--- _id: '11657' 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 runs a factor 7.5× faster on average when using 32 threads. To further speed up computations, we also give a version of our algorithm that performs random edge contractions as preprocessing. This version achieves a lower running time and better parallel scalability at the expense of a higher error rate. article_processing_charge: No article_type: original author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Alexander full_name: Noe, Alexander last_name: Noe - first_name: Christian full_name: Schulz, Christian last_name: Schulz - first_name: Darren full_name: Strash, Darren last_name: Strash citation: ama: Henzinger MH, Noe A, Schulz C, Strash D. Practical minimum cut algorithms. ACM Journal of Experimental Algorithmics. 2018;23:1-22. doi:10.1145/3274662 apa: Henzinger, M. H., Noe, A., Schulz, C., & Strash, D. (2018). Practical minimum cut algorithms. ACM Journal of Experimental Algorithmics. Association for Computing Machinery. https://doi.org/10.1145/3274662 chicago: Henzinger, Monika H, Alexander Noe, Christian Schulz, and Darren Strash. “Practical Minimum Cut Algorithms.” ACM Journal of Experimental Algorithmics. Association for Computing Machinery, 2018. https://doi.org/10.1145/3274662. ieee: M. H. Henzinger, A. Noe, C. Schulz, and D. Strash, “Practical minimum cut algorithms,” ACM Journal of Experimental Algorithmics, vol. 23. Association for Computing Machinery, pp. 1–22, 2018. ista: Henzinger MH, Noe A, Schulz C, Strash D. 2018. Practical minimum cut algorithms. ACM Journal of Experimental Algorithmics. 23, 1–22. mla: Henzinger, Monika H., et al. “Practical Minimum Cut Algorithms.” ACM Journal of Experimental Algorithmics, vol. 23, Association for Computing Machinery, 2018, pp. 1–22, doi:10.1145/3274662. short: M.H. Henzinger, A. Noe, C. Schulz, D. Strash, ACM Journal of Experimental Algorithmics 23 (2018) 1–22. date_created: 2022-07-27T08:28:26Z date_published: 2018-10-01T00:00:00Z date_updated: 2022-09-09T11:32:52Z day: '01' doi: 10.1145/3274662 extern: '1' external_id: arxiv: - '1708.06127' intvolume: ' 23' keyword: - Theoretical Computer Science language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.06127 month: '10' oa: 1 oa_version: Preprint page: 1-22 publication: ACM Journal of Experimental Algorithmics publication_identifier: eissn: - 1084-6654 issn: - 1084-6654 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Practical minimum cut algorithms type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2018' ... --- _id: '11667' abstract: - lang: eng text: The focus of classic mechanism design has been on truthful direct-revelation mechanisms. In the context of combinatorial auctions, the truthful direct-revelation mechanism that maximizes social welfare is the Vickrey-Clarke-Groves mechanism. For many valuation spaces, computing the allocation and payments of the VCG mechanism, however, is a computationally hard problem. We thus study the performance of the VCG mechanism when bidders are forced to choose bids from a subspace of the valuation space for which the VCG outcome can be computed efficiently. We prove improved upper bounds on the welfare loss for restrictions to additive bids and upper and lower bounds for restrictions to non-additive bids. These bounds show that increased expressiveness can give rise to additional equilibria of poorer efficiency. article_number: '5' article_processing_charge: No article_type: original author: - first_name: Paul full_name: Dütting, Paul last_name: Dütting - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Martin full_name: Starnberger, Martin last_name: Starnberger citation: ama: Dütting P, Henzinger MH, Starnberger M. Valuation compressions in VCG-based combinatorial auctions. ACM Transactions on Economics and Computation. 2018;6(2). doi:10.1145/3232860 apa: Dütting, P., Henzinger, M. H., & Starnberger, M. (2018). Valuation compressions in VCG-based combinatorial auctions. ACM Transactions on Economics and Computation. Association for Computing Machinery. https://doi.org/10.1145/3232860 chicago: Dütting, Paul, Monika H Henzinger, and Martin Starnberger. “Valuation Compressions in VCG-Based Combinatorial Auctions.” ACM Transactions on Economics and Computation. Association for Computing Machinery, 2018. https://doi.org/10.1145/3232860. ieee: P. Dütting, M. H. Henzinger, and M. Starnberger, “Valuation compressions in VCG-based combinatorial auctions,” ACM Transactions on Economics and Computation, vol. 6, no. 2. Association for Computing Machinery, 2018. ista: Dütting P, Henzinger MH, Starnberger M. 2018. Valuation compressions in VCG-based combinatorial auctions. ACM Transactions on Economics and Computation. 6(2), 5. mla: Dütting, Paul, et al. “Valuation Compressions in VCG-Based Combinatorial Auctions.” ACM Transactions on Economics and Computation, vol. 6, no. 2, 5, Association for Computing Machinery, 2018, doi:10.1145/3232860. short: P. Dütting, M.H. Henzinger, M. Starnberger, ACM Transactions on Economics and Computation 6 (2018). date_created: 2022-07-27T11:46:46Z date_published: 2018-05-01T00:00:00Z date_updated: 2022-09-09T12:04:42Z day: '01' doi: 10.1145/3232860 extern: '1' external_id: arxiv: - '1310.3153' intvolume: ' 6' issue: '2' keyword: - Theory of computation - Algorithmic game theory and mechanism design - Applied computing - Economics - Simplified mechanisms - Combinatorial auctions with item bidding - Price of anarchy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1310.3153 month: '05' oa: 1 oa_version: Preprint publication: ACM Transactions on Economics and Computation publication_identifier: eissn: - 2167-8383 issn: - 2167-8375 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Valuation compressions in VCG-based combinatorial auctions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2018' ... --- _id: '11664' abstract: - lang: eng text: "We present a deterministic incremental algorithm for exactly maintaining the size of a minimum cut with O(log3 n log log2 n) amortized time per edge insertion and O(1) query time. This result partially answers an open question posed by Thorup (2007). It also stays in sharp contrast to a polynomial conditional lower bound for the fully dynamic weighted minimum cut problem. Our algorithm is obtained by combining a sparsification technique of Kawarabayashi and Thorup (2015) or its recent improvement by Henzinger, Rao, and Wang (2017), and an exact incremental algorithm of Henzinger (1997).\r\n\r\nWe also study space-efficient incremental algorithms for the minimum cut problem. Concretely, we show that there exists an O(nlog n/ε2) space Monte Carlo algorithm that can process a stream of edge insertions starting from an empty graph, and with high probability, the algorithm maintains a (1+ε)-approximation to the minimum cut. The algorithm has O((α (n) log3 n)/ε 2) amortized update time and constant query time, where α (n) stands for the inverse of Ackermann function." acknowledgement: "We thank the two anonymous reviewers for their suggestions and comments, which improved the\r\nquality of the article." article_number: '17' article_processing_charge: No article_type: original author: - first_name: Gramoz full_name: Goranci, Gramoz last_name: Goranci - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Mikkel full_name: Thorup, Mikkel last_name: Thorup citation: ama: Goranci G, Henzinger MH, Thorup M. Incremental exact min-cut in polylogarithmic amortized update time. ACM Transactions on Algorithms. 2018;14(2). doi:10.1145/3174803 apa: Goranci, G., Henzinger, M. H., & Thorup, M. (2018). Incremental exact min-cut in polylogarithmic amortized update time. ACM Transactions on Algorithms. Association for Computing Machinery. https://doi.org/10.1145/3174803 chicago: Goranci, Gramoz, Monika H Henzinger, and Mikkel Thorup. “Incremental Exact Min-Cut in Polylogarithmic Amortized Update Time.” ACM Transactions on Algorithms. Association for Computing Machinery, 2018. https://doi.org/10.1145/3174803. ieee: G. Goranci, M. H. Henzinger, and M. Thorup, “Incremental exact min-cut in polylogarithmic amortized update time,” ACM Transactions on Algorithms, vol. 14, no. 2. Association for Computing Machinery, 2018. ista: Goranci G, Henzinger MH, Thorup M. 2018. Incremental exact min-cut in polylogarithmic amortized update time. ACM Transactions on Algorithms. 14(2), 17. mla: Goranci, Gramoz, et al. “Incremental Exact Min-Cut in Polylogarithmic Amortized Update Time.” ACM Transactions on Algorithms, vol. 14, no. 2, 17, Association for Computing Machinery, 2018, doi:10.1145/3174803. short: G. Goranci, M.H. Henzinger, M. Thorup, ACM Transactions on Algorithms 14 (2018). date_created: 2022-07-27T11:29:39Z date_published: 2018-04-01T00:00:00Z date_updated: 2022-09-09T11:38:14Z day: '01' doi: 10.1145/3174803 extern: '1' external_id: arxiv: - '1611.06500' intvolume: ' 14' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1611.06500 month: '04' oa: 1 oa_version: Preprint publication: ACM Transactions on Algorithms publication_identifier: eissn: - 1549-6333 issn: - 1549-6325 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Incremental exact min-cut in polylogarithmic amortized update time type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2018' ... --- _id: '11757' abstract: - lang: eng text: We develop a dynamic version of the primal-dual method for optimization problems, and apply it to obtain the following results. (1) For the dynamic set-cover problem, we maintain an O ( f 2)-approximately optimal solution in O ( f · log(m + n)) amortized update time, where f is the maximum “frequency” of an element, n is the number of sets, and m is the maximum number of elements in the universe at any point in time. (2) For the dynamic b-matching problem, we maintain an O (1)-approximately optimal solution in O (log3 n) amortized update time, where n is the number of nodes in the graph. article_processing_charge: No article_type: original author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Giuseppe full_name: Italiano, Giuseppe last_name: Italiano citation: ama: Bhattacharya S, Henzinger MH, Italiano G. Dynamic algorithms via the primal-dual method. Information and Computation. 2018;261(08):219-239. doi:10.1016/j.ic.2018.02.005 apa: Bhattacharya, S., Henzinger, M. H., & Italiano, G. (2018). Dynamic algorithms via the primal-dual method. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2018.02.005 chicago: Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe Italiano. “Dynamic Algorithms via the Primal-Dual Method.” Information and Computation. Elsevier, 2018. https://doi.org/10.1016/j.ic.2018.02.005. ieee: S. Bhattacharya, M. H. Henzinger, and G. Italiano, “Dynamic algorithms via the primal-dual method,” Information and Computation, vol. 261, no. 08. Elsevier, pp. 219–239, 2018. ista: Bhattacharya S, Henzinger MH, Italiano G. 2018. Dynamic algorithms via the primal-dual method. Information and Computation. 261(08), 219–239. mla: Bhattacharya, Sayan, et al. “Dynamic Algorithms via the Primal-Dual Method.” Information and Computation, vol. 261, no. 08, Elsevier, 2018, pp. 219–39, doi:10.1016/j.ic.2018.02.005. short: S. Bhattacharya, M.H. Henzinger, G. Italiano, Information and Computation 261 (2018) 219–239. date_created: 2022-08-08T11:20:03Z date_published: 2018-08-01T00:00:00Z date_updated: 2023-02-10T07:27:39Z day: '01' doi: 10.1016/j.ic.2018.02.005 extern: '1' intvolume: ' 261' issue: '08' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.ic.2018.02.005 month: '08' oa: 1 oa_version: Published Version page: 219-239 publication: Information and Computation publication_identifier: issn: - 0890-5401 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Dynamic algorithms via the primal-dual method type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 261 year: '2018' ... --- _id: '11828' 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." alternative_title: - LIPIcs article_number: '40' article_processing_charge: No author: - first_name: Gramoz full_name: Goranci, Gramoz last_name: Goranci - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Pan full_name: Peng, Pan last_name: Peng citation: ama: 'Goranci G, Henzinger MH, Peng P. Dynamic effective resistances and approximate schur complement on separable graphs. In: 26th Annual European Symposium on Algorithms. Vol 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.ESA.2018.40' apa: 'Goranci, G., Henzinger, M. H., & Peng, P. (2018). Dynamic effective resistances and approximate schur complement on separable graphs. In 26th Annual European Symposium on Algorithms (Vol. 112). Helsinki, Finland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2018.40' chicago: Goranci, Gramoz, Monika H Henzinger, and Pan Peng. “Dynamic Effective Resistances and Approximate Schur Complement on Separable Graphs.” In 26th Annual European Symposium on Algorithms, Vol. 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ESA.2018.40. ieee: G. Goranci, M. H. Henzinger, and P. Peng, “Dynamic effective resistances and approximate schur complement on separable graphs,” in 26th Annual European Symposium on Algorithms, Helsinki, Finland, 2018, vol. 112. ista: 'Goranci G, Henzinger MH, 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.' mla: Goranci, Gramoz, et al. “Dynamic Effective Resistances and Approximate Schur Complement on Separable Graphs.” 26th Annual European Symposium on Algorithms, vol. 112, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.ESA.2018.40. short: G. Goranci, M.H. Henzinger, P. Peng, in:, 26th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. conference: end_date: 2018-08-22 location: Helsinki, Finland name: 'ESA: Annual European Symposium on Algorithms' start_date: 2018-08-20 date_created: 2022-08-12T08:26:42Z date_published: 2018-08-14T00:00:00Z date_updated: 2023-02-16T11:08:08Z day: '14' doi: 10.4230/LIPICS.ESA.2018.40 extern: '1' external_id: arxiv: - '1802.09111' intvolume: ' 112' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPIcs.ESA.2018.40 month: '08' oa: 1 oa_version: Published Version publication: 26th Annual European Symposium on Algorithms publication_identifier: isbn: - '9783959770811' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Dynamic effective resistances and approximate schur complement on separable graphs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2018' ... --- _id: '11827' abstract: - lang: eng text: We study the metric facility location problem with client insertions and deletions. This setting differs from the classic dynamic facility location problem, where the set of clients remains the same, but the metric space can change over time. We show a deterministic algorithm that maintains a constant factor approximation to the optimal solution in worst-case time O~(2^{O(kappa^2)}) per client insertion or deletion in metric spaces while answering queries about the cost in O(1) time, where kappa denotes the doubling dimension of the metric. For metric spaces with bounded doubling dimension, the update time is polylogarithmic in the parameters of the problem. alternative_title: - LIPIcs article_number: '39' article_processing_charge: No author: - first_name: 'Gramoz ' full_name: 'Goranci, Gramoz ' last_name: Goranci - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Dariusz full_name: Leniowski, Dariusz last_name: Leniowski citation: ama: 'Goranci G, Henzinger MH, Leniowski D. A tree structure for dynamic facility location. In: 26th Annual European Symposium on Algorithms. Vol 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.ESA.2018.39' apa: 'Goranci, G., Henzinger, M. H., & Leniowski, D. (2018). A tree structure for dynamic facility location. In 26th Annual European Symposium on Algorithms (Vol. 112). Helsinki, Finland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2018.39' chicago: Goranci, Gramoz , Monika H Henzinger, and Dariusz Leniowski. “A Tree Structure for Dynamic Facility Location.” In 26th Annual European Symposium on Algorithms, Vol. 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ESA.2018.39. ieee: G. Goranci, M. H. Henzinger, and D. Leniowski, “A tree structure for dynamic facility location,” in 26th Annual European Symposium on Algorithms, Helsinki, Finland, 2018, vol. 112. ista: 'Goranci G, Henzinger MH, Leniowski D. 2018. A tree structure for dynamic facility location. 26th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 112, 39.' mla: Goranci, Gramoz, et al. “A Tree Structure for Dynamic Facility Location.” 26th Annual European Symposium on Algorithms, vol. 112, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.ESA.2018.39. short: G. Goranci, M.H. Henzinger, D. Leniowski, in:, 26th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. conference: end_date: 2018-08-22 location: Helsinki, Finland name: 'ESA: Annual European Symposium on Algorithms' start_date: 2018-08-20 date_created: 2022-08-12T08:20:57Z date_published: 2018-08-14T00:00:00Z date_updated: 2023-02-16T10:50:51Z day: '14' doi: 10.4230/LIPICS.ESA.2018.39 extern: '1' external_id: arxiv: - '1909.06653' intvolume: ' 112' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPIcs.ESA.2018.39 month: '08' oa: 1 oa_version: Published Version publication: 26th Annual European Symposium on Algorithms publication_identifier: isbn: - '9783959770811' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: A tree structure for dynamic facility location type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2018' ... --- _id: '11768' abstract: - lang: eng text: "In the decremental single-source shortest paths (SSSP) problem, we want to maintain the distances between a given source node s and every other node in an n-node m-edge graph G undergoing edge deletions. While its static counterpart can be solved in near-linear time, this decremental problem is much more challenging even in the undirected unweighted case. In this case, the classic O(mn) total update time of Even and Shiloach [16] has been the fastest known algorithm for three decades. At the cost of a (1+ϵ)-approximation factor, the running time was recently improved to n2+o(1) by Bernstein and Roditty [9]. In this article, we bring the running time down to near-linear: We give a (1+ϵ)-approximation algorithm with m1+o(1) expected total update time, thus obtaining near-linear time. Moreover, we obtain m1+o(1) log W time for the weighted case, where the edge weights are integers from 1 to W. The only prior work on weighted graphs in o(mn) time is the mn0.9 + o(1)-time algorithm by Henzinger et al. [18, 19], which works for directed graphs with quasi-polynomial edge weights. The expected running time bound of our algorithm holds against an oblivious adversary.\r\n\r\nIn contrast to the previous results, which rely on maintaining a sparse emulator, our algorithm relies on maintaining a so-called sparse (h, ϵ)-hop set introduced by Cohen [12] in the PRAM literature. An (h, ϵ)-hop set of a graph G=(V, E) is a set F of weighted edges such that the distance between any pair of nodes in G can be (1+ϵ)-approximated by their h-hop distance (given by a path containing at most h edges) on G′=(V, E ∪ F). Our algorithm can maintain an (no(1), ϵ)-hop set of near-linear size in near-linear time under edge deletions. It is the first of its kind to the best of our knowledge. To maintain approximate distances using this hop set, we extend the monotone Even-Shiloach tree of Henzinger et al. [20] and combine it with the bounded-hop SSSP technique of Bernstein [4, 5] and Mądry [27]. These two new tools might be of independent interest." article_processing_charge: No article_type: original author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: Henzinger MH, Krinninger S, Nanongkai D. Decremental single-source shortest paths on undirected graphs in near-linear total update time. Journal of the ACM. 2018;65(6):1-40. doi:10.1145/3218657 apa: Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2018). Decremental single-source shortest paths on undirected graphs in near-linear total update time. Journal of the ACM. Association for Computing Machinery. https://doi.org/10.1145/3218657 chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” Journal of the ACM. Association for Computing Machinery, 2018. https://doi.org/10.1145/3218657. ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Decremental single-source shortest paths on undirected graphs in near-linear total update time,” Journal of the ACM, vol. 65, no. 6. Association for Computing Machinery, pp. 1–40, 2018. ista: Henzinger MH, Krinninger S, Nanongkai D. 2018. Decremental single-source shortest paths on undirected graphs in near-linear total update time. Journal of the ACM. 65(6), 1–40. mla: Henzinger, Monika H., et al. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” Journal of the ACM, vol. 65, no. 6, Association for Computing Machinery, 2018, pp. 1–40, doi:10.1145/3218657. short: M.H. Henzinger, S. Krinninger, D. Nanongkai, Journal of the ACM 65 (2018) 1–40. date_created: 2022-08-08T12:33:17Z date_published: 2018-12-01T00:00:00Z date_updated: 2023-02-21T16:30:41Z day: '01' doi: 10.1145/3218657 extern: '1' external_id: arxiv: - '1512.08148' intvolume: ' 65' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1512.08148 month: '12' oa: 1 oa_version: Preprint page: 1-40 publication: Journal of the ACM publication_identifier: eissn: - 1557-735X issn: - 0004-5411 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '11855' relation: earlier_version status: public scopus_import: '1' status: public title: Decremental single-source shortest paths on undirected graphs in near-linear total update time type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 65 year: '2018' ... --- _id: '11872' 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]. article_processing_charge: No author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Deeparnab full_name: Chakrabarty, Deeparnab last_name: Chakrabarty - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: 'Bhattacharya S, Chakrabarty D, Henzinger MH, Nanongkai D. Dynamic algorithms for graph coloring. In: 29th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2018:1-20. doi:10.1137/1.9781611975031.1' apa: 'Bhattacharya, S., Chakrabarty, D., Henzinger, M. H., & Nanongkai, D. (2018). Dynamic algorithms for graph coloring. In 29th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1–20). New Orleans, LA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611975031.1' chicago: Bhattacharya, Sayan, Deeparnab Chakrabarty, Monika H Henzinger, and Danupon Nanongkai. “Dynamic Algorithms for Graph Coloring.” In 29th Annual ACM-SIAM Symposium on Discrete Algorithms, 1–20. Society for Industrial and Applied Mathematics, 2018. https://doi.org/10.1137/1.9781611975031.1. ieee: S. Bhattacharya, D. Chakrabarty, M. H. Henzinger, and D. Nanongkai, “Dynamic algorithms for graph coloring,” in 29th Annual ACM-SIAM Symposium on Discrete Algorithms, New Orleans, LA, United States, 2018, pp. 1–20. ista: 'Bhattacharya S, Chakrabarty D, Henzinger MH, Nanongkai D. 2018. Dynamic algorithms for graph coloring. 29th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1–20.' mla: Bhattacharya, Sayan, et al. “Dynamic Algorithms for Graph Coloring.” 29th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2018, pp. 1–20, doi:10.1137/1.9781611975031.1. short: S. Bhattacharya, D. Chakrabarty, M.H. Henzinger, D. Nanongkai, in:, 29th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2018, pp. 1–20. conference: end_date: 2018-01-10 location: New Orleans, LA, United States name: 'SODA: Symposium on Discrete Algorithms' start_date: 2018-01-07 date_created: 2022-08-16T12:07:14Z date_published: 2018-01-01T00:00:00Z date_updated: 2023-02-17T11:39:01Z day: '01' doi: 10.1137/1.9781611975031.1 extern: '1' external_id: arxiv: - '1711.04355' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.04355 month: '01' oa: 1 oa_version: Preprint page: 1 - 20 publication: 29th Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: eisbn: - 978-161197503-1 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: Dynamic algorithms for graph coloring type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '11882' 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. article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Alexander full_name: Noe, Alexander last_name: Noe - first_name: Christian full_name: Schulz, Christian last_name: Schulz - first_name: Darren full_name: Strash, Darren last_name: Strash citation: ama: 'Henzinger MH, Noe A, Schulz C, Strash D. Practical minimum cut algorithms. In: 20th Workshop on Algorithm Engineering and Experiments. Society for Industrial and Applied Mathematics; 2018:48-61. doi:10.1137/1.9781611975055.5' apa: 'Henzinger, M. H., Noe, A., Schulz, C., & Strash, D. (2018). Practical minimum cut algorithms. In 20th Workshop on Algorithm Engineering and Experiments (pp. 48–61). New Orleans, LA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611975055.5' chicago: Henzinger, Monika H, Alexander Noe, Christian Schulz, and Darren Strash. “Practical Minimum Cut Algorithms.” In 20th Workshop on Algorithm Engineering and Experiments, 48–61. Society for Industrial and Applied Mathematics, 2018. https://doi.org/10.1137/1.9781611975055.5. ieee: M. H. Henzinger, A. Noe, C. Schulz, and D. Strash, “Practical minimum cut algorithms,” in 20th Workshop on Algorithm Engineering and Experiments, New Orleans, LA, United States, 2018, pp. 48–61. ista: 'Henzinger MH, 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.' mla: Henzinger, Monika H., et al. “Practical Minimum Cut Algorithms.” 20th Workshop on Algorithm Engineering and Experiments, Society for Industrial and Applied Mathematics, 2018, pp. 48–61, doi:10.1137/1.9781611975055.5. short: M.H. 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. conference: end_date: 2018-01-08 location: New Orleans, LA, United States name: 'ALENEX: Symposium on Algorithm Engineering and Experiments' start_date: 2018-01-07 date_created: 2022-08-17T07:04:57Z date_published: 2018-01-01T00:00:00Z date_updated: 2023-02-17T14:03:39Z day: '01' doi: 10.1137/1.9781611975055.5 extern: '1' external_id: arxiv: - '1708.06127' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.06127 month: '01' oa: 1 oa_version: Preprint page: 48-61 publication: 20th Workshop on Algorithm Engineering and Experiments publication_identifier: eisbn: - 978-1-61197-505-5 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: Practical minimum cut algorithms type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '11890' abstract: - lang: eng text: "We present the first deterministic data structures for maintaining approximate minimum vertex cover and maximum matching in a fully dynamic graph \U0001D43A=(\U0001D449,\U0001D438), with |\U0001D449|=\U0001D45B and |\U0001D438|=\U0001D45A, in \U0001D45C(\U0001D45A‾‾√) time per update. In particular, for minimum vertex cover, we provide deterministic data structures for maintaining a (2+\U0001D716) approximation in \U0001D442(log\U0001D45B/\U0001D7162) amortized time per update. For maximum matching, we show how to maintain a (3+\U0001D716) approximation in \U0001D442(min(\U0001D45B√/\U0001D716,\U0001D45A1/3/\U0001D7162) amortized time per update and a (4+\U0001D716) approximation in \U0001D442(\U0001D45A1/3/\U0001D7162) 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]." article_processing_charge: No article_type: original author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Giuseppe F. full_name: Italiano, Giuseppe F. last_name: Italiano citation: ama: Bhattacharya S, Henzinger MH, Italiano GF. Deterministic fully dynamic data structures for vertex cover and matching. SIAM Journal on Computing. 2018;47(3):859-887. doi:10.1137/140998925 apa: Bhattacharya, S., Henzinger, M. H., & Italiano, G. F. (2018). Deterministic fully dynamic data structures for vertex cover and matching. SIAM Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/140998925 chicago: Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe F. Italiano. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics, 2018. https://doi.org/10.1137/140998925. ieee: S. Bhattacharya, M. H. Henzinger, and G. F. Italiano, “Deterministic fully dynamic data structures for vertex cover and matching,” SIAM Journal on Computing, vol. 47, no. 3. Society for Industrial & Applied Mathematics, pp. 859–887, 2018. ista: Bhattacharya S, Henzinger MH, Italiano GF. 2018. Deterministic fully dynamic data structures for vertex cover and matching. SIAM Journal on Computing. 47(3), 859–887. mla: Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” SIAM Journal on Computing, vol. 47, no. 3, Society for Industrial & Applied Mathematics, 2018, pp. 859–87, doi:10.1137/140998925. short: S. Bhattacharya, M.H. Henzinger, G.F. Italiano, SIAM Journal on Computing 47 (2018) 859–887. date_created: 2022-08-17T08:21:23Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-02-21T16:31:30Z day: '01' doi: 10.1137/140998925 extern: '1' external_id: arxiv: - '1412.1318' intvolume: ' 47' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1412.1318 month: '05' oa: 1 oa_version: Preprint page: 859-887 publication: SIAM Journal on Computing publication_identifier: eissn: - 1095-7111 issn: - 0097-5397 publication_status: published publisher: Society for Industrial & Applied Mathematics quality_controlled: '1' related_material: record: - id: '11875' relation: earlier_version status: public scopus_import: '1' status: public title: Deterministic fully dynamic data structures for vertex cover and matching type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2018' ... --- _id: '11911' 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. alternative_title: - LIPIcs article_number: '3' article_processing_charge: No author: - first_name: Sonja full_name: Biedermann, Sonja last_name: Biedermann - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Christian full_name: Schulz, Christian last_name: Schulz - first_name: Bernhard full_name: Schuster, Bernhard last_name: Schuster citation: ama: 'Biedermann S, Henzinger MH, Schulz C, Schuster B. Memetic graph clustering. In: 17th International Symposium on Experimental Algorithms. Vol 103. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.SEA.2018.3' apa: 'Biedermann, S., Henzinger, M. H., Schulz, C., & Schuster, B. (2018). Memetic graph clustering. In 17th International Symposium on Experimental Algorithms (Vol. 103). L’Aquila, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SEA.2018.3' chicago: Biedermann, Sonja, Monika H Henzinger, Christian Schulz, and Bernhard Schuster. “Memetic Graph Clustering.” In 17th International Symposium on Experimental Algorithms, Vol. 103. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.SEA.2018.3. ieee: S. Biedermann, M. H. Henzinger, C. Schulz, and B. Schuster, “Memetic graph clustering,” in 17th International Symposium on Experimental Algorithms, L’Aquila, Italy, 2018, vol. 103. ista: 'Biedermann S, Henzinger MH, Schulz C, Schuster B. 2018. Memetic graph clustering. 17th International Symposium on Experimental Algorithms. SEA: Symposium on Experimental Algorithms, LIPIcs, vol. 103, 3.' mla: Biedermann, Sonja, et al. “Memetic Graph Clustering.” 17th International Symposium on Experimental Algorithms, vol. 103, 3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.SEA.2018.3. short: S. Biedermann, M.H. Henzinger, C. Schulz, B. Schuster, in:, 17th International Symposium on Experimental Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. conference: end_date: 2018-07-29 location: L'Aquila, Italy name: 'SEA: Symposium on Experimental Algorithms' start_date: 2018-07-27 date_created: 2022-08-18T06:49:40Z date_published: 2018-07-01T00:00:00Z date_updated: 2023-02-16T11:45:14Z day: '01' doi: 10.4230/LIPICS.SEA.2018.3 extern: '1' external_id: arxiv: - '1802.07034' intvolume: ' 103' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPICS.SEA.2018.3 month: '07' oa: 1 oa_version: Published Version publication: 17th International Symposium on Experimental Algorithms publication_identifier: isbn: - '9783959770705' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Memetic graph clustering type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 103 year: '2018' ... --- _id: '11958' 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. article_processing_charge: No article_type: letter_note author: - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Menny full_name: Shalom, Menny last_name: Shalom - first_name: Markus full_name: Antonietti, Markus last_name: Antonietti - first_name: Peter H. full_name: Seeberger, Peter H. last_name: Seeberger - first_name: Kerry full_name: Gilmore, Kerry last_name: Gilmore citation: ama: Pieber B, Shalom M, Antonietti M, Seeberger PH, Gilmore K. Continuous heterogeneous photocatalysis in serial micro-batch reactors. Angewandte Chemie International Edition. 2018;57(31):9976-9979. doi:10.1002/anie.201712568 apa: Pieber, B., Shalom, M., Antonietti, M., Seeberger, P. H., & Gilmore, K. (2018). Continuous heterogeneous photocatalysis in serial micro-batch reactors. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201712568 chicago: Pieber, Bartholomäus, Menny Shalom, Markus Antonietti, Peter H. Seeberger, and Kerry Gilmore. “Continuous Heterogeneous Photocatalysis in Serial Micro-Batch Reactors.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201712568. ieee: B. Pieber, M. Shalom, M. Antonietti, P. H. Seeberger, and K. Gilmore, “Continuous heterogeneous photocatalysis in serial micro-batch reactors,” Angewandte Chemie International Edition, 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.” Angewandte Chemie International Edition, vol. 57, no. 31, Wiley, 2018, pp. 9976–79, doi:10.1002/anie.201712568. short: B. Pieber, M. Shalom, M. Antonietti, P.H. Seeberger, K. Gilmore, Angewandte Chemie International Edition 57 (2018) 9976–9979. date_created: 2022-08-24T10:57:25Z date_published: 2018-07-26T00:00:00Z date_updated: 2023-02-21T10:09:18Z day: '26' doi: 10.1002/anie.201712568 extern: '1' external_id: pmid: - '29377383' intvolume: ' 57' issue: '31' language: - iso: eng month: '07' oa_version: None page: 9976-9979 pmid: 1 publication: Angewandte Chemie International Edition publication_identifier: eissn: - ' 1521-3773' issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Continuous heterogeneous photocatalysis in serial micro-batch reactors type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2018' ... --- _id: '1215' abstract: - lang: eng 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." 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. article_processing_charge: Yes (via OA deal) author: - first_name: Franco full_name: Flandoli, Franco last_name: Flandoli - first_name: Francesco full_name: Russo, Francesco last_name: Russo - first_name: Giovanni A full_name: Zanco, Giovanni A id: 47491882-F248-11E8-B48F-1D18A9856A87 last_name: Zanco citation: ama: Flandoli F, Russo F, Zanco GA. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 2018;31(2):789-826. doi:10.1007/s10959-016-0724-2 apa: Flandoli, F., Russo, F., & Zanco, G. A. (2018). Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. Springer. https://doi.org/10.1007/s10959-016-0724-2 chicago: Flandoli, Franco, Francesco Russo, and Giovanni A Zanco. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability. Springer, 2018. https://doi.org/10.1007/s10959-016-0724-2. ieee: F. Flandoli, F. Russo, and G. A. Zanco, “Infinite-dimensional calculus under weak spatial regularity of the processes,” Journal of Theoretical Probability, vol. 31, no. 2. Springer, pp. 789–826, 2018. 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. mla: Flandoli, Franco, et al. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability, vol. 31, no. 2, Springer, 2018, pp. 789–826, doi:10.1007/s10959-016-0724-2. short: F. Flandoli, F. Russo, G.A. Zanco, Journal of Theoretical Probability 31 (2018) 789–826. date_created: 2018-12-11T11:50:45Z date_published: 2018-06-01T00:00:00Z date_updated: 2021-01-12T06:49:09Z day: '01' ddc: - '519' department: - _id: JaMa doi: 10.1007/s10959-016-0724-2 file: - access_level: open_access checksum: 47686d58ec21c164540f1a980ff2163f content_type: application/pdf creator: system date_created: 2018-12-12T10:17:13Z date_updated: 2020-07-14T12:44:39Z file_id: '5266' file_name: IST-2016-712-v1+1_s10959-016-0724-2.pdf file_size: 671125 relation: main_file file_date_updated: 2020-07-14T12:44:39Z has_accepted_license: '1' intvolume: ' 31' issue: '2' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 789-826 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Journal of Theoretical Probability publication_status: published publisher: Springer publist_id: '6119' pubrep_id: '712' quality_controlled: '1' scopus_import: 1 status: public title: Infinite-dimensional calculus under weak spatial regularity of the processes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2018' ... --- _id: '124' abstract: - lang: eng text: By investigating the in situ chemical and O-isotope compositions of olivine in lightly sintered dust agglomerates from the early Solar System, we constrain their origins and the retention of dust in the protoplanetary disk. The grain sizes of silicates in these agglomeratic olivine (AO) chondrules indicate that the grain sizes of chondrule precursors in the Renazzo-like carbonaceous (CR) chondrites ranged from <1 to 80 µm. We infer this grain size range to be equivalent to the size range for dust in the early Solar System. AO chondrules may contain, but are not solely composed of, recycled fragments of earlier formed chondrules. They also contain 16O-rich olivine related to amoeboid olivine aggregates and represent the best record of chondrule-precursor materials. AO chondrules contain one or more large grains, sometimes similar to FeO-poor (type I) and/or FeO-rich (type II) chondrules, while others contain a type II chondrule core. These morphologies are consistent with particle agglomeration by electrostatic charging of grains during collision, a process that may explain solid agglomeration in the protoplanetary disk in the micrometer size regime. The petrographic, isotopic, and chemical compositions of AO chondrules are consistent with chondrule formation by large-scale shocks, bow shocks, and current sheets. The petrographic, isotopic, and chemical similarities between AO chondrules in CR chondrites and chondrule-like objects from comet 81P/Wild 2 indicate that comets contain AO chondrules. We infer that these AO chondrules likely formed in the inner Solar System and migrated to the comet forming region at least 3 Ma after the formation of the first Solar System solids. Observations made in this study imply that the protoplanetary disk retained a dusty disk at least ∼3.7 Ma after the formation of the first Solar System solids, longer than half of the dusty accretion disks observed around other stars. author: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Devin full_name: Schrader, Devin last_name: Schrader - first_name: Kazuhide full_name: Nagashima, Kazuhide last_name: Nagashima - first_name: Jemma full_name: Davidson, Jemma last_name: Davidson - first_name: Timothy full_name: Mccoy, Timothy last_name: Mccoy - first_name: Harold full_name: Conolly Jr, Harold last_name: Conolly Jr - first_name: Dante full_name: Lauretta, Dante last_name: Lauretta citation: ama: 'Waitukaitis SR, Schrader D, Nagashima K, et al. The retention of dust in protoplanetary disks: evidence from agglomeration olivine chondrules from the outer solar system. Geochimica et Cosmochimica Acta. 2018;223:405-421. doi:10.1016/j.gca.2017.12.014' apa: 'Waitukaitis, S. R., Schrader, D., Nagashima, K., Davidson, J., Mccoy, T., Conolly Jr, H., & Lauretta, D. (2018). The retention of dust in protoplanetary disks: evidence from agglomeration olivine chondrules from the outer solar system. Geochimica et Cosmochimica Acta. Elsevier. https://doi.org/10.1016/j.gca.2017.12.014' chicago: 'Waitukaitis, Scott R, Devin Schrader, Kazuhide Nagashima, Jemma Davidson, Timothy Mccoy, Harold Conolly Jr, and Dante Lauretta. “The Retention of Dust in Protoplanetary Disks: Evidence from Agglomeration Olivine Chondrules from the Outer Solar System.” Geochimica et Cosmochimica Acta. Elsevier, 2018. https://doi.org/10.1016/j.gca.2017.12.014.' ieee: 'S. R. Waitukaitis et al., “The retention of dust in protoplanetary disks: evidence from agglomeration olivine chondrules from the outer solar system,” Geochimica et Cosmochimica Acta, vol. 223. Elsevier, pp. 405–421, 2018.' ista: 'Waitukaitis SR, Schrader D, Nagashima K, Davidson J, Mccoy T, Conolly Jr H, Lauretta D. 2018. The retention of dust in protoplanetary disks: evidence from agglomeration olivine chondrules from the outer solar system. Geochimica et Cosmochimica Acta. 223, 405–421.' mla: 'Waitukaitis, Scott R., et al. “The Retention of Dust in Protoplanetary Disks: Evidence from Agglomeration Olivine Chondrules from the Outer Solar System.” Geochimica et Cosmochimica Acta, vol. 223, Elsevier, 2018, pp. 405–21, doi:10.1016/j.gca.2017.12.014.' short: S.R. Waitukaitis, D. Schrader, K. Nagashima, J. Davidson, T. Mccoy, H. Conolly Jr, D. Lauretta, Geochimica et Cosmochimica Acta 223 (2018) 405–421. date_created: 2018-12-11T11:44:45Z date_published: 2018-02-15T00:00:00Z date_updated: 2021-01-12T06:49:19Z day: '15' doi: 10.1016/j.gca.2017.12.014 extern: '1' intvolume: ' 223' language: - iso: eng month: '02' oa_version: None page: 405 - 421 publication: Geochimica et Cosmochimica Acta publication_status: published publisher: Elsevier publist_id: '7930' quality_controlled: '1' status: public title: 'The retention of dust in protoplanetary disks: evidence from agglomeration olivine chondrules from the outer solar system' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 223 year: '2018' ... --- _id: '125' abstract: - lang: eng text: Many fields of study, including medical imaging, granular physics, colloidal physics, and active matter, require the precise identification and tracking of particle-like objects in images. While many algorithms exist to track particles in diffuse conditions, these often perform poorly when particles are densely packed together—as in, for example, solid-like systems of granular materials. Incorrect particle identification can have significant effects on the calculation of physical quantities, which makes the development of more precise and faster tracking algorithms a worthwhile endeavor. In this work, we present a new tracking algorithm to identify particles in dense systems that is both highly accurate and fast. We demonstrate the efficacy of our approach by analyzing images of dense, solid-state granular media, where we achieve an identification error of 5% in the worst evaluated cases. Going further, we propose a parallelization strategy for our algorithm using a GPU, which results in a speedup of up to 10× when compared to a sequential CPU implementation in C and up to 40× when compared to the reference MATLAB library widely used for particle tracking. Our results extend the capabilities of state-of-the-art particle tracking methods by allowing fast, high-fidelity detection in dense media at high resolutions. author: - first_name: Mauricio full_name: Cerda, Mauricio last_name: Cerda - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Cristóbal full_name: Navarro, Cristóbal last_name: Navarro - first_name: Juan full_name: Silva, Juan last_name: Silva - first_name: Nicolás full_name: Mujica, Nicolás last_name: Mujica - first_name: Nancy full_name: Hitschfeld, Nancy last_name: Hitschfeld citation: ama: Cerda M, Waitukaitis SR, Navarro C, Silva J, Mujica N, Hitschfeld N. A high-speed tracking algorithm for dense granular media. Computer Physics Communications. 2018;227:8-16. doi:10.1016/j.cpc.2018.02.010 apa: Cerda, M., Waitukaitis, S. R., Navarro, C., Silva, J., Mujica, N., & Hitschfeld, N. (2018). A high-speed tracking algorithm for dense granular media. Computer Physics Communications. Elsevier. https://doi.org/10.1016/j.cpc.2018.02.010 chicago: Cerda, Mauricio, Scott R Waitukaitis, Cristóbal Navarro, Juan Silva, Nicolás Mujica, and Nancy Hitschfeld. “A High-Speed Tracking Algorithm for Dense Granular Media.” Computer Physics Communications. Elsevier, 2018. https://doi.org/10.1016/j.cpc.2018.02.010. ieee: M. Cerda, S. R. Waitukaitis, C. Navarro, J. Silva, N. Mujica, and N. Hitschfeld, “A high-speed tracking algorithm for dense granular media,” Computer Physics Communications, vol. 227. Elsevier, pp. 8–16, 2018. ista: Cerda M, Waitukaitis SR, Navarro C, Silva J, Mujica N, Hitschfeld N. 2018. A high-speed tracking algorithm for dense granular media. Computer Physics Communications. 227, 8–16. mla: Cerda, Mauricio, et al. “A High-Speed Tracking Algorithm for Dense Granular Media.” Computer Physics Communications, vol. 227, Elsevier, 2018, pp. 8–16, doi:10.1016/j.cpc.2018.02.010. short: M. Cerda, S.R. Waitukaitis, C. Navarro, J. Silva, N. Mujica, N. Hitschfeld, Computer Physics Communications 227 (2018) 8–16. date_created: 2018-12-11T11:44:45Z date_published: 2018-06-01T00:00:00Z date_updated: 2021-01-12T06:49:23Z day: '01' doi: 10.1016/j.cpc.2018.02.010 extern: '1' intvolume: ' 227' language: - iso: eng month: '06' oa_version: None page: 8 - 16 publication: Computer Physics Communications publication_status: published publisher: Elsevier publist_id: '7928' quality_controlled: '1' status: public title: A high-speed tracking algorithm for dense granular media type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 227 year: '2018' ... --- _id: '126' abstract: - lang: eng text: The Leidenfrost effect occurs when a liquid or stiff sublimable solid near a hot surface creates enough vapor beneath it to lift itself up and float. In contrast, vaporizable soft solids, e.g., hydrogels, have been shown to exhibit persistent bouncing - the elastic Leidenfrost effect. By carefully lowering hydrogel spheres towards a hot surface, we discover that they are also capable of floating. The bounce-to-float transition is controlled by the approach velocity and temperature, analogously to the "dynamic Leidenfrost effect." For the floating regime, we measure power-law scalings for the gap geometry, which we explain with a model that couples the vaporization rate to the spherical shape. Our results reveal that hydrogels are a promising pathway for controlling floating Leidenfrost objects through shape. acknowledgement: We acknowledge funding from the Netherlands Organization for Scientific Research through Grants VICI No. NWO- 680-47-609 (M. v. H. and S. W.) and VENI No. NWO-680- 47-453 (S. W.), and from the German Science Foundation through Grant No. HA8467/1-1 (K. H.). article_number: '048001 ' author: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Kirsten full_name: Harth, Kirsten last_name: Harth - first_name: Martin full_name: Van Hecke, Martin last_name: Van Hecke citation: ama: 'Waitukaitis SR, Harth K, Van Hecke M. From bouncing to floating: the Leidenfrost effect with hydrogel spheres. Physical Review Letters. 2018;121(4). doi:10.1103/PhysRevLett.121.048001' apa: 'Waitukaitis, S. R., Harth, K., & Van Hecke, M. (2018). From bouncing to floating: the Leidenfrost effect with hydrogel spheres. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.048001' chicago: 'Waitukaitis, Scott R, Kirsten Harth, and Martin Van Hecke. “From Bouncing to Floating: The Leidenfrost Effect with Hydrogel Spheres.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.048001.' ieee: 'S. R. Waitukaitis, K. Harth, and M. Van Hecke, “From bouncing to floating: the Leidenfrost effect with hydrogel spheres,” Physical Review Letters, vol. 121, no. 4. American Physical Society, 2018.' ista: 'Waitukaitis SR, Harth K, Van Hecke M. 2018. From bouncing to floating: the Leidenfrost effect with hydrogel spheres. Physical Review Letters. 121(4), 048001.' mla: 'Waitukaitis, Scott R., et al. “From Bouncing to Floating: The Leidenfrost Effect with Hydrogel Spheres.” Physical Review Letters, vol. 121, no. 4, 048001, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.048001.' short: S.R. Waitukaitis, K. Harth, M. Van Hecke, Physical Review Letters 121 (2018). date_created: 2018-12-11T11:44:46Z date_published: 2018-07-25T00:00:00Z date_updated: 2021-01-12T06:49:27Z day: '25' doi: 10.1103/PhysRevLett.121.048001 extern: '1' intvolume: ' 121' issue: '4' language: - iso: eng month: '07' oa_version: None publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7927' quality_controlled: '1' status: public title: 'From bouncing to floating: the Leidenfrost effect with hydrogel spheres' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 121 year: '2018' ... --- _id: '127' abstract: - lang: eng text: The ideas of topology are breaking ground in origami-based metamaterials. Experiments now show that certain shapes — doughnuts included — exhibit topological bistability, and can be made to click between different topologically stable states. author: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: Waitukaitis SR. Clicks for doughnuts. Nature Physics. 2018;14(8):777-778. doi:10.1038/s41567-018-0160-6 apa: Waitukaitis, S. R. (2018). Clicks for doughnuts. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/s41567-018-0160-6 chicago: Waitukaitis, Scott R. “Clicks for Doughnuts.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-018-0160-6. ieee: S. R. Waitukaitis, “Clicks for doughnuts,” Nature Physics, vol. 14, no. 8. Nature Publishing Group, pp. 777–778, 2018. ista: Waitukaitis SR. 2018. Clicks for doughnuts. Nature Physics. 14(8), 777–778. mla: Waitukaitis, Scott R. “Clicks for Doughnuts.” Nature Physics, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 777–78, doi:10.1038/s41567-018-0160-6. short: S.R. Waitukaitis, Nature Physics 14 (2018) 777–778. date_created: 2018-12-11T11:44:46Z date_published: 2018-05-28T00:00:00Z date_updated: 2021-01-12T06:49:31Z day: '28' doi: 10.1038/s41567-018-0160-6 extern: '1' intvolume: ' 14' issue: '8' language: - iso: eng month: '05' oa_version: None page: 777 - 778 publication: Nature Physics publication_status: published publisher: Nature Publishing Group publist_id: '7926' status: public title: Clicks for doughnuts type: journal_article user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2018' ... --- _id: '174' abstract: - lang: eng text: We survey recent efforts to quantify failures of the Hasse principle in families of rationally connected varieties. alternative_title: - Proceedings of Symposia in Pure Mathematics article_processing_charge: No author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: 'Browning TD. How often does the Hasse principle hold? In: Vol 97. American Mathematical Society; 2018:89-102. doi:10.1090/pspum/097.2/01700' apa: 'Browning, T. D. (2018). How often does the Hasse principle hold? (Vol. 97, pp. 89–102). Presented at the Algebraic Geometry, Salt Lake City, Utah, USA: American Mathematical Society. https://doi.org/10.1090/pspum/097.2/01700' chicago: Browning, Timothy D. “How Often Does the Hasse Principle Hold?,” 97:89–102. American Mathematical Society, 2018. https://doi.org/10.1090/pspum/097.2/01700. ieee: T. D. Browning, “How often does the Hasse principle hold?,” presented at the Algebraic Geometry, Salt Lake City, Utah, USA, 2018, vol. 97, no. 2, pp. 89–102. ista: Browning TD. 2018. How often does the Hasse principle hold? Algebraic Geometry, Proceedings of Symposia in Pure Mathematics, vol. 97, 89–102. mla: Browning, Timothy D. How Often Does the Hasse Principle Hold? Vol. 97, no. 2, American Mathematical Society, 2018, pp. 89–102, doi:10.1090/pspum/097.2/01700. short: T.D. Browning, in:, American Mathematical Society, 2018, pp. 89–102. conference: end_date: 2015-07-10 location: Salt Lake City, Utah, USA name: Algebraic Geometry start_date: 2015-07-06 date_created: 2018-12-11T11:45:01Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T06:52:54Z day: '01' doi: 10.1090/pspum/097.2/01700 extern: '1' intvolume: ' 97' issue: '2' language: - iso: eng month: '01' oa_version: None page: 89 - 102 publication_status: published publisher: American Mathematical Society quality_controlled: '1' status: public title: How often does the Hasse principle hold? type: conference user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 97 year: '2018' ... --- _id: '176' abstract: - lang: eng text: For a general class of non-negative functions defined on integral ideals of number fields, upper bounds are established for their average over the values of certain principal ideals that are associated to irreducible binary forms with integer coefficients. article_processing_charge: No article_type: original author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Efthymios full_name: Sofos, Efthymios last_name: Sofos citation: ama: Browning TD, Sofos E. Averages of arithmetic functions over principal ideals. International Journal of Nuber Theory. 2018;15(3):547-567. doi:10.1142/S1793042119500283 apa: Browning, T. D., & Sofos, E. (2018). Averages of arithmetic functions over principal ideals. International Journal of Nuber Theory. World Scientific Publishing. https://doi.org/10.1142/S1793042119500283 chicago: Browning, Timothy D, and Efthymios Sofos. “Averages of Arithmetic Functions over Principal Ideals.” International Journal of Nuber Theory. World Scientific Publishing, 2018. https://doi.org/10.1142/S1793042119500283. ieee: T. D. Browning and E. Sofos, “Averages of arithmetic functions over principal ideals,” International Journal of Nuber Theory, vol. 15, no. 3. World Scientific Publishing, pp. 547–567, 2018. ista: Browning TD, Sofos E. 2018. Averages of arithmetic functions over principal ideals. International Journal of Nuber Theory. 15(3), 547–567. mla: Browning, Timothy D., and Efthymios Sofos. “Averages of Arithmetic Functions over Principal Ideals.” International Journal of Nuber Theory, vol. 15, no. 3, World Scientific Publishing, 2018, pp. 547–67, doi:10.1142/S1793042119500283. short: T.D. Browning, E. Sofos, International Journal of Nuber Theory 15 (2018) 547–567. date_created: 2018-12-11T11:45:01Z date_published: 2018-11-16T00:00:00Z date_updated: 2021-01-12T06:53:01Z day: '16' doi: 10.1142/S1793042119500283 extern: '1' external_id: arxiv: - '1706.04331' intvolume: ' 15' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1706.04331 month: '11' oa: 1 oa_version: Preprint page: 547-567 publication: International Journal of Nuber Theory publication_status: published publisher: World Scientific Publishing status: public title: Averages of arithmetic functions over principal ideals type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 15 year: '2018' ... --- _id: '178' abstract: - lang: eng text: We give an upper bound for the number of rational points of height at most B, lying on a surface defined by a quadratic form Q. The bound shows an explicit dependence on Q. It is optimal with respect to B, and is also optimal for typical forms Q. article_processing_charge: No author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Roger full_name: Heath-Brown, Roger last_name: Heath-Brown citation: ama: Browning TD, Heath-Brown R. Counting rational points on quadric surfaces. Discrete Analysis. 2018;15:1-29. doi:10.19086/da.4375 apa: Browning, T. D., & Heath-Brown, R. (2018). Counting rational points on quadric surfaces. Discrete Analysis. Alliance of Diamond Open Access Journals. https://doi.org/10.19086/da.4375 chicago: Browning, Timothy D, and Roger Heath-Brown. “Counting Rational Points on Quadric Surfaces.” Discrete Analysis. Alliance of Diamond Open Access Journals, 2018. https://doi.org/10.19086/da.4375. ieee: T. D. Browning and R. Heath-Brown, “Counting rational points on quadric surfaces,” Discrete Analysis, vol. 15. Alliance of Diamond Open Access Journals, pp. 1–29, 2018. ista: Browning TD, Heath-Brown R. 2018. Counting rational points on quadric surfaces. Discrete Analysis. 15, 1–29. mla: Browning, Timothy D., and Roger Heath-Brown. “Counting Rational Points on Quadric Surfaces.” Discrete Analysis, vol. 15, Alliance of Diamond Open Access Journals, 2018, pp. 1–29, doi:10.19086/da.4375. short: T.D. Browning, R. Heath-Brown, Discrete Analysis 15 (2018) 1–29. date_created: 2018-12-11T11:45:02Z date_published: 2018-09-07T00:00:00Z date_updated: 2022-08-26T09:13:02Z day: '07' ddc: - '512' doi: 10.19086/da.4375 extern: '1' external_id: arxiv: - '1801.00979' intvolume: ' 15' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1801.00979 month: '09' oa: 1 oa_version: Preprint page: 1 - 29 publication: Discrete Analysis publication_identifier: eissn: - 2397-3129 publication_status: published publisher: Alliance of Diamond Open Access Journals quality_controlled: '1' status: public title: Counting rational points on quadric surfaces tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2018' ... --- _id: '185' abstract: - lang: eng text: We resolve in the affirmative conjectures of A. Skopenkov and Repovš (1998), and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the setting of approximating maps of graphs on 2-dimensional surfaces by embeddings. Our proof of this result is constructive and almost immediately implies an efficient algorithm for testing whether a given piecewise linear map of a graph in a surface is approximable by an embedding. More precisely, an instance of this problem consists of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact surface M given as the union of a set of pairwise disjoint discs corresponding to the clusters and a set of pairwise disjoint "pipes" corresponding to the bundles, connecting certain pairs of these discs. We are to decide whether G can be embedded inside M so that the vertices in every cluster are drawn in the corresponding disc, the edges in every bundle pass only through its corresponding pipe, and every edge crosses the boundary of each disc at most once. alternative_title: - Leibniz International Proceedings in Information, LIPIcs article_number: '39' author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Jan full_name: Kynčl, Jan last_name: Kynčl citation: ama: 'Fulek R, Kynčl J. Hanani-Tutte for approximating maps of graphs. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.39' apa: 'Fulek, R., & Kynčl, J. (2018). Hanani-Tutte for approximating maps of graphs (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.39' chicago: Fulek, Radoslav, and Jan Kynčl. “Hanani-Tutte for Approximating Maps of Graphs,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.39. ieee: 'R. Fulek and J. Kynčl, “Hanani-Tutte for approximating maps of graphs,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.' ista: 'Fulek R, Kynčl J. 2018. Hanani-Tutte for approximating maps of graphs. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 39.' mla: Fulek, Radoslav, and Jan Kynčl. Hanani-Tutte for Approximating Maps of Graphs. Vol. 99, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.39. short: R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. conference: end_date: 2018-06-14 location: Budapest, Hungary name: 'SoCG: Symposium on Computational Geometry' start_date: 2018-06-11 date_created: 2018-12-11T11:45:04Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T06:53:36Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.4230/LIPIcs.SoCG.2018.39 file: - access_level: open_access checksum: f1b94f1a75b37c414a1f61d59fb2cd4c content_type: application/pdf creator: dernst date_created: 2018-12-17T12:33:52Z date_updated: 2020-07-14T12:45:19Z file_id: '5701' file_name: 2018_LIPIcs_Fulek.pdf file_size: 718857 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 99' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 261FA626-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02281 name: Eliminating intersections in drawings of graphs publication_identifier: isbn: - 978-3-95977-066-8 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7735' quality_controlled: '1' scopus_import: 1 status: public title: Hanani-Tutte for approximating maps of graphs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 99 year: '2018' ... --- _id: '188' abstract: - lang: eng text: Smallest enclosing spheres of finite point sets are central to methods in topological data analysis. Focusing on Bregman divergences to measure dissimilarity, we prove bounds on the location of the center of a smallest enclosing sphere. These bounds depend on the range of radii for which Bregman balls are convex. acknowledgement: This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund alternative_title: - Leibniz International Proceedings in Information, LIPIcs author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Ziga full_name: Virk, Ziga last_name: Virk - first_name: Hubert full_name: Wagner, Hubert id: 379CA8B8-F248-11E8-B48F-1D18A9856A87 last_name: Wagner citation: ama: 'Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:35:1-35:13. doi:10.4230/LIPIcs.SoCG.2018.35' apa: 'Edelsbrunner, H., Virk, Z., & Wagner, H. (2018). Smallest enclosing spheres and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.35' chicago: Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.35. ieee: 'H. Edelsbrunner, Z. Virk, and H. Wagner, “Smallest enclosing spheres and Chernoff points in Bregman geometry,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 35:1-35:13.' ista: 'Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13.' mla: Edelsbrunner, Herbert, et al. Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13, doi:10.4230/LIPIcs.SoCG.2018.35. short: H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13. conference: end_date: 2018-06-14 location: Budapest, Hungary name: 'SoCG: Symposium on Computational Geometry' start_date: 2018-06-11 date_created: 2018-12-11T11:45:05Z date_published: 2018-06-11T00:00:00Z date_updated: 2021-01-12T06:53:48Z day: '11' ddc: - '000' department: - _id: HeEd doi: 10.4230/LIPIcs.SoCG.2018.35 file: - access_level: open_access checksum: 7509403803b3ac1aee94bbc2ad293d21 content_type: application/pdf creator: dernst date_created: 2018-12-17T16:31:31Z date_updated: 2020-07-14T12:45:20Z file_id: '5724' file_name: 2018_LIPIcs_Edelsbrunner.pdf file_size: 489080 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 99' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 35:1 - 35:13 project: - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7733' quality_controlled: '1' scopus_import: 1 status: public title: Smallest enclosing spheres and Chernoff points in Bregman geometry tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 99 year: '2018' ... --- _id: '2015' abstract: - lang: eng text: We consider the problem of learning a Bayesian network or directed acyclic graph model from observational data. A number of constraint‐based, score‐based and hybrid algorithms have been developed for this purpose. Statistical consistency guarantees of these algorithms rely on the faithfulness assumption, which has been shown to be restrictive especially for graphs with cycles in the skeleton. We here propose the sparsest permutation (SP) algorithm, showing that learning Bayesian networks is possible under strictly weaker assumptions than faithfulness. This comes at a computational price, thereby indicating a statistical‐computational trade‐off for causal inference algorithms. In the Gaussian noiseless setting, we prove that the SP algorithm boils down to finding the permutation of the variables with the sparsest Cholesky decomposition of the inverse covariance matrix, which is equivalent to ℓ0‐penalized maximum likelihood estimation. We end with a simulation study showing that in line with the proven stronger consistency guarantees, and the SP algorithm compares favourably to standard causal inference algorithms in terms of accuracy for a given sample size. article_number: e183 article_processing_charge: No article_type: original author: - first_name: Garvesh full_name: Raskutti, Garvesh last_name: Raskutti - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 citation: ama: Raskutti G, Uhler C. Learning directed acyclic graphs based on sparsest permutations. STAT. 2018;7(1). doi:10.1002/sta4.183 apa: Raskutti, G., & Uhler, C. (2018). Learning directed acyclic graphs based on sparsest permutations. STAT. Wiley. https://doi.org/10.1002/sta4.183 chicago: Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based on Sparsest Permutations.” STAT. Wiley, 2018. https://doi.org/10.1002/sta4.183. ieee: G. Raskutti and C. Uhler, “Learning directed acyclic graphs based on sparsest permutations,” STAT, vol. 7, no. 1. Wiley, 2018. ista: Raskutti G, Uhler C. 2018. Learning directed acyclic graphs based on sparsest permutations. STAT. 7(1), e183. mla: Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based on Sparsest Permutations.” STAT, vol. 7, no. 1, e183, Wiley, 2018, doi:10.1002/sta4.183. short: G. Raskutti, C. Uhler, STAT 7 (2018). date_created: 2018-12-11T11:55:13Z date_published: 2018-04-17T00:00:00Z date_updated: 2021-01-12T06:54:44Z day: '17' doi: 10.1002/sta4.183 extern: '1' external_id: arxiv: - '1307.0366' intvolume: ' 7' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1307.0366 month: '04' oa: 1 oa_version: Preprint publication: STAT publication_status: published publisher: Wiley publist_id: '5061' quality_controlled: '1' status: public title: Learning directed acyclic graphs based on sparsest permutations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2018' ... --- _id: '306' abstract: - lang: eng text: A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data. article_number: e00596 author: - first_name: Andrea full_name: De Martino, Andrea last_name: De Martino - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 citation: ama: De Martino A, De Martino D. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 2018;4(4). doi:10.1016/j.heliyon.2018.e00596 apa: De Martino, A., & De Martino, D. (2018). An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. Elsevier. https://doi.org/10.1016/j.heliyon.2018.e00596 chicago: De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon. Elsevier, 2018. https://doi.org/10.1016/j.heliyon.2018.e00596. ieee: A. De Martino and D. De Martino, “An introduction to the maximum entropy approach and its application to inference problems in biology,” Heliyon, vol. 4, no. 4. Elsevier, 2018. ista: De Martino A, De Martino D. 2018. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 4(4), e00596. mla: De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon, vol. 4, no. 4, e00596, Elsevier, 2018, doi:10.1016/j.heliyon.2018.e00596. short: A. De Martino, D. De Martino, Heliyon 4 (2018). date_created: 2018-12-11T11:45:44Z date_published: 2018-04-01T00:00:00Z date_updated: 2021-01-12T07:40:46Z day: '01' ddc: - '530' department: - _id: GaTk doi: 10.1016/j.heliyon.2018.e00596 ec_funded: 1 file: - access_level: open_access checksum: 67010cf5e3b3e0637c659371714a715a content_type: application/pdf creator: dernst date_created: 2019-02-06T07:36:24Z date_updated: 2020-07-14T12:45:59Z file_id: '5929' file_name: 2018_Heliyon_DeMartino.pdf file_size: 994490 relation: main_file file_date_updated: 2020-07-14T12:45:59Z has_accepted_license: '1' intvolume: ' 4' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Heliyon publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: 1 status: public title: An introduction to the maximum entropy approach and its application to inference problems in biology tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2018' ... --- _id: '3300' abstract: - lang: eng text: "This book first explores the origins of this idea, grounded in theoretical work on temporal logic and automata. The editors and authors are among the world's leading researchers in this domain, and they contributed 32 chapters representing a thorough view of the development and application of the technique. Topics covered include binary decision diagrams, symbolic model checking, satisfiability modulo theories, partial-order reduction, abstraction, interpolation, concurrency, security protocols, games, probabilistic model checking, and process algebra, and chapters on the transfer of theory to industrial practice, property specification languages for hardware, and verification of real-time systems and hybrid systems.\r\n\r\nThe book will be valuable for researchers and graduate students engaged with the development of formal methods and verification tools." article_processing_charge: No author: - first_name: Edmund M. full_name: Clarke, Edmund M. last_name: Clarke - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Helmut full_name: Veith, Helmut last_name: Veith - first_name: Roderick full_name: Bloem, Roderick last_name: Bloem citation: ama: 'Clarke EM, Henzinger TA, Veith H, Bloem R. Handbook of Model Checking. 1st ed. Cham: Springer Nature; 2018. doi:10.1007/978-3-319-10575-8' apa: 'Clarke, E. M., Henzinger, T. A., Veith, H., & Bloem, R. (2018). Handbook of Model Checking (1st ed.). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-10575-8' chicago: 'Clarke, Edmund M., Thomas A Henzinger, Helmut Veith, and Roderick Bloem. Handbook of Model Checking. 1st ed. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-10575-8.' ieee: 'E. M. Clarke, T. A. Henzinger, H. Veith, and R. Bloem, Handbook of Model Checking, 1st ed. Cham: Springer Nature, 2018.' ista: 'Clarke EM, Henzinger TA, Veith H, Bloem R. 2018. Handbook of Model Checking 1st ed., Cham: Springer Nature, XLVIII, 1212p.' mla: Clarke, Edmund M., et al. Handbook of Model Checking. 1st ed., Springer Nature, 2018, doi:10.1007/978-3-319-10575-8. short: E.M. Clarke, T.A. Henzinger, H. Veith, R. Bloem, Handbook of Model Checking, 1st ed., Springer Nature, Cham, 2018. date_created: 2018-12-11T12:02:32Z date_published: 2018-06-08T00:00:00Z date_updated: 2021-12-21T10:49:36Z day: '08' department: - _id: ToHe doi: 10.1007/978-3-319-10575-8 edition: '1' language: - iso: eng month: '06' oa_version: None page: XLVIII, 1212 place: Cham publication_identifier: eisbn: - 978-3-319-10575-8 isbn: - 978-3-319-10574-1 publication_status: published publisher: Springer Nature publist_id: '3340' quality_controlled: '1' scopus_import: '1' status: public title: Handbook of Model Checking type: book user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2018' ... --- _id: '37' abstract: - lang: eng text: Developmental processes are inherently dynamic and understanding them requires quantitative measurements of gene and protein expression levels in space and time. While live imaging is a powerful approach for obtaining such data, it is still a challenge to apply it over long periods of time to large tissues, such as the embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression and signaling activity patterns in this organ can be studied by collecting tissue sections at different developmental stages. In combination with immunohistochemistry, this allows for measuring the levels of multiple developmental regulators in a quantitative manner with high spatiotemporal resolution. The mean protein expression levels over time, as well as embryo-to-embryo variability can be analyzed. A key aspect of the approach is the ability to compare protein levels across different samples. This requires a number of considerations in sample preparation, imaging and data analysis. Here we present a protocol for obtaining time course data of dorsoventral expression patterns from mouse and chick neural tube in the first 3 days of neural tube development. The described workflow starts from embryo dissection and ends with a processed dataset. Software scripts for data analysis are included. The protocol is adaptable and instructions that allow the user to modify different steps are provided. Thus, the procedure can be altered for analysis of time-lapse images and applied to systems other than the neural tube. alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Marcin P full_name: Zagórski, Marcin P id: 343DA0DC-F248-11E8-B48F-1D18A9856A87 last_name: Zagórski orcid: 0000-0001-7896-7762 - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: 'Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Vol 1863. MIMB. Springer Nature; 2018:47-63. doi:10.1007/978-1-4939-8772-6_4' apa: Zagórski, M. P., & Kicheva, A. (2018). Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In Morphogen Gradients (Vol. 1863, pp. 47–63). Springer Nature. https://doi.org/10.1007/978-1-4939-8772-6_4 chicago: Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” In Morphogen Gradients , 1863:47–63. MIMB. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-8772-6_4. ieee: M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube,” in Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63. ista: 'Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods in Molecular Biology, vol. 1863, 47–63.' mla: Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63, doi:10.1007/978-1-4939-8772-6_4. short: M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63. date_created: 2018-12-11T11:44:17Z date_published: 2018-10-16T00:00:00Z date_updated: 2021-01-12T07:49:03Z day: '16' ddc: - '570' department: - _id: AnKi doi: 10.1007/978-1-4939-8772-6_4 ec_funded: 1 file: - access_level: open_access checksum: 2a97d0649fdcfcf1bdca7c8ad1dce71b content_type: application/pdf creator: dernst date_created: 2020-10-13T14:20:37Z date_updated: 2020-10-13T14:20:37Z file_id: '8656' file_name: 2018_MIMB_Zagorski.pdf file_size: 4906815 relation: main_file success: 1 file_date_updated: 2020-10-13T14:20:37Z has_accepted_license: '1' intvolume: ' 1863' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 47 - 63 project: - _id: B6FC0238-B512-11E9-945C-1524E6697425 call_identifier: H2020 grant_number: '680037' name: Coordination of Patterning And Growth In the Spinal Cord publication: 'Morphogen Gradients ' publication_identifier: isbn: - 978-1-4939-8771-9 issn: - 1064-3745 publication_status: published publisher: Springer Nature publist_id: '8018' quality_controlled: '1' scopus_import: '1' series_title: MIMB status: public title: Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1863 year: '2018' ... --- _id: '305' abstract: - lang: eng text: The hanging-drop network (HDN) is a technology platform based on a completely open microfluidic network at the bottom of an inverted, surface-patterned substrate. The platform is predominantly used for the formation, culturing, and interaction of self-assembled spherical microtissues (spheroids) under precisely controlled flow conditions. Here, we describe design, fabrication, and operation of microfluidic hanging-drop networks. acknowledgement: This work was financially supported by FP7 of the EU through the project “Body on a chip,” ICT-FET-296257, and the ERC Advanced Grant “NeuroCMOS” (contract 267351), as well as by an individual Ambizione Grant 142440 from the Swiss National Science Foundation for Olivier Frey. The research leading to these results also received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734]. We would like to thank Alexander Stettler, ETH Zurich for his expertise and support in the cleanroom, and we acknowledge the Single Cell Unit of D-BSSE, ETH Zurich for assistance in microscopy issues. M.L. is grateful to the members of the Guet and Tkačik groups, IST Austria, for valuable comments and support. alternative_title: - MIMB author: - first_name: Patrick full_name: Misun, Patrick last_name: Misun - first_name: Axel full_name: Birchler, Axel last_name: Birchler - first_name: Moritz full_name: Lang, Moritz id: 29E0800A-F248-11E8-B48F-1D18A9856A87 last_name: Lang - first_name: Andreas full_name: Hierlemann, Andreas last_name: Hierlemann - first_name: Olivier full_name: Frey, Olivier last_name: Frey citation: ama: Misun P, Birchler A, Lang M, Hierlemann A, Frey O. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 2018;1771:183-202. doi:10.1007/978-1-4939-7792-5_15 apa: Misun, P., Birchler, A., Lang, M., Hierlemann, A., & Frey, O. (2018). Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-4939-7792-5_15 chicago: Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology. Springer, 2018. https://doi.org/10.1007/978-1-4939-7792-5_15. ieee: P. Misun, A. Birchler, M. Lang, A. Hierlemann, and O. Frey, “Fabrication and operation of microfluidic hanging drop networks,” Methods in Molecular Biology, vol. 1771. Springer, pp. 183–202, 2018. ista: Misun P, Birchler A, Lang M, Hierlemann A, Frey O. 2018. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 1771, 183–202. mla: Misun, Patrick, et al. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology, vol. 1771, Springer, 2018, pp. 183–202, doi:10.1007/978-1-4939-7792-5_15. short: P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular Biology 1771 (2018) 183–202. date_created: 2018-12-11T11:45:43Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T07:40:42Z day: '01' department: - _id: CaGu - _id: GaTk doi: 10.1007/978-1-4939-7792-5_15 ec_funded: 1 intvolume: ' 1771' language: - iso: eng month: '01' oa_version: None page: 183 - 202 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Methods in Molecular Biology publication_status: published publisher: Springer publist_id: '7574' quality_controlled: '1' scopus_import: 1 status: public title: Fabrication and operation of microfluidic hanging drop networks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1771 year: '2018' ... --- _id: '325' abstract: - lang: eng text: Probabilistic programs extend classical imperative programs with real-valued random variables and random branching. The most basic liveness property for such programs is the termination property. The qualitative (aka almost-sure) termination problem asks whether a given program program terminates with probability 1. While ranking functions provide a sound and complete method for non-probabilistic programs, the extension of them to probabilistic programs is achieved via ranking supermartingales (RSMs). Although deep theoretical results have been established about RSMs, their application to probabilistic programs with nondeterminism has been limited only to programs of restricted control-flow structure. For non-probabilistic programs, lexicographic ranking functions provide a compositional and practical approach for termination analysis of real-world programs. In this work we introduce lexicographic RSMs and show that they present a sound method for almost-sure termination of probabilistic programs with nondeterminism. We show that lexicographic RSMs provide a tool for compositional reasoning about almost-sure termination, and for probabilistic programs with linear arithmetic they can be synthesized efficiently (in polynomial time). We also show that with additional restrictions even asymptotic bounds on expected termination time can be obtained through lexicographic RSMs. Finally, we present experimental results on benchmarks adapted from previous work to demonstrate the effectiveness of our approach. article_number: '34' author: - first_name: Sheshansh full_name: Agrawal, Sheshansh last_name: Agrawal - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny citation: ama: 'Agrawal S, Chatterjee K, Novotný P. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. In: Vol 2. ACM; 2018. doi:10.1145/3158122' apa: 'Agrawal, S., Chatterjee, K., & Novotný, P. (2018). Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs (Vol. 2). Presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/3158122' chicago: 'Agrawal, Sheshansh, Krishnendu Chatterjee, and Petr Novotný. “Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs,” Vol. 2. ACM, 2018. https://doi.org/10.1145/3158122.' ieee: 'S. Agrawal, K. Chatterjee, and P. Novotný, “Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs,” presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA, 2018, vol. 2, no. POPL.' ista: 'Agrawal S, Chatterjee K, Novotný P. 2018. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. POPL: Principles of Programming Languages vol. 2, 34.' mla: 'Agrawal, Sheshansh, et al. Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs. Vol. 2, no. POPL, 34, ACM, 2018, doi:10.1145/3158122.' short: S. Agrawal, K. Chatterjee, P. Novotný, in:, ACM, 2018. conference: end_date: 2018-01-13 location: Los Angeles, CA, USA name: 'POPL: Principles of Programming Languages' start_date: 2018-01-07 date_created: 2018-12-11T11:45:50Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T07:42:07Z day: '01' department: - _id: KrCh doi: 10.1145/3158122 external_id: arxiv: - '1709.04037' intvolume: ' 2' issue: POPL language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1709.04037 month: '01' oa: 1 oa_version: Preprint project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: ACM publist_id: '7540' quality_controlled: '1' status: public title: 'Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2018' ... --- _id: '394' abstract: - lang: eng text: 'The valley pseudospin in monolayer transition metal dichalcogenides (TMDs) has been proposed as a new way to manipulate information in various optoelectronic devices. This relies on a large valley polarization that remains stable over long time scales (hundreds of nanoseconds). However, time-resolved measurements report valley lifetimes of only a few picoseconds. This has been attributed to mechanisms such as phonon-mediated intervalley scattering and a precession of the valley pseudospin through electron-hole exchange. Here we use transient spin grating to directly measure the valley depolarization lifetime in monolayer MoSe2. We find a fast valley decay rate that scales linearly with the excitation density at different temperatures. This establishes the presence of strong exciton-exciton Coulomb exchange interactions enhancing the valley depolarization. Our work highlights the microscopic processes inhibiting the efficient use of the exciton valley pseudospin in monolayer TMDs. ' author: - first_name: Fahad full_name: Mahmood, Fahad last_name: Mahmood - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 - first_name: Yi full_name: Lee, Yi last_name: Lee - first_name: Jing full_name: Kong, Jing last_name: Kong - first_name: Nuh full_name: Gedik, Nuh last_name: Gedik citation: ama: Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. 2018;18(1):223-228. doi:10.1021/acs.nanolett.7b03953 apa: Mahmood, F., Alpichshev, Z., Lee, Y., Kong, J., & Gedik, N. (2018). Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b03953 chicago: Mahmood, Fahad, Zhanybek Alpichshev, Yi Lee, Jing Kong, and Nuh Gedik. “Observation of Exciton-Exciton Interaction Mediated Valley Depolarization in Monolayer MoSe2.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.7b03953. ieee: F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, and N. Gedik, “Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2,” Nano Letters, vol. 18, no. 1. American Chemical Society, pp. 223–228, 2018. ista: Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. 2018. Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. 18(1), 223–228. mla: Mahmood, Fahad, et al. “Observation of Exciton-Exciton Interaction Mediated Valley Depolarization in Monolayer MoSe2.” Nano Letters, vol. 18, no. 1, American Chemical Society, 2018, pp. 223–28, doi:10.1021/acs.nanolett.7b03953. short: F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, N. Gedik, Nano Letters 18 (2018) 223–228. date_created: 2018-12-11T11:46:13Z date_published: 2018-01-10T00:00:00Z date_updated: 2021-01-12T07:53:20Z day: '10' doi: 10.1021/acs.nanolett.7b03953 extern: '1' external_id: arxiv: - '1712.07925' intvolume: ' 18' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.07925 month: '01' oa: 1 oa_version: Submitted Version page: 223 - 228 publication: Nano Letters publication_status: published publisher: American Chemical Society publist_id: '7435' quality_controlled: '1' status: public title: Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2018' ... --- _id: '408' abstract: - lang: eng text: Adventitious roots (AR) are de novo formed roots that emerge from any part of the plant or from callus in tissue culture, except root tissue. The plant tissue origin and the method by which they are induced determine the physiological properties of emerged ARs. Hence, a standard method encompassing all types of AR does not exist. Here we describe a method for the induction and analysis of AR that emerge from the etiolated hypocotyl of dicot plants. The hypocotyl is formed during embryogenesis and shows a determined developmental pattern which usually does not involve AR formation. However, the hypocotyl shows propensity to form de novo roots under specific circumstances such as removal of the root system, high humidity or flooding, or during de-etiolation. The hypocotyl AR emerge from a pericycle-like cell layer surrounding the vascular tissue of the central cylinder, which is reminiscent to the developmental program of lateral roots. Here we propose an easy protocol for in vitro hypocotyl AR induction from etiolated Arabidopsis seedlings. alternative_title: - MIMB article_processing_charge: No author: - first_name: Hoang full_name: Trinh, Hoang last_name: Trinh - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: Danny full_name: Geelen, Danny last_name: Geelen citation: ama: 'Trinh H, Verstraeten I, Geelen D. In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . Vol 1761. Springer Nature; 2018:95-102. doi:10.1007/978-1-4939-7747-5_7' apa: Trinh, H., Verstraeten, I., & Geelen, D. (2018). In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In Root Development (Vol. 1761, pp. 95–102). Springer Nature. https://doi.org/10.1007/978-1-4939-7747-5_7 chicago: Trinh, Hoang, Inge Verstraeten, and Danny Geelen. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” In Root Development , 1761:95–102. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-7747-5_7. ieee: H. Trinh, I. Verstraeten, and D. Geelen, “In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls,” in Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102. ista: 'Trinh H, Verstraeten I, Geelen D. 2018.In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . MIMB, vol. 1761, 95–102.' mla: Trinh, Hoang, et al. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102, doi:10.1007/978-1-4939-7747-5_7. short: H. Trinh, I. Verstraeten, D. Geelen, in:, Root Development , Springer Nature, 2018, pp. 95–102. date_created: 2018-12-11T11:46:18Z date_published: 2018-03-01T00:00:00Z date_updated: 2021-01-12T07:54:21Z day: '01' department: - _id: JiFr doi: 10.1007/978-1-4939-7747-5_7 external_id: pmid: - '29525951' intvolume: ' 1761' language: - iso: eng month: '03' oa_version: None page: 95 - 102 pmid: 1 publication: 'Root Development ' publication_identifier: issn: - 1064-3745 publication_status: published publisher: Springer Nature publist_id: '7421' quality_controlled: '1' scopus_import: '1' status: public title: In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1761 year: '2018' ... --- _id: '411' abstract: - lang: eng text: Immunolocalization is a valuable tool for cell biology research that allows to rapidly determine the localization and expression levels of endogenous proteins. In plants, whole-mount in situ immunolocalization remains a challenging method, especially in tissues protected by waxy layers and complex cell wall carbohydrates. Here, we present a robust method for whole-mount in situ immunolocalization in primary root meristems and lateral root primordia in Arabidopsis thaliana. For good epitope preservation, fixation is done in an alkaline paraformaldehyde/glutaraldehyde mixture. This fixative is suitable for detecting a wide range of proteins, including integral transmembrane proteins and proteins peripherally attached to the plasma membrane. From initiation until emergence from the primary root, lateral root primordia are surrounded by several layers of differentiated tissues with a complex cell wall composition that interferes with the efficient penetration of all buffers. Therefore, immunolocalization in early lateral root primordia requires a modified method, including a strong solvent treatment for removal of hydrophobic barriers and a specific cocktail of cell wall-degrading enzymes. The presented method allows for easy, reliable, and high-quality in situ detection of the subcellular localization of endogenous proteins in primary and lateral root meristems without the need of time-consuming crosses or making translational fusions to fluorescent proteins. alternative_title: - Methods in Molecular Biology author: - first_name: Michael full_name: Karampelias, Michael last_name: Karampelias - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste citation: ama: 'Karampelias M, Tejos R, Friml J, Vanneste S. Optimized whole mount in situ immunolocalization for Arabidopsis thaliana  root meristems and lateral root primordia. In: Ristova D, Barbez E, eds. Root Development. Methods and Protocols. Vol 1761. MIMB. Springer; 2018:131-143. doi:10.1007/978-1-4939-7747-5_10' apa: Karampelias, M., Tejos, R., Friml, J., & Vanneste, S. (2018). Optimized whole mount in situ immunolocalization for Arabidopsis thaliana  root meristems and lateral root primordia. In D. Ristova & E. Barbez (Eds.), Root Development. Methods and Protocols (Vol. 1761, pp. 131–143). Springer. https://doi.org/10.1007/978-1-4939-7747-5_10 chicago: Karampelias, Michael, Ricardo Tejos, Jiří Friml, and Steffen Vanneste. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana  Root Meristems and Lateral Root Primordia.” In Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, 1761:131–43. MIMB. Springer, 2018. https://doi.org/10.1007/978-1-4939-7747-5_10. ieee: M. Karampelias, R. Tejos, J. Friml, and S. Vanneste, “Optimized whole mount in situ immunolocalization for Arabidopsis thaliana  root meristems and lateral root primordia,” in Root Development. Methods and Protocols, vol. 1761, D. Ristova and E. Barbez, Eds. Springer, 2018, pp. 131–143. ista: 'Karampelias M, Tejos R, Friml J, Vanneste S. 2018.Optimized whole mount in situ immunolocalization for Arabidopsis thaliana  root meristems and lateral root primordia. In: Root Development. Methods and Protocols. Methods in Molecular Biology, vol. 1761, 131–143.' mla: Karampelias, Michael, et al. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana  Root Meristems and Lateral Root Primordia.” Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, vol. 1761, Springer, 2018, pp. 131–43, doi:10.1007/978-1-4939-7747-5_10. short: M. Karampelias, R. Tejos, J. Friml, S. Vanneste, in:, D. Ristova, E. Barbez (Eds.), Root Development. Methods and Protocols, Springer, 2018, pp. 131–143. date_created: 2018-12-11T11:46:20Z date_published: 2018-03-11T00:00:00Z date_updated: 2021-01-12T07:54:34Z day: '11' department: - _id: JiFr doi: 10.1007/978-1-4939-7747-5_10 editor: - first_name: Daniela full_name: Ristova, Daniela last_name: Ristova - first_name: Elke full_name: Barbez, Elke last_name: Barbez intvolume: ' 1761' language: - iso: eng month: '03' oa_version: None page: 131 - 143 publication: Root Development. Methods and Protocols publication_status: published publisher: Springer publist_id: '7418' quality_controlled: '1' scopus_import: 1 series_title: MIMB status: public title: Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 1761 year: '2018' ... --- _id: '456' abstract: - lang: eng text: 'Inhibition of the endoplasmic reticulum stress pathway may hold the key to Zika virus-associated microcephaly treatment. ' article_number: eaar7514 author: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: 'Novarino G. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 2018;10(423). doi:10.1126/scitranslmed.aar7514' apa: 'Novarino, G. (2018). Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aar7514' chicago: 'Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” Science Translational Medicine. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/scitranslmed.aar7514.' ieee: 'G. Novarino, “Zika-associated microcephaly: Reduce the stress and race for the treatment,” Science Translational Medicine, vol. 10, no. 423. American Association for the Advancement of Science, 2018.' ista: 'Novarino G. 2018. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 10(423), eaar7514.' mla: 'Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” Science Translational Medicine, vol. 10, no. 423, eaar7514, American Association for the Advancement of Science, 2018, doi:10.1126/scitranslmed.aar7514.' short: G. Novarino, Science Translational Medicine 10 (2018). date_created: 2018-12-11T11:46:34Z date_published: 2018-01-10T00:00:00Z date_updated: 2021-01-12T07:59:42Z day: '10' department: - _id: GaNo doi: 10.1126/scitranslmed.aar7514 intvolume: ' 10' issue: '423' language: - iso: eng month: '01' oa_version: None publication: Science Translational Medicine publication_status: published publisher: American Association for the Advancement of Science publist_id: '7365' quality_controlled: '1' scopus_import: 1 status: public title: 'Zika-associated microcephaly: Reduce the stress and race for the treatment' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2018' ... --- _id: '53' abstract: - lang: eng text: In 2013, a publication repository was implemented at IST Austria and 2015 after a thorough preparation phase a data repository was implemented - both based on the Open Source Software EPrints. In this text, designed as field report, we will reflect on our experiences with Open Source Software in general and specifically with EPrints regarding technical aspects but also regarding their characteristics of the user community. The second part is a pleading for including the end users in the process of implementation, adaption and evaluation. author: - first_name: Barbara full_name: Petritsch, Barbara id: 406048EC-F248-11E8-B48F-1D18A9856A87 last_name: Petritsch orcid: 0000-0003-2724-4614 - first_name: Jana full_name: Porsche, Jana id: 3252EDC2-F248-11E8-B48F-1D18A9856A87 last_name: Porsche citation: ama: 'Petritsch B, Porsche J. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 2018;71(1):199-206. doi:10.31263/voebm.v71i1.1993' apa: 'Petritsch, B., & Porsche, J. (2018). IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v71i1.1993' chicago: 'Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018. https://doi.org/10.31263/voebm.v71i1.1993.' ieee: 'B. Petritsch and J. Porsche, “IST PubRep and IST DataRep: the institutional repositories at IST Austria,” VÖB Mitteilungen, vol. 71, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 199–206, 2018.' ista: 'Petritsch B, Porsche J. 2018. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 71(1), 199–206.' mla: 'Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen, vol. 71, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018, pp. 199–206, doi:10.31263/voebm.v71i1.1993.' short: B. Petritsch, J. Porsche, VÖB Mitteilungen 71 (2018) 199–206. date_created: 2018-12-11T11:44:22Z date_published: 2018-10-01T00:00:00Z date_updated: 2021-01-12T08:01:26Z day: '01' ddc: - '020' department: - _id: E-Lib doi: 10.31263/voebm.v71i1.1993 file: - access_level: open_access checksum: 7ac61bade5f37db011ca435ebcf86797 content_type: application/pdf creator: dernst date_created: 2018-12-17T12:40:27Z date_updated: 2020-07-14T12:46:38Z file_id: '5702' file_name: 2018_VOEB_Petritsch.pdf file_size: 509434 relation: main_file file_date_updated: 2020-07-14T12:46:38Z has_accepted_license: '1' intvolume: ' 71' issue: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 199 - 206 publication: VÖB Mitteilungen publication_status: published publisher: Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare publist_id: '8001' scopus_import: 1 status: public title: 'IST PubRep and IST DataRep: the institutional repositories at IST Austria' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 71 year: '2018' ... --- _id: '536' abstract: - lang: eng text: 'We consider the problem of consensus in the challenging classic model. In this model, the adversary is adaptive; it can choose which processors crash at any point during the course of the algorithm. Further, communication is via asynchronous message passing: there is no known upper bound on the time to send a message from one processor to another, and all messages and coin flips are seen by the adversary. We describe a new randomized consensus protocol with expected message complexity O(n2log2n) when fewer than n / 2 processes may fail by crashing. This is an almost-linear improvement over the best previously known protocol, and within logarithmic factors of a known Ω(n2) message lower bound. The protocol further ensures that no process sends more than O(nlog3n) messages in expectation, which is again within logarithmic factors of optimal. We also present a generalization of the algorithm to an arbitrary number of failures t, which uses expected O(nt+t2log2t) total messages. Our approach is to build a message-efficient, resilient mechanism for aggregating individual processor votes, implementing the message-passing equivalent of a weak shared coin. Roughly, in our protocol, a processor first announces its votes to small groups, then propagates them to increasingly larger groups as it generates more and more votes. To bound the number of messages that an individual process might have to send or receive, the protocol progressively increases the weight of generated votes. The main technical challenge is bounding the impact of votes that are still “in flight” (generated, but not fully propagated) on the final outcome of the shared coin, especially since such votes might have different weights. We achieve this by leveraging the structure of the algorithm, and a technical argument based on martingale concentration bounds. Overall, we show that it is possible to build an efficient message-passing implementation of a shared coin, and in the process (almost-optimally) solve the classic consensus problem in the asynchronous message-passing model.' article_processing_charge: Yes (via OA deal) author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: James full_name: Aspnes, James last_name: Aspnes - first_name: Valerie full_name: King, Valerie last_name: King - first_name: Jared full_name: Saia, Jared last_name: Saia citation: ama: Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized consensus. Distributed Computing. 2018;31(6):489-501. doi:10.1007/s00446-017-0315-1 apa: Alistarh, D.-A., Aspnes, J., King, V., & Saia, J. (2018). Communication-efficient randomized consensus. Distributed Computing. Springer. https://doi.org/10.1007/s00446-017-0315-1 chicago: Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient Randomized Consensus.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-017-0315-1. ieee: D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient randomized consensus,” Distributed Computing, vol. 31, no. 6. Springer, pp. 489–501, 2018. ista: Alistarh D-A, Aspnes J, King V, Saia J. 2018. Communication-efficient randomized consensus. Distributed Computing. 31(6), 489–501. mla: Alistarh, Dan-Adrian, et al. “Communication-Efficient Randomized Consensus.” Distributed Computing, vol. 31, no. 6, Springer, 2018, pp. 489–501, doi:10.1007/s00446-017-0315-1. short: D.