[{"alternative_title":["LNCS"],"date_published":"2008-11-01T00:00:00Z","page":"143-154","month":"11","intvolume":"      5303","date_updated":"2024-11-18T10:22:43Z","oa_version":"None","publication_identifier":{"eisbn":["9783540886884"],"eissn":["0302-9743"],"issn":["1611-3349"],"isbn":["9783540886853"]},"status":"public","doi":"10.1007/978-3-540-88688-4_11","volume":5303,"article_processing_charge":"No","abstract":[{"text":"Matching of rigid shapes is an important problem in numerous applications across the boundary of computer vision, pattern recognition and computer graphics communities. A particularly challenging setting of this problem is partial matching, where the two shapes are dissimilar in general, but have significant similar parts. In this paper, we show a rigorous approach allowing to find matching parts of rigid shapes with controllable size and regularity. The regularity term we use is similar to the spirit of the Mumford-Shah functional, extended to non-Euclidean spaces. Numerical experiments show that the regularized partial matching produces better results compared to the non-regularized one.","lang":"eng"}],"citation":{"short":"A.M. Bronstein, M.M. Bronstein, in:, 10th European Conference on Computer Vision, Springer Berlin Heidelberg, 2008, pp. 143–154.","ista":"Bronstein AM, Bronstein MM. 2008. Regularized partial matching of rigid shapes. 10th European Conference on Computer Vision. ECCV: European Conference on Computer Vision, LNCS, vol. 5303, 143–154.","ama":"Bronstein AM, Bronstein MM. Regularized partial matching of rigid shapes. In: <i>10th European Conference on Computer Vision</i>. Vol 5303. Springer Berlin Heidelberg; 2008:143-154. doi:<a href=\"https://doi.org/10.1007/978-3-540-88688-4_11\">10.1007/978-3-540-88688-4_11</a>","mla":"Bronstein, Alex M., and Michael M. Bronstein. “Regularized Partial Matching of Rigid Shapes.” <i>10th European Conference on Computer Vision</i>, vol. 5303, Springer Berlin Heidelberg, 2008, pp. 143–54, doi:<a href=\"https://doi.org/10.1007/978-3-540-88688-4_11\">10.1007/978-3-540-88688-4_11</a>.","ieee":"A. M. Bronstein and M. M. Bronstein, “Regularized partial matching of rigid shapes,” in <i>10th European Conference on Computer Vision</i>, Marseille, France, 2008, vol. 5303, pp. 143–154.","apa":"Bronstein, A. M., &#38; Bronstein, M. M. (2008). Regularized partial matching of rigid shapes. In <i>10th European Conference on Computer Vision</i> (Vol. 5303, pp. 143–154). Marseille, France: Springer Berlin Heidelberg. <a href=\"https://doi.org/10.1007/978-3-540-88688-4_11\">https://doi.org/10.1007/978-3-540-88688-4_11</a>","chicago":"Bronstein, Alex M., and Michael M. Bronstein. “Regularized Partial Matching of Rigid Shapes.” In <i>10th European Conference on Computer Vision</i>, 5303:143–54. Springer Berlin Heidelberg, 2008. <a href=\"https://doi.org/10.1007/978-3-540-88688-4_11\">https://doi.org/10.1007/978-3-540-88688-4_11</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","scopus_import":"1","conference":{"name":"ECCV: European Conference on Computer Vision","location":"Marseille, France","start_date":"2008-10-12","end_date":"2008-10-18"},"day":"01","_id":"18337","author":[{"last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander","orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander"},{"last_name":"Bronstein","full_name":"Bronstein, Michael M.","first_name":"Michael M."}],"date_created":"2024-10-15T11:20:54Z","publisher":"Springer Berlin Heidelberg","publication_status":"published","extern":"1","publication":"10th European Conference on Computer Vision","title":"Regularized partial matching of rigid shapes","language":[{"iso":"eng"}],"type":"conference","year":"2008"},{"scopus_import":"1","quality_controlled":"1","day":"01","author":[{"id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","last_name":"Bronstein","first_name":"Alexander","full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730"},{"first_name":"Michael M.","full_name":"Bronstein, Michael M.","last_name":"Bronstein"},{"last_name":"Bruckstein","first_name":"Alfred M.","full_name":"Bruckstein, Alfred M."},{"first_name":"Ron","full_name":"Kimmel, Ron","last_name":"Kimmel"}],"_id":"18355","publisher":"Springer Nature","publication_status":"published","date_created":"2024-10-15T11:20:54Z","extern":"1","status":"public","doi":"10.1007/s11263-007-0078-4","abstract":[{"text":"Analysis of deformable two-dimensional shapes is an important problem, encountered in numerous pattern recognition, computer vision and computer graphics applications. In this paper, we address three major problems in the analysis of non-rigid shapes: similarity, partial similarity, and correspondence. We present an axiomatic construction of similarity criteria for deformation-invariant shape comparison, based on intrinsic geometric properties of the shapes, and show that such criteria are related to the Gromov-Hausdorff distance. Next, we extend the problem of similarity computation to shapes which have similar parts but are dissimilar when considered as a whole, and present a construction of set-valued distances, based on the notion of Pareto optimality. Finally, we show that the correspondence between non-rigid shapes can be obtained as a byproduct of the non-rigid similarity problem. As a numerical framework, we use the generalized multidimensional scaling (GMDS) method, which is the numerical core of the three problems addressed in this paper.","lang":"eng"}],"article_processing_charge":"No","volume":78,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bronstein, Alex M., et al. “Analysis of Two-Dimensional Non-Rigid Shapes.” <i>International Journal of Computer Vision</i>, vol. 78, Springer Nature, 2008, pp. 67–88, doi:<a href=\"https://doi.org/10.1007/s11263-007-0078-4\">10.1007/s11263-007-0078-4</a>.","ama":"Bronstein AM, Bronstein MM, Bruckstein AM, Kimmel R. Analysis of two-dimensional non-rigid shapes. <i>International Journal of Computer Vision</i>. 2008;78:67-88. doi:<a href=\"https://doi.org/10.1007/s11263-007-0078-4\">10.1007/s11263-007-0078-4</a>","ista":"Bronstein AM, Bronstein MM, Bruckstein AM, Kimmel R. 2008. Analysis of two-dimensional non-rigid shapes. International Journal of Computer Vision. 78, 67–88.","short":"A.M. Bronstein, M.M. Bronstein, A.M. Bruckstein, R. Kimmel, International Journal of Computer Vision 78 (2008) 67–88.","chicago":"Bronstein, Alex M., Michael M. Bronstein, Alfred M. Bruckstein, and Ron Kimmel. “Analysis of Two-Dimensional Non-Rigid Shapes.” <i>International Journal of Computer Vision</i>. Springer Nature, 2008. <a href=\"https://doi.org/10.1007/s11263-007-0078-4\">https://doi.org/10.1007/s11263-007-0078-4</a>.","apa":"Bronstein, A. M., Bronstein, M. M., Bruckstein, A. M., &#38; Kimmel, R. (2008). Analysis of two-dimensional non-rigid shapes. <i>International Journal of Computer Vision</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11263-007-0078-4\">https://doi.org/10.1007/s11263-007-0078-4</a>","ieee":"A. M. Bronstein, M. M. Bronstein, A. M. Bruckstein, and R. Kimmel, “Analysis of two-dimensional non-rigid shapes,” <i>International Journal of Computer Vision</i>, vol. 78. Springer Nature, pp. 67–88, 2008."},"year":"2008","type":"journal_article","publication":"International Journal of Computer Vision","title":"Analysis of two-dimensional non-rigid shapes","language":[{"iso":"eng"}],"month":"06","intvolume":"        78","date_updated":"2024-10-22T07:22:49Z","date_published":"2008-06-01T00:00:00Z","OA_type":"closed access","page":"67-88","article_type":"original","publication_identifier":{"issn":["0920-5691","1573-1405"]},"oa_version":"None"},{"date_published":"2008-07-01T00:00:00Z","date_updated":"2024-11-18T10:18:28Z","month":"07","oa_version":"None","publication_identifier":{"isbn":["9781424423392"],"issn":["2160-7508"]},"citation":{"apa":"Bronstein, A. M., &#38; Bronstein, M. M. (2008). Not only size matters: Regularized partial matching of nonrigid shapes. In <i>2008 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops</i>. Anchorage, AK, United States: IEEE. <a href=\"https://doi.org/10.1109/cvprw.2008.4563077\">https://doi.org/10.1109/cvprw.2008.4563077</a>","ieee":"A. M. Bronstein and M. M. Bronstein, “Not only size matters: Regularized partial matching of nonrigid shapes,” in <i>2008 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops</i>, Anchorage, AK, United States, 2008.","chicago":"Bronstein, Alex M., and Michael M. Bronstein. “Not Only Size Matters: Regularized Partial Matching of Nonrigid Shapes.” In <i>2008 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops</i>. IEEE, 2008. <a href=\"https://doi.org/10.1109/cvprw.2008.4563077\">https://doi.org/10.1109/cvprw.2008.4563077</a>.","ista":"Bronstein AM, Bronstein MM. 2008. Not only size matters: Regularized partial matching of nonrigid shapes. 