\">10.1016/j.cub.2012.11.034</a>","apa":"Tragust, S., Mitteregger, B., Barone, V., Konrad, M., Ugelvig, L. V., &#38; Cremer, S. (2013). Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2012.11.034\">https://doi.org/10.1016/j.cub.2012.11.034</a>","chicago":"Tragust, Simon, Barbara Mitteregger, Vanessa Barone, Matthias Konrad, Line V Ugelvig, and Sylvia Cremer. “Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2012.11.034\">https://doi.org/10.1016/j.cub.2012.11.034</a>."},"intvolume":"        23","status":"public","date_updated":"2023-09-07T12:05:08Z","year":"2013","doi":"10.1016/j.cub.2012.11.034","day":"07","issue":"1","title":"Ants disinfect fungus-exposed brood by oral uptake and spread of their poison"},{"date_published":"2013-05-01T00:00:00Z","publist_id":"3796","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"publisher":"Elsevier","oa_version":"None","quality_controlled":"1","_id":"2939","acknowledgement":"The authors thank Herbert Edelsbrunner for many helpful discussions and suggestions. Moreover, they are grateful for the careful reviews that helped to improve the quality of the paper.","citation":{"chicago":"Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">https://doi.org/10.1016/j.comgeo.2012.02.010</a>.","apa":"Chen, C., &#38; Kerber, M. (2013). An output sensitive algorithm for persistent homology. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">https://doi.org/10.1016/j.comgeo.2012.02.010</a>","ama":"Chen C, Kerber M. An output sensitive algorithm for persistent homology. <i>Computational Geometry: Theory and Applications</i>. 2013;46(4):435-447. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">10.1016/j.comgeo.2012.02.010</a>","ista":"Chen C, Kerber M. 2013. An output sensitive algorithm for persistent homology. Computational Geometry: Theory and Applications. 46(4), 435–447.","mla":"Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology.” <i>Computational Geometry: Theory and Applications</i>, vol. 46, no. 4, Elsevier, 2013, pp. 435–47, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">10.1016/j.comgeo.2012.02.010</a>.","short":"C. Chen, M. Kerber, Computational Geometry: Theory and Applications 46 (2013) 435–447.","ieee":"C. Chen and M. Kerber, “An output sensitive algorithm for persistent homology,” <i>Computational Geometry: Theory and Applications</i>, vol. 46, no. 4. Elsevier, pp. 435–447, 2013."},"publication_status":"published","abstract":[{"lang":"eng","text":"In this paper, we present the first output-sensitive algorithm to compute the persistence diagram of a filtered simplicial complex. For any Γ &gt; 0, it returns only those homology classes with persistence at least Γ. Instead of the classical reduction via column operations, our algorithm performs rank computations on submatrices of the boundary matrix. For an arbitrary constant δ ∈ (0, 1), the running time is O (C (1 - δ) Γ R d (n) log n), where C (1 - δ) Γ is the number of homology classes with persistence at least (1 - δ) Γ, n is the total number of simplices in the complex, d its dimension, and R d (n) is the complexity of computing the rank of an n × n matrix with O (d n) nonzero entries. Depending on the choice of the rank algorithm, this yields a deterministic O (C (1 - δ) Γ n 2.376) algorithm, an O (C (1 - δ) Γ n 2.28) Las-Vegas algorithm, or an O (C (1 - δ) Γ n 2 + ε{lunate}) Monte-Carlo algorithm for an arbitrary ε{lunate} &gt; 0. The space complexity of the Monte-Carlo version is bounded by O (d n) = O (n log n)."}],"date_updated":"2023-02-23T11:24:10Z","publication":"Computational Geometry: Theory and Applications","status":"public","scopus_import":1,"intvolume":"        46","month":"05","author":[{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chao","full_name":"Chen, Chao"},{"id":"36E4574A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8030-9299","last_name":"Kerber","first_name":"Michael","full_name":"Kerber, Michael"}],"language":[{"iso":"eng"}],"type":"journal_article","page":"435 - 447","year":"2013","date_created":"2018-12-11T12:00:27Z","volume":46,"related_material":{"record":[{"status":"public","id":"3367","relation":"earlier_version"}]},"issue":"4","title":"An output sensitive algorithm for persistent homology","day":"01","doi":"10.1016/j.comgeo.2012.02.010"},{"volume":7785,"ddc":["000"],"related_material":{"record":[{"relation":"later_version","id":"1479","status":"public"}]},"file_date_updated":"2020-07-14T12:45:54Z","date_created":"2018-12-11T12:00:27Z","page":"23 - 39","conference":{"name":"TCC: Theory of Cryptography Conference","location":"Tokyo, Japan","end_date":"2013-03-06","start_date":"2013-03-03"},"language":[{"iso":"eng"}],"author":[{"full_name":"Krenn, Stephan","first_name":"Stephan","last_name":"Krenn","orcid":"0000-0003-2835-9093","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"},{"full_name":"Wadia, Akshay","first_name":"Akshay","last_name":"Wadia"}],"month":"01","type":"conference","scopus_import":1,"abstract":[{"lang":"eng","text":"A chain rule for an entropy notion H(.) states that the entropy H(X) of a variable X decreases by at most l if conditioned on an l-bit string A, i.e., H(X|A)&gt;= H(X)-l. More generally, it satisfies a chain rule for conditional entropy if H(X|Y,A)&gt;= H(X|Y)-l.\r\n\r\nAll natural information theoretic entropy notions we are aware of (like Shannon or min-entropy) satisfy some kind of chain rule for conditional entropy. Moreover, many computational entropy notions (like Yao entropy, unpredictability entropy and several variants of HILL entropy) satisfy the chain rule for conditional entropy, though here not only the quantity decreases by l, but also the quality of the entropy decreases exponentially in l. However, for \r\nthe standard notion of conditional HILL entropy (the computational equivalent of min-entropy) the existence of such a rule was unknown so far.\r\n\r\nIn this paper, we prove that for conditional HILL entropy no meaningful chain rule exists, assuming the existence of one-way permutations: there exist distributions X,Y,A, where A is a distribution over a single bit, but  $H(X|Y)&gt;&gt;H(X|Y,A)$, even if we simultaneously allow for a massive degradation in the quality of the entropy.