[{"publist_id":"4668","abstract":[{"text":"The problem of minimizing the Potts energy function frequently occurs in computer vision applications. One way to tackle this NP-hard problem was proposed by Kovtun [19, 20]. It identifies a part of an optimal solution by running k maxflow computations, where k is the number of labels. The number of “labeled” pixels can be significant in some applications, e.g. 50-93% in our tests for stereo. We show how to reduce the runtime to O (log k) maxflow computations (or one parametric maxflow computation). Furthermore, the output of our algorithm allows to speed-up the subsequent alpha expansion for the unlabeled part, or can be used as it is for time-critical applications. To derive our technique, we generalize the algorithm of Felzenszwalb et al. [7] for Tree Metrics . We also show a connection to k-submodular functions from combinatorial optimization, and discuss k-submodular relaxations for general energy functions.","lang":"eng"}],"type":"conference","oa_version":"Preprint","date_created":"2018-12-11T11:56:43Z","date_updated":"2021-01-12T06:56:28Z","author":[{"id":"4B60654C-F248-11E8-B48F-1D18A9856A87","last_name":"Gridchyn","first_name":"Igor","full_name":"Gridchyn, Igor"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"}],"publisher":"IEEE","department":[{"_id":"JoCs"},{"_id":"VlKo"}],"publication_status":"published","title":"Potts model, parametric maxflow and k-submodular functions","status":"public","_id":"2276","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","day":"01","month":"12","language":[{"iso":"eng"}],"doi":"10.1109/ICCV.2013.288","date_published":"2013-12-01T00:00:00Z","conference":{"name":"ICCV: International Conference on Computer Vision","location":"Sydney, Australia","start_date":"2013-12-01","end_date":"2013-12-08"},"page":"2320 - 2327","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1310.1771"}],"citation":{"ama":"Gridchyn I, Kolmogorov V. Potts model, parametric maxflow and k-submodular functions. In: IEEE; 2013:2320-2327. doi:10.1109/ICCV.2013.288","ista":"Gridchyn I, Kolmogorov V. 2013. Potts model, parametric maxflow and k-submodular functions. ICCV: International Conference on Computer Vision, 2320–2327.","apa":"Gridchyn, I., & Kolmogorov, V. (2013). Potts model, parametric maxflow and k-submodular functions (pp. 2320–2327). Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.288","ieee":"I. Gridchyn and V. Kolmogorov, “Potts model, parametric maxflow and k-submodular functions,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2013, pp. 2320–2327.","mla":"Gridchyn, Igor, and Vladimir Kolmogorov. Potts Model, Parametric Maxflow and k-Submodular Functions. IEEE, 2013, pp. 2320–27, doi:10.1109/ICCV.2013.288.","short":"I. Gridchyn, V. Kolmogorov, in:, IEEE, 2013, pp. 2320–2327.","chicago":"Gridchyn, Igor, and Vladimir Kolmogorov. “Potts Model, Parametric Maxflow and k-Submodular Functions,” 2320–27. IEEE, 2013. https://doi.org/10.1109/ICCV.2013.288."},"external_id":{"arxiv":["1310.1771"]}},{"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1204.0235"}],"external_id":{"arxiv":["1204.0235"]},"language":[{"iso":"eng"}],"doi":"10.1137/120872309","month":"11","publisher":"Society for Industrial and Applied Mathematics ","department":[{"_id":"CaUh"}],"publication_status":"published","year":"2013","volume":55,"date_created":"2018-12-11T11:56:44Z","date_updated":"2021-01-12T06:56:30Z","author":[{"last_name":"Uhler","first_name":"Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline"},{"first_name":"Stephen","last_name":"Wright","full_name":"Wright, Stephen"}],"publist_id":"4655","page":"671 - 706","citation":{"ama":"Uhler C, Wright S. Packing ellipsoids with overlap. SIAM Review. 2013;55(4):671-706. doi:10.1137/120872309","ieee":"C. Uhler and S. Wright, “Packing ellipsoids with overlap,” SIAM Review, vol. 55, no. 4. Society for Industrial and Applied Mathematics , pp. 671–706, 2013.","apa":"Uhler, C., & Wright, S. (2013). Packing ellipsoids with overlap. SIAM Review. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/120872309","ista":"Uhler C, Wright S. 2013. Packing ellipsoids with overlap. SIAM Review. 55(4), 671–706.","short":"C. Uhler, S. Wright, SIAM Review 55 (2013) 671–706.","mla":"Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.” SIAM Review, vol. 55, no. 4, Society for Industrial and Applied Mathematics , 2013, pp. 671–706, doi:10.1137/120872309.","chicago":"Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.” SIAM Review. Society for Industrial and Applied Mathematics , 2013. https://doi.org/10.1137/120872309."},"publication":"SIAM Review","date_published":"2013-11-07T00:00:00Z","scopus_import":1,"day":"07","intvolume":" 55","status":"public","title":"Packing ellipsoids with overlap","_id":"2280","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","issue":"4","abstract":[{"text":"The problem of packing ellipsoids of different sizes and shapes into an ellipsoidal container so as to minimize a measure of overlap between ellipsoids is considered. A bilevel optimization formulation is given, together with an algorithm for the general case and a simpler algorithm for the special case in which all ellipsoids are in fact spheres. Convergence results are proved and computational experience is described and illustrated. The motivating application-chromosome organization in the human cell nucleus-is discussed briefly, and some illustrative results are presented.","lang":"eng"}]},{"department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","publication_status":"published","year":"2013","volume":3,"date_updated":"2021-01-12T06:56:32Z","date_created":"2018-12-11T11:56:47Z","author":[{"first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda"},{"first_name":"Spencer","last_name":"Barrett","full_name":"Barrett, Spencer"}],"license":"https://creativecommons.org/licenses/by/4.0/","publist_id":"4644","file_date_updated":"2020-07-14T12:45:37Z","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1002/ece3.465","month":"03","intvolume":" 3","title":"The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant","status":"public","ddc":["576"],"_id":"2287","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"5290","checksum":"b5531bab4c0dec396bf5c8497fe178bf","date_created":"2018-12-12T10:17:35Z","date_updated":"2020-07-14T12:45:37Z","access_level":"open_access","file_name":"IST-2016-416-v1+1_Pickup_et_al-2013-Ecology_and_Evolution.pdf","file_size":626949,"content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","pubrep_id":"416","type":"journal_article","issue":"3","abstract":[{"text":"Negative frequency-dependent selection should result in equal sex ratios in large populations of dioecious flowering plants, but deviations from equality are commonly reported. A variety of ecological and genetic factors can explain biased sex ratios, although the mechanisms involved are not well understood. Most dioecious species are long-lived and/or clonal complicating efforts to identify stages during the life cycle when biases develop. We investigated the demographic correlates of sex-ratio variation in two chromosome races of Rumex hastatulus, an annual, wind-pollinated colonizer of open habitats from the southern USA. We examined sex ratios in 46 populations and evaluated the hypothesis that the proximity of males in the local mating environment, through its influence on gametophytic selection, is the primary cause of female-biased sex ratios. Female-biased sex ratios characterized most populations of R. hastatulus (mean sex ratio = 0.62), with significant female bias in 89% of populations. Large, high-density populations had the highest proportion of females, whereas smaller, low-density populations had sex ratios closer to equality. Progeny sex ratios were more female biased when males were in closer proximity to females, a result consistent with the gametophytic selection hypothesis. Our results suggest that interactions between demographic and genetic factors are probably the main cause of female-biased sex ratios in R. hastatulus. The annual life cycle of this species may limit the scope for selection against males and may account for the weaker degree of bias in comparison with perennial Rumex species.","lang":"eng"}],"page":"629 - 639","citation":{"short":"M. Pickup, S. Barrett, Ecology and Evolution 3 (2013) 629–639.","mla":"Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology and Evolution, vol. 3, no. 3, Wiley-Blackwell, 2013, pp. 629–39, doi:10.1002/ece3.465.","chicago":"Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology and Evolution. Wiley-Blackwell, 2013. https://doi.org/10.1002/ece3.465.","ama":"Pickup M, Barrett S. