[{"abstract":[{"lang":"eng","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."}],"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"scopus_import":"1","external_id":{"isi":["000351830500290"],"arxiv":["1310.1771"]},"doi":"10.1109/ICCV.2013.288","publisher":"IEEE","isi":1,"page":"2320 - 2327","status":"public","date_created":"2018-12-11T11:56:43Z","arxiv":1,"date_updated":"2025-09-29T14:27:49Z","day":"01","type":"conference","date_published":"2013-12-01T00:00:00Z","publication_status":"published","oa_version":"Preprint","year":"2013","corr_author":"1","author":[{"id":"4B60654C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1807-1929","full_name":"Gridchyn, Igor","last_name":"Gridchyn","first_name":"Igor"},{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"citation":{"chicago":"Gridchyn, Igor, and Vladimir Kolmogorov. “Potts Model, Parametric Maxflow and k-Submodular Functions,” 2320–27. IEEE, 2013. <a href=\"https://doi.org/10.1109/ICCV.2013.288\">https://doi.org/10.1109/ICCV.2013.288</a>.","short":"I. Gridchyn, V. Kolmogorov, in:, IEEE, 2013, pp. 2320–2327.","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., &#38; 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. <a href=\"https://doi.org/10.1109/ICCV.2013.288\">https://doi.org/10.1109/ICCV.2013.288</a>","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. <i>Potts Model, Parametric Maxflow and k-Submodular Functions</i>. IEEE, 2013, pp. 2320–27, doi:<a href=\"https://doi.org/10.1109/ICCV.2013.288\">10.1109/ICCV.2013.288</a>.","ama":"Gridchyn I, Kolmogorov V. Potts model, parametric maxflow and k-submodular functions. In: IEEE; 2013:2320-2327. doi:<a href=\"https://doi.org/10.1109/ICCV.2013.288\">10.1109/ICCV.2013.288</a>"},"month":"12","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1310.1771","open_access":"1"}],"department":[{"_id":"JoCs"},{"_id":"VlKo"}],"conference":{"name":"ICCV: International Conference on Computer Vision","end_date":"2013-12-08","start_date":"2013-12-01","location":"Sydney, Australia"},"publist_id":"4668","quality_controlled":"1","_id":"2276","title":"Potts model, parametric maxflow and k-submodular functions"},{"has_accepted_license":"1","ddc":["570"],"oa":1,"publist_id":"4667","department":[{"_id":"GaTk"}],"quality_controlled":"1","intvolume":"         9","file":[{"creator":"system","date_created":"2018-12-12T10:14:36Z","file_size":3115568,"file_id":"5089","access_level":"open_access","date_updated":"2020-07-14T12:45:36Z","content_type":"application/pdf","relation":"main_file","checksum":"46722afc4f7eabb0831165d9c1b171ad","file_name":"IST-2016-410-v1+1_journal.pcbi.1003344.pdf"}],"title":"Transformation of stimulus correlations by the retina","_id":"2277","year":"2013","oa_version":"Published Version","publication_status":"published","date_published":"2013-12-05T00:00:00Z","author":[{"full_name":"Simmons, Kristina","first_name":"Kristina","last_name":"Simmons"},{"full_name":"Prentice, Jason","first_name":"Jason","last_name":"Prentice"},{"last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Homann, Jan","last_name":"Homann","first_name":"Jan"},{"last_name":"Yee","first_name":"Heather","full_name":"Yee, Heather"},{"last_name":"Palmer","first_name":"Stephanie","full_name":"Palmer, Stephanie"},{"full_name":"Nelson, Philip","last_name":"Nelson","first_name":"Philip"},{"full_name":"Balasubramanian, Vijay","last_name":"Balasubramanian","first_name":"Vijay"}],"related_material":{"record":[{"id":"9752","relation":"research_data","status":"public"}]},"month":"12","issue":"12","citation":{"mla":"Simmons, Kristina, et al. “Transformation of Stimulus Correlations by the Retina.” <i>PLoS Computational Biology</i>, vol. 9, no. 12, e1003344, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003344\">10.1371/journal.pcbi.1003344</a>.","apa":"Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2013). Transformation of stimulus correlations by the retina. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003344\">https://doi.org/10.1371/journal.pcbi.1003344</a>","ieee":"K. Simmons <i>et al.</i>, “Transformation of stimulus correlations by the retina,” <i>PLoS Computational Biology</i>, vol. 9, no. 12. Public Library of Science, 2013.","ama":"Simmons K, Prentice J, Tkačik G, et al. Transformation of stimulus correlations by the retina. <i>PLoS Computational Biology</i>. 2013;9(12). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003344\">10.1371/journal.pcbi.1003344</a>","ista":"Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2013. Transformation of stimulus correlations by the retina. PLoS Computational Biology. 9(12), e1003344.","short":"K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, PLoS Computational Biology 9 (2013).","chicago":"Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Transformation of Stimulus Correlations by the Retina.” <i>PLoS Computational Biology</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pcbi.1003344\">https://doi.org/10.1371/journal.pcbi.1003344</a>."},"isi":1,"file_date_updated":"2020-07-14T12:45:36Z","publisher":"Public Library of Science","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"PLoS Computational Biology","status":"public","date_created":"2018-12-11T11:56:43Z","type":"journal_article","day":"05","date_updated":"2025-09-29T14:27:23Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","abstract":[{"text":"Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible.","lang":"eng"}],"scopus_import":"1","language":[{"iso":"eng"}],"article_number":"e1003344","volume":9,"doi":"10.1371/journal.pcbi.1003344","external_id":{"isi":["000329364800028"]},"pubrep_id":"410"},{"volume":126,"external_id":{"isi":["000326392500009"]},"doi":"10.1242/jcs.125617","abstract":[{"text":"It is firmly established that interactions between neurons and glia are fundamental across species for the correct establishment of a functional brain. Here, we found that the glia of the Drosophila larval brain display an essential non-autonomous role during the development of the optic lobe. The optic lobe develops from neuroepithelial cells that proliferate by dividing symmetrically until they switch to asymmetric/differentiative divisions that generate neuroblasts. The proneural gene lethal of scute (l9sc) is transiently activated by the epidermal growth factor receptor (EGFR)-Ras signal transduction pathway at the leading edge of a proneural wave that sweeps from medial to lateral neuroepithelium, promoting this switch. This process is tightly regulated by the tissue-autonomous function within the neuroepithelium of multiple signaling pathways, including EGFR-Ras and Notch. This study shows that the Notch ligand Serrate (Ser) is expressed in the glia and it forms a complex in vivo with Notch and Canoe, which colocalize at the adherens junctions of neuroepithelial cells. This complex is crucial for interactions between glia and neuroepithelial cells during optic