[{"type":"journal_article","issue":"5","extern":"1","year":"2005","status":"public","intvolume":"        88","date_published":"2005-05-01T00:00:00Z","oa":1,"date_created":"2018-12-11T12:03:13Z","publication":"Biophysical Journal","fulldoi":"https://doi.org/10.1529/biophysj.105.059774","publication_status":"published","publist_id":"2985","pmid":1,"article_type":"original","OA_type":"green","volume":88,"page":"37 - 39","das_tickbox":"1","OA_place":"repository","day":"01","author":[{"first_name":"Harald L","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","last_name":"Janovjak"},{"first_name":"Tanuj","full_name":"Sapra, Tanuj","last_name":"Sapra"},{"last_name":"Mueller","first_name":"Daniel","full_name":"Mueller, Daniel"}],"external_id":{"pmid":["15792967"]},"date_updated":"2026-07-02T07:29:18Z","publisher":"Biophysical Society","_id":"3416","title":"Complex stability of single proteins explored by forced unfolding experiments","abstract":[{"lang":"eng","text":"In the last decade atomic force microscopy has been used to measure the mechanical stability of single proteins. These force spectroscopy experiments have shown that many water-soluble and membrane proteins unfold via one or more intermediates. Recently, Li and co-workers found a linear correlation between the unfolding force of the native state and the intermediate in fibronectin, which they suggested indicated the presence of a molecular memory or multiple unfolding pathways (1). Here, we apply two independent methods in combination with Monte Carlo simulations to analyze the unfolding of α-helices E and D of bacteriorhodopsin (BR). We show that correlation analysis of unfolding forces is very sensitive to errors in force calibration of the instrument. In contrast, a comparison of relative forces provides a robust measure for the stability of unfolding intermediates. The proposed approach detects three energetically different states of α-helices E and D in trimeric BR. These states are not observed for monomeric BR and indicate that substantial information is hidden in forced unfolding experiments of single proteins."}],"publication_identifier":{"issn":["0006-3495"],"eissn":["1542-0086"]},"citation":{"ieee":"H. L. Janovjak, T. Sapra, and D. Mueller, “Complex stability of single proteins explored by forced unfolding experiments,” <i>Biophysical Journal</i>, vol. 88, no. 5. Biophysical Society, pp. 37–39, 2005.","ista":"Janovjak HL, Sapra T, Mueller D. 2005. Complex stability of single proteins explored by forced unfolding experiments. Biophysical Journal. 88(5), 37–39.","short":"H.L. Janovjak, T. Sapra, D. Mueller, Biophysical Journal 88 (2005) 37–39.","chicago":"Janovjak, Harald L, Tanuj Sapra, and Daniel Mueller. “Complex Stability of Single Proteins Explored by Forced Unfolding Experiments.” <i>Biophysical Journal</i>. Biophysical Society, 2005. <a href=\"https://doi.org/10.1529/biophysj.105.059774\">https://doi.org/10.1529/biophysj.105.059774</a>.","ama":"Janovjak HL, Sapra T, Mueller D. Complex stability of single proteins explored by forced unfolding experiments. <i>Biophysical Journal</i>. 2005;88(5):37-39. doi:<a href=\"https://doi.org/10.1529/biophysj.105.059774\">10.1529/biophysj.105.059774</a>","mla":"Janovjak, Harald L., et al. “Complex Stability of Single Proteins Explored by Forced Unfolding Experiments.” <i>Biophysical Journal</i>, vol. 88, no. 5, Biophysical Society, 2005, pp. 37–39, doi:<a href=\"https://doi.org/10.1529/biophysj.105.059774\">10.1529/biophysj.105.059774</a>.","apa":"Janovjak, H. L., Sapra, T., &#38; Mueller, D. (2005). Complex stability of single proteins explored by forced unfolding experiments. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1529/biophysj.105.059774\">https://doi.org/10.1529/biophysj.105.059774</a>"},"doi":"10.1529/biophysj.105.059774","article_processing_charge":"No","oa_version":"None","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305525/","open_access":"1"}],"month":"05","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}]},{"day":"12","author":[{"last_name":"Dodis","full_name":"Dodis, Yevgeniy","first_name":"Yevgeniy"},{"full_name":"Oliveira, Roberto","first_name":"Roberto","last_name":"Oliveira"},{"first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"page":"449 - 466","das_tickbox":"1","volume":3621,"OA_type":"closed access","conference":{"location":" Santa Barbara, CA, United States","end_date":"2005-08-18","name":"CRYPTO: International Cryptology Conference","start_date":"2005-08-14"},"publist_id":"3470","publication":"25th Annual International Cryptology Conference","fulldoi":"https://doi.org/10.1007/11535218_27","publication_status":"published","date_published":"2005-09-12T00:00:00Z","date_created":"2018-12-11T12:02:03Z","type":"conference","extern":"1","status":"public","year":"2005","intvolume":"      3621","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"09","language":[{"iso":"eng"}],"oa_version":"None","alternative_title":["LNCS"],"publication_identifier":{"isbn":["9783540281146"],"eisbn":["9783540318705"]},"abstract":[{"lang":"eng","text":"The Full-Domain Hash (FDH) signature scheme [3] forms one the most basic usages of random oracles. It works with a family F of trapdoor permutations (TDP), where the signature of m is computed as f−1(h(m)) (here f ∈R F and h is modelled as a random oracle). It is known to be existentially unforgeable for any TDP family F [3], although a much tighter security reduction is known for a restrictive class of TDP’s [10,14] — namely, those induced by a family of claw-free permutations (CFP) pairs. The latter result was shown [11] to match the best possible “black-box” security reduction in the random oracle model, irrespective of the TDP family F (e.g., RSA) one might use.\r\nIn this work we investigate the question if it is possible to instantiate the random oracle h with a “real” family of hash functions H such that the corresponding schemes can be proven secure in the standard model, under some natural assumption on the family F. Our main result rules out the existence of such instantiations for any assumption on F which (1) is satisfied by a family of random permutations; and (2) does not allow the attacker to invert f ∈R F on an a-priori unbounded number of points. Moreover, this holds even if the choice of H can arbitrarily depend on f. As an immediate corollary, we rule out instantiating FDH based on general claw-free permutations, which shows that in order to prove the security of FDH in the standard model one must utilize significantly more structure on F than what is sufficient for the best proof of security in the random oracle model."}],"doi":"10.1007/11535218_27","citation":{"apa":"Dodis, Y., Oliveira, R., &#38; Pietrzak, K. Z. (2005). On the generic insecurity of the full domain hash. In <i>25th Annual International Cryptology Conference</i> (Vol. 3621, pp. 449–466).  Santa Barbara, CA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/11535218_27\">https://doi.org/10.1007/11535218_27</a>","mla":"Dodis, Yevgeniy, et al. “On the Generic Insecurity of the Full Domain Hash.” <i>25th Annual International Cryptology Conference</i>, vol. 3621, Springer Nature, 2005, pp. 449–66, doi:<a href=\"https://doi.org/10.1007/11535218_27\">10.1007/11535218_27</a>.","ista":"Dodis Y, Oliveira R, Pietrzak KZ. 2005. On the generic insecurity of the full domain hash. 25th Annual International Cryptology Conference. CRYPTO: International Cryptology Conference, LNCS, vol. 3621, 449–466.","ieee":"Y. Dodis, R. Oliveira, and K. Z. Pietrzak, “On the generic insecurity of the full domain hash,” in <i>25th Annual International Cryptology Conference</i>,  Santa Barbara, CA, United States, 2005, vol. 3621, pp. 449–466.","ama":"Dodis Y, Oliveira R, Pietrzak KZ. On the generic insecurity of the full domain hash. In: <i>25th Annual International Cryptology Conference</i>. Vol 3621. Springer Nature; 2005:449-466. doi:<a href=\"https://doi.org/10.1007/11535218_27\">10.1007/11535218_27</a>","chicago":"Dodis, Yevgeniy, Roberto Oliveira, and Krzysztof Z Pietrzak. “On the Generic Insecurity of the Full Domain Hash.” In <i>25th Annual International Cryptology Conference</i>, 3621:449–66. Springer Nature, 2005. <a href=\"https://doi.org/10.1007/11535218_27\">https://doi.org/10.1007/11535218_27</a>.","short":"Y. Dodis, R. Oliveira, K.Z. Pietrzak, in:, 25th Annual International Cryptology Conference, Springer Nature, 2005, pp. 449–466."},"article_processing_charge":"No","title":"On the generic insecurity of the full domain hash","acknowledgement":"Supported by NSF CAREER Award CCR-0133806 and TC Grant No.CCR-0311095. Supported by the Swiss National Science Foundation, project No. 200020-103847/1","date_updated":"2026-07-02T08:05:18Z","_id":"3212","publisher":"Springer Nature"},{"type":"conference","status":"public","extern":"1","year":"2005","intvolume":"         2","date_published":"2005-07-25T00:00:00Z","date_created":"2018-12-11T12:01:52Z","publication":"Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 2 ","fulldoi":"https://doi.org/10.1109/CVPR.2005.91","publication_status":"published","publist_id":"3502","conference":{"end_date":"2005-06-25","name":"CVPR: Computer Vision and Pattern Recognition","start_date":"2005-06-20","location":"San Diego, CA, United States"},"OA_type":"closed access","volume":2,"page":"407 - 414","das_tickbox":"1","day":"25","author":[{"last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"},{"last_name":"Criminisi","first_name":"Antonio","full_name":"Criminisi, Antonio"},{"last_name":"Blake","first_name":"Andrew","full_name":"Blake, Andrew"},{"first_name":"Geoffrey","full_name":"Cross, Geoffrey","last_name":"Cross"},{"first_name":"Carsten","full_name":"Rother, Carsten","last_name":"Rother"}],"date_updated":"2026-07-02T09:00:36Z","_id":"3183","publisher":"IEEE","title":"Bi-layer segmentation of binocular stereo video","publication_identifier":{"issn":["1063-6919"],"isbn":["0769523722"]},"abstract":[{"lang":"eng","text":"This paper describes two algorithms capable of real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, contrast and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves stereo in an extended 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour model that is learned on the fly, and stereo disparities are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC), does not directly solve stereo. Instead the stereo match likelihood is marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar perfomance, substantially better than stereo or colour/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output."