\r\n\r\nThe idea underlying our construction is based on a surprising connection between the chain rule for HILL entropy and deniable encryption. "}],"_id":"2940","alternative_title":["LNCS"],"publisher":"Springer","project":[{"grant_number":"259668","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3795","ec_funded":1,"doi":"10.1007/978-3-642-36594-2_2","day":"29","has_accepted_license":"1","title":"A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it","year":"2013","oa":1,"status":"public","intvolume":"      7785","date_updated":"2023-02-23T10:00:43Z","citation":{"mla":"Krenn, Stephan, et al. <i>A Counterexample to the Chain Rule for Conditional HILL Entropy, and What Deniable Encryption Has to Do with It</i>. Edited by Amit Sahai, vol. 7785, Springer, 2013, pp. 23–39, doi:<a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">10.1007/978-3-642-36594-2_2</a>.","short":"S. Krenn, K.Z. Pietrzak, A. Wadia, in:, A. Sahai (Ed.), Springer, 2013, pp. 23–39.","ieee":"S. Krenn, K. Z. Pietrzak, and A. Wadia, “A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it,” presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan, 2013, vol. 7785, pp. 23–39.","ista":"Krenn S, Pietrzak KZ, Wadia A. 2013. A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. TCC: Theory of Cryptography Conference, LNCS, vol. 7785, 23–39.","apa":"Krenn, S., Pietrzak, K. Z., &#38; Wadia, A. (2013). A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. In A. Sahai (Ed.) (Vol. 7785, pp. 23–39). Presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan: Springer. <a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">https://doi.org/10.1007/978-3-642-36594-2_2</a>","ama":"Krenn S, Pietrzak KZ, Wadia A. A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. In: Sahai A, ed. Vol 7785. Springer; 2013:23-39. doi:<a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">10.1007/978-3-642-36594-2_2</a>","chicago":"Krenn, Stephan, Krzysztof Z Pietrzak, and Akshay Wadia. “A Counterexample to the Chain Rule for Conditional HILL Entropy, and What Deniable Encryption Has to Do with It.” edited by Amit Sahai, 7785:23–39. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">https://doi.org/10.1007/978-3-642-36594-2_2</a>."},"publication_status":"published","editor":[{"first_name":"Amit","full_name":"Sahai, Amit","last_name":"Sahai"}],"quality_controlled":"1","file":[{"date_updated":"2020-07-14T12:45:54Z","file_name":"2013_LNCS_Krenn.pdf","access_level":"open_access","relation":"main_file","file_size":414823,"checksum":"beb0cc1c0579da2d2e84394230a5da78","file_id":"5875","content_type":"application/pdf","date_created":"2019-01-22T14:11:11Z","creator":"dernst"}],"oa_version":"Submitted Version","department":[{"_id":"KrPi"}],"date_published":"2013-01-29T00:00:00Z"},{"quality_controlled":"1","publication_status":"published","citation":{"apa":"Aeschbacher, S., Futschik, A., &#38; Beaumont, M. (2013). Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mec.12165\">https://doi.org/10.1111/mec.12165</a>","ama":"Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . <i>Molecular Ecology</i>. 2013;22(4):987-1002. doi:<a href=\"https://doi.org/10.1111/mec.12165\">10.1111/mec.12165</a>","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” <i>Molecular Ecology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/mec.12165\">https://doi.org/10.1111/mec.12165</a>.","ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” <i>Molecular Ecology</i>, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002, 2013.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002.","mla":"Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” <i>Molecular Ecology</i>, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:<a href=\"https://doi.org/10.1111/mec.12165\">10.1111/mec.12165</a>.","ista":"Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 22(4), 987–1002."},"date_published":"2013-02-01T00:00:00Z","department":[{"_id":"NiBa"}],"oa_version":"None","year":"2013","title":"Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ","issue":"4","doi":"10.1111/mec.12165","day":"01","date_updated":"2023-02-23T14:07:19Z","intvolume":"        22","status":"public","acknowledgement":"This study has made use of the computational resources provided by IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk). The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk). S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation, St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).","_id":"2944","abstract":[{"lang":"eng","text":"We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"publist_id":"3788","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley-Blackwell","page":"987 - 1002","date_created":"2018-12-11T12:00:28Z","related_material":{"record":[{"id":"9758","relation":"research_data","status":"public"}]},"volume":22,"publication":"Molecular Ecology","scopus_import":1,"type":"journal_article","month":"02","language":[{"iso":"eng"}],"author":[{"last_name":"Aeschbacher","full_name":"Aeschbacher, Simon","first_name":"Simon","id":"2D35326E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Futschik","full_name":"Futschik, Andreas","first_name":"Andreas"},{"first_name":"Mark","full_name":"Beaumont, Mark","last_name":"Beaumont"}]},{"scopus_import":1,"type":"conference","conference":{"start_date":"2012-11-05","end_date":"2012-11-09","location":"Daejeon, Korea","name":"ACCV: Asian Conference on Computer Vision"},"author":[{"first_name":"Tatiana","full_name":"Tommasi, Tatiana","last_name":"Tommasi"},{"last_name":"Quadrianto","full_name":"Quadrianto, Novi","first_name":"Novi"},{"last_name":"Caputo","full_name":"Caputo, Barbara","first_name":"Barbara"},{"first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"month":"04","date_created":"2018-12-11T12:00:30Z","page":"1 - 15","file_date_updated":"2020-07-14T12:45:55Z","ddc":["000"],"volume":7724,"publist_id":"3784","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"acknowledgement":"This work was supported by the PASCAL 2 Network of Excellence (TT) and by the Newton International Fellowship (NQ)","_id":"2948","abstract":[{"lang":"eng","text":"Many visual datasets are traditionally used to analyze the performance of different learning techniques. The evaluation is usually done within each dataset, therefore it is questionable if such results are a reliable indicator of true generalization ability. We propose here an algorithm to exploit the existing data resources when learning on a new multiclass problem. Our main idea is to identify an image representation that decomposes orthogonally into two subspaces: a part specific to each dataset, and a part generic to, and therefore shared between, all the considered source sets. This allows us to use the generic representation as un-biased reference knowledge for a novel classification task. By casting the method in the multi-view setting, we also make it possible to use different features for different databases. We call the algorithm MUST, Multitask Unaligned Shared knowledge Transfer. Through extensive experiments on five public datasets, we show that MUST consistently improves the cross-datasets generalization performance."}],"intvolume":"      7724","status":"public","date_updated":"2020-08-11T10:09:54Z","oa":1,"year":"2013","doi":"10.1007/978-3-642-37331-2_1","day":"04","has_accepted_license":"1","title":"Beyond dataset bias: Multi-task unaligned shared knowledge transfer","date_published":"2013-04-04T00:00:00Z","series_title":"Lecture Notes in Computer Science","oa_version":"Submitted Version","file":[{"date_created":"2019-01-22T14:03:11Z","file_id":"5874","content_type":"application/pdf","creator":"dernst","date_updated":"2020-07-14T12:45:55Z","relation":"main_file","access_level":"open_access","file_size":1513620,"checksum":"a0a7234a89e2192af655b0d0ae3bf445","file_name":"2012_ACCV_Tommasi.pdf"}],"department":[{"_id":"ChLa"}],"quality_controlled":"1","publication_status":"published","citation":{"ama":"Tommasi T, Quadrianto N, Caputo B, Lampert C. Beyond dataset bias: Multi-task unaligned shared knowledge transfer. 