lobe development. Ser is tissue-autonomously required in the glia where it activates Notch to regulate its proliferation, and non-autonomously in the neuroepithelium where Ser induces Notch signaling to avoid the premature activation of the EGFR-Ras pathway and hence of L9sc. Interestingly, different Notch activity reporters showed very different expression patterns in the glia and in the neuroepithelium, suggesting the existence of tissue-specific factors that promote the expression of particular Notch target genes or/and a reporter response dependent on different thresholds of Notch signaling.","lang":"eng"}],"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"scopus_import":"1","status":"public","date_created":"2018-12-11T11:56:43Z","date_updated":"2025-09-29T14:26:53Z","day":"01","type":"journal_article","publication":"Journal of Cell Science","publisher":"Company of Biologists","isi":1,"page":"4873 - 4884","author":[{"full_name":"Pérez Gómez, Raquel","first_name":"Raquel","last_name":"Pérez Gómez"},{"first_name":"Jana","last_name":"Slovakova","full_name":"Slovakova, Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rives Quinto","first_name":"Noemí","full_name":"Rives Quinto, Noemí"},{"full_name":"Krejčí, Alena","last_name":"Krejčí","first_name":"Alena"},{"first_name":"Ana","last_name":"Carmena","full_name":"Carmena, Ana"}],"issue":"21","citation":{"ista":"Pérez Gómez R, Slovakova J, Rives Quinto N, Krejčí A, Carmena A. 2013. A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development. Journal of Cell Science. 126(21), 4873–4884.","chicago":"Pérez Gómez, Raquel, Jana Slovakova, Noemí Rives Quinto, Alena Krejčí, and Ana Carmena. “A Serrate-Notch-Canoe Complex Mediates Essential Interactions between Glia and Neuroepithelial Cells during Drosophila Optic Lobe Development.” <i>Journal of Cell Science</i>. Company of Biologists, 2013. <a href=\"https://doi.org/10.1242/jcs.125617\">https://doi.org/10.1242/jcs.125617</a>.","short":"R. Pérez Gómez, J. Slovakova, N. Rives Quinto, A. Krejčí, A. Carmena, Journal of Cell Science 126 (2013) 4873–4884.","mla":"Pérez Gómez, Raquel, et al. “A Serrate-Notch-Canoe Complex Mediates Essential Interactions between Glia and Neuroepithelial Cells during Drosophila Optic Lobe Development.” <i>Journal of Cell Science</i>, vol. 126, no. 21, Company of Biologists, 2013, pp. 4873–84, doi:<a href=\"https://doi.org/10.1242/jcs.125617\">10.1242/jcs.125617</a>.","apa":"Pérez Gómez, R., Slovakova, J., Rives Quinto, N., Krejčí, A., &#38; Carmena, A. (2013). A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.125617\">https://doi.org/10.1242/jcs.125617</a>","ieee":"R. Pérez Gómez, J. Slovakova, N. Rives Quinto, A. Krejčí, and A. Carmena, “A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development,” <i>Journal of Cell Science</i>, vol. 126, no. 21. Company of Biologists, pp. 4873–4884, 2013.","ama":"Pérez Gómez R, Slovakova J, Rives Quinto N, Krejčí A, Carmena A. A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development. <i>Journal of Cell Science</i>. 2013;126(21):4873-4884. doi:<a href=\"https://doi.org/10.1242/jcs.125617\">10.1242/jcs.125617</a>"},"month":"11","date_published":"2013-11-01T00:00:00Z","publication_status":"published","oa_version":"None","year":"2013","intvolume":"       126","quality_controlled":"1","_id":"2278","title":"A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development","department":[{"_id":"CaHe"}],"publist_id":"4658"},{"volume":8172,"external_id":{"arxiv":["1302.4248"]},"doi":"10.1007/978-3-319-02444-8_10","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We consider two-player games played on weighted directed graphs with mean-payoff and total-payoff objectives, two classical quantitative objectives. While for single-dimensional games the complexity and memory bounds for both objectives coincide, we show that in contrast to multi-dimensional mean-payoff games that are known to be coNP-complete, multi-dimensional total-payoff games are undecidable. We introduce conservative approximations of these objectives, where the payoff is considered over a local finite window sliding along a play, instead of the whole play. For single dimension, we show that (i) if the window size is polynomial, deciding the winner takes polynomial time, and (ii) the existence of a bounded window can be decided in NP ∩ coNP, and is at least as hard as solving mean-payoff games. For multiple dimensions, we show that (i) the problem with fixed window size is EXPTIME-complete, and (ii) there is no primitive-recursive algorithm to decide the existence of a bounded window."}],"article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:56:44Z","status":"public","day":"01","series_title":"Lecture Notes in Computer Science","type":"conference","arxiv":1,"date_updated":"2025-09-23T09:29:54Z","ec_funded":1,"publisher":"Springer","page":"118 - 132","acknowledgement":"279307; ERC; Fonds National de la Reserche Luxembourg;  279499; ERC; Fonds National de la Reserche Luxembourg","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"first_name":"Mickael","last_name":"Randour","full_name":"Randour, Mickael"},{"full_name":"Raskin, Jean","last_name":"Raskin","first_name":"Jean"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"523"}]},"citation":{"ista":"Chatterjee K, Doyen L, Randour M, Raskin J. 2013. Looking at mean-payoff and total-payoff through windows. 8172, 118–132.","short":"K. Chatterjee, L. Doyen, M. Randour, J. Raskin, 8172 (2013) 118–132.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Mickael Randour, and Jean Raskin. “Looking at Mean-Payoff and Total-Payoff through Windows.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-319-02444-8_10\">https://doi.org/10.1007/978-3-319-02444-8_10</a>.","ama":"Chatterjee K, Doyen L, Randour M, Raskin J. Looking at mean-payoff and total-payoff through windows. 2013;8172:118-132. doi:<a href=\"https://doi.org/10.1007/978-3-319-02444-8_10\">10.1007/978-3-319-02444-8_10</a>","mla":"Chatterjee, Krishnendu, et al. <i>Looking at Mean-Payoff and Total-Payoff through Windows</i>. Vol. 8172, Springer, 2013, pp. 118–32, doi:<a href=\"https://doi.org/10.1007/978-3-319-02444-8_10\">10.1007/978-3-319-02444-8_10</a>.","apa":"Chatterjee, K., Doyen, L., Randour, M., &#38; Raskin, J. (2013). Looking at mean-payoff and total-payoff through windows. Presented at the ATVA: Automated Technology for Verification and Analysis, Hanoi, Vietnam: Springer. <a href=\"https://doi.org/10.1007/978-3-319-02444-8_10\">https://doi.org/10.1007/978-3-319-02444-8_10</a>","ieee":"K. Chatterjee, L. Doyen, M. Randour, and J. Raskin, “Looking at mean-payoff and total-payoff through windows,” vol. 8172. Springer, pp. 118–132, 2013."