}],"citation":{"apa":"Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., &#38; Rother, C. (2005). Bi-layer segmentation of binocular stereo video. In <i>Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 2 </i> (Vol. 2, pp. 407–414). San Diego, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2005.91\">https://doi.org/10.1109/CVPR.2005.91</a>","mla":"Kolmogorov, Vladimir, et al. “Bi-Layer Segmentation of Binocular Stereo Video.” <i>Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 2 </i>, vol. 2, IEEE, 2005, pp. 407–14, doi:<a href=\"https://doi.org/10.1109/CVPR.2005.91\">10.1109/CVPR.2005.91</a>.","ista":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2005. Bi-layer segmentation of binocular stereo video. Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 2 . CVPR: Computer Vision and Pattern Recognition vol. 2, 407–414.","ieee":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Bi-layer segmentation of binocular stereo video,” in <i>Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 2 </i>, San Diego, CA, United States, 2005, vol. 2, pp. 407–414.","ama":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Bi-layer segmentation of binocular stereo video. In: <i>Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 2 </i>. Vol 2. IEEE; 2005:407-414. doi:<a href=\"https://doi.org/10.1109/CVPR.2005.91\">10.1109/CVPR.2005.91</a>","chicago":"Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross, and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video.” In <i>Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 2 </i>, 2:407–14. IEEE, 2005. <a href=\"https://doi.org/10.1109/CVPR.2005.91\">https://doi.org/10.1109/CVPR.2005.91</a>.","short":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 2 , IEEE, 2005, pp. 407–414."},"doi":"10.1109/CVPR.2005.91","article_processing_charge":"No","oa_version":"None","main_file_link":[{"url":"http://research.microsoft.com/pubs/67281/criminisi_cvpr2005.pdf"}],"month":"07","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"oa_version":"None","month":"12","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"doi":"10.1109/ICCV.2005.252","citation":{"mla":"Kolmogorov, Vladimir, and Yuri Boykov. “What Metrics Can Be Approximated by Geo Cuts or Global Optimization of Length Area and Flux.” <i>Proceedings of the Tenth IEEE International Conference on Computer Vision Volume 1</i>, vol. 1, IEEE, 2005, pp. 564–71, doi:<a href=\"https://doi.org/10.1109/ICCV.2005.252\">10.1109/ICCV.2005.252</a>.","apa":"Kolmogorov, V., &#38; Boykov, Y. (2005). What metrics can be approximated by geo cuts or global optimization of length area and flux. In <i>Proceedings of the Tenth IEEE International Conference on Computer Vision Volume 1</i> (Vol. 1, pp. 564–571). NW Washington, DC, United States: IEEE. <a href=\"https://doi.org/10.1109/ICCV.2005.252\">https://doi.org/10.1109/ICCV.2005.252</a>","chicago":"Kolmogorov, Vladimir, and Yuri Boykov. “What Metrics Can Be Approximated by Geo Cuts or Global Optimization of Length Area and Flux.” In <i>Proceedings of the Tenth IEEE International Conference on Computer Vision Volume 1</i>, 1:564–71. IEEE, 2005. <a href=\"https://doi.org/10.1109/ICCV.2005.252\">https://doi.org/10.1109/ICCV.2005.252</a>.","short":"V. Kolmogorov, Y. Boykov, in:, Proceedings of the Tenth IEEE International Conference on Computer Vision Volume 1, IEEE, 2005, pp. 564–571.","ama":"Kolmogorov V, Boykov Y. What metrics can be approximated by geo cuts or global optimization of length area and flux. In: <i>Proceedings of the Tenth IEEE International Conference on Computer Vision Volume 1</i>. Vol 1. IEEE; 2005:564-571. doi:<a href=\"https://doi.org/10.1109/ICCV.2005.252\">10.1109/ICCV.2005.252</a>","ieee":"V. Kolmogorov and Y. Boykov, “What metrics can be approximated by geo cuts or global optimization of length area and flux,” in <i>Proceedings of the Tenth IEEE International Conference on Computer Vision Volume 1</i>, NW Washington, DC, United States, 2005, vol. 1, pp. 564–571.","ista":"Kolmogorov V, Boykov Y. 2005. What metrics can be approximated by geo cuts or global optimization of length area and flux. Proceedings of the Tenth IEEE International Conference on Computer Vision Volume 1. ICCV: International Conference on Computer Vision vol. 1, 564–571."},"publication_identifier":{"eissn":["2380-7504"],"issn":["1550-5499"]},"abstract":[{"text":"In the work of the authors (2003), we showed that graph cuts can find hypersurfaces of globally minimal length (or area) under any Riemannian metric. Here we show that graph cuts on directed regular grids can approximate a significantly more general class of continuous non-symmetric metrics. Using submodularity condition (Boros and Hammer, 2002 and Kolmogorov and Zabih, 2004), we obtain a tight characterization of graph-representable metrics. Such &quot;submodular&quot; metrics have an elegant geometric interpretation via hypersurface functionals combining length/area and flux. Practically speaking, we attend 'geo-cuts' algorithm to a wider class of geometrically motivated hypersurface functionals and show how to globally optimize any combination of length/area and flux of a given vector field. The concept of flux was recently introduced into computer vision by Vasilevskiy and Siddiqi (2002) but it was mainly studied within variational framework so far. We are first to show that flux can be integrated into graph cuts as well. Combining geometric concepts of flux and length/area within the global optimization framework of graph cuts allows principled discrete segmentation models and advances the slate of the art for the graph cuts methods in vision. In particular we address the &quot;shrinking&quot; problem of graph cuts, improve segmentation of long thin objects, and introduce useful shape constraints.","lang":"eng"}],"article_processing_charge":"No","_id":"3182","publisher":"IEEE","date_updated":"2026-07-02T08:53:55Z","title":"What metrics can be approximated by geo cuts or global optimization of length area and flux","das_tickbox":"1","page":"564 - 571","day":"05","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"},{"last_name":"Boykov","first_name":"Yuri","full_name":"Boykov, Yuri"}],"OA_type":"closed access","volume":1,"publication":"Proceedings of the Tenth IEEE International Conference on Computer Vision Volume 1","publication_status":"published","fulldoi":"https://doi.org/10.1109/ICCV.2005.252","publist_id":"3501","conference":{"end_date":"2005-10-20","name":"ICCV: International Conference on Computer Vision","start_date":"2005-10-17","location":"NW Washington, DC, United States"},"type":"conference","intvolume":"         1","year":"2005","status":"public","extern":"1","date_published":"2005-12-05T00:00:00Z","date_created":"2018-12-11T12:01:52Z"},{"article_processing_charge":"No","abstract":[{"lang":"eng","text":"This paper addresses the novel problem of automatically synthesizing an output image from a large collection of different input images. The synthesized image, called a digital tapestry, can be viewed as a visual summary or a virtual 'thumbnail' of all the images in the input collection. The problem of creating the tapestry is cast as a multi-class labeling problem such that each region in the tapestry is constructed from input image blocks that are salient and such that neighboring blocks satisfy spatial compatibility. This is formulated using a Markov Random Field and optimized via the graph cut based expansion move algorithm. The standard expansion move algorithm can only handle energies with metric terms, while our energy contains non-metric (soft and hard) constraints. Therefore we propose two novel contributions. First, we extend the expansion move algorithm for energy functions with non-metric hard constraints. Secondly, we modify it for functions with &quot;almost&quot; metric soft terms, and show that it gives good results in practice. The proposed framework was tested on several consumer photograph collections, and the results are presented."}],"publication_identifier":{"issn":["1063-6919"],"isbn":["0769523722"]},"citation":{"ieee":"C. Rother, S. Kumar, V. Kolmogorov, and A. Blake, “Digital tapestry,” in <i>Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 1</i>, San Diego, CA, United States, 2005, vol. 1, pp. 589–596.","ista":"Rother C, Kumar S, Kolmogorov V, Blake A. 2005. Digital tapestry. Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 1. CVPR: Computer Vision and Pattern Recognition vol. 1, 589–596.","chicago":"Rother, Carsten, Sanjiv Kumar, Vladimir Kolmogorov, and Andrew Blake. “Digital Tapestry.” In <i>Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 1</i>, 1:589–96. IEEE, 2005. <a href=\"https://doi.org/10.1109/CVPR.2005.130\">https://doi.org/10.1109/CVPR.2005.130</a>.","short":"C. Rother, S. Kumar, V. Kolmogorov, A. Blake, in:, Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 1, IEEE, 2005, pp. 589–596.","ama":"Rother C, Kumar S, Kolmogorov V, Blake A. Digital tapestry. In: <i>Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 1</i>. Vol 1. IEEE; 2005:589-596. doi:<a href=\"https://doi.org/10.1109/CVPR.2005.130\">10.1109/CVPR.2005.130</a>","mla":"Rother, Carsten, et al. “Digital Tapestry.” <i>Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 1</i>, vol. 1, IEEE, 2005, pp. 589–96, doi:<a href=\"https://doi.org/10.1109/CVPR.2005.130\">10.1109/CVPR.2005.130</a>.","apa":"Rother, C., Kumar, S., Kolmogorov, V., &#38; Blake, A. (2005). Digital tapestry. In <i>Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 1</i> (Vol. 1, pp. 589–596). San Diego, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2005.130\">https://doi.org/10.1109/CVPR.2005.130</a>"},"doi":"10.1109/CVPR.2005.130","title":"Digital tapestry","date_updated":"2026-07-02T09:06:43Z","publisher":"IEEE","_id":"3175","language":[{"iso":"eng"}],"month":"07","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","main_file_link":[{"url":"http://research.microsoft.com/en-us/um/people/ablake/papers/ablake/rother_cvpr05.pdf"}],"oa_version":"None","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2005-06-25","start_date":"2005-06-20","location":"San Diego, CA, United States"},"publist_id":"3503","fulldoi":"https://doi.org/10.1109/CVPR.2005.130","publication_status":"published","publication":"Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Volume 1","date_created":"2018-12-11T12:01:50Z","date_published":"2005-07-25T00:00:00Z","extern":"1","year":"2005","status":"public","intvolume":"         1","type":"conference","author":[{"last_name":"Rother","full_name":"Rother, Carsten","first_name":"Carsten"},{"full_name":"Kumar, Sanjiv","first_name":"Sanjiv","last_name":"Kumar"},{"last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir"},{"first_name":"Andrew","full_name":"Blake, Andrew","last_name":"Blake"}],"day":"25","page":"589 - 596","das_tickbox":"1","volume":1,"OA_type":"closed access"},{"author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir"},{"last_name":"Wainwright","full_name":"Wainwright, Martin","first_name":"Martin"}],"day":"01","OA_place":"repository","das_tickbox":"1","page":"316 - 323","OA_type":"green","conference":{"start_date":"2005-07-26","name":"UAI: Uncertainty in Artificial Intelligence","end_date":"2005-07-29","location":"Edinburgh, Scotland"},"publist_id":"3500","arxiv":1,"publication_status":"published","publication":"Proceedings of the Twenty-First Conference on Uncertainty in Artificial Intelligence","date_created":"2018-12-11T12:01:51Z","oa":1,"date_published":"2005-07-01T00:00:00Z","year":"2005","status":"public","extern":"1","type":"conference","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"month":"07","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1207.1395","open_access":"1"}],"oa_version":"Preprint","article_processing_charge":"No","citation":{"apa":"Kolmogorov, V., &#38; Wainwright, M. (2005). On the optimality of tree reweighted max product message passing. In <i>Proceedings of the Twenty-First Conference on Uncertainty in Artificial Intelligence</i> (pp. 316–323). Edinburgh, Scotland: AUAI Press.","mla":"Kolmogorov, Vladimir, and Martin Wainwright. “On the Optimality of Tree Reweighted Max Product Message Passing.” <i>Proceedings of the Twenty-First Conference on Uncertainty in Artificial Intelligence</i>, AUAI Press, 2005, pp. 316–23.","ama":"Kolmogorov V, Wainwright M. On the optimality of tree reweighted max product message passing. In: <i>Proceedings of the Twenty-First Conference on Uncertainty in Artificial Intelligence</i>. AUAI Press; 2005:316-323.","short":"V. Kolmogorov, M. Wainwright, in:, Proceedings of the Twenty-First Conference on Uncertainty in Artificial Intelligence, AUAI Press, 2005, pp. 316–323.","chicago":"Kolmogorov, Vladimir, and Martin Wainwright. “On the Optimality of Tree Reweighted Max Product Message Passing.” In <i>Proceedings of the Twenty-First Conference on Uncertainty in Artificial Intelligence</i>, 316–23. AUAI Press, 2005.","ista":"Kolmogorov V, Wainwright M. 2005. On the optimality of tree reweighted max product message passing. Proceedings of the Twenty-First Conference on Uncertainty in Artificial Intelligence. UAI: Uncertainty in Artificial Intelligence, 316–323.","ieee":"V. Kolmogorov and M. Wainwright, “On the optimality of tree reweighted max product message passing,” in <i>Proceedings of the Twenty-First Conference on Uncertainty in Artificial Intelligence</i>, Edinburgh, Scotland, 2005, pp. 316–323."},"abstract":[{"text":"Tree-reweighted max-product (TRW) message passing [9] is a modified form of the ordinary max-product algorithm for attempting to find minimal energy configurations in Markov random field with cycles. For a TRW fixed point satisfying the strong tree agreement condition, the algorithm outputs a configuration that is provably optimal. In this paper, we focus on the case of binary variables with pairwise couplings, and establish stronger properties of TRW fixed points that satisfy only the milder condition of weak tree agreement (WTA). First, we demonstrate how it is possible to identify part of the optimal solution - i.e., a provably optimal solution for a subset of nodes - without knowing a complete solution. Second, we show that for submodular functions, a WTA fixed point always yields a globally optimal solution. We establish that for binary variables, any WTA fixed point always achieves the global maximum of the linear programming relaxation underlying the TRW method.","lang":"eng"}],"publication_identifier":{"isbn":["9780974903910"]},"title":"On the optimality of tree reweighted max product message passing","_id":"3181","publisher":"AUAI Press","date_updated":"2026-07-02T08:19:20Z","external_id":{"arxiv":["1207.1395"]}},{"author":[{"last_name":"Bellare","first_name":"Mihir","full_name":"Bellare, Mihir"},{"first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"},{"last_name":"Rogaway","first_name":"Phillip","full_name":"Rogaway, Phillip"}],"day":"12","OA_place":"publisher","page":"527 - 545","volume":3621,"OA_type":"gold","publist_id":"3469","conference":{"start_date":"2005-08-14","name":"CRYPTO: International Cryptology Conference","end_date":"2005-08-18","location":"Santa Barbara, CA, United States"},"fulldoi":"https://doi.org/10.1007/11535218_32","publication_status":"published","publication":"25th Annual International Cryptology Conference","date_created":"2018-12-11T12:02:02Z","date_published":"2005-09-12T00:00:00Z","year":"2005","extern":"1","status":"public","intvolume":"      3621","type":"conference","month":"09","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"oa_version":"None","alternative_title":["LNCS"],"article_processing_charge":"No","publication_identifier":{"isbn":["9783540281146"],"eisbn":["9783540318705"]},"abstract":[{"text":"We present an improved bound on the advantage of any q-query adversary at distinguishing between the CBC MAC over a random n-bit permutation and a random function outputting n bits. The result assumes that no message queried is a prefix of any other, as is the case when all messages to be MACed have the same length. We go on to give an improved analysis of the encrypted CBC MAC, where there is no restriction on queried messages. Letting m be the block length of the longest query, our bounds are about mq2/2n for the basic CBC MAC and mo(1)q2/2n for the encrypted CBC MAC, improving prior bounds of m2q2/2n. The new bounds translate into improved guarantees on the probability of forging these MACs.","lang":"eng"}],"doi":"10.1007/11535218_32","citation":{"chicago":"Bellare, Mihir, Krzysztof Z Pietrzak, and Phillip Rogaway. “Improved Security Analyses for CBC MACs.” In <i>25th Annual International Cryptology Conference</i>, 3621:527–45. Springer Nature, 2005. <a href=\"https://doi.org/10.1007/11535218_32\">https://doi.org/10.1007/11535218_32</a>.","short":"M. Bellare, K.Z. Pietrzak, P. Rogaway, in:, 25th Annual International Cryptology Conference, Springer Nature, 2005, pp. 527–545.","ama":"Bellare M, Pietrzak KZ, Rogaway P. Improved security analyses for CBC MACs. In: <i>25th Annual International Cryptology Conference</i>. Vol 3621. Springer Nature; 2005:527-545. doi:<a href=\"https://doi.org/10.1007/11535218_32\">10.1007/11535218_32</a>","ieee":"M. Bellare, K. Z. Pietrzak, and P. Rogaway, “Improved security analyses for CBC MACs,” in <i>25th Annual International Cryptology Conference</i>, Santa Barbara, CA, United States, 2005, vol. 3621, pp. 527–545.","ista":"Bellare M, Pietrzak KZ, Rogaway P. 2005. Improved security analyses for CBC MACs. 25th Annual International Cryptology Conference. CRYPTO: International Cryptology Conference, LNCS, vol. 3621, 527–545.","mla":"Bellare, Mihir, et al. “Improved Security Analyses for CBC MACs.” <i>25th Annual International Cryptology Conference</i>, vol. 3621, Springer Nature, 2005, pp. 527–45, doi:<a href=\"https://doi.org/10.1007/11535218_32\">10.1007/11535218_32</a>.","apa":"Bellare, M., Pietrzak, K. Z., &#38; Rogaway, P. (2005). Improved security analyses for CBC MACs. In <i>25th Annual International Cryptology Conference</i> (Vol. 3621, pp. 527–545). Santa Barbara, CA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/11535218_32\">https://doi.org/10.1007/11535218_32</a>"},"title":"Improved security analyses for CBC MACs","date_updated":"2026-07-02T07:55:53Z","_id":"3211","publisher":"Springer Nature","acknowledgement":"Pietrzak was supported by the Swiss National Science Foundation, project No. 200020-103847/1."},{"oa_version":"None","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"06","date_updated":"2026-07-03T10:56:31Z","_id":"4249","publisher":"Wiley-Blackwell","external_id":{"pmid":["16050097"]},"title":"Speciation through competition: A critical review","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We examined causes of speciation in asexual populations in both sympatry and parapatry, providing an alternative explanation for the speciation patterns reported by Dieckmann and Doebeli (1999) and Doebeli and Dieckmann (2003). Both in sympatry and parapatry, they find that speciation occurs relatively easily. We reveal that in the sympatric clonal model, the equilibrium distribution is continuous and the disruptive selection driving evolution of discrete clusters is only transient. Hence, if discrete phenotypes are to remain stable in the sympatric sexual model, there should be some source of nontransient disruptive selection that will drive evolution of assortment. We analyze sexually reproducing populations using the Bulmer’s infinitesimal model and show that cost-free assortment alone leads to speciation and disruptive selection only arises when the optimal distribution cannot be matched—in this example, because the phenotypic range is limited. In addition, Doebeli and Dieckmann’s analyses assumed a high genetic variance and a high mutation rate. Thus, these theoretical models do not support the conclusion that sympatric speciation is a likely outcome of competition for resources. In their parapatric model (Doebeli and Dieckmann 2003), clustering into distinct phenotypes is driven by edge effects, rather than by frequency-dependent competition."