2013;7724:1-15. doi:<a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">10.1007/978-3-642-37331-2_1</a>","apa":"Tommasi, T., Quadrianto, N., Caputo, B., &#38; Lampert, C. (2013). Beyond dataset bias: Multi-task unaligned shared knowledge transfer. Presented at the ACCV: Asian Conference on Computer Vision, Daejeon, Korea: Springer. <a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">https://doi.org/10.1007/978-3-642-37331-2_1</a>","chicago":"Tommasi, Tatiana, Novi Quadrianto, Barbara Caputo, and Christoph Lampert. “Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">https://doi.org/10.1007/978-3-642-37331-2_1</a>.","mla":"Tommasi, Tatiana, et al. <i>Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer</i>. Vol. 7724, Springer, 2013, pp. 1–15, doi:<a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">10.1007/978-3-642-37331-2_1</a>.","short":"T. Tommasi, N. Quadrianto, B. Caputo, C. Lampert, 7724 (2013) 1–15.","ieee":"T. Tommasi, N. Quadrianto, B. Caputo, and C. Lampert, “Beyond dataset bias: Multi-task unaligned shared knowledge transfer,” vol. 7724. Springer, pp. 1–15, 2013.","ista":"Tommasi T, Quadrianto N, Caputo B, Lampert C. 2013. Beyond dataset bias: Multi-task unaligned shared knowledge transfer. 7724, 1–15."}},{"type":"journal_article","month":"04","author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Alfaro","full_name":"De Alfaro, Luca","first_name":"Luca"},{"last_name":"Faella","full_name":"Faella, Marco","first_name":"Marco"},{"first_name":"Ritankar","full_name":"Majumdar, Ritankar","last_name":"Majumdar"},{"full_name":"Raman, Vishwanath","first_name":"Vishwanath","last_name":"Raman"}],"language":[{"iso":"eng"}],"scopus_import":1,"intvolume":"        42","status":"public","date_updated":"2021-01-12T07:41:10Z","publication":"Formal Methods in System Design","day":"01","doi":"10.1007/s10703-012-0170-4","issue":"2","title":"Code aware resource management","volume":42,"date_created":"2018-12-11T12:01:29Z","year":"2013","page":"142 - 174","oa_version":"None","publisher":"Springer","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3583","date_published":"2013-04-01T00:00:00Z","abstract":[{"lang":"eng","text":"Multithreaded programs coordinate their interaction through synchronization primitives like mutexes and semaphores, which are managed by an OS-provided resource manager. We propose algorithms for the automatic construction of code-aware resource managers for multithreaded embedded applications. Such managers use knowledge about the structure and resource usage (mutex and semaphore usage) of the threads to guarantee deadlock freedom and progress while managing resources in an efficient way. Our algorithms compute managers as winning strategies in certain infinite games, and produce a compact code description of these strategies. We have implemented the algorithms in the tool Cynthesis. Given a multithreaded program in C, the tool produces C code implementing a code-aware resource manager. We show in experiments that Cynthesis produces compact resource managers within a few minutes on a set of embedded benchmarks with up to 6 threads. © 2012 Springer Science+Business Media, LLC."}],"citation":{"ista":"Chatterjee K, De Alfaro L, Faella M, Majumdar R, Raman V. 2013. Code aware resource management. Formal Methods in System Design. 42(2), 142–174.","mla":"Chatterjee, Krishnendu, et al. “Code Aware Resource Management.” <i>Formal Methods in System Design</i>, vol. 42, no. 2, Springer, 2013, pp. 142–74, doi:<a href=\"https://doi.org/10.1007/s10703-012-0170-4\">10.1007/s10703-012-0170-4</a>.","short":"K. Chatterjee, L. De Alfaro, M. Faella, R. Majumdar, V. Raman, Formal Methods in System Design 42 (2013) 142–174.","ieee":"K. Chatterjee, L. De Alfaro, M. Faella, R. Majumdar, and V. Raman, “Code aware resource management,” <i>Formal Methods in System Design</i>, vol. 42, no. 2. Springer, pp. 142–174, 2013.","chicago":"Chatterjee, Krishnendu, Luca De Alfaro, Marco Faella, Ritankar Majumdar, and Vishwanath Raman. “Code Aware Resource Management.” <i>Formal Methods in System Design</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s10703-012-0170-4\">https://doi.org/10.1007/s10703-012-0170-4</a>.","ama":"Chatterjee K, De Alfaro L, Faella M, Majumdar R, Raman V. Code aware resource management. <i>Formal Methods in System Design</i>. 2013;42(2):142-174. doi:<a href=\"https://doi.org/10.1007/s10703-012-0170-4\">10.1007/s10703-012-0170-4</a>","apa":"Chatterjee, K., De Alfaro, L., Faella, M., Majumdar, R., &#38; Raman, V. (2013). Code aware resource management. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-012-0170-4\">https://doi.org/10.1007/s10703-012-0170-4</a>"},"publication_status":"published","acknowledgement":"This research was supported in part by the National Science Foundation CAREER award CCR-0132780, by the ONR grant N00014-02-1-0671, by the National Science Foundation grants CCR-0427202 and CCR-0234690, and by the ARP award TO.030.MM.D.","_id":"3116","quality_controlled":"1"},{"type":"journal_article","language":[{"iso":"eng"}],"month":"10","author":[{"last_name":"Dubuis","first_name":"Julien","full_name":"Dubuis, Julien"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper"},{"last_name":"Wieschaus","first_name":"Eric","full_name":"Wieschaus, Eric"},{"full_name":"Gregor, Thomas","first_name":"Thomas","last_name":"Gregor"},{"first_name":"William","full_name":"Bialek, William","last_name":"Bialek"}],"scopus_import":1,"publication":"PNAS","file_date_updated":"2020-07-14T12:46:06Z","volume":110,"ddc":["570"],"date_created":"2018-12-11T12:02:19Z","page":"16301 - 16308","publisher":"National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3387","abstract":[{"lang":"eng","text":"Cells in a developing embryo have no direct way of &quot;measuring&quot; their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus form a code for &quot;positional information.&quot; We show how to measure this information, in bits, using the gap genes in the Drosophila embryo as an example. Individual genes carry nearly two bits of information, twice as much as expected if the expression patterns consisted only of on/off domains separated by sharp boundaries. Taken together, four gap genes carry enough information to define a cell's location with an error bar of ~1% along the anterior-posterior axis of the embryo. This precision is nearly enough for each cell to have a unique identity, which is the maximum information the system can use, and is nearly constant along the length of the embryo. We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network."