[{"date_created":"2022-08-12T08:26:42Z","publication":"26th Annual European Symposium on Algorithms","title":"Dynamic effective resistances and approximate schur complement on separable graphs","main_file_link":[{"open_access":"1","url":"https://doi.org/10.4230/LIPIcs.ESA.2018.40"}],"arxiv":1,"date_updated":"2024-11-06T12:16:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"abstract":[{"lang":"eng","text":"We consider the problem of dynamically maintaining (approximate) all-pairs effective resistances in separable graphs, which are those that admit an n^{c}-separator theorem for some c<1. We give a fully dynamic algorithm that maintains (1+epsilon)-approximations of the all-pairs effective resistances of an n-vertex graph G undergoing edge insertions and deletions with O~(sqrt{n}/epsilon^2) worst-case update time and O~(sqrt{n}/epsilon^2) worst-case query time, if G is guaranteed to be sqrt{n}-separable (i.e., it is taken from a class satisfying a sqrt{n}-separator theorem) and its separator can be computed in O~(n) time. Our algorithm is built upon a dynamic algorithm for maintaining approximate Schur complement that approximately preserves pairwise effective resistances among a set of terminals for separable graphs, which might be of independent interest.\r\nWe complement our result by proving that for any two fixed vertices s and t, no incremental or decremental algorithm can maintain the s-t effective resistance for sqrt{n}-separable graphs with worst-case update time O(n^{1/2-delta}) and query time O(n^{1-delta}) for any delta>0, unless the Online Matrix Vector Multiplication (OMv) conjecture is false.\r\nWe further show that for general graphs, no incremental or decremental algorithm can maintain the s-t effective resistance problem with worst-case update time O(n^{1-delta}) and query-time O(n^{2-delta}) for any delta >0, unless the OMv conjecture is false."}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"       112","author":[{"last_name":"Goranci","first_name":"Gramoz","full_name":"Goranci, Gramoz"},{"last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"},{"last_name":"Peng","first_name":"Pan","full_name":"Peng, Pan"}],"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"arxiv":["1802.09111"]},"publication_status":"published","extern":"1","status":"public","year":"2018","date_published":"2018-08-14T00:00:00Z","alternative_title":["LIPIcs"],"corr_author":"1","citation":{"chicago":"Goranci, Gramoz, Monika Henzinger, and Pan Peng. “Dynamic Effective Resistances and Approximate Schur Complement on Separable Graphs.” In <i>26th Annual European Symposium on Algorithms</i>, Vol. 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPICS.ESA.2018.40\">https://doi.org/10.4230/LIPICS.ESA.2018.40</a>.","short":"G. Goranci, M. Henzinger, P. Peng, in:, 26th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Goranci, Gramoz, et al. “Dynamic Effective Resistances and Approximate Schur Complement on Separable Graphs.” <i>26th Annual European Symposium on Algorithms</i>, vol. 112, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPICS.ESA.2018.40\">10.4230/LIPICS.ESA.2018.40</a>.","ista":"Goranci G, Henzinger M, Peng P. 2018. Dynamic effective resistances and approximate schur complement on separable graphs. 26th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 112, 40.","ieee":"G. Goranci, M. Henzinger, and P. Peng, “Dynamic effective resistances and approximate schur complement on separable graphs,” in <i>26th Annual European Symposium on Algorithms</i>, Helsinki, Finland, 2018, vol. 112.","apa":"Goranci, G., Henzinger, M., &#38; Peng, P. (2018). Dynamic effective resistances and approximate schur complement on separable graphs. In <i>26th Annual European Symposium on Algorithms</i> (Vol. 112). Helsinki, Finland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.ESA.2018.40\">https://doi.org/10.4230/LIPICS.ESA.2018.40</a>","ama":"Goranci G, Henzinger M, Peng P. Dynamic effective resistances and approximate schur complement on separable graphs. In: <i>26th Annual European Symposium on Algorithms</i>. Vol 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPICS.ESA.2018.40\">10.4230/LIPICS.ESA.2018.40</a>"},"oa_version":"Published Version","month":"08","type":"conference","scopus_import":"1","article_processing_charge":"No","article_number":"40","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959770811"]},"day":"14","doi":"10.4230/LIPICS.ESA.2018.40","volume":112,"_id":"11828","conference":{"name":"ESA: Annual European Symposium on Algorithms","end_date":"2018-08-22","location":"Helsinki, Finland","start_date":"2018-08-20"}},{"conference":{"name":"SODA: Symposium on Discrete Algorithms","end_date":"2018-01-10","location":"New Orleans, LA, United States","start_date":"2018-01-07"},"_id":"11872","doi":"10.1137/1.9781611975031.1","day":"01","publication_identifier":{"eisbn":["978-161197503-1"]},"article_processing_charge":"No","page":"1 - 20","scopus_import":"1","month":"01","type":"conference","oa_version":"Preprint","citation":{"ista":"Bhattacharya S, Chakrabarty D, Henzinger M, Nanongkai D. 2018. Dynamic algorithms for graph coloring. 29th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1–20.","ieee":"S. Bhattacharya, D. Chakrabarty, M. Henzinger, and D. Nanongkai, “Dynamic algorithms for graph coloring,” in <i>29th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, New Orleans, LA, United States, 2018, pp. 1–20.","apa":"Bhattacharya, S., Chakrabarty, D., Henzinger, M., &#38; Nanongkai, D. (2018). Dynamic algorithms for graph coloring. In <i>29th Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 1–20). New Orleans, LA, United States: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611975031.1\">https://doi.org/10.1137/1.9781611975031.1</a>","ama":"Bhattacharya S, Chakrabarty D, Henzinger M, Nanongkai D. Dynamic algorithms for graph coloring. In: <i>29th Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 2018:1-20. doi:<a href=\"https://doi.org/10.1137/1.9781611975031.1\">10.1137/1.9781611975031.1</a>","mla":"Bhattacharya, Sayan, et al. “Dynamic Algorithms for Graph Coloring.” <i>29th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Society for Industrial and Applied Mathematics, 2018, pp. 1–20, doi:<a href=\"https://doi.org/10.1137/1.9781611975031.1\">10.1137/1.9781611975031.1</a>.","short":"S. Bhattacharya, D. Chakrabarty, M. Henzinger, D. Nanongkai, in:, 29th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2018, pp. 1–20.","chicago":"Bhattacharya, Sayan, Deeparnab Chakrabarty, Monika Henzinger, and Danupon Nanongkai. “Dynamic Algorithms for Graph Coloring.” In <i>29th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 1–20. Society for Industrial and Applied Mathematics, 2018. <a href=\"https://doi.org/10.1137/1.9781611975031.1\">https://doi.org/10.1137/1.9781611975031.1</a>."},"extern":"1","status":"public","publication_status":"published","date_published":"2018-01-01T00:00:00Z","year":"2018","language":[{"iso":"eng"}],"external_id":{"arxiv":["1711.04355"]},"quality_controlled":"1","author":[{"first_name":"Sayan","full_name":"Bhattacharya, Sayan","last_name":"Bhattacharya"},{"last_name":"Chakrabarty","full_name":"Chakrabarty, Deeparnab","first_name":"Deeparnab"},{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"last_name":"Nanongkai","first_name":"Danupon","full_name":"Nanongkai, Danupon"}],"publisher":"Society for Industrial and Applied Mathematics","abstract":[{"lang":"eng","text":"We design fast dynamic algorithms for proper vertex and edge colorings in a graph undergoing edge insertions and deletions. In the static setting, there are simple linear time algorithms for (Δ + 1)- vertex coloring and (2Δ – 1)-edge coloring in a graph with maximum degree Δ. It is natural to ask if we can efficiently maintain such colorings in the dynamic setting as well. We get the following three results. (1) We present a randomized algorithm which maintains a (Δ + 1)-vertex coloring with O(log Δ) expected amortized update time. (2) We present a deterministic algorithm which maintains a (1 + o(1)Δ-vertex coloring with O(polylog Δ) amortized update time. (3) We present a simple, deterministic algorithm which maintains a (2Δ – 1)-edge coloring with O(log Δ) worst-case update time. This improves the recent O(Δ)-edge coloring algorithm with  worst-case update time [4]."}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.04355"}],"date_updated":"2024-11-06T12:20:35Z","publication":"29th Annual ACM-SIAM Symposium on Discrete Algorithms","title":"Dynamic algorithms for graph coloring","date_created":"2022-08-16T12:07:14Z"},{"external_id":{"arxiv":["1708.06127"]},"language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"ista":"Henzinger M, Noe A, Schulz C, Strash D. 2018. Practical minimum cut algorithms. 20th Workshop on Algorithm Engineering and Experiments. ALENEX: Symposium on Algorithm Engineering and Experiments, 48–61.","ieee":"M. Henzinger, A. Noe, C. Schulz, and D. Strash, “Practical minimum cut algorithms,” in <i>20th Workshop on Algorithm Engineering and Experiments</i>, New Orleans, LA, United States, 2018, pp. 48–61.","apa":"Henzinger, M., Noe, A., Schulz, C., &#38; Strash, D. (2018). Practical minimum cut algorithms. In <i>20th Workshop on Algorithm Engineering and Experiments</i> (pp. 48–61). New Orleans, LA, United States: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611975055.5\">https://doi.org/10.1137/1.9781611975055.5</a>","ama":"Henzinger M, Noe A, Schulz C, Strash D. Practical minimum cut algorithms. In: <i>20th Workshop on Algorithm Engineering and Experiments</i>. Society for Industrial and Applied Mathematics; 2018:48-61. doi:<a href=\"https://doi.org/10.1137/1.9781611975055.5\">10.1137/1.9781611975055.5</a>","mla":"Henzinger, Monika, et al. “Practical Minimum Cut Algorithms.” <i>20th Workshop on Algorithm Engineering and Experiments</i>, Society for Industrial and Applied Mathematics, 2018, pp. 48–61, doi:<a href=\"https://doi.org/10.1137/1.9781611975055.5\">10.1137/1.9781611975055.5</a>.","short":"M. Henzinger, A. Noe, C. Schulz, D. Strash, in:, 20th Workshop on Algorithm Engineering and Experiments, Society for Industrial and Applied Mathematics, 2018, pp. 48–61.","chicago":"Henzinger, Monika, Alexander Noe, Christian Schulz, and Darren Strash. “Practical Minimum Cut Algorithms.” In <i>20th Workshop on Algorithm Engineering and Experiments</i>, 48–61. Society for Industrial and Applied Mathematics, 2018. <a href=\"https://doi.org/10.1137/1.9781611975055.5\">https://doi.org/10.1137/1.9781611975055.5</a>."