}],"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"doi":"10.1111/j.0014-3820.2005.tb01771.x","citation":{"apa":"Polechova, J., &#38; Barton, N. H. (2005). Speciation through competition: A critical review. <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.0014-3820.2005.tb01771.x\">https://doi.org/10.1111/j.0014-3820.2005.tb01771.x</a>","mla":"Polechova, Jitka, and Nicholas H. Barton. “Speciation through Competition: A Critical Review.” <i>Evolution; International Journal of Organic Evolution</i>, vol. 59, no. 6, Wiley-Blackwell, 2005, pp. 1194–210, doi:<a href=\"https://doi.org/10.1111/j.0014-3820.2005.tb01771.x\">10.1111/j.0014-3820.2005.tb01771.x</a>.","ista":"Polechova J, Barton NH. 2005. Speciation through competition: A critical review. Evolution; International Journal of Organic Evolution. 59(6), 1194–1210.","ieee":"J. Polechova and N. H. Barton, “Speciation through competition: A critical review,” <i>Evolution; International Journal of Organic Evolution</i>, vol. 59, no. 6. Wiley-Blackwell, pp. 1194–1210, 2005.","ama":"Polechova J, Barton NH. Speciation through competition: A critical review. <i>Evolution; International Journal of Organic Evolution</i>. 2005;59(6):1194-1210. doi:<a href=\"https://doi.org/10.1111/j.0014-3820.2005.tb01771.x\">10.1111/j.0014-3820.2005.tb01771.x</a>","chicago":"Polechova, Jitka, and Nicholas H Barton. “Speciation through Competition: A Critical Review.” <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell, 2005. <a href=\"https://doi.org/10.1111/j.0014-3820.2005.tb01771.x\">https://doi.org/10.1111/j.0014-3820.2005.tb01771.x</a>.","short":"J. Polechova, N.H. Barton, Evolution; International Journal of Organic Evolution 59 (2005) 1194–1210."},"pmid":1,"article_type":"original","OA_type":"closed access","volume":59,"page":"1194 - 1210","das_tickbox":"1","author":[{"first_name":"Jitka","full_name":"Polechova, Jitka","last_name":"Polechova","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"day":"01","year":"2005","extern":"1","status":"public","intvolume":"        59","type":"journal_article","issue":"6","date_created":"2018-12-11T12:07:50Z","date_published":"2005-06-01T00:00:00Z","fulldoi":"https://doi.org/10.1111/j.0014-3820.2005.tb01771.x","publication_status":"published","publication":"Evolution; International Journal of Organic Evolution","publist_id":"1849"},{"oa_version":"None","month":"03","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"article_processing_charge":"No","abstract":[{"text":"In finite populations subject to selection, genetic drift generates negative linkage disequilibrium, on average, even if selection acts independently (i.e. multiplicatively) upon all loci. Negative disequilibrium reduces the variance in fitness and hence, by FISHER's Fundamental Theorem (1930), slows the rate of increase in mean fitness. Modifiers that increase recombination eliminate the negative disequilibria that impede selection and consequently increase in frequency by 'hitch-hiking'. In addition, recombinant progeny are more fit on average than non-recombinant progeny when there is negative linkage disequilibrium and loci interact multiplicatively. For both these reasons, stochastic fluctuations in linkage disequilibrium in finite populations favor the evolution of increased rates of recombination, even in the absence of epistatic interactions among loci and even when disequilibrium is initially absent. The method developed within this paper quantifies the strength of selection on a modifier allele that increases recombination due to stochastically generated linkage disequilibria. The analysis indicates that, in a population subject to multiplicative selection, genetic associations generated by drift do select for increased recombination, a result that is confirmed by Monte Carlo simulations. Selection for a modifier that increases recombination is highest when linkage among all loci is tight, when beneficial alleles rise from low to high frequency, and when the population size is small.","lang":"eng"}],"publication_identifier":{"issn":["0016-6731"],"eissn":["1943-2631"]},"doi":"10.1534/genetics.104.032821","citation":{"mla":"Barton, Nicholas H., and Sarah Otto. “Evolution of Recombination Due to Random Drift.” <i>Genetics</i>, vol. 169, no. 4, Genetics Society of America, 2005, pp. 2353–70, doi:<a href=\"https://doi.org/10.1534/genetics.104.032821\">10.1534/genetics.104.032821</a>.","apa":"Barton, N. H., &#38; Otto, S. (2005). Evolution of recombination due to random drift. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.104.032821\">https://doi.org/10.1534/genetics.104.032821</a>","chicago":"Barton, Nicholas H, and Sarah Otto. “Evolution of Recombination Due to Random Drift.” <i>Genetics</i>. Genetics Society of America, 2005. <a href=\"https://doi.org/10.1534/genetics.104.032821\">https://doi.org/10.1534/genetics.104.032821</a>.","short":"N.H. Barton, S. Otto, Genetics 169 (2005) 2353–2370.","ama":"Barton NH, Otto S. Evolution of recombination due to random drift. <i>Genetics</i>. 2005;169(4):2353-2370. doi:<a href=\"https://doi.org/10.1534/genetics.104.032821\">10.1534/genetics.104.032821</a>","ieee":"N. H. Barton and S. Otto, “Evolution of recombination due to random drift,” <i>Genetics</i>, vol. 169, no. 4. Genetics Society of America, pp. 2353–2370, 2005.","ista":"Barton NH, Otto S. 2005. Evolution of recombination due to random drift. Genetics. 169(4), 2353–2370."},"date_updated":"2026-07-03T08:18:26Z","publisher":"Genetics Society of America","_id":"4251","external_id":{"pmid":["15687279"]},"title":"Evolution of recombination due to random drift","page":"2353 - 2370","das_tickbox":"1","author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"last_name":"Otto","full_name":"Otto, Sarah","first_name":"Sarah"}],"day":"01","pmid":1,"OA_type":"closed access","article_type":"original","volume":169,"fulldoi":"https://doi.org/10.1534/genetics.104.032821","publication_status":"published","publication":"Genetics","publist_id":"1846","extern":"1","year":"2005","status":"public","intvolume":"       169","type":"journal_article","issue":"4","date_created":"2018-12-11T12:07:51Z","date_published":"2005-03-01T00:00:00Z"},{"language":[{"iso":"eng"}],"month":"07","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"None","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1569515/"}],"citation":{"ista":"Johnson T, Barton NH. 2005. Theoretical models of selection and mutationon quantitative traits. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 360(1459), 1411–1425.","ieee":"T. Johnson and N. H. Barton, “Theoretical models of selection and mutationon quantitative traits,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 360, no. 1459. Royal Society, The, pp. 1411–1425, 2005.","ama":"Johnson T, Barton NH. Theoretical models of selection and mutationon quantitative traits. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2005;360(1459):1411-1425. doi:<a href=\"https://doi.org/10.1098/rstb.2005.1667\">10.1098/rstb.2005.1667</a>","chicago":"Johnson, Toby, and Nicholas H Barton. “Theoretical Models of Selection and Mutationon Quantitative Traits.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The, 2005. <a href=\"https://doi.org/10.1098/rstb.2005.1667\">https://doi.org/10.1098/rstb.2005.1667</a>.","short":"T. Johnson, N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 360 (2005) 1411–1425.","apa":"Johnson, T., &#38; Barton, N. H. (2005). Theoretical models of selection and mutationon quantitative traits. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rstb.2005.1667\">https://doi.org/10.1098/rstb.2005.1667</a>","mla":"Johnson, Toby, and Nicholas H. Barton. “Theoretical Models of Selection and Mutationon Quantitative Traits.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 360, no. 1459, Royal Society, The, 2005, pp. 1411–25, doi:<a href=\"https://doi.org/10.1098/rstb.2005.1667\">10.1098/rstb.2005.1667</a>."},"doi":"10.1098/rstb.2005.1667","abstract":[{"lang":"eng","text":"Empirical studies of quantitative genetic variation have revealed robust patterns that are observed both across traits and across species. However, these patterns have no compelling explanation, and some of the observations even appear to be mutually incompatible. We review and extend a major class of theoretical models, ‘mutation–selection models’, that have been proposed to explain quantitative genetic variation. We also briefly review an alternative class of ‘balancing selection models’. We consider to what extent the models are compatible with the general observations, and argue that a key issue is understanding and modelling pleiotropy. We discuss some"}],"publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"article_processing_charge":"No","title":"Theoretical models of selection and mutationon quantitative traits","external_id":{"pmid":["16048784"]},"publisher":"Royal Society, The","_id":"4252","date_updated":"2026-07-03T10:17:54Z","day":"29","author":[{"first_name":"Toby","full_name":"Johnson, Toby","last_name":"Johnson"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"das_tickbox":"1","page":"1411 - 1425","OA_place":"repository","volume":360,"article_type":"original","OA_type":"green","pmid":1,"publist_id":"1847","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","publication_status":"published","fulldoi":"https://doi.org/10.1098/rstb.2005.1667","oa":1,"date_published":"2005-07-29T00:00:00Z","date_created":"2018-12-11T12:07:51Z","issue":"1459","type":"journal_article","intvolume":"       360","extern":"1","status":"public","year":"2005"},{"publication_status":"published","article_processing_charge":"No","fulldoi":"https://doi.org/10.1109/CVPR.2005.90","publication":"Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition","doi":"10.1109/CVPR.2005.90","citation":{"short":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2005, pp. 1186–1186.","chicago":"Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross, and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video.” In <i>Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>, 1186–1186. IEEE, 2005. <a href=\"https://doi.org/10.1109/CVPR.2005.90\">https://doi.org/10.1109/CVPR.2005.90</a>.","ama":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Bi-layer segmentation of binocular stereo video. In: <i>Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2005:1186-1186. doi:<a href=\"https://doi.org/10.1109/CVPR.2005.90\">10.1109/CVPR.2005.90</a>","ieee":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Bi-layer segmentation of binocular stereo video,” in <i>Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>, San Diego, CA, United States, 2005, pp. 1186–1186.","ista":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2005. Bi-layer segmentation of binocular stereo video. Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Computer Vision and Pattern Recognition, 1186–1186.","mla":"Kolmogorov, Vladimir, et al. “Bi-Layer Segmentation of Binocular Stereo Video.” <i>Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2005, pp. 1186–1186, doi:<a href=\"https://doi.org/10.1109/CVPR.2005.90\">10.1109/CVPR.2005.90</a>.","apa":"Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., &#38; Rother, C. (2005). Bi-layer segmentation of binocular stereo video. In <i>Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i> (pp. 1186–1186). San Diego, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2005.90\">https://doi.org/10.1109/CVPR.2005.90</a>"},"abstract":[{"lang":"eng","text":"This paper demonstrates the high quality, real-time segmentation techniques. We achieve real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, contrast and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, layered dynamic programming (LDP), solves stereo in an extended 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour model that is learned on the fly, and stereo disparities are obtained by dynamic programming. The second algorithm, layered graph cut (LGC), does not directly solve stereo. Instead the stereo match likelihood is marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than stereo or colour/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output.\r\n"}],"publication_identifier":{"isbn":["0769523722"],"issn":["1063-6919"]},"conference":{"end_date":"2005-06-25","name":"CVPR: Computer Vision and Pattern Recognition","start_date":"2005-06-20","location":"San Diego, CA, United States"},"publist_id":"3504","_id":"3176","publisher":"IEEE","date_updated":"2026-07-15T12:24:09Z","year":"2005","extern":"1","status":"public","type":"conference","date_created":"2018-12-11T12:01:50Z","title":"Bi-layer segmentation of binocular stereo video","date_published":"2005-06-20T00:00:00Z","OA_place":"repository","oa_version":"None","das_tickbox":"1","page":"1186 - 1186","author":[{"first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"},{"full_name":"Criminisi, Antonio","first_name":"Antonio","last_name":"Criminisi"},{"first_name":"Andrew","full_name":"Blake, Andrew","last_name":"Blake"},{"last_name":"Cross","full_name":"Cross, Geoffrey","first_name":"Geoffrey"},{"last_name":"Rother","full_name":"Rother, Carsten","first_name":"Carsten"}],"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"06","day":"20","OA_type":"green"},{"article_processing_charge":"No","doi":"10.1038/sj.emboj.7600659","citation":{"ista":"Weijers D, Benková E, Jäger K, Schlereth A, Hamann T, Kientz M, Wilmoth J, Reed J, Jürgens G. 2005. Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators. EMBO Journal. 24(10), 1874–1885.","ieee":"D. Weijers <i>et al.</i>, “Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators,” <i>EMBO Journal</i>, vol. 24, no. 10. Wiley-Blackwell, pp. 1874–1885, 2005.","ama":"Weijers D, Benková E, Jäger K, et al. Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators. <i>EMBO Journal</i>. 2005;24(10):1874-1885. doi:<a href=\"https://doi.org/10.1038/sj.emboj.7600659\">10.1038/sj.emboj.7600659</a>","chicago":"Weijers, Dolf, Eva Benková, Katja Jäger, Alexandra Schlereth, Thorsten Hamann, Marika Kientz, Jill Wilmoth, Jason Reed, and Gerd Jürgens. “Developmental Specificity of Auxin Response by Pairs of ARF and Aux/IAA Transcriptional Regulators.” <i>EMBO Journal</i>. Wiley-Blackwell, 2005. <a href=\"https://doi.org/10.1038/sj.emboj.7600659\">https://doi.org/10.1038/sj.emboj.7600659</a>.","short":"D. Weijers, E. Benková, K. Jäger, A. Schlereth, T. Hamann, M. Kientz, J. Wilmoth, J. Reed, G. Jürgens, EMBO Journal 24 (2005) 1874–1885.","apa":"Weijers, D., Benková, E., Jäger, K., Schlereth, A., Hamann, T., Kientz, M., … Jürgens, G. (2005). Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/sj.emboj.7600659\">https://doi.org/10.1038/sj.emboj.7600659</a>","mla":"Weijers, Dolf, et al. “Developmental Specificity of Auxin Response by Pairs of ARF and Aux/IAA Transcriptional Regulators.” <i>EMBO Journal</i>, vol. 24, no. 10, Wiley-Blackwell, 2005, pp. 1874–85, doi:<a href=\"https://doi.org/10.1038/sj.emboj.7600659\">10.1038/sj.emboj.7600659</a>."},"publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"abstract":[{"lang":"eng","text":"The plant hormone auxin elicits many specific context-dependent developmental responses. Auxin promotes degradation of Aux/IAA proteins that prevent transcription factors of the auxin response factor (ARF) family from regulating auxin-responsive target genes. Aux/IAAs and ARFs are represented by large gene families in Arabidopsis. Here we show that stabilization of BDL/IAA12 or its sister protein IAA13 prevents MP/ARF5-dependent embryonic root formation whereas stabilized SHY2/IAA3 interferes with seedling growth. Although both bdl and shy2-2 proteins inhibited MP/ARF5-dependent reporter gene activation, shy2-2 was much less efficient than bdl to interfere with embryonic root initiation when expressed from the BDL promoter. Similarly, MP was much more efficient than ARF16 in this process. When expressed from the SHY2 promoter, both shy2-2 and bdl inhibited cell elongation and auxin-induced gene expression in the seedling hypocotyl. By contrast, gravitropism and auxin-induced gene expression in the root, which were promoted by functionally redundant NPH4/ARF7 and ARF19 proteins, were inhibited by shy2-2, but not by bdl protein. Our results suggest that auxin signals are converted into specific responses by matching pairs of coexpressed ARF and Aux/IAA proteins."}],"_id":"2867","publisher":"Wiley-Blackwell","date_updated":"2026-07-15T13:21:20Z","external_id":{"pmid":["15889151"]},"title":"Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1142592/","open_access":"1"}],"oa_version":"None","language":[{"iso":"eng"}],"month":"05","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","fulldoi":"https://doi.org/10.1038/sj.emboj.7600659","publication":"EMBO Journal","publist_id":"3918","intvolume":"        24","year":"2005","status":"public","extern":"1","issue":"10","type":"journal_article","date_created":"2018-12-11T12:00:01Z","oa":1,"date_published":"2005-05-18T00:00:00Z","das_tickbox":"1","page":"1874 - 1885","author":[{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva"},{"first_name":"Katja","full_name":"Jäger, Katja","last_name":"Jäger"},{"full_name":"Schlereth, Alexandra","first_name":"Alexandra","last_name":"Schlereth"},{"last_name":"Hamann","first_name":"Thorsten","full_name":"Hamann, Thorsten"},{"last_name":"Kientz","first_name":"Marika","full_name":"Kientz, Marika"},{"last_name":"Wilmoth","first_name":"Jill","full_name":"Wilmoth, Jill"},{"full_name":"Reed, Jason","first_name":"Jason","last_name":"Reed"},{"full_name":"Jürgens, Gerd","first_name":"Gerd","last_name":"Jürgens"}],"day":"18","article_type":"original","pmid":1,"volume":24},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"month":"07","oa_version":"None","title":"Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis","date_updated":"2026-07-15T12:50:09Z","publisher":"American Society of Plant Biologists","_id":"3004","external_id":{"pmid":["16055631"]},"article_processing_charge":"No","abstract":[{"text":"Molecular mechanisms of pattern formation in the plant embryo are not well understood. Recent molecular and cellular studies, in conjunction with earlier microsurgical, physiological, and genetic work, are now starting to define the outlines of a model where gradients of the signaling molecule auxin play a central role in embryo patterning. It is relatively clear how these gradients are established and interpreted, but how they are maintained is still unresolved. Here, we have studied the contributions of auxin biosynthesis, conjugation, and transport pathways to the maintenance of embryonic auxin gradients. Auxin homeostasis in the embryo was manipulated by region-specific conditional expression of indoleacetic acid-tryptophan monooxygenase or indoleacetic acid-lysine synthetase, bacterial enzymes for auxin biosynthesis or conjugation. Neither manipulation of auxin biosynthesis nor of auxin conjugation interfered with auxin gradients and patterning in the embryo. This result suggests a compensatory mechanism for buffering auxin gradients in the embryo. Chemical and genetic inhibition revealed that auxin transport activity, in particular that of the PIN-FORMED1 (PIN1) and PIN4 proteins, is a major factor in the maintenance of these gradients.","lang":"eng"}],"publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"citation":{"ieee":"D. Weijers <i>et al.</i>, “Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis,” <i>Plant Cell</i>, vol. 17, no. 9. American Society of Plant Biologists, pp. 2517–2526, 2005.","ista":"Weijers D, Sauer M, Meurette O, Friml J, Ljung K, Sandberg G, Hooykaas P, Offringa R. 2005. Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis. Plant Cell. 17(9), 2517–2526.","chicago":"Weijers, Dolf, Michael Sauer, Olivier Meurette, Jiří Friml, Karin Ljung, Göran Sandberg, Paul Hooykaas, and Remko Offringa. “Maintenance of Embryonic Auxin Distribution for Apical Basal Patterning by PIN FORMED Dependent Auxin Transport in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2005. <a href=\"https://doi.org/10.1105/tpc.105.034637\">https://doi.org/10.1105/tpc.105.034637</a>.","short":"D. Weijers, M. Sauer, O. Meurette, J. Friml, K. Ljung, G. Sandberg, P. Hooykaas, R. Offringa, Plant Cell 17 (2005) 2517–2526.","ama":"Weijers D, Sauer M, Meurette O, et al. Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis. <i>Plant Cell</i>. 2005;17(9):2517-2526. doi:<a href=\"https://doi.org/10.1105/tpc.105.034637\">10.1105/tpc.105.034637</a>","mla":"Weijers, Dolf, et al. “Maintenance of Embryonic Auxin Distribution for Apical Basal Patterning by PIN FORMED Dependent Auxin Transport in Arabidopsis.” <i>Plant Cell</i>, vol. 17, no. 9, American Society of Plant Biologists, 2005, pp. 2517–26, doi:<a href=\"https://doi.org/10.1105/tpc.105.034637\">10.1105/tpc.105.034637</a>.","apa":"Weijers, D., Sauer, M., Meurette, O., Friml, J., Ljung, K., Sandberg, G., … Offringa, R. (2005). Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.105.034637\">https://doi.org/10.1105/tpc.105.034637</a>"},"doi":"10.1105/tpc.105.034637","volume":17,"pmid":1,"article_type":"original","OA_type":"closed access","author":[{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"first_name":"Michael","full_name":"Sauer, Michael","last_name":"Sauer"},{"last_name":"Meurette","full_name":"Meurette, Olivier","first_name":"Olivier"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí"},{"last_name":"Ljung","full_name":"Ljung, Karin","first_name":"Karin"},{"first_name":"Göran","full_name":"Sandberg, Göran","last_name":"Sandberg"},{"first_name":"Paul","full_name":"Hooykaas, Paul","last_name":"Hooykaas"},{"last_name":"Offringa","first_name":"Remko","full_name":"Offringa, Remko"}],"day":"29","page":"2517 - 2526","das_tickbox":"1","date_created":"2018-12-11T12:00:48Z","date_published":"2005-07-29T00:00:00Z","status":"public","year":"2005","extern":"1","intvolume":"        17","type":"journal_article","issue":"9","publist_id":"3698","fulldoi":"https://doi.org/10.1105/tpc.105.034637","publication_status":"published","publication":"Plant Cell"},{"type":"journal_article","issue":"20","extern":"1","status":"public","year":"2005","intvolume":"       132","date_published":"2005-10-01T00:00:00Z","date_created":"2018-12-11T12:00:48Z","publication":"Development","fulldoi":"https://doi.org/10.1242/dev.02027","publication_status":"published","publist_id":"3700","pmid":1,"OA_type":"closed access","article_type":"original","volume":132,"page":"4521 - 4531","das_tickbox":"1","day":"01","author":[{"last_name":"Vieten","full_name":"Vieten, Anne","first_name":"Anne"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"last_name":"Wiśniewska","first_name":"Justyna","full_name":"Wiśniewska, Justyna"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva"},{"last_name":"Benjamins","first_name":"René","full_name":"Benjamins, René"},{"full_name":"Beeckman, Tom","first_name":"Tom","last_name":"Beeckman"},{"last_name":"Luschnig","first_name":"Christian","full_name":"Luschnig, Christian"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí"}],"external_id":{"pmid":["16192309 "]},"date_updated":"2026-07-15T12:56:50Z","publisher":"Company of Biologists","_id":"3003","title":"Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression","abstract":[{"text":"Plant development displays an exceptional plasticity and adaptability that involves the dynamic, asymmetric distribution of the phytohormone auxin. Polar auxin flow, which requires polarly localized transport facilitators of the PIN family, largely contributes to the establishment and maintenance of the auxin gradients. Functionally overlapping action of PIN proteins mediates multiple developmental processes, including embryo formation, organ development and tropisms. Here we show that PIN proteins exhibit synergistic interactions, which involve cross-regulation of PIN gene expression in pin mutants or plants with inhibited auxin transport. Auxin itself positively feeds back on PIN gene expression in a tissue-specific manner through an AUX/IAA-dependent signalling pathway. This regulatory switch is indicative of a mechanism by which the loss of a specific PIN protein is compensated for by auxin-dependent ectopic: expression of its homologues. The compensatory properties of the PIN-dependent transport network might enable the stabilization of auxin gradients and potentially contribute to the robustness of plant adaptive development.","lang":"eng"}],"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"citation":{"apa":"Vieten, A., Vanneste, S., Wiśniewska, J., Benková, E., Benjamins, R., Beeckman, T., … Friml, J. (2005). Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.02027\">https://doi.org/10.1242/dev.02027</a>","mla":"Vieten, Anne, et al. “Functional Redundancy of PIN Proteins Is Accompanied by Auxin-Dependent Cross-Regulation of PIN Expression.” <i>Development</i>, vol. 132, no. 20, Company of Biologists, 2005, pp. 4521–31, doi:<a href=\"https://doi.org/10.1242/dev.02027\">10.1242/dev.02027</a>.","ista":"Vieten A, Vanneste S, Wiśniewska J, Benková E, Benjamins R, Beeckman T, Luschnig C, Friml J. 2005. Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression. Development. 132(20), 4521–4531.","ieee":"A. Vieten <i>et al.</i>, “Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression,” <i>Development</i>, vol. 132, no. 20. Company of Biologists, pp. 4521–4531, 2005.","ama":"Vieten A, Vanneste S, Wiśniewska J, et al. Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression. <i>Development</i>. 2005;132(20):4521-4531. doi:<a href=\"https://doi.org/10.1242/dev.02027\">10.1242/dev.02027</a>","short":"A. Vieten, S. Vanneste, J. Wiśniewska, E. Benková, R. Benjamins, T. Beeckman, C. Luschnig, J. Friml, Development 132 (2005) 4521–4531.","chicago":"Vieten, Anne, Steffen Vanneste, Justyna Wiśniewska, Eva Benková, René Benjamins, Tom Beeckman, Christian Luschnig, and Jiří Friml. “Functional Redundancy of PIN Proteins Is Accompanied by Auxin-Dependent Cross-Regulation of PIN Expression.” <i>Development</i>. Company of Biologists, 2005. <a href=\"https://doi.org/10.1242/dev.02027\">https://doi.org/10.1242/dev.02027</a>."},"doi":"10.1242/dev.02027","article_processing_charge":"No","oa_version":"None","language":[{"iso":"eng"}],"month":"10","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"author":[{"last_name":"Paciorek","full_name":"Paciorek, Tomasz","first_name":"Tomasz"},{"first_name":"Eva","full_name":"Zažímalová, Eva","last_name":"Zažímalová"},{"last_name":"Ruthardt","first_name":"Nadia","full_name":"Ruthardt, Nadia"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"last_name":"Stierhof","full_name":"Stierhof, York","first_name":"York"},{"last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen","first_name":"Jürgen"},{"last_name":"Morris","full_name":"Morris, David","first_name":"David"},{"last_name":"Emans","full_name":"Emans, Neil","first_name":"Neil"},{"last_name":"Jürgens","first_name":"Gerd","full_name":"Jürgens, Gerd"},{"first_name":"Niko","full_name":"Geldner, Niko","last_name":"Geldner"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"}],"day":"30","das_tickbox":"1","page":"1251 - 1256","volume":435,"article_type":"original","pmid":1,"publist_id":"3702","publication_status":"published","fulldoi":"https://doi.org/10.1038/nature03633","publication":"Nature","date_created":"2018-12-11T12:00:47Z","date_published":"2005-06-30T00:00:00Z","intvolume":"       435","year":"2005","extern":"1","status":"public","issue":"7046","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"month":"06","oa_version":"None","article_processing_charge":"No","doi":"10.1038/nature03633","citation":{"short":"T. Paciorek, E. Zažímalová, N. Ruthardt, J. Petrášek, Y. Stierhof, J. Kleine Vehn, D. Morris, N. Emans, G. Jürgens, N. Geldner, J. Friml, Nature 435 (2005) 1251–1256.","chicago":"Paciorek, Tomasz, Eva Zažímalová, Nadia Ruthardt, Jan Petrášek, York Stierhof, Jürgen Kleine Vehn, David Morris, et al. “Auxin Inhibits Endocytosis and Promotes Its Own Efflux from Cells.” <i>Nature</i>. Nature Publishing Group, 2005. <a href=\"https://doi.org/10.1038/nature03633\">https://doi.org/10.1038/nature03633</a>.","ama":"Paciorek T, Zažímalová E, Ruthardt N, et al. Auxin inhibits endocytosis and promotes its own efflux from cells. <i>Nature</i>. 2005;435(7046):1251-1256. doi:<a href=\"https://doi.org/10.1038/nature03633\">10.1038/nature03633</a>","ieee":"T. Paciorek <i>et al.</i>, “Auxin inhibits endocytosis and promotes its own efflux from cells,” <i>Nature</i>, vol. 435, no. 7046. Nature Publishing Group, pp. 1251–1256, 2005.","ista":"Paciorek T, Zažímalová E, Ruthardt N, Petrášek J, Stierhof Y, Kleine Vehn J, Morris D, Emans N, Jürgens G, Geldner N, Friml J. 2005. Auxin inhibits endocytosis and promotes its own efflux from cells. Nature. 435(7046), 1251–1256.","mla":"Paciorek, Tomasz, et al. “Auxin Inhibits Endocytosis and Promotes Its Own Efflux from Cells.” <i>Nature</i>, vol. 435, no. 7046, Nature Publishing Group, 2005, pp. 1251–56, doi:<a href=\"https://doi.org/10.1038/nature03633\">10.1038/nature03633</a>.","apa":"Paciorek, T., Zažímalová, E., Ruthardt, N., Petrášek, J., Stierhof, Y., Kleine Vehn, J., … Friml, J. (2005). Auxin inhibits endocytosis and promotes its own efflux from cells. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature03633\">https://doi.org/10.1038/nature03633</a>"},"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"abstract":[{"text":"One of the mechanisms by which signalling molecules regulate cellular behaviour is modulating subcellular protein translocation. This mode of regulation is often based on specialized vesicle trafficking, termed constitutive cycling, which consists of repeated internalization and recycling of proteins to and from the plasma membrane. No such mechanism of hormone action has been shown in plants although several proteins, including the PIN auxin efflux facilitators, exhibit constitutive cycling. Here we show that a major regulator of plant development, auxin, inhibits endocytosis. This effect is specific to biologically active auxins and requires activity of the Calossin-like protein BIG. By inhibiting the internalization step of PIN constitutive cycling, auxin increases levels of PINs at the plasma membrane. Concomitantly, auxin promotes its own efflux from cells by a vesicle-trafficking-dependent mechanism. Furthermore, asymmetric auxin translocation during gravitropism is correlated with decreased PIN internalization. Our data imply a previously undescribed mode of plant hormone action: by modulating PIN protein trafficking, auxin regulates PIN abundance and activity at the cell surface, providing a mechanism for the feedback regulation of auxin transport.","lang":"eng"}],"title":"Auxin inhibits endocytosis and promotes its own efflux from cells","publisher":"Nature Publishing Group","_id":"3001","date_updated":"2026-07-15T13:02:15Z","external_id":{"pmid":["15988527 "]}},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"12","language":[{"iso":"eng"}],"oa_version":"None","title":"Immunological self tolerance: Lessons from mathematical modeling","publisher":"Elsevier","_id":"2895","date_updated":"2026-07-15T13:16:15Z","acknowledgement":"The work was financially supported by Fundação para a Ciência e Tecnologia: grants  P/BIA/10094/1998,  POCTI/36413/99,  and  POCTI/MGI/46477/2002; and fellowships to JF (Praxis/BCC/18972/98), JS (BD/13546/97), KL (SFRH/BPD+/1157/2002), DM (SFRH/BD/2960/2000) and TP (SFRH/BD/10550/2002).","article_processing_charge":"No","citation":{"apa":"Carneiro, J., Paixao, T., Milutinovic, D., Sousa, J., Leon, K., Gardner, R., &#38; Faro, J. (2005). Immunological self tolerance: Lessons from mathematical modeling. <i>Journal of Computational and Applied Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cam.2004.10.025\">https://doi.org/10.1016/j.cam.2004.10.025</a>","mla":"Carneiro, Jorge, et al. “Immunological Self Tolerance: Lessons from Mathematical Modeling.” <i>Journal of Computational and Applied Mathematics</i>, vol. 184, no. 1, Elsevier, 2005, pp. 77–100, doi:<a href=\"https://doi.org/10.1016/j.cam.2004.10.025\">10.1016/j.cam.2004.10.025</a>.","ista":"Carneiro J, Paixao T, Milutinovic D, Sousa J, Leon K, Gardner R, Faro J. 2005. Immunological self tolerance: Lessons from mathematical modeling. Journal of Computational and Applied Mathematics. 184(1), 77–100.","ieee":"J. Carneiro <i>et al.</i>, “Immunological self tolerance: Lessons from mathematical modeling,” <i>Journal of Computational and Applied Mathematics</i>, vol. 184, no. 1. Elsevier, pp. 77–100, 2005.","ama":"Carneiro J, Paixao T, Milutinovic D, et al. Immunological self tolerance: Lessons from mathematical modeling. <i>Journal of Computational and Applied Mathematics</i>. 2005;184(1):77-100. doi:<a href=\"https://doi.org/10.1016/j.cam.2004.10.025\">10.1016/j.cam.2004.10.025</a>","chicago":"Carneiro, Jorge, Tiago Paixao, Dejan Milutinovic, João Sousa, Kalet Leon, Rui Gardner, and Jose Faro. “Immunological Self Tolerance: Lessons from Mathematical Modeling.” <i>Journal of Computational and Applied Mathematics</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.cam.2004.10.025\">https://doi.org/10.1016/j.cam.2004.10.025</a>.","short":"J. Carneiro, T. Paixao, D. Milutinovic, J. Sousa, K. Leon, R. Gardner, J. Faro, Journal of Computational and Applied Mathematics 184 (2005) 77–100."},"doi":"10.1016/j.cam.2004.10.025","abstract":[{"text":"One of the fundamental properties of the immune system is its capacity to avoid autoimmune diseases. The mechanism underlying this process, known as self-tolerance, is hitherto unresolved but seems to involve the control of clonal expansion of autoreactive lymphocytes. This article reviews mathematical modeling of self-tolerance, addressing two specific hypotheses. The first hypothesis posits that self-tolerance is mediated by tuning of activation thresholds, which makes autoreactive T lymphocytes reversibly &quot;anergic&quot; and unable to proliferate. The second hypothesis posits that the proliferation of autoreactive T lymphocytes is instead controlled by specific regulatory T lymphocytes. Models representing the population dynamics of autoreactive T lymphocytes according to these two hypotheses were derived. For each model we identified how cell density affects tolerance, and predicted the corresponding phase spaces and bifurcations. We show that the simple induction of proliferative anergy, as modeled here, has a density dependence that is only partially compatible with adoptive transfers of tolerance, and that the models of tolerance mediated by specific regulatory T cells are closer to the observations.","lang":"eng"}],"publication_identifier":{"eissn":["1879-1778"],"issn":["0377-0427"]},"volume":184,"OA_type":"free access","article_type":"original","author":[{"last_name":"Carneiro","full_name":"Carneiro, Jorge","first_name":"Jorge"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","orcid":"0000-0003-2361-3953","first_name":"Tiago","full_name":"Paixao, Tiago"},{"first_name":"Dejan","full_name":"Milutinovic, Dejan","last_name":"Milutinovic"},{"first_name":"João","full_name":"Sousa, João","last_name":"Sousa"},{"last_name":"Leon","first_name":"Kalet","full_name":"Leon, Kalet"},{"last_name":"Gardner","full_name":"Gardner, Rui","first_name":"Rui"},{"full_name":"Faro, Jose","first_name":"Jose","last_name":"Faro"}],"day":"01","das_tickbox":"1","page":"77 - 100","date_created":"2018-12-11T12:00:12Z","date_published":"2005-12-01T00:00:00Z","intvolume":"       184","extern":"1","status":"public","year":"2005","issue":"1","type":"journal_article","publist_id":"3863","publication_status":"published","fulldoi":"https://doi.org/10.1016/j.cam.2004.10.025","publication":"Journal of Computational and Applied Mathematics"},{"title":"A developmental switch in the response of DRG neurons to ETS transcription factor signaling","external_id":{"pmid":["15836427"]},"publisher":"Public Library of Science","_id":"3143","date_updated":"2026-07-15T12:28:30Z","doi":"10.1371/journal.pbio.0030159","citation":{"apa":"Hippenmeyer, S., Vrieseling, E., Sigrist, M., Portmann, T., Laengle, C., Ladle, D., &#38; Arber, S. (2005). A developmental switch in the response of DRG neurons to ETS transcription factor signaling. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.0030159\">https://doi.org/10.1371/journal.pbio.0030159</a>","mla":"Hippenmeyer, Simon, et al. “A Developmental Switch in the Response of DRG Neurons to ETS Transcription Factor Signaling.” <i>PLoS Biology</i>, vol. 3, no. 5, Public Library of Science, 2005, pp. 0878–90, doi:<a href=\"https://doi.org/10.1371/journal.pbio.0030159\">10.1371/journal.pbio.0030159</a>.","ama":"Hippenmeyer S, Vrieseling E, Sigrist M, et al. A developmental switch in the response of DRG neurons to ETS transcription factor signaling. <i>PLoS Biology</i>. 2005;3(5):0878-0890. doi:<a href=\"https://doi.org/10.1371/journal.pbio.0030159\">10.1371/journal.pbio.0030159</a>","short":"S. Hippenmeyer, E. Vrieseling, M. Sigrist, T. Portmann, C. Laengle, D. Ladle, S. Arber, PLoS Biology 3 (2005) 0878–0890.","chicago":"Hippenmeyer, Simon, Eline Vrieseling, Markus Sigrist, Thomas Portmann, Celia Laengle, David Ladle, and Silvia Arber. “A Developmental Switch in the Response of DRG Neurons to ETS Transcription Factor Signaling.” <i>PLoS Biology</i>. Public Library of Science, 2005. <a href=\"https://doi.org/10.1371/journal.pbio.0030159\">https://doi.org/10.1371/journal.pbio.0030159</a>.","ista":"Hippenmeyer S, Vrieseling E, Sigrist M, Portmann T, Laengle C, Ladle D, Arber S. 2005. A developmental switch in the response of DRG neurons to ETS transcription factor signaling. PLoS Biology. 3(5), 0878–0890.","ieee":"S. Hippenmeyer <i>et al.</i>, “A developmental switch in the response of DRG neurons to ETS transcription factor signaling,” <i>PLoS Biology</i>, vol. 3, no. 5. Public Library of Science, pp. 0878–0890, 2005."},"publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"abstract":[{"lang":"eng","text":"Two ETS transcription factors of the Pea3 subfamily are induced in subpopulations of dorsal root ganglion (DRG) sensory and spinal motor neurons by target-derived factors. Their expression controls late aspects of neuronal differentiation such as target invasion and branching. Here, we show that the late onset of ETS gene expression is an essential requirement for normal sensory neuron differentiation. We provide genetic evidence in the mouse that precocious ETS expression in DRG sensory neurons perturbs axonal projections, the acquisition of terminal differentiation markers, and their dependence on neurotrophic support. Together, our findings indicate that DRG sensory neurons exhibit a temporal developmental switch that can be revealed by distinct responses to ETS transcription factor signaling at sequential steps of neuronal maturation."