}],"_id":"3261","pmid":1,"external_id":{"pmid":["24089448"]},"oa":1,"intvolume":"       110","status":"public","date_updated":"2021-01-12T07:42:13Z","doi":"10.1073/pnas.1315642110","day":"08","has_accepted_license":"1","issue":"41","title":"Positional information, in bits","year":"2013","file":[{"relation":"main_file","access_level":"open_access","file_size":1670548,"checksum":"ecd859fe52a562193027d428b5524a8d","file_name":"2013_PNAS_Dubuis.pdf","date_updated":"2020-07-14T12:46:06Z","creator":"dernst","date_created":"2019-01-22T13:53:23Z","file_id":"5873","content_type":"application/pdf"}],"oa_version":"Published Version","department":[{"_id":"GaTk"}],"date_published":"2013-10-08T00:00:00Z","citation":{"chicago":"Dubuis, Julien, Gašper Tkačik, Eric Wieschaus, Thomas Gregor, and William Bialek. “Positional Information, in Bits.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1315642110\">https://doi.org/10.1073/pnas.1315642110</a>.","apa":"Dubuis, J., Tkačik, G., Wieschaus, E., Gregor, T., &#38; Bialek, W. (2013). Positional information, in bits. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1315642110\">https://doi.org/10.1073/pnas.1315642110</a>","ama":"Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. Positional information, in bits. <i>PNAS</i>. 2013;110(41):16301-16308. doi:<a href=\"https://doi.org/10.1073/pnas.1315642110\">10.1073/pnas.1315642110</a>","ista":"Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. 2013. Positional information, in bits. PNAS. 110(41), 16301–16308.","mla":"Dubuis, Julien, et al. “Positional Information, in Bits.” <i>PNAS</i>, vol. 110, no. 41, National Academy of Sciences, 2013, pp. 16301–08, doi:<a href=\"https://doi.org/10.1073/pnas.1315642110\">10.1073/pnas.1315642110</a>.","short":"J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, W. Bialek, PNAS 110 (2013) 16301–16308.","ieee":"J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, and W. Bialek, “Positional information, in bits,” <i>PNAS</i>, vol. 110, no. 41. National Academy of Sciences, pp. 16301–16308, 2013."},"publication_status":"published","quality_controlled":"1"},{"date_updated":"2021-01-12T07:42:38Z","publication":"Encyclopedia of Systems Biology","status":"public","intvolume":"         3","language":[{"iso":"eng"}],"month":"01","author":[{"full_name":"Quadrianto, Novi","first_name":"Novi","last_name":"Quadrianto"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"}],"type":"encyclopedia_article","page":"1069 - 1069","year":"2013","date_created":"2018-12-11T12:02:39Z","volume":3,"title":"Kernel based learning","doi":"10.1007/978-1-4419-9863-7_604","day":"01","date_published":"2013-01-01T00:00:00Z","publist_id":"3314","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChLa"}],"publisher":"Springer","oa_version":"None","quality_controlled":"1","_id":"3321","editor":[{"first_name":"Werner","full_name":"Dubitzky, Werner","last_name":"Dubitzky"},{"last_name":"Wolkenhauer","full_name":"Wolkenhauer, Olaf","first_name":"Olaf"},{"last_name":"Cho","first_name":"Kwang","full_name":"Cho, Kwang"},{"last_name":"Yokota","first_name":"Hiroki","full_name":"Yokota, Hiroki"}],"publication_status":"published","citation":{"chicago":"Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” In <i>Encyclopedia of Systems Biology</i>, edited by Werner Dubitzky, Olaf Wolkenhauer, Kwang Cho, and Hiroki Yokota, 3:1069–1069. Springer, 2013. <a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">https://doi.org/10.1007/978-1-4419-9863-7_604</a>.","apa":"Quadrianto, N., &#38; Lampert, C. (2013). Kernel based learning. In W. Dubitzky, O. Wolkenhauer, K. Cho, &#38; H. Yokota (Eds.), <i>Encyclopedia of Systems Biology</i> (Vol. 3, pp. 1069–1069). Springer. <a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">https://doi.org/10.1007/978-1-4419-9863-7_604</a>","ama":"Quadrianto N, Lampert C. Kernel based learning. In: Dubitzky W, Wolkenhauer O, Cho K, Yokota H, eds. <i>Encyclopedia of Systems Biology</i>. Vol 3. Springer; 2013:1069-1069. doi:<a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">10.1007/978-1-4419-9863-7_604</a>","ista":"Quadrianto N, Lampert C. 2013.Kernel based learning. In: Encyclopedia of Systems Biology. vol. 3, 1069–1069.","ieee":"N. Quadrianto and C. Lampert, “Kernel based learning,” in <i>Encyclopedia of Systems Biology</i>, vol. 3, W. Dubitzky, O. Wolkenhauer, K. Cho, and H. Yokota, Eds. Springer, 2013, pp. 1069–1069.","mla":"Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” <i>Encyclopedia of Systems Biology</i>, edited by Werner Dubitzky et al., vol. 3, Springer, 2013, pp. 1069–1069, doi:<a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">10.1007/978-1-4419-9863-7_604</a>.","short":"N. Quadrianto, C. Lampert, in:, W. Dubitzky, O. Wolkenhauer, K. Cho, H. Yokota (Eds.), Encyclopedia of Systems Biology, Springer, 2013, pp. 1069–1069."}},{"year":"2013","doi":"10.3390/plants2040650","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)"},"keyword":["Plant Science","Ecology","Ecology","Evolution","Behavior and Systematics"],"day":"21","has_accepted_license":"1","issue":"4","title":"Calcium: The missing link in auxin action","publication_identifier":{"issn":["2223-7747"]},"intvolume":"         2","status":"public","date_updated":"2022-03-21T12:15:29Z","external_id":{"pmid":["27137397"]},"license":"https://creativecommons.org/licenses/by/3.0/","oa":1,"quality_controlled":"1","publication_status":"published","citation":{"chicago":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” <i>Plants</i>. MDPI, 2013. <a href=\"https://doi.org/10.3390/plants2040650\">https://doi.org/10.3390/plants2040650</a>.","ama":"Vanneste S, Friml J. Calcium: The missing link in auxin action. <i>Plants</i>. 2013;2(4):650-675. doi:<a href=\"https://doi.org/10.3390/plants2040650\">10.3390/plants2040650</a>","apa":"Vanneste, S., &#38; Friml, J. (2013). Calcium: The missing link in auxin action. <i>Plants</i>. MDPI. <a href=\"https://doi.org/10.3390/plants2040650\">https://doi.org/10.3390/plants2040650</a>","ista":"Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants. 2(4), 650–675.","mla":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” <i>Plants</i>, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:<a href=\"https://doi.org/10.3390/plants2040650\">10.3390/plants2040650</a>.","short":"S. Vanneste, J. Friml, Plants 2 (2013) 650–675.","ieee":"S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” <i>Plants</i>, vol. 2, no. 4. MDPI, pp. 650–675, 2013."