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 2013;3(3):629-639. doi:10.1002/ece3.465","ieee":"M. Pickup and S. Barrett, “The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant,” Ecology and Evolution, vol. 3, no. 3. Wiley-Blackwell, pp. 629–639, 2013.","apa":"Pickup, M., & Barrett, S. (2013). The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.465","ista":"Pickup M, Barrett S. 2013. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 3(3), 629–639."},"publication":"Ecology and Evolution","date_published":"2013-03-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01"},{"month":"11","project":[{"call_identifier":"FWF","name":"Control of Epithelial Cell Layer Spreading in Zebrafish","grant_number":"I 930-B20","_id":"252ABD0A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://hal.upmc.fr/hal-00983313/"}],"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"doi":"10.1038/ncb2869","publist_id":"4652","department":[{"_id":"CaHe"}],"publisher":"Nature Publishing Group","publication_status":"published","acknowledgement":"This work was supported by the IST Austria and MPI-CBG ","year":"2013","volume":15,"date_created":"2018-12-11T11:56:45Z","date_updated":"2023-02-21T17:02:44Z","related_material":{"record":[{"id":"1403","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Pedro","last_name":"Campinho","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8526-5416","full_name":"Campinho, Pedro"},{"last_name":"Behrndt","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","full_name":"Behrndt, Martin"},{"last_name":"Ranft","first_name":"Jonas","full_name":"Ranft, Jonas"},{"first_name":"Thomas","last_name":"Risler","full_name":"Risler, Thomas"},{"first_name":"Nicolas","last_name":"Minc","full_name":"Minc, Nicolas"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"scopus_import":1,"day":"10","page":"1405 - 1414","citation":{"short":"P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, C.-P.J. Heisenberg, Nature Cell Biology 15 (2013) 1405–1414.","mla":"Campinho, Pedro, et al. “Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” Nature Cell Biology, vol. 15, Nature Publishing Group, 2013, pp. 1405–14, doi:10.1038/ncb2869.","chicago":"Campinho, Pedro, Martin Behrndt, Jonas Ranft, Thomas Risler, Nicolas Minc, and Carl-Philipp J Heisenberg. “Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” Nature Cell Biology. Nature Publishing Group, 2013. https://doi.org/10.1038/ncb2869.","ama":"Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nature Cell Biology. 2013;15:1405-1414. doi:10.1038/ncb2869","apa":"Campinho, P., Behrndt, M., Ranft, J., Risler, T., Minc, N., & Heisenberg, C.-P. J. (2013). Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2869","ieee":"P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, and C.-P. J. Heisenberg, “Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly,” Nature Cell Biology, vol. 15. Nature Publishing Group, pp. 1405–1414, 2013.","ista":"Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. 2013. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nature Cell Biology. 15, 1405–1414."},"publication":"Nature Cell Biology","date_published":"2013-11-10T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Epithelial spreading is a common and fundamental aspect of various developmental and disease-related processes such as epithelial closure and wound healing. A key challenge for epithelial tissues undergoing spreading is to increase their surface area without disrupting epithelial integrity. Here we show that orienting cell divisions by tension constitutes an efficient mechanism by which the enveloping cell layer (EVL) releases anisotropic tension while undergoing spreading during zebrafish epiboly. The control of EVL cell-division orientation by tension involves cell elongation and requires myosin II activity to align the mitotic spindle with the main tension axis. We also found that in the absence of tension-oriented cell divisions and in the presence of increased tissue tension, EVL cells undergo ectopic fusions, suggesting that the reduction of tension anisotropy by oriented cell divisions is required to prevent EVL cells from fusing. We conclude that cell-division orientation by tension constitutes a key mechanism for limiting tension anisotropy and thus promoting tissue spreading during EVL epiboly."}],"intvolume":" 15","status":"public","title":"Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2282","oa_version":"Submitted Version"},{"scopus_import":1,"month":"11","day":"14","publication":"Naturwissenschaften","citation":{"ama":"Pull C, Hughes W, Brown M. Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger . Naturwissenschaften. 2013;100(12):1125-1136. doi:10.1007/s00114-013-1115-5","apa":"Pull, C., Hughes, W., & Brown, M. (2013). Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger . Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-013-1115-5","ieee":"C. Pull, W. Hughes, and M. Brown, “Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger ,” Naturwissenschaften, vol. 100, no. 12. Springer, pp. 1125–1136, 2013.","ista":"Pull C, Hughes W, Brown M. 2013. Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger . Naturwissenschaften. 100(12), 1125–1136.","short":"C. Pull, W. Hughes, M. Brown, Naturwissenschaften 100 (2013) 1125–1136.","mla":"Pull, Christopher, et al. “Tolerating an Infection: An Indirect Benefit of Co-Founding Queen Associations in the Ant Lasius Niger .” Naturwissenschaften, vol. 100, no. 12, Springer, 2013, pp. 1125–36, doi:10.1007/s00114-013-1115-5.","chicago":"Pull, Christopher, William Hughes, and Markus Brown. “Tolerating an Infection: An Indirect Benefit of Co-Founding Queen Associations in the Ant Lasius Niger .” Naturwissenschaften. Springer, 2013. https://doi.org/10.1007/s00114-013-1115-5."},"quality_controlled":"1","page":"1125 - 1136","date_published":"2013-11-14T00:00:00Z","doi":"10.1007/s00114-013-1115-5","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Pathogens exert a strong selection pressure on organisms to evolve effective immune defences. In addition to individual immunity, social organisms can act cooperatively to produce collective defences. In many ant species, queens have the option to found a colony alone or in groups with other, often unrelated, conspecifics. These associations are transient, usually lasting only as long as each queen benefits from the presence of others. In fact, once the first workers emerge, queens fight to the death for dominance. One potential advantage of co-founding may be that queens benefit from collective disease defences, such as mutual grooming, that act against common soil pathogens. We test this hypothesis by exposing single and co-founding queens to a fungal parasite, in order to assess whether queens in co-founding associations have improved survival. Surprisingly, co-foundresses exposed to the entomopathogenic fungus Metarhizium did not engage in cooperative disease defences, and consequently, we find no direct benefit of multiple queens on survival. However, an indirect benefit was observed, with parasite-exposed queens producing more brood when they co-founded, than when they were alone. We suggest this is due to a trade-off between reproduction and immunity. Additionally, we report an extraordinary ability of the queens to tolerate an infection for long periods after parasite exposure. Our study suggests that there are no social immunity benefits for co-founding ant queens, but that in parasite-rich environments, the presence of additional queens may nevertheless improve the chances of colony founding success."