},"month":"01","oa_version":"Preprint","publication_status":"published","year":"2013","date_published":"2013-01-01T00:00:00Z","quality_controlled":"1","alternative_title":["LNCS"],"intvolume":"      8172","_id":"2279","title":"Looking at mean-payoff and total-payoff through windows","oa":1,"department":[{"_id":"KrCh"}],"publist_id":"4656","conference":{"end_date":"2013-10-18","start_date":"2013-10-15","name":"ATVA: Automated Technology for Verification and Analysis","location":"Hanoi, Vietnam"},"main_file_link":[{"url":"http://arxiv.org/abs/1302.4248","open_access":"1"}]},{"doi":"10.1137/120872309","external_id":{"isi":["000327502800002"],"arxiv":["1204.0235"]},"volume":55,"scopus_import":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","abstract":[{"lang":"eng","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."}],"type":"journal_article","day":"07","date_updated":"2025-09-29T14:26:18Z","arxiv":1,"status":"public","date_created":"2018-12-11T11:56:44Z","page":"671 - 706","isi":1,"publisher":"Society for Industrial and Applied Mathematics ","publication":"SIAM Review","month":"11","issue":"4","citation":{"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.","chicago":"Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.” <i>SIAM Review</i>. Society for Industrial and Applied Mathematics , 2013. <a href=\"https://doi.org/10.1137/120872309\">https://doi.org/10.1137/120872309</a>.","ama":"Uhler C, Wright S. Packing ellipsoids with overlap. <i>SIAM Review</i>. 2013;55(4):671-706. doi:<a href=\"https://doi.org/10.1137/120872309\">10.1137/120872309</a>","mla":"Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.” <i>SIAM Review</i>, vol. 55, no. 4, Society for Industrial and Applied Mathematics , 2013, pp. 671–706, doi:<a href=\"https://doi.org/10.1137/120872309\">10.1137/120872309</a>.","ieee":"C. Uhler and S. Wright, “Packing ellipsoids with overlap,” <i>SIAM Review</i>, vol. 55, no. 4. Society for Industrial and Applied Mathematics , pp. 671–706, 2013.","apa":"Uhler, C., &#38; Wright, S. (2013). Packing ellipsoids with overlap. <i>SIAM Review</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/120872309\">https://doi.org/10.1137/120872309</a>"},"author":[{"first_name":"Caroline","last_name":"Uhler","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wright, Stephen","last_name":"Wright","first_name":"Stephen"}],"year":"2013","publication_status":"published","oa_version":"Preprint","date_published":"2013-11-07T00:00:00Z","title":"Packing ellipsoids with overlap","_id":"2280","quality_controlled":"1","intvolume":"        55","publist_id":"4655","department":[{"_id":"CaUh"}],"main_file_link":[{"url":"http://arxiv.org/abs/1204.0235","open_access":"1"}],"oa":1},{"publisher":"Nature Publishing Group","publication":"Nature Cell Biology","isi":1,"acknowledgement":"This work was supported by the IST Austria and MPI-CBG ","page":"1405 - 1414","date_created":"2018-12-11T11:56:45Z","status":"public","date_updated":"2026-03-09T14:56:18Z","type":"journal_article","day":"10","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"article_processing_charge":"No","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."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"scopus_import":"1","volume":15,"project":[{"grant_number":"I930-B20","name":"Control of Epithelial Cell Layer Spreading in Zebrafish","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"doi":"10.1038/ncb2869","external_id":{"isi":["000327944200005"]},"oa":1,"main_file_link":[{"url":"http://hal.upmc.fr/hal-00983313/","open_access":"1"}],"publist_id":"4652","department":[{"_id":"CaHe"}],"intvolume":"        15","quality_controlled":"1","title":"Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly","_id":"2282","date_published":"2013-11-10T00:00:00Z","year":"2013","publication_status":"published","oa_version":"Submitted Version","corr_author":"1","author":[{"id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8526-5416","full_name":"Campinho, Pedro","first_name":"Pedro","last_name":"Campinho"},{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","first_name":"Martin","full_name":"Behrndt, Martin"},{"full_name":"Ranft, Jonas","first_name":"Jonas","last_name":"Ranft"},{"full_name":"Risler, Thomas","last_name":"Risler","first_name":"Thomas"},{"full_name":"Minc, Nicolas","last_name":"Minc","first_name":"Nicolas"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"month":"11","citation":{"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. <i>Nature Cell Biology</i>. 2013;15:1405-1414. doi:<a href=\"https://doi.org/10.1038/ncb2869\">10.1038/ncb2869</a>","mla":"Campinho, Pedro, et al. “Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” <i>Nature Cell Biology</i>, vol. 15, Nature Publishing Group, 2013, pp. 1405–14, doi:<a href=\"https://doi.org/10.1038/ncb2869\">10.1038/ncb2869</a>.","apa":"Campinho, P., Behrndt, M., Ranft, J., Risler, T., Minc, N., &#38; Heisenberg, C.-P. J. (2013). Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb2869\">https://doi.org/10.1038/ncb2869</a>","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,” <i>Nature Cell Biology</i>, 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.","short":"P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, C.-P.J. Heisenberg, Nature Cell Biology 15 (2013) 1405–1414.","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.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/ncb2869\">https://doi.org/10.1038/ncb2869</a>."},"related_material":{"record":[{"id":"1403","relation":"dissertation_contains","status":"public"}]}},{"corr_author":"1","year":"2013","publication_status":"published","oa_version":"None","date_published":"2013-11-14T00:00:00Z","month":"11","citation":{"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.","chicago":"Pull, Christopher, William Hughes, and Markus Brown. “Tolerating an Infection: An Indirect Benefit of Co-Founding Queen Associations in the Ant Lasius Niger .” <i>Naturwissenschaften</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s00114-013-1115-5\">https://doi.org/10.1007/s00114-013-1115-5</a>.","ama":"Pull C, Hughes W, Brown M. Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger . <i>Naturwissenschaften</i>. 2013;100(12):1125-1136. doi:<a href=\"https://doi.org/10.1007/s00114-013-1115-5\">10.1007/s00114-013-1115-5</a>","mla":"Pull, Christopher, et al. “Tolerating an Infection: An Indirect Benefit of Co-Founding Queen Associations in the Ant Lasius Niger .” <i>Naturwissenschaften</i>, vol. 100, no. 12, Springer, 2013, pp. 1125–36, doi:<a href=\"https://doi.org/10.1007/s00114-013-1115-5\">10.1007/s00114-013-1115-5</a>.","apa":"Pull, C., Hughes, W., &#38; Brown, M. (2013). Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger . <i>Naturwissenschaften</i>. Springer. <a href=\"https://doi.org/10.1007/s00114-013-1115-5\">https://doi.org/10.1007/s00114-013-1115-5</a>","ieee":"C. Pull, W. Hughes, and M. Brown, “Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger ,” <i>Naturwissenschaften</i>, vol. 100, no. 12. Springer, pp. 1125–1136, 2013."