},"publication_status":"published","extern":"1","status":"public","date_published":"2018-01-01T00:00:00Z","year":"2018","author":[{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger"},{"full_name":"Noe, Alexander","first_name":"Alexander","last_name":"Noe"},{"first_name":"Christian","full_name":"Schulz, Christian","last_name":"Schulz"},{"first_name":"Darren","full_name":"Strash, Darren","last_name":"Strash"}],"abstract":[{"lang":"eng","text":"The minimum cut problem for an undirected edge-weighted graph asks us to divide its set of nodes into two blocks while minimizing the weight sum of the cut edges. Here, we introduce a linear-time algorithm to compute near-minimum cuts. Our algorithm is based on cluster contraction using label propagation and Padberg and Rinaldi's contraction heuristics [SIAM Review, 1991]. We give both sequential and shared-memory parallel implementations of our algorithm. Extensive experiments on both real-world and generated instances show that our algorithm finds the optimal cut on nearly all instances significantly faster than other state-of-the-art exact algorithms, and our error rate is lower than that of other heuristic algorithms. In addition, our parallel algorithm shows good scalability."}],"oa":1,"publisher":"Society for Industrial and Applied Mathematics","publication":"20th Workshop on Algorithm Engineering and Experiments","title":"Practical minimum cut algorithms","date_created":"2022-08-17T07:04:57Z","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.06127"}],"date_updated":"2024-11-06T12:22:09Z","day":"01","doi":"10.1137/1.9781611975055.5","publication_identifier":{"eisbn":["978-1-61197-505-5"]},"conference":{"start_date":"2018-01-07","location":"New Orleans, LA, United States","name":"ALENEX: Symposium on Algorithm Engineering and Experiments","end_date":"2018-01-08"},"_id":"11882","page":"48-61","scopus_import":"1","article_processing_charge":"No","month":"01","type":"conference","oa_version":"Preprint"},{"external_id":{"arxiv":["1412.1318"]},"language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"mla":"Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” <i>SIAM Journal on Computing</i>, vol. 47, no. 3, Society for Industrial &#38; Applied Mathematics, 2018, pp. 859–87, doi:<a href=\"https://doi.org/10.1137/140998925\">10.1137/140998925</a>.","ista":"Bhattacharya S, Henzinger M, Italiano GF. 2018. Deterministic fully dynamic data structures for vertex cover and matching. SIAM Journal on Computing. 47(3), 859–887.","apa":"Bhattacharya, S., Henzinger, M., &#38; Italiano, G. F. (2018). Deterministic fully dynamic data structures for vertex cover and matching. <i>SIAM Journal on Computing</i>. Society for Industrial &#38; Applied Mathematics. <a href=\"https://doi.org/10.1137/140998925\">https://doi.org/10.1137/140998925</a>","ama":"Bhattacharya S, Henzinger M, Italiano GF. Deterministic fully dynamic data structures for vertex cover and matching. <i>SIAM Journal on Computing</i>. 2018;47(3):859-887. doi:<a href=\"https://doi.org/10.1137/140998925\">10.1137/140998925</a>","ieee":"S. Bhattacharya, M. Henzinger, and G. F. Italiano, “Deterministic fully dynamic data structures for vertex cover and matching,” <i>SIAM Journal on Computing</i>, vol. 47, no. 3. Society for Industrial &#38; Applied Mathematics, pp. 859–887, 2018.","chicago":"Bhattacharya, Sayan, Monika Henzinger, and Giuseppe F. Italiano. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” <i>SIAM Journal on Computing</i>. Society for Industrial &#38; Applied Mathematics, 2018. <a href=\"https://doi.org/10.1137/140998925\">https://doi.org/10.1137/140998925</a>.","short":"S. Bhattacharya, M. Henzinger, G.F. Italiano, SIAM Journal on Computing 47 (2018) 859–887."},"year":"2018","date_published":"2018-05-01T00:00:00Z","extern":"1","publication_status":"published","status":"public","author":[{"last_name":"Bhattacharya","first_name":"Sayan","full_name":"Bhattacharya, Sayan"},{"last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","first_name":"Monika H"},{"last_name":"Italiano","full_name":"Italiano, Giuseppe F.","first_name":"Giuseppe F."}],"intvolume":"        47","issue":"3","abstract":[{"text":"We present the first deterministic data structures for maintaining approximate minimum vertex cover and maximum matching in a fully dynamic graph 𝐺=(𝑉,𝐸), with |𝑉|=𝑛 and |𝐸|=𝑚, in 𝑜(𝑚‾‾√) time per update. In particular, for minimum vertex cover, we provide deterministic data structures for maintaining a (2+𝜖) approximation in 𝑂(log𝑛/𝜖2) amortized time per update. For maximum matching, we show how to maintain a (3+𝜖) approximation in 𝑂(min(𝑛√/𝜖,𝑚1/3/𝜖2) amortized time per update and a (4+𝜖) approximation in 𝑂(𝑚1/3/𝜖2) worst-case time per update. Our data structure for fully dynamic minimum vertex cover is essentially near-optimal and settles an open problem by Onak and Rubinfeld [in 42nd ACM Symposium on Theory of Computing, Cambridge, MA, ACM, 2010, pp. 457--464].","lang":"eng"}],"oa":1,"publisher":"Society for Industrial & Applied Mathematics","title":"Deterministic fully dynamic data structures for vertex cover and matching","publication":"SIAM Journal on Computing","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"11875"}]},"date_created":"2022-08-17T08:21:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://arxiv.org/abs/1412.1318","open_access":"1"}],"date_updated":"2024-11-06T12:22:54Z","arxiv":1,"doi":"10.1137/140998925","day":"01","publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"_id":"11890","volume":47,"article_type":"original","page":"859-887","scopus_import":"1","article_processing_charge":"No","type":"journal_article","month":"05","oa_version":"Preprint"},{"conference":{"start_date":"2018-07-27","name":"SEA: Symposium on Experimental Algorithms","end_date":"2018-07-29","location":"L'Aquila, Italy"},"volume":103,"_id":"11911","day":"01","doi":"10.4230/LIPICS.SEA.2018.3","publication_identifier":{"isbn":["9783959770705"],"issn":["1868-8969"]},"article_number":"3","article_processing_charge":"No","scopus_import":"1","month":"07","type":"conference","oa_version":"Published Version","alternative_title":["LIPIcs"],"citation":{"ista":"Biedermann S, Henzinger M, Schulz C, Schuster B. 2018. Memetic graph clustering. 17th International Symposium on Experimental Algorithms. SEA: Symposium on Experimental Algorithms, LIPIcs, vol. 103, 3.","ama":"Biedermann S, Henzinger M, Schulz C, Schuster B. Memetic graph clustering. In: <i>17th International Symposium on Experimental Algorithms</i>. Vol 103. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPICS.SEA.2018.3\">10.4230/LIPICS.SEA.2018.3</a>","ieee":"S. Biedermann, M. Henzinger, C. Schulz, and B. Schuster, “Memetic graph clustering,” in <i>17th International Symposium on Experimental Algorithms</i>, L’Aquila, Italy, 2018, vol. 103.","apa":"Biedermann, S., Henzinger, M., Schulz, C., &#38; Schuster, B. (2018). Memetic graph clustering. In <i>17th International Symposium on Experimental Algorithms</i> (Vol. 103). L’Aquila, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.SEA.2018.3\">https://doi.org/10.4230/LIPICS.SEA.2018.3</a>","mla":"Biedermann, Sonja, et al. “Memetic Graph Clustering.” <i>17th International Symposium on Experimental Algorithms</i>, vol. 103, 3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPICS.SEA.2018.3\">10.4230/LIPICS.SEA.2018.3</a>.","short":"S. Biedermann, M. Henzinger, C. Schulz, B. Schuster, in:, 17th International Symposium on Experimental Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","chicago":"Biedermann, Sonja, Monika Henzinger, Christian Schulz, and Bernhard Schuster. “Memetic Graph Clustering.” In <i>17th International Symposium on Experimental Algorithms</i>, Vol. 103. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPICS.SEA.2018.3\">https://doi.org/10.4230/LIPICS.SEA.2018.3</a>."},"status":"public","extern":"1","publication_status":"published","year":"2018","date_published":"2018-07-01T00:00:00Z","external_id":{"arxiv":["1802.07034"]},"language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"first_name":"Sonja","full_name":"Biedermann, Sonja","last_name":"Biedermann"},{"first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"last_name":"Schulz","full_name":"Schulz, Christian","first_name":"Christian"},{"last_name":"Schuster","full_name":"Schuster, Bernhard","first_name":"Bernhard"}],"intvolume":"       103","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","abstract":[{"lang":"eng","text":"It is common knowledge that there is no single best strategy for graph clustering, which justifies a plethora of existing approaches. In this paper, we present a general memetic algorithm, VieClus, to tackle the graph clustering problem. This algorithm can be adapted to optimize different objective functions. A key component of our contribution are natural recombine operators that employ ensemble clusterings as well as multi-level techniques. Lastly, we combine these techniques with a scalable communication protocol, producing a system that is able to compute high-quality solutions in a short amount of time. We instantiate our scheme with local search for modularity and show that our algorithm successfully improves or reproduces all entries of the 10th DIMACS implementation challenge under consideration using a small amount of time."