},"article_type":"original","date_published":"2013-10-21T00:00:00Z","file":[{"creator":"dernst","success":1,"date_created":"2022-03-21T12:12:56Z","file_id":"10916","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":670188,"checksum":"fb4ff2e820e344e253c9197544610be6","file_name":"2013_Plants_Vanneste.pdf","date_updated":"2022-03-21T12:12:56Z"}],"oa_version":"Published Version","department":[{"_id":"JiFr"}],"date_created":"2022-03-21T07:13:49Z","page":"650-675","file_date_updated":"2022-03-21T12:12:56Z","ddc":["580"],"volume":2,"scopus_import":"1","publication":"Plants","article_processing_charge":"No","type":"journal_article","author":[{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"month":"10","_id":"10895","pmid":1,"abstract":[{"lang":"eng","text":"Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. "}],"publisher":"MDPI","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"place":"Berlin, Heidelberg","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"publisher":"Springer Nature","ec_funded":1,"abstract":[{"lang":"eng","text":"Taking images is an efficient way to collect data about the physical world. It can be done fast and in exquisite detail. By definition, image processing is the field that concerns itself with the computation aimed at harnessing the information contained in images [10]. This talk is concerned with topological information. Our main thesis is that persistent homology [5] is a useful method to quantify and summarize topological information, building a bridge that connects algebraic topology with applications. We provide supporting evidence for this thesis by touching upon four technical developments in the overlap between persistent homology and image processing."}],"acknowledgement":"This research is partially supported by the European Science Foundation (ESF) under the Research Network Programme, the European Union under the Toposys Project FP7-ICT-318493-STREP, the Russian Government under the Mega Project 11.G34.31.0053.","_id":"10897","type":"conference","language":[{"iso":"eng"}],"author":[{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"}],"conference":{"name":"GbRPR: Graph-based Representations in Pattern Recognition","location":"Vienna, Austria","end_date":"2013-05-17","start_date":"2013-05-15"},"month":"06","publication":"Graph-Based Representations in Pattern Recognition","article_processing_charge":"No","scopus_import":"1","volume":7877,"page":"182-183","date_created":"2022-03-21T07:30:33Z","department":[{"_id":"HeEd"}],"series_title":"LNCS","oa_version":"None","date_published":"2013-06-01T00:00:00Z","citation":{"short":"H. Edelsbrunner, in:, Graph-Based Representations in Pattern Recognition, Springer Nature, Berlin, Heidelberg, 2013, pp. 182–183.","mla":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” <i>Graph-Based Representations in Pattern Recognition</i>, vol. 7877, Springer Nature, 2013, pp. 182–83, doi:<a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">10.1007/978-3-642-38221-5_19</a>.","ieee":"H. Edelsbrunner, “Persistent homology in image processing,” in <i>Graph-Based Representations in Pattern Recognition</i>, Vienna, Austria, 2013, vol. 7877, pp. 182–183.","ista":"Edelsbrunner H. 2013. Persistent homology in image processing. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNCS vol. 7877, 182–183.","ama":"Edelsbrunner H. Persistent homology in image processing. In: <i>Graph-Based Representations in Pattern Recognition</i>. Vol 7877. LNCS. Berlin, Heidelberg: Springer Nature; 2013:182-183. doi:<a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">10.1007/978-3-642-38221-5_19</a>","apa":"Edelsbrunner, H. (2013). Persistent homology in image processing. In <i>Graph-Based Representations in Pattern Recognition</i> (Vol. 7877, pp. 182–183). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">https://doi.org/10.1007/978-3-642-38221-5_19</a>","chicago":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” In <i>Graph-Based Representations in Pattern Recognition</i>, 7877:182–83. LNCS. Berlin, Heidelberg: Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">https://doi.org/10.1007/978-3-642-38221-5_19</a>."},"publication_status":"published","quality_controlled":"1","date_updated":"2023-09-05T15:10:20Z","intvolume":"      7877","status":"public","title":"Persistent homology in image processing","publication_identifier":{"eisbn":["9783642382215"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783642382208"]},"doi":"10.1007/978-3-642-38221-5_19","day":"01","year":"2013"},{"_id":"10898","quality_controlled":"1","publication_status":"published","citation":{"apa":"Haas, A., Lippautz, M., Henzinger, T. A., Payer, H., Sokolova, A., Kirsch, C. M., &#38; Sezgin, A. (2013). Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. Ischia, Italy: ACM Press. <a href=\"https://doi.org/10.1145/2482767.2482789\">https://doi.org/10.1145/2482767.2482789</a>","ama":"Haas A, Lippautz M, Henzinger TA, et al. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In: <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. ACM Press; 2013. doi:<a href=\"https://doi.org/10.1145/2482767.2482789\">10.1145/2482767.2482789</a>","chicago":"Haas, Andreas, Michael Lippautz, Thomas A Henzinger, Hannes Payer, Ana Sokolova, Christoph M. Kirsch, and Ali Sezgin. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” In <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. ACM Press, 2013. <a href=\"https://doi.org/10.1145/2482767.2482789\">https://doi.org/10.1145/2482767.2482789</a>.","ieee":"A. Haas <i>et al.</i>, “Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation,” in <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>, Ischia, Italy, 2013, no. 5.","short":"A. Haas, M. Lippautz, T.A. Henzinger, H. Payer, A. Sokolova, C.M. Kirsch, A. Sezgin, in:, Proceedings of the ACM International Conference on Computing Frontiers - CF ’13, ACM Press, 2013.","mla":"Haas, Andreas, et al. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>, no. 5, 17, ACM Press, 2013, doi:<a href=\"https://doi.org/10.1145/2482767.2482789\">10.1145/2482767.2482789</a>.","ista":"Haas A, Lippautz M, Henzinger TA, Payer H, Sokolova A, Kirsch CM, Sezgin A. 2013. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. CF: Conference on Computing Frontiers, 17."},"abstract":[{"lang":"eng","text":"A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered."}],"date_published":"2013-05-01T00:00:00Z","publisher":"ACM Press","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"year":"2013","date_created":"2022-03-21T07:33:22Z","doi":"10.1145/2482767.2482789","article_number":"17","day":"01","publication_identifier":{"isbn":["978-145032053-5"]},"title":"Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation","issue":"5","status":"public","scopus_import":"1","article_processing_charge":"No","publication":"Proceedings of the ACM International Conference on Computing Frontiers - CF '13","date_updated":"2022-06-21T08:01:19Z","author":[{"full_name":"Haas, Andreas","first_name":"Andreas","last_name":"Haas"},{"last_name":"Lippautz","full_name":"Lippautz, Michael","first_name":"Michael"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Payer","full_name":"Payer, Hannes","first_name":"Hannes"},{"first_name":"Ana","full_name":"Sokolova, Ana","last_name":"Sokolova"},{"first_name":"Christoph M.","full_name":"Kirsch, Christoph M.","last_name":"Kirsch"},{"id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","full_name":"Sezgin, Ali","first_name":"Ali"}],"conference":{"end_date":"2013-05-16","start_date":"2013-05-14","name":"CF: Conference on Computing Frontiers","location":"Ischia, Italy"},"month":"05","language":[{"iso":"eng"}],"type":"conference"},{"doi":"10.1016/b978-0-12-384719-5.00031-9","day":"01","keyword":["Adaptive landscape","Cline","Coalescent process","Gene flow","Hybrid zone","Local adaptation","Natural selection","Neutral theory","Population structure","Speciation"],"publication_identifier":{"isbn":["978-0-12-384720-1"]},"title":"Differentiation","year":"2013","date_created":"2022-03-21T07:46:22Z","page":"508-515","month":"01","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"language":[{"iso":"eng"}],"type":"book_chapter","status":"public","scopus_import":"1","article_processing_charge":"No","publication":"Encyclopedia of Biodiversity","date_updated":"2022-06-20T09:18:06Z","citation":{"chicago":"Barton, Nicholas H. “Differentiation.” In <i>Encyclopedia of Biodiversity</i>, 2nd ed., 508–15. Elsevier, 2013. <a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">https://doi.org/10.1016/b978-0-12-384719-5.00031-9</a>.","ama":"Barton NH. Differentiation. In: <i>Encyclopedia of Biodiversity</i>. 