},"issue":"12","author":[{"last_name":"Pull","first_name":"Christopher","full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hughes, William","first_name":"William","last_name":"Hughes"},{"last_name":"Brown","first_name":"Markus","full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"4649","department":[{"_id":"SyCr"}],"title":"Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger ","_id":"2283","quality_controlled":"1","intvolume":"       100","scopus_import":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","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."}],"doi":"10.1007/s00114-013-1115-5","external_id":{"isi":["000328850200004"]},"volume":100,"page":"1125  - 1136","isi":1,"publisher":"Springer","publication":"Naturwissenschaften","type":"journal_article","day":"14","date_updated":"2025-09-29T14:24:42Z","date_created":"2018-12-11T11:56:45Z","status":"public"},{"intvolume":"        13","quality_controlled":"1","title":"Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies","_id":"2284","file":[{"content_type":"application/pdf","relation":"main_file","checksum":"c16ef36f2a10786a7885e19c4528d707","file_name":"IST-2016-402-v1+1_1471-2148-13-225.pdf","creator":"system","file_size":281736,"date_created":"2018-12-12T10:13:41Z","file_id":"5026","access_level":"open_access","date_updated":"2020-07-14T12:45:37Z"}],"oa":1,"has_accepted_license":"1","ddc":["570"],"publist_id":"4647","department":[{"_id":"SyCr"}],"author":[{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Tragust","full_name":"Tragust, Simon"},{"full_name":"Ugelvig, Line V","first_name":"Line V","last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883"},{"first_name":"Michel","last_name":"Chapuisat","full_name":"Chapuisat, Michel"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer"}],"month":"10","issue":"1","citation":{"short":"S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, BMC Evolutionary Biology 13 (2013).","chicago":"Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia Cremer. “Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2148-13-225\">https://doi.org/10.1186/1471-2148-13-225</a>.","ista":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2013. Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. BMC Evolutionary Biology. 13(1), 225.","ama":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. <i>BMC Evolutionary Biology</i>. 2013;13(1). doi:<a href=\"https://doi.org/10.1186/1471-2148-13-225\">10.1186/1471-2148-13-225</a>","apa":"Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., &#38; Cremer, S. (2013). Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-13-225\">https://doi.org/10.1186/1471-2148-13-225</a>","ieee":"S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies,” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1. BioMed Central, 2013.","mla":"Tragust, Simon, et al. “Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1, 225, BioMed Central, 2013, doi:<a href=\"https://doi.org/10.1186/1471-2148-13-225\">10.1186/1471-2148-13-225</a>."},"related_material":{"record":[{"id":"9753","status":"public","relation":"research_data"}]},"date_published":"2013-10-14T00:00:00Z","year":"2013","publication_status":"published","oa_version":"Published Version","corr_author":"1","status":"public","date_created":"2018-12-11T11:56:46Z","date_updated":"2025-09-29T14:24:13Z","type":"journal_article","day":"14","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"BioMed Central","ec_funded":1,"publication":"BMC Evolutionary Biology","isi":1,"file_date_updated":"2020-07-14T12:45:37Z","acknowledgement":"The study was funded by the European Research Council (Marie Curie ERG 036569) and Marie Curie IEF 302204 to LVU\r\nCC BY 2.0\r\n","volume":13,"pubrep_id":"402","project":[{"_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071"},{"name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425"}],"doi":"10.1186/1471-2148-13-225","external_id":{"isi":["000326620500001"]},"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal-originally described for honeybees as &quot;hygienic behaviour&quot;-is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"article_number":"225","scopus_import":"1"},{"oa":1,"department":[{"_id":"CaHe"}],"publist_id":"4645","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817470/"}],"quality_controlled":"1","intvolume":"        32","_id":"2286","title":"The force and effect of cell proliferation","publication_status":"published","oa_version":"Submitted Version","year":"2013","date_published":"2013-10-04T00:00:00Z","corr_author":"1","author":[{"orcid":"0000-0002-8526-5416","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","full_name":"Campinho, Pedro","last_name":"Campinho","first_name":"Pedro"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"issue":"21","citation":{"ieee":"P. Campinho and C.-P. J. Heisenberg, “The force and effect of cell proliferation,” <i>EMBO Journal</i>, vol. 32, no. 21. Wiley-Blackwell, pp. 2783–2784, 2013.","apa":"Campinho, P., &#38; Heisenberg, C.-P. J. (2013). The force and effect of cell proliferation. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2013.225\">https://doi.org/10.1038/emboj.2013.225</a>","mla":"Campinho, Pedro, and Carl-Philipp J. Heisenberg. “The Force and Effect of Cell Proliferation.” <i>EMBO Journal</i>, vol. 32, no. 21, Wiley-Blackwell, 2013, pp. 2783–84, doi:<a href=\"https://doi.org/10.1038/emboj.2013.225\">10.1038/emboj.2013.225</a>.","ama":"Campinho P, Heisenberg C-PJ. The force and effect of cell proliferation. <i>EMBO Journal</i>. 2013;32(21):2783-2784. doi:<a href=\"https://doi.org/10.1038/emboj.2013.225\">10.1038/emboj.2013.225</a>","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.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2013.225\">https://doi.org/10.1038/emboj.2013.225</a>.","ista":"Campinho P, Heisenberg C-PJ. 2013. The force and effect of cell proliferation. EMBO Journal. 32(21), 2783–2784."},"month":"10","isi":1,"publication":"EMBO Journal","publisher":"Wiley-Blackwell","page":"2783 - 2784","pmid":1,"date_created":"2018-12-11T11:56:46Z","status":"public","day":"04","type":"journal_article","date_updated":"2025-09-29T14:23:43Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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."}],"article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"volume":32,"external_id":{"isi":["000326504900001"],"pmid":["24097062"]},"doi":"10.1038/emboj.2013.225"},{"quality_controlled":"1","intvolume":"         3","file":[{"file_id":"5290","date_created":"2018-12-12T10:17:35Z","file_size":626949,"creator":"system","date_updated":"2020-07-14T12:45:37Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"IST-2016-416-v1+1_Pickup_et_al-2013-Ecology_and_Evolution.pdf","checksum":"b5531bab4c0dec396bf5c8497fe178bf"}],"title":"The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant","_id":"2287","has_accepted_license":"1","ddc":["576"],"oa":1,"publist_id":"4644","department":[{"_id":"NiBa"}],"author":[{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup","full_name":"Pickup, Melinda"},{"last_name":"Barrett","first_name":"Spencer","full_name":"Barrett, Spencer"}],"month":"03","issue":"3","citation":{"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.","chicago":"Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” <i>Ecology and Evolution</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1002/ece3.465\">https://doi.org/10.1002/ece3.465</a>.","short":"M. Pickup, S. Barrett, Ecology and Evolution 3 (2013) 629–639.","ama":"Pickup M, Barrett S. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. <i>Ecology and Evolution</i>. 2013;3(3):629-639. doi:<a href=\"https://doi.org/10.1002/ece3.465\">10.1002/ece3.465</a>","mla":"Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” <i>Ecology and Evolution</i>, vol. 3, no. 3, Wiley-Blackwell, 2013, pp. 629–39, doi:<a href=\"https://doi.org/10.1002/ece3.465\">10.1002/ece3.465</a>.","ieee":"M. Pickup and S. Barrett, “The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant,” <i>Ecology and Evolution</i>, vol. 3, no. 3. Wiley-Blackwell, pp. 629–639, 2013.","apa":"Pickup, M., &#38; Barrett, S. (2013). The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. <i>Ecology and Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/ece3.465\">https://doi.org/10.1002/ece3.465</a>"},"year":"2013","publication_status":"published","oa_version":"Published Version","date_published":"2013-03-01T00:00:00Z","corr_author":"1","status":"public","date_created":"2018-12-11T11:56:47Z","type":"journal_article","day":"01","date_updated":"2025-09-29T14:23:14Z","isi":1,"file_date_updated":"2020-07-14T12:45:37Z","publisher":"Wiley-Blackwell","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Ecology and Evolution","page":"629 - 639","volume":3,"doi":"10.1002/ece3.465","external_id":{"isi":["000316124100015"]},"pubrep_id":"416","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","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"}],"scopus_import":"1","language":[{"iso":"eng"}]},{"type":"conference_editor","publication_identifier":{"isbn":["978-3-642-40707-9"]},"day":"01","date_updated":"2024-10-09T20:55:17Z","title":"Computational Methods in Systems Biology","_id":"2288","alternative_title":["LNCS"],"quality_controlled":"1","intvolume":"      8130","date_created":"2018-12-11T11:56:47Z","status":"public","publist_id":"4643","conference":{"end_date":"2013-09-24","start_date":"2013-09-22","name":"CMSB: Computational Methods in Systems Biology","location":"Klosterneuburg, Austria"},"department":[{"_id":"ToHe"}],"publisher":"Springer","doi":"10.1007/978-3-642-40708-6","month":"07","citation":{"short":"A. Gupta, T.A. Henzinger, eds., Computational Methods in Systems Biology, Springer, 2013.","chicago":"Gupta, Ashutosh, and Thomas A Henzinger, eds. <i>Computational Methods in Systems Biology</i>. Vol. 8130. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-40708-6\">https://doi.org/10.1007/978-3-642-40708-6</a>.","ista":"Gupta A, Henzinger TA eds. 2013. Computational Methods in Systems Biology, Springer,p.","ama":"Gupta A, Henzinger TA, eds. <i>Computational Methods in Systems Biology</i>. Vol 8130. Springer; 2013. doi:<a href=\"https://doi.org/10.1007/978-3-642-40708-6\">10.1007/978-3-642-40708-6</a>","ieee":"A. Gupta and T. A. Henzinger, Eds., <i>Computational Methods in Systems Biology</i>, vol. 8130. Springer, 2013.","apa":"Gupta, A., &#38; Henzinger, T. A. (Eds.). (2013). <i>Computational Methods in Systems Biology</i> (Vol. 8130). Presented at the CMSB: Computational Methods in Systems Biology, Klosterneuburg, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-642-40708-6\">https://doi.org/10.1007/978-3-642-40708-6</a>","mla":"Gupta, Ashutosh, and Thomas A. Henzinger, editors. <i>Computational Methods in Systems Biology</i>. Vol. 8130, Springer, 2013, doi:<a href=\"https://doi.org/10.1007/978-3-642-40708-6\">10.1007/978-3-642-40708-6</a>."},"volume":8130,"editor":[{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"language":[{"iso":"eng"}],"corr_author":"1","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa_version":"None","date_published":"2013-07-01T00:00:00Z","abstract":[{"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.","lang":"eng"}]},{"page":"331 - 344","publisher":"Springer","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"publication":"Computer Science Research and Development","file_date_updated":"2020-07-14T12:45:37Z","date_updated":"2024-10-09T20:55:17Z","type":"journal_article","day":"05","date_created":"2018-12-11T11:56:47Z","status":"public","language":[{"iso":"eng"}],"scopus_import":1,"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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"626","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/s00450-013-0251-7","volume":28,"publist_id":"4642","department":[{"_id":"ToHe"}],"oa":1,"has_accepted_license":"1","ddc":["000"],"title":"Quantitative reactive modeling and verification","_id":"2289","file":[{"relation":"main_file","content_type":"application/pdf","file_name":"IST-2016-626-v1+1_s00450-013-0251-7.pdf","checksum":"f117a00f9f046165bfa95595681e08a0","file_id":"5308","date_created":"2018-12-12T10:17:51Z","file_size":570361,"creator":"system","date_updated":"2020-07-14T12:45:37Z","access_level":"open_access"}],"intvolume":"        28","quality_controlled":"1","corr_author":"1","date_published":"2013-10-05T00:00:00Z","year":"2013","publication_status":"published","oa_version":"Published Version","month":"10","issue":"4","citation":{"ama":"Henzinger TA. Quantitative reactive modeling and verification. <i>Computer Science Research and Development</i>. 2013;28(4):331-344. doi:<a href=\"https://doi.org/10.1007/s00450-013-0251-7\">10.1007/s00450-013-0251-7</a>","ieee":"T. A. Henzinger, “Quantitative reactive modeling and verification,” <i>Computer Science Research and Development</i>, vol. 28, no. 4. Springer, pp. 331–344, 2013.","apa":"Henzinger, T. A. (2013). Quantitative reactive modeling and verification. <i>Computer Science Research and Development</i>. Springer. <a href=\"https://doi.org/10.1007/s00450-013-0251-7\">https://doi.org/10.1007/s00450-013-0251-7</a>","mla":"Henzinger, Thomas A. “Quantitative Reactive Modeling and Verification.” <i>Computer Science Research and Development</i>, vol. 28, no. 4, Springer, 2013, pp. 331–44, doi:<a href=\"https://doi.org/10.1007/s00450-013-0251-7\">10.1007/s00450-013-0251-7</a>.","short":"T.A. Henzinger, Computer Science Research and Development 28 (2013) 331–344.","chicago":"Henzinger, Thomas A. “Quantitative Reactive Modeling and Verification.” <i>Computer Science Research and Development</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s00450-013-0251-7\">https://doi.org/10.1007/s00450-013-0251-7</a>.","ista":"Henzinger TA. 2013. Quantitative reactive modeling and verification. Computer Science Research and Development. 