}],"issue":"12","publist_id":"4649","_id":"2283","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger ","publication_status":"published","publisher":"Springer","intvolume":" 100","department":[{"_id":"SyCr"}],"author":[{"full_name":"Pull, Christopher","first_name":"Christopher","last_name":"Pull","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982"},{"first_name":"William","last_name":"Hughes","full_name":"Hughes, William"},{"first_name":"Markus","last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus"}],"date_updated":"2021-01-12T06:56:31Z","date_created":"2018-12-11T11:56:45Z","oa_version":"None","volume":100},{"month":"10","quality_controlled":"1","external_id":{"pmid":["24097062"]},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817470/"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/emboj.2013.225","publist_id":"4645","publisher":"Wiley-Blackwell","department":[{"_id":"CaHe"}],"publication_status":"published","pmid":1,"year":"2013","volume":32,"date_updated":"2021-01-12T06:56:32Z","date_created":"2018-12-11T11:56:46Z","author":[{"full_name":"Campinho, Pedro","orcid":"0000-0002-8526-5416","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","last_name":"Campinho","first_name":"Pedro"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"scopus_import":1,"day":"04","page":"2783 - 2784","citation":{"mla":"Campinho, Pedro, and Carl-Philipp J. Heisenberg. “The Force and Effect of Cell Proliferation.” EMBO Journal, vol. 32, no. 21, Wiley-Blackwell, 2013, pp. 2783–84, doi:10.1038/emboj.2013.225.","short":"P. Campinho, C.-P.J. Heisenberg, EMBO Journal 32 (2013) 2783–2784.","chicago":"Campinho, Pedro, and Carl-Philipp J Heisenberg. “The Force and Effect of Cell Proliferation.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2013.225.","ama":"Campinho P, Heisenberg C-PJ. The force and effect of cell proliferation. EMBO Journal. 2013;32(21):2783-2784. doi:10.1038/emboj.2013.225","ista":"Campinho P, Heisenberg C-PJ. 2013. The force and effect of cell proliferation. EMBO Journal. 32(21), 2783–2784.","apa":"Campinho, P., & Heisenberg, C.-P. J. (2013). The force and effect of cell proliferation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2013.225","ieee":"P. Campinho and C.-P. J. Heisenberg, “The force and effect of cell proliferation,” EMBO Journal, vol. 32, no. 21. Wiley-Blackwell, pp. 2783–2784, 2013."},"publication":"EMBO Journal","date_published":"2013-10-04T00:00:00Z","type":"journal_article","issue":"21","abstract":[{"lang":"eng","text":"The spatiotemporal control of cell divisions is a key factor in epithelial morphogenesis and patterning. Mao et al (2013) now describe how differential rates of proliferation within the Drosophila wing disc epithelium give rise to anisotropic tissue tension in peripheral/proximal regions of the disc. Such global tissue tension anisotropy in turn determines the orientation of cell divisions by controlling epithelial cell elongation."}],"intvolume":" 32","title":"The force and effect of cell proliferation","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2286","oa_version":"Submitted Version"},{"month":"10","doi":"10.1007/s00450-013-0251-7","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"quality_controlled":"1","publist_id":"4642","ec_funded":1,"file_date_updated":"2020-07-14T12:45:37Z","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"volume":28,"date_updated":"2021-01-12T06:56:33Z","date_created":"2018-12-11T11:56:47Z","year":"2013","department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","has_accepted_license":"1","day":"05","scopus_import":1,"date_published":"2013-10-05T00:00:00Z","citation":{"short":"T.A. Henzinger, Computer Science Research and Development 28 (2013) 331–344.","mla":"Henzinger, Thomas A. “Quantitative Reactive Modeling and Verification.” Computer Science Research and Development, vol. 28, no. 4, Springer, 2013, pp. 331–44, doi:10.1007/s00450-013-0251-7.","chicago":"Henzinger, Thomas A. “Quantitative Reactive Modeling and Verification.” Computer Science Research and Development. Springer, 2013. https://doi.org/10.1007/s00450-013-0251-7.","ama":"Henzinger TA. Quantitative reactive modeling and verification. Computer Science Research and Development. 2013;28(4):331-344. doi:10.1007/s00450-013-0251-7","ieee":"T. A. Henzinger, “Quantitative reactive modeling and verification,” Computer Science Research and Development, vol. 28, no. 4. Springer, pp. 331–344, 2013.","apa":"Henzinger, T. A. (2013). Quantitative reactive modeling and verification. Computer Science Research and Development. Springer. https://doi.org/10.1007/s00450-013-0251-7","ista":"Henzinger TA. 2013. Quantitative reactive modeling and verification. Computer Science Research and Development. 28(4), 331–344."},"publication":"Computer Science Research and Development","page":"331 - 344","issue":"4","abstract":[{"text":"Formal verification aims to improve the quality of software by detecting errors before they do harm. At the basis of formal verification is the logical notion of correctness, which purports to capture whether or not a program behaves as desired. We suggest that the boolean partition of software into correct and incorrect programs falls short of the practical need to assess the behavior of software in a more nuanced fashion against multiple criteria. We therefore propose to introduce quantitative fitness measures for programs, specifically for measuring the function, performance, and robustness of reactive programs such as concurrent processes. This article describes the goals of the ERC Advanced Investigator Project QUAREM. The project aims to build and evaluate a theory of quantitative fitness measures for reactive models. Such a theory must strive to obtain quantitative generalizations of the paradigms that have been success stories in qualitative reactive modeling, such as compositionality, property-preserving abstraction and abstraction refinement, model checking, and synthesis. The theory will be evaluated not only in the context of software and hardware engineering, but also in the context of systems biology. In particular, we will use the quantitative reactive models and fitness measures developed in this project for testing hypotheses about the mechanisms behind data from biological experiments.","lang":"eng"}],"type":"journal_article","pubrep_id":"626","oa_version":"Published Version","file":[{"file_name":"IST-2016-626-v1+1_s00450-013-0251-7.pdf","access_level":"open_access","file_size":570361,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5308","date_updated":"2020-07-14T12:45:37Z","date_created":"2018-12-12T10:17:51Z","checksum":"f117a00f9f046165bfa95595681e08a0"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2289","intvolume":" 28","ddc":["000"],"title":"Quantitative reactive modeling and verification","status":"public"},{"date_published":"2013-10-01T00:00:00Z","publication":"PNAS","citation":{"short":"Y. Boutté, K. Jonsson, H. Mcfarlane, E. Johnson, D. Gendre, R. Swarup, J. Friml, L. Samuels, S. Robert, R. Bhalerao, PNAS 110 (2013) 16259–16264.","mla":"Boutté, Yohann, et al. “ECHIDNA Mediated Post Golgi Trafficking of Auxin Carriers for Differential Cell Elongation.” PNAS, vol. 110, no. 40, National Academy of Sciences, 2013, pp. 16259–64, doi:10.1073/pnas.1309057110.","chicago":"Boutté, Yohann, Kristoffer Jonsson, Heather Mcfarlane, Errin Johnson, Delphine Gendre, Ranjan Swarup, Jiří Friml, Lacey Samuels, Stéphanie Robert, and Rishikesh Bhalerao. “ECHIDNA Mediated Post Golgi Trafficking of Auxin Carriers for Differential Cell Elongation.