2008 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops. CVPR: Conference on Computer Vision and Pattern Recognition.","short":"A.M. Bronstein, M.M. Bronstein, in:, 2008 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, IEEE, 2008.","mla":"Bronstein, Alex M., and Michael M. Bronstein. “Not Only Size Matters: Regularized Partial Matching of Nonrigid Shapes.” <i>2008 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops</i>, IEEE, 2008, doi:<a href=\"https://doi.org/10.1109/cvprw.2008.4563077\">10.1109/cvprw.2008.4563077</a>.","ama":"Bronstein AM, Bronstein MM. Not only size matters: Regularized partial matching of nonrigid shapes. In: <i>2008 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops</i>. IEEE; 2008. doi:<a href=\"https://doi.org/10.1109/cvprw.2008.4563077\">10.1109/cvprw.2008.4563077</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Partial matching is probably one of the most challenging problems in nonrigid shape analysis. The problem consists of matching similar parts of shapes that are dissimilar on the whole and can assume different forms by undergoing nonrigid deformations. Conceptually, two shapes can be considered partially matching if they have significant similar parts, with the simplest definition of significance being the size of the parts. Thus, partial matching can be defined as a multicriterion optimization problem trying to simultaneously maximize the similarity and the size of these parts. In this paper, we propose a different definition of significance, taking into account the regularity of parts besides their size. The regularity term proposed here is similar to the spirit of the Mumford-Shah functional. Numerical experiments show that the regularized partial matching produces semantically better results compared to the non-regularized one."}],"article_processing_charge":"No","doi":"10.1109/cvprw.2008.4563077","status":"public","extern":"1","publication_status":"published","_id":"18381","author":[{"orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander","first_name":"Alexander","last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6"},{"full_name":"Bronstein, Michael M.","first_name":"Michael M.","last_name":"Bronstein"}],"publisher":"IEEE","date_created":"2024-10-15T11:20:54Z","conference":{"location":"Anchorage, AK, United States","start_date":"2008-06-23","name":"CVPR: Conference on Computer Vision and Pattern Recognition","end_date":"2008-06-28"},"day":"01","quality_controlled":"1","scopus_import":"1","language":[{"iso":"eng"}],"title":"Not only size matters: Regularized partial matching of nonrigid shapes","publication":"2008 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops","type":"conference","year":"2008"},{"citation":{"chicago":"Weber, Ofir, Yohai S. Devir, Alex M. Bronstein, Michael M. Bronstein, and Ron Kimmel. “Parallel Algorithms for Approximation of Distance Maps on Parametric Surfaces.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2008. <a href=\"https://doi.org/10.1145/1409625.1409626\">https://doi.org/10.1145/1409625.1409626</a>.","ieee":"O. Weber, Y. S. Devir, A. M. Bronstein, M. M. Bronstein, and R. Kimmel, “Parallel algorithms for approximation of distance maps on parametric surfaces,” <i>ACM Transactions on Graphics</i>, vol. 27, no. 4. Association for Computing Machinery, 2008.","apa":"Weber, O., Devir, Y. S., Bronstein, A. M., Bronstein, M. M., &#38; Kimmel, R. (2008). Parallel algorithms for approximation of distance maps on parametric surfaces. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/1409625.1409626\">https://doi.org/10.1145/1409625.1409626</a>","ama":"Weber O, Devir YS, Bronstein AM, Bronstein MM, Kimmel R. Parallel algorithms for approximation of distance maps on parametric surfaces. <i>ACM Transactions on Graphics</i>. 2008;27(4). doi:<a href=\"https://doi.org/10.1145/1409625.1409626\">10.1145/1409625.1409626</a>","mla":"Weber, Ofir, et al. “Parallel Algorithms for Approximation of Distance Maps on Parametric Surfaces.” <i>ACM Transactions on Graphics</i>, vol. 27, no. 4, 104, Association for Computing Machinery, 2008, doi:<a href=\"https://doi.org/10.1145/1409625.1409626\">10.1145/1409625.1409626</a>.","ista":"Weber O, Devir YS, Bronstein AM, Bronstein MM, Kimmel R. 2008. Parallel algorithms for approximation of distance maps on parametric surfaces. ACM Transactions on Graphics. 27(4), 104.","short":"O. Weber, Y.S. Devir, A.M. Bronstein, M.M. Bronstein, R. Kimmel, ACM Transactions on Graphics 27 (2008)."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","doi":"10.1145/1409625.1409626","volume":27,"article_processing_charge":"No","abstract":[{"text":"We present an efficient O(n) numerical algorithm for first-order approximation of geodesic distances on geometry images, where n is the number of points on the surface. The structure of our algorithm allows efficient implementation on parallel architectures. Two implementations on a SIMD processor and on a GPU are discussed. Numerical results demonstrate up to four orders of magnitude improvement in execution time compared to the state-of-the-art algorithms.","lang":"eng"}],"_id":"18431","publication_status":"published","publisher":"Association for Computing Machinery","date_created":"2024-10-15T11:20:55Z","author":[{"last_name":"Weber","full_name":"Weber, Ofir","first_name":"Ofir"},{"first_name":"Yohai S.","full_name":"Devir, Yohai S.","last_name":"Devir"},{"id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","last_name":"Bronstein","first_name":"Alexander","full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730"},{"full_name":"Bronstein, Michael M.","first_name":"Michael M.","last_name":"Bronstein"},{"first_name":"Ron","full_name":"Kimmel, Ron","last_name":"Kimmel"}],"extern":"1","quality_controlled":"1","scopus_import":"1","day":"01","language":[{"iso":"eng"}],"publication":"ACM Transactions on Graphics","title":"Parallel algorithms for approximation of distance maps on parametric surfaces","type":"journal_article","year":"2008","issue":"4","article_number":"104","date_published":"2008-10-01T00:00:00Z","date_updated":"2024-12-18T14:46:45Z","month":"10","intvolume":"        27","oa_version":"None","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]}},{"type":"journal_article","year":"2008","issue":"10","title":"Environmental heterogeneity generates fluctuating selection on a secondary sexual trait","publication":"Current Biology","language":[{"iso":"eng"}],"day":"20","quality_controlled":"1","extern":"1","_id":"7752","publisher":"Elsevier","publication_status":"published","date_created":"2020-04-30T11:02:13Z","author":[{"first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"last_name":"Pilkington","full_name":"Pilkington, Jill G.","first_name":"Jill G."},{"first_name":"Tim H.","full_name":"Clutton-Brock, Tim H.","last_name":"Clutton-Brock"},{"last_name":"Pemberton","first_name":"Josephine M.","full_name":"Pemberton, Josephine M."},{"last_name":"Kruuk","first_name":"Loeske. E.B.","full_name":"Kruuk, Loeske. E.B."}],"volume":18,"article_processing_charge":"No","doi":"10.1016/j.cub.2008.04.059","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Robinson, Matthew Richard, et al. “Environmental Heterogeneity Generates Fluctuating Selection on a Secondary Sexual Trait.” <i>Current Biology</i>, vol. 18, no. 10, Elsevier, 2008, pp. 751–57, doi:<a href=\"https://doi.org/10.1016/j.cub.2008.04.059\">10.1016/j.cub.2008.04.059</a>.","ama":"Robinson MR, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. Environmental heterogeneity generates fluctuating selection on a secondary sexual trait. <i>Current Biology</i>. 2008;18(10):751-757. doi:<a href=\"https://doi.org/10.1016/j.cub.2008.04.059\">10.1016/j.cub.2008.04.059</a>","short":"M.R. Robinson, J.G. Pilkington, T.H. Clutton-Brock, J.M. Pemberton, L.E.B. Kruuk, Current Biology 18 (2008) 751–757.","ista":"Robinson MR, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. 2008. Environmental heterogeneity generates fluctuating selection on a secondary sexual trait. Current Biology. 18(10), 751–757.","chicago":"Robinson, Matthew Richard, Jill G. Pilkington, Tim H. Clutton-Brock, Josephine M. Pemberton, and Loeske. E.B. Kruuk. “Environmental Heterogeneity Generates Fluctuating Selection on a Secondary Sexual Trait.” <i>Current Biology</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.cub.2008.04.059\">https://doi.org/10.1016/j.cub.2008.04.059</a>.","apa":"Robinson, M. R., Pilkington, J. G., Clutton-Brock, T. H., Pemberton, J. M., &#38; Kruuk, L. E. B. (2008). Environmental heterogeneity generates fluctuating selection on a secondary sexual trait. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2008.04.059\">https://doi.org/10.1016/j.cub.2008.04.059</a>","ieee":"M. R. Robinson, J. G. Pilkington, T. H. Clutton-Brock, J. M. Pemberton, and L. E. B. Kruuk, “Environmental heterogeneity generates fluctuating selection on a secondary sexual trait,” <i>Current Biology</i>, vol. 18, no. 10. Elsevier, pp. 751–757, 2008."