28(4), 331–344."},"author":[{"first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}]},{"author":[{"full_name":"Boutté, Yohann","first_name":"Yohann","last_name":"Boutté"},{"full_name":"Jonsson, Kristoffer","last_name":"Jonsson","first_name":"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"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"first_name":"Lacey","last_name":"Samuels","full_name":"Samuels, Lacey"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"full_name":"Bhalerao, Rishikesh","first_name":"Rishikesh","last_name":"Bhalerao"}],"month":"10","citation":{"mla":"Boutté, Yohann, et al. “ECHIDNA Mediated Post Golgi Trafficking of Auxin Carriers for Differential Cell Elongation.” <i>PNAS</i>, vol. 110, no. 40, National Academy of Sciences, 2013, pp. 16259–64, doi:<a href=\"https://doi.org/10.1073/pnas.1309057110\">10.1073/pnas.1309057110</a>.","ieee":"Y. Boutté <i>et al.</i>, “ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation,” <i>PNAS</i>, 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. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1309057110\">https://doi.org/10.1073/pnas.1309057110</a>","ama":"Boutté Y, Jonsson K, Mcfarlane H, et al. ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. <i>PNAS</i>. 2013;110(40):16259-16264. doi:<a href=\"https://doi.org/10.1073/pnas.1309057110\">10.1073/pnas.1309057110</a>","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.","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.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1309057110\">https://doi.org/10.1073/pnas.1309057110</a>.","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."},"issue":"40","year":"2013","publication_status":"published","oa_version":"Submitted Version","date_published":"2013-10-01T00:00:00Z","quality_controlled":"1","intvolume":"       110","title":"ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation","_id":"2290","oa":1,"publist_id":"4639","department":[{"_id":"JiFr"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791722/","open_access":"1"}],"volume":110,"doi":"10.1073/pnas.1309057110","external_id":{"pmid":["24043780"],"isi":["000325105500090"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","abstract":[{"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.","lang":"eng"}],"scopus_import":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:56:48Z","status":"public","type":"journal_article","day":"01","date_updated":"2025-09-29T14:22:33Z","isi":1,"publisher":"National Academy of Sciences","publication":"PNAS","page":"16259 - 16264","pmid":1},{"main_file_link":[{"url":"http://eprint.iacr.org/2013/492","open_access":"1"}],"department":[{"_id":"KrPi"}],"page":"115 - 129","conference":{"location":"New Orleans, LA, United States","name":"CSF: Computer Security Foundations","end_date":"2013-09-28","start_date":"2013-09-26"},"publist_id":"4637","oa":1,"publisher":"IEEE","isi":1,"_id":"2291","date_updated":"2025-09-29T14:22:06Z","title":"Cryptographically enforced RBAC","day":"01","type":"conference","date_created":"2018-12-11T11:56:48Z","status":"public","quality_controlled":"1","language":[{"iso":"eng"}],"scopus_import":"1","date_published":"2013-09-01T00:00:00Z","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"}],"article_processing_charge":"No","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Submitted Version","year":"2013","citation":{"chicago":"Ferrara, Anna, Georg Fuchsbauer, and Bogdan Warinschi. “Cryptographically Enforced RBAC,” 115–29. IEEE, 2013. <a href=\"https://doi.org/10.1109/CSF.2013.15\">https://doi.org/10.1109/CSF.2013.15</a>.","short":"A. Ferrara, G. Fuchsbauer, B. Warinschi, in:, IEEE, 2013, pp. 115–129.","ista":"Ferrara A, Fuchsbauer G, Warinschi B. 2013. Cryptographically enforced RBAC. CSF: Computer Security Foundations, 115–129.","apa":"Ferrara, A., Fuchsbauer, G., &#38; Warinschi, B. (2013). Cryptographically enforced RBAC (pp. 115–129). Presented at the CSF: Computer Security Foundations, New Orleans, LA, United States: IEEE. <a href=\"https://doi.org/10.1109/CSF.2013.15\">https://doi.org/10.1109/CSF.2013.15</a>","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. <i>Cryptographically Enforced RBAC</i>. IEEE, 2013, pp. 115–29, doi:<a href=\"https://doi.org/10.1109/CSF.2013.15\">10.1109/CSF.2013.15</a>.","ama":"Ferrara A, Fuchsbauer G, Warinschi B. Cryptographically enforced RBAC. In: IEEE; 2013:115-129. doi:<a href=\"https://doi.org/10.1109/CSF.2013.15\">10.1109/CSF.2013.15</a>"},"month":"09","external_id":{"isi":["000335225600008"]},"doi":"10.1109/CSF.2013.15","author":[{"full_name":"Ferrara, Anna","first_name":"Anna","last_name":"Ferrara"},{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer","first_name":"Georg"},{"full_name":"Warinschi, Bogdan","last_name":"Warinschi","first_name":"Bogdan"}]},{"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","year":"2013","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"}],"date_published":"2013-08-08T00:00:00Z","doi":"10.1007/978-3-642-40313-2","citation":{"ama":"Chatterjee K, Sgall J, eds. <i>Mathematical Foundations of Computer Science 2013</i>. Vol 8087. Springer; 2013:VI-854. doi:<a href=\"https://doi.org/10.1007/978-3-642-40313-2\">10.1007/978-3-642-40313-2</a>","mla":"Chatterjee, Krishnendu, and Jiri Sgall, editors. <i>Mathematical Foundations of Computer Science 2013</i>. Vol. 8087, Springer, 2013, p. VI-854, doi:<a href=\"https://doi.org/10.1007/978-3-642-40313-2\">10.1007/978-3-642-40313-2</a>.","apa":"Chatterjee, K., &#38; Sgall, J. (Eds.). (2013). <i>Mathematical Foundations of Computer Science 2013</i> (Vol. 8087, p. VI-854). Presented at the MFCS: Mathematical Foundations of Computer Science, Klosterneuburg, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-642-40313-2\">https://doi.org/10.1007/978-3-642-40313-2</a>","ieee":"K. Chatterjee and J. Sgall, Eds., <i>Mathematical Foundations of Computer Science 2013</i>, vol. 8087. Springer, 2013, p. VI-854.","ista":"Chatterjee K, Sgall J eds. 2013. Mathematical Foundations of Computer Science 2013, Springer,p.","short":"K. Chatterjee, J. Sgall, eds., Mathematical Foundations of Computer Science 2013, Springer, 2013.","chicago":"Chatterjee, Krishnendu, and Jiri Sgall, eds. <i>Mathematical Foundations of Computer Science 2013</i>. Vol. 8087. Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-40313-2\">https://doi.org/10.1007/978-3-642-40313-2</a>."