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1309057110.","ama":"Boutté Y, Jonsson K, Mcfarlane H, et al. ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. PNAS. 2013;110(40):16259-16264. doi:10.1073/pnas.1309057110","ieee":"Y. Boutté et al., “ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation,” PNAS, vol. 110, no. 40. National Academy of Sciences, pp. 16259–16264, 2013.","apa":"Boutté, Y., Jonsson, K., Mcfarlane, H., Johnson, E., Gendre, D., Swarup, R., … Bhalerao, R. (2013). ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1309057110","ista":"Boutté Y, Jonsson K, Mcfarlane H, Johnson E, Gendre D, Swarup R, Friml J, Samuels L, Robert S, Bhalerao R. 2013. ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. PNAS. 110(40), 16259–16264."},"page":"16259 - 16264","day":"01","scopus_import":1,"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2290","title":"ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation","status":"public","intvolume":" 110","abstract":[{"lang":"eng","text":"The plant hormone indole-acetic acid (auxin) is essential for many aspects of plant development. Auxin-mediated growth regulation typically involves the establishment of an auxin concentration gradient mediated by polarly localized auxin transporters. The localization of auxin carriers and their amount at the plasma membrane are controlled by membrane trafficking processes such as secretion, endocytosis, and recycling. In contrast to endocytosis or recycling, how the secretory pathway mediates the localization of auxin carriers is not well understood. In this study we have used the differential cell elongation process during apical hook development to elucidate the mechanisms underlying the post-Golgi trafficking of auxin carriers in Arabidopsis. We show that differential cell elongation during apical hook development is defective in Arabidopsis mutant echidna (ech). ECH protein is required for the trans-Golgi network (TGN)-mediated trafficking of the auxin influx carrier AUX1 to the plasma membrane. In contrast, ech mutation only marginally perturbs the trafficking of the highly related auxin influx carrier LIKE-AUX1-3 or the auxin efflux carrier PIN-FORMED-3, both also involved in hook development. Electron tomography reveals that the trafficking defects in ech mutant are associated with the perturbation of secretory vesicle genesis from the TGN. Our results identify differential mechanisms for the post-Golgi trafficking of de novo-synthesized auxin carriers to plasma membrane from the TGN and reveal how trafficking of auxin influx carriers mediates the control of differential cell elongation in apical hook development."}],"issue":"40","type":"journal_article","doi":"10.1073/pnas.1309057110","language":[{"iso":"eng"}],"external_id":{"pmid":["24043780"]},"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791722/","open_access":"1"}],"quality_controlled":"1","month":"10","author":[{"last_name":"Boutté","first_name":"Yohann","full_name":"Boutté, Yohann"},{"last_name":"Jonsson","first_name":"Kristoffer","full_name":"Jonsson, Kristoffer"},{"first_name":"Heather","last_name":"Mcfarlane","full_name":"Mcfarlane, Heather"},{"last_name":"Johnson","first_name":"Errin","full_name":"Johnson, Errin"},{"first_name":"Delphine","last_name":"Gendre","full_name":"Gendre, Delphine"},{"full_name":"Swarup, Ranjan","first_name":"Ranjan","last_name":"Swarup"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Samuels, Lacey","first_name":"Lacey","last_name":"Samuels"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"last_name":"Bhalerao","first_name":"Rishikesh","full_name":"Bhalerao, Rishikesh"}],"date_updated":"2021-01-12T06:56:33Z","date_created":"2018-12-11T11:56:48Z","volume":110,"year":"2013","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","publist_id":"4639"},{"language":[{"iso":"eng"}],"date_published":"2013-12-01T00:00:00Z","doi":"10.1109/ICCV.2013.139","conference":{"name":"ICCV: International Conference on Computer Vision","start_date":"2013-12-01","location":"Sydney, Australia","end_date":"2013-12-08"},"project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036"}],"quality_controlled":"1","citation":{"ieee":"T. Kazmar, E. Kvon, A. Stark, and C. Lampert, “Drosophila Embryo Stage Annotation using Label Propagation,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2013.","apa":"Kazmar, T., Kvon, E., Stark, A., & Lampert, C. (2013). Drosophila Embryo Stage Annotation using Label Propagation. Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.139","ista":"Kazmar T, Kvon E, Stark A, Lampert C. 2013. Drosophila Embryo Stage Annotation using Label Propagation. ICCV: International Conference on Computer Vision.","ama":"Kazmar T, Kvon E, Stark A, Lampert C. Drosophila Embryo Stage Annotation using Label Propagation. In: IEEE; 2013. doi:10.1109/ICCV.2013.139","chicago":"Kazmar, Tomas, Evgeny Kvon, Alexander Stark, and Christoph Lampert. “Drosophila Embryo Stage Annotation Using Label Propagation.” IEEE, 2013. https://doi.org/10.1109/ICCV.2013.139.","short":"T. Kazmar, E. Kvon, A. Stark, C. Lampert, in:, IEEE, 2013.","mla":"Kazmar, Tomas, et al. Drosophila Embryo Stage Annotation Using Label Propagation. IEEE, 2013, doi:10.1109/ICCV.2013.139."},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.cv-foundation.org/openaccess/ICCV2013.py"}],"day":"01","month":"12","scopus_import":1,"oa_version":"Submitted Version","date_created":"2018-12-11T11:56:49Z","date_updated":"2021-01-12T06:56:35Z","author":[{"first_name":"Tomas","last_name":"Kazmar","full_name":"Kazmar, Tomas"},{"full_name":"Kvon, Evgeny","last_name":"Kvon","first_name":"Evgeny"},{"full_name":"Stark, Alexander","first_name":"Alexander","last_name":"Stark"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"}],"publisher":"IEEE","department":[{"_id":"ChLa"}],"status":"public","publication_status":"published","title":"Drosophila Embryo Stage Annotation using Label Propagation","_id":"2294","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","ec_funded":1,"publist_id":"4634","abstract":[{"text":"In this work we propose a system for automatic classification of Drosophila embryos into developmental stages.\r\nWhile the system is designed to solve an actual problem in biological research, we believe that the principle underly-\r\ning it is interesting not only for biologists, but also for researchers in computer vision. The main idea is to combine two orthogonal sources of information: one is a classifier trained on strongly invariant features, which makes it applicable to images of very different conditions, but also leads to rather noisy predictions. The other is a label propagation step based on a more powerful similarity measure that however is only consistent within specific subsets of the data at a time.