},"publication_identifier":{"issn":["0960-9822"]},"article_type":"original","oa_version":"None","intvolume":"        18","month":"05","date_updated":"2021-01-12T08:15:17Z","date_published":"2008-05-20T00:00:00Z","page":"751-757"},{"date_published":"2008-11-01T00:00:00Z","acknowledgement":"This work was supported in part by NIH grants R01 GM078598 and U54 LM008748.","intvolume":"         4","month":"11","date_updated":"2021-01-12T08:19:16Z","publist_id":"6800","title":"Hypermutable non-synonymous sites are under stronger negative selection","publication":"PLoS Genetics","type":"journal_article","issue":"11","year":"2008","volume":4,"abstract":[{"text":"Mutation rate varies greatly between nucleotide sites of the human genome and depends both on the global genomic location and the local sequence context of a site. In particular, CpG context elevates the mutation rate by an order of magnitude. Mutations also vary widely in their effect on the molecular function, phenotype, and fitness. Independence of the probability of occurrence of a new mutation's effect has been a fundamental premise in genetics. However, highly mutable contexts may be preserved by negative selection at important sites but destroyed by mutation at sites under no selection. Thus, there may be a positive correlation between the rate of mutations at a nucleotide site and the magnitude of their effect on fitness. We studied the impact of CpG context on the rate of human-chimpanzee divergence and on intrahuman nucleotide diversity at non-synonymous coding sites. We compared nucleotides that occupy identical positions within codons of identical amino acids and only differ by being within versus outside CpG context. Nucleotides within CpG context are under a stronger negative selection, as revealed by their lower, proportionally to the mutation rate, rate of evolution and nucleotide diversity. In particular, the probability of fixation of a non-synonymous transition at a CpG site is two times lower than at a CpG site. Thus, sites with different mutation rates are not necessarily selectively equivalent. This suggests that the mutation rate may complement sequence conservation as a characteristic predictive of functional importance of nucleotide sites.","lang":"eng"}],"doi":"10.1371/journal.pgen.1000281","status":"public","citation":{"ama":"Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S. Hypermutable non-synonymous sites are under stronger negative selection. <i>PLoS Genetics</i>. 2008;4(11). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1000281\">10.1371/journal.pgen.1000281</a>","mla":"Schmidt, Steffen, et al. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” <i>PLoS Genetics</i>, vol. 4, no. 11, Public Library of Science, 2008, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1000281\">10.1371/journal.pgen.1000281</a>.","short":"S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, S. Sunyaev, PLoS Genetics 4 (2008).","ista":"Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S. 2008. Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genetics. 4(11).","chicago":"Schmidt, Steffen, Anna Gerasimova, Fyodor Kondrashov, Ivan Adzuhbei, Alexey Kondrashov, and Shamil Sunyaev. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” <i>PLoS Genetics</i>. Public Library of Science, 2008. <a href=\"https://doi.org/10.1371/journal.pgen.1000281\">https://doi.org/10.1371/journal.pgen.1000281</a>.","ieee":"S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, and S. Sunyaev, “Hypermutable non-synonymous sites are under stronger negative selection,” <i>PLoS Genetics</i>, vol. 4, no. 11. Public Library of Science, 2008.","apa":"Schmidt, S., Gerasimova, A., Kondrashov, F., Adzuhbei, I., Kondrashov, A., &#38; Sunyaev, S. (2008). Hypermutable non-synonymous sites are under stronger negative selection. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1000281\">https://doi.org/10.1371/journal.pgen.1000281</a>"},"day":"01","quality_controlled":0,"extern":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"844","publisher":"Public Library of Science","author":[{"full_name":"Schmidt, Steffen","first_name":"Steffen","last_name":"Schmidt"},{"first_name":"Anna","full_name":"Gerasimova, Anna","last_name":"Gerasimova"},{"last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov"},{"last_name":"Adzuhbei","first_name":"Ivan","full_name":"Adzuhbei, Ivan A"},{"first_name":"Alexey","full_name":"Kondrashov, Alexey S","last_name":"Kondrashov"},{"last_name":"Sunyaev","first_name":"Shamil","full_name":"Sunyaev, Shamil R"}],"date_created":"2018-12-11T11:48:48Z","publication_status":"published"},{"intvolume":"       380","month":"07","date_updated":"2021-01-12T08:19:34Z","date_published":"2008-07-18T00:00:00Z","page":"726-741","article_type":"original","publication_identifier":{"issn":["0022-2836"]},"oa_version":"None","keyword":["Molecular Biology"],"day":"18","quality_controlled":"1","extern":"1","publication_status":"published","_id":"8480","publisher":"Elsevier","author":[{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"last_name":"Brutscher","first_name":"Bernhard","full_name":"Brutscher, Bernhard"},{"last_name":"Konrat","first_name":"Robert","full_name":"Konrat, Robert"},{"full_name":"Tollinger, Martin","first_name":"Martin","last_name":"Tollinger"}],"date_created":"2020-09-18T10:12:29Z","article_processing_charge":"No","volume":380,"abstract":[{"lang":"eng","text":"The KIX domain of the transcription co-activator CBP is a three-helix bundle protein that folds via rapid accumulation of an intermediate state, followed by a slower folding phase. Recent NMR relaxation dispersion studies revealed the presence of a low-populated (excited) state of KIX that exists in equilibrium with the natively folded form under non-denaturing conditions, and likely represents the equilibrium analog of the folding intermediate. Here, we combine amide hydrogen/deuterium exchange measurements using rapid NMR data acquisition techniques with backbone 15N and 13C relaxation dispersion experiments to further investigate the equilibrium folding of the KIX domain. Residual structure within the folding intermediate is detected by both methods, and their combination enables reliable quantification of the amount of persistent residual structure. Three well-defined folding subunits are found, which display variable stability and correspond closely to the individual helices in the native state. While two of the three helices (α2 and α3) are partially formed in the folding intermediate (to ∼ 50% and ∼ 80%, respectively, at 20 °C), the third helix is disordered. The observed helical content within the excited state exceeds the helical propensities predicted for the corresponding peptide regions, suggesting that the two helices are weakly mutually stabilized, while methyl 13C relaxation dispersion data indicate that a defined packing arrangement is unlikely. Temperature-dependent experiments reveal that the largest enthalpy and entropy changes along the folding reaction occur during the final transition from the intermediate to the native state. Our experimental data are consistent with a folding mechanism where helices α2 and α3 form rapidly, although to different extents, while helix α1 consolidates only as folding proceeds to complete the native state-structure."}],"status":"public","doi":"10.1016/j.jmb.2008.05.040","citation":{"mla":"Schanda, Paul, et al. “Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange NMR Spectroscopy.” <i>Journal of Molecular Biology</i>, vol. 380, no. 4, Elsevier, 2008, pp. 726–41, doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">10.1016/j.jmb.2008.05.040</a>.","ama":"Schanda P, Brutscher B, Konrat R, Tollinger M. Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. <i>Journal of Molecular Biology</i>. 2008;380(4):726-741. doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">10.1016/j.jmb.2008.05.040</a>","short":"P. Schanda, B. Brutscher, R. Konrat, M. Tollinger, Journal of Molecular Biology 380 (2008) 726–741.","ista":"Schanda P, Brutscher B, Konrat R, Tollinger M. 2008. Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal of Molecular Biology. 380(4), 726–741.","chicago":"Schanda, Paul, Bernhard Brutscher, Robert Konrat, and Martin Tollinger. “Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange NMR Spectroscopy.” <i>Journal of Molecular Biology</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">https://doi.org/10.1016/j.jmb.2008.05.040</a>.","apa":"Schanda, P., Brutscher, B., Konrat, R., &#38; Tollinger, M. (2008). Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">https://doi.org/10.1016/j.jmb.2008.05.040</a>","ieee":"P. Schanda, B. Brutscher, R. Konrat, and M. Tollinger, “Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy,” <i>Journal of Molecular Biology</i>, vol. 380, no. 4. Elsevier, pp. 726–741, 2008."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","year":"2008","type":"journal_article","title":"Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy","publication":"Journal of Molecular Biology","language":[{"iso":"eng"}]},{"oa_version":"None","keyword":["Molecular Biology"],"publication_identifier":{"issn":["0022-2836"]},"article_type":"original","page":"386-403","date_published":"2008-07-04T00:00:00Z","date_updated":"2021-01-12T08:19:34Z","intvolume":"       380","month":"07","language":[{"iso":"eng"}],"title":"Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge","publication":"Journal of Molecular Biology","type":"journal_article","issue":"2","year":"2008","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Bersch B, Favier A, Schanda P, et al. Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. <i>Journal of Molecular Biology</i>. 2008;380(2):386-403. doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">10.1016/j.jmb.2008.05.017</a>","mla":"Bersch, Beate, et al. “Molecular Structure and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during Copper Challenge.” <i>Journal of Molecular Biology</i>, vol. 380, no. 2, Elsevier, 2008, pp. 386–403, doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">10.1016/j.jmb.2008.05.017</a>.","ista":"Bersch B, Favier A, Schanda P, van Aelst S, Vallaeys T, Covès J, Mergeay M, Wattiez R. 2008. Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. Journal of Molecular Biology. 380(2), 386–403.","short":"B. Bersch, A. Favier, P. Schanda, S. van Aelst, T. Vallaeys, J. Covès, M. Mergeay, R. Wattiez, Journal of Molecular Biology 380 (2008) 386–403.","chicago":"Bersch, Beate, Adrien Favier, Paul Schanda, Sébastien van Aelst, Tatiana Vallaeys, Jacques Covès, Max Mergeay, and Ruddy Wattiez. “Molecular Structure and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during Copper Challenge.” <i>Journal of Molecular Biology</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">https://doi.org/10.1016/j.jmb.2008.05.017</a>.","ieee":"B. Bersch <i>et al.