},"month":"08","volume":8087,"editor":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Sgall, Jiri","first_name":"Jiri","last_name":"Sgall"}],"page":"VI - 854","department":[{"_id":"KrCh"}],"publist_id":"4636","conference":{"location":"Klosterneuburg, Austria","name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2013-08-26","end_date":"2013-08-30"},"publisher":"Springer","series_title":"Lecture Notes in Computer Science","day":"08","type":"conference_editor","publication_identifier":{"isbn":["978-3-642-40312-5"]},"_id":"2292","title":"Mathematical Foundations of Computer Science 2013","date_updated":"2020-08-11T10:09:45Z","quality_controlled":"1","alternative_title":["LNCS"],"intvolume":"      8087","status":"public","date_created":"2018-12-11T11:56:48Z"},{"external_id":{"isi":["000351830500103"]},"doi":"10.1109/ICCV.2013.107","project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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"}],"article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:56:49Z","status":"public","day":"01","type":"conference","date_updated":"2025-09-29T14:20:45Z","isi":1,"ec_funded":1,"publisher":"IEEE","page":"825 - 832","author":[{"id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308","last_name":"Sharmanska","first_name":"Viktoriia","full_name":"Sharmanska, Viktoriia"},{"full_name":"Quadrianto, Novi","last_name":"Quadrianto","first_name":"Novi"},{"first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ama":"Sharmanska V, Quadrianto N, Lampert C. Learning to rank using privileged information. In: IEEE; 2013:825-832. doi:<a href=\"https://doi.org/10.1109/ICCV.2013.107\">10.1109/ICCV.2013.107</a>","mla":"Sharmanska, Viktoriia, et al. <i>Learning to Rank Using Privileged Information</i>. IEEE, 2013, pp. 825–32, doi:<a href=\"https://doi.org/10.1109/ICCV.2013.107\">10.1109/ICCV.2013.107</a>.","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.","apa":"Sharmanska, V., Quadrianto, N., &#38; Lampert, C. (2013). Learning to rank using privileged information (pp. 825–832). Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. <a href=\"https://doi.org/10.1109/ICCV.2013.107\">https://doi.org/10.1109/ICCV.2013.107</a>","ista":"Sharmanska V, Quadrianto N, Lampert C. 2013. Learning to rank using privileged information. ICCV: International Conference on Computer Vision, 825–832.","chicago":"Sharmanska, Viktoriia, Novi Quadrianto, and Christoph Lampert. “Learning to Rank Using Privileged Information,” 825–32. IEEE, 2013. <a href=\"https://doi.org/10.1109/ICCV.2013.107\">https://doi.org/10.1109/ICCV.2013.107</a>.","short":"V. Sharmanska, N. Quadrianto, C. Lampert, in:, IEEE, 2013, pp. 825–832."},"month":"12","publication_status":"published","oa_version":"Submitted Version","year":"2013","date_published":"2013-12-01T00:00:00Z","quality_controlled":"1","_id":"2293","title":"Learning to rank using privileged information","oa":1,"department":[{"_id":"ChLa"}],"conference":{"name":"ICCV: International Conference on Computer Vision","start_date":"2013-12-01","end_date":"2013-12-08","location":"Sydney, Australia"},"publist_id":"4635","main_file_link":[{"url":"www.cv-foundation.org/openaccess/content_iccv_2013/papers/Sharmanska_Learning_to_Rank_2013_ICCV_paper.pdf","open_access":"1"}]},{"conference":{"start_date":"2013-12-01","end_date":"2013-12-08","name":"ICCV: International Conference on Computer Vision","location":"Sydney, Australia"},"publist_id":"4634","department":[{"_id":"ChLa"}],"main_file_link":[{"url":"http://www.cv-foundation.org/openaccess/ICCV2013.py","open_access":"1"}],"oa":1,"title":"Drosophila Embryo Stage Annotation using Label Propagation","_id":"2294","quality_controlled":"1","year":"2013","publication_status":"published","oa_version":"Submitted Version","date_published":"2013-12-01T00:00:00Z","month":"12","citation":{"mla":"Kazmar, Tomas, et al. <i>Drosophila Embryo Stage Annotation Using Label Propagation</i>. IEEE, 2013, doi:<a href=\"https://doi.org/10.1109/ICCV.2013.139\">10.1109/ICCV.2013.139</a>.","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., &#38; Lampert, C. (2013). Drosophila Embryo Stage Annotation using Label Propagation. Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. <a href=\"https://doi.org/10.1109/ICCV.2013.139\">https://doi.org/10.1109/ICCV.2013.139</a>","ama":"Kazmar T, Kvon E, Stark A, Lampert C. Drosophila Embryo Stage Annotation using Label Propagation. In: IEEE; 2013. doi:<a href=\"https://doi.org/10.1109/ICCV.2013.139\">10.1109/ICCV.2013.139</a>","ista":"Kazmar T, Kvon E, Stark A, Lampert C. 2013. Drosophila Embryo Stage Annotation using Label Propagation. ICCV: International Conference on Computer Vision.","short":"T. Kazmar, E. Kvon, A. Stark, C. Lampert, in:, IEEE, 2013.","chicago":"Kazmar, Tomas, Evgeny Kvon, Alexander Stark, and Christoph Lampert. “Drosophila Embryo Stage Annotation Using Label Propagation.” IEEE, 2013. <a href=\"https://doi.org/10.1109/ICCV.2013.139\">https://doi.org/10.1109/ICCV.2013.139</a>."},"author":[{"last_name":"Kazmar","first_name":"Tomas","full_name":"Kazmar, Tomas"},{"first_name":"Evgeny","last_name":"Kvon","full_name":"Kvon, Evgeny"},{"full_name":"Stark, Alexander","last_name":"Stark","first_name":"Alexander"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph"}],"isi":1,"ec_funded":1,"publisher":"IEEE","type":"conference","day":"01","date_updated":"2025-09-29T14:20:15Z","date_created":"2018-12-11T11:56:49Z","status":"public","scopus_import":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","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"}],"doi":"10.1109/ICCV.2013.139","external_id":{"isi":["000351830500136"]},"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"}]},{"doi":"10.4230/LIPIcs.CSL.2013.165","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"pubrep_id":"756","volume":23,"scopus_import":1,"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, we establish decidability (with optimal EXPTIME-complete complexity) of the qualitative analysis problems for POMDPs with all parity objectives under finite-memory strategies. We also establish asymptotically optimal (exponential) memory bounds."}],"day":"27","series_title":"Leibniz International Proceedings in Informatics","type":"conference","date_updated":"2025-09-18T11:38:38Z","status":"public","date_created":"2018-12-11T11:56:50Z","page":"165 - 180","file_date_updated":"2020-07-14T12:45:37Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5400"},{"id":"1477","relation":"later_version","status":"public"}]},"citation":{"ieee":"K. Chatterjee, M. Chmelik, and M. Tracol, “What is decidable about partially observable Markov decision processes with omega-regular objectives,” vol. 23. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 165–180, 2013.","apa":"Chatterjee, K., Chmelik, M., &#38; Tracol, M. (2013). What is decidable about partially observable Markov decision processes with omega-regular objectives. Presented at the CSL: Computer Science Logic, Torino, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.165\">https://doi.org/10.4230/LIPIcs.CSL.2013.165</a>","mla":"Chatterjee, Krishnendu, et al. <i>What Is Decidable about Partially Observable Markov Decision Processes with Omega-Regular Objectives</i>. Vol. 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 165–80, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.165\">10.4230/LIPIcs.CSL.2013.165</a>.","ama":"Chatterjee K, Chmelik M, Tracol M. What is decidable about partially observable Markov decision processes with omega-regular objectives. 