\r\nIn our biological setup, the information sources are the shape and the staining patterns of embryo images. We show\r\nexperimentally that while neither of the methods can be used by itself to achieve satisfactory results, their combina-\r\ntion achieves prediction quality comparable to human performance.","lang":"eng"}],"type":"conference"},{"date_updated":"2020-08-11T10:09:45Z","date_created":"2018-12-11T11:56:48Z","oa_version":"None","volume":8087,"status":"public","title":"Mathematical Foundations of Computer Science 2013","publication_status":"published","editor":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Jiri","last_name":"Sgall","full_name":"Sgall, Jiri"}],"department":[{"_id":"KrCh"}],"intvolume":" 8087","publisher":"Springer","_id":"2292","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"This book constitutes the thoroughly refereed conference proceedings of the 38th International Symposium on Mathematical Foundations of Computer Science, MFCS 2013, held in Klosterneuburg, Austria, in August 2013. The 67 revised full papers presented together with six invited talks were carefully selected from 191 submissions. Topics covered include algorithmic game theory, algorithmic learning theory, algorithms and data structures, automata, formal languages, bioinformatics, complexity, computational geometry, computer-assisted reasoning, concurrency theory, databases and knowledge-based systems, foundations of computing, logic in computer science, models of computation, semantics and verification of programs, and theoretical issues in artificial intelligence.","lang":"eng"}],"publist_id":"4636","alternative_title":["LNCS"],"type":"conference_editor","language":[{"iso":"eng"}],"conference":{"start_date":"2013-08-26","location":"Klosterneuburg, Austria","end_date":"2013-08-30","name":"MFCS: Mathematical Foundations of Computer Science"},"doi":"10.1007/978-3-642-40313-2","date_published":"2013-08-08T00:00:00Z","quality_controlled":"1","page":"VI - 854","citation":{"chicago":"Chatterjee, Krishnendu, and Jiri Sgall, eds. Mathematical Foundations of Computer Science 2013. Vol. 8087. Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40313-2.","short":"K. Chatterjee, J. Sgall, eds., Mathematical Foundations of Computer Science 2013, Springer, 2013.","mla":"Chatterjee, Krishnendu, and Jiri Sgall, editors. Mathematical Foundations of Computer Science 2013. Vol. 8087, Springer, 2013, p. VI-854, doi:10.1007/978-3-642-40313-2.","apa":"Chatterjee, K., & Sgall, J. (Eds.). (2013). Mathematical Foundations of Computer Science 2013 (Vol. 8087, p. VI-854). Presented at the MFCS: Mathematical Foundations of Computer Science, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-40313-2","ieee":"K. Chatterjee and J. Sgall, Eds., Mathematical Foundations of Computer Science 2013, vol. 8087. Springer, 2013, p. VI-854.","ista":"Chatterjee K, Sgall J eds. 2013. Mathematical Foundations of Computer Science 2013, Springer,p.","ama":"Chatterjee K, Sgall J, eds. Mathematical Foundations of Computer Science 2013. Vol 8087. Springer; 2013:VI-854. doi:10.1007/978-3-642-40313-2"},"day":"08","month":"08","publication_identifier":{"isbn":["978-3-642-40312-5"]},"series_title":"Lecture Notes in Computer Science","scopus_import":1},{"scopus_import":1,"day":"01","month":"12","quality_controlled":"1","project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"}],"page":"825 - 832","citation":{"apa":"Sharmanska, V., Quadrianto, N., & Lampert, C. (2013). Learning to rank using privileged information (pp. 825–832). Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.107","ieee":"V. Sharmanska, N. Quadrianto, and C. Lampert, “Learning to rank using privileged information,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2013, pp. 825–832.","ista":"Sharmanska V, Quadrianto N, Lampert C. 2013. Learning to rank using privileged information. ICCV: International Conference on Computer Vision, 825–832.","ama":"Sharmanska V, Quadrianto N, Lampert C. Learning to rank using privileged information. In: IEEE; 2013:825-832. doi:10.1109/ICCV.2013.107","chicago":"Sharmanska, Viktoriia, Novi Quadrianto, and Christoph Lampert. “Learning to Rank Using Privileged Information,” 825–32. IEEE, 2013. https://doi.org/10.1109/ICCV.2013.107.","short":"V. Sharmanska, N. Quadrianto, C. Lampert, in:, IEEE, 2013, pp. 825–832.","mla":"Sharmanska, Viktoriia, et al. Learning to Rank Using Privileged Information. IEEE, 2013, pp. 825–32, doi:10.1109/ICCV.2013.107."},"main_file_link":[{"open_access":"1","url":"www.cv-foundation.org/openaccess/content_iccv_2013/papers/Sharmanska_Learning_to_Rank_2013_ICCV_paper.pdf"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"ICCV: International Conference on Computer Vision","start_date":"2013-12-01","location":"Sydney, Australia","end_date":"2013-12-08"},"doi":"10.1109/ICCV.2013.107","date_published":"2013-12-01T00:00:00Z","type":"conference","abstract":[{"text":"Many computer vision problems have an asymmetric distribution of information between training and test time. In this work, we study the case where we are given additional information about the training data, which however will not be available at test time. This situation is called learning using privileged information (LUPI). We introduce two maximum-margin techniques that are able to make use of this additional source of information, and we show that the framework is applicable to several scenarios that have been studied in computer vision before. Experiments with attributes, bounding boxes, image tags and rationales as additional information in object classification show promising results.","lang":"eng"}],"ec_funded":1,"publist_id":"4635","title":"Learning to rank using privileged information","publication_status":"published","status":"public","department":[{"_id":"ChLa"}],"publisher":"IEEE","year":"2013","_id":"2293","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T10:36:41Z","date_created":"2018-12-11T11:56:49Z","oa_version":"Submitted Version","author":[{"id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308","first_name":"Viktoriia","last_name":"Sharmanska","full_name":"Sharmanska, Viktoriia"},{"first_name":"Novi","last_name":"Quadrianto","full_name":"Quadrianto, Novi"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}]},{"scopus_import":1,"day":"01","month":"09","main_file_link":[{"url":"http://eprint.iacr.org/2013/492","open_access":"1"}],"citation":{"ama":"Ferrara A, Fuchsbauer G, Warinschi B. Cryptographically enforced RBAC. In: IEEE; 2013:115-129. doi:10.1109/CSF.2013.15","ista":"Ferrara A, Fuchsbauer G, Warinschi B. 2013. Cryptographically enforced RBAC. CSF: Computer Security Foundations, 115–129.","apa":"Ferrara, A., Fuchsbauer, G., & Warinschi, B. (2013). Cryptographically enforced RBAC (pp. 115–129). Presented at the CSF: Computer Security Foundations, New Orleans, LA, United States: IEEE. https://doi.org/10.1109/CSF.2013.15","ieee":"A. Ferrara, G. Fuchsbauer, and B. Warinschi, “Cryptographically enforced RBAC,” presented at the CSF: Computer Security Foundations, New Orleans, LA, United States, 2013, pp. 115–129.","mla":"Ferrara, Anna, et al. Cryptographically Enforced RBAC. IEEE, 2013, pp. 115–29, doi:10.1109/CSF.2013.15.","short":"A. Ferrara, G. Fuchsbauer, B. Warinschi, in:, IEEE, 2013, pp. 115–129.","chicago":"Ferrara, Anna, Georg Fuchsbauer, and Bogdan Warinschi. “Cryptographically Enforced RBAC,” 115–29. IEEE, 2013. https://doi.org/10.1109/CSF.2013.15."},"oa":1,"quality_controlled":"1","page":"115 - 129","conference":{"name":"CSF: Computer Security Foundations","end_date":"2013-09-28","location":"New Orleans, LA, United States","start_date":"2013-09-26"},"date_published":"2013-09-01T00:00:00Z","doi":"10.1109/CSF.2013.15","language":[{"iso":"eng"}],"type":"conference","abstract":[{"lang":"eng","text":"Cryptographic access control promises to offer easily distributed trust and broader applicability, while reducing reliance on low-level online monitors. Traditional implementations of cryptographic access control rely on simple cryptographic primitives whereas recent endeavors employ primitives with richer functionality and security guarantees. Worryingly, few of the existing cryptographic access-control schemes come with precise guarantees, the gap between the policy specification and the implementation being analyzed only informally, if at all. In this paper we begin addressing this shortcoming. Unlike prior work that targeted ad-hoc policy specification, we look at the well-established Role-Based Access Control (RBAC) model, as used in a typical file system. In short, we provide a precise syntax for a computational version of RBAC, offer rigorous definitions for cryptographic policy enforcement of a large class of RBAC security policies, and demonstrate that an implementation based on attribute-based encryption meets our security notions. We view our main contribution as being at the conceptual level. Although