}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"date_updated":"2024-11-06T11:57:15Z","main_file_link":[{"url":"https://doi.org/10.4230/LIPICS.SEA.2018.3","open_access":"1"}],"publication":"17th International Symposium on Experimental Algorithms","title":"Memetic graph clustering","date_created":"2022-08-18T06:49:40Z"},{"_id":"11958","volume":57,"day":"26","doi":"10.1002/anie.201712568","publication_identifier":{"eissn":[" 1521-3773"],"issn":["1433-7851"]},"article_type":"letter_note","article_processing_charge":"No","page":"9976-9979","scopus_import":"1","type":"journal_article","month":"07","oa_version":"None","citation":{"short":"B. Pieber, M. Shalom, M. Antonietti, P.H. Seeberger, K. Gilmore, Angewandte Chemie International Edition 57 (2018) 9976–9979.","chicago":"Pieber, Bartholomäus, Menny Shalom, Markus Antonietti, Peter H. Seeberger, and Kerry Gilmore. “Continuous Heterogeneous Photocatalysis in Serial Micro-Batch Reactors.” <i>Angewandte Chemie International Edition</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/anie.201712568\">https://doi.org/10.1002/anie.201712568</a>.","ama":"Pieber B, Shalom M, Antonietti M, Seeberger PH, Gilmore K. Continuous heterogeneous photocatalysis in serial micro-batch reactors. <i>Angewandte Chemie International Edition</i>. 2018;57(31):9976-9979. doi:<a href=\"https://doi.org/10.1002/anie.201712568\">10.1002/anie.201712568</a>","apa":"Pieber, B., Shalom, M., Antonietti, M., Seeberger, P. H., &#38; Gilmore, K. (2018). Continuous heterogeneous photocatalysis in serial micro-batch reactors. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201712568\">https://doi.org/10.1002/anie.201712568</a>","ieee":"B. Pieber, M. Shalom, M. Antonietti, P. H. Seeberger, and K. Gilmore, “Continuous heterogeneous photocatalysis in serial micro-batch reactors,” <i>Angewandte Chemie International Edition</i>, vol. 57, no. 31. Wiley, pp. 9976–9979, 2018.","ista":"Pieber B, Shalom M, Antonietti M, Seeberger PH, Gilmore K. 2018. Continuous heterogeneous photocatalysis in serial micro-batch reactors. Angewandte Chemie International Edition. 57(31), 9976–9979.","mla":"Pieber, Bartholomäus, et al. “Continuous Heterogeneous Photocatalysis in Serial Micro-Batch Reactors.” <i>Angewandte Chemie International Edition</i>, vol. 57, no. 31, Wiley, 2018, pp. 9976–79, doi:<a href=\"https://doi.org/10.1002/anie.201712568\">10.1002/anie.201712568</a>."},"date_published":"2018-07-26T00:00:00Z","year":"2018","status":"public","extern":"1","publication_status":"published","language":[{"iso":"eng"}],"external_id":{"pmid":["29377383"]},"quality_controlled":"1","author":[{"last_name":"Pieber","first_name":"Bartholomäus","orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","full_name":"Pieber, Bartholomäus"},{"last_name":"Shalom","full_name":"Shalom, Menny","first_name":"Menny"},{"last_name":"Antonietti","full_name":"Antonietti, Markus","first_name":"Markus"},{"last_name":"Seeberger","full_name":"Seeberger, Peter H.","first_name":"Peter H."},{"first_name":"Kerry","full_name":"Gilmore, Kerry","last_name":"Gilmore"}],"intvolume":"        57","issue":"31","publisher":"Wiley","abstract":[{"lang":"eng","text":"Solid reagents, leaching catalysts, and heterogeneous photocatalysts are commonly employed in batch processes but are ill-suited for continuous-flow chemistry. Heterogeneous catalysts for thermal reactions are typically used in packed-bed reactors, which cannot be penetrated by light and thus are not suitable for photocatalytic reactions involving solids. We demonstrate that serial micro-batch reactors (SMBRs) allow for the continuous utilization of solid materials together with liquids and gases in flow. This technology was utilized to develop selective and efficient fluorination reactions using a modified graphitic carbon nitride heterogeneous catalyst instead of costly homogeneous metal polypyridyl complexes. The merger of this inexpensive, recyclable catalyst and the SMBR approach enables sustainable and scalable photocatalysis."}],"date_updated":"2023-02-21T10:09:18Z","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Continuous heterogeneous photocatalysis in serial micro-batch reactors","publication":"Angewandte Chemie International Edition","date_created":"2022-08-24T10:57:25Z"},{"publication":"ACM Transaction on Graphics","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/interactive-software-tool-makes-complex-mold-design-simple/","description":"News on IST Homepage"}]},"title":"CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds","date_created":"2018-12-11T11:44:09Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2025-03-31T15:58:16Z","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"6a5368bc86c4e1a9fcfe588fd1f14ee8","creator":"system","file_name":"IST-2018-1037-v1+1_CoreCavity-AuthorVersion.pdf","file_size":104225664,"file_id":"5360","date_created":"2018-12-12T10:18:38Z","access_level":"open_access","date_updated":"2020-07-14T12:44:38Z"},{"file_size":377743553,"file_name":"IST-2018-1037-v1+2_CoreCavity-Supplemental.zip","creator":"system","checksum":"3861e693ba47c51f3ec7b7867d573a61","relation":"main_file","content_type":"application/zip","access_level":"open_access","date_updated":"2020-07-14T12:44:38Z","file_id":"5361","date_created":"2018-12-12T10:18:39Z"},{"file_id":"5362","date_created":"2018-12-12T10:18:41Z","date_updated":"2020-07-14T12:44:38Z","access_level":"open_access","checksum":"490040c685ed869536e2a18f5a906b94","content_type":"video/vnd.objectvideo","relation":"main_file","file_name":"IST-2018-1037-v1+3_CoreCavity-Video.mp4","file_size":162634396,"creator":"system"},{"checksum":"be7fc8b229adda727419b6504b3b9352","content_type":"image/jpeg","relation":"main_file","file_name":"IST-2018-1037-v1+4_CoreCavity-RepresentativeImage.jpg","file_size":527972,"creator":"system","file_id":"5363","date_created":"2018-12-12T10:18:42Z","access_level":"open_access","date_updated":"2020-07-14T12:44:38Z"}],"abstract":[{"lang":"eng","text":"Molding is a popular mass production method, in which the initial expenses for the mold are offset by the low per-unit production cost. However, the physical fabrication constraints of the molding technique commonly restrict the shape of moldable objects. For a complex shape, a decomposition of the object into moldable parts is a common strategy to address these constraints, with plastic model kits being a popular and illustrative example. However, conducting such a decomposition requires considerable expertise, and it depends on the technical aspects of the fabrication technique, as well as aesthetic considerations. We present an interactive technique to create such decompositions for two-piece molding, in which each part of the object is cast between two rigid mold pieces. Given the surface description of an object, we decompose its thin-shell equivalent into moldable parts by first performing a coarse decomposition and then utilizing an active contour model for the boundaries between individual parts. Formulated as an optimization problem, the movement of the contours is guided by an energy reflecting fabrication constraints to ensure the moldability of each part. Simultaneously, the user is provided with editing capabilities to enforce aesthetic guidelines. Our interactive interface provides control of the contour positions by allowing, for example, the alignment of part boundaries with object features. Our technique enables a novel workflow, as it empowers novice users to explore the design space, and it generates fabrication-ready two-piece molds that can be used either for casting or industrial injection molding of free-form objects."}],"oa":1,"publisher":"ACM","ec_funded":1,"has_accepted_license":"1","author":[{"last_name":"Nakashima","full_name":"Nakashima, Kazutaka","first_name":"Kazutaka"},{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","first_name":"Thomas","last_name":"Auzinger"},{"last_name":"Iarussi","first_name":"Emmanuel","id":"33F19F16-F248-11E8-B48F-1D18A9856A87","full_name":"Iarussi, Emmanuel"},{"first_name":"Ran","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X","last_name":"Zhang"},{"first_name":"Takeo","full_name":"Igarashi, Takeo","last_name":"Igarashi"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","first_name":"Bernd"}],"issue":"4","intvolume":"        37","external_id":{"isi":["000448185000096"]},"language":[{"iso":"eng"}],"quality_controlled":"1","file_date_updated":"2020-07-14T12:44:38Z","citation":{"chicago":"Nakashima, Kazutaka, Thomas Auzinger, Emmanuel Iarussi, Ran Zhang, Takeo Igarashi, and Bernd Bickel. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” <i>ACM Transaction on Graphics</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3197517.3201341\">https://doi.org/10.1145/3197517.3201341</a>.","short":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, B. Bickel, ACM Transaction on Graphics 37 (2018).","mla":"Nakashima, Kazutaka, et al. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” <i>ACM Transaction on Graphics</i>, vol. 37, no. 4, 135, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3197517.3201341\">10.1145/3197517.3201341</a>.","ista":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. 2018. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 37(4), 135.","ieee":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, and B. Bickel, “CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds,” <i>ACM Transaction on Graphics</i>, vol. 37, no. 4. ACM, 2018.","apa":"Nakashima, K., Auzinger, T., Iarussi, E., Zhang, R., Igarashi, T., &#38; Bickel, B. (2018). CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. <i>ACM Transaction on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3197517.3201341\">https://doi.org/10.1145/3197517.3201341</a>","ama":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. <i>ACM Transaction on Graphics</i>. 