-A. Alistarh, J. Aspnes, V. King, J. Saia, Distributed Computing 31 (2018) 489–501. date_created: 2018-12-11T11:47:01Z date_published: 2018-11-01T00:00:00Z date_updated: 2023-02-23T12:23:25Z day: '01' ddc: - '000' department: - _id: DaAl doi: 10.1007/s00446-017-0315-1 file: - access_level: open_access checksum: 69b46e537acdcac745237ddb853fcbb5 content_type: application/pdf creator: dernst date_created: 2019-01-22T07:25:51Z date_updated: 2020-07-14T12:46:38Z file_id: '5867' file_name: 2017_DistribComp_Alistarh.pdf file_size: 595707 relation: main_file file_date_updated: 2020-07-14T12:46:38Z has_accepted_license: '1' intvolume: ' 31' issue: '6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 489-501 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Distributed Computing publication_identifier: issn: - '01782770' publication_status: published publisher: Springer publist_id: '7281' quality_controlled: '1' scopus_import: 1 status: public title: Communication-efficient randomized consensus tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2018' ... --- _id: '554' abstract: - lang: eng text: We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a first-order phase transition and, in the limit (Formula presented.), we determine the critical temperature to be (Formula presented.) to leading order. Here, (Formula presented.) is the critical temperature of the free Bose gas, ρ is the density of the gas and a is the scattering length of the pair-interaction potential V. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula in the limit (Formula presented.). author: - first_name: Marcin M full_name: Napiórkowski, Marcin M id: 4197AD04-F248-11E8-B48F-1D18A9856A87 last_name: Napiórkowski - first_name: Robin full_name: Reuvers, Robin last_name: Reuvers - first_name: Jan full_name: Solovej, Jan last_name: Solovej citation: ama: 'Napiórkowski MM, Reuvers R, Solovej J. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 2018;360(1):347-403. doi:10.1007/s00220-017-3064-x' apa: 'Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-017-3064-x' chicago: 'Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” Communications in Mathematical Physics. Springer, 2018. https://doi.org/10.1007/s00220-017-3064-x.' ieee: 'M. M. Napiórkowski, R. Reuvers, and J. Solovej, “The Bogoliubov free energy functional II: The dilute Limit,” Communications in Mathematical Physics, vol. 360, no. 1. Springer, pp. 347–403, 2018.' ista: 'Napiórkowski MM, Reuvers R, Solovej J. 2018. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 360(1), 347–403.' mla: 'Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” Communications in Mathematical Physics, vol. 360, no. 1, Springer, 2018, pp. 347–403, doi:10.1007/s00220-017-3064-x.' short: M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical Physics 360 (2018) 347–403. date_created: 2018-12-11T11:47:09Z date_published: 2018-05-01T00:00:00Z date_updated: 2021-01-12T08:02:35Z day: '01' department: - _id: RoSe doi: 10.1007/s00220-017-3064-x external_id: arxiv: - '1511.05953' intvolume: ' 360' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1511.05953 month: '05' oa: 1 oa_version: Submitted Version page: 347-403 project: - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems publication: Communications in Mathematical Physics publication_identifier: issn: - '00103616' publication_status: published publisher: Springer publist_id: '7260' quality_controlled: '1' scopus_import: 1 status: public title: 'The Bogoliubov free energy functional II: The dilute Limit' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 360 year: '2018' ... --- _id: '562' abstract: - lang: eng text: Primary neuronal cell culture preparations are widely used to investigate synaptic functions. This chapter describes a detailed protocol for the preparation of a neuronal cell culture in which giant calyx-type synaptic terminals are formed. This chapter also presents detailed protocols for utilizing the main technical advantages provided by such a preparation, namely, labeling and imaging of synaptic organelles and electrophysiological recordings directly from presynaptic terminals. alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Dimitar full_name: Dimitrov, Dimitar last_name: Dimitrov - first_name: Laurent full_name: Guillaud, Laurent last_name: Guillaud - first_name: Kohgaku full_name: Eguchi, Kohgaku id: 2B7846DC-F248-11E8-B48F-1D18A9856A87 last_name: Eguchi orcid: 0000-0002-6170-2546 - first_name: Tomoyuki full_name: Takahashi, Tomoyuki last_name: Takahashi citation: ama: 'Dimitrov D, Guillaud L, Eguchi K, Takahashi T. Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Skaper SD, ed. Neurotrophic Factors. Vol 1727. Springer; 2018:201-215. doi:10.1007/978-1-4939-7571-6_15' apa: Dimitrov, D., Guillaud, L., Eguchi, K., & Takahashi, T. (2018). Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In S. D. Skaper (Ed.), Neurotrophic Factors (Vol. 1727, pp. 201–215). Springer. https://doi.org/10.1007/978-1-4939-7571-6_15 chicago: Dimitrov, Dimitar, Laurent Guillaud, Kohgaku Eguchi, and Tomoyuki Takahashi. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” In Neurotrophic Factors, edited by Stephen D. Skaper, 1727:201–15. Springer, 2018. https://doi.org/10.1007/978-1-4939-7571-6_15. ieee: D. Dimitrov, L. Guillaud, K. Eguchi, and T. Takahashi, “Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses,” in Neurotrophic Factors, vol. 1727, S. D. Skaper, Ed. Springer, 2018, pp. 201–215. ista: 'Dimitrov D, Guillaud L, Eguchi K, Takahashi T. 2018.Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Neurotrophic Factors. Methods in Molecular Biology, vol. 1727, 201–215.' mla: Dimitrov, Dimitar, et al. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” Neurotrophic Factors, edited by Stephen D. Skaper, vol. 1727, Springer, 2018, pp. 201–15, doi:10.1007/978-1-4939-7571-6_15. short: D. Dimitrov, L. Guillaud, K. Eguchi, T. Takahashi, in:, S.D. Skaper (Ed.), Neurotrophic Factors, Springer, 2018, pp. 201–215. date_created: 2018-12-11T11:47:11Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T08:03:05Z day: '01' ddc: - '570' department: - _id: RySh doi: 10.1007/978-1-4939-7571-6_15 editor: - first_name: Stephen D. full_name: Skaper, Stephen D. last_name: Skaper external_id: pmid: - '29222783' file: - access_level: open_access checksum: 8aa174ca65a56fbb19e9f88cff3ac3fd content_type: application/pdf creator: dernst date_created: 2019-11-19T07:47:43Z date_updated: 2020-07-14T12:47:09Z file_id: '7046' file_name: 2018_NeurotrophicFactors_Dimitrov.pdf file_size: 787407 relation: main_file file_date_updated: 2020-07-14T12:47:09Z has_accepted_license: '1' intvolume: ' 1727' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 201 - 215 pmid: 1 publication: Neurotrophic Factors publication_status: published publisher: Springer publist_id: '7252' quality_controlled: '1' scopus_import: 1 status: public title: Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1727 year: '2018' ... --- _id: '59' abstract: - lang: eng text: Graph-based games are an important tool in computer science. They have applications in synthesis, verification, refinement, and far beyond. We review graphbased games with objectives on infinite plays. We give definitions and algorithms to solve the games and to give a winning strategy. The objectives we consider are mostly Boolean, but we also look at quantitative graph-based games and their objectives. Synthesis aims to turn temporal logic specifications into correct reactive systems. We explain the reduction of synthesis to graph-based games (or equivalently tree automata) using synthesis of LTL specifications as an example. We treat the classical approach that uses determinization of parity automata and more modern approaches. author: - first_name: Roderick full_name: Bloem, Roderick last_name: Bloem - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann citation: ama: 'Bloem R, Chatterjee K, Jobstmann B. Graph games and reactive synthesis. In: Henzinger TA, Clarke EM, Veith H, Bloem R, eds. Handbook of Model Checking. 1st ed. Springer; 2018:921-962. doi:10.1007/978-3-319-10575-8_27' apa: Bloem, R., Chatterjee, K., & Jobstmann, B. (2018). Graph games and reactive synthesis. In T. A. Henzinger, E. M. Clarke, H. Veith, & R. Bloem (Eds.), Handbook of Model Checking (1st ed., pp. 921–962). Springer. https://doi.org/10.1007/978-3-319-10575-8_27 chicago: Bloem, Roderick, Krishnendu Chatterjee, and Barbara Jobstmann. “Graph Games and Reactive Synthesis.” In Handbook of Model Checking, edited by Thomas A Henzinger, Edmund M. Clarke, Helmut Veith, and Roderick Bloem, 1st ed., 921–62. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_27. ieee: R. Bloem, K. Chatterjee, and B. Jobstmann, “Graph games and reactive synthesis,” in Handbook of Model Checking, 1st ed., T. A. Henzinger, E. M. Clarke, H. Veith, and R. Bloem, Eds. Springer, 2018, pp. 921–962. ista: 'Bloem R, Chatterjee K, Jobstmann B. 2018.Graph games and reactive synthesis. In: Handbook of Model Checking. , 921–962.' mla: Bloem, Roderick, et al. “Graph Games and Reactive Synthesis.” Handbook of Model Checking, edited by Thomas A Henzinger et al., 1st ed., Springer, 2018, pp. 921–62, doi:10.1007/978-3-319-10575-8_27. short: R. Bloem, K. Chatterjee, B. Jobstmann, in:, T.A. Henzinger, E.M. Clarke, H. Veith, R. Bloem (Eds.), Handbook of Model Checking, 1st ed., Springer, 2018, pp. 921–962. date_created: 2018-12-11T11:44:24Z date_published: 2018-05-19T00:00:00Z date_updated: 2021-01-12T08:05:10Z day: '19' department: - _id: KrCh doi: 10.1007/978-3-319-10575-8_27 edition: '1' editor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Edmund M. full_name: Clarke, Edmund M. last_name: Clarke - first_name: Helmut full_name: Veith, Helmut last_name: Veith - first_name: Roderick full_name: Bloem, Roderick last_name: Bloem language: - iso: eng month: '05' oa_version: None page: 921 - 962 publication: Handbook of Model Checking publication_identifier: isbn: - 978-3-319-10574-1 publication_status: published publisher: Springer publist_id: '7995' quality_controlled: '1' scopus_import: 1 status: public title: Graph games and reactive synthesis type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '60' abstract: - lang: eng text: Model checking is a computer-assisted method for the analysis of dynamical systems that can be modeled by state-transition systems. Drawing from research traditions in mathematical logic, programming languages, hardware design, and theoretical computer science, model checking is now widely used for the verification of hardware and software in industry. This chapter is an introduction and short survey of model checking. The chapter aims to motivate and link the individual chapters of the handbook, and to provide context for readers who are not familiar with model checking. author: - first_name: Edmund full_name: Clarke, Edmund last_name: Clarke - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Helmut full_name: Veith, Helmut last_name: Veith citation: ama: 'Clarke E, Henzinger TA, Veith H. Introduction to model checking. In: Henzinger TA, ed. Handbook of Model Checking. Handbook of Model Checking. Springer; 2018:1-26. doi:10.1007/978-3-319-10575-8_1' apa: Clarke, E., Henzinger, T. A., & Veith, H. (2018). Introduction to model checking. In T. A. Henzinger (Ed.), Handbook of Model Checking (pp. 1–26). Springer. https://doi.org/10.1007/978-3-319-10575-8_1 chicago: Clarke, Edmund, Thomas A Henzinger, and Helmut Veith. “Introduction to Model Checking.” In Handbook of Model Checking, edited by Thomas A Henzinger, 1–26. Handbook of Model Checking. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_1. ieee: E. Clarke, T. A. Henzinger, and H. Veith, “Introduction to model checking,” in Handbook of Model Checking, T. A. Henzinger, Ed. Springer, 2018, pp. 1–26. ista: 'Clarke E, Henzinger TA, Veith H. 2018.Introduction to model checking. In: Handbook of Model Checking. , 1–26.' mla: Clarke, Edmund, et al. “Introduction to Model Checking.” Handbook of Model Checking, edited by Thomas A Henzinger, Springer, 2018, pp. 1–26, doi:10.1007/978-3-319-10575-8_1. short: E. Clarke, T.A. Henzinger, H. Veith, in:, T.A. Henzinger (Ed.), Handbook of Model Checking, Springer, 2018, pp. 1–26. date_created: 2018-12-11T11:44:25Z date_published: 2018-05-19T00:00:00Z date_updated: 2021-01-12T08:05:35Z day: '19' department: - _id: ToHe doi: 10.1007/978-3-319-10575-8_1 editor: - first_name: Thomas A full_name: Henzinger, Thomas A last_name: Henzinger language: - iso: eng month: '05' oa_version: None page: 1 - 26 publication: Handbook of Model Checking publication_status: published publisher: Springer publist_id: '7994' quality_controlled: '1' scopus_import: 1 series_title: Handbook of Model Checking status: public title: Introduction to model checking type: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '61' abstract: - lang: eng text: 'We prove that there is no strongly regular graph (SRG) with parameters (460; 153; 32; 60). The proof is based on a recent lower bound on the number of 4-cliques in a SRG and some applications of Euclidean representation of SRGs. ' article_processing_charge: No author: - first_name: Andriy full_name: Bondarenko, Andriy last_name: Bondarenko - first_name: Anton full_name: Mellit, Anton id: 388D3134-F248-11E8-B48F-1D18A9856A87 last_name: Mellit - first_name: Andriy full_name: Prymak, Andriy last_name: Prymak - first_name: Danylo full_name: Radchenko, Danylo last_name: Radchenko - first_name: Maryna full_name: Viazovska, Maryna last_name: Viazovska citation: ama: 'Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. Springer; 2018:131-134. doi:10.1007/978-3-319-72456-0_7' apa: Bondarenko, A., Mellit, A., Prymak, A., Radchenko, D., & Viazovska, M. (2018). There is no strongly regular graph with parameters (460; 153; 32; 60). In Contemporary Computational Mathematics (pp. 131–134). Springer. https://doi.org/10.1007/978-3-319-72456-0_7 chicago: Bondarenko, Andriy, Anton Mellit, Andriy Prymak, Danylo Radchenko, and Maryna Viazovska. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” In Contemporary Computational Mathematics, 131–34. Springer, 2018. https://doi.org/10.1007/978-3-319-72456-0_7. ieee: A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, and M. Viazovska, “There is no strongly regular graph with parameters (460; 153; 32; 60),” in Contemporary Computational Mathematics, Springer, 2018, pp. 131–134. ista: 'Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. 2018.There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. , 131–134.' mla: Bondarenko, Andriy, et al. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” Contemporary Computational Mathematics, Springer, 2018, pp. 131–34, doi:10.1007/978-3-319-72456-0_7. short: A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, M. Viazovska, in:, Contemporary Computational Mathematics, Springer, 2018, pp. 131–134. date_created: 2018-12-11T11:44:25Z date_published: 2018-05-23T00:00:00Z date_updated: 2021-01-12T08:06:06Z day: '23' department: - _id: TaHa doi: 10.1007/978-3-319-72456-0_7 extern: '1' external_id: arxiv: - '1509.06286' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1509.06286 month: '05' oa: 1 oa_version: Preprint page: 131 - 134 publication: Contemporary Computational Mathematics publication_status: published publisher: Springer publist_id: '7993' quality_controlled: '1' status: public title: There is no strongly regular graph with parameters (460; 153; 32; 60) type: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6111' abstract: - lang: eng text: 'Neurons develop elaborate morphologies that provide a model for understanding cellular architecture. By studying C. elegans sensory dendrites, we previously identified genes that act to promote the extension of ciliated sensory dendrites during embryogenesis. Interestingly, the nonciliated dendrite of the oxygen-sensing neuron URX is not affected by these genes, suggesting it develops through a distinct mechanism. Here, we use a visual forward genetic screen to identify mutants that affect URX dendrite morphogenesis. We find that disruption of the MAP kinase MAPK-15 or the βH-spectrin SMA-1 causes a phenotype opposite to what we had seen before: dendrites extend normally during embryogenesis but begin to overgrow as the animals reach adulthood, ultimately extending up to 150% of their normal length. SMA-1 is broadly expressed and acts non-cell-autonomously, while MAPK-15 is expressed in many sensory neurons including URX and acts cell-autonomously. MAPK-15 acts at the time of overgrowth, localizes at the dendrite ending, and requires its kinase activity, suggesting it acts locally in time and space to constrain dendrite growth. Finally, we find that the oxygen-sensing guanylate cyclase GCY-35, which normally localizes at the dendrite ending, is localized throughout the overgrown region, and that overgrowth can be suppressed by overexpressing GCY-35 or by genetically mimicking elevated cGMP signaling. These results suggest that overgrowth may correspond to expansion of a sensory compartment at the dendrite ending, reminiscent of the remodeling of sensory cilia or dendritic spines. Thus, in contrast to established pathways that promote dendrite growth during early development, our results reveal a distinct mechanism that constrains dendrite growth throughout the life of the animal, possibly by controlling the size of a sensory compartment at the dendrite ending.' article_number: e1007435 author: - first_name: Ian G. full_name: McLachlan, Ian G. last_name: McLachlan - first_name: Isabel full_name: Beets, Isabel last_name: Beets - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: Maxwell G. full_name: Heiman, Maxwell G. last_name: Heiman citation: ama: McLachlan IG, Beets I, de Bono M, Heiman MG. A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. 2018;14(6). doi:10.1371/journal.pgen.1007435 apa: McLachlan, I. G., Beets, I., de Bono, M., & Heiman, M. G. (2018). A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007435 chicago: McLachlan, Ian G., Isabel Beets, Mario de Bono, and Maxwell G. Heiman. “A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis Elegans Sensory Dendrite throughout the Life of the Organism.” PLOS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007435. ieee: I. G. McLachlan, I. Beets, M. de Bono, and M. G. Heiman, “A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism,” PLOS Genetics, vol. 14, no. 6. Public Library of Science, 2018. ista: McLachlan IG, Beets I, de Bono M, Heiman MG. 2018. A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. 14(6), e1007435. mla: McLachlan, Ian G., et al. “A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis Elegans Sensory Dendrite throughout the Life of the Organism.” PLOS Genetics, vol. 14, no. 6, e1007435, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007435. short: I.G. McLachlan, I. Beets, M. de Bono, M.G. Heiman, PLOS Genetics 14 (2018). date_created: 2019-03-19T13:09:28Z date_published: 2018-06-07T00:00:00Z date_updated: 2021-01-12T08:06:11Z day: '07' ddc: - '570' doi: 10.1371/journal.pgen.1007435 extern: '1' external_id: pmid: - '29879119' file: - access_level: open_access checksum: 622036b945365dbc575bea2768aa9bc8 content_type: application/pdf creator: kschuh date_created: 2019-03-19T13:18:01Z date_updated: 2020-07-14T12:47:19Z file_id: '6112' file_name: 2018_PLOS_McLachlan.pdf file_size: 13011506 relation: main_file file_date_updated: 2020-07-14T12:47:19Z has_accepted_license: '1' intvolume: ' 14' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: PLOS Genetics publication_identifier: issn: - 1553-7404 publication_status: published publisher: Public Library of Science quality_controlled: '1' status: public title: A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2018' ... --- _id: '6109' abstract: - lang: eng text: Neuropeptides are ubiquitous modulators of behavior and physiology. They are packaged in specialized secretory organelles called dense core vesicles (DCVs) that are released upon neural stimulation. Unlike synaptic vesicles, which can be recycled and refilled close to release sites, DCVs must be replenished by de novo synthesis in the cell body. Here, we dissect DCV cell biology in vivo in a Caenorhabditis elegans sensory neuron whose tonic activity we can control using a natural stimulus. We express fluorescently tagged neuropeptides in the neuron and define parameters that describe their subcellular distribution. We measure these parameters at high and low neural activity in 187 mutants defective in proteins implicated in membrane traffic, neuroendocrine secretion, and neuronal or synaptic activity. Using unsupervised hierarchical clustering methods, we analyze these data and identify 62 groups of genes with similar mutant phenotypes. We explore the function of a subset of these groups. We recapitulate many previous findings, validating our paradigm. We uncover a large battery of proteins involved in recycling DCV membrane proteins, something hitherto poorly explored. We show that the unfolded protein response promotes DCV production, which may contribute to intertissue communication of stress. We also find evidence that different mechanisms of priming and exocytosis may operate at high and low neural activity. Our work provides a defined framework to study DCV biology at different neural activity levels. author: - first_name: Patrick full_name: Laurent, Patrick last_name: Laurent - first_name: QueeLim full_name: Ch’ng, QueeLim last_name: Ch’ng - first_name: Maëlle full_name: Jospin, Maëlle last_name: Jospin - first_name: Changchun full_name: Chen, Changchun last_name: Chen - first_name: Ramiro full_name: Lorenzo, Ramiro last_name: Lorenzo - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. 2018;115(29):E6890-E6899. doi:10.1073/pnas.1714610115 apa: Laurent, P., Ch’ng, Q., Jospin, M., Chen, C., Lorenzo, R., & de Bono, M. (2018). Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1714610115 chicago: Laurent, Patrick, QueeLim Ch’ng, Maëlle Jospin, Changchun Chen, Ramiro Lorenzo, and Mario de Bono. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1714610115. ieee: P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, and M. de Bono, “Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron,” Proceedings of the National Academy of Sciences, vol. 115, no. 29. National Academy of Sciences, pp. E6890–E6899, 2018. ista: Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. 2018. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. 115(29), E6890–E6899. mla: Laurent, Patrick, et al. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National Academy of Sciences, vol. 115, no. 29, National Academy of Sciences, 2018, pp. E6890–99, doi:10.1073/pnas.1714610115. short: P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, M. de Bono, Proceedings of the National Academy of Sciences 115 (2018) E6890–E6899. date_created: 2019-03-19T12:41:33Z date_published: 2018-07-17T00:00:00Z date_updated: 2021-01-12T08:06:09Z day: '17' ddc: - '570' doi: 10.1073/pnas.1714610115 extern: '1' external_id: pmid: - '29959203' file: - access_level: open_access checksum: 5e81665377441cdd8d99ab952c534319 content_type: application/pdf creator: kschuh date_created: 2019-03-19T13:01:58Z date_updated: 2020-07-14T12:47:19Z file_id: '6110' file_name: 2018_PNAS_Laurent.pdf file_size: 1567765 relation: main_file file_date_updated: 2020-07-14T12:47:19Z has_accepted_license: '1' intvolume: ' 115' issue: '29' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: E6890-E6899 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' status: public title: Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2018' ... --- _id: '6164' abstract: - lang: eng text: In this paper, we propose an algorithm to build discrete spherical shell having integer center and real-valued inner and outer radii on the face-centered cubic (FCC) grid. We address the problem by mapping it to a 2D scenario and building the shell layer by layer on hexagonal grids with additive manufacturing in mind. The layered hexagonal grids get shifted according to need as we move from one layer to another and forms the FCC grid in 3D. However, we restrict our computation strictly to 2D in order to utilize symmetry and simplicity. alternative_title: - LNCS article_processing_charge: No author: - first_name: Girish full_name: Koshti, Girish last_name: Koshti - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Gaëlle full_name: Largeteau-Skapin, Gaëlle last_name: Largeteau-Skapin - first_name: Rita full_name: Zrour, Rita last_name: Zrour - first_name: Eric full_name: Andres, Eric last_name: Andres - first_name: Partha full_name: Bhowmick, Partha last_name: Bhowmick citation: ama: 'Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. In: 19th International Workshop. Vol 11255. Cham: Springer; 2018:82-96. doi:10.1007/978-3-030-05288-1_7' apa: 'Koshti, G., Biswas, R., Largeteau-Skapin, G., Zrour, R., Andres, E., & Bhowmick, P. (2018). Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. In 19th International Workshop (Vol. 11255, pp. 82–96). Cham: Springer. https://doi.org/10.1007/978-3-030-05288-1_7' chicago: 'Koshti, Girish, Ranita Biswas, Gaëlle Largeteau-Skapin, Rita Zrour, Eric Andres, and Partha Bhowmick. “Sphere Construction on the FCC Grid Interpreted as Layered Hexagonal Grids in 3D.” In 19th International Workshop, 11255:82–96. Cham: Springer, 2018. https://doi.org/10.1007/978-3-030-05288-1_7.' ieee: G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, and P. Bhowmick, “Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D,” in 19th International Workshop, Porto, Portugal, 2018, vol. 11255, pp. 82–96. ista: 'Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. 2018. Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. 19th International Workshop. IWCIA: International Workshop on Combinatorial Image Analysis, LNCS, vol. 11255, 82–96.' mla: Koshti, Girish, et al. “Sphere Construction on the FCC Grid Interpreted as Layered Hexagonal Grids in 3D.” 19th International Workshop, vol. 11255, Springer, 2018, pp. 82–96, doi:10.1007/978-3-030-05288-1_7. short: G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, P. Bhowmick, in:, 19th International Workshop, Springer, Cham, 2018, pp. 82–96. conference: end_date: 2018-11-24 location: Porto, Portugal name: 'IWCIA: International Workshop on Combinatorial Image Analysis' start_date: 2018-11-22 date_created: 2019-03-21T12:16:58Z date_published: 2018-11-22T00:00:00Z date_updated: 2022-01-27T15:26:39Z day: '22' doi: 10.1007/978-3-030-05288-1_7 extern: '1' intvolume: ' 11255' language: - iso: eng month: '11' oa_version: None page: 82-96 place: Cham publication: 19th International Workshop publication_identifier: eisbn: - 978-3-030-05288-1 eissn: - 1611-3349 isbn: - 978-3-030-05287-4 issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' status: public title: Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 11255 year: '2018' ... --- _id: '6354' abstract: - lang: eng text: Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow. acknowledgement: ' FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.)' article_number: e3018 author: - first_name: Shuxia full_name: Fan, Shuxia last_name: Fan - first_name: Michael full_name: Lorenz, Michael last_name: Lorenz - first_name: Steffen full_name: Massberg, Steffen last_name: Massberg - first_name: Florian R full_name: Gärtner, Florian R id: 397A88EE-F248-11E8-B48F-1D18A9856A87 last_name: Gärtner orcid: 0000-0001-6120-3723 citation: ama: Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018 apa: Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018 chicago: Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol, 2018. https://doi.org/10.21769/bioprotoc.3018. ieee: S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol, 2018. ista: Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 8(18), e3018. mla: Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018. short: S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018). date_created: 2019-04-29T09:40:33Z date_published: 2018-09-20T00:00:00Z date_updated: 2021-01-12T08:07:12Z day: '20' ddc: - '570' department: - _id: MiSi doi: 10.21769/bioprotoc.3018 ec_funded: 1 file: - access_level: open_access checksum: d4588377e789da7f360b553ae02c5119 content_type: application/pdf creator: dernst date_created: 2019-04-30T08:04:33Z date_updated: 2020-07-14T12:47:28Z file_id: '6360' file_name: 2018_BioProtocol_Fan.pdf file_size: 2928337 relation: main_file file_date_updated: 2020-07-14T12:47:28Z has_accepted_license: '1' intvolume: ' 8' issue: '18' keyword: - Platelets - Cell migration - Bacteria - Shear flow - Fibrinogen - E. coli language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 260AA4E2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '747687' name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells publication: Bio-Protocol publication_identifier: issn: - 2331-8325 publication_status: published publisher: Bio-Protocol quality_controlled: '1' status: public title: Platelet migration and bacterial trapping assay under flow tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2018' ... --- _id: '6368' abstract: - lang: eng text: An optical network of superconducting quantum bits (qubits) is an appealing platform for quantum communication and distributed quantum computing, but developing a quantum-compatible link between the microwave and optical domains remains an outstanding challenge. Operating at T < 100 mK temperatures, as required for quantum electrical circuits, we demonstrate a mechanically mediated microwave–optical converter with 47% conversion efficiency, and use a classical feed-forward protocol to reduce added noise to 38 photons. The feed-forward protocol harnesses our discovery that noise emitted from the two converter output ports is strongly correlated because both outputs record thermal motion of the same mechanical mode. We also discuss a quantum feed-forward protocol that, given high system efficiencies, would allow quantum information to be transferred even when thermal phonons enter the mechanical element faster than the electro-optic conversion rate. author: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: P. S. full_name: Burns, P. S. last_name: Burns - first_name: M. D. full_name: Urmey, M. D. last_name: Urmey - first_name: R. W. full_name: Peterson, R. W. last_name: Peterson - first_name: N. S. full_name: Kampel, N. S. last_name: Kampel - first_name: B. M. full_name: Brubaker, B. M. last_name: Brubaker - first_name: G. full_name: Smith, G. last_name: Smith - first_name: K. W. full_name: Lehnert, K. W. last_name: Lehnert - first_name: C. A. full_name: Regal, C. A. last_name: Regal citation: ama: Higginbotham AP, Burns PS, Urmey MD, et al. Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. 2018;14(10):1038-1042. doi:10.1038/s41567-018-0210-0 apa: Higginbotham, A. P., Burns, P. S., Urmey, M. D., Peterson, R. W., Kampel, N. S., Brubaker, B. M., … Regal, C. A. (2018). Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-018-0210-0 chicago: Higginbotham, Andrew P, P. S. Burns, M. D. Urmey, R. W. Peterson, N. S. Kampel, B. M. Brubaker, G. Smith, K. W. Lehnert, and C. A. Regal. “Harnessing Electro-Optic Correlations in an Efficient Mechanical Converter.” Nature Physics. Springer Nature, 2018. https://doi.org/10.1038/s41567-018-0210-0. ieee: A. P. Higginbotham et al., “Harnessing electro-optic correlations in an efficient mechanical converter,” Nature Physics, vol. 14, no. 10. Springer Nature, pp. 1038–1042, 2018. ista: Higginbotham AP, Burns PS, Urmey MD, Peterson RW, Kampel NS, Brubaker BM, Smith G, Lehnert KW, Regal CA. 2018. Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. 14(10), 1038–1042. mla: Higginbotham, Andrew P., et al. “Harnessing Electro-Optic Correlations in an Efficient Mechanical Converter.” Nature Physics, vol. 14, no. 10, Springer Nature, 2018, pp. 1038–42, doi:10.1038/s41567-018-0210-0. short: A.P. Higginbotham, P.S. Burns, M.D. Urmey, R.W. Peterson, N.S. Kampel, B.M. Brubaker, G. Smith, K.W. Lehnert, C.A. Regal, Nature Physics 14 (2018) 1038–1042. date_created: 2019-05-03T09:17:20Z date_published: 2018-10-01T00:00:00Z date_updated: 2021-01-12T08:07:15Z day: '01' doi: 10.1038/s41567-018-0210-0 extern: '1' external_id: arxiv: - '1712.06535' intvolume: ' 14' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.06535 month: '10' oa: 1 oa_version: Preprint page: 1038-1042 publication: Nature Physics publication_identifier: issn: - 1745-2473 - 1745-2481 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Harnessing electro-optic correlations in an efficient mechanical converter type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2018' ... --- _id: '6369' abstract: - lang: eng text: We construct a metamaterial from radio-frequency harmonic oscillators, and find two topologically distinct phases resulting from dissipation engineered into the system. These phases are distinguished by a quantized value of bulk energy transport. The impulse response of our circuit is measured and used to reconstruct the band structure and winding number of circuit eigenfunctions around a dark mode. Our results demonstrate that dissipative topological transport can occur in a wider class of physical systems than considered before. article_number: '220301' author: - first_name: Eric I. full_name: Rosenthal, Eric I. last_name: Rosenthal - first_name: Nicole K. full_name: Ehrlich, Nicole K. last_name: Ehrlich - first_name: Mark S. full_name: Rudner, Mark S. last_name: Rudner - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: K. W. full_name: Lehnert, K. W. last_name: Lehnert citation: ama: Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. Topological phase transition measured in a dissipative metamaterial. Physical Review B. 2018;97(22). doi:10.1103/physrevb.97.220301 apa: Rosenthal, E. I., Ehrlich, N. K., Rudner, M. S., Higginbotham, A. P., & Lehnert, K. W. (2018). Topological phase transition measured in a dissipative metamaterial. Physical Review B. American Physical Society (APS). https://doi.org/10.1103/physrevb.97.220301 chicago: Rosenthal, Eric I., Nicole K. Ehrlich, Mark S. Rudner, Andrew P Higginbotham, and K. W. Lehnert. “Topological Phase Transition Measured in a Dissipative Metamaterial.” Physical Review B. American Physical Society (APS), 2018. https://doi.org/10.1103/physrevb.97.220301. ieee: E. I. Rosenthal, N. K. Ehrlich, M. S. Rudner, A. P. Higginbotham, and K. W. Lehnert, “Topological phase transition measured in a dissipative metamaterial,” Physical Review B, vol. 97, no. 22. American Physical Society (APS), 2018. ista: Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. 