2nd ed. Elsevier; 2013:508-515. doi:<a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">10.1016/b978-0-12-384719-5.00031-9</a>","apa":"Barton, N. H. (2013). Differentiation. In <i>Encyclopedia of Biodiversity</i> (2nd ed., pp. 508–515). Elsevier. <a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">https://doi.org/10.1016/b978-0-12-384719-5.00031-9</a>","ista":"Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515.","ieee":"N. H. Barton, “Differentiation,” in <i>Encyclopedia of Biodiversity</i>, 2nd ed., Elsevier, 2013, pp. 508–515.","short":"N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515.","mla":"Barton, Nicholas H. “Differentiation.” <i>Encyclopedia of Biodiversity</i>, 2nd ed., Elsevier, 2013, pp. 508–15, doi:<a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">10.1016/b978-0-12-384719-5.00031-9</a>."},"publication_status":"published","_id":"10899","quality_controlled":"1","publisher":"Elsevier","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"edition":"2","date_published":"2013-01-01T00:00:00Z"},{"publication_identifier":{"isbn":["9781627034258"],"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["9781627034265"]},"title":"Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations","day":"03","doi":"10.1007/978-1-62703-426-5_14","year":"2013","external_id":{"pmid":["23625502"]},"date_updated":"2023-09-05T13:15:33Z","status":"public","intvolume":"      1013","editor":[{"last_name":"Cardona","first_name":"Astrid","full_name":"Cardona, Astrid"},{"first_name":"Eroboghene","full_name":"Ubogu, Eroboghene","last_name":"Ubogu"}],"citation":{"ista":"Weber M, Sixt MK. 2013.Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Chemokines. Methods in Molecular Biology, vol. 1013, 215–226.","ieee":"M. Weber and M. K. Sixt, “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations,” in <i>Chemokines</i>, vol. 1013, A. Cardona and E. Ubogu, Eds. Totowa, NJ: Humana Press, 2013, pp. 215–226.","short":"M. Weber, M.K. Sixt, in:, A. Cardona, E. Ubogu (Eds.), Chemokines, Humana Press, Totowa, NJ, 2013, pp. 215–226.","mla":"Weber, Michele, and Michael K. Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” <i>Chemokines</i>, edited by Astrid Cardona and Eroboghene Ubogu, vol. 1013, Humana Press, 2013, pp. 215–26, doi:<a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">10.1007/978-1-62703-426-5_14</a>.","chicago":"Weber, Michele, and Michael K Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” In <i>Chemokines</i>, edited by Astrid Cardona and Eroboghene Ubogu, 1013:215–26. MIMB. Totowa, NJ: Humana Press, 2013. <a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">https://doi.org/10.1007/978-1-62703-426-5_14</a>.","apa":"Weber, M., &#38; Sixt, M. K. (2013). Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In A. Cardona &#38; E. Ubogu (Eds.), <i>Chemokines</i> (Vol. 1013, pp. 215–226). Totowa, NJ: Humana Press. <a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">https://doi.org/10.1007/978-1-62703-426-5_14</a>","ama":"Weber M, Sixt MK. Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Cardona A, Ubogu E, eds. <i>Chemokines</i>. Vol 1013. MIMB. Totowa, NJ: Humana Press; 2013:215-226. doi:<a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">10.1007/978-1-62703-426-5_14</a>"},"publication_status":"published","quality_controlled":"1","department":[{"_id":"MiSi"}],"oa_version":"None","series_title":"MIMB","date_published":"2013-04-03T00:00:00Z","volume":1013,"page":"215-226","date_created":"2022-03-21T07:47:41Z","month":"04","language":[{"iso":"eng"}],"author":[{"last_name":"Weber","full_name":"Weber, Michele","first_name":"Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt"}],"type":"book_chapter","article_processing_charge":"No","publication":"Chemokines","scopus_import":"1","abstract":[{"text":"Leukocyte migration through the interstitial space is crucial for the maintenance of tolerance and immunity. The main cues for leukocyte trafficking are chemokines thought to directionally guide these cells towards their targets. However, model systems that facilitate quantification of chemokine-guided leukocyte migration in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted mouse ears that allows the visualization of chemokine-dependent dendritic cell (DC) motility in the dermal interstitium in real time. We present methods for the preparation of mouse ear sheets and their use in multidimensional confocal imaging experiments to monitor and analyze the directional migration of fluorescently labelled DCs through the dermis and into afferent lymphatic vessels. The assay provides a more physiological approach to study leukocyte migration than in vitro three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen gels and transwell assays.","lang":"eng"}],"pmid":1,"_id":"10900","acknowledgement":"We would like to thank Alexander Eichner and Ingrid de Vries for discussion and critical reading of the manuscript, and Mary Frank for assistance with the recording of videos and images in Fig. 1. M.S. is supported through funding from the German Research Foundation (DFG). M.W. acknowledges the Alexander von Humboldt Foundation for funding.","alternative_title":["Methods in Molecular Biology"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","place":"Totowa, NJ","publisher":"Humana Press"},{"date_updated":"2023-09-05T15:10:38Z","status":"public","intvolume":"      7810","year":"2013","title":"How to travel between languages","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783642370649"],"eissn":["1611-3349"],"isbn":["9783642370632"]},"day":"15","doi":"10.1007/978-3-642-37064-9_20","date_published":"2013-04-15T00:00:00Z","department":[{"_id":"KrCh"}],"oa_version":"None","series_title":"LNCS","quality_controlled":"1","publication_status":"published","citation":{"ieee":"K. Chatterjee, S. Chaubal, and S. Rubin, “How to travel between languages,” in <i>7th International Conference on Language and Automata Theory and Applications</i>, Bilbao, Spain, 2013, vol. 7810, pp. 214–225.","short":"K. Chatterjee, S. Chaubal, S. Rubin, in:, 7th International Conference on Language and Automata Theory and Applications, Springer Nature, Berlin, Heidelberg, 2013, pp. 214–225.","mla":"Chatterjee, Krishnendu, et al. “How to Travel between Languages.” <i>7th International Conference on Language and Automata Theory and Applications</i>, vol. 7810, Springer Nature, 2013, pp. 214–25, doi:<a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">10.1007/978-3-642-37064-9_20</a>.","ista":"Chatterjee K, Chaubal S, Rubin S. 2013. How to travel between languages. 