2018;37(4). doi:<a href=\"https://doi.org/10.1145/3197517.3201341\">10.1145/3197517.3201341</a>"},"publication_status":"published","status":"public","date_published":"2018-08-04T00:00:00Z","year":"2018","month":"08","type":"journal_article","oa_version":"Submitted Version","pubrep_id":"1037","department":[{"_id":"BeBi"}],"isi":1,"ddc":["004","516","670"],"scopus_import":"1","article_processing_charge":"No","publist_id":"8044","article_number":"135","doi":"10.1145/3197517.3201341","day":"04","volume":37,"project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"},{"grant_number":"642841","name":"Distributed 3D Object Design","_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"_id":"12"},{"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by/4.0/","intvolume":"        31","issue":"2","author":[{"full_name":"Flandoli, Franco","first_name":"Franco","last_name":"Flandoli"},{"full_name":"Russo, Francesco","first_name":"Francesco","last_name":"Russo"},{"id":"47491882-F248-11E8-B48F-1D18A9856A87","full_name":"Zanco, Giovanni A","first_name":"Giovanni A","last_name":"Zanco"}],"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000432743300007"]},"year":"2018","date_published":"2018-06-01T00:00:00Z","publication_status":"published","status":"public","corr_author":"1","file_date_updated":"2020-07-14T12:44:39Z","citation":{"mla":"Flandoli, Franco, et al. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” <i>Journal of Theoretical Probability</i>, vol. 31, no. 2, Springer, 2018, pp. 789–826, doi:<a href=\"https://doi.org/10.1007/s10959-016-0724-2\">10.1007/s10959-016-0724-2</a>.","ista":"Flandoli F, Russo F, Zanco GA. 2018. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 31(2), 789–826.","apa":"Flandoli, F., Russo, F., &#38; Zanco, G. A. (2018). Infinite-dimensional calculus under weak spatial regularity of the processes. <i>Journal of Theoretical Probability</i>. Springer. <a href=\"https://doi.org/10.1007/s10959-016-0724-2\">https://doi.org/10.1007/s10959-016-0724-2</a>","ieee":"F. Flandoli, F. Russo, and G. A. Zanco, “Infinite-dimensional calculus under weak spatial regularity of the processes,” <i>Journal of Theoretical Probability</i>, vol. 31, no. 2. Springer, pp. 789–826, 2018.","ama":"Flandoli F, Russo F, Zanco GA. Infinite-dimensional calculus under weak spatial regularity of the processes. <i>Journal of Theoretical Probability</i>. 2018;31(2):789-826. doi:<a href=\"https://doi.org/10.1007/s10959-016-0724-2\">10.1007/s10959-016-0724-2</a>","chicago":"Flandoli, Franco, Francesco Russo, and Giovanni A Zanco. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” <i>Journal of Theoretical Probability</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s10959-016-0724-2\">https://doi.org/10.1007/s10959-016-0724-2</a>.","short":"F. Flandoli, F. Russo, G.A. Zanco, Journal of Theoretical Probability 31 (2018) 789–826."},"date_created":"2018-12-11T11:50:45Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The second named author benefited partially from the support of the “FMJH Program Gaspard Monge in Optimization and Operations Research” (Project 2014-1607H). He is also grateful for the invitation to the Department of Mathematics of the University of Pisa. The third named author is grateful for the invitation to ENSTA.","title":"Infinite-dimensional calculus under weak spatial regularity of the processes","publication":"Journal of Theoretical Probability","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T09:36:02Z","oa":1,"abstract":[{"text":"Two generalizations of Itô formula to infinite-dimensional spaces are given.\r\nThe first one, in Hilbert spaces, extends the classical one by taking advantage of\r\ncancellations when they occur in examples and it is applied to the case of a group\r\ngenerator. The second one, based on the previous one and a limit procedure, is an Itô\r\nformula in a special class of Banach spaces having a product structure with the noise\r\nin a Hilbert component; again the key point is the extension due to a cancellation. This\r\nextension to Banach spaces and in particular the specific cancellation are motivated\r\nby path-dependent Itô calculus.","lang":"eng"}],"file":[{"date_updated":"2020-07-14T12:44:39Z","access_level":"open_access","date_created":"2018-12-12T10:17:13Z","file_id":"5266","file_name":"IST-2016-712-v1+1_s10959-016-0724-2.pdf","file_size":671125,"creator":"system","checksum":"47686d58ec21c164540f1a980ff2163f","relation":"main_file","content_type":"application/pdf"}],"publisher":"Springer","publist_id":"6119","doi":"10.1007/s10959-016-0724-2","tmp":{"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","image":"/images/cc_by.png"},"day":"01","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"_id":"1215","volume":31,"oa_version":"Published Version","type":"journal_article","month":"06","pubrep_id":"712","scopus_import":"1","isi":1,"ddc":["519"],"department":[{"_id":"JaMa"}],"page":"789-826","article_processing_charge":"Yes (via OA deal)"},{"publisher":"IEEE","ec_funded":1,"abstract":[{"text":"The accuracy of information retrieval systems is often measured using complex loss functions such as the average precision (AP) or the normalized discounted cumulative gain (NDCG). Given a set of positive and negative samples, the parameters of a retrieval system can be estimated by minimizing these loss functions. However, the non-differentiability and non-decomposability of these loss functions does not allow for simple gradient based optimization algorithms. This issue is generally circumvented by either optimizing a structured hinge-loss upper bound to the loss function or by using asymptotic methods like the direct-loss minimization framework. Yet, the high computational complexity of loss-augmented inference, which is necessary for both the frameworks, prohibits its use in large training data sets. To alleviate this deficiency, we present a novel quicksort flavored algorithm for a large class of non-decomposable loss functions. We provide a complete characterization of the loss functions that are amenable to our algorithm, and show that it includes both AP and NDCG based loss functions. Furthermore, we prove that no comparison based algorithm can improve upon the computational complexity of our approach asymptotically. We demonstrate the effectiveness of our approach in the context of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning models for a variety of vision tasks. We show that our approach provides significantly better results than simpler decomposable loss functions, while requiring a comparable training time.","lang":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.08269"}],"arxiv":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2024-11-04T13:52:32Z","title":"Efficient optimization for rank-based loss functions","publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","date_created":"2018-12-11T11:45:33Z","citation":{"mla":"Mohapatra, Pritish, et al. “Efficient Optimization for Rank-Based Loss Functions.” <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2018, pp. 3693–701, doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00389\">10.1109/cvpr.2018.00389</a>.","ista":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. 2018. Efficient optimization for rank-based loss functions. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 3693–3701.","apa":"Mohapatra, P., Rolinek, M., Jawahar, C. V., Kolmogorov, V., &#38; Kumar, M. P. (2018). Efficient optimization for rank-based loss functions. In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 3693–3701). Salt Lake City, UT, USA: IEEE. <a href=\"https://doi.org/10.1109/cvpr.2018.00389\">https://doi.org/10.1109/cvpr.2018.00389</a>","ieee":"P. Mohapatra, M. Rolinek, C. V. Jawahar, V. Kolmogorov, and M. P. Kumar, “Efficient optimization for rank-based loss functions,” in <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Salt Lake City, UT, USA, 2018, pp. 3693–3701.","ama":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. Efficient optimization for rank-based loss functions. In: <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2018:3693-3701. doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00389\">10.1109/cvpr.2018.00389</a>","chicago":"Mohapatra, Pritish, Michal Rolinek, C V Jawahar, Vladimir Kolmogorov, and M Pawan Kumar. “Efficient Optimization for Rank-Based Loss Functions.” In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 3693–3701. IEEE, 2018. <a href=\"https://doi.org/10.1109/cvpr.2018.00389\">https://doi.org/10.1109/cvpr.2018.00389</a>.","short":"P. Mohapatra, M. Rolinek, C.V. Jawahar, V. Kolmogorov, M.P. Kumar, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–3701."},"year":"2018","date_published":"2018-06-28T00:00:00Z","status":"public","publication_status":"published","external_id":{"arxiv":["1604.08269"],"isi":["000457843603087"]},"language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"last_name":"Mohapatra","full_name":"Mohapatra, Pritish","first_name":"Pritish"},{"last_name":"Rolinek","first_name":"Michal","full_name":"Rolinek, Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jawahar","full_name":"Jawahar, C V","first_name":"C V"},{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"},{"full_name":"Kumar, M Pawan","first_name":"M Pawan","last_name":"Kumar"}],"article_processing_charge":"No","department":[{"_id":"VlKo"}],"page":"3693-3701","scopus_import":"1","isi":1,"type":"conference","month":"06","oa_version":"Preprint","conference":{"location":"Salt Lake City, UT, USA","name":"CVPR: Conference on Computer Vision and Pattern Recognition","end_date":"2018-06-22","start_date":"2018-06-18"},"_id":"273","project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"day":"28","doi":"10.1109/cvpr.2018.00389","publication_identifier":{"isbn":["9781538664209"]}},{"type":"journal_article","month":"04","oa_version":"Published Version","department":[{"_id":"MiSi"},{"_id":"Bio"}],"page":"2205 - 2221","scopus_import":"1","ddc":["570"],"isi":1,"article_processing_charge":"No","publist_id":"7627","day":"12","tmp":{"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","image":"/images/cc_by.png"},"doi":"10.1083/jcb.201612051","_id":"275","project":[{"call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"Y 564-B12"},{"call_identifier":"FP7","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","_id":"25A603A2-B435-11E9-9278-68D0E5697425"}],"volume":217,"title":"Lymphatic exosomes promote dendritic cell migration along guidance cues","publication":"Journal of Cell Biology","date_created":"2018-12-11T11:45:33Z","acknowledgement":"M. Brown was supported by the Cell Communication in Health and Disease Graduate Study Program of the Austrian Science Fund and Medizinische Universität Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland postdoctoral research grant (287853). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 668036 (RELENT).","pmid":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2025-04-14T13:10:20Z","abstract":[{"lang":"eng","text":"Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified &gt; 1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments."}],"file":[{"date_created":"2018-12-17T12:50:07Z","file_id":"5704","access_level":"open_access","date_updated":"2020-07-14T12:45:45Z","checksum":"9c7eba51a35c62da8c13f98120b64df4","content_type":"application/pdf","relation":"main_file","file_size":2252043,"file_name":"2018_JournalCellBiology_Brown.pdf","creator":"dernst"}],"oa":1,"publisher":"Rockefeller University Press","ec_funded":1,"has_accepted_license":"1","author":[{"first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus","last_name":"Brown"},{"last_name":"Johnson","full_name":"Johnson, Louise","first_name":"Louise"},{"last_name":"Leone","full_name":"Leone, Dario","first_name":"Dario"},{"full_name":"Májek, Peter","first_name":"Peter","last_name":"Májek"},{"first_name":"Kari","full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri"},{"last_name":"Senfter","full_name":"Senfter, Daniel","first_name":"Daniel"},{"last_name":"Bukosza","first_name":"Nora","full_name":"Bukosza, Nora"},{"last_name":"Schachner","full_name":"Schachner, Helga","first_name":"Helga"},{"full_name":"Asfour, Gabriele","first_name":"Gabriele","last_name":"Asfour"},{"full_name":"Langer, Brigitte","first_name":"Brigitte","last_name":"Langer"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild"},{"first_name":"Katja","full_name":"Parapatics, Katja","last_name":"Parapatics"},{"last_name":"Hong","full_name":"Hong, Young","first_name":"Young"},{"last_name":"Bennett","full_name":"Bennett, Keiryn","first_name":"Keiryn"},{"last_name":"Kain","full_name":"Kain, Renate","first_name":"Renate"},{"full_name":"Detmar, Michael","first_name":"Michael","last_name":"Detmar"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"last_name":"Jackson","full_name":"Jackson, David","first_name":"David"},{"full_name":"Kerjaschki, Dontscho","first_name":"Dontscho","last_name":"Kerjaschki"}],"intvolume":"       217","issue":"6","external_id":{"pmid":["29650776"],"isi":["000438077800026"]},"language":[{"iso":"eng"}],"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:45Z","corr_author":"1","citation":{"chicago":"Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri, Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1083/jcb.201612051\">https://doi.org/10.1083/jcb.201612051</a>.","short":"M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza, H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett, R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology 217 (2018) 2205–2221.","mla":"Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” <i>Journal of Cell Biology</i>, vol. 217, no. 6, Rockefeller University Press, 2018, pp. 2205–21, doi:<a href=\"https://doi.org/10.1083/jcb.201612051\">10.1083/jcb.201612051</a>.","ista":"Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N, Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K, Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6), 2205–2221.","ama":"Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell migration along guidance cues. <i>Journal of Cell Biology</i>. 2018;217(6):2205-2221. doi:<a href=\"https://doi.org/10.1083/jcb.201612051\">10.1083/jcb.201612051</a>","ieee":"M. Brown <i>et al.</i>, “Lymphatic exosomes promote dendritic cell migration along guidance cues,” <i>Journal of Cell Biology</i>, vol. 217, no. 6. Rockefeller University Press, pp. 2205–2221, 2018.","apa":"Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D., … Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along guidance cues. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201612051\">https://doi.org/10.1083/jcb.201612051</a>"},"year":"2018","date_published":"2018-04-12T00:00:00Z","status":"public","publication_status":"published"},{"article_processing_charge":"No","department":[{"_id":"MiSi"}],"ddc":["570"],"isi":1,"scopus_import":"1","month":"06","type":"journal_article","oa_version":"Published Version","volume":13,"_id":"276","tmp":{"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","image":"/images/cc_by.png"},"doi":"10.1371/journal.pone.0198330","day":"07","publist_id":"7626","article_number":"e0198330","article_type":"original","publisher":"Public Library of Science","abstract":[{"text":"Directed migration of cells relies on their ability to sense directional guidance cues and to interact with pericellular structures in order to transduce contractile cytoskeletal- into mechanical forces. These biomechanical processes depend highly on microenvironmental factors such as exposure to 2D surfaces or 3D matrices. In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell migration are mostly derived from intravital microscopy or collagen-based in vitro assays. Both approaches offer only limited controlla-bility of experimental conditions. Here, we developed an automated microfluidic system that allows positioning of cells in 3D microenvironments containing highly controlled diffusion-based chemokine gradients. Tracking migration in such gradients was feasible in real time at the single cell level. Moreover, the setup allowed on-chip immunocytochemistry and thus linking of functional with phenotypical properties in individual cells. Spatially defined retrieval of cells from the device allows down-stream off-chip analysis. Using dendritic cells as a model, our setup specifically allowed us for the first time to quantitate key migration characteristics of cells exposed to identical gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration properties between 2D and 3D migration were distinct. Morphological features of cells migrating in an in vitro 3D environment were similar to those of cells migrating in animal tissues, but different from cells migrating on a surface. Our system thus offers a highly controllable in vitro-mimic of a 3D environment that cells traffic in vivo.","lang":"eng"}],"file":[{"date_updated":"2020-07-14T12:45:45Z","access_level":"open_access","date_created":"2018-12-17T14:10:32Z","file_id":"5709","creator":"dernst","file_size":7682167,"file_name":"2018_Plos_Frick.pdf","relation":"main_file","content_type":"application/pdf","checksum":"95fc5dc3938b3ad3b7697d10c83cc143"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-13T09:00:15Z","publication":"PLoS One","title":"Nano-scale microfluidics to study 3D chemotaxis at the single cell level","acknowledgement":"This work was supported by the Swiss National Science Foundation (MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863 to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.), a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409) to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","date_created":"2018-12-11T11:45:34Z","file_date_updated":"2020-07-14T12:45:45Z","citation":{"ieee":"C. Frick <i>et al.</i>, “Nano-scale microfluidics to study 3D chemotaxis at the single cell level,” <i>PLoS One</i>, vol. 13, no. 6. Public Library of Science, 2018.","apa":"Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M., … Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single cell level. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0198330\">https://doi.org/10.1371/journal.pone.0198330</a>","ama":"Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. <i>PLoS One</i>. 2018;13(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0198330\">10.1371/journal.pone.0198330</a>","ista":"Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 13(6), e0198330.","mla":"Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” <i>PLoS One</i>, vol. 13, no. 6, e0198330, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pone.0198330\">10.1371/journal.pone.0198330</a>.","short":"C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T. Schroeder, M. Mehling, PLoS One 13 (2018).","chicago":"Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” <i>PLoS One</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pone.0198330\">https://doi.org/10.1371/journal.pone.0198330</a>."},"status":"public","publication_status":"published","year":"2018","date_published":"2018-06-07T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"isi":["000434384900031"]},"quality_controlled":"1","author":[{"last_name":"Frick","first_name":"Corina","full_name":"Frick, Corina"},{"full_name":"Dettinger, Philip","first_name":"Philip","last_name":"Dettinger"},{"orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg","first_name":"Jörg","last_name":"Renkawitz"},{"first_name":"Annaïse","full_name":"Jauch, Annaïse","last_name":"Jauch"},{"last_name":"Berger","first_name":"Christoph","full_name":"Berger, Christoph"},{"last_name":"Recher","first_name":"Mike","full_name":"Recher, Mike"},{"full_name":"Schroeder, Timm","first_name":"Timm","last_name":"Schroeder"},{"last_name":"Mehling","first_name":"Matthias","full_name":"Mehling, Matthias"}],"issue":"6","intvolume":"        13","has_accepted_license":"1"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-08T13:21:05Z","publication":"Plant Molecular Biology","title":"An armadillo-domain protein participates in a telomerase interaction network","date_created":"2018-12-11T11:45:34Z","publisher":"Springer","abstract":[{"text":"Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2. Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions. We previously identified interaction of the C-terminal domain of Arabidopsis telomerase reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing protein. Here we explore protein–protein interactions of the ARM protein, AtTERT domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both the N- and C-terminal domains of AtTERT in different cellular compartments. ARM interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly or through interaction with POT1a. The putative human ARM homolog co-precipitates telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis arm mutants shows no obvious changes in telomere length or telomerase activity, suggesting that ARM is not essential for telomere maintenance. The observed interactions with telomerase and Myb-like domain proteins (TRF-like family I) may therefore reflect possible non-telomeric functions. Transcript levels of several DNA repair and ribosomal genes are affected in arm mutants, and ARM, likely in association with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric functions of telomerase, and can also perform its own telomerase-independent functions.","lang":"eng"}],"file":[{"file_size":1150679,"file_name":"2018_PlantMolecBio_Dokladal.pdf","creator":"dernst","checksum":"451ae47616e6af2533099f596b2a47fb","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:45:45Z","access_level":"open_access","file_id":"7834","date_created":"2020-05-14T12:23:08Z"}],"oa":1,"author":[{"full_name":"Dokládal, Ladislav","first_name":"Ladislav","last_name":"Dokládal"},{"last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","full_name":"Honys, David","last_name":"Honys"},{"full_name":"Dupláková, Nikoleta","first_name":"Nikoleta","last_name":"Dupláková"},{"last_name":"Lee","full_name":"Lee, Lan","first_name":"Lan"},{"last_name":"Gelvin","full_name":"Gelvin, Stanton","first_name":"Stanton"},{"full_name":"Sýkorová, Eva","first_name":"Eva","last_name":"Sýkorová"}],"issue":"5","intvolume":"        97","has_accepted_license":"1","citation":{"short":"L. Dokládal, E. Benková, D. Honys, N. Dupláková, L. Lee, S. Gelvin, E. Sýkorová, Plant Molecular Biology 97 (2018) 407–420.","chicago":"Dokládal, Ladislav, Eva Benková, David Honys, Nikoleta Dupláková, Lan Lee, Stanton Gelvin, and Eva Sýkorová. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” <i>Plant Molecular Biology</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s11103-018-0747-4\">https://doi.org/10.1007/s11103-018-0747-4</a>.","ieee":"L. Dokládal <i>et al.</i>, “An armadillo-domain protein participates in a telomerase interaction network,” <i>Plant Molecular Biology</i>, vol. 97, no. 5. Springer, pp. 407–420, 2018.","ama":"Dokládal L, Benková E, Honys D, et al. An armadillo-domain protein participates in a telomerase interaction network. <i>Plant Molecular Biology</i>. 2018;97(5):407-420. doi:<a href=\"https://doi.org/10.1007/s11103-018-0747-4\">10.1007/s11103-018-0747-4</a>","apa":"Dokládal, L., Benková, E., Honys, D., Dupláková, N., Lee, L., Gelvin, S., &#38; Sýkorová, E. (2018). An armadillo-domain protein participates in a telomerase interaction network. <i>Plant Molecular Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s11103-018-0747-4\">https://doi.org/10.1007/s11103-018-0747-4</a>","ista":"Dokládal L, Benková E, Honys D, Dupláková N, Lee L, Gelvin S, Sýkorová E. 2018. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 97(5), 407–420.","mla":"Dokládal, Ladislav, et al. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” <i>Plant Molecular Biology</i>, vol. 97, no. 5, Springer, 2018, pp. 407–20, doi:<a href=\"https://doi.org/10.1007/s11103-018-0747-4\">10.1007/s11103-018-0747-4</a>."},"file_date_updated":"2020-07-14T12:45:45Z","publication_status":"published","status":"public","date_published":"2018-06-12T00:00:00Z","year":"2018","language":[{"iso":"eng"}],"external_id":{"isi":["000438981700009"]},"quality_controlled":"1","month":"06","type":"journal_article","oa_version":"Submitted Version","article_processing_charge":"No","page":"407 - 420","department":[{"_id":"EvBe"}],"ddc":["580"],"isi":1,"scopus_import":"1","publist_id":"7625","article_type":"original","volume":97,"_id":"277","doi":"10.1007/s11103-018-0747-4","day":"12"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2025-04-15T08:30:30Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"9811"},{"status":"public","relation":"research_data","id":"9812"}]},"publication":"Genome Biology","title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","date_created":"2018-12-11T11:45:35Z","publisher":"BioMed Central","ec_funded":1,"abstract":[{"lang":"eng","text":"Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments."}],"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:45:47Z","date_created":"2018-12-17T14:05:01Z","file_id":"5708","creator":"dernst","file_name":"2018_GenomeBiology_Zapata.pdf","file_size":1414722,"content_type":"application/pdf","relation":"main_file","checksum":"f3e4922486bd9bf1483271bdbed394a7"}],"oa":1,"author":[{"full_name":"Zapata, Luis","first_name":"Luis","last_name":"Zapata"},{"first_name":"Oriol","full_name":"Pich, Oriol","last_name":"Pich"},{"last_name":"Serrano","full_name":"Serrano, Luis","first_name":"Luis"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"last_name":"Ossowski","full_name":"Ossowski, Stephan","first_name":"Stephan"},{"full_name":"Schaefer, Martin","first_name":"Martin","last_name":"Schaefer"}],"intvolume":"        19","has_accepted_license":"1","file_date_updated":"2020-07-14T12:45:47Z","citation":{"mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” <i>Genome Biology</i>, vol. 19, 67, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>.","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” <i>Genome Biology</i>, vol. 19. BioMed Central, 2018.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. <i>Genome Biology</i>. 2018;19. doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” <i>Genome Biology</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018)."},"publication_status":"published","status":"public","date_published":"2018-05-31T00:00:00Z","year":"2018","external_id":{"isi":["000433986200001"]},"language":[{"iso":"eng"}],"quality_controlled":"1","month":"05","type":"journal_article","oa_version":"Published Version","article_processing_charge":"No","department":[{"_id":"FyKo"}],"ddc":["570"],"isi":1,"scopus_import":"1","publist_id":"7620","article_number":"67","volume":19,"project":[{"call_identifier":"FP7","_id":"26120F5C-B435-11E9-9278-68D0E5697425","grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution"}],"_id":"279","day":"31","tmp":{"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","image":"/images/cc_by.png"},"doi":"10.1186/s13059-018-1434-0"},{"citation":{"mla":"Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” <i>Nature Plants</i>, vol. 4, no. 6, Nature Publishing Group, 2018, pp. 365–75, doi:<a href=\"https://doi.org/10.1038/s41477-018-0160-7\">10.1038/s41477-018-0160-7</a>.","apa":"Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., … Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0160-7\">https://doi.org/10.1038/s41477-018-0160-7</a>","ieee":"Z. Gao <i>et al.</i>, “KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis,” <i>Nature Plants</i>, vol. 4, no. 6. Nature Publishing Group, pp. 365–375, 2018.","ama":"Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. <i>Nature Plants</i>. 2018;4(6):365-375. doi:<a href=\"https://doi.org/10.1038/s41477-018-0160-7\">10.1038/s41477-018-0160-7</a>","ista":"Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375.","chicago":"Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans, Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0160-7\">https://doi.org/10.1038/s41477-018-0160-7</a>.","short":"Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle, K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375."},"date_published":"2018-05-28T00:00:00Z","year":"2018","publication_status":"published","status":"public","external_id":{"isi":["000435571000017"]},"language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"last_name":"Gao","full_name":"Gao, Zhen","first_name":"Zhen"},{"full_name":"Daneva, Anna","first_name":"Anna","last_name":"Daneva"},{"full_name":"Salanenka, Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","first_name":"Yuliya","last_name":"Salanenka"},{"last_name":"Van Durme","first_name":"Matthias","full_name":"Van Durme, Matthias"},{"first_name":"Marlies","full_name":"Huysmans, Marlies","last_name":"Huysmans"},{"last_name":"Lin","first_name":"Zongcheng","full_name":"Lin, Zongcheng"},{"full_name":"De Winter, Freya","first_name":"Freya","last_name":"De Winter"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"last_name":"Karimi","full_name":"Karimi, Mansour","first_name":"Mansour"},{"full_name":"Van De Velde, Jan","first_name":"Jan","last_name":"Van De Velde"},{"first_name":"Klaas","full_name":"Vandepoele, Klaas","last_name":"Vandepoele"},{"first_name":"Davy","full_name":"Van De Walle, Davy","last_name":"Van De Walle"},{"last_name":"Dewettinck","first_name":"Koen","full_name":"Dewettinck, Koen"},{"full_name":"Lambrecht, Bart","first_name":"Bart","last_name":"Lambrecht"},{"full_name":"Nowack, Moritz","first_name":"Moritz","last_name":"Nowack"}],"intvolume":"         4","issue":"6","publisher":"Nature Publishing Group","abstract":[{"text":"Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span.","lang":"eng"}],"date_updated":"2023-09-13T08:24:17Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis","publication":"Nature Plants","date_created":"2018-12-11T11:45:35Z","acknowledgement":"We gratefully acknowledge funding from the Chinese Scholarship Council (CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek (FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.), the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH (project number 639234 to M.K.N.).","_id":"280","volume":4,"doi":"10.1038/s41477-018-0160-7","day":"28","publist_id":"7619","article_processing_charge":"No","department":[{"_id":"JiFr"}],"page":"365 - 375","scopus_import":"1","isi":1,"type":"journal_article","month":"05","oa_version":"None"},{"language":[{"iso":"eng"}],"external_id":{"isi":["000440014100020"]},"quality_controlled":"1","citation":{"chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.301018\">https://doi.org/10.1534/genetics.118.301018</a>.