</i>, “Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge,” <i>Journal of Molecular Biology</i>, vol. 380, no. 2. Elsevier, pp. 386–403, 2008.","apa":"Bersch, B., Favier, A., Schanda, P., van Aelst, S., Vallaeys, T., Covès, J., … Wattiez, R. (2008). Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">https://doi.org/10.1016/j.jmb.2008.05.017</a>"},"volume":380,"abstract":[{"text":"The copK gene is localized on the pMOL30 plasmid of Cupriavidus metallidurans CH34 within the complex cop cluster of genes, for which 21 genes have been identified. The expression of the corresponding periplasmic CopK protein is strongly upregulated in the presence of copper, leading to a high periplasmic accumulation. The structure and metal-binding properties of CopK were investigated by NMR and mass spectrometry. The protein is dimeric in the apo state with a dissociation constant in the range of 10- 5 M estimated from analytical ultracentrifugation. Mass spectrometry revealed that CopK has two high-affinity Cu(I)-binding sites per monomer with different Cu(I) affinities. Binding of Cu(II) was observed but appeared to be non-specific. The solution structure of apo-CopK revealed an all-β fold formed of two β-sheets in perpendicular orientation with an unstructured C-terminal tail. The dimer interface is formed by the surface of the C-terminal β-sheet. Binding of the first Cu(I)-ion induces a major structural modification involving dissociation of the dimeric apo-protein. Backbone chemical shifts determined for the 1Cu(I)-bound form confirm the conservation of the N-terminal β-sheet, while the last strand of the C-terminal sheet appears in slow conformational exchange. We hypothesize that the partial disruption of the C-terminal β-sheet is related to dimer dissociation. NH-exchange data acquired on the apo-protein are consistent with a lower thermodynamic stability of the C-terminal sheet. CopK contains seven methionine residues, five of which appear highly conserved. Chemical shift data suggest implication of two or three methionines (Met54, Met38, Met28) in the first Cu(I) site. Addition of a second Cu(I) ion further increases protein plasticity. Comparison of the structural and metal-binding properties of CopK with other periplasmic copper-binding proteins reveals two conserved features within these functionally related proteins: the all-β fold and the methionine-rich Cu(I)-binding site.","lang":"eng"}],"article_processing_charge":"No","status":"public","doi":"10.1016/j.jmb.2008.05.017","extern":"1","publication_status":"published","_id":"8481","author":[{"first_name":"Beate","full_name":"Bersch, Beate","last_name":"Bersch"},{"last_name":"Favier","full_name":"Favier, Adrien","first_name":"Adrien"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul"},{"full_name":"van Aelst, Sébastien","first_name":"Sébastien","last_name":"van Aelst"},{"first_name":"Tatiana","full_name":"Vallaeys, Tatiana","last_name":"Vallaeys"},{"first_name":"Jacques","full_name":"Covès, Jacques","last_name":"Covès"},{"last_name":"Mergeay","full_name":"Mergeay, Max","first_name":"Max"},{"first_name":"Ruddy","full_name":"Wattiez, Ruddy","last_name":"Wattiez"}],"publisher":"Elsevier","date_created":"2020-09-18T10:12:37Z","day":"04","quality_controlled":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"T. Kern, P. Schanda, and B. Brutscher, “Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load,” <i>Journal of Magnetic Resonance</i>, vol. 190, no. 2. Elsevier, pp. 333–338, 2008.","apa":"Kern, T., Schanda, P., &#38; Brutscher, B. (2008). Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">https://doi.org/10.1016/j.jmr.2007.11.015</a>","chicago":"Kern, Thomas, Paul Schanda, and Bernhard Brutscher. “Sensitivity-Enhanced IPAP-SOFAST-HMQC for Fast-Pulsing 2D NMR with Reduced Radiofrequency Load.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">https://doi.org/10.1016/j.jmr.2007.11.015</a>.","short":"T. Kern, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 190 (2008) 333–338.","ista":"Kern T, Schanda P, Brutscher B. 2008. Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic Resonance. 190(2), 333–338.","ama":"Kern T, Schanda P, Brutscher B. Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. <i>Journal of Magnetic Resonance</i>. 2008;190(2):333-338. doi:<a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">10.1016/j.jmr.2007.11.015</a>","mla":"Kern, Thomas, et al. “Sensitivity-Enhanced IPAP-SOFAST-HMQC for Fast-Pulsing 2D NMR with Reduced Radiofrequency Load.” <i>Journal of Magnetic Resonance</i>, vol. 190, no. 2, Elsevier, 2008, pp. 333–38, doi:<a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">10.1016/j.jmr.2007.11.015</a>."},"doi":"10.1016/j.jmr.2007.11.015","status":"public","volume":190,"abstract":[{"lang":"eng","text":"The SOFAST-HMQC experiment [P. Schanda, B. Brutscher, Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds, J. Am. Chem. Soc. 127 (2005) 8014–8015] allows recording two-dimensional correlation spectra of macromolecules such as proteins in only a few seconds acquisition time. To achieve the highest possible sensitivity, SOFAST-HMQC experiments are preferably performed on high-field NMR spectrometers equipped with cryogenically cooled probes. The duty cycle of over 80% in fast-pulsing SOFAST-HMQC experiments, however, may cause problems when using a cryogenic probe. Here we introduce SE-IPAP-SOFAST-HMQC, a new pulse sequence that provides comparable sensitivity to standard SOFAST-HMQC, while avoiding heteronuclear decoupling during 1H detection, and thus significantly reducing the radiofrequency load of the probe during the experiment. The experiment is also attractive for fast and sensitive measurement of heteronuclear one-bond spin coupling constants."}],"article_processing_charge":"No","_id":"8482","publication_status":"published","author":[{"full_name":"Kern, Thomas","first_name":"Thomas","last_name":"Kern"},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"last_name":"Brutscher","full_name":"Brutscher, Bernhard","first_name":"Bernhard"}],"date_created":"2020-09-18T10:12:46Z","publisher":"Elsevier","extern":"1","quality_controlled":"1","day":"01","language":[{"iso":"eng"}],"publication":"Journal of Magnetic Resonance","title":"Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load","type":"journal_article","issue":"2","year":"2008","page":"333-338","date_published":"2008-02-01T00:00:00Z","date_updated":"2021-01-12T08:19:35Z","month":"02","intvolume":"       190","oa_version":"None","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"article_type":"letter_note","publication_identifier":{"issn":["1090-7807"]}},{"article_type":"original","publication_identifier":{"issn":["0036-1445","1095-7200"]},"oa_version":"None","keyword":["Theoretical Computer Science","Applied Mathematics","Computational Mathematics"],"intvolume":"        50","month":"11","date_updated":"2021-01-12T08:19:46Z","date_published":"2008-11-05T00:00:00Z","page":"702-720","type":"journal_article","issue":"4","year":"2008","title":"Geometry of Arnold diffusion","publication":"SIAM Review","language":[{"iso":"eng"}],"day":"05","quality_controlled":"1","extern":"1","_id":"8509","publication_status":"published","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","first_name":"Vadim"},{"last_name":"Levi","first_name":"Mark","full_name":"Levi, Mark"}],"publisher":"Society for Industrial & Applied Mathematics","date_created":"2020-09-18T10:48:12Z","abstract":[{"lang":"eng","text":"The goal of this paper is to present to nonspecialists what is perhaps the simplest possible geometrical picture explaining the mechanism of Arnold diffusion. We choose to speak of a specific model—that of geometric rays in a periodic optical medium. This model is equivalent to that of a particle in a periodic potential in ${\\mathbb R}^{n}$ with energy prescribed and to the geodesic flow in a Riemannian metric on ${\\mathbb R}^{n} $."}],"volume":50,"article_processing_charge":"No","status":"public","doi":"10.1137/070703235","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” <i>SIAM Review</i>. Society for Industrial &#38; Applied Mathematics, 2008. <a href=\"https://doi.org/10.1137/070703235\">https://doi.org/10.1137/070703235</a>.","ieee":"V. Kaloshin and M. Levi, “Geometry of Arnold diffusion,” <i>SIAM Review</i>, vol. 50, no. 4. Society for Industrial &#38; Applied Mathematics, pp. 702–720, 2008.","apa":"Kaloshin, V., &#38; Levi, M. (2008). Geometry of Arnold diffusion. <i>SIAM Review</i>. Society for Industrial &#38; Applied Mathematics. <a href=\"https://doi.org/10.1137/070703235\">https://doi.org/10.1137/070703235</a>","ama":"Kaloshin V, Levi M. Geometry of Arnold diffusion. <i>SIAM Review</i>. 2008;50(4):702-720. doi:<a href=\"https://doi.org/10.1137/070703235\">10.1137/070703235</a>","mla":"Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” <i>SIAM Review</i>, vol. 50, no. 4, Society for Industrial &#38; Applied Mathematics, 2008, pp. 702–20, doi:<a href=\"https://doi.org/10.1137/070703235\">10.1137/070703235</a>.","ista":"Kaloshin V, Levi M. 2008. Geometry of Arnold diffusion. SIAM Review. 50(4), 702–720.","short":"V. Kaloshin, M. Levi, SIAM Review 50 (2008) 702–720."