we work with RBAC for concreteness, our general methodology could guide future research for uses of cryptography in other access-control models. \r\n"}],"publist_id":"4637","_id":"2291","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Cryptographically enforced RBAC","publication_status":"published","status":"public","department":[{"_id":"KrPi"}],"publisher":"IEEE","author":[{"full_name":"Ferrara, Anna","last_name":"Ferrara","first_name":"Anna"},{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg"},{"first_name":"Bogdan","last_name":"Warinschi","full_name":"Warinschi, Bogdan"}],"date_updated":"2021-01-12T06:56:34Z","date_created":"2018-12-11T11:56:48Z","oa_version":"Submitted Version"},{"alternative_title":["LNCS"],"type":"conference_editor","publist_id":"4643","abstract":[{"lang":"eng","text":"This book constitutes the proceedings of the 11th International Conference on Computational Methods in Systems Biology, CMSB 2013, held in Klosterneuburg, Austria, in September 2013. The 15 regular papers included in this volume were carefully reviewed and selected from 27 submissions. They deal with computational models for all levels, from molecular and cellular, to organs and entire organisms."}],"publisher":"Springer","intvolume":" 8130","editor":[{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","first_name":"Ashutosh","full_name":"Gupta, Ashutosh"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"}],"department":[{"_id":"ToHe"}],"status":"public","title":"Computational Methods in Systems Biology","publication_status":"published","year":"2013","_id":"2288","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":8130,"oa_version":"None","date_created":"2018-12-11T11:56:47Z","date_updated":"2019-08-02T12:37:44Z","publication_identifier":{"isbn":["978-3-642-40707-9"]},"day":"01","month":"07","quality_controlled":"1","citation":{"chicago":"Gupta, Ashutosh, and Thomas A Henzinger, eds. Computational Methods in Systems Biology. Vol. 8130. Springer, 2013. https://doi.org/10.1007/978-3-642-40708-6.","mla":"Gupta, Ashutosh, and Thomas A. Henzinger, editors. Computational Methods in Systems Biology. Vol. 8130, Springer, 2013, doi:10.1007/978-3-642-40708-6.","short":"A. Gupta, T.A. Henzinger, eds., Computational Methods in Systems Biology, Springer, 2013.","ista":"Gupta A, Henzinger TA eds. 2013. Computational Methods in Systems Biology, Springer,p.","apa":"Gupta, A., & Henzinger, T. A. (Eds.). (2013). Computational Methods in Systems Biology (Vol. 8130). Presented at the CMSB: Computational Methods in Systems Biology, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-40708-6","ieee":"A. Gupta and T. A. Henzinger, Eds., Computational Methods in Systems Biology, vol. 8130. Springer, 2013.","ama":"Gupta A, Henzinger TA, eds. Computational Methods in Systems Biology. Vol 8130. Springer; 2013. doi:10.1007/978-3-642-40708-6"},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-40708-6","date_published":"2013-07-01T00:00:00Z","conference":{"name":"CMSB: Computational Methods in Systems Biology","start_date":"2013-09-22","location":"Klosterneuburg, Austria","end_date":"2013-09-24"}},{"file":[{"relation":"main_file","file_id":"4824","checksum":"907edd33a5892e3af093365f1fd57ed7","date_updated":"2020-07-14T12:45:37Z","date_created":"2018-12-12T10:10:36Z","access_level":"open_access","file_name":"IST-2014-196-v1+1_sas13.pdf","content_type":"application/pdf","file_size":299004,"creator":"system"}],"oa_version":"Submitted Version","pubrep_id":"196","intvolume":" 7935","status":"public","ddc":["000","004"],"title":"Local shape analysis for overlaid data structures","_id":"2298","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We present a shape analysis for programs that manipulate overlaid data structures which share sets of objects. The abstract domain contains Separation Logic formulas that (1) combine a per-object separating conjunction with a per-field separating conjunction and (2) constrain a set of variables interpreted as sets of objects. The definition of the abstract domain operators is based on a notion of homomorphism between formulas, viewed as graphs, used recently to define optimal decision procedures for fragments of the Separation Logic. Based on a Frame Rule that supports the two versions of the separating conjunction, the analysis is able to reason in a modular manner about non-overlaid data structures and then, compose information only at a few program points, e.g., procedure returns. We have implemented this analysis in a prototype tool and applied it on several interesting case studies that manipulate overlaid and nested linked lists.\r\n"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2013-01-01T00:00:00Z","page":"150 - 171","citation":{"ama":"Dragoi C, Enea C, Sighireanu M. Local shape analysis for overlaid data structures. In: Vol 7935. Springer; 2013:150-171. doi:10.1007/978-3-642-38856-9_10","ista":"Dragoi C, Enea C, Sighireanu M. 2013. Local shape analysis for overlaid data structures. SAS: Static Analysis Symposium, LNCS, vol. 7935, 150–171.","apa":"Dragoi, C., Enea, C., & Sighireanu, M. (2013). Local shape analysis for overlaid data structures (Vol. 7935, pp. 150–171). Presented at the SAS: Static Analysis Symposium, Seattle, WA, United States: Springer. https://doi.org/10.1007/978-3-642-38856-9_10","ieee":"C. Dragoi, C. Enea, and M. Sighireanu, “Local shape analysis for overlaid data structures,” presented at the SAS: Static Analysis Symposium, Seattle, WA, United States, 2013, vol. 7935, pp. 150–171.","mla":"Dragoi, Cezara, et al. Local Shape Analysis for Overlaid Data Structures. Vol. 7935, Springer, 2013, pp. 150–71, doi:10.1007/978-3-642-38856-9_10.","short":"C. Dragoi, C. Enea, M. Sighireanu, in:, Springer, 2013, pp. 150–171.","chicago":"Dragoi, Cezara, Constantin Enea, and Mihaela Sighireanu. “Local Shape Analysis for Overlaid Data Structures,” 7935:150–71. Springer, 2013. https://doi.org/10.1007/978-3-642-38856-9_10."},"has_accepted_license":"1","day":"01","scopus_import":1,"volume":7935,"date_created":"2018-12-11T11:56:50Z","date_updated":"2021-01-12T06:56:36Z","author":[{"full_name":"Dragoi, Cezara","last_name":"Dragoi","first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Enea, Constantin","first_name":"Constantin","last_name":"Enea"},{"first_name":"Mihaela","last_name":"Sighireanu","full_name":"Sighireanu, Mihaela"}],"publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2013","publist_id":"4630","ec_funded":1,"file_date_updated":"2020-07-14T12:45:37Z","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-38856-9_10","conference":{"end_date":"2013-06-22","location":"Seattle, WA, United States","start_date":"2013-06-20","name":"SAS: Static Analysis Symposium"},"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"month":"01"},{"issue":"5-6","abstract":[{"lang":"eng","text":"The standard hardware design flow involves: (a) design of an integrated circuit using a hardware description language, (b) extensive functional and formal verification, and (c) logical synthesis. However, the above-mentioned processes consume significant effort and time. An alternative approach is to use a formal specification language as a high-level hardware description language and synthesize hardware from formal specifications. Our work is a case study of the synthesis of the widely and industrially used AMBA AHB protocol from formal specifications. Bloem et al. presented the first formal specifications for the AMBA AHB Arbiter and synthesized the AHB Arbiter circuit. However, in the first formal specification some important assumptions were missing. Our contributions are as follows: (a) We present detailed formal specifications for the AHB Arbiter incorporating the missing details, and obtain significant improvements in the synthesis results (both with respect to the number of gates in the synthesized circuit and with respect to the time taken to synthesize the circuit), and (b) we present formal specifications to generate compact circuits for the remaining two main components of AMBA AHB, namely, AHB Master and AHB Slave. Thus with systematic description we are able to automatically and completely synthesize an important and widely used industrial protocol."