}],"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"month":"04","oa_version":"None","date_published":"2005-04-26T00:00:00Z","date_created":"2018-12-11T12:01:38Z","issue":"5","type":"journal_article","intvolume":"         3","status":"public","extern":"1","year":"2005","publist_id":"3552","publication":"PLoS Biology","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","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_status":"published","fulldoi":"https://doi.org/10.1371/journal.pbio.0030159","volume":3,"article_type":"original","OA_type":"gold","pmid":1,"day":"26","author":[{"first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"last_name":"Vrieseling","full_name":"Vrieseling, Eline","first_name":"Eline"},{"full_name":"Sigrist, Markus","first_name":"Markus","last_name":"Sigrist"},{"full_name":"Portmann, Thomas","first_name":"Thomas","last_name":"Portmann"},{"last_name":"Laengle","full_name":"Laengle, Celia","first_name":"Celia"},{"last_name":"Ladle","full_name":"Ladle, David","first_name":"David"},{"full_name":"Arber, Silvia","first_name":"Silvia","last_name":"Arber"}],"das_tickbox":"1","license":"https://creativecommons.org/licenses/by/4.0/","page":"0878 - 0890","OA_place":"publisher"},{"publist_id":"4099","publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"abstract":[{"text":"We present the results of an experimental investigation of the effect of a magnetic field on the stability of convection in a liquid metal. A rectangular container of gallium is subjected to a horizontal temperature gradient and a uniform magnetic field is applied separately in three directions. The magnetic field suppresses the oscillation most effectively when it is applied in the vertical direction and is least efficient when applied in the direction of the temperature gradient. The critical temperature difference required for the onset of oscillations is found to scale exponentially with the magnitude of the magnetic field for all three orientations. Comparisons are made with available theory and qualitative differences are discussed.","lang":"eng"}],"publication":"Journal of Fluid Mechanics","doi":"10.1017/S0022112005006762","citation":{"ama":"Hof B, Juel A, Mullin T. Magnetohydrodynamic damping of oscillations in low-Prandtl-number convection. <i>Journal of Fluid Mechanics</i>. 2005;545:193-201. doi:<a href=\"https://doi.org/10.1017/S0022112005006762\">10.1017/S0022112005006762</a>","chicago":"Hof, Björn, Anne Juel, and Tom Mullin. “Magnetohydrodynamic Damping of Oscillations in Low-Prandtl-Number Convection.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2005. <a href=\"https://doi.org/10.1017/S0022112005006762\">https://doi.org/10.1017/S0022112005006762</a>.","short":"B. Hof, A. Juel, T. Mullin, Journal of Fluid Mechanics 545 (2005) 193–201.","ista":"Hof B, Juel A, Mullin T. 2005. Magnetohydrodynamic damping of oscillations in low-Prandtl-number convection. Journal of Fluid Mechanics. 545, 193–201.","ieee":"B. Hof, A. Juel, and T. Mullin, “Magnetohydrodynamic damping of oscillations in low-Prandtl-number convection,” <i>Journal of Fluid Mechanics</i>, vol. 545. Cambridge University Press, pp. 193–201, 2005.","apa":"Hof, B., Juel, A., &#38; Mullin, T. (2005). Magnetohydrodynamic damping of oscillations in low-Prandtl-number convection. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0022112005006762\">https://doi.org/10.1017/S0022112005006762</a>","mla":"Hof, Björn, et al. “Magnetohydrodynamic Damping of Oscillations in Low-Prandtl-Number Convection.” <i>Journal of Fluid Mechanics</i>, vol. 545, Cambridge University Press, 2005, pp. 193–201, doi:<a href=\"https://doi.org/10.1017/S0022112005006762\">10.1017/S0022112005006762</a>."},"fulldoi":"https://doi.org/10.1017/S0022112005006762","article_processing_charge":"No","publication_status":"published","title":"Magnetohydrodynamic damping of oscillations in low-Prandtl-number convection","date_published":"2005-12-25T00:00:00Z","date_created":"2018-12-11T11:59:37Z","type":"journal_article","date_updated":"2026-07-29T10:59:51Z","status":"public","year":"2005","extern":"1","publisher":"Cambridge University Press","_id":"2790","intvolume":"       545","day":"25","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"12","author":[{"first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"},{"last_name":"Juel","full_name":"Juel, Anne","first_name":"Anne"},{"full_name":"Mullin, Tom","first_name":"Tom","last_name":"Mullin"}],"page":"193 - 201","oa_version":"None","volume":545,"OA_type":"closed access","article_type":"original"},{"oa_version":"None","month":"11","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"pmid":["16384146 "]},"publisher":"American Physical Society","_id":"2788","date_updated":"2026-07-29T11:15:02Z","title":"Turbulence regeneration in pipe flow at moderate reynolds numbers","citation":{"ama":"Hof B, Van Doorne C, Westerweel J, Nieuwstadt F. Turbulence regeneration in pipe flow at moderate reynolds numbers. <i>Physical Review Letters</i>. 2005;95(21). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.95.214502\">10.1103/PhysRevLett.95.214502</a>","chicago":"Hof, Björn, Casimir Van Doorne, Jerry Westerweel, and Frans Nieuwstadt. “Turbulence Regeneration in Pipe Flow at Moderate Reynolds Numbers.” <i>Physical Review Letters</i>. American Physical Society, 2005. <a href=\"https://doi.org/10.1103/PhysRevLett.95.214502\">https://doi.org/10.1103/PhysRevLett.95.214502</a>.","short":"B. Hof, C. Van Doorne, J. Westerweel, F. Nieuwstadt, Physical Review Letters 95 (2005).","ista":"Hof B, Van Doorne C, Westerweel J, Nieuwstadt F. 2005. Turbulence regeneration in pipe flow at moderate reynolds numbers. Physical Review Letters. 95(21).","ieee":"B. Hof, C. Van Doorne, J. Westerweel, and F. Nieuwstadt, “Turbulence regeneration in pipe flow at moderate reynolds numbers,” <i>Physical Review Letters</i>, vol. 95, no. 21. American Physical Society, 2005.","apa":"Hof, B., Van Doorne, C., Westerweel, J., &#38; Nieuwstadt, F. (2005). Turbulence regeneration in pipe flow at moderate reynolds numbers. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.95.214502\">https://doi.org/10.1103/PhysRevLett.95.214502</a>","mla":"Hof, Björn, et al. “Turbulence Regeneration in Pipe Flow at Moderate Reynolds Numbers.” <i>Physical Review Letters</i>, vol. 95, no. 21, American Physical Society, 2005, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.95.214502\">10.1103/PhysRevLett.95.214502</a>."},"doi":"10.1103/PhysRevLett.95.214502","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"abstract":[{"text":"We present the results of an experimental investigation into the nature and structure of turbulent pipe flow at moderate Reynolds numbers. A turbulence regeneration mechanism is identified which sustains a symmetric traveling wave within the flow. The periodicity of the mechanism allows comparison to the wavelength of numerically observed exact traveling wave solutions and close agreement is found. The advection speed of the upstream turbulence laminar interface in the experimental flow is observed to form a lower bound on the phase velocities of the exact traveling wave solutions. Overall our observations suggest that the dynamics of the turbulent flow at moderate Reynolds numbers are governed by unstable nonlinear traveling waves.","lang":"eng"}],"article_processing_charge":"No","article_type":"original","OA_type":"closed access","pmid":1,"volume":95,"day":"17","author":[{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn"},{"last_name":"Van Doorne","full_name":"Van Doorne, Casimir","first_name":"Casimir"},{"last_name":"Westerweel","first_name":"Jerry","full_name":"Westerweel, Jerry"},{"last_name":"Nieuwstadt","first_name":"Frans","full_name":"Nieuwstadt, Frans"}],"issue":"21","type":"journal_article","intvolume":"        95","status":"public","year":"2005","extern":"1","date_published":"2005-11-17T00:00:00Z","date_created":"2018-12-11T11:59:36Z","publication":"Physical Review Letters","publication_status":"published","fulldoi":"https://doi.org/10.1103/PhysRevLett.95.214502","publist_id":"4101"},{"type":"journal_article","issue":"6","extern":"1","status":"public","year":"2005","intvolume":"        17","date_published":"2005-07-01T00:00:00Z","date_created":"2018-12-11T11:59:22Z","publication":"Reviews in Mathematical Physics","fulldoi":"https://doi.org/10.1142/S0129055X0500242X","publication_status":"published","publist_id":"4148","OA_type":"closed access","article_type":"original","volume":17,"page":"669 - 743","day":"01","author":[{"first_name":"David","full_name":"Eng, David","last_name":"Eng"},{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László","first_name":"László"}],"date_updated":"2026-07-29T11:19:15Z","publisher":"World Scientific Publishing","_id":"2744","title":"The linear Boltzmann equation as the low density limit of a random Schrödinger equation","publication_identifier":{"issn":["0129-055X"],"eissn":["1793-6659"]},"abstract":[{"lang":"eng","text":"We study the long time evolution of a quantum particle interacting with a random potential in the Boltzmann-Grad low density limit. We prove that the phase space density of the quantum evolution defined through the Husimi function converges weakly to a linear Boltzmann equation. The Boltzmann collision kernel is given by the full quantum scattering cross-section of the obstacle potential."}],"doi":"10.1142/S0129055X0500242X","citation":{"ieee":"D. Eng and L. Erdös, “The linear Boltzmann equation as the low density limit of a random Schrödinger equation,” <i>Reviews in Mathematical Physics</i>, vol. 17, no. 6. World Scientific Publishing, pp. 669–743, 2005.","ista":"Eng D, Erdös L. 2005. The linear Boltzmann equation as the low density limit of a random Schrödinger equation. Reviews in Mathematical Physics. 17(6), 669–743.","chicago":"Eng, David, and László Erdös. “The Linear Boltzmann Equation as the Low Density Limit of a Random Schrödinger Equation.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2005. <a href=\"https://doi.org/10.1142/S0129055X0500242X\">https://doi.org/10.1142/S0129055X0500242X</a>.","short":"D. Eng, L. Erdös, Reviews in Mathematical Physics 17 (2005) 669–743.","ama":"Eng D, Erdös L. The linear Boltzmann equation as the low density limit of a random Schrödinger equation. <i>Reviews in Mathematical Physics</i>. 2005;17(6):669-743. doi:<a href=\"https://doi.org/10.1142/S0129055X0500242X\">10.1142/S0129055X0500242X</a>","mla":"Eng, David, and László Erdös. “The Linear Boltzmann Equation as the Low Density Limit of a Random Schrödinger Equation.” <i>Reviews in Mathematical Physics</i>, vol. 17, no. 6, World Scientific Publishing, 2005, pp. 669–743, doi:<a href=\"https://doi.org/10.1142/S0129055X0500242X\">10.1142/S0129055X0500242X</a>.","apa":"Eng, D., &#38; Erdös, L. (2005). The linear Boltzmann equation as the low density limit of a random Schrödinger equation. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129055X0500242X\">https://doi.org/10.1142/S0129055X0500242X</a>"},"article_processing_charge":"No","oa_version":"None","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"month":"07"}]