}},{"language":[{"iso":"eng"}],"publication":"Bulletin of the American Mathematical Society","title":"An example of Arnold diffusion for near-integrable Hamiltonians","year":"2008","type":"journal_article","issue":"3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable Hamiltonians.” <i>Bulletin of the American Mathematical Society</i>. American Mathematical Society, 2008. <a href=\"https://doi.org/10.1090/s0273-0979-08-01211-1\">https://doi.org/10.1090/s0273-0979-08-01211-1</a>.","ieee":"V. Kaloshin and M. Levi, “An example of Arnold diffusion for near-integrable Hamiltonians,” <i>Bulletin of the American Mathematical Society</i>, vol. 45, no. 3. American Mathematical Society, pp. 409–427, 2008.","apa":"Kaloshin, V., &#38; Levi, M. (2008). An example of Arnold diffusion for near-integrable Hamiltonians. <i>Bulletin of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/s0273-0979-08-01211-1\">https://doi.org/10.1090/s0273-0979-08-01211-1</a>","ama":"Kaloshin V, Levi M. An example of Arnold diffusion for near-integrable Hamiltonians. <i>Bulletin of the American Mathematical Society</i>. 2008;45(3):409-427. doi:<a href=\"https://doi.org/10.1090/s0273-0979-08-01211-1\">10.1090/s0273-0979-08-01211-1</a>","mla":"Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable Hamiltonians.” <i>Bulletin of the American Mathematical Society</i>, vol. 45, no. 3, American Mathematical Society, 2008, pp. 409–27, doi:<a href=\"https://doi.org/10.1090/s0273-0979-08-01211-1\">10.1090/s0273-0979-08-01211-1</a>.","short":"V. Kaloshin, M. Levi, Bulletin of the American Mathematical Society 45 (2008) 409–427.","ista":"Kaloshin V, Levi M. 2008. An example of Arnold diffusion for near-integrable Hamiltonians. Bulletin of the American Mathematical Society. 45(3), 409–427."},"doi":"10.1090/s0273-0979-08-01211-1","status":"public","article_processing_charge":"No","volume":45,"abstract":[{"lang":"eng","text":"In this paper, using the ideas of Bessi and Mather, we present a simple mechanical system exhibiting Arnold diffusion. This system of a particle in a small periodic potential can be also interpreted as ray propagation in a periodic optical medium with a near-constant index of refraction. Arnold diffusion in this context manifests itself as an arbitrary finite change of direction for nearly constant index of refraction."}],"_id":"8510","publication_status":"published","publisher":"American Mathematical Society","date_created":"2020-09-18T10:48:20Z","author":[{"orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","first_name":"Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"first_name":"Mark","full_name":"Levi, Mark","last_name":"Levi"}],"extern":"1","quality_controlled":"1","day":"01","keyword":["Applied Mathematics","General Mathematics"],"oa_version":"None","article_type":"original","publication_identifier":{"issn":["0273-0979"]},"page":"409-427","date_published":"2008-07-01T00:00:00Z","date_updated":"2021-01-12T08:19:47Z","month":"07","intvolume":"        45"},{"publication":"BMC Evolutionary Biology","title":"Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene","issue":"1","year":"2008","type":"journal_article","doi":"10.1186/1471-2148-8-180","status":"public","abstract":[{"lang":"eng","text":"Background. The arginine vasopressin V1a receptor (V1aR) modulates social cognition and behavior in a wide variety of species. Variation in a repetitive microsatellite element in the 5′ flanking region of the V1aR gene (AVPR1A) in rodents has been associated with variation in brain V1aR expression and in social behavior. In humans, the 5′ flanking region of AVPR1A contains a tandem duplication of two ∼350 bp, microsatellite-containing elements located approximately 3.5 kb upstream of the transcription start site. The first block, referred to as DupA, contains a polymorphic (GT) 25microsatellite; the second block, DupB, has a complex (CT) 4-(TT)-(CT)8-(GT)24polymorphic motif, known as RS3. Polymorphisms in RS3 have been associated with variation in sociobehavioral traits in humans, including autism spectrum disorders. Thus, evolution of these regions may have contributed to variation in social behavior in primates. We examined the structure of these regions in six ape, six monkey, and one prosimian species. Results. Both tandem repeat blocks are present upstream of the AVPR1A coding region in five of the ape species we investigated, while monkeys have only one copy of this region. As in humans, the microsatellites within DupA and DupB are polymorphic in many primate species. Furthermore, both single (lacking DupB) and duplicated alleles (containing both DupA and DupB) are present in chimpanzee (Pan troglodytes) populations with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles, respectively, based on the analysis of 47 wild-caught individuals. Finally, a phylogenetic reconstruction suggests two alternate evolutionary histories for this locus. Conclusion. There is no obvious relationship between the presence of the RS3 duplication and social organization in primates. However, polymorphisms identified in some species may be useful in future genetic association studies. In particular, the presence of both single and duplicated alleles in chimpanzees provides a unique opportunity to assess the functional role of this duplication in contributing to variation in social behavior in primates. While our initial studies show no signs of directional selection on this locus in chimps, pharmacological and genetic association studies support a potential role for this region in influencing V1aR expression and social behavior."}],"volume":8,"citation":{"chicago":"Donaldson, Zoe, Fyodor Kondrashov, Andrea Putnam, Yaohui Bai, Tara Stoinski, Elizabeth Hammock, and Larry Young. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2008. <a href=\"https://doi.org/10.1186/1471-2148-8-180\">https://doi.org/10.1186/1471-2148-8-180</a>.","ieee":"Z. Donaldson <i>et al.</i>, “Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene,” <i>BMC Evolutionary Biology</i>, vol. 8, no. 1. BioMed Central, 2008.","apa":"Donaldson, Z., Kondrashov, F., Putnam, A., Bai, Y., Stoinski, T., Hammock, E., &#38; Young, L. (2008). Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-8-180\">https://doi.org/10.1186/1471-2148-8-180</a>","ama":"Donaldson Z, Kondrashov F, Putnam A, et al. Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. <i>BMC Evolutionary Biology</i>. 2008;8(1). doi:<a href=\"https://doi.org/10.1186/1471-2148-8-180\">10.1186/1471-2148-8-180</a>","mla":"Donaldson, Zoe, et al. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” <i>BMC Evolutionary Biology</i>, vol. 8, no. 1, BioMed Central, 2008, doi:<a href=\"https://doi.org/10.1186/1471-2148-8-180\">10.1186/1471-2148-8-180</a>.","short":"Z. Donaldson, F. Kondrashov, A. Putnam, Y. Bai, T. Stoinski, E. Hammock, L. Young, BMC Evolutionary Biology 8 (2008).","ista":"Donaldson Z, Kondrashov F, Putnam A, Bai Y, Stoinski T, Hammock E, Young L. 2008. Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. 8(1)."},"quality_controlled":0,"day":"01","author":[{"last_name":"Donaldson","full_name":"Donaldson, Zoe R","first_name":"Zoe"},{"last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","first_name":"Fyodor"},{"last_name":"Putnam","first_name":"Andrea","full_name":"Putnam, Andrea S"},{"last_name":"Bai","first_name":"Yaohui","full_name":"Bai, Yaohui"},{"last_name":"Stoinski","full_name":"Stoinski, Tara S","first_name":"Tara"},{"last_name":"Hammock","first_name":"Elizabeth","full_name":"Hammock, Elizabeth A"},{"last_name":"Young","full_name":"Young, Larry","first_name":"Larry"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"895","date_created":"2018-12-11T11:49:04Z","publication_status":"published","publisher":"BioMed Central","extern":1,"acknowledgement":"We thank the caretakers at Zoo Atlanta and Yerkes National Primate Center for help with procuring specimens. Additional DNA samples were supplied by Bill Hopkins, Emory University (chimpanzee), Allyson Bennet, Wake Forest University (chimpanzee, rhesus macaque, bonnet macaque), Mar Sanchez, Emory University (rhesus macaque), and Anne Yoder, Duke University (galago). Susan Lambeth, M.D. Anderson Cancer Center, and Katie Chace, Yerkes National Primate Center, helped provide records regarding the origins of wild born chimps at these centers. We would like to thank Dr Lisa McGraw and two anonymous reviewers for their com- ments on this manuscript. This work was supported by NSF IBN-9876754, NIH RR00165, NIMH56897 (LJY), MH64692 (LJY) and a Howard Hughes Predoctoral Fellowship (ZRD).\n","date_published":"2008-01-01T00:00:00Z","month":"01","intvolume":"         8","publist_id":"6753","date_updated":"2021-01-12T08:21:29Z"},{"year":"2008","issue":"10","type":"journal_article","title":"Nested genes and increasing organizational complexity of metazoan genomes","publication":"Trends in Genetics","day":"01","quality_controlled":0,"extern":1,"author":[{"last_name":"Assis","first_name":"Raquel","full_name":"Assis, Raquel"},{"first_name":"Alexey","full_name":"Kondrashov, Alexey S","last_name":"Kondrashov"},{"full_name":"Koonin, Eugene V","first_name":"Eugene","last_name":"Koonin"},{"last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov"}],"_id":"907","publication_status":"published","publisher":"Elsevier","date_created":"2018-12-11T11:49:08Z","volume":24,"abstract":[{"text":"The most common form of protein-coding gene overlap in eukaryotes is a simple nested structure, whereby one gene is embedded in an intron of another. Analysis of nested protein-coding genes in vertebrates, fruit flies and nematodes revealed substantially higher rates of evolutionary gains than losses. The accumulation of nested gene structures could not be attributed to any obvious functional relationships between the genes involved and represents an increase of the organizational complexity of animal genomes via a neutral process.","lang":"eng"}],"doi":"10.1016/j.tig.2008.08.003","status":"public","citation":{"apa":"Assis, R., Kondrashov, A., Koonin, E., &#38; Kondrashov, F. (2008). Nested genes and increasing organizational complexity of metazoan genomes. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2008.08.003\">https://doi.org/10.1016/j.tig.2008.08.003</a>","ieee":"R. Assis, A. Kondrashov, E. Koonin, and F. Kondrashov, “Nested genes and increasing organizational complexity of metazoan genomes,” <i>Trends in Genetics</i>, vol. 24, no. 10. Elsevier, pp. 475–478, 2008.","chicago":"Assis, Raquel, Alexey Kondrashov, Eugene Koonin, and Fyodor Kondrashov. “Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” <i>Trends in Genetics</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.tig.2008.08.003\">https://doi.org/10.1016/j.tig.2008.08.003</a>.","short":"R. Assis, A. Kondrashov, E. Koonin, F. Kondrashov, Trends in Genetics 24 (2008) 475–478.","ista":"Assis R, Kondrashov A, Koonin E, Kondrashov F. 2008. Nested genes and increasing organizational complexity of metazoan genomes. Trends in Genetics. 24(10), 475–478.","mla":"Assis, Raquel, et al. “Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” <i>Trends in Genetics</i>, vol. 24, no. 10, Elsevier, 2008, pp. 475–78, doi:<a href=\"https://doi.org/10.1016/j.tig.2008.08.003\">10.1016/j.tig.2008.08.003</a>.","ama":"Assis R, Kondrashov A, Koonin E, Kondrashov F. Nested genes and increasing organizational complexity of metazoan genomes. <i>Trends in Genetics</i>. 2008;24(10):475-478. doi:<a href=\"https://doi.org/10.1016/j.tig.2008.08.003\">10.1016/j.tig.2008.08.003</a>"},"intvolume":"        24","month":"10","date_updated":"2021-01-12T08:21:49Z","publist_id":"6743","date_published":"2008-10-01T00:00:00Z","page":"475 - 478"},{"scopus_import":"1","quality_controlled":"1","date_created":"2021-06-04T11:49:32Z","status":"public","volume":456,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Zilberman, D., Coleman-Derr, D., Ballinger, T., &#38; Henikoff, S. (2008). Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature07324\">https://doi.org/10.1038/nature07324</a>","ieee":"D. Zilberman, D. Coleman-Derr, T. Ballinger, and S. Henikoff, “Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks,” <i>Nature</i>, vol. 456, no. 7218. Springer Nature, pp. 125–129, 2008.","chicago":"Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” <i>Nature</i>. Springer Nature, 2008. <a href=\"https://doi.org/10.1038/nature07324\">https://doi.org/10.1038/nature07324</a>.","short":"D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008) 125–129.","ista":"Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. 2008. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 456(7218), 125–129.","mla":"Zilberman, Daniel, et al. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” <i>Nature</i>, vol. 456, no. 7218, Springer Nature, 2008, pp. 125–29, doi:<a href=\"https://doi.org/10.1038/nature07324\">10.1038/nature07324</a>.","ama":"Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. <i>Nature</i>. 2008;456(7218):125-129. doi:<a href=\"https://doi.org/10.1038/nature07324\">10.1038/nature07324</a>"},"pmid":1,"year":"2008","issue":"7218","type":"journal_article","publication":"Nature","title":"Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks","language":[{"iso":"eng"}],"intvolume":"       456","date_published":"2008-11-06T00:00:00Z","page":"125-129","department":[{"_id":"DaZi"}],"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"day":"06","publisher":"Springer Nature","_id":"9457","external_id":{"pmid":["18815594"]},"publication_status":"published","author":[{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel"},{"last_name":"Coleman-Derr","first_name":"Devin","full_name":"Coleman-Derr, Devin"},{"first_name":"Tracy","full_name":"Ballinger, Tracy","last_name":"Ballinger"},{"last_name":"Henikoff","first_name":"Steven","full_name":"Henikoff, Steven"}],"extern":"1","doi":"10.1038/nature07324","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation1–6. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development4,5, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer7. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation."}],"month":"11","date_updated":"2021-12-14T08:54:36Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877514/"}],"oa":1,"article_type":"letter_note","oa_version":"Submitted Version","keyword":["Multidisciplinary"]},{"date_updated":"2021-12-14T08:54:07Z","month":"10","article_type":"review","oa_version":"None","extern":"1","_id":"9537","publisher":"Elsevier ","author":[{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"external_id":{"pmid":["18774331"]},"publication_status":"published","abstract":[{"lang":"eng","text":"DNA methylation is an ancient process found in all domains of life. Although the enzymes that mediate methylation have remained highly conserved, DNA methylation has been adapted for a variety of uses throughout evolution, including defense against transposable elements and control of gene expression. Defects in DNA methylation are linked to human diseases, including cancer. Methylation has been lost several times in the course of animal and fungal evolution, thus limiting the opportunity for study in common model organisms. In the past decade, plants have emerged as a premier model system for genetic dissection of DNA methylation. A recent combination of plant genetics with powerful genomic approaches has led to a number of exciting discoveries and promises many more."}],"article_processing_charge":"No","doi":"10.1016/j.pbi.2008.07.004","intvolume":"        11","page":"554-559","date_published":"2008-10-01T00:00:00Z","department":[{"_id":"DaZi"}],"publication_identifier":{"issn":["1369-5266"]},"date_created":"2021-06-08T13:13:37Z","scopus_import":"1","quality_controlled":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” <i>Current Opinion in Plant Biology</i>. Elsevier , 2008. <a href=\"https://doi.org/10.1016/j.pbi.2008.07.004\">https://doi.org/10.1016/j.pbi.2008.07.004</a>.","apa":"Zilberman, D. (2008). The evolving functions of DNA methylation. <i>Current Opinion in Plant Biology</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.pbi.2008.07.004\">https://doi.org/10.1016/j.pbi.2008.07.004</a>","ieee":"D. Zilberman, “The evolving functions of DNA methylation,” <i>Current Opinion in Plant Biology</i>, vol. 11, no. 5. Elsevier , pp. 554–559, 2008.","mla":"Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” <i>Current Opinion in Plant Biology</i>, vol. 11, no. 5, Elsevier , 2008, pp. 554–59, doi:<a href=\"https://doi.org/10.1016/j.pbi.2008.07.004\">10.1016/j.pbi.2008.07.004</a>.","ama":"Zilberman D. The evolving functions of DNA methylation. <i>Current Opinion in Plant Biology</i>. 2008;11(5):554-559. doi:<a href=\"https://doi.org/10.1016/j.pbi.2008.07.004\">10.1016/j.pbi.2008.07.004</a>","ista":"Zilberman D. 2008. The evolving functions of DNA methylation. Current Opinion in Plant Biology. 11(5), 554–559.","short":"D. Zilberman, Current Opinion in Plant Biology 11 (2008) 554–559."},"volume":11,"status":"public","issue":"5","year":"2008","type":"journal_article","pmid":1,"language":[{"iso":"eng"}],"title":"The evolving functions of DNA methylation","publication":"Current Opinion in Plant Biology"},{"quality_controlled":0,"day":"01","_id":"965","publisher":"Elsevier","publication_status":"published","date_created":"2018-12-11T11:49:26Z","author":[{"last_name":"Morozov","first_name":"Alexei","full_name":"Morozov, Alexei Y"},{"orcid":"0000-0002-2399-5827","full_name":"Maksym Serbyn","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"extern":1,"doi":"10.1007/s11232-008-0026-7","status":"public","volume":154,"abstract":[{"text":"We give many examples of applying Bogoliubov's forest formula to iterative solutions of various nonlinear equations. The same formula describes an extremely wide class of objects, from an ordinary quadratic equation to renormalization in quantum field theory.","lang":"eng"}],"citation":{"ieee":"A. Morozov and M. Serbyn, “Nonlinear algebra and Bogoliubov’s recursion,” <i>Theoretical and Mathematical Physics</i>, vol. 154, no. 2. Elsevier, pp. 270–293, 2008.","apa":"Morozov, A., &#38; Serbyn, M. (2008). Nonlinear algebra and Bogoliubov’s recursion. <i>Theoretical and Mathematical Physics</i>. Elsevier. <a href=\"https://doi.org/10.1007/s11232-008-0026-7\">https://doi.org/10.1007/s11232-008-0026-7</a>","chicago":"Morozov, Alexei, and Maksym Serbyn. “Nonlinear Algebra and Bogoliubov’s Recursion.” <i>Theoretical and Mathematical Physics</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1007/s11232-008-0026-7\">https://doi.org/10.1007/s11232-008-0026-7</a>.","ista":"Morozov A, Serbyn M. 2008. Nonlinear algebra and Bogoliubov’s recursion. Theoretical and Mathematical Physics. 154(2), 270–293.","short":"A. Morozov, M. Serbyn, Theoretical and Mathematical Physics 154 (2008) 270–293.","ama":"Morozov A, Serbyn M. Nonlinear algebra and Bogoliubov’s recursion. <i>Theoretical and Mathematical Physics</i>. 