}],"type":"journal_article","pubrep_id":"87","file":[{"relation":"main_file","file_id":"4910","date_updated":"2020-07-14T12:45:37Z","date_created":"2018-12-12T10:11:53Z","checksum":"57b06a732dd8d6349190dba6b5b0d33b","file_name":"IST-2012-87-v1+1_Synthesis_of_AMBA_AHB_from_formal_specifications-_A_case_study.pdf","access_level":"open_access","content_type":"application/pdf","file_size":277372,"creator":"system"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2299","intvolume":" 15","title":"Synthesis of AMBA AHB from formal specification: A case study","ddc":["000"],"status":"public","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2013-10-01T00:00:00Z","citation":{"short":"Y. Godhal, K. Chatterjee, T.A. Henzinger, International Journal on Software Tools for Technology Transfer 15 (2013) 585–601.","mla":"Godhal, Yashdeep, et al. “Synthesis of AMBA AHB from Formal Specification: A Case Study.” International Journal on Software Tools for Technology Transfer, vol. 15, no. 5–6, Springer, 2013, pp. 585–601, doi:10.1007/s10009-011-0207-9.","chicago":"Godhal, Yashdeep, Krishnendu Chatterjee, and Thomas A Henzinger. “Synthesis of AMBA AHB from Formal Specification: A Case Study.” International Journal on Software Tools for Technology Transfer. Springer, 2013. https://doi.org/10.1007/s10009-011-0207-9.","ama":"Godhal Y, Chatterjee K, Henzinger TA. Synthesis of AMBA AHB from formal specification: A case study. International Journal on Software Tools for Technology Transfer. 2013;15(5-6):585-601. doi:10.1007/s10009-011-0207-9","ieee":"Y. Godhal, K. Chatterjee, and T. A. 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The presentation includes a discussion of Bose-Einstein condensation, the excitation spectrum for trapped gases and its relation to superfluidity, as well as the appearance of quantized vortices in rotating systems. All these properties are intensely being studied in current experiments on cold atomic gases. We will give a description of the mathematics involved in understanding these phenomena, starting from the underlying many-body Schrödinger equation."}],"issue":"2","_id":"2297","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Hot topics in cold gases: A mathematical physics perspective","intvolume":" 8","oa_version":"Preprint","scopus_import":1,"day":"24","publication":"Japanese Journal of Mathematics","citation":{"short":"R. Seiringer, Japanese Journal of Mathematics 8 (2013) 185–232.","mla":"Seiringer, Robert. “Hot Topics in Cold Gases: A Mathematical Physics Perspective.” Japanese Journal of Mathematics, vol. 8, no. 2, Springer, 2013, pp. 185–232, doi:10.1007/s11537-013-1264-5.","chicago":"Seiringer, Robert. “Hot Topics in Cold Gases: A Mathematical Physics Perspective.” Japanese Journal of Mathematics. Springer, 2013. https://doi.org/10.1007/s11537-013-1264-5.","ama":"Seiringer R. Hot topics in cold gases: A mathematical physics perspective. Japanese Journal of Mathematics. 2013;8(2):185-232. doi:10.1007/s11537-013-1264-5","ieee":"R. Seiringer, “Hot topics in cold gases: A mathematical physics perspective,” Japanese Journal of Mathematics, vol. 8, no. 2. Springer, pp. 185–232, 2013.","apa":"Seiringer, R. (2013). Hot topics in cold gases: A mathematical physics perspective. Japanese Journal of Mathematics. Springer. https://doi.org/10.1007/s11537-013-1264-5","ista":"Seiringer R. 2013. 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Hierzu werden konkrete Anwendungsprojekte beschrieben. Der Band wendet sich dabei sowohl an Personen aus der Bibliothekspraxis als auch an Personen aus dem Bibliotheksmanagement, die noch nicht mit dem Thema vertraut sind.","lang":"ger"}],"_id":"2306","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["020"],"status":"public","title":"(Open) Linked Data in Bibliotheken","intvolume":" 50","pubrep_id":"725","oa_version":"Published 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(2013). (Open) Linked Data in Bibliotheken (Vol. 50). De Gruyter. https://doi.org/10.1515/9783110278736","ieee":"P. Danowski and A. Pohl, (Open) Linked Data in Bibliotheken, vol. 50. De Gruyter, 2013.","ista":"Danowski P, Pohl A. 2013. (Open) Linked Data in Bibliotheken, De Gruyter,p.","ama":"Danowski P, Pohl A. (Open) Linked Data in Bibliotheken. Vol 50. De Gruyter; 2013. doi:10.1515/9783110278736","chicago":"Danowski, Patrick, and Adrian Pohl. (Open) Linked Data in Bibliotheken. Vol. 50. De Gruyter, 2013. https://doi.org/10.1515/9783110278736.","short":"P. Danowski, A. Pohl, (Open) Linked Data in Bibliotheken, De Gruyter, 2013.","mla":"Danowski, Patrick, and Adrian Pohl. (Open) Linked Data in Bibliotheken. Vol. 50, De Gruyter, 2013, doi:10.1515/9783110278736."},"date_published":"2013-09-13T00:00:00Z","file_date_updated":"2020-07-14T12:45:38Z","publist_id":"4621","year":"2013","publication_status":"published","publisher":"De Gruyter","department":[{"_id":"E-Lib"}],"author":[{"orcid":"0000-0002-6026-4409","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","last_name":"Danowski","first_name":"Patrick","full_name":"Danowski, Patrick"},{"last_name":"Pohl","first_name":"Adrian","full_name":"Pohl, Adrian"}],"date_created":"2018-12-11T11:56:53Z","date_updated":"2021-12-21T12:17:19Z","volume":50,"month":"09","publication_identifier":{"isbn":[" 978-3-11-027634-3"],"issn":["2191-3587"],"eisbn":["9-783-1102-7873-6"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1515/9783110278736","language":[{"iso":"ger"}]},{"type":"conference","abstract":[{"lang":"eng","text":"We describe the design and implementation of P, a domain-specific language to write asynchronous event driven code. P allows the programmer to specify the system as a collection of interacting state machines, which communicate with each other using events. P unifies modeling and programming into one activity for the programmer. Not only can a P program be compiled into executable code, but it can also be tested using model checking techniques. P allows the programmer to specify the environment, used to "close" the system during testing, as nondeterministic ghost machines. Ghost machines are erased during compilation to executable code; a type system ensures that the erasure is semantics preserving. The P language is designed so that a P program can be checked for responsiveness-the ability to handle every event in a timely manner. By default, a machine needs to handle every event that arrives in every state. But handling every event in every state is impractical. The language provides a notion of deferred events where the programmer can annotate when she wants to delay processing an event. The default safety checker looks for presence of unhan-dled events. The language also provides default liveness checks that an event cannot be potentially deferred forever. P was used to implement and verify the core of the USB device driver stack that ships with Microsoft Windows 8. The resulting driver is more reliable and performs better than its prior incarnation (which did not use P); we have more confidence in the robustness of its design due to the language abstractions and verification provided by P."