2013;23:165-180. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.165\">10.4230/LIPIcs.CSL.2013.165</a>","short":"K. Chatterjee, M. Chmelik, M. Tracol, 23 (2013) 165–180.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. “What Is Decidable about Partially Observable Markov Decision Processes with Omega-Regular Objectives.” Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.165\">https://doi.org/10.4230/LIPIcs.CSL.2013.165</a>.","ista":"Chatterjee K, Chmelik M, Tracol M. 2013. What is decidable about partially observable Markov decision processes with omega-regular objectives. 23, 165–180."},"month":"08","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","first_name":"Martin","last_name":"Chmelik"},{"full_name":"Tracol, Mathieu","first_name":"Mathieu","last_name":"Tracol","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","oa_version":"Published Version","year":"2013","date_published":"2013-08-27T00:00:00Z","file":[{"creator":"system","file_id":"4766","date_created":"2018-12-12T10:09:42Z","file_size":345171,"access_level":"open_access","date_updated":"2020-07-14T12:45:37Z","content_type":"application/pdf","relation":"main_file","file_name":"IST-2017-756-v1+1_2.pdf","checksum":"ba2828322955574d9283bea0e17a37a6"}],"_id":"2295","title":"What is decidable about partially observable Markov decision processes with omega-regular objectives","quality_controlled":"1","alternative_title":["LIPIcs"],"intvolume":"        23","department":[{"_id":"KrCh"}],"conference":{"location":"Torino, Italy","name":"CSL: Computer Science Logic","start_date":"2013-09-02","end_date":"2013-09-05"},"publist_id":"4633","ddc":["000"],"has_accepted_license":"1","oa":1},{"language":[{"iso":"eng"}],"scopus_import":"1","article_processing_charge":"No","abstract":[{"text":"We present an overview of mathematical results on the low temperature properties of dilute quantum gases, which have been obtained in the past few years. 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.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1007/s11537-013-1264-5","external_id":{"arxiv":["0908.3686"],"isi":["000324648700001"]},"volume":8,"page":"185 - 232","publisher":"Springer","publication":"Japanese Journal of Mathematics","isi":1,"arxiv":1,"date_updated":"2025-09-29T14:19:17Z","type":"journal_article","day":"24","date_created":"2018-12-11T11:56:50Z","status":"public","corr_author":"1","date_published":"2013-09-24T00:00:00Z","year":"2013","publication_status":"published","oa_version":"Preprint","month":"09","issue":"2","citation":{"apa":"Seiringer, R. (2013). Hot topics in cold gases: A mathematical physics perspective. <i>Japanese Journal of Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s11537-013-1264-5\">https://doi.org/10.1007/s11537-013-1264-5</a>","ieee":"R. Seiringer, “Hot topics in cold gases: A mathematical physics perspective,” <i>Japanese Journal of Mathematics</i>, vol. 8, no. 2. Springer, pp. 185–232, 2013.","mla":"Seiringer, Robert. “Hot Topics in Cold Gases: A Mathematical Physics Perspective.” <i>Japanese Journal of Mathematics</i>, vol. 8, no. 2, Springer, 2013, pp. 185–232, doi:<a href=\"https://doi.org/10.1007/s11537-013-1264-5\">10.1007/s11537-013-1264-5</a>.","ama":"Seiringer R. Hot topics in cold gases: A mathematical physics perspective. <i>Japanese Journal of Mathematics</i>. 2013;8(2):185-232. doi:<a href=\"https://doi.org/10.1007/s11537-013-1264-5\">10.1007/s11537-013-1264-5</a>","chicago":"Seiringer, Robert. “Hot Topics in Cold Gases: A Mathematical Physics Perspective.” <i>Japanese Journal of Mathematics</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s11537-013-1264-5\">https://doi.org/10.1007/s11537-013-1264-5</a>.","short":"R. Seiringer, Japanese Journal of Mathematics 8 (2013) 185–232.","ista":"Seiringer R. 2013. Hot topics in cold gases: A mathematical physics perspective. Japanese Journal of Mathematics. 8(2), 185–232."},"author":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer"}],"main_file_link":[{"url":"http://arxiv.org/abs/0908.3686","open_access":"1"}],"publist_id":"4631","department":[{"_id":"RoSe"}],"oa":1,"title":"Hot topics in cold gases: A mathematical physics perspective","_id":"2297","intvolume":"         8","quality_controlled":"1"},{"file_date_updated":"2020-07-14T12:45:37Z","ec_funded":1,"publisher":"Springer","page":"150 - 171","status":"public","date_created":"2018-12-11T11:56:50Z","type":"conference","day":"01","date_updated":"2021-01-12T06:56:36Z","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"}],"scopus_import":1,"language":[{"iso":"eng"}],"volume":7935,"doi":"10.1007/978-3-642-38856-9_10","pubrep_id":"196","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"}],"has_accepted_license":"1","ddc":["000","004"],"oa":1,"conference":{"end_date":"2013-06-22","start_date":"2013-06-20","name":"SAS: Static Analysis Symposium","location":"Seattle, WA, United States"},"publist_id":"4630","department":[{"_id":"ToHe"}],"alternative_title":["LNCS"],"quality_controlled":"1","intvolume":"      7935","file":[{"checksum":"907edd33a5892e3af093365f1fd57ed7","file_name":"IST-2014-196-v1+1_sas13.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:45:37Z","creator":"system","date_created":"2018-12-12T10:10:36Z","file_size":299004,"file_id":"4824"}],"title":"Local shape analysis for overlaid data structures","_id":"2298","year":"2013","publication_status":"published","oa_version":"Submitted Version","date_published":"2013-01-01T00:00:00Z","author":[{"first_name":"Cezara","last_name":"Dragoi","full_name":"Dragoi, Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Enea","first_name":"Constantin","full_name":"Enea, Constantin"},{"full_name":"Sighireanu, Mihaela","last_name":"Sighireanu","first_name":"Mihaela"}],"month":"01","citation":{"ama":"Dragoi C, Enea C, Sighireanu M. Local shape analysis for overlaid data structures. In: Vol 7935. Springer; 2013:150-171. doi:<a href=\"https://doi.org/10.1007/978-3-642-38856-9_10\">10.1007/978-3-642-38856-9_10</a>","mla":"Dragoi, Cezara, et al. <i>Local Shape Analysis for Overlaid Data Structures</i>. Vol. 7935, Springer, 2013, pp. 150–71, doi:<a href=\"https://doi.org/10.1007/978-3-642-38856-9_10\">10.1007/978-3-642-38856-9_10</a>.","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.","apa":"Dragoi, C., Enea, C., &#38; 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. <a href=\"https://doi.org/10.1007/978-3-642-38856-9_10\">https://doi.org/10.1007/978-3-642-38856-9_10</a>","ista":"Dragoi C, Enea C, Sighireanu M. 2013. Local shape analysis for overlaid data structures. SAS: Static Analysis Symposium, LNCS, vol. 7935, 150–171.","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. <a href=\"https://doi.org/10.1007/978-3-642-38856-9_10\">https://doi.org/10.1007/978-3-642-38856-9_10</a>."}}]