2008;154(2):270-293. doi:<a href=\"https://doi.org/10.1007/s11232-008-0026-7\">10.1007/s11232-008-0026-7</a>","mla":"Morozov, Alexei, and Maksym Serbyn. “Nonlinear Algebra and Bogoliubov’s Recursion.” <i>Theoretical and Mathematical Physics</i>, vol. 154, no. 2, Elsevier, 2008, pp. 270–93, doi:<a href=\"https://doi.org/10.1007/s11232-008-0026-7\">10.1007/s11232-008-0026-7</a>."},"issue":"2","type":"journal_article","year":"2008","publication":"Theoretical and Mathematical Physics","title":"Nonlinear algebra and Bogoliubov's recursion","month":"01","intvolume":"       154","publist_id":"6437","date_updated":"2021-01-12T08:22:17Z","date_published":"2008-01-01T00:00:00Z","acknowledgement":"This work is supported in part by the Dynasty Foundation (M. N. S.),  the\nRussian Foundation for Basic Research (Grant No\ns. 07-02-00878 and 07-02-00645), a joint grant (Grant\nNo. 06-01-92059-CE), the NWO (Project No. 047.011.2004.026), INTAS (Grant No. 05-1000008-7865), the\nProgram for Supporting Leading Scientific School\ns (Grant No. NSh-8004.2006.2), and also by a project\n(Project No. ANR-05-BLAN-0029-01, A. Yu. M.).","main_file_link":[{"url":"https://arxiv.org/abs/hep-th/0703258","open_access":"1"}],"page":"270 - 293","oa":1},{"quality_controlled":"1","day":"30","_id":"7320","publisher":"Elsevier","author":[{"last_name":"Flückiger","full_name":"Flückiger, Reto","first_name":"Reto"},{"last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander"},{"first_name":"Denis","full_name":"Kramer, Denis","last_name":"Kramer"},{"last_name":"Wokaun","full_name":"Wokaun, Alexander","first_name":"Alexander"},{"last_name":"Scherer","first_name":"Günther G.","full_name":"Scherer, Günther G."},{"last_name":"Büchi","first_name":"Felix N.","full_name":"Büchi, Felix N."}],"date_created":"2020-01-15T12:21:36Z","publication_status":"published","extern":"1","doi":"10.1016/j.electacta.2008.07.034","status":"public","abstract":[{"text":"A comparative, experimental diffusivity study of gas diffusion layer (GDL) materials for polymer electrolyte fuel cells (PEFC) is presented for the first time. The GDL plays an important role for electrochemical losses due to gas transport limitations at high current densities. Characterization and optimization of these layers is therefore essential to improve power density. A recently developed method which allows for fast diffusimetry is applied and data compared to the literature values. Measurements are made as a function of direction and compression and the effect of different binder structures and hydrophobic treatments on effective diffusivities are discussed. A better understanding of the results is gained by including novel GDL cross-section images and a meaningful unit cell model for the interpretation of the data. The diffusivity data is valuable for GDL manufacturers and future PEFC models. The study reveals that a binder–fiber ratio larger than 50% has a negative impact on the effective diffusion properties. The hydrophobic treatment which is necessary to improve the water management can impede diffusion and thus reduce the power density. Furthermore binder has an isotropic effect while compression pronounces the in-plane orientation of the fibers.","lang":"eng"}],"article_processing_charge":"No","volume":54,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Flückiger, Reto, Stefan Alexander Freunberger, Denis Kramer, Alexander Wokaun, Günther G. Scherer, and Felix N. Büchi. “Anisotropic, Effective Diffusivity of Porous Gas Diffusion Layer Materials for PEFC.” <i>Electrochimica Acta</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.electacta.2008.07.034\">https://doi.org/10.1016/j.electacta.2008.07.034</a>.","apa":"Flückiger, R., Freunberger, S. A., Kramer, D., Wokaun, A., Scherer, G. G., &#38; Büchi, F. N. (2008). Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC. <i>Electrochimica Acta</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.electacta.2008.07.034\">https://doi.org/10.1016/j.electacta.2008.07.034</a>","ieee":"R. Flückiger, S. A. Freunberger, D. Kramer, A. Wokaun, G. G. Scherer, and F. N. Büchi, “Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC,” <i>Electrochimica Acta</i>, vol. 54, no. 2. Elsevier, pp. 551–559, 2008.","mla":"Flückiger, Reto, et al. “Anisotropic, Effective Diffusivity of Porous Gas Diffusion Layer Materials for PEFC.” <i>Electrochimica Acta</i>, vol. 54, no. 2, Elsevier, 2008, pp. 551–59, doi:<a href=\"https://doi.org/10.1016/j.electacta.2008.07.034\">10.1016/j.electacta.2008.07.034</a>.","ama":"Flückiger R, Freunberger SA, Kramer D, Wokaun A, Scherer GG, Büchi FN. Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC. <i>Electrochimica Acta</i>. 2008;54(2):551-559. doi:<a href=\"https://doi.org/10.1016/j.electacta.2008.07.034\">10.1016/j.electacta.2008.07.034</a>","short":"R. Flückiger, S.A. Freunberger, D. Kramer, A. Wokaun, G.G. Scherer, F.N. Büchi, Electrochimica Acta 54 (2008) 551–559.","ista":"Flückiger R, Freunberger SA, Kramer D, Wokaun A, Scherer GG, Büchi FN. 2008. Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC. Electrochimica Acta. 54(2), 551–559."},"issue":"2","year":"2008","type":"journal_article","publication":"Electrochimica Acta","title":"Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC","language":[{"iso":"eng"}],"month":"12","intvolume":"        54","date_updated":"2021-01-12T08:13:02Z","date_published":"2008-12-30T00:00:00Z","page":"551-559","publication_identifier":{"issn":["0013-4686"]},"article_type":"original","oa_version":"None"},{"issue":"7","year":"2008","type":"journal_article","language":[{"iso":"eng"}],"publication":"Journal of The Electrochemical Society","title":"Cell interaction phenomena in polymer electrolyte fuel cell stacks","_id":"7321","author":[{"first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger"},{"last_name":"Schneider","full_name":"Schneider, Ingo A.","first_name":"Ingo A."},{"first_name":"Pang-Chieh","full_name":"Sui, Pang-Chieh","last_name":"Sui"},{"last_name":"Wokaun","first_name":"Alexander","full_name":"Wokaun, Alexander"},{"last_name":"Djilali","full_name":"Djilali, Nedjib","first_name":"Nedjib"},{"last_name":"Büchi","first_name":"Felix N.","full_name":"Büchi, Felix N."}],"date_created":"2020-01-15T12:21:47Z","publication_status":"published","publisher":"The Electrochemical Society","extern":"1","quality_controlled":"1","day":"08","citation":{"chicago":"Freunberger, Stefan Alexander, Ingo A. Schneider, Pang-Chieh Sui, Alexander Wokaun, Nedjib Djilali, and Felix N. Büchi. “Cell Interaction Phenomena in Polymer Electrolyte Fuel Cell Stacks.” <i>Journal of The Electrochemical Society</i>. The Electrochemical Society, 2008. <a href=\"https://doi.org/10.1149/1.2913095\">https://doi.org/10.1149/1.2913095</a>.","ieee":"S. A. Freunberger, I. A. Schneider, P.-C. Sui, A. Wokaun, N. Djilali, and F. N. Büchi, “Cell interaction phenomena in polymer electrolyte fuel cell stacks,” <i>Journal of The Electrochemical Society</i>, vol. 155, no. 7. The Electrochemical Society, 2008.","apa":"Freunberger, S. A., Schneider, I. A., Sui, P.-C., Wokaun, A., Djilali, N., &#38; Büchi, F. N. (2008). Cell interaction phenomena in polymer electrolyte fuel cell stacks. <i>Journal of The Electrochemical Society</i>. The Electrochemical Society. <a href=\"https://doi.org/10.1149/1.2913095\">https://doi.org/10.1149/1.2913095</a>","ama":"Freunberger SA, Schneider IA, Sui P-C, Wokaun A, Djilali N, Büchi FN. Cell interaction phenomena in polymer electrolyte fuel cell stacks. <i>Journal of The Electrochemical Society</i>. 2008;155(7). doi:<a href=\"https://doi.org/10.1149/1.2913095\">10.1149/1.2913095</a>","mla":"Freunberger, Stefan Alexander, et al. “Cell Interaction Phenomena in Polymer Electrolyte Fuel Cell Stacks.” <i>Journal of The Electrochemical Society</i>, vol. 155, no. 7, B704, The Electrochemical Society, 2008, doi:<a href=\"https://doi.org/10.1149/1.2913095\">10.1149/1.2913095</a>.","short":"S.A. Freunberger, I.A. Schneider, P.-C. Sui, A. Wokaun, N. Djilali, F.N. Büchi, Journal of The Electrochemical Society 155 (2008).","ista":"Freunberger SA, Schneider IA, Sui P-C, Wokaun A, Djilali N, Büchi FN. 2008. Cell interaction phenomena in polymer electrolyte fuel cell stacks. Journal of The Electrochemical Society. 155(7), B704."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","doi":"10.1149/1.2913095","abstract":[{"text":"Cell interaction phenomena in polymer electrolyte fuel cell stacks that arise from imbalance between adjacent cells are investigated in detail experimentally and theoretically. A specialized two-cell stack with advanced localized diagnostics was developed and used to analyze the mechanism and effect of cell-to-cell coupling as a result of operationally relevant variations in reactant feed flow. Contributions to overall and local voltage changes with respect to uniformly operated cells are scrutinized. Unequal operation of the cells causes in-plane current in the bipolar plate to redistribute current and result in inhomogeneous polarization. Both increasing and decreasing polarization along the air-flow path reduces cell power as compared to isopotential operation. A two-dimensional model based on a commercial computational fluid dynamics code is used to back and extend the experimental results to more general cases. Furthermore, the experimental setup presented allowed for the first time to perform simultaneous localized electrochemical impedance spectroscopy beyond the single-cell level. The mechanism of mutual cell interaction on local and integral spectra is revealed. Results show that virtually identical operation of the cells is essential to obtain meaningful integral spectra.","lang":"eng"}],"volume":155,"article_processing_charge":"No","publication_identifier":{"issn":["0013-4651"]},"article_type":"original","oa_version":"None","date_updated":"2021-01-12T08:13:03Z","month":"05","intvolume":"       155","date_published":"2008-05-08T00:00:00Z","article_number":"B704"},{"oa_version":"None","article_type":"original","publication_identifier":{"issn":["1572-6657"]},"page":"63-77","date_published":"2008-01-01T00:00:00Z","date_updated":"2021-01-12T08:13:03Z","intvolume":"       612","month":"01","language":[{"iso":"eng"}],"title":"Electrochemical diffusimetry of fuel cell gas diffusion layers","publication":"Journal of Electroanalytical Chemistry","year":"2008","type":"journal_article","issue":"1","citation":{"ista":"Kramer D, Freunberger SA, Flückiger R, Schneider IA, Wokaun A, Büchi FN, Scherer GG. 2008. Electrochemical diffusimetry of fuel cell gas diffusion layers. Journal of Electroanalytical Chemistry. 