7th International Conference on Language and Automata Theory and Applications. LATA: Conference on Language and Automata Theory and ApplicationsLNCS, LNCS, vol. 7810, 214–225.","apa":"Chatterjee, K., Chaubal, S., &#38; Rubin, S. (2013). How to travel between languages. In <i>7th International Conference on Language and Automata Theory and Applications</i> (Vol. 7810, pp. 214–225). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">https://doi.org/10.1007/978-3-642-37064-9_20</a>","ama":"Chatterjee K, Chaubal S, Rubin S. How to travel between languages. In: <i>7th International Conference on Language and Automata Theory and Applications</i>. Vol 7810. LNCS. Berlin, Heidelberg: Springer Nature; 2013:214-225. doi:<a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">10.1007/978-3-642-37064-9_20</a>","chicago":"Chatterjee, Krishnendu, Siddhesh Chaubal, and Sasha Rubin. “How to Travel between Languages.” In <i>7th International Conference on Language and Automata Theory and Applications</i>, 7810:214–25. LNCS. Berlin, Heidelberg: Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">https://doi.org/10.1007/978-3-642-37064-9_20</a>."},"article_processing_charge":"No","publication":"7th International Conference on Language and Automata Theory and Applications","scopus_import":"1","language":[{"iso":"eng"}],"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Siddhesh","full_name":"Chaubal, Siddhesh","last_name":"Chaubal"},{"id":"2EC51194-F248-11E8-B48F-1D18A9856A87","last_name":"Rubin","first_name":"Sasha","full_name":"Rubin, Sasha"}],"conference":{"name":"LATA: Conference on Language and Automata Theory and Applications","location":"Bilbao, Spain","start_date":"2013-04-02","end_date":"2013-04-05"},"month":"04","type":"conference","page":"214-225","date_created":"2022-03-21T07:56:21Z","volume":7810,"ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","place":"Berlin, Heidelberg","publisher":"Springer Nature","project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"_id":"10902","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award. Thanks to Gabriele Puppis for suggesting the problem of identifying a deterministic transducer to compute the optimal cost, and to Martin Chmelik for his comments on the introduction.","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We consider how to edit strings from a source language so that the edited strings belong to a target language, where the languages are given as deterministic finite automata. Non-streaming (or offline) transducers perform edits given the whole source string. We show that the class of deterministic one-pass transducers with registers along with increment and min operation suffices for computing optimal edit distance, whereas the same class of transducers without the min operation is not sufficient. Streaming (or online) transducers perform edits as the letters of the source string are received. We present a polynomial time algorithm for the partial-repair problem that given a bound α asks for the construction of a deterministic streaming transducer (if one exists) that ensures that the ‘maximum fraction’ η of the strings of the source language are edited, within cost α, to the target language."}]},{"publist_id":"6821","ec_funded":1,"project":[{"grant_number":"207362","call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis"}],"publisher":"Frontiers Research Foundation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"827","abstract":[{"lang":"eng","text":"As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed."}],"scopus_import":1,"publication":"Frontiers in Plant Science","type":"journal_article","author":[{"last_name":"O'Brien","full_name":"O'Brien, José","first_name":"José"},{"last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"language":[{"iso":"eng"}],"month":"11","date_created":"2018-12-11T11:48:43Z","file_date_updated":"2020-07-14T12:48:11Z","volume":4,"ddc":["580"],"date_published":"2013-11-19T00:00:00Z","oa_version":"Published Version","file":[{"file_name":"2013_FrontiersPlant_OBrien.pdf","file_size":953299,"checksum":"fdc25ddd1bf9a99b99f662cdbafeddd4","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:48:11Z","creator":"dernst","content_type":"application/pdf","file_id":"5903","date_created":"2019-01-31T10:40:38Z"}],"department":[{"_id":"EvBe"}],"quality_controlled":"1","citation":{"apa":"O’Brien, J., &#38; Benková, E. (2013). Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>","ama":"O’Brien J, Benková E. Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>","chicago":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>.","ieee":"J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic stress responses,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013.","short":"J. O’Brien, E. Benková, Frontiers in Plant Science 4 (2013).","mla":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>, vol. 4, 451, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>.","ista":"O’Brien J, Benková E. 2013. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 4, 451."},"publication_status":"published","intvolume":"         4","status":"public","date_updated":"2021-01-12T08:17:50Z","license":"https://creativecommons.org/licenses/by/4.0/","oa":1,"year":"2013","day":"19","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_number":"451","doi":"10.3389/fpls.2013.00451","title":"Cytokinin cross talking during biotic and abiotic stress responses","has_accepted_license":"1"},{"abstract":[{"text":"The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed.","lang":"eng"}],"_id":"828","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Frontiers Research Foundation","project":[{"call_identifier":"FP7","grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"publist_id":"6820","volume":4,"ddc":["580"],"file_date_updated":"2020-07-14T12:48:11Z","date_created":"2018-12-11T11:48:43Z","month":"12","author":[{"full_name":"Cuesta, Candela","first_name":"Candela","last_name":"Cuesta","orcid":"0000-0003-1923-2410","id":"33A3C818-F248-11E8-B48F-1D18A9856A87"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","last_name":"Wabnik","first_name":"Krzysztof T","full_name":"Wabnik, Krzysztof T"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Frontiers in Plant Science","scopus_import":1,"citation":{"mla":"Cuesta, Candela, et al. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>, vol. 4, 537, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>.","short":"C. Cuesta, K.T. Wabnik, E. Benková, Frontiers in Plant Science 4 (2013).","ieee":"C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root architecture dynamics,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013.","ista":"Cuesta C, Wabnik KT, Benková E. 2013. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 4, 537.","ama":"Cuesta C, Wabnik KT, Benková E. Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>","apa":"Cuesta, C., Wabnik, K. T., &#38; Benková, E. (2013). Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>","chicago":"Cuesta, Candela, Krzysztof T Wabnik, and Eva Benková. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>."},"publication_status":"published","quality_controlled":"1","department":[{"_id":"EvBe"}],"oa_version":"Published Version","file":[{"creator":"dernst","date_created":"2019-01-31T10:36:43Z","content_type":"application/pdf","file_id":"5902","checksum":"0185b3c4d7df9a94bd3ce5a66d213506","file_size":710835,"relation":"main_file","access_level":"open_access","file_name":"2013_FrontiersPlant_Cuesta.pdf","date_updated":"2020-07-14T12:48:11Z"}],"date_published":"2013-12-26T00:00:00Z","has_accepted_license":"1","title":"Systems approaches to study root architecture dynamics","article_number":"537","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"26","doi":"10.3389/fpls.2013.00537","year":"2013","oa":1,"date_updated":"2021-01-12T08:17:52Z","status":"public","intvolume":"         4"},{"date_updated":"2023-09-07T11:40:43Z","intvolume":"      8044","status":"public","oa":1,"external_id":{"arxiv":["1303.5251"]},"year":"2013","title":"TTP: Tool for tumor progression","doi":"10.1007/978-3-642-39799-8_6","day":"01","date_published":"2013-01-01T00:00:00Z","department":[{"_id":"KrCh"}],"series_title":"Lecture Notes in Computer Science","oa_version":"Preprint","quality_controlled":"1","arxiv":1,"publication_status":"published","citation":{"ama":"Reiter J, Božić I, Chatterjee K, Nowak M. TTP: Tool for tumor progression. In: <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>. Vol 8044. Lecture Notes in Computer Science. Springer; 2013:101-106. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>","apa":"Reiter, J., Božić, I., Chatterjee, K., &#38; Nowak, M. (2013). TTP: Tool for tumor progression. In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i> (Vol. 8044, pp. 101–106). St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>","chicago":"Reiter, Johannes, Ivana Božić, Krishnendu Chatterjee, and Martin Nowak. “TTP: Tool for Tumor Progression.” In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, 8044:101–6. Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>.","short":"J. Reiter, I. Božić, K. Chatterjee, M. Nowak, in:, Proceedings of 25th Int. Conf. on Computer Aided Verification, Springer, 2013, pp. 101–106.","mla":"Reiter, Johannes, et al. “TTP: Tool for Tumor Progression.” <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, vol. 8044, Springer, 2013, pp. 101–06, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>.","ieee":"J. Reiter, I. Božić, K. Chatterjee, and M. Nowak, “TTP: Tool for tumor progression,” in <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, St. Petersburg, Russia, 2013, vol. 8044, pp. 101–106.","ista":"Reiter J, Božić I, Chatterjee K, Nowak M. 2013. TTP: Tool for tumor progression. Proceedings of 25th Int. Conf. on Computer Aided Verification. CAV: Computer Aided VerificationLecture Notes in Computer Science, LNCS, vol. 8044, 101–106."},"publication":"Proceedings of 25th Int. Conf. on Computer Aided Verification","scopus_import":1,"type":"conference","month":"01","conference":{"name":"CAV: Computer Aided Verification","location":"St. Petersburg, Russia","end_date":"2013-07-19","start_date":"2013-07-13"},"language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","first_name":"Johannes","full_name":"Reiter, Johannes"},{"first_name":"Ivana","full_name":"Božić, Ivana","last_name":"Božić"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"page":"101 - 106","date_created":"2018-12-11T11:55:08Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5399"},{"status":"public","id":"1400","relation":"dissertation_contains"}]},"volume":8044,"ec_funded":1,"publist_id":"5077","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1303.5251"}],"publisher":"Springer","alternative_title":["LNCS"],"_id":"2000","abstract":[{"lang":"eng","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."}]},{"abstract":[{"text":"Traditional statistical methods for confidentiality protection of statistical databases do not scale well to deal with GWAS databases especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual’s privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially-private approach to penalized logistic regression.","lang":"eng"}],"publication_status":"published","citation":{"chicago":"Uhler, Caroline, Aleksandra Slavkovic, and Stephen Fienberg. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University, 2013. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>.","ama":"Uhler C, Slavkovic A, Fienberg S. Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. 2013;5(1):137-166. doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>","apa":"Uhler, C., Slavkovic, A., &#38; Fienberg, S. (2013). Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>","ista":"Uhler C, Slavkovic A, Fienberg S. 2013. Privacy-preserving data sharing for genome-wide association studies. Journal of Privacy and Confidentiality . 5(1), 137–166.","short":"C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality  5 (2013) 137–166.","mla":"Uhler, Caroline, et al. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1, Carnegie Mellon University, 2013, pp. 137–66, doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>.","ieee":"C. Uhler, A. Slavkovic, and S. Fienberg, “Privacy-preserving data sharing for genome-wide association studies,” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1. Carnegie Mellon University, pp. 137–166, 2013."},"quality_controlled":"1","_id":"2009","department":[{"_id":"CaUh"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"http://repository.cmu.edu/jpc/vol5/iss1/6"}],"publisher":"Carnegie Mellon University","oa_version":"Published Version","date_published":"2013-08-01T00:00:00Z","publist_id":"5067","issue":"1","title":"Privacy-preserving data sharing for genome-wide association studies","volume":5,"doi":"10.29012/jpc.v5i1.629","day":"01","page":"137 - 166","date_created":"2018-12-11T11:55:11Z","year":"2013","type":"journal_article","author":[{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","first_name":"Caroline","last_name":"Uhler"},{"full_name":"Slavkovic, Aleksandra","first_name":"Aleksandra","last_name":"Slavkovic"},{"full_name":"Fienberg, Stephen","first_name":"Stephen","last_name":"Fienberg"}],"language":[{"iso":"eng"}],"month":"08","oa":1,"publication":"Journal of Privacy and Confidentiality ","date_updated":"2021-01-12T06:54:41Z","article_processing_charge":"No","intvolume":"         5","status":"public"}]