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” <i>Genetics</i>, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:<a href=\"https://doi.org/10.1534/genetics.118.301018\">10.1534/genetics.118.301018</a>.","ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” <i>Genetics</i>, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018.","ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. <i>Genetics</i>. 2018;209(4):1279-1303. doi:<a href=\"https://doi.org/10.1534/genetics.118.301018\">10.1534/genetics.118.301018</a>","apa":"Sachdeva, H., &#38; Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.301018\">https://doi.org/10.1534/genetics.118.301018</a>","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303."},"publication_status":"published","status":"public","year":"2018","date_published":"2018-08-01T00:00:00Z","author":[{"last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani","first_name":"Himani"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"}],"issue":"4","intvolume":"       209","abstract":[{"lang":"eng","text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci."}],"oa":1,"publisher":"Genetics Society of America","publication":"Genetics","title":"Introgression of a block of genome under infinitesimal selection","date_created":"2018-12-11T11:45:36Z","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/early/2017/11/30/227082"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-13T08:22:32Z","day":"01","doi":"10.1534/genetics.118.301018","volume":209,"_id":"282","publist_id":"7617","page":"1279 - 1303","department":[{"_id":"NiBa"}],"isi":1,"scopus_import":"1","article_processing_charge":"No","month":"08","type":"journal_article","oa_version":"Submitted Version"},{"has_accepted_license":"1","author":[{"first_name":"Rosa Maria","full_name":"Ceinos, Rosa Maria","last_name":"Ceinos"},{"first_name":"Elena","full_name":"Frigato, Elena","last_name":"Frigato"},{"first_name":"Cristina","full_name":"Pagano, Cristina","last_name":"Pagano"},{"last_name":"Frohlich","first_name":"Nadine","full_name":"Frohlich, Nadine"},{"last_name":"Negrini","first_name":"Pietro","full_name":"Negrini, Pietro"},{"last_name":"Cavallari","first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","full_name":"Cavallari, Nicola"},{"first_name":"Daniela","full_name":"Vallone, Daniela","last_name":"Vallone"},{"last_name":"Fuselli","first_name":"Silvia","full_name":"Fuselli, Silvia"},{"last_name":"Bertolucci","full_name":"Bertolucci, Cristiano","first_name":"Cristiano"},{"first_name":"Nicholas S","full_name":"Foulkes, Nicholas S","last_name":"Foulkes"}],"issue":"1","intvolume":"         8","language":[{"iso":"eng"}],"external_id":{"isi":["000434640800008"]},"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:49Z","citation":{"mla":"Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” <i>Scientific Reports</i>, vol. 8, no. 1, 8754, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-27080-2\">10.1038/s41598-018-27080-2</a>.","ieee":"R. M. Ceinos <i>et al.</i>, “Mutations in blind cavefish target the light regulated circadian clock gene period 2,” <i>Scientific Reports</i>, vol. 8, no. 1. Nature Publishing Group, 2018.","apa":"Ceinos, R. M., Frigato, E., Pagano, C., Frohlich, N., Negrini, P., Cavallari, N., … Foulkes, N. S. (2018). Mutations in blind cavefish target the light regulated circadian clock gene period 2. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-018-27080-2\">https://doi.org/10.1038/s41598-018-27080-2</a>","ama":"Ceinos RM, Frigato E, Pagano C, et al. Mutations in blind cavefish target the light regulated circadian clock gene period 2. <i>Scientific Reports</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-27080-2\">10.1038/s41598-018-27080-2</a>","ista":"Ceinos RM, Frigato E, Pagano C, Frohlich N, Negrini P, Cavallari N, Vallone D, Fuselli S, Bertolucci C, Foulkes NS. 2018. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 8(1), 8754.","chicago":"Ceinos, Rosa Maria, Elena Frigato, Cristina Pagano, Nadine Frohlich, Pietro Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci, and Nicholas S Foulkes. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” <i>Scientific Reports</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41598-018-27080-2\">https://doi.org/10.1038/s41598-018-27080-2</a>.","short":"R.M. Ceinos, E. Frigato, C. Pagano, N. Frohlich, P. Negrini, N. Cavallari, D. Vallone, S. Fuselli, C. Bertolucci, N.S. Foulkes, Scientific Reports 8 (2018)."},"status":"public","publication_status":"published","date_published":"2018-06-08T00:00:00Z","year":"2018","publication":"Scientific Reports","title":"Mutations in blind cavefish target the light regulated circadian clock gene period 2","date_created":"2018-12-11T11:45:36Z","date_updated":"2023-09-13T08:59:27Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors.","lang":"eng"}],"file":[{"file_id":"5707","date_created":"2018-12-17T13:04:46Z","date_updated":"2020-07-14T12:45:49Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"9c3942d772f84f3df032ffde0ed9a8ea","creator":"dernst","file_size":1855324,"file_name":"2018_ScientificReports_Ceinos.pdf"}],"oa":1,"publisher":"Nature Publishing Group","publist_id":"7616","article_number":"8754","tmp":{"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","image":"/images/cc_by.png"},"day":"08","doi":"10.1038/s41598-018-27080-2","volume":8,"_id":"283","month":"06","type":"journal_article","oa_version":"Published Version","department":[{"_id":"EvBe"}],"isi":1,"ddc":["570"],"scopus_import":"1","article_processing_charge":"No"},{"scopus_import":"1","department":[{"_id":"LaEr"}],"page":"65 - 80","article_processing_charge":"No","oa_version":"Preprint","type":"journal_article","month":"06","publication_identifier":{"eissn":["2064-8316"],"issn":["0001-6969"]},"day":"04","doi":"10.14232/actasm-018-753-y","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"_id":"284","volume":84,"article_type":"original","publist_id":"7615","oa":1,"abstract":[{"lang":"eng","text":"Borel probability measures living on metric spaces are fundamental\r\nmathematical objects. There are several meaningful distance functions that make the collection of the probability measures living on a certain space a metric space. We are interested in the description of the structure of the isometries of such metric spaces. We overview some of the recent results of the topic and we also provide some new ones concerning the Wasserstein distance. More specifically, we consider the space of all Borel probability measures on the unit sphere of a Euclidean space endowed with the Wasserstein metric W_p for arbitrary p &gt;= 1, and we show that the action of a Wasserstein isometry on the set of Dirac measures is induced by an isometry of the underlying unit sphere."}],"ec_funded":1,"publisher":"Springer Nature","date_created":"2018-12-11T11:45:36Z","acknowledgement":"The author was supported by the ISTFELLOW program of the Institute of Science and Technol- ogy Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office, NKFIH (grant no. K124152).","title":"Maps on probability measures preserving certain distances - a survey and some new results","publication":"Acta Scientiarum Mathematicarum","date_updated":"2025-04-15T06:50:21Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.03305"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"arxiv":["1802.03305"]},"date_published":"2018-06-04T00:00:00Z","year":"2018","status":"public","publication_status":"published","citation":{"short":"D. Virosztek, Acta Scientiarum Mathematicarum 84 (2018) 65–80.","chicago":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” <i>Acta Scientiarum Mathematicarum</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.14232/actasm-018-753-y\">https://doi.org/10.14232/actasm-018-753-y</a>.","ieee":"D. Virosztek, “Maps on probability measures preserving certain distances - a survey and some new results,” <i>Acta Scientiarum Mathematicarum</i>, vol. 84, no. 1–2. Springer Nature, pp. 65–80, 2018.","ama":"Virosztek D. Maps on probability measures preserving certain distances - a survey and some new results. <i>Acta Scientiarum Mathematicarum</i>. 2018;84(1-2):65-80. doi:<a href=\"https://doi.org/10.14232/actasm-018-753-y\">10.14232/actasm-018-753-y</a>","apa":"Virosztek, D. (2018). Maps on probability measures preserving certain distances - a survey and some new results. <i>Acta Scientiarum Mathematicarum</i>. Springer Nature. <a href=\"https://doi.org/10.14232/actasm-018-753-y\">https://doi.org/10.14232/actasm-018-753-y</a>","ista":"Virosztek D. 2018. Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. 84(1–2), 65–80.","mla":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” <i>Acta Scientiarum Mathematicarum</i>, vol. 84, no. 1–2, Springer Nature, 2018, pp. 65–80, doi:<a href=\"https://doi.org/10.14232/actasm-018-753-y\">10.14232/actasm-018-753-y</a>."