612(1), 63–77.","short":"D. Kramer, S.A. Freunberger, R. Flückiger, I.A. Schneider, A. Wokaun, F.N. Büchi, G.G. Scherer, Journal of Electroanalytical Chemistry 612 (2008) 63–77.","ama":"Kramer D, Freunberger SA, Flückiger R, et al. Electrochemical diffusimetry of fuel cell gas diffusion layers. <i>Journal of Electroanalytical Chemistry</i>. 2008;612(1):63-77. doi:<a href=\"https://doi.org/10.1016/j.jelechem.2007.09.014\">10.1016/j.jelechem.2007.09.014</a>","mla":"Kramer, Denis, et al. “Electrochemical Diffusimetry of Fuel Cell Gas Diffusion Layers.” <i>Journal of Electroanalytical Chemistry</i>, vol. 612, no. 1, Elsevier, 2008, pp. 63–77, doi:<a href=\"https://doi.org/10.1016/j.jelechem.2007.09.014\">10.1016/j.jelechem.2007.09.014</a>.","ieee":"D. Kramer <i>et al.</i>, “Electrochemical diffusimetry of fuel cell gas diffusion layers,” <i>Journal of Electroanalytical Chemistry</i>, vol. 612, no. 1. Elsevier, pp. 63–77, 2008.","apa":"Kramer, D., Freunberger, S. A., Flückiger, R., Schneider, I. A., Wokaun, A., Büchi, F. N., &#38; Scherer, G. G. (2008). Electrochemical diffusimetry of fuel cell gas diffusion layers. <i>Journal of Electroanalytical Chemistry</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jelechem.2007.09.014\">https://doi.org/10.1016/j.jelechem.2007.09.014</a>","chicago":"Kramer, Denis, Stefan Alexander Freunberger, Reto Flückiger, Ingo A. Schneider, Alexander Wokaun, Felix N. Büchi, and Günther G. Scherer. “Electrochemical Diffusimetry of Fuel Cell Gas Diffusion Layers.” <i>Journal of Electroanalytical Chemistry</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.jelechem.2007.09.014\">https://doi.org/10.1016/j.jelechem.2007.09.014</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":612,"article_processing_charge":"No","abstract":[{"lang":"eng","text":"The gas diffusion layers (GDLs) of a membrane electrode assembly (MEA) serve as link between flow field and porous electrode within a polymer electrolyte fuel cell. Beside ensuring sufficient electrical and thermal contact between the whole electrode area and the flow field, these typically 200–400 μm thick porous structures enable the access of educts to the electrode area which would be occluded by the flow field lands if the flow field is directly attached to the electrode. Hence, the characterisation of properties pertaining to mass transport of educts and products through these structures is indispensable whilst examining the contribution of the GDLs to the overall electrochemical characteristics of a MEA. A fast and cost effective method to measure the effective diffusivity of a GDL is presented. Electrochemical impedance spectroscopy is applied to measure the effective ionic conductivity of an electrolyte-soaked GDL. Taking advantage of the analogy between Ficks and Ohms law, this provides a measure for the effective diffusivity. The method is described in detail, including experimental as well as theoretical aspects, and selected results, highlighting the anisotropy and dependence on the degree of compression, are shown. Moreover, a two-dimensional model consisting of regularly spaced ellipses is developed to represent the porous structure of the GDL, and by using conformal maps, the agreement between this model and experiment with respect to the sensitivity of the effective diffusivity towards compression is shown."}],"status":"public","doi":"10.1016/j.jelechem.2007.09.014","extern":"1","_id":"7322","date_created":"2020-01-15T12:21:57Z","publication_status":"published","publisher":"Elsevier","author":[{"first_name":"Denis","full_name":"Kramer, Denis","last_name":"Kramer"},{"last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Flückiger, Reto","first_name":"Reto","last_name":"Flückiger"},{"last_name":"Schneider","full_name":"Schneider, Ingo A.","first_name":"Ingo A."},{"last_name":"Wokaun","full_name":"Wokaun, Alexander","first_name":"Alexander"},{"first_name":"Felix N.","full_name":"Büchi, Felix N.","last_name":"Büchi"},{"full_name":"Scherer, Günther G.","first_name":"Günther G.","last_name":"Scherer"}],"day":"01","quality_controlled":"1"},{"type":"conference","year":"2008","publication":"3rd International Conference on Fuel Cell Science, Engineering and Technology","title":"Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks","language":[{"iso":"eng"}],"quality_controlled":"1","day":"13","conference":{"end_date":"2005-05-25","name":"International conference on fuel cell science, engineering and technology","start_date":"2005-05-23","location":"Ypsilanti, MI, United States"},"author":[{"full_name":"Santis, Marco","first_name":"Marco","last_name":"Santis"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander"},{"last_name":"Papra","full_name":"Papra, Matthias","first_name":"Matthias"},{"last_name":"Büchi","full_name":"Büchi, Felix N.","first_name":"Felix N."}],"_id":"7425","publication_status":"published","publisher":"ASMEDC","date_created":"2020-01-31T10:14:45Z","extern":"1","status":"public","doi":"10.1115/fuelcell2005-74116","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The propagation of single cell performance losses to adjacent cells in a polymer electrolyte fuel cell stack is studied by means of local current density measurements in a two cell stack. In this stack, the working conditions of adjacent cells can be controlled independently in order to deliberately change the performance of one cell (inducing cell) and study the coupling effects to the adjacent cell (response cell), while keeping the working conditions of the later one unchanged. The experiments have shown that changes in the current density distribution caused by lowering of the air stoichiometry in the inducing cell cause changes in the current density distribution of the response cell in the order of 60% of the change of the inducing cell, even when the air stoichiometry of the response cell is kept constant. The losses in cell voltage of the inducing cell cause losses in cell voltage of the response cell in a magnitude between 30 and 50%."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Santis, M., Freunberger, S. A., Papra, M., &#38; Büchi, F. N. (2008). Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks. In <i>3rd International Conference on Fuel Cell Science, Engineering and Technology</i> (pp. 763–765). Ypsilanti, MI, United States: ASMEDC. <a href=\"https://doi.org/10.1115/fuelcell2005-74116\">https://doi.org/10.1115/fuelcell2005-74116</a>","ieee":"M. Santis, S. A. Freunberger, M. Papra, and F. N. Büchi, “Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks,” in <i>3rd International Conference on Fuel Cell Science, Engineering and Technology</i>, Ypsilanti, MI, United States, 2008, pp. 763–765.","chicago":"Santis, Marco, Stefan Alexander Freunberger, Matthias Papra, and Felix N. Büchi. “Experimental Investigation of the Propagation of Local Current Density Variations to Adjacent Cells in PEFC Stacks.” In <i>3rd International Conference on Fuel Cell Science, Engineering and Technology</i>, 763–65. ASMEDC, 2008. <a href=\"https://doi.org/10.1115/fuelcell2005-74116\">https://doi.org/10.1115/fuelcell2005-74116</a>.","ista":"Santis M, Freunberger SA, Papra M, Büchi FN. 2008. Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks. 3rd International Conference on Fuel Cell Science, Engineering and Technology. International conference on fuel cell science, engineering and technology, 763–765.","short":"M. Santis, S.A. Freunberger, M. Papra, F.N. Büchi, in:, 3rd International Conference on Fuel Cell Science, Engineering and Technology, ASMEDC, 2008, pp. 763–765.","mla":"Santis, Marco, et al. “Experimental Investigation of the Propagation of Local Current Density Variations to Adjacent Cells in PEFC Stacks.” <i>3rd International Conference on Fuel Cell Science, Engineering and Technology</i>, ASMEDC, 2008, pp. 763–65, doi:<a href=\"https://doi.org/10.1115/fuelcell2005-74116\">10.1115/fuelcell2005-74116</a>.","ama":"Santis M, Freunberger SA, Papra M, Büchi FN. Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks. In: <i>3rd International Conference on Fuel Cell Science, Engineering and Technology</i>. ASMEDC; 2008:763-765. doi:<a href=\"https://doi.org/10.1115/fuelcell2005-74116\">10.1115/fuelcell2005-74116</a>"},"publication_identifier":{"isbn":["0791837645","0791837572"]},"oa_version":"None","month":"10","date_updated":"2021-01-12T08:13:33Z","date_published":"2008-10-13T00:00:00Z","page":"763-765"}]