}],"ec_funded":1,"publist_id":"4626","year":"2013","_id":"2301","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"P: Safe asynchronous event-driven programming","publisher":"ACM","department":[{"_id":"ToHe"}],"author":[{"full_name":"Desai, Ankush","last_name":"Desai","first_name":"Ankush"},{"last_name":"Gupta","first_name":"Vivek","full_name":"Gupta, Vivek"},{"first_name":"Ethan","last_name":"Jackson","full_name":"Jackson, Ethan"},{"first_name":"Shaz","last_name":"Qadeer","full_name":"Qadeer, Shaz"},{"full_name":"Rajamani, Sriram","first_name":"Sriram","last_name":"Rajamani"},{"full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","last_name":"Zufferey","first_name":"Damien"}],"date_created":"2018-12-11T11:56:52Z","date_updated":"2021-01-12T06:56:38Z","oa_version":"None","scopus_import":1,"day":"01","month":"06","publication":"Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation","main_file_link":[{"url":"http://research.microsoft.com/pubs/191069/pldi212_desai.pdf"}],"citation":{"chicago":"Desai, Ankush, Vivek Gupta, Ethan Jackson, Shaz Qadeer, Sriram Rajamani, and Damien Zufferey. “P: Safe Asynchronous Event-Driven Programming.” In Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, 321–31. ACM, 2013. https://doi.org/10.1145/2491956.2462184.","mla":"Desai, Ankush, et al. “P: Safe Asynchronous Event-Driven Programming.” Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, ACM, 2013, pp. 321–31, doi:10.1145/2491956.2462184.","short":"A. Desai, V. Gupta, E. Jackson, S. Qadeer, S. Rajamani, D. Zufferey, in:, Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, ACM, 2013, pp. 321–331.","ista":"Desai A, Gupta V, Jackson E, Qadeer S, Rajamani S, Zufferey D. 2013. P: Safe asynchronous event-driven programming. Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Languages Design and Implementation, 321–331.","apa":"Desai, A., Gupta, V., Jackson, E., Qadeer, S., Rajamani, S., & Zufferey, D. (2013). P: Safe asynchronous event-driven programming. In Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 321–331). Seattle, WA, United States: ACM. https://doi.org/10.1145/2491956.2462184","ieee":"A. Desai, V. Gupta, E. Jackson, S. Qadeer, S. Rajamani, and D. Zufferey, “P: Safe asynchronous event-driven programming,” in Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, Seattle, WA, United States, 2013, pp. 321–331.","ama":"Desai A, Gupta V, Jackson E, Qadeer S, Rajamani S, Zufferey D. P: Safe asynchronous event-driven programming. In: Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation. 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If the strength of the ferromagnetic coupling J is larger than a critical value Jc, then the ground state is homogeneous and ferromagnetic. As the critical value is approached from smaller values of J, it is believed that the ground state consists of a periodic array of stripes (d=2) or slabs (d=3), all of the same size and alternating magnetization. Here we prove rigorously that the ground state energy per site converges to that of the optimal periodic striped or slabbed state, in the limit that J tends to the ferromagnetic transition point. While this theorem does not prove rigorously that the ground state is precisely striped or slabbed, it does prove that in any suitably large box the ground state is striped or slabbed with high probability."}],"_id":"2300","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 88","status":"public","title":"Realization of stripes and slabs in two and three dimensions","oa_version":"Preprint","scopus_import":1,"day":"01","citation":{"ama":"Giuliani A, Lieb É, Seiringer R. Realization of stripes and slabs in two and three dimensions. Physical Review B. 2013;88(6). doi:10.1103/PhysRevB.88.064401","ista":"Giuliani A, Lieb É, Seiringer R. 2013. Realization of stripes and slabs in two and three dimensions. Physical Review B. 88(6), 064401.","ieee":"A. Giuliani, É. Lieb, and R. Seiringer, “Realization of stripes and slabs in two and three dimensions,” Physical Review B, vol. 88, no. 6. American Physical Society, 2013.","apa":"Giuliani, A., Lieb, É., & Seiringer, R. (2013). Realization of stripes and slabs in two and three dimensions. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.88.064401","mla":"Giuliani, Alessandro, et al. “Realization of Stripes and Slabs in Two and Three Dimensions.” Physical Review B, vol. 88, no. 6, 064401, American Physical Society, 2013, doi:10.1103/PhysRevB.88.064401.","short":"A. Giuliani, É. Lieb, R. Seiringer, Physical Review B 88 (2013).","chicago":"Giuliani, Alessandro, Élliott Lieb, and Robert Seiringer. “Realization of Stripes and Slabs in Two and Three Dimensions.” Physical Review B. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.88.064401."},"publication":"Physical Review B","date_published":"2013-08-01T00:00:00Z","article_number":"064401","publist_id":"4627","year":"2013","department":[{"_id":"RoSe"}],"publisher":"American Physical Society","publication_status":"published","author":[{"full_name":"Giuliani, Alessandro","last_name":"Giuliani","first_name":"Alessandro"},{"last_name":"Lieb","first_name":"Élliott","full_name":"Lieb, Élliott"},{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"volume":88,"date_updated":"2021-01-12T06:56:38Z","date_created":"2018-12-11T11:56:51Z","month":"08","oa":1,"external_id":{"arxiv":["1305.5323"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1305.5323"}],"quality_controlled":"1","doi":"10.1103/PhysRevB.88.064401","language":[{"iso":"eng"}]},{"title":"Dissection of gene function at clonal level using mosaic analysis with double markers","publication_status":"published","status":"public","department":[{"_id":"SiHi"}],"publisher":"Springer","intvolume":" 8","_id":"2303","year":"2013","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by IST Austria institutional funds.","date_updated":"2021-01-12T06:56:39Z","date_created":"2018-12-11T11:56:52Z","volume":8,"oa_version":"None","author":[{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"type":"journal_article","abstract":[{"lang":"eng","text":"MADM (Mosaic Analysis with Double Markers) technology offers a genetic approach in mice to visualize and concomitantly manipulate genetically defined cells at clonal level and single cell resolution. MADM employs Cre recombinase/loxP-dependent interchromosomal mitotic recombination to reconstitute two split marker genes—green GFP and red tdTomato—and can label sparse clones of homozygous mutant cells in one color and wild-type cells in the other color in an otherwise unlabeled background. At present, major MADM applications include lineage tracing, single cell labeling, conditional knockouts in small populations of cells and induction of uniparental chromosome disomy to assess effects of genomic imprinting. MADM can be applied universally in the mouse with the sole limitation being the specificity of the promoter controlling Cre recombinase expression. Here I review recent developments and extensions of the MADM technique and give an overview of the major discoveries and progresses enabled by the implementation of the novel genetic MADM tools."}],"publist_id":"4624","issue":"6","article_type":"review","quality_controlled":"1","page":"557 - 568","publication":"Frontiers in Biology","citation":{"chicago":"Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using Mosaic Analysis with Double Markers.” Frontiers in Biology. Springer, 2013. https://doi.org/10.1007/s11515-013-1279-6.","mla":"Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using Mosaic Analysis with Double Markers.” Frontiers in Biology, vol. 8, no. 6, Springer, 2013, pp. 557–68, doi:10.1007/s11515-013-1279-6.","short":"S. Hippenmeyer, Frontiers in Biology 8 (2013) 557–568.","ista":"Hippenmeyer S. 2013. Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. 8(6), 557–568.","ieee":"S. Hippenmeyer, “Dissection of gene function at clonal level using mosaic analysis with double markers,” Frontiers in Biology, vol. 8, no. 6. Springer, pp. 557–568, 2013.","apa":"Hippenmeyer, S. (2013). Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. Springer. https://doi.org/10.1007/s11515-013-1279-6","ama":"Hippenmeyer S. Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. 2013;8(6):557-568. doi:10.1007/s11515-013-1279-6"},"language":[{"iso":"eng"}],"date_published":"2013-09-03T00:00:00Z","doi":"10.1007/s11515-013-1279-6","scopus_import":1,"month":"09","day":"03"}]