},"intvolume":"        84","issue":"1-2","author":[{"last_name":"Virosztek","first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1109-5511","full_name":"Virosztek, Daniel"}]},{"arxiv":1,"date_updated":"2025-07-10T11:52:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"On the treewidth of triangulated 3-manifolds","related_material":{"record":[{"status":"public","relation":"later_version","id":"7093"}]},"date_created":"2018-12-11T11:45:37Z","acknowledgement":"Research of the second author was supported by the Einstein Foundation (project “Einstein Visiting Fellow Santos”) and by the Simons Foundation (“Simons Visiting Professors” program).","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","abstract":[{"lang":"eng","text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how &quot;simple&quot; or &quot;thin&quot; a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth. In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs). We derive these results from work of Agol and of Scharlemann and Thompson, by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 48(k+1) (resp. 4(3k+1))."}],"file":[{"date_created":"2018-12-17T15:32:38Z","file_id":"5713","access_level":"open_access","date_updated":"2020-07-14T12:45:51Z","content_type":"application/pdf","relation":"main_file","checksum":"530d084116778135d5bffaa317479cac","creator":"dernst","file_size":642522,"file_name":"2018_LIPIcs_Huszar.pdf"}],"oa":1,"author":[{"last_name":"Huszár","first_name":"Kristóf","full_name":"Huszár, Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5445-5057"},{"full_name":"Spreer, Jonathan","first_name":"Jonathan","last_name":"Spreer"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"intvolume":"        99","has_accepted_license":"1","alternative_title":["LIPIcs"],"citation":{"ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">10.4230/LIPIcs.SoCG.2018.46</a>","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","apa":"Huszár, K., Spreer, J., &#38; Wagner, U. (2018). On the treewidth of triangulated 3-manifolds (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">https://doi.org/10.4230/LIPIcs.SoCG.2018.46</a>","ista":"Huszár K, Spreer J, Wagner U. 2018. On the treewidth of triangulated 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 46.","mla":"Huszár, Kristóf, et al. <i>On the Treewidth of Triangulated 3-Manifolds</i>. Vol. 99, 46, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">10.4230/LIPIcs.SoCG.2018.46</a>.","short":"K. Huszár, J. Spreer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">https://doi.org/10.4230/LIPIcs.SoCG.2018.46</a>."},"file_date_updated":"2020-07-14T12:45:51Z","date_published":"2018-06-01T00:00:00Z","year":"2018","status":"public","publication_status":"published","external_id":{"arxiv":["1712.00434"]},"language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","month":"06","oa_version":"Submitted Version","article_processing_charge":"No","department":[{"_id":"UlWa"}],"scopus_import":"1","ddc":["516","000"],"publist_id":"7614","article_number":"46","conference":{"start_date":"2018-06-11","end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary"},"_id":"285","volume":99,"tmp":{"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","image":"/images/cc_by.png"},"doi":"10.4230/LIPIcs.SoCG.2018.46","day":"01","publication_identifier":{"issn":["1868-8969"]}},{"ec_funded":1,"publisher":"Wiley","abstract":[{"text":"Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. ","lang":"eng"}],"date_updated":"2025-04-15T07:11:03Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:45:37Z","acknowledgement":"ERC, Grant/Award Number: 250152","title":"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering","publication":"Molecular Ecology Resources","related_material":{"record":[{"id":"5583","relation":"popular_science","status":"public"}]},"year":"2018","date_published":"2018-09-01T00:00:00Z","status":"public","publication_status":"published","citation":{"chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” <i>Molecular Ecology Resources</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/1755-0998.12782\">https://doi.org/10.1111/1755-0998.12782</a>.","short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.","mla":"Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” <i>Molecular Ecology Resources</i>, vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:<a href=\"https://doi.org/10.1111/1755-0998.12782\">10.1111/1755-0998.12782</a>.","apa":"Ellis, T., Field, D., &#38; Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.12782\">https://doi.org/10.1111/1755-0998.12782</a>","ieee":"T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering,” <i>Molecular Ecology Resources</i>, vol. 18, no. 5. Wiley, pp. 988–999, 2018.","ama":"Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. <i>Molecular Ecology Resources</i>. 2018;18(5):988-999. doi:<a href=\"https://doi.org/10.1111/1755-0998.12782\">10.1111/1755-0998.12782</a>","ista":"Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 18(5), 988–999."},"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000441753000007"]},"intvolume":"        18","issue":"5","author":[{"last_name":"Ellis","first_name":"Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas"},{"last_name":"Field","first_name":"David","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"article_processing_charge":"No","scopus_import":"1","isi":1,"department":[{"_id":"NiBa"}],"page":"988 - 999","oa_version":"None","type":"journal_article","month":"09","_id":"286","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"volume":18,"doi":"10.1111/1755-0998.12782","day":"01"},{"volume":23,"project":[{"_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","call_identifier":"H2020"}],"_id":"287","doi":"10.2741/4651","day":"01","article_processing_charge":"No","isi":1,"scopus_import":"1","page":"1391 - 1406","department":[{"_id":"JoFi"}],"oa_version":"Submitted Version","month":"03","type":"journal_article","publication_status":"published","status":"public","year":"2018","date_published":"2018-03-01T00:00:00Z","citation":{"ista":"Salari V, Barzanjeh S, Cifra M, Simon C, Scholkmann F, Alirezaei Z, Tuszynski J. 2018. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 23(8), 1391–1406.","ama":"Salari V, Barzanjeh S, Cifra M, et al. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. <i>Frontiers in Bioscience - Landmark</i>. 2018;23(8):1391-1406. doi:<a href=\"https://doi.org/10.2741/4651\">10.2741/4651</a>","ieee":"V. Salari <i>et al.</i>, “Electromagnetic fields and optomechanics In cancer diagnostics and treatment,” <i>Frontiers in Bioscience - Landmark</i>, vol. 23, no. 8. Frontiers in Bioscience, pp. 1391–1406, 2018.","apa":"Salari, V., Barzanjeh, S., Cifra, M., Simon, C., Scholkmann, F., Alirezaei, Z., &#38; Tuszynski, J. (2018). Electromagnetic fields and optomechanics In cancer diagnostics and treatment. <i>Frontiers in Bioscience - Landmark</i>. Frontiers in Bioscience. <a href=\"https://doi.org/10.2741/4651\">https://doi.org/10.2741/4651</a>","mla":"Salari, Vahid, et al. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” <i>Frontiers in Bioscience - Landmark</i>, vol. 23, no. 8, Frontiers in Bioscience, 2018, pp. 1391–406, doi:<a href=\"https://doi.org/10.2741/4651\">10.2741/4651</a>.","short":"V. Salari, S. Barzanjeh, M. Cifra, C. Simon, F. Scholkmann, Z. Alirezaei, J. Tuszynski, Frontiers in Bioscience - Landmark 23 (2018) 1391–1406.","chicago":"Salari, Vahid, Shabir Barzanjeh, Michal Cifra, Christoph Simon, Felix Scholkmann, Zahra Alirezaei, and Jack Tuszynski. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” <i>Frontiers in Bioscience - Landmark</i>. Frontiers in Bioscience, 2018. <a href=\"https://doi.org/10.2741/4651\">https://doi.org/10.2741/4651</a>."},"quality_controlled":"1","external_id":{"isi":["000439042800001"],"pmid":["29293441"]},"language":[{"iso":"eng"}],"issue":"8","intvolume":"        23","author":[{"full_name":"Salari, Vahid","first_name":"Vahid","last_name":"Salari"},{"last_name":"Barzanjeh","first_name":"Shabir","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cifra, Michal","first_name":"Michal","last_name":"Cifra"},{"last_name":"Simon","full_name":"Simon, Christoph","first_name":"Christoph"},{"last_name":"Scholkmann","full_name":"Scholkmann, Felix","first_name":"Felix"},{"full_name":"Alirezaei, Zahra","first_name":"Zahra","last_name":"Alirezaei"},{"full_name":"Tuszynski, Jack","first_name":"Jack","last_name":"Tuszynski"}],"ec_funded":1,"publisher":"Frontiers in Bioscience","oa":1,"abstract":[{"text":"In this paper, we discuss biological effects of electromagnetic (EM) fields in the context of cancer biology. In particular, we review the nanomechanical properties of microtubules (MTs), the latter being one of the most successful targets for cancer therapy. We propose an investigation on the coupling of electromagnetic radiation to mechanical vibrations of MTs as an important basis for biological and medical applications. In our opinion, optomechanical methods can accurately monitor and control the mechanical properties of isolated MTs in a liquid environment. Consequently, studying nanomechanical properties of MTs may give useful information for future applications to diagnostic and therapeutic technologies involving non-invasive externally applied physical fields. For example, electromagnetic fields or high intensity ultrasound can be used therapeutically avoiding harmful side effects of chemotherapeutic agents or classical radiation therapy.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2024-10-22T09:36:28Z","pmid":1,"main_file_link":[{"url":"https://www.bioscience.org/2018/v23/af/4651/fulltext.htm","open_access":"1"}],"acknowledgement":"The work of SB has been supported by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska Curie grant agreement No MSC-IF 707438 SUPEREOM. JAT gratefully acknowledges funding support from NSERC (Canada) for his research. MC acknowledges support from the Czech Science Foundation, projects 15-17102S and 17-11898S and he participates in COST Action BM1309, CA15211 and bilateral exchange project between Czech and Slovak Academies of Sciences, SAV-15-22.","date_created":"2018-12-11T11:45:37Z","publication":"Frontiers in Bioscience - Landmark","title":"Electromagnetic fields and optomechanics In cancer diagnostics and treatment"}]