2018. Topological phase transition measured in a dissipative metamaterial. Physical Review B. 97(22), 220301. mla: Rosenthal, Eric I., et al. “Topological Phase Transition Measured in a Dissipative Metamaterial.” Physical Review B, vol. 97, no. 22, 220301, American Physical Society (APS), 2018, doi:10.1103/physrevb.97.220301. short: E.I. Rosenthal, N.K. Ehrlich, M.S. Rudner, A.P. Higginbotham, K.W. Lehnert, Physical Review B 97 (2018). date_created: 2019-05-03T09:29:49Z date_published: 2018-06-04T00:00:00Z date_updated: 2021-01-12T08:07:16Z day: '04' doi: 10.1103/physrevb.97.220301 extern: '1' external_id: arxiv: - '1802.02243' intvolume: ' 97' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.02243 month: '06' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: issn: - 2469-9950 - 2469-9969 publication_status: published publisher: American Physical Society (APS) quality_controlled: '1' status: public title: Topological phase transition measured in a dissipative metamaterial type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 97 year: '2018' ... --- _id: '6459' author: - first_name: Barbara full_name: Petritsch, Barbara id: 406048EC-F248-11E8-B48F-1D18A9856A87 last_name: Petritsch orcid: 0000-0003-2724-4614 citation: ama: Petritsch B. Open Access at IST Austria 2009-2017. IST Austria; 2018. doi:10.5281/zenodo.1410279 apa: 'Petritsch, B. (2018). Open Access at IST Austria 2009-2017. Presented at the Open-Access-Tage, Graz, Austria: IST Austria. https://doi.org/10.5281/zenodo.1410279' chicago: Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018. https://doi.org/10.5281/zenodo.1410279. ieee: B. Petritsch, Open Access at IST Austria 2009-2017. IST Austria, 2018. ista: Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p. mla: Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018, doi:10.5281/zenodo.1410279. short: B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018. conference: end_date: 2018-09-26 location: Graz, Austria name: Open-Access-Tage start_date: 2018-09-24 date_created: 2019-05-16T07:27:14Z date_published: 2018-09-24T00:00:00Z date_updated: 2020-07-14T23:06:21Z day: '24' ddc: - '020' department: - _id: E-Lib doi: 10.5281/zenodo.1410279 file: - access_level: open_access checksum: 9063ab4d10ea93353c3a03bbf53fbcf1 content_type: application/pdf creator: dernst date_created: 2019-05-16T07:26:25Z date_updated: 2020-07-14T12:47:30Z file_id: '6460' file_name: Poster_Beitrag_125_Petritsch.pdf file_size: 1967778 relation: main_file file_date_updated: 2020-07-14T12:47:30Z has_accepted_license: '1' keyword: - Open Access - Publication Analysis language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication_status: published publisher: IST Austria status: public title: Open Access at IST Austria 2009-2017 tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference_poster user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6525' abstract: - lang: eng text: This chapter finds an agreement of equivariant indices of semi-classical homomorphisms between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface. On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs bundles, whose mirror was proposed by Hitchin to be certain even exterior powers of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present. The agreement arises from a mysterious functional equation. This gives strong computational evidence for Hitchin’s proposal. author: - first_name: Tamás full_name: Hausel, Tamás id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Anton full_name: Mellit, Anton id: 388D3134-F248-11E8-B48F-1D18A9856A87 last_name: Mellit - first_name: Du full_name: Pei, Du last_name: Pei citation: ama: 'Hausel T, Mellit A, Pei D. Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. Oxford University Press; 2018:189-218. doi:10.1093/oso/9780198802013.003.0009' apa: 'Hausel, T., Mellit, A., & Pei, D. (2018). Mirror symmetry with branes by equivariant verlinde formulas. In Geometry and Physics: Volume I (pp. 189–218). Oxford University Press. https://doi.org/10.1093/oso/9780198802013.003.0009' chicago: 'Hausel, Tamás, Anton Mellit, and Du Pei. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” In Geometry and Physics: Volume I, 189–218. Oxford University Press, 2018. https://doi.org/10.1093/oso/9780198802013.003.0009.' ieee: 'T. Hausel, A. Mellit, and D. Pei, “Mirror symmetry with branes by equivariant verlinde formulas,” in Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.' ista: 'Hausel T, Mellit A, Pei D. 2018.Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. , 189–218.' mla: 'Hausel, Tamás, et al. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218, doi:10.1093/oso/9780198802013.003.0009.' short: 'T. Hausel, A. Mellit, D. Pei, in:, Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.' date_created: 2019-06-06T12:42:01Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T08:07:52Z day: '01' department: - _id: TaHa doi: 10.1093/oso/9780198802013.003.0009 language: - iso: eng month: '01' oa_version: None page: 189-218 publication: 'Geometry and Physics: Volume I' publication_identifier: isbn: - '9780198802013' - '9780191840500' publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: 1 status: public title: Mirror symmetry with branes by equivariant verlinde formulas type: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6664' abstract: - lang: eng text: Reed-Muller (RM) and polar codes are a class of capacity-achieving channel coding schemes with the same factor graph representation. Low-complexity decoding algorithms fall short in providing a good error-correction performance for RM and polar codes. Using the symmetric group of RM and polar codes, the specific decoding algorithm can be carried out on multiple permutations of the factor graph to boost the error-correction performance. However, this approach results in high decoding complexity. In this paper, we first derive the total number of factor graph permutations on which the decoding can be performed. We further propose a successive permutation (SP) scheme which finds the permutations on the fly, thus the decoding always progresses on a single factor graph permutation. We show that SP can be used to improve the error-correction performance of RM and polar codes under successive-cancellation (SC) and SC list (SCL) decoding, while keeping the memory requirements of the decoders unaltered. Our results for RM and polar codes of length 128 and rate 0.5 show that when SP is used and at a target frame error rate of 10 -4 , up to 0.5 dB and 0.1 dB improvement can be achieved for RM and polar codes respectively. author: - first_name: Seyyed Ali full_name: Hashemi, Seyyed Ali last_name: Hashemi - first_name: Nghia full_name: Doan, Nghia last_name: Doan - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: 'Warren ' full_name: 'Gross, Warren ' last_name: Gross citation: ama: 'Hashemi SA, Doan N, Mondelli M, Gross W. Decoding Reed-Muller and polar codes by successive factor graph permutations. In: 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing. IEEE; 2018:1-5. doi:10.1109/istc.2018.8625281' apa: 'Hashemi, S. A., Doan, N., Mondelli, M., & Gross, W. (2018). Decoding Reed-Muller and polar codes by successive factor graph permutations. In 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing (pp. 1–5). Hong Kong, China: IEEE. https://doi.org/10.1109/istc.2018.8625281' chicago: Hashemi, Seyyed Ali, Nghia Doan, Marco Mondelli, and Warren Gross. “Decoding Reed-Muller and Polar Codes by Successive Factor Graph Permutations.” In 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, 1–5. IEEE, 2018. https://doi.org/10.1109/istc.2018.8625281. ieee: S. A. Hashemi, N. Doan, M. Mondelli, and W. Gross, “Decoding Reed-Muller and polar codes by successive factor graph permutations,” in 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, Hong Kong, China, 2018, pp. 1–5. ista: 'Hashemi SA, Doan N, Mondelli M, Gross W. 2018. Decoding Reed-Muller and polar codes by successive factor graph permutations. 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing. ISTC: Symposium on Turbo Codes & Iterative Information Processing, 1–5.' mla: Hashemi, Seyyed Ali, et al. “Decoding Reed-Muller and Polar Codes by Successive Factor Graph Permutations.” 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, IEEE, 2018, pp. 1–5, doi:10.1109/istc.2018.8625281. short: S.A. Hashemi, N. Doan, M. Mondelli, W. Gross, in:, 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, IEEE, 2018, pp. 1–5. conference: end_date: 2018-12-07 location: Hong Kong, China name: 'ISTC: Symposium on Turbo Codes & Iterative Information Processing' start_date: 2018-12-03 date_created: 2019-07-23T09:12:43Z date_published: 2018-12-01T00:00:00Z date_updated: 2021-01-12T08:08:29Z day: '01' doi: 10.1109/istc.2018.8625281 extern: '1' external_id: arxiv: - '1807.03912' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1807.03912 month: '12' oa: 1 oa_version: Preprint page: 1-5 publication: 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing publication_status: published publisher: IEEE quality_controlled: '1' status: public title: Decoding Reed-Muller and polar codes by successive factor graph permutations type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6674' abstract: - lang: eng text: Polar codes represent one of the major recent breakthroughs in coding theory and, because of their attractive features, they have been selected for the incoming 5G standard. As such, a lot of attention has been devoted to the development of decoding algorithms with good error performance and efficient hardware implementation. One of the leading candidates in this regard is represented by successive-cancellation list (SCL) decoding. However, its hardware implementation requires a large amount of memory. Recently, a partitioned SCL (PSCL) decoder has been proposed to significantly reduce the memory consumption. In this paper, we consider the paradigm of PSCL decoding from a practical standpoint, and we provide several improvements. First, by changing the target signal-to-noise ratio and consequently modifying the construction of the code, we are able to improve the performance at no additional computational, latency, or memory cost. Second, we bridge the performance gap between SCL and PSCL decoding by introducing a generalized PSCL decoder and a layered PSCL decoder. In this way, we obtain almost the same performance of the SCL decoder with a significantly lower memory requirement, as testified by hardware implementation results. Third, we present an optimal scheme to allocate cyclic redundancy checks. Finally, we provide a lower bound on the list size that guarantees optimal maximum a posteriori performance for the binary erasure channel. author: - first_name: Seyyed Ali full_name: Hashemi, Seyyed Ali last_name: Hashemi - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: S. Hamed full_name: Hassani, S. Hamed last_name: Hassani - first_name: Carlo full_name: Condo, Carlo last_name: Condo - first_name: Rudiger L. full_name: Urbanke, Rudiger L. last_name: Urbanke - first_name: Warren J. full_name: Gross, Warren J. last_name: Gross citation: ama: 'Hashemi SA, Mondelli M, Hassani SH, Condo C, Urbanke RL, Gross WJ. Decoder partitioning: Towards practical list decoding of polar codes. IEEE Transactions on Communications. 2018;66(9):3749-3759. doi:10.1109/tcomm.2018.2832207' apa: 'Hashemi, S. A., Mondelli, M., Hassani, S. H., Condo, C., Urbanke, R. L., & Gross, W. J. (2018). Decoder partitioning: Towards practical list decoding of polar codes. IEEE Transactions on Communications. IEEE. https://doi.org/10.1109/tcomm.2018.2832207' chicago: 'Hashemi, Seyyed Ali, Marco Mondelli, S. Hamed Hassani, Carlo Condo, Rudiger L. Urbanke, and Warren J. Gross. “Decoder Partitioning: Towards Practical List Decoding of Polar Codes.” IEEE Transactions on Communications. IEEE, 2018. https://doi.org/10.1109/tcomm.2018.2832207.' ieee: 'S. A. Hashemi, M. Mondelli, S. H. Hassani, C. Condo, R. L. Urbanke, and W. J. Gross, “Decoder partitioning: Towards practical list decoding of polar codes,” IEEE Transactions on Communications, vol. 66, no. 9. IEEE, pp. 3749–3759, 2018.' ista: 'Hashemi SA, Mondelli M, Hassani SH, Condo C, Urbanke RL, Gross WJ. 2018. Decoder partitioning: Towards practical list decoding of polar codes. IEEE Transactions on Communications. 66(9), 3749–3759.' mla: 'Hashemi, Seyyed Ali, et al. “Decoder Partitioning: Towards Practical List Decoding of Polar Codes.” IEEE Transactions on Communications, vol. 66, no. 9, IEEE, 2018, pp. 3749–59, doi:10.1109/tcomm.2018.2832207.' short: S.A. Hashemi, M. Mondelli, S.H. Hassani, C. Condo, R.L. Urbanke, W.J. Gross, IEEE Transactions on Communications 66 (2018) 3749–3759. date_created: 2019-07-24T08:59:41Z date_published: 2018-09-01T00:00:00Z date_updated: 2021-01-12T08:08:31Z day: '01' doi: 10.1109/tcomm.2018.2832207 extern: '1' intvolume: ' 66' issue: '9' language: - iso: eng month: '09' oa_version: None page: 3749-3759 publication: IEEE Transactions on Communications publication_identifier: eissn: - 1558-0857 publication_status: published publisher: IEEE quality_controlled: '1' status: public title: 'Decoder partitioning: Towards practical list decoding of polar codes' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 66 year: '2018' ... --- _id: '6728' abstract: - lang: eng text: Polar codes are a channel coding scheme for the next generation of wireless communications standard (5G). The belief propagation (BP) decoder allows for parallel decoding of polar codes, making it suitable for high throughput applications. However, the error-correction performance of polar codes under BP decoding is far from the requirements of 5G. It has been shown that the error-correction performance of BP can be improved if the decoding is performed on multiple permuted factor graphs of polar codes. However, a different BP decoding scheduling is required for each factor graph permutation which results in the design of a different decoder for each permutation. Moreover, the selection of the different factor graph permutations is at random, which prevents the decoder to achieve a desirable error correction performance with a small number of permutations. In this paper, we first show that the permutations on the factor graph can be mapped into suitable permutations on the codeword positions. As a result, we can make use of a single decoder for all the permutations. In addition, we introduce a method to construct a set of predetermined permutations which can provide the correct codeword if the decoding fails on the original permutation. We show that for the 5G polar code of length 1024, the error-correction performance of the proposed decoder is more than 0.25 dB better than that of the BP decoder with the same number of random permutations at the frame error rate of 10 -4 . author: - first_name: Nghia full_name: Doan, Nghia last_name: Doan - first_name: Seyyed Ali full_name: Hashemi, Seyyed Ali last_name: Hashemi - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Warren J. full_name: Gross, Warren J. last_name: Gross citation: ama: 'Doan N, Hashemi SA, Mondelli M, Gross WJ. On the decoding of polar codes on permuted factor graphs. In: 2018 IEEE Global Communications Conference . IEEE; 2018. doi:10.1109/glocom.2018.8647308' apa: 'Doan, N., Hashemi, S. A., Mondelli, M., & Gross, W. J. (2018). On the decoding of polar codes on permuted factor graphs. In 2018 IEEE Global Communications Conference . Abu Dhabi, United Arab Emirates: IEEE. https://doi.org/10.1109/glocom.2018.8647308' chicago: Doan, Nghia, Seyyed Ali Hashemi, Marco Mondelli, and Warren J. Gross. “On the Decoding of Polar Codes on Permuted Factor Graphs.” In 2018 IEEE Global Communications Conference . IEEE, 2018. https://doi.org/10.1109/glocom.2018.8647308. ieee: N. Doan, S. A. Hashemi, M. Mondelli, and W. J. Gross, “On the decoding of polar codes on permuted factor graphs,” in 2018 IEEE Global Communications Conference , Abu Dhabi, United Arab Emirates, 2018. ista: 'Doan N, Hashemi SA, Mondelli M, Gross WJ. 2018. On the decoding of polar codes on permuted factor graphs. 2018 IEEE Global Communications Conference . GLOBECOM: Global Communications Conference.' mla: Doan, Nghia, et al. “On the Decoding of Polar Codes on Permuted Factor Graphs.” 2018 IEEE Global Communications Conference , IEEE, 2018, doi:10.1109/glocom.2018.8647308. short: N. Doan, S.A. Hashemi, M. Mondelli, W.J. Gross, in:, 2018 IEEE Global Communications Conference , IEEE, 2018. conference: end_date: 2018-12-13 location: Abu Dhabi, United Arab Emirates name: 'GLOBECOM: Global Communications Conference' start_date: 2018-12-09 date_created: 2019-07-30T06:43:15Z date_published: 2018-12-01T00:00:00Z date_updated: 2021-01-12T08:08:42Z day: '01' doi: 10.1109/glocom.2018.8647308 extern: '1' external_id: arxiv: - '1806.11195' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.11195 month: '12' oa: 1 oa_version: Preprint publication: '2018 IEEE Global Communications Conference ' publication_identifier: isbn: - '9781538647271' publication_status: published publisher: IEEE quality_controlled: '1' status: public title: On the decoding of polar codes on permuted factor graphs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6678' abstract: - lang: eng text: We survey coding techniques that enable reliable transmission at rates that approach the capacity of an arbitrary discrete memoryless channel. In particular, we take the point of view of modern coding theory and discuss how recent advances in coding for symmetric channels help provide more efficient solutions for the asymmetric case. We consider, in more detail, three basic coding paradigms. The first one is Gallager's scheme that consists of concatenating a linear code with a non-linear mapping so that the input distribution can be appropriately shaped. We explicitly show that both polar codes and spatially coupled codes can be employed in this scenario. Furthermore, we derive a scaling law between the gap to capacity, the cardinality of the input and output alphabets, and the required size of the mapper. The second one is an integrated scheme in which the code is used both for source coding, in order to create codewords distributed according to the capacity-achieving input distribution, and for channel coding, in order to provide error protection. Such a technique has been recently introduced by Honda and Yamamoto in the context of polar codes, and we show how to apply it also to the design of sparse graph codes. The third paradigm is based on an idea of Böcherer and Mathar, and separates the two tasks of source coding and channel coding by a chaining construction that binds together several codewords. We present conditions for the source code and the channel code, and we describe how to combine any source code with any channel code that fulfill those conditions, in order to provide capacity-achieving schemes for asymmetric channels. In particular, we show that polar codes, spatially coupled codes, and homophonic codes are suitable as basic building blocks of the proposed coding strategy. Rather than focusing on the exact details of the schemes, the purpose of this tutorial is to present different coding techniques that can then be implemented with many variants. There is no absolute winner and, in order to understand the most suitable technique for a specific application scenario, we provide a detailed comparison that takes into account several performance metrics. article_type: original author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani - first_name: 'Rudiger ' full_name: 'Urbanke, Rudiger ' last_name: Urbanke citation: ama: Mondelli M, Hassani H, Urbanke R. How to achieve the capacity of asymmetric channels. IEEE Transactions on Information Theory. 2018;64(5):3371-3393. doi:10.1109/tit.2018.2789885 apa: Mondelli, M., Hassani, H., & Urbanke, R. (2018). How to achieve the capacity of asymmetric channels. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/tit.2018.2789885 chicago: Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “How to Achieve the Capacity of Asymmetric Channels.” IEEE Transactions on Information Theory. IEEE, 2018. https://doi.org/10.1109/tit.2018.2789885. ieee: M. Mondelli, H. Hassani, and R. Urbanke, “How to achieve the capacity of asymmetric channels,” IEEE Transactions on Information Theory, vol. 64, no. 5. IEEE, pp. 3371–3393, 2018. ista: Mondelli M, Hassani H, Urbanke R. 2018. How to achieve the capacity of asymmetric channels. IEEE Transactions on Information Theory. 64(5), 3371–3393. mla: Mondelli, Marco, et al. “How to Achieve the Capacity of Asymmetric Channels.” IEEE Transactions on Information Theory, vol. 64, no. 5, IEEE, 2018, pp. 3371–93, doi:10.1109/tit.2018.2789885. short: M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Information Theory 64 (2018) 3371–3393. date_created: 2019-07-24T12:38:49Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-02-23T12:50:46Z day: '01' doi: 10.1109/tit.2018.2789885 extern: '1' external_id: arxiv: - '1406.7373' intvolume: ' 64' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1406.7373 month: '05' oa: 1 oa_version: Preprint page: 3371-3393 publication: IEEE Transactions on Information Theory publication_identifier: issn: - 0018-9448 - 1557-9654 publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '6740' relation: earlier_version status: public status: public title: How to achieve the capacity of asymmetric channels type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 64 year: '2018' ... --- _id: '690' abstract: - lang: eng text: We consider spectral properties and the edge universality of sparse random matrices, the class of random matrices that includes the adjacency matrices of the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density up to the spectral edges. Under a suitable condition on the sparsity, we also prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations if a deterministic shift of the spectral edge due to the sparsity is included. For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom fluctuations of the second largest eigenvalue when p is much larger than N−2/3 with a deterministic shift of order (Np)−1. article_number: 543-616 author: - first_name: Jii full_name: Lee, Jii last_name: Lee - first_name: Kevin full_name: Schnelli, Kevin id: 434AD0AE-F248-11E8-B48F-1D18A9856A87 last_name: Schnelli orcid: 0000-0003-0954-3231 citation: ama: Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 2018;171(1-2). doi:10.1007/s00440-017-0787-8 apa: Lee, J., & Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-017-0787-8 chicago: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields. Springer, 2018. https://doi.org/10.1007/s00440-017-0787-8. ieee: J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random matrices,” Probability Theory and Related Fields, vol. 171, no. 1–2. Springer, 2018. ista: Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 171(1–2), 543–616. mla: Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields, vol. 171, no. 1–2, 543–616, Springer, 2018, doi:10.1007/s00440-017-0787-8. short: J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018). date_created: 2018-12-11T11:47:56Z date_published: 2018-06-14T00:00:00Z date_updated: 2021-01-12T08:09:33Z day: '14' department: - _id: LaEr doi: 10.1007/s00440-017-0787-8 ec_funded: 1 external_id: arxiv: - '1605.08767' intvolume: ' 171' issue: 1-2 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1605.08767 month: '06' oa: 1 oa_version: Preprint project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Probability Theory and Related Fields publication_status: published publisher: Springer publist_id: '7017' quality_controlled: '1' scopus_import: 1 status: public title: Local law and Tracy–Widom limit for sparse random matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 171 year: '2018' ... --- _id: '6675' abstract: - lang: eng text: 'We present a coding paradigm that provides a new achievable rate for the primitive relay channel by combining compress-and-forward and decode-and-forward with a chaining construction. In the primitive relay channel model, the source broadcasts a message to the relay and to the destination; and the relay facilitates this communication by sending an additional message to the destination through a separate channel. Two well-known coding approaches for this setting are decode-and-forward and compress-and-forward: in the former, the relay decodes the message and sends some of the information to the destination; in the latter, the relay does not attempt to decode, but it sends a compressed description of the received sequence to the destination via Wyner-Ziv coding. In our scheme, we transmit over pairs of blocks and we use compress-and-forward for the first block and decode-and-forward for the second. In particular, in the first block, the relay does not attempt to decode and it sends only a part of the compressed description of the received sequence; in the second block, the relay decodes the message and sends this information plus the remaining part of the compressed sequence relative to the first block. As a result, we strictly outperform both compress-and- forward and decode-and-forward. Furthermore, this paradigm can be implemented with a low-complexity polar coding scheme that has the typical attractive features of polar codes, i.e., quasi-linear encoding/decoding complexity and super-polynomial decay of the error probability. Throughout the paper we consider as a running example the special case of the erasure relay channel and we compare the rates achievable by our proposed scheme with the existing upper and lower bounds.' author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani - first_name: Rudiger full_name: Urbanke, Rudiger last_name: Urbanke citation: ama: 'Mondelli M, Hassani H, Urbanke R. A new coding paradigm for the primitive relay channel. In: 2018 IEEE International Symposium on Information Theory. IEEE; 2018:351-355. doi:10.1109/isit.2018.8437479' apa: 'Mondelli, M., Hassani, H., & Urbanke, R. (2018). A new coding paradigm for the primitive relay channel. In 2018 IEEE International Symposium on Information Theory (pp. 351–355). Vail, CO, United States: IEEE. https://doi.org/10.1109/isit.2018.8437479' chicago: Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “A New Coding Paradigm for the Primitive Relay Channel.” In 2018 IEEE International Symposium on Information Theory, 351–55. IEEE, 2018. https://doi.org/10.1109/isit.2018.8437479. ieee: M. Mondelli, H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive relay channel,” in 2018 IEEE International Symposium on Information Theory, Vail, CO, United States, 2018, pp. 351–355. ista: 'Mondelli M, Hassani H, Urbanke R. 2018. A new coding paradigm for the primitive relay channel. 2018 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory , 351–355.' mla: Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.” 2018 IEEE International Symposium on Information Theory, IEEE, 2018, pp. 351–55, doi:10.1109/isit.2018.8437479. short: M. Mondelli, H. Hassani, R. Urbanke, in:, 2018 IEEE International Symposium on Information Theory, IEEE, 2018, pp. 351–355. conference: end_date: 2018-06-22 location: Vail, CO, United States name: 'ISIT: International Symposium on Information Theory ' start_date: 2018-06-17 date_created: 2019-07-24T09:10:38Z date_published: 2018-06-16T00:00:00Z date_updated: 2023-02-23T12:56:49Z day: '16' doi: 10.1109/isit.2018.8437479 extern: '1' external_id: arxiv: - '1801.03153' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1801.03153 month: '06' oa: 1 oa_version: Preprint page: 351-355 publication: 2018 IEEE International Symposium on Information Theory publication_identifier: eissn: - 2157-8117 publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '7007' relation: later_version status: public status: public title: A new coding paradigm for the primitive relay channel type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '703' abstract: - lang: eng text: We consider the NP-hard problem of MAP-inference for undirected discrete graphical models. We propose a polynomial time and practically efficient algorithm for finding a part of its optimal solution. Specifically, our algorithm marks some labels of the considered graphical model either as (i) optimal, meaning that they belong to all optimal solutions of the inference problem; (ii) non-optimal if they provably do not belong to any solution. With access to an exact solver of a linear programming relaxation to the MAP-inference problem, our algorithm marks the maximal possible (in a specified sense) number of labels. We also present a version of the algorithm, which has access to a suboptimal dual solver only and still can ensure the (non-)optimality for the marked labels, although the overall number of the marked labels may decrease. We propose an efficient implementation, which runs in time comparable to a single run of a suboptimal dual solver. Our method is well-scalable and shows state-of-the-art results on computational benchmarks from machine learning and computer vision. author: - first_name: Alexander full_name: Shekhovtsov, Alexander last_name: Shekhovtsov - first_name: Paul full_name: Swoboda, Paul id: 446560C6-F248-11E8-B48F-1D18A9856A87 last_name: Swoboda - first_name: Bogdan full_name: Savchynskyy, Bogdan last_name: Savchynskyy citation: ama: Shekhovtsov A, Swoboda P, Savchynskyy B. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2018;40(7):1668-1682. doi:10.1109/TPAMI.2017.2730884 apa: Shekhovtsov, A., Swoboda, P., & Savchynskyy, B. (2018). Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2017.2730884 chicago: Shekhovtsov, Alexander, Paul Swoboda, and Bogdan Savchynskyy. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2017.2730884. ieee: A. Shekhovtsov, P. Swoboda, and B. Savchynskyy, “Maximum persistency via iterative relaxed inference with graphical models,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7. IEEE, pp. 1668–1682, 2018. ista: Shekhovtsov A, Swoboda P, Savchynskyy B. 2018. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(7), 1668–1682. mla: Shekhovtsov, Alexander, et al. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7, IEEE, 2018, pp. 1668–82, doi:10.1109/TPAMI.2017.2730884. short: A. Shekhovtsov, P. Swoboda, B. Savchynskyy, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1668–1682. date_created: 2018-12-11T11:48:01Z date_published: 2018-07-01T00:00:00Z date_updated: 2021-01-12T08:11:32Z day: '01' department: - _id: VlKo doi: 10.1109/TPAMI.2017.2730884 external_id: arxiv: - '1508.07902' intvolume: ' 40' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1508.07902 month: '07' oa: 1 oa_version: Preprint page: 1668-1682 publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_identifier: issn: - '01628828' publication_status: published publisher: IEEE publist_id: '6992' quality_controlled: '1' scopus_import: 1 status: public title: Maximum persistency via iterative relaxed inference with graphical models type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 40 year: '2018' ... --- _id: '7063' abstract: - lang: eng text: The high-pressure synthesis and incommensurately modulated structure are reported for the new compound Sr2Pt8−xAs, with x = 0.715 (5). The structure consists of Sr2Pt3As layers alternating with Pt-only corrugated grids. Ab initio calculations predict a metallic character with a dominant role of the Pt d electrons. The electrical resistivity (ρ) and Seebeck coefficient confirm the metallic character, but surprisingly, ρ showed a near-flat temperature dependence. This observation fits the description of the Mooij correlation for electrical resistivity in disordered metals, originally developed for statistically distributed point defects. The discussed material has a long-range crystallographic order, but the high concentration of Pt vacancies, incommensurately ordered, strongly influences the electronic conduction properties. This result extends the range of validity of the Mooij correlation to long-range ordered incommensurately modulated vacancies. Motivated by the layered structure, the resistivity anisotropy was measured in a focused-ion-beam micro-fabricated well oriented single crystal. A low resistivity anisotropy indicates that the layers are electrically coupled and conduction channels along different directions are intermixed. article_processing_charge: No article_type: original author: - first_name: Edoardo full_name: Martino, Edoardo last_name: Martino - first_name: Alla full_name: Arakcheeva, Alla last_name: Arakcheeva - first_name: Gabriel full_name: Autès, Gabriel last_name: Autès - first_name: Andrea full_name: Pisoni, Andrea last_name: Pisoni - first_name: Maja D. full_name: Bachmann, Maja D. last_name: Bachmann - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Toni full_name: Helm, Toni last_name: Helm - first_name: Oleg V. full_name: Yazyev, Oleg V. last_name: Yazyev - first_name: Philip J. W. full_name: Moll, Philip J. W. last_name: Moll - first_name: László full_name: Forró, László last_name: Forró - first_name: Sergiy full_name: Katrych, Sergiy last_name: Katrych citation: ama: 'Martino E, Arakcheeva A, Autès G, et al. Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity. IUCrJ. 2018;5(4):470-477. doi:10.1107/s2052252518007303' apa: 'Martino, E., Arakcheeva, A., Autès, G., Pisoni, A., Bachmann, M. D., Modic, K. A., … Katrych, S. (2018). Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity. IUCrJ. International Union of Crystallography (IUCr). https://doi.org/10.1107/s2052252518007303' chicago: 'Martino, Edoardo, Alla Arakcheeva, Gabriel Autès, Andrea Pisoni, Maja D. Bachmann, Kimberly A Modic, Toni Helm, et al. “Sr2Pt8−xAs: A Layered Incommensurately Modulated Metal with Saturated Resistivity.” IUCrJ. International Union of Crystallography (IUCr), 2018. https://doi.org/10.1107/s2052252518007303.' ieee: 'E. Martino et al., “Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity,” IUCrJ, vol. 5, no. 4. International Union of Crystallography (IUCr), pp. 470–477, 2018.' ista: 'Martino E, Arakcheeva A, Autès G, Pisoni A, Bachmann MD, Modic KA, Helm T, Yazyev OV, Moll PJW, Forró L, Katrych S. 2018. Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity. IUCrJ. 5(4), 470–477.' mla: 'Martino, Edoardo, et al. “Sr2Pt8−xAs: A Layered Incommensurately Modulated Metal with Saturated Resistivity.” IUCrJ, vol. 5, no. 4, International Union of Crystallography (IUCr), 2018, pp. 470–77, doi:10.1107/s2052252518007303.' short: E. Martino, A. Arakcheeva, G. Autès, A. Pisoni, M.D. Bachmann, K.A. Modic, T. Helm, O.V. Yazyev, P.J.W. Moll, L. Forró, S. Katrych, IUCrJ 5 (2018) 470–477. date_created: 2019-11-19T13:11:15Z date_published: 2018-07-01T00:00:00Z date_updated: 2021-01-12T08:11:38Z day: '01' ddc: - '530' doi: 10.1107/s2052252518007303 extern: '1' file: - access_level: open_access checksum: 5c6180c7d19da599dd50a067eb2efd50 content_type: application/pdf creator: dernst date_created: 2019-11-20T14:00:27Z date_updated: 2020-07-14T12:47:48Z file_id: '7090' file_name: 2018_IUCrJ_Martino.pdf file_size: 1563353 relation: main_file file_date_updated: 2020-07-14T12:47:48Z has_accepted_license: '1' intvolume: ' 5' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 470-477 publication: IUCrJ publication_identifier: eissn: - 2052-2525 publication_status: published publisher: International Union of Crystallography (IUCr) quality_controlled: '1' status: public title: 'Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2018' ... --- _id: '7062' abstract: - lang: eng text: 'Weyl fermions are a recently discovered ingredient for correlated states of electronic matter. A key difficulty has been that real materials also contain non-Weyl quasiparticles, and disentangling the experimental signatures has proven challenging. Here we use magnetic fields up to 95 T to drive the Weyl semimetal TaAs far into its quantum limit, where only the purely chiral 0th Landau levels of the Weyl fermions are occupied. We find the electrical resistivity to be nearly independent of magnetic field up to 50 T: unusual for conventional metals but consistent with the chiral anomaly for Weyl fermions. Above 50 T we observe a two-order-of-magnitude increase in resistivity, indicating that a gap opens in the chiral Landau levels. Above 80 T we observe strong ultrasonic attenuation below 2 K, suggesting a mesoscopically textured state of matter. These results point the way to inducing new correlated states of matter in the quantum limit of Weyl semimetals.' article_number: '2217' article_processing_charge: No article_type: original author: - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Arkady full_name: Shekhter, Arkady last_name: Shekhter - first_name: Yi full_name: Zhang, Yi last_name: Zhang - first_name: Eun-Ah full_name: Kim, Eun-Ah last_name: Kim - first_name: Philip J. W. full_name: Moll, Philip J. W. last_name: Moll - first_name: Maja D. full_name: Bachmann, Maja D. last_name: Bachmann - first_name: M. K. full_name: Chan, M. K. last_name: Chan - first_name: J. B. full_name: Betts, J. B. last_name: Betts - first_name: F. full_name: Balakirev, F. last_name: Balakirev - first_name: A. full_name: Migliori, A. last_name: Migliori - first_name: N. J. full_name: Ghimire, N. J. last_name: Ghimire - first_name: E. D. full_name: Bauer, E. D. last_name: Bauer - first_name: F. full_name: Ronning, F. last_name: Ronning - first_name: R. D. full_name: McDonald, R. D. last_name: McDonald citation: ama: Ramshaw BJ, Modic KA, Shekhter A, et al. Quantum limit transport and destruction of the Weyl nodes in TaAs. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-04542-9 apa: Ramshaw, B. J., Modic, K. A., Shekhter, A., Zhang, Y., Kim, E.-A., Moll, P. J. W., … McDonald, R. D. (2018). Quantum limit transport and destruction of the Weyl nodes in TaAs. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04542-9 chicago: Ramshaw, B. J., Kimberly A Modic, Arkady Shekhter, Yi Zhang, Eun-Ah Kim, Philip J. W. Moll, Maja D. Bachmann, et al. “Quantum Limit Transport and Destruction of the Weyl Nodes in TaAs.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04542-9. ieee: B. J. Ramshaw et al., “Quantum limit transport and destruction of the Weyl nodes in TaAs,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018. ista: Ramshaw BJ, Modic KA, Shekhter A, Zhang Y, Kim E-A, Moll PJW, Bachmann MD, Chan MK, Betts JB, Balakirev F, Migliori A, Ghimire NJ, Bauer ED, Ronning F, McDonald RD. 2018. Quantum limit transport and destruction of the Weyl nodes in TaAs. Nature Communications. 9(1), 2217. mla: Ramshaw, B. J., et al. “Quantum Limit Transport and Destruction of the Weyl Nodes in TaAs.” Nature Communications, vol. 9, no. 1, 2217, Springer Nature, 2018, doi:10.1038/s41467-018-04542-9. short: B.J. Ramshaw, K.A. Modic, A. Shekhter, Y. Zhang, E.-A. Kim, P.J.W. Moll, M.D. Bachmann, M.K. Chan, J.B. Betts, F. Balakirev, A. Migliori, N.J. Ghimire, E.D. Bauer, F. Ronning, R.D. McDonald, Nature Communications 9 (2018). date_created: 2019-11-19T13:10:33Z date_published: 2018-06-07T00:00:00Z date_updated: 2021-01-12T08:11:38Z day: '07' ddc: - '530' doi: 10.1038/s41467-018-04542-9 extern: '1' file: - access_level: open_access checksum: 9c53f9a1f06a4d83d5fe879d2478b7d7 content_type: application/pdf creator: dernst date_created: 2019-11-20T13:55:44Z date_updated: 2020-07-14T12:47:48Z file_id: '7089' file_name: 2018_NatureComm_Ramshaw.pdf file_size: 1794797 relation: main_file file_date_updated: 2020-07-14T12:47:48Z has_accepted_license: '1' intvolume: ' 9' issue: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Quantum limit transport and destruction of the Weyl nodes in TaAs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7059' abstract: - lang: eng text: Unusual behavior in quantum materials commonly arises from their effective low-dimensional physics, reflecting the underlying anisotropy in the spin and charge degrees of freedom. Here we introduce the magnetotropic coefficient k = ∂2F/∂θ2, the second derivative of the free energy F with respect to the magnetic field orientation θ in the crystal. We show that the magnetotropic coefficient can be quantitatively determined from a shift in the resonant frequency of a commercially available atomic force microscopy cantilever under magnetic field. This detection method enables part per 100 million sensitivity and the ability to measure magnetic anisotropy in nanogram-scale samples, as demonstrated on the Weyl semimetal NbP. Measurement of the magnetotropic coefficient in the spin-liquid candidate RuCl3 highlights its sensitivity to anisotropic phase transitions and allows a quantitative comparison to other thermodynamic coefficients via the Ehrenfest relations. article_processing_charge: No article_type: original author: - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Maja D. full_name: Bachmann, Maja D. last_name: Bachmann - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - first_name: F. full_name: Arnold, F. last_name: Arnold - first_name: K. R. full_name: Shirer, K. R. last_name: Shirer - first_name: Amelia full_name: Estry, Amelia last_name: Estry - first_name: J. B. full_name: Betts, J. B. last_name: Betts - first_name: Nirmal J. full_name: Ghimire, Nirmal J. last_name: Ghimire - first_name: E. D. full_name: Bauer, E. D. last_name: Bauer - first_name: Marcus full_name: Schmidt, Marcus last_name: Schmidt - first_name: Michael full_name: Baenitz, Michael last_name: Baenitz - first_name: E. full_name: Svanidze, E. last_name: Svanidze - first_name: Ross D. full_name: McDonald, Ross D. last_name: McDonald - first_name: Arkady full_name: Shekhter, Arkady last_name: Shekhter - first_name: Philip J. W. full_name: Moll, Philip J. W. last_name: Moll citation: ama: Modic KA, Bachmann MD, Ramshaw BJ, et al. Resonant torsion magnetometry in anisotropic quantum materials. Nature Communications. 2018;9(1):3975. doi:10.1038/s41467-018-06412-w apa: Modic, K. A., Bachmann, M. D., Ramshaw, B. J., Arnold, F., Shirer, K. R., Estry, A., … Moll, P. J. W. (2018). Resonant torsion magnetometry in anisotropic quantum materials. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-06412-w chicago: Modic, Kimberly A, Maja D. Bachmann, B. J. Ramshaw, F. Arnold, K. R. Shirer, Amelia Estry, J. B. Betts, et al. “Resonant Torsion Magnetometry in Anisotropic Quantum Materials.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-06412-w. ieee: K. A. Modic et al., “Resonant torsion magnetometry in anisotropic quantum materials,” Nature Communications, vol. 9, no. 1. Springer Nature, p. 3975, 2018. ista: Modic KA, Bachmann MD, Ramshaw BJ, Arnold F, Shirer KR, Estry A, Betts JB, Ghimire NJ, Bauer ED, Schmidt M, Baenitz M, Svanidze E, McDonald RD, Shekhter A, Moll PJW. 2018. Resonant torsion magnetometry in anisotropic quantum materials. Nature Communications. 9(1), 3975. mla: Modic, Kimberly A., et al. “Resonant Torsion Magnetometry in Anisotropic Quantum Materials.” Nature Communications, vol. 9, no. 1, Springer Nature, 2018, p. 3975, doi:10.1038/s41467-018-06412-w. short: K.A. Modic, M.D. Bachmann, B.J. Ramshaw, F. Arnold, K.R. Shirer, A. Estry, J.B. Betts, N.J. Ghimire, E.D. Bauer, M. Schmidt, M. Baenitz, E. Svanidze, R.D. McDonald, A. Shekhter, P.J.W. Moll, Nature Communications 9 (2018) 3975. date_created: 2019-11-19T13:02:20Z date_published: 2018-09-28T00:00:00Z date_updated: 2021-01-12T08:11:37Z day: '28' ddc: - '530' doi: 10.1038/s41467-018-06412-w extern: '1' file: - access_level: open_access checksum: 46a313c816e66899d4dad2cf3583e5b0 content_type: application/pdf creator: dernst date_created: 2019-11-20T12:48:58Z date_updated: 2020-07-14T12:47:48Z file_id: '7088' file_name: 2018_NatureComm_Modic.pdf file_size: 1257681 relation: main_file file_date_updated: 2020-07-14T12:47:48Z has_accepted_license: '1' intvolume: ' 9' issue: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '3975' publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Resonant torsion magnetometry in anisotropic quantum materials tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7058' abstract: - lang: eng text: We examine recent magnetic torque measurements in two compounds, γ−Li2IrO3 and RuCl3, which have been discussed as possible realizations of the Kitaev model. The analysis of the reported discontinuity in torque, as an external magnetic field is rotated across the c axis in both crystals, suggests that they have a translationally invariant chiral spin order of the form ⟨Si⋅(Sj×Sk)⟩≠0 in the ground state and persisting over a very wide range of magnetic field and temperature. An extraordinary |B|B2 dependence of the torque for small fields, beside the usual B2 part, is predicted by the chiral spin order. Data for small fields are available for γ−Li2IrO3 and are found to be consistent with the prediction upon further analysis. Other experiments such as inelastic scattering and thermal Hall effect and several questions raised by the discovery of chiral spin order, including its topological consequences, are discussed. article_number: '205110 ' article_processing_charge: No article_type: original author: - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - first_name: A. full_name: Shekhter, A. last_name: Shekhter - first_name: C. M. full_name: Varma, C. M. last_name: Varma citation: ama: Modic KA, Ramshaw BJ, Shekhter A, Varma CM. Chiral spin order in some purported Kitaev spin-liquid compounds. Physical Review B. 2018;98(20). doi:10.1103/physrevb.98.205110 apa: Modic, K. A., Ramshaw, B. J., Shekhter, A., & Varma, C. M. (2018). Chiral spin order in some purported Kitaev spin-liquid compounds. Physical Review B. APS. https://doi.org/10.1103/physrevb.98.205110 chicago: Modic, Kimberly A, B. J. Ramshaw, A. Shekhter, and C. M. Varma. “Chiral Spin Order in Some Purported Kitaev Spin-Liquid Compounds.” Physical Review B. APS, 2018. https://doi.org/10.1103/physrevb.98.205110. ieee: K. A. Modic, B. J. Ramshaw, A. Shekhter, and C. M. Varma, “Chiral spin order in some purported Kitaev spin-liquid compounds,” Physical Review B, vol. 98, no. 20. APS, 2018. ista: Modic KA, Ramshaw BJ, Shekhter A, Varma CM. 2018. Chiral spin order in some purported Kitaev spin-liquid compounds. Physical Review B. 98(20), 205110. mla: Modic, Kimberly A., et al. “Chiral Spin Order in Some Purported Kitaev Spin-Liquid Compounds.” Physical Review B, vol. 98, no. 20, 205110, APS, 2018, doi:10.1103/physrevb.98.205110. short: K.A. Modic, B.J. Ramshaw, A. Shekhter, C.M. Varma, Physical Review B 98 (2018). date_created: 2019-11-19T13:01:31Z date_published: 2018-11-05T00:00:00Z date_updated: 2021-01-12T08:11:36Z day: '05' doi: 10.1103/physrevb.98.205110 extern: '1' external_id: arxiv: - '1807.06637' intvolume: ' 98' issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1807.06637 month: '11' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: APS quality_controlled: '1' status: public title: Chiral spin order in some purported Kitaev spin-liquid compounds type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 98 year: '2018' ... --- _id: '7060' abstract: - lang: eng text: The anomalous metallic state in the high-temperature superconducting cuprates is masked by superconductivity near a quantum critical point. Applying high magnetic fields to suppress superconductivity has enabled detailed studies of the normal state, yet the direct effect of strong magnetic fields on the metallic state is poorly understood. We report the high-field magnetoresistance of thin-film La2–xSrxCuO4 cuprate in the vicinity of the critical doping, 0.161 ≤ p ≤ 0.190. We find that the metallic state exposed by suppressing superconductivity is characterized by magnetoresistance that is linear in magnetic fields up to 80 tesla. The magnitude of the linear-in-field resistivity mirrors the magnitude and doping evolution of the well-known linear-in-temperature resistivity that has been associated with quantum criticality in high-temperature superconductors. article_processing_charge: No article_type: original author: - first_name: P. full_name: Giraldo-Gallo, P. last_name: Giraldo-Gallo - first_name: J. A. full_name: Galvis, J. A. last_name: Galvis - first_name: Z. full_name: Stegen, Z. last_name: Stegen - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: F. F. full_name: Balakirev, F. F. last_name: Balakirev - first_name: J. B. full_name: Betts, J. B. last_name: Betts - first_name: X. full_name: Lian, X. last_name: Lian - first_name: C. full_name: Moir, C. last_name: Moir - first_name: S. C. full_name: Riggs, S. C. last_name: Riggs - first_name: J. full_name: Wu, J. last_name: Wu - first_name: A. T. full_name: Bollinger, A. T. last_name: Bollinger - first_name: X. full_name: He, X. last_name: He - first_name: I. full_name: Božović, I. last_name: Božović - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - first_name: R. D. full_name: McDonald, R. D. last_name: McDonald - first_name: G. S. full_name: Boebinger, G. S. last_name: Boebinger - first_name: A. full_name: Shekhter, A. last_name: Shekhter citation: ama: Giraldo-Gallo P, Galvis JA, Stegen Z, et al. Scale-invariant magnetoresistance in a cuprate superconductor. Science. 2018;361(6401):479-481. doi:10.1126/science.aan3178 apa: Giraldo-Gallo, P., Galvis, J. A., Stegen, Z., Modic, K. A., Balakirev, F. F., Betts, J. B., … Shekhter, A. (2018). Scale-invariant magnetoresistance in a cuprate superconductor. Science. AAAS. https://doi.org/10.1126/science.aan3178 chicago: Giraldo-Gallo, P., J. A. Galvis, Z. Stegen, Kimberly A Modic, F. F. Balakirev, J. B. Betts, X. Lian, et al. “Scale-Invariant Magnetoresistance in a Cuprate Superconductor.” Science. AAAS, 2018. https://doi.org/10.1126/science.aan3178. ieee: P. Giraldo-Gallo et al., “Scale-invariant magnetoresistance in a cuprate superconductor,” Science, vol. 361, no. 6401. AAAS, pp. 479–481, 2018. ista: Giraldo-Gallo P, Galvis JA, Stegen Z, Modic KA, Balakirev FF, Betts JB, Lian X, Moir C, Riggs SC, Wu J, Bollinger AT, He X, Božović I, Ramshaw BJ, McDonald RD, Boebinger GS, Shekhter A. 2018. Scale-invariant magnetoresistance in a cuprate superconductor. Science. 361(6401), 479–481. mla: Giraldo-Gallo, P., et al. “Scale-Invariant Magnetoresistance in a Cuprate Superconductor.” Science, vol. 361, no. 6401, AAAS, 2018, pp. 479–81, doi:10.1126/science.aan3178. short: P. Giraldo-Gallo, J.A. Galvis, Z. Stegen, K.A. Modic, F.F. Balakirev, J.B. Betts, X. Lian, C. Moir, S.C. Riggs, J. Wu, A.T. Bollinger, X. He, I. Božović, B.J. Ramshaw, R.D. McDonald, G.S. Boebinger, A. Shekhter, Science 361 (2018) 479–481. date_created: 2019-11-19T13:03:16Z date_published: 2018-08-03T00:00:00Z date_updated: 2021-01-12T08:11:37Z day: '03' doi: 10.1126/science.aan3178 extern: '1' intvolume: ' 361' issue: '6401' language: - iso: eng month: '08' oa_version: None page: 479-481 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: AAAS quality_controlled: '1' status: public title: Scale-invariant magnetoresistance in a cuprate superconductor type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 361 year: '2018' ... --- _id: '7116' abstract: - lang: eng text: 'Training deep learning models has received tremendous research interest recently. In particular, there has been intensive research on reducing the communication cost of training when using multiple computational devices, through reducing the precision of the underlying data representation. Naturally, such methods induce system trade-offs—lowering communication precision could de-crease communication overheads and improve scalability; but, on the other hand, it can also reduce the accuracy of training. In this paper, we study this trade-off space, and ask:Can low-precision communication consistently improve the end-to-end performance of training modern neural networks, with no accuracy loss?From the performance point of view, the answer to this question may appear deceptively easy: compressing communication through low precision should help when the ratio between communication and computation is high. However, this answer is less straightforward when we try to generalize this principle across various neural network architectures (e.g., AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g., EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL), and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is not clear how a realistic realization of all these factors maps to the speed up provided by low-precision communication. In this paper, we conduct an empirical study to answer this question and report the insights.' article_processing_charge: No author: - first_name: Demjan full_name: Grubic, Demjan last_name: Grubic - first_name: Leo full_name: Tam, Leo last_name: Tam - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Ce full_name: Zhang, Ce last_name: Zhang citation: ama: 'Grubic D, Tam L, Alistarh D-A, Zhang C. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In: Proceedings of the 21st International Conference on Extending Database Technology. OpenProceedings; 2018:145-156. doi:10.5441/002/EDBT.2018.14' apa: 'Grubic, D., Tam, L., Alistarh, D.-A., & Zhang, C. (2018). Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In Proceedings of the 21st International Conference on Extending Database Technology (pp. 145–156). Vienna, Austria: OpenProceedings. https://doi.org/10.5441/002/EDBT.2018.14' chicago: 'Grubic, Demjan, Leo Tam, Dan-Adrian Alistarh, and Ce Zhang. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” In Proceedings of the 21st International Conference on Extending Database Technology, 145–56. OpenProceedings, 2018. https://doi.org/10.5441/002/EDBT.2018.14.' ieee: 'D. Grubic, L. Tam, D.-A. Alistarh, and C. Zhang, “Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study,” in Proceedings of the 21st International Conference on Extending Database Technology, Vienna, Austria, 2018, pp. 145–156.' ista: 'Grubic D, Tam L, Alistarh D-A, Zhang C. 2018. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. Proceedings of the 21st International Conference on Extending Database Technology. EDBT: Conference on Extending Database Technology, 145–156.' mla: 'Grubic, Demjan, et al. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–56, doi:10.5441/002/EDBT.2018.14.' short: D. Grubic, L. Tam, D.-A. Alistarh, C. Zhang, in:, Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–156. conference: end_date: 2018-03-29 location: Vienna, Austria name: 'EDBT: Conference on Extending Database Technology' start_date: 2018-03-26 date_created: 2019-11-26T14:19:11Z date_published: 2018-03-26T00:00:00Z date_updated: 2023-02-23T12:59:17Z day: '26' ddc: - '000' department: - _id: DaAl doi: 10.5441/002/EDBT.2018.14 file: - access_level: open_access checksum: ec979b56abc71016d6e6adfdadbb4afe content_type: application/pdf creator: dernst date_created: 2019-11-26T14:23:04Z date_updated: 2020-07-14T12:47:49Z file_id: '7118' file_name: 2018_OpenProceedings_Grubic.pdf file_size: 1603204 relation: main_file file_date_updated: 2020-07-14T12:47:49Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 145-156 publication: Proceedings of the 21st International Conference on Extending Database Technology publication_identifier: isbn: - '9783893180783' issn: - 2367-2005 publication_status: published publisher: OpenProceedings quality_controlled: '1' scopus_import: 1 status: public title: 'Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '7126' abstract: - lang: eng text: In the Minimum Description Length (MDL) principle, learning from the data is equivalent to an optimal coding problem. We show that the codes that achieve optimal compression in MDL are critical in a very precise sense. First, when they are taken as generative models of samples, they generate samples with broad empirical distributions and with a high value of the relevance, defined as the entropy of the empirical frequencies. These results are derived for different statistical models (Dirichlet model, independent and pairwise dependent spin models, and restricted Boltzmann machines). Second, MDL codes sit precisely at a second order phase transition point where the symmetry between the sampled outcomes is spontaneously broken. The order parameter controlling the phase transition is the coding cost of the samples. The phase transition is a manifestation of the optimality of MDL codes, and it arises because codes that achieve a higher compression do not exist. These results suggest a clear interpretation of the widespread occurrence of statistical criticality as a characterization of samples which are maximally informative on the underlying generative process. article_number: '755' article_processing_charge: No article_type: original author: - first_name: Ryan J full_name: Cubero, Ryan J id: 850B2E12-9CD4-11E9-837F-E719E6697425 last_name: Cubero orcid: 0000-0003-0002-1867 - first_name: Matteo full_name: Marsili, Matteo last_name: Marsili - first_name: Yasser full_name: Roudi, Yasser last_name: Roudi citation: ama: Cubero RJ, Marsili M, Roudi Y. Minimum description length codes are critical. Entropy. 2018;20(10). doi:10.3390/e20100755 apa: Cubero, R. J., Marsili, M., & Roudi, Y. (2018). Minimum description length codes are critical. Entropy. MDPI. https://doi.org/10.3390/e20100755 chicago: Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Minimum Description Length Codes Are Critical.” Entropy. MDPI, 2018. https://doi.org/10.3390/e20100755. ieee: R. J. Cubero, M. Marsili, and Y. Roudi, “Minimum description length codes are critical,” Entropy, vol. 20, no. 10. MDPI, 2018. ista: Cubero RJ, Marsili M, Roudi Y. 2018. Minimum description length codes are critical. Entropy. 20(10), 755. mla: Cubero, Ryan J., et al. “Minimum Description Length Codes Are Critical.” Entropy, vol. 20, no. 10, 755, MDPI, 2018, doi:10.3390/e20100755. short: R.J. Cubero, M. Marsili, Y. Roudi, Entropy 20 (2018). date_created: 2019-11-26T22:18:05Z date_published: 2018-10-01T00:00:00Z date_updated: 2021-01-12T08:11:56Z day: '01' ddc: - '519' doi: 10.3390/e20100755 extern: '1' file: - access_level: open_access checksum: d642b7b661e1d5066b62e6ea9986b917 content_type: application/pdf creator: rcubero date_created: 2019-11-26T22:23:08Z date_updated: 2020-07-14T12:47:50Z file_id: '7127' file_name: entropy-20-00755-v2.pdf file_size: 1366813 relation: main_file file_date_updated: 2020-07-14T12:47:50Z has_accepted_license: '1' intvolume: ' 20' issue: '10' keyword: - Minimum Description Length - normalized maximum likelihood - statistical criticality - phase transitions - large deviations language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Entropy publication_identifier: issn: - 1099-4300 publication_status: published publisher: MDPI quality_controlled: '1' status: public title: Minimum description length codes are critical tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2018' ... --- _id: '7277' abstract: - lang: eng text: 'Solid alkali metal carbonates are universal passivation layer components of intercalation battery materials and common side products in metal‐O2 batteries, and are believed to form and decompose reversibly in metal‐O2/CO2 cells. In these cathodes, Li2CO3 decomposes to CO2 when exposed to potentials above 3.8 V vs. Li/Li+. However, O2 evolution, as would be expected according to the decomposition reaction 2 Li2CO3→4 Li++4 e−+2 CO2+O2, is not detected. O atoms are thus unaccounted for, which was previously ascribed to unidentified parasitic reactions. Here, we show that highly reactive singlet oxygen (1O2) forms upon oxidizing Li2CO3 in an aprotic electrolyte and therefore does not evolve as O2. These results have substantial implications for the long‐term cyclability of batteries: they underpin the importance of avoiding 1O2 in metal‐O2 batteries, question the possibility of a reversible metal‐O2/CO2 battery based on a carbonate discharge product, and help explain the interfacial reactivity of transition‐metal cathodes with residual Li2CO3.' article_processing_charge: No article_type: original author: - first_name: Nika full_name: Mahne, Nika last_name: Mahne - first_name: Sara E. full_name: Renfrew, Sara E. last_name: Renfrew - first_name: Bryan D. full_name: McCloskey, Bryan D. last_name: McCloskey - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. Electrochemical oxidation of Lithium Carbonate generates singlet oxygen. Angewandte Chemie International Edition. 2018;57(19):5529-5533. doi:10.1002/anie.201802277 apa: Mahne, N., Renfrew, S. E., McCloskey, B. D., & Freunberger, S. A. (2018). Electrochemical oxidation of Lithium Carbonate generates singlet oxygen. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201802277 chicago: Mahne, Nika, Sara E. Renfrew, Bryan D. McCloskey, and Stefan Alexander Freunberger. “Electrochemical Oxidation of Lithium Carbonate Generates Singlet Oxygen.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201802277. ieee: N. Mahne, S. E. Renfrew, B. D. McCloskey, and S. A. Freunberger, “Electrochemical oxidation of Lithium Carbonate generates singlet oxygen,” Angewandte Chemie International Edition, vol. 57, no. 19. Wiley, pp. 5529–5533, 2018. ista: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. 2018. Electrochemical oxidation of Lithium Carbonate generates singlet oxygen. Angewandte Chemie International Edition. 57(19), 5529–5533. mla: Mahne, Nika, et al. “Electrochemical Oxidation of Lithium Carbonate Generates Singlet Oxygen.” Angewandte Chemie International Edition, vol. 57, no. 19, Wiley, 2018, pp. 5529–33, doi:10.1002/anie.201802277. short: N. Mahne, S.E. Renfrew, B.D. McCloskey, S.A. Freunberger, Angewandte Chemie International Edition 57 (2018) 5529–5533. date_created: 2020-01-15T07:20:09Z date_published: 2018-03-15T00:00:00Z date_updated: 2021-01-12T08:12:42Z day: '15' ddc: - '540' doi: 10.1002/anie.201802277 extern: '1' file: - access_level: open_access checksum: 45868d0adc2d13a506bb9a59eb4f409c content_type: application/pdf creator: dernst date_created: 2020-01-22T16:28:31Z date_updated: 2020-07-14T12:47:55Z file_id: '7357' file_name: 2018_AngewChemie_Mahne.pdf file_size: 657963 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 57' issue: '19' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 5529-5533 publication: Angewandte Chemie International Edition publication_identifier: issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Electrochemical oxidation of Lithium Carbonate generates singlet oxygen tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2018' ... --- _id: '7271' abstract: - lang: eng text: The recent demand of multifunctional materials and devices for advanced applications in energy conversion and data storage resulted into a revival of multiferroics, that is, materials characterized by the coexistence of ferromagnetism and ferroelectricity. Despite intense efforts made in the past decade, single-phase room temperature multiferroics are yet to be discovered/fabricated. Nanostructured ferroic materials could potentially exhibit multiferroism since a high fraction of their atoms/ions are superficial, thereby altering significantly the properties of the bulk phase. Alternately, a magnetic order can be induced into ferroelectric materials upon aliovalent doping with magnetic ions. Here, we report on the synthesis of aggregate-free single-phase transition-metal-doped BaTiO3 quasi-monodisperse cuboidal nanocrystals (NC) which exhibit multiferroic properties at room temperature and can be suitable for applications in data storage. The proposed synthetic route allows the inclusion of a high concentration of magnetic ions such as Mn+ (M = Cr, Mn, Fe, Co) up to a nominal concentration of 4% without the formation of any secondary phase. The size of the nanocrystals was controlled in a wide range from ∼15 up to ∼70 nm by varying the reaction time from 48 to 144 h. The presence of unpaired electrons and their magnetic ordering have been probed by electron paramagnetic resonance spectroscopy (EPR), and a vibrating sample magnetometer (VSM). Likewise, an acentric structure, associated with the existence of a dielectric polarization, was observed by lattice dynamics analysis and piezoresponse force microscopy (PFM). These results show that high-quality titanium-containing perovskite nanocrystals which display multiferroic properties at room temperature can be fabricated via soft solution-based synthetic routes, and the properties of these materials can be modulated by changing the size of the nanocrystals and the concentration of the dopant thereby opening the door to the design and study of single-phase multiferroic materials. article_processing_charge: No article_type: original author: - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: John full_name: McCracken, John last_name: McCracken - first_name: Aurelian full_name: Rotaru, Aurelian last_name: Rotaru - first_name: Gabriel full_name: Caruntu, Gabriel last_name: Caruntu citation: ama: Costanzo T, McCracken J, Rotaru A, Caruntu G. Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties. ACS Applied Nano Materials. 2018;1(9):4863-4874. doi:10.1021/acsanm.8b01036 apa: Costanzo, T., McCracken, J., Rotaru, A., & Caruntu, G. (2018). Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties. ACS Applied Nano Materials. ACS. https://doi.org/10.1021/acsanm.8b01036 chicago: Costanzo, Tommaso, John McCracken, Aurelian Rotaru, and Gabriel Caruntu. “Quasi-Monodisperse Transition-Metal-Doped BaTiO3 (M = Cr, Mn, Fe, Co) Colloidal Nanocrystals with Multiferroic Properties.” ACS Applied Nano Materials. ACS, 2018. https://doi.org/10.1021/acsanm.8b01036. ieee: T. Costanzo, J. McCracken, A. Rotaru, and G. Caruntu, “Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties,” ACS Applied Nano Materials, vol. 1, no. 9. ACS, pp. 4863–4874, 2018. ista: Costanzo T, McCracken J, Rotaru A, Caruntu G. 2018. Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties. ACS Applied Nano Materials. 1(9), 4863–4874. mla: Costanzo, Tommaso, et al. “Quasi-Monodisperse Transition-Metal-Doped BaTiO3 (M = Cr, Mn, Fe, Co) Colloidal Nanocrystals with Multiferroic Properties.” ACS Applied Nano Materials, vol. 1, no. 9, ACS, 2018, pp. 4863–74, doi:10.1021/acsanm.8b01036. short: T. Costanzo, J. McCracken, A. Rotaru, G. Caruntu, ACS Applied Nano Materials 1 (2018) 4863–4874. date_created: 2020-01-13T21:58:27Z date_published: 2018-09-28T00:00:00Z date_updated: 2023-02-23T13:02:57Z day: '28' doi: 10.1021/acsanm.8b01036 extern: '1' intvolume: ' 1' issue: '9' language: - iso: eng month: '09' oa_version: None page: 4863-4874 publication: ACS Applied Nano Materials publication_identifier: issn: - 2574-0970 publication_status: published publisher: ACS quality_controlled: '1' status: public title: Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2018' ... --- _id: '7287' abstract: - lang: eng text: Passivation layers on electrode materials are ubiquitous in nonaqueous battery chemistries and strongly govern performance and lifetime. They comprise breakdown products of the electrolyte including carbonate, alkyl carbonates, alkoxides, carboxylates, and polymers. Parasitic chemistry in metal–O2 batteries forms similar products and is tied to the deviation of the O2 balance from the ideal stoichiometry during formation/decomposition of alkaline peroxides or superoxides. Accurate and integral quantification of carbonaceous species and peroxides or superoxides in battery electrodes remains, however, elusive. We present a refined procedure to quantify them accurately and sensitively by pointing out and rectifying pitfalls of previous procedures. Carbonaceous compounds are differentiated into inorganic and organic ones. We combine mass and UV–vis spectrometry to quantify evolved O2 and complexed peroxide and CO2 evolved from carbonaceous compounds by acid treatment and Fenton’s reaction. The capabilities of the method are exemplified by means of Li–O2 and Na–O2 cathodes, graphite anodes, and LiNi0.8Co0.15Al0.05O2 cathodes. article_processing_charge: No article_type: letter_note author: - first_name: Bettina full_name: Schafzahl, Bettina last_name: Schafzahl - first_name: Eléonore full_name: Mourad, Eléonore last_name: Mourad - first_name: Lukas full_name: Schafzahl, Lukas last_name: Schafzahl - first_name: Yann K. full_name: Petit, Yann K. last_name: Petit - first_name: Anjana R. full_name: Raju, Anjana R. last_name: Raju - first_name: Musthafa Ottakam full_name: Thotiyl, Musthafa Ottakam last_name: Thotiyl - first_name: Martin full_name: Wilkening, Martin last_name: Wilkening - first_name: Christian full_name: Slugovc, Christian last_name: Slugovc - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Schafzahl B, Mourad E, Schafzahl L, et al. Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase. ACS Energy Letters. 2018;3(1):170-176. doi:10.1021/acsenergylett.7b01111 apa: Schafzahl, B., Mourad, E., Schafzahl, L., Petit, Y. K., Raju, A. R., Thotiyl, M. O., … Freunberger, S. A. (2018). Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase. ACS Energy Letters. ACS. https://doi.org/10.1021/acsenergylett.7b01111 chicago: Schafzahl, Bettina, Eléonore Mourad, Lukas Schafzahl, Yann K. Petit, Anjana R. Raju, Musthafa Ottakam Thotiyl, Martin Wilkening, Christian Slugovc, and Stefan Alexander Freunberger. “Quantifying Total Superoxide, Peroxide, and Carbonaceous Compounds in Metal–O2 Batteries and the Solid Electrolyte Interphase.” ACS Energy Letters. ACS, 2018. https://doi.org/10.1021/acsenergylett.7b01111. ieee: B. Schafzahl et al., “Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase,” ACS Energy Letters, vol. 3, no. 1. ACS, pp. 170–176, 2018. ista: Schafzahl B, Mourad E, Schafzahl L, Petit YK, Raju AR, Thotiyl MO, Wilkening M, Slugovc C, Freunberger SA. 2018. Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase. ACS Energy Letters. 3(1), 170–176. mla: Schafzahl, Bettina, et al. “Quantifying Total Superoxide, Peroxide, and Carbonaceous Compounds in Metal–O2 Batteries and the Solid Electrolyte Interphase.” ACS Energy Letters, vol. 3, no. 1, ACS, 2018, pp. 170–76, doi:10.1021/acsenergylett.7b01111. short: B. Schafzahl, E. Mourad, L. Schafzahl, Y.K. Petit, A.R. Raju, M.O. Thotiyl, M. Wilkening, C. Slugovc, S.A. Freunberger, ACS Energy Letters 3 (2018) 170–176. date_created: 2020-01-15T12:13:52Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T08:12:46Z day: '01' ddc: - '540' - '543' - '546' - '547' doi: 10.1021/acsenergylett.7b01111 extern: '1' file: - access_level: open_access checksum: 461ccf575ba077af90314fe72d20521e content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T14:19:36Z date_updated: 2020-07-14T12:47:55Z file_id: '8049' file_name: O2 TIOC_fin_incl_SI.pdf file_size: 1892355 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 3' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 170-176 publication: ACS Energy Letters publication_identifier: issn: - 2380-8195 - 2380-8195 publication_status: published publisher: ACS quality_controlled: '1' status: public title: Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2018' ... --- _id: '7285' abstract: - lang: eng text: Hydrogelation, the self-assembly of molecules into soft, water-loaded networks, is one way to bridge the structural gap between single molecules and functional materials. The potential of hydrogels, such as those based on perylene bisimides, lies in their chemical, physical, optical, and electronic properties, which are governed by the supramolecular structure of the gel. However, the structural motifs and their precise role for long-range conductivity are yet to be explored. Here, we present a comprehensive structural picture of a perylene bisimide hydrogel, suggesting that its long-range conductivity is limited by charge transfer between electronic backbones. We reveal nanocrystalline ribbon-like structures as the electronic and structural backbone units between which charge transfer is mediated by polar solvent bridges. We exemplify this effect with sensing, where exposure to polar vapor enhances conductivity by 5 orders of magnitude, emphasizing the crucial role of the interplay between structural motif and surrounding medium for the rational design of devices based on nanocrystalline hydrogels. article_processing_charge: No article_type: original author: - first_name: Max full_name: Burian, Max last_name: Burian - first_name: Francesco full_name: Rigodanza, Francesco last_name: Rigodanza - first_name: Nicola full_name: Demitri, Nicola last_name: Demitri - first_name: Luka full_name: D̵ord̵ević, Luka last_name: D̵ord̵ević - first_name: Silvia full_name: Marchesan, Silvia last_name: Marchesan - first_name: Tereza full_name: Steinhartova, Tereza last_name: Steinhartova - first_name: Ilse full_name: Letofsky-Papst, Ilse last_name: Letofsky-Papst - first_name: Ivan full_name: Khalakhan, Ivan last_name: Khalakhan - first_name: Eléonore full_name: Mourad, Eléonore last_name: Mourad - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Heinz full_name: Amenitsch, Heinz last_name: Amenitsch - first_name: Maurizio full_name: Prato, Maurizio last_name: Prato - first_name: Zois full_name: Syrgiannis, Zois last_name: Syrgiannis citation: ama: Burian M, Rigodanza F, Demitri N, et al. Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels. ACS Nano. 2018;12(6):5800-5806. doi:10.1021/acsnano.8b01689 apa: Burian, M., Rigodanza, F., Demitri, N., D̵ord̵ević, L., Marchesan, S., Steinhartova, T., … Syrgiannis, Z. (2018). Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels. ACS Nano. ACS. https://doi.org/10.1021/acsnano.8b01689 chicago: Burian, Max, Francesco Rigodanza, Nicola Demitri, Luka D̵ord̵ević, Silvia Marchesan, Tereza Steinhartova, Ilse Letofsky-Papst, et al. “Inter-Backbone Charge Transfer as Prerequisite for Long-Range Conductivity in Perylene Bisimide Hydrogels.” ACS Nano. ACS, 2018. https://doi.org/10.1021/acsnano.8b01689. ieee: M. Burian et al., “Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels,” ACS Nano, vol. 12, no. 6. ACS, pp. 5800–5806, 2018. ista: Burian M, Rigodanza F, Demitri N, D̵ord̵ević L, Marchesan S, Steinhartova T, Letofsky-Papst I, Khalakhan I, Mourad E, Freunberger SA, Amenitsch H, Prato M, Syrgiannis Z. 2018. Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels. ACS Nano. 12(6), 5800–5806. mla: Burian, Max, et al. “Inter-Backbone Charge Transfer as Prerequisite for Long-Range Conductivity in Perylene Bisimide Hydrogels.” ACS Nano, vol. 12, no. 6, ACS, 2018, pp. 5800–06, doi:10.1021/acsnano.8b01689. short: M. Burian, F. Rigodanza, N. Demitri, L. D̵ord̵ević, S. Marchesan, T. Steinhartova, I. Letofsky-Papst, I. Khalakhan, E. Mourad, S.A. Freunberger, H. Amenitsch, M. Prato, Z. Syrgiannis, ACS Nano 12 (2018) 5800–5806. date_created: 2020-01-15T12:13:25Z date_published: 2018-06-05T00:00:00Z date_updated: 2021-01-12T08:12:46Z day: '05' ddc: - '540' - '541' doi: 10.1021/acsnano.8b01689 extern: '1' file: - access_level: open_access checksum: 050f7f0ba5d845c5c71779ef14ad5ef3 content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T14:56:40Z date_updated: 2020-07-14T12:47:55Z file_id: '8052' file_name: Manuscript 20092017_subm.pdf file_size: 1333353 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 12' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 5800-5806 publication: ACS Nano publication_identifier: issn: - 1936-0851 publication_status: published publisher: ACS quality_controlled: '1' status: public title: Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2018' ... --- _id: '7286' abstract: - lang: eng text: The solid electrolyte interphase (SEI) in Li and Na ion batteries forms when highly reducing or oxidizing electrode materials come into contact with a liquid organic electrolyte. Its ability to form a mechanically robust, ion-conducting, and electron-insulating layer critically determines performance, cycle life, and safety. Li or Na alkyl carbonates (LiAC and NaAC, respectively) are lead SEI components in state-of-the-art carbonate based electrolytes, and our fundamental understanding of their charge transport and mechanical properties may hold the key to designing electrolytes forming an improved SEI. We synthesized a homologous series of LiACs and NaACs from methyl to octyl analogues and characterized them with respect to structure, ionic conductivity, and stiffness. The compounds assume layered structures except for the lithium methyl carbonate. Room-temperature conductivities were found to be ∼10–9 S cm–1 for lithium methyl carbonate, <10–12 S cm–1 for the other LiACs, and <10–12 S cm–1 for the NaACs with ion transport mostly attributed to grain boundaries. While LiACs show stiffnesses of ∼1 GPa, NaACs become significantly softer with increasing chain lengths. These findings will help to more precisely interpret the complex results from charge transport and mechanical characterization of real SEIs and can give a rationale for influencing the SEI’s mechanical properties via the electrolyte. article_processing_charge: No article_type: original author: - first_name: Lukas full_name: Schafzahl, Lukas last_name: Schafzahl - first_name: Heike full_name: Ehmann, Heike last_name: Ehmann - first_name: Manfred full_name: Kriechbaum, Manfred last_name: Kriechbaum - first_name: Jürgen full_name: Sattelkow, Jürgen last_name: Sattelkow - first_name: Thomas full_name: Ganner, Thomas last_name: Ganner - first_name: Harald full_name: Plank, Harald last_name: Plank - first_name: Martin full_name: Wilkening, Martin last_name: Wilkening - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: 'Schafzahl L, Ehmann H, Kriechbaum M, et al. Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties. Chemistry of Materials. 2018;30(10):3338-3345. doi:10.1021/acs.chemmater.8b00750' apa: 'Schafzahl, L., Ehmann, H., Kriechbaum, M., Sattelkow, J., Ganner, T., Plank, H., … Freunberger, S. A. (2018). Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties. Chemistry of Materials. ACS. https://doi.org/10.1021/acs.chemmater.8b00750' chicago: 'Schafzahl, Lukas, Heike Ehmann, Manfred Kriechbaum, Jürgen Sattelkow, Thomas Ganner, Harald Plank, Martin Wilkening, and Stefan Alexander Freunberger. “Long-Chain Li and Na Alkyl Carbonates as Solid Electrolyte Interphase Components: Structure, Ion Transport, and Mechanical Properties.” Chemistry of Materials. ACS, 2018. https://doi.org/10.1021/acs.chemmater.8b00750.' ieee: 'L. Schafzahl et al., “Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties,” Chemistry of Materials, vol. 30, no. 10. ACS, pp. 3338–3345, 2018.' ista: 'Schafzahl L, Ehmann H, Kriechbaum M, Sattelkow J, Ganner T, Plank H, Wilkening M, Freunberger SA. 2018. Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties. Chemistry of Materials. 30(10), 3338–3345.' mla: 'Schafzahl, Lukas, et al. “Long-Chain Li and Na Alkyl Carbonates as Solid Electrolyte Interphase Components: Structure, Ion Transport, and Mechanical Properties.” Chemistry of Materials, vol. 30, no. 10, ACS, 2018, pp. 3338–45, doi:10.1021/acs.chemmater.8b00750.' short: L. Schafzahl, H. Ehmann, M. Kriechbaum, J. Sattelkow, T. Ganner, H. Plank, M. Wilkening, S.A. Freunberger, Chemistry of Materials 30 (2018) 3338–3345. date_created: 2020-01-15T12:13:37Z date_published: 2018-05-03T00:00:00Z date_updated: 2021-01-12T08:12:46Z day: '03' doi: 10.1021/acs.chemmater.8b00750 extern: '1' intvolume: ' 30' issue: '10' language: - iso: eng month: '05' oa_version: None page: 3338-3345 publication: Chemistry of Materials publication_identifier: eissn: - 1520-5002 issn: - 0897-4756 publication_status: published publisher: ACS quality_controlled: '1' status: public title: 'Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2018' ... --- _id: '7407' abstract: - lang: eng text: 'Proofs of space (PoS) [Dziembowski et al., CRYPTO''15] are proof systems where a prover can convince a verifier that he "wastes" disk space. PoS were introduced as a more ecological and economical replacement for proofs of work which are currently used to secure blockchains like Bitcoin. In this work we investigate extensions of PoS which allow the prover to embed useful data into the dedicated space, which later can be recovered. Our first contribution is a security proof for the original PoS from CRYPTO''15 in the random oracle model (the original proof only applied to a restricted class of adversaries which can store a subset of the data an honest prover would store). When this PoS is instantiated with recent constructions of maximally depth robust graphs, our proof implies basically optimal security. As a second contribution we show three different extensions of this PoS where useful data can be embedded into the space required by the prover. Our security proof for the PoS extends (non-trivially) to these constructions. We discuss how some of these variants can be used as proofs of catalytic space (PoCS), a notion we put forward in this work, and which basically is a PoS where most of the space required by the prover can be used to backup useful data. Finally we discuss how one of the extensions is a candidate construction for a proof of replication (PoR), a proof system recently suggested in the Filecoin whitepaper. ' alternative_title: - LIPIcs article_processing_charge: No author: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Pietrzak KZ. Proofs of catalytic space. In: 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019). Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:59:1-59:25. doi:10.4230/LIPICS.ITCS.2019.59' apa: 'Pietrzak, K. Z. (2018). Proofs of catalytic space. In 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019) (Vol. 124, p. 59:1-59:25). San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.59' chicago: Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” In 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019), 124:59:1-59:25. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ITCS.2019.59. ieee: K. Z. Pietrzak, “Proofs of catalytic space,” in 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019), San Diego, CA, United States, 2018, vol. 124, p. 59:1-59:25. ista: 'Pietrzak KZ. 2018. Proofs of catalytic space. 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019). ITCS: Innovations in theoretical Computer Science Conference, LIPIcs, vol. 124, 59:1-59:25.' mla: Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019), vol. 124, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25, doi:10.4230/LIPICS.ITCS.2019.59. short: K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science  Conference (ITCS 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25. conference: end_date: 2019-01-12 location: San Diego, CA, United States name: 'ITCS: Innovations in theoretical Computer Science Conference' start_date: 2019-01-10 date_created: 2020-01-30T09:16:05Z date_published: 2018-12-31T00:00:00Z date_updated: 2021-01-12T08:13:26Z day: '31' ddc: - '000' department: - _id: KrPi doi: 10.4230/LIPICS.ITCS.2019.59 ec_funded: 1 file: - access_level: open_access checksum: 5cebb7f7849a3beda898f697d755dd96 content_type: application/pdf creator: dernst date_created: 2020-02-04T08:17:52Z date_updated: 2020-07-14T12:47:57Z file_id: '7443' file_name: 2018_LIPIcs_Pietrzak.pdf file_size: 822884 relation: main_file file_date_updated: 2020-07-14T12:47:57Z has_accepted_license: '1' intvolume: ' 124' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2018/194 month: '12' oa: 1 oa_version: Published Version page: 59:1-59:25 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: 10th Innovations in Theoretical Computer Science Conference (ITCS 2019) publication_identifier: isbn: - 978-3-95977-095-8 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Proofs of catalytic space tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 124 year: '2018' ... --- _id: '7458' abstract: - lang: eng text: The coupling between magnetic and electric subsystems in composites of ferromagnetic and ferroelectric phases is a product property that is facilitated by mechanical strain that arises due to magnetostriction and the piezoelectric effect in the constituent phases. Such multiferroic composites are of immense interests for studies on the physics of electromagnetic coupling and for use in a variety of applications. Here, we focus on magneto-electric (ME) coupling in nanocomposites. Particular emphasis is on core-shell particles and coaxial fibers, thin film heterostructures, and planar structures with a variety of mechanical connectivity. A brief review of models that predict strong ME effects in nanostructures is followed by synthesis and characterization. Core-shell particulate composites can be prepared by hydrothermal processes and chemical or deoxyribonucleic acid-assisted assembly. Electrospinning techniques have been utilized to prepare defect free core-shell nanofibers. Core-shell particles and fibers can be assembled into superstructures with the aid of magnetic and electric fields and characterized for possible use in advanced technologies. Chemical-vapor deposition techniques have been shown to be effective for the preparation of heterostructures of ferrites and ferroelectrics. Exotic planar multiferroic structures with potential for enhancing ME coupling strengths are also considered. Scanning probe microscopy techniques are ideal for probing the nature of direct- and converse-ME coupling in individual nanostructures. Magnetoelectric characterization of assemblies of nanocomposites can be done by ME voltage coefficient, magnetic field induced polarization, and magneto-dielectric effects. We conclude with a brief discussion on possible avenues for strengthening the product properties in the nanocomposites. article_number: '061101' article_processing_charge: No article_type: original author: - first_name: Dwight full_name: Viehland, Dwight last_name: Viehland - first_name: Jie Fang full_name: Li, Jie Fang last_name: Li - first_name: Yaodong full_name: Yang, Yaodong last_name: Yang - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: Amin full_name: Yourdkhani, Amin last_name: Yourdkhani - first_name: Gabriel full_name: Caruntu, Gabriel last_name: Caruntu - first_name: Peng full_name: Zhou, Peng last_name: Zhou - first_name: Tianjin full_name: Zhang, Tianjin last_name: Zhang - first_name: Tianqian full_name: Li, Tianqian last_name: Li - first_name: Arunava full_name: Gupta, Arunava last_name: Gupta - first_name: Maksym full_name: Popov, Maksym last_name: Popov - first_name: Gopalan full_name: Srinivasan, Gopalan last_name: Srinivasan citation: ama: 'Viehland D, Li JF, Yang Y, et al. Tutorial: Product properties in multiferroic nanocomposites. Journal of Applied Physics. 2018;124(6). doi:10.1063/1.5038726' apa: 'Viehland, D., Li, J. F., Yang, Y., Costanzo, T., Yourdkhani, A., Caruntu, G., … Srinivasan, G. (2018). Tutorial: Product properties in multiferroic nanocomposites. Journal of Applied Physics. AIP. https://doi.org/10.1063/1.5038726' chicago: 'Viehland, Dwight, Jie Fang Li, Yaodong Yang, Tommaso Costanzo, Amin Yourdkhani, Gabriel Caruntu, Peng Zhou, et al. “Tutorial: Product Properties in Multiferroic Nanocomposites.” Journal of Applied Physics. AIP, 2018. https://doi.org/10.1063/1.5038726.' ieee: 'D. Viehland et al., “Tutorial: Product properties in multiferroic nanocomposites,” Journal of Applied Physics, vol. 124, no. 6. AIP, 2018.' ista: 'Viehland D, Li JF, Yang Y, Costanzo T, Yourdkhani A, Caruntu G, Zhou P, Zhang T, Li T, Gupta A, Popov M, Srinivasan G. 2018. Tutorial: Product properties in multiferroic nanocomposites. Journal of Applied Physics. 124(6), 061101.' mla: 'Viehland, Dwight, et al. “Tutorial: Product Properties in Multiferroic Nanocomposites.” Journal of Applied Physics, vol. 124, no. 6, 061101, AIP, 2018, doi:10.1063/1.5038726.' short: D. Viehland, J.F. Li, Y. Yang, T. Costanzo, A. Yourdkhani, G. Caruntu, P. Zhou, T. Zhang, T. Li, A. Gupta, M. Popov, G. Srinivasan, Journal of Applied Physics 124 (2018). date_created: 2020-02-05T14:18:22Z date_published: 2018-08-10T00:00:00Z date_updated: 2023-02-23T13:08:29Z day: '10' doi: 10.1063/1.5038726 extern: '1' intvolume: ' 124' issue: '6' language: - iso: eng month: '08' oa_version: None publication: Journal of Applied Physics publication_identifier: issn: - 0021-8979 - 1089-7550 publication_status: published publisher: AIP quality_controlled: '1' status: public title: 'Tutorial: Product properties in multiferroic nanocomposites' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 124 year: '2018' ... --- _id: '7717' abstract: - lang: eng text: "Background: DNA methylation levels change along with age, but few studies have examined the variation in the rate of such changes between individuals.\r\nMethods: We performed a longitudinal analysis to quantify the variation in the rate of change of DNA methylation between individuals using whole blood DNA methylation array profiles collected at 2–4 time points (N = 2894) in 954 individuals (67–90 years).\r\nResults: After stringent quality control, we identified 1507 DNA methylation CpG sites (rsCpGs) with statistically significant variation in the rate of change (random slope) of DNA methylation among individuals in a mixed linear model analysis. Genes in the vicinity of these rsCpGs were found to be enriched in Homeobox transcription factors and the Wnt signalling pathway, both of which are related to ageing processes. Furthermore, we investigated the SNP effect on the random slope. We found that 4 out of 1507 rsCpGs had one significant (P < 5 × 10−8/1507) SNP effect and 343 rsCpGs had at least one SNP effect (436 SNP-probe pairs) reaching genome-wide significance (P < 5 × 10−8). Ninety-five percent of the significant (P < 5 × 10−8) SNPs are on different chromosomes from their corresponding probes.\r\nConclusions: We identified CpG sites that have variability in the rate of change of DNA methylation between individuals, and our results suggest a genetic basis of this variation. Genes around these CpG sites have been reported to be involved in the ageing process." article_number: '75' article_processing_charge: No article_type: original author: - first_name: Qian full_name: Zhang, Qian last_name: Zhang - first_name: Riccardo E full_name: Marioni, Riccardo E last_name: Marioni - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Jon full_name: Higham, Jon last_name: Higham - first_name: Duncan full_name: Sproul, Duncan last_name: Sproul - first_name: Naomi R full_name: Wray, Naomi R last_name: Wray - first_name: Ian J full_name: Deary, Ian J last_name: Deary - first_name: Allan F full_name: McRae, Allan F last_name: McRae - first_name: Peter M full_name: Visscher, Peter M last_name: Visscher citation: ama: Zhang Q, Marioni RE, Robinson MR, et al. Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Medicine. 2018;10(1). doi:10.1186/s13073-018-0585-7 apa: Zhang, Q., Marioni, R. E., Robinson, M. R., Higham, J., Sproul, D., Wray, N. R., … Visscher, P. M. (2018). Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-018-0585-7 chicago: Zhang, Qian, Riccardo E Marioni, Matthew Richard Robinson, Jon Higham, Duncan Sproul, Naomi R Wray, Ian J Deary, Allan F McRae, and Peter M Visscher. “Genotype Effects Contribute to Variation in Longitudinal Methylome Patterns in Older People.” Genome Medicine. Springer Nature, 2018. https://doi.org/10.1186/s13073-018-0585-7. ieee: Q. Zhang et al., “Genotype effects contribute to variation in longitudinal methylome patterns in older people,” Genome Medicine, vol. 10, no. 1. Springer Nature, 2018. ista: Zhang Q, Marioni RE, Robinson MR, Higham J, Sproul D, Wray NR, Deary IJ, McRae AF, Visscher PM. 2018. Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Medicine. 10(1), 75. mla: Zhang, Qian, et al. “Genotype Effects Contribute to Variation in Longitudinal Methylome Patterns in Older People.” Genome Medicine, vol. 10, no. 1, 75, Springer Nature, 2018, doi:10.1186/s13073-018-0585-7. short: Q. Zhang, R.E. Marioni, M.R. Robinson, J. Higham, D. Sproul, N.R. Wray, I.J. Deary, A.F. McRae, P.M. Visscher, Genome Medicine 10 (2018). date_created: 2020-04-30T10:42:50Z date_published: 2018-10-22T00:00:00Z date_updated: 2021-01-12T08:15:04Z day: '22' doi: 10.1186/s13073-018-0585-7 extern: '1' intvolume: ' 10' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1186/s13073-018-0585-7 month: '10' oa: 1 oa_version: Published Version publication: Genome Medicine publication_identifier: issn: - 1756-994X publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Genotype effects contribute to variation in longitudinal methylome patterns in older people type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2018' ... --- _id: '7718' abstract: - lang: eng text: Flores Island, Indonesia, was inhabited by the small-bodied hominin species Homo floresiensis, which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale single-nucleotide polymorphism data and whole-genome sequences from a contemporary human pygmy population living on Flores near the cave where H. floresiensis was found. The genomes of Flores pygmies reveal a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins. Modern individuals bear the signatures of recent positive selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related to diet, and polygenic selection acting on standing variation that contributed to their short-stature phenotype. Thus, multiple independent instances of hominin insular dwarfism occurred on Flores. article_processing_charge: No article_type: original author: - first_name: Serena full_name: Tucci, Serena last_name: Tucci - first_name: Samuel H. full_name: Vohr, Samuel H. last_name: Vohr - first_name: Rajiv C. full_name: McCoy, Rajiv C. last_name: McCoy - first_name: Benjamin full_name: Vernot, Benjamin last_name: Vernot - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Chiara full_name: Barbieri, Chiara last_name: Barbieri - first_name: Brad J. full_name: Nelson, Brad J. last_name: Nelson - first_name: Wenqing full_name: Fu, Wenqing last_name: Fu - first_name: Gludhug A. full_name: Purnomo, Gludhug A. last_name: Purnomo - first_name: Herawati full_name: Sudoyo, Herawati last_name: Sudoyo - first_name: Evan E. full_name: Eichler, Evan E. last_name: Eichler - first_name: Guido full_name: Barbujani, Guido last_name: Barbujani - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Joshua M. full_name: Akey, Joshua M. last_name: Akey - first_name: Richard E. full_name: Green, Richard E. last_name: Green citation: ama: Tucci S, Vohr SH, McCoy RC, et al. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science. 2018;361(6401):511-516. doi:10.1126/science.aar8486 apa: Tucci, S., Vohr, S. H., McCoy, R. C., Vernot, B., Robinson, M. R., Barbieri, C., … Green, R. E. (2018). Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aar8486 chicago: Tucci, Serena, Samuel H. Vohr, Rajiv C. McCoy, Benjamin Vernot, Matthew Richard Robinson, Chiara Barbieri, Brad J. Nelson, et al. “Evolutionary History and Adaptation of a Human Pygmy Population of Flores Island, Indonesia.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aar8486. ieee: S. Tucci et al., “Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia,” Science, vol. 361, no. 6401. American Association for the Advancement of Science, pp. 511–516, 2018. ista: Tucci S, Vohr SH, McCoy RC, Vernot B, Robinson MR, Barbieri C, Nelson BJ, Fu W, Purnomo GA, Sudoyo H, Eichler EE, Barbujani G, Visscher PM, Akey JM, Green RE. 2018. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science. 361(6401), 511–516. mla: Tucci, Serena, et al. “Evolutionary History and Adaptation of a Human Pygmy Population of Flores Island, Indonesia.” Science, vol. 361, no. 6401, American Association for the Advancement of Science, 2018, pp. 511–16, doi:10.1126/science.aar8486. short: S. Tucci, S.H. Vohr, R.C. McCoy, B. Vernot, M.R. Robinson, C. Barbieri, B.J. Nelson, W. Fu, G.A. Purnomo, H. Sudoyo, E.E. Eichler, G. Barbujani, P.M. Visscher, J.M. Akey, R.E. Green, Science 361 (2018) 511–516. date_created: 2020-04-30T10:43:24Z date_published: 2018-08-03T00:00:00Z date_updated: 2021-01-12T08:15:04Z day: '03' doi: 10.1126/science.aar8486 extern: '1' external_id: pmid: - '30072539' intvolume: ' 361' issue: '6401' language: - iso: eng month: '08' oa_version: None page: 511-516 pmid: 1 publication: Science publication_identifier: issn: - 0036-8075 - 1095-9203 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' status: public title: Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 361 year: '2018' ... --- _id: '7712' abstract: - lang: eng text: 'Male pattern baldness (MPB) is a sex-limited, age-related, complex trait. We study MPB genetics in 205,327 European males from the UK Biobank. Here we show that MPB is strongly heritable and polygenic, with pedigree-heritability of 0.62 (SE = 0.03) estimated from close relatives, and SNP-heritability of 0.39 (SE = 0.01) from conventionally-unrelated males. We detect 624 near-independent genome-wide loci, contributing SNP-heritability of 0.25 (SE = 0.01), of which 26 X-chromosome loci explain 11.6%. Autosomal genetic variance is enriched for common variants and regions of lower linkage disequilibrium. We identify plausible genetic correlations between MPB and multiple sex-limited markers of earlier puberty, increased bone mineral density (rg = 0.15) and pancreatic β-cell function (rg = 0.12). Correlations with reproductive traits imply an effect on fitness, consistent with an estimated linear selection gradient of -0.018 per MPB standard deviation. Overall, we provide genetic insights into MPB: a phenotype of interest in its own right, with value as a model sex-limited, complex trait.' article_number: '5407' article_processing_charge: No article_type: original author: - first_name: Chloe X. full_name: Yap, Chloe X. last_name: Yap - first_name: Julia full_name: Sidorenko, Julia last_name: Sidorenko - first_name: Yang full_name: Wu, Yang last_name: Wu - first_name: Kathryn E. full_name: Kemper, Kathryn E. last_name: Kemper - first_name: Jian full_name: Yang, Jian last_name: Yang - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Yap CX, Sidorenko J, Wu Y, et al. Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. 2018;9. doi:10.1038/s41467-018-07862-y apa: Yap, C. X., Sidorenko, J., Wu, Y., Kemper, K. E., Yang, J., Wray, N. R., … Visscher, P. M. (2018). Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-07862-y chicago: Yap, Chloe X., Julia Sidorenko, Yang Wu, Kathryn E. Kemper, Jian Yang, Naomi R. Wray, Matthew Richard Robinson, and Peter M. Visscher. “Dissection of Genetic Variation and Evidence for Pleiotropy in Male Pattern Baldness.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-07862-y. ieee: C. X. Yap et al., “Dissection of genetic variation and evidence for pleiotropy in male pattern baldness,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Yap CX, Sidorenko J, Wu Y, Kemper KE, Yang J, Wray NR, Robinson MR, Visscher PM. 2018. Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. 9, 5407. mla: Yap, Chloe X., et al. “Dissection of Genetic Variation and Evidence for Pleiotropy in Male Pattern Baldness.” Nature Communications, vol. 9, 5407, Springer Nature, 2018, doi:10.1038/s41467-018-07862-y. short: C.X. Yap, J. Sidorenko, Y. Wu, K.E. Kemper, J. Yang, N.R. Wray, M.R. Robinson, P.M. Visscher, Nature Communications 9 (2018). date_created: 2020-04-30T10:41:19Z date_published: 2018-12-20T00:00:00Z date_updated: 2021-01-12T08:15:02Z day: '20' doi: 10.1038/s41467-018-07862-y extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-018-07862-y month: '12' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Dissection of genetic variation and evidence for pleiotropy in male pattern baldness type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7716' abstract: - lang: eng text: Genomic prediction has the potential to contribute to precision medicine. However, to date, the utility of such predictors is limited due to low accuracy for most traits. Here theory and simulation study are used to demonstrate that widespread pleiotropy among phenotypes can be utilised to improve genomic risk prediction. We show how a genetic predictor can be created as a weighted index that combines published genome-wide association study (GWAS) summary statistics across many different traits. We apply this framework to predict risk of schizophrenia and bipolar disorder in the Psychiatric Genomics consortium data, finding substantial heterogeneity in prediction accuracy increases across cohorts. For six additional phenotypes in the UK Biobank data, we find increases in prediction accuracy ranging from 0.7% for height to 47% for type 2 diabetes, when using a multi-trait predictor that combines published summary statistics from multiple traits, as compared to a predictor based only on one trait. article_number: '989' article_processing_charge: No article_type: original author: - first_name: Robert M. full_name: Maier, Robert M. last_name: Maier - first_name: Zhihong full_name: Zhu, Zhihong last_name: Zhu - first_name: Sang Hong full_name: Lee, Sang Hong last_name: Lee - first_name: Maciej full_name: Trzaskowski, Maciej last_name: Trzaskowski - first_name: Douglas M. full_name: Ruderfer, Douglas M. last_name: Ruderfer - first_name: Eli A. full_name: Stahl, Eli A. last_name: Stahl - first_name: Stephan full_name: Ripke, Stephan last_name: Ripke - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Jian full_name: Yang, Jian last_name: Yang - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Maier RM, Zhu Z, Lee SH, et al. Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications. 2018;9. doi:10.1038/s41467-017-02769-6 apa: Maier, R. M., Zhu, Z., Lee, S. H., Trzaskowski, M., Ruderfer, D. M., Stahl, E. A., … Robinson, M. R. (2018). Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-02769-6 chicago: Maier, Robert M., Zhihong Zhu, Sang Hong Lee, Maciej Trzaskowski, Douglas M. Ruderfer, Eli A. Stahl, Stephan Ripke, et al. “Improving Genetic Prediction by Leveraging Genetic Correlations among Human Diseases and Traits.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02769-6. ieee: R. M. Maier et al., “Improving genetic prediction by leveraging genetic correlations among human diseases and traits,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Maier RM, Zhu Z, Lee SH, Trzaskowski M, Ruderfer DM, Stahl EA, Ripke S, Wray NR, Yang J, Visscher PM, Robinson MR. 2018. Improving genetic prediction by leveraging genetic correlations among human diseases and traits. Nature Communications. 9, 989. mla: Maier, Robert M., et al. “Improving Genetic Prediction by Leveraging Genetic Correlations among Human Diseases and Traits.” Nature Communications, vol. 9, 989, Springer Nature, 2018, doi:10.1038/s41467-017-02769-6. short: R.M. Maier, Z. Zhu, S.H. Lee, M. Trzaskowski, D.M. Ruderfer, E.A. Stahl, S. Ripke, N.R. Wray, J. Yang, P.M. Visscher, M.R. Robinson, Nature Communications 9 (2018). date_created: 2020-04-30T10:42:29Z date_published: 2018-03-07T00:00:00Z date_updated: 2021-01-12T08:15:03Z day: '07' doi: 10.1038/s41467-017-02769-6 extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-017-02769-6 month: '03' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Improving genetic prediction by leveraging genetic correlations among human diseases and traits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7715' abstract: - lang: eng text: Preference for mates with similar phenotypes; that is, assortative mating, is widely observed in humans1,2,3,4,5 and has evolutionary consequences6,7,8. Under Fisher's classical theory6, assortative mating is predicted to induce a signature in the genome at trait-associated loci that can be detected and quantified. Here, we develop and apply a method to quantify assortative mating on a specific trait by estimating the correlation (θ) between genetic predictors of the trait from single nucleotide polymorphisms on odd- versus even-numbered chromosomes. We show by theory and simulation that the effect of assortative mating can be quantified in the presence of population stratification. We applied this approach to 32 complex traits and diseases using single nucleotide polymorphism data from ~400,000 unrelated individuals of European ancestry. We found significant evidence of assortative mating for height (θ = 3.2%) and educational attainment (θ = 2.7%), both of which were consistent with theoretical predictions. Overall, our results imply that assortative mating involves multiple traits and affects the genomic architecture of loci that are associated with these traits, and that the consequence of mate choice can be detected from a random sample of genomes. article_processing_charge: No article_type: original author: - first_name: Loic full_name: Yengo, Loic last_name: Yengo - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Matthew C. full_name: Keller, Matthew C. last_name: Keller - first_name: Kathryn E. full_name: Kemper, Kathryn E. last_name: Kemper - first_name: Yuanhao full_name: Yang, Yuanhao last_name: Yang - first_name: Maciej full_name: Trzaskowski, Maciej last_name: Trzaskowski - first_name: Jacob full_name: Gratten, Jacob last_name: Gratten - first_name: Patrick full_name: Turley, Patrick last_name: Turley - first_name: David full_name: Cesarini, David last_name: Cesarini - first_name: Daniel J. full_name: Benjamin, Daniel J. last_name: Benjamin - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Michael E. full_name: Goddard, Michael E. last_name: Goddard - first_name: Jian full_name: Yang, Jian last_name: Yang - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Yengo L, Robinson MR, Keller MC, et al. Imprint of assortative mating on the human genome. Nature Human Behaviour. 2018;2(12):948-954. doi:10.1038/s41562-018-0476-3 apa: Yengo, L., Robinson, M. R., Keller, M. C., Kemper, K. E., Yang, Y., Trzaskowski, M., … Visscher, P. M. (2018). Imprint of assortative mating on the human genome. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-018-0476-3 chicago: Yengo, Loic, Matthew Richard Robinson, Matthew C. Keller, Kathryn E. Kemper, Yuanhao Yang, Maciej Trzaskowski, Jacob Gratten, et al. “Imprint of Assortative Mating on the Human Genome.” Nature Human Behaviour. Springer Nature, 2018. https://doi.org/10.1038/s41562-018-0476-3. ieee: L. Yengo et al., “Imprint of assortative mating on the human genome,” Nature Human Behaviour, vol. 2, no. 12. Springer Nature, pp. 948–954, 2018. ista: Yengo L, Robinson MR, Keller MC, Kemper KE, Yang Y, Trzaskowski M, Gratten J, Turley P, Cesarini D, Benjamin DJ, Wray NR, Goddard ME, Yang J, Visscher PM. 2018. Imprint of assortative mating on the human genome. Nature Human Behaviour. 2(12), 948–954. mla: Yengo, Loic, et al. “Imprint of Assortative Mating on the Human Genome.” Nature Human Behaviour, vol. 2, no. 12, Springer Nature, 2018, pp. 948–54, doi:10.1038/s41562-018-0476-3. short: L. Yengo, M.R. Robinson, M.C. Keller, K.E. Kemper, Y. Yang, M. Trzaskowski, J. Gratten, P. Turley, D. Cesarini, D.J. Benjamin, N.R. Wray, M.E. Goddard, J. Yang, P.M. Visscher, Nature Human Behaviour 2 (2018) 948–954. date_created: 2020-04-30T10:42:12Z date_published: 2018-11-26T00:00:00Z date_updated: 2021-01-12T08:15:03Z day: '26' doi: 10.1038/s41562-018-0476-3 extern: '1' intvolume: ' 2' issue: '12' language: - iso: eng month: '11' oa_version: None page: 948-954 publication: Nature Human Behaviour publication_identifier: issn: - 2397-3374 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Imprint of assortative mating on the human genome type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2018' ... --- _id: '7714' abstract: - lang: eng text: Health risk factors such as body mass index (BMI) and serum cholesterol are associated with many common diseases. It often remains unclear whether the risk factors are cause or consequence of disease, or whether the associations are the result of confounding. We develop and apply a method (called GSMR) that performs a multi-SNP Mendelian randomization analysis using summary-level data from genome-wide association studies to test the causal associations of BMI, waist-to-hip ratio, serum cholesterols, blood pressures, height, and years of schooling (EduYears) with common diseases (sample sizes of up to 405,072). We identify a number of causal associations including a protective effect of LDL-cholesterol against type-2 diabetes (T2D) that might explain the side effects of statins on T2D, a protective effect of EduYears against Alzheimer’s disease, and bidirectional associations with opposite effects (e.g., higher BMI increases the risk of T2D but the effect of T2D on BMI is negative). article_number: '224' article_processing_charge: No article_type: original author: - first_name: Zhihong full_name: Zhu, Zhihong last_name: Zhu - first_name: Zhili full_name: Zheng, Zhili last_name: Zheng - first_name: Futao full_name: Zhang, Futao last_name: Zhang - first_name: Yang full_name: Wu, Yang last_name: Wu - first_name: Maciej full_name: Trzaskowski, Maciej last_name: Trzaskowski - first_name: Robert full_name: Maier, Robert last_name: Maier - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: John J. full_name: McGrath, John J. last_name: McGrath - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Jian full_name: Yang, Jian last_name: Yang citation: ama: Zhu Z, Zheng Z, Zhang F, et al. Causal associations between risk factors and common diseases inferred from GWAS summary data. Nature Communications. 2018;9. doi:10.1038/s41467-017-02317-2 apa: Zhu, Z., Zheng, Z., Zhang, F., Wu, Y., Trzaskowski, M., Maier, R., … Yang, J. (2018). Causal associations between risk factors and common diseases inferred from GWAS summary data. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-02317-2 chicago: Zhu, Zhihong, Zhili Zheng, Futao Zhang, Yang Wu, Maciej Trzaskowski, Robert Maier, Matthew Richard Robinson, et al. “Causal Associations between Risk Factors and Common Diseases Inferred from GWAS Summary Data.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02317-2. ieee: Z. Zhu et al., “Causal associations between risk factors and common diseases inferred from GWAS summary data,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Zhu Z, Zheng Z, Zhang F, Wu Y, Trzaskowski M, Maier R, Robinson MR, McGrath JJ, Visscher PM, Wray NR, Yang J. 2018. Causal associations between risk factors and common diseases inferred from GWAS summary data. Nature Communications. 9, 224. mla: Zhu, Zhihong, et al. “Causal Associations between Risk Factors and Common Diseases Inferred from GWAS Summary Data.” Nature Communications, vol. 9, 224, Springer Nature, 2018, doi:10.1038/s41467-017-02317-2. short: Z. Zhu, Z. Zheng, F. Zhang, Y. Wu, M. Trzaskowski, R. Maier, M.R. Robinson, J.J. McGrath, P.M. Visscher, N.R. Wray, J. Yang, Nature Communications 9 (2018). date_created: 2020-04-30T10:41:55Z date_published: 2018-01-15T00:00:00Z date_updated: 2021-01-12T08:15:03Z day: '15' doi: 10.1038/s41467-017-02317-2 extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-017-02317-2 month: '01' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Causal associations between risk factors and common diseases inferred from GWAS summary data type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7713' abstract: - lang: eng text: There are mean differences in complex traits among global human populations. We hypothesize that part of the phenotypic differentiation is due to natural selection. To address this hypothesis, we assess the differentiation in allele frequencies of trait-associated SNPs among African, Eastern Asian, and European populations for ten complex traits using data of large sample size (up to ~405,000). We show that SNPs associated with height (P=2.46×10−5), waist-to-hip ratio (P=2.77×10−4), and schizophrenia (P=3.96×10−5) are significantly more differentiated among populations than matched “control” SNPs, suggesting that these trait-associated SNPs have undergone natural selection. We further find that SNPs associated with height (P=2.01×10−6) and schizophrenia (P=5.16×10−18) show significantly higher variance in linkage disequilibrium (LD) scores across populations than control SNPs. Our results support the hypothesis that natural selection has shaped the genetic differentiation of complex traits, such as height and schizophrenia, among worldwide populations. article_number: '1865' article_processing_charge: No article_type: original author: - first_name: Jing full_name: Guo, Jing last_name: Guo - first_name: Yang full_name: Wu, Yang last_name: Wu - first_name: Zhihong full_name: Zhu, Zhihong last_name: Zhu - first_name: Zhili full_name: Zheng, Zhili last_name: Zheng - first_name: Maciej full_name: Trzaskowski, Maciej last_name: Trzaskowski - first_name: Jian full_name: Zeng, Jian last_name: Zeng - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Jian full_name: Yang, Jian last_name: Yang citation: ama: Guo J, Wu Y, Zhu Z, et al. Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications. 2018;9. doi:10.1038/s41467-018-04191-y apa: Guo, J., Wu, Y., Zhu, Z., Zheng, Z., Trzaskowski, M., Zeng, J., … Yang, J. (2018). Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04191-y chicago: Guo, Jing, Yang Wu, Zhihong Zhu, Zhili Zheng, Maciej Trzaskowski, Jian Zeng, Matthew Richard Robinson, Peter M. Visscher, and Jian Yang. “Global Genetic Differentiation of Complex Traits Shaped by Natural Selection in Humans.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04191-y. ieee: J. Guo et al., “Global genetic differentiation of complex traits shaped by natural selection in humans,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Guo J, Wu Y, Zhu Z, Zheng Z, Trzaskowski M, Zeng J, Robinson MR, Visscher PM, Yang J. 2018. Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications. 9, 1865. mla: Guo, Jing, et al. “Global Genetic Differentiation of Complex Traits Shaped by Natural Selection in Humans.” Nature Communications, vol. 9, 1865, Springer Nature, 2018, doi:10.1038/s41467-018-04191-y. short: J. Guo, Y. Wu, Z. Zhu, Z. Zheng, M. Trzaskowski, J. Zeng, M.R. Robinson, P.M. Visscher, J. Yang, Nature Communications 9 (2018). date_created: 2020-04-30T10:41:36Z date_published: 2018-05-14T00:00:00Z date_updated: 2021-01-12T08:15:02Z day: '14' doi: 10.1038/s41467-018-04191-y extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-018-04191-y month: '05' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Global genetic differentiation of complex traits shaped by natural selection in humans type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7721' abstract: - lang: eng text: 'The availability of genome-wide genetic data on hundreds of thousands of people has led to an equally rapid growth in methodologies available to analyse these data. While the motivation for undertaking genome-wide association studies (GWAS) is identification of genetic markers associated with complex traits, once generated these data can be used for many other analyses. GWAS have demonstrated that complex traits exhibit a highly polygenic genetic architecture, often with shared genetic risk factors across traits. New methods to analyse data from GWAS are increasingly being used to address a diverse set of questions about the aetiology of complex traits and diseases, including psychiatric disorders. Here, we give an overview of some of these methods and present examples of how they have contributed to our understanding of psychiatric disorders. We consider: (i) estimation of the extent of genetic influence on traits, (ii) uncovering of shared genetic control between traits, (iii) predictions of genetic risk for individuals, (iv) uncovering of causal relationships between traits, (v) identifying causal single-nucleotide polymorphisms and genes or (vi) the detection of genetic heterogeneity. This classification helps organise the large number of recently developed methods, although some could be placed in more than one category. While some methods require GWAS data on individual people, others simply use GWAS summary statistics data, allowing novel well-powered analyses to be conducted at a low computational burden.' article_processing_charge: No article_type: original author: - first_name: R. M. full_name: Maier, R. M. last_name: Maier - first_name: P. M. full_name: Visscher, P. M. last_name: Visscher - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: N. R. full_name: Wray, N. R. last_name: Wray citation: ama: 'Maier RM, Visscher PM, Robinson MR, Wray NR. Embracing polygenicity: A review of methods and tools for psychiatric genetics research. Psychological Medicine. 2018;48(7):1055-1067. doi:10.1017/s0033291717002318' apa: 'Maier, R. M., Visscher, P. M., Robinson, M. R., & Wray, N. R. (2018). Embracing polygenicity: A review of methods and tools for psychiatric genetics research. Psychological Medicine. Cambridge University Press. https://doi.org/10.1017/s0033291717002318' chicago: 'Maier, R. M., P. M. Visscher, Matthew Richard Robinson, and N. R. Wray. “Embracing Polygenicity: A Review of Methods and Tools for Psychiatric Genetics Research.” Psychological Medicine. Cambridge University Press, 2018. https://doi.org/10.1017/s0033291717002318.' ieee: 'R. M. Maier, P. M. Visscher, M. R. Robinson, and N. R. Wray, “Embracing polygenicity: A review of methods and tools for psychiatric genetics research,” Psychological Medicine, vol. 48, no. 7. Cambridge University Press, pp. 1055–1067, 2018.' ista: 'Maier RM, Visscher PM, Robinson MR, Wray NR. 2018. Embracing polygenicity: A review of methods and tools for psychiatric genetics research. Psychological Medicine. 48(7), 1055–1067.' mla: 'Maier, R. M., et al. “Embracing Polygenicity: A Review of Methods and Tools for Psychiatric Genetics Research.” Psychological Medicine, vol. 48, no. 7, Cambridge University Press, 2018, pp. 1055–67, doi:10.1017/s0033291717002318.' short: R.M. Maier, P.M. Visscher, M.R. Robinson, N.R. Wray, Psychological Medicine 48 (2018) 1055–1067. date_created: 2020-04-30T10:44:35Z date_published: 2018-05-01T00:00:00Z date_updated: 2021-01-12T08:15:05Z day: '01' doi: 10.1017/s0033291717002318 extern: '1' intvolume: ' 48' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1017/s0033291717002318 month: '05' oa: 1 oa_version: Published Version page: 1055-1067 publication: Psychological Medicine publication_identifier: issn: - 0033-2917 - 1469-8978 publication_status: published publisher: Cambridge University Press quality_controlled: '1' status: public title: 'Embracing polygenicity: A review of methods and tools for psychiatric genetics research' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2018' ... --- _id: '7723' abstract: - lang: eng text: Genome-wide association studies (GWAS) have identified thousands of loci that are robustly associated with complex diseases. The use of linear mixed model (LMM) methodology for GWAS is becoming more prevalent due to its ability to control for population structure and cryptic relatedness and to increase power. The odds ratio (OR) is a common measure of the association of a disease with an exposure (e.g., a genetic variant) and is readably available from logistic regression. However, when the LMM is applied to all-or-none traits it provides estimates of genetic effects on the observed 0–1 scale, a different scale to that in logistic regression. This limits the comparability of results across studies, for example in a meta-analysis, and makes the interpretation of the magnitude of an effect from an LMM GWAS difficult. In this study, we derived transformations from the genetic effects estimated under the LMM to the OR that only rely on summary statistics. To test the proposed transformations, we used real genotypes from two large, publicly available data sets to simulate all-or-none phenotypes for a set of scenarios that differ in underlying model, disease prevalence, and heritability. Furthermore, we applied these transformations to GWAS summary statistics for type 2 diabetes generated from 108,042 individuals in the UK Biobank. In both simulation and real-data application, we observed very high concordance between the transformed OR from the LMM and either the simulated truth or estimates from logistic regression. The transformations derived and validated in this study improve the comparability of results from prospective and already performed LMM GWAS on complex diseases by providing a reliable transformation to a common comparative scale for the genetic effects. article_processing_charge: No article_type: original author: - first_name: Luke R. full_name: Lloyd-Jones, Luke R. last_name: Lloyd-Jones - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Jian full_name: Yang, Jian last_name: Yang - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Lloyd-Jones LR, Robinson MR, Yang J, Visscher PM. Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. 2018;208(4):1397-1408. doi:10.1534/genetics.117.300360 apa: Lloyd-Jones, L. R., Robinson, M. R., Yang, J., & Visscher, P. M. (2018). Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300360 chicago: Lloyd-Jones, Luke R., Matthew Richard Robinson, Jian Yang, and Peter M. Visscher. “Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300360. ieee: L. R. Lloyd-Jones, M. R. Robinson, J. Yang, and P. M. Visscher, “Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1397–1408, 2018. ista: Lloyd-Jones LR, Robinson MR, Yang J, Visscher PM. 2018. Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio. Genetics. 208(4), 1397–1408. mla: Lloyd-Jones, Luke R., et al. “Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1397–408, doi:10.1534/genetics.117.300360. short: L.R. Lloyd-Jones, M.R. Robinson, J. Yang, P.M. Visscher, Genetics 208 (2018) 1397–1408. date_created: 2020-04-30T10:45:19Z date_published: 2018-04-01T00:00:00Z date_updated: 2021-01-12T08:15:06Z day: '01' doi: 10.1534/genetics.117.300360 extern: '1' intvolume: ' 208' issue: '4' language: - iso: eng month: '04' oa_version: None page: 1397-1408 publication: Genetics publication_identifier: issn: - 0016-6731 - 1943-2631 publication_status: published publisher: Genetics Society of America quality_controlled: '1' status: public title: Transformation of summary statistics from linear mixed model association on all-or-none traits to odds ratio type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 208 year: '2018' ... --- _id: '7722' abstract: - lang: eng text: We develop a Bayesian mixed linear model that simultaneously estimates single-nucleotide polymorphism (SNP)-based heritability, polygenicity (proportion of SNPs with nonzero effects), and the relationship between SNP effect size and minor allele frequency for complex traits in conventionally unrelated individuals using genome-wide SNP data. We apply the method to 28 complex traits in the UK Biobank data (N = 126,752) and show that on average, 6% of SNPs have nonzero effects, which in total explain 22% of phenotypic variance. We detect significant (P < 0.05/28) signatures of natural selection in the genetic architecture of 23 traits, including reproductive, cardiovascular, and anthropometric traits, as well as educational attainment. The significant estimates of the relationship between effect size and minor allele frequency in complex traits are consistent with a model of negative (or purifying) selection, as confirmed by forward simulation. We conclude that negative selection acts pervasively on the genetic variants associated with human complex traits. article_processing_charge: No article_type: original author: - first_name: Jian full_name: Zeng, Jian last_name: Zeng - first_name: Ronald full_name: de Vlaming, Ronald last_name: de Vlaming - first_name: Yang full_name: Wu, Yang last_name: Wu - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Luke R. full_name: Lloyd-Jones, Luke R. last_name: Lloyd-Jones - first_name: Loic full_name: Yengo, Loic last_name: Yengo - first_name: Chloe X. full_name: Yap, Chloe X. last_name: Yap - first_name: Angli full_name: Xue, Angli last_name: Xue - first_name: Julia full_name: Sidorenko, Julia last_name: Sidorenko - first_name: Allan F. full_name: McRae, Allan F. last_name: McRae - first_name: Joseph E. full_name: Powell, Joseph E. last_name: Powell - first_name: Grant W. full_name: Montgomery, Grant W. last_name: Montgomery - first_name: Andres full_name: Metspalu, Andres last_name: Metspalu - first_name: Tonu full_name: Esko, Tonu last_name: Esko - first_name: Greg full_name: Gibson, Greg last_name: Gibson - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Jian full_name: Yang, Jian last_name: Yang citation: ama: Zeng J, de Vlaming R, Wu Y, et al. Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. 2018;50(5):746-753. doi:10.1038/s41588-018-0101-4 apa: Zeng, J., de Vlaming, R., Wu, Y., Robinson, M. R., Lloyd-Jones, L. R., Yengo, L., … Yang, J. (2018). Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-018-0101-4 chicago: Zeng, Jian, Ronald de Vlaming, Yang Wu, Matthew Richard Robinson, Luke R. Lloyd-Jones, Loic Yengo, Chloe X. Yap, et al. “Signatures of Negative Selection in the Genetic Architecture of Human Complex Traits.” Nature Genetics. Springer Nature, 2018. https://doi.org/10.1038/s41588-018-0101-4. ieee: J. Zeng et al., “Signatures of negative selection in the genetic architecture of human complex traits,” Nature Genetics, vol. 50, no. 5. Springer Nature, pp. 746–753, 2018. ista: Zeng J, de Vlaming R, Wu Y, Robinson MR, Lloyd-Jones LR, Yengo L, Yap CX, Xue A, Sidorenko J, McRae AF, Powell JE, Montgomery GW, Metspalu A, Esko T, Gibson G, Wray NR, Visscher PM, Yang J. 2018. Signatures of negative selection in the genetic architecture of human complex traits. Nature Genetics. 50(5), 746–753. mla: Zeng, Jian, et al. “Signatures of Negative Selection in the Genetic Architecture of Human Complex Traits.” Nature Genetics, vol. 50, no. 5, Springer Nature, 2018, pp. 746–53, doi:10.1038/s41588-018-0101-4. short: J. Zeng, R. de Vlaming, Y. Wu, M.R. Robinson, L.R. Lloyd-Jones, L. Yengo, C.X. Yap, A. Xue, J. Sidorenko, A.F. McRae, J.E. Powell, G.W. Montgomery, A. Metspalu, T. Esko, G. Gibson, N.R. Wray, P.M. Visscher, J. Yang, Nature Genetics 50 (2018) 746–753. date_created: 2020-04-30T10:44:57Z date_published: 2018-04-16T00:00:00Z date_updated: 2021-01-12T08:15:06Z day: '16' doi: 10.1038/s41588-018-0101-4 extern: '1' intvolume: ' 50' issue: '5' language: - iso: eng month: '04' oa_version: None page: 746-753 publication: Nature Genetics publication_identifier: issn: - 1061-4036 - 1546-1718 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Signatures of negative selection in the genetic architecture of human complex traits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2018' ... --- _id: '7724' abstract: - lang: eng text: Modern molecular genetic datasets, primarily collected to study the biology of human health and disease, can be used to directly measure the action of natural selection and reveal important features of contemporary human evolution. Here we leverage the UK Biobank data to test for the presence of linear and nonlinear natural selection in a contemporary population of the United Kingdom. We obtain phenotypic and genetic evidence consistent with the action of linear/directional selection. Phenotypic evidence suggests that stabilizing selection, which acts to reduce variance in the population without necessarily modifying the population mean, is widespread and relatively weak in comparison with estimates from other species. article_processing_charge: No article_type: original author: - first_name: Jaleal S. full_name: Sanjak, Jaleal S. last_name: Sanjak - first_name: Julia full_name: Sidorenko, Julia last_name: Sidorenko - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Kevin R. full_name: Thornton, Kevin R. last_name: Thornton - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. 2018;115(1):151-156. doi:10.1073/pnas.1707227114 apa: Sanjak, J. S., Sidorenko, J., Robinson, M. R., Thornton, K. R., & Visscher, P. M. (2018). Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1707227114 chicago: Sanjak, Jaleal S., Julia Sidorenko, Matthew Richard Robinson, Kevin R. Thornton, and Peter M. Visscher. “Evidence of Directional and Stabilizing Selection in Contemporary Humans.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1707227114. ieee: J. S. Sanjak, J. Sidorenko, M. R. Robinson, K. R. Thornton, and P. M. Visscher, “Evidence of directional and stabilizing selection in contemporary humans,” Proceedings of the National Academy of Sciences, vol. 115, no. 1. Proceedings of the National Academy of Sciences, pp. 151–156, 2018. ista: Sanjak JS, Sidorenko J, Robinson MR, Thornton KR, Visscher PM. 2018. Evidence of directional and stabilizing selection in contemporary humans. Proceedings of the National Academy of Sciences. 115(1), 151–156. mla: Sanjak, Jaleal S., et al. “Evidence of Directional and Stabilizing Selection in Contemporary Humans.” Proceedings of the National Academy of Sciences, vol. 115, no. 1, Proceedings of the National Academy of Sciences, 2018, pp. 151–56, doi:10.1073/pnas.1707227114. short: J.S. Sanjak, J. Sidorenko, M.R. Robinson, K.R. Thornton, P.M. Visscher, Proceedings of the National Academy of Sciences 115 (2018) 151–156. date_created: 2020-04-30T10:45:43Z date_published: 2018-01-02T00:00:00Z date_updated: 2021-01-12T08:15:07Z day: '02' doi: 10.1073/pnas.1707227114 extern: '1' intvolume: ' 115' issue: '1' language: - iso: eng month: '01' oa_version: None page: 151-156 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1073/pnas.1806837115 status: public title: Evidence of directional and stabilizing selection in contemporary humans type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2018' ... --- _id: '7754' abstract: - lang: eng text: Creating a selective gel that filters particles based on their interactions is a major goal of nanotechnology, with far-reaching implications from drug delivery to controlling assembly pathways. However, this is particularly difficult when the particles are larger than the gel’s characteristic mesh size because such particles cannot passively pass through the gel. Thus, filtering requires the interacting particles to transiently reorganize the gel’s internal structure. While significant advances, e.g., in DNA engineering, have enabled the design of nano-materials with programmable interactions, it is not clear what physical principles such a designer gel could exploit to achieve selective permeability. We present an equilibrium mechanism where crosslink binding dynamics are affected by interacting particles such that particle diffusion is enhanced. In addition to revealing specific design rules for manufacturing selective gels, our results have the potential to explain the origin of selective permeability in certain biological materials, including the nuclear pore complex. article_number: '4348' article_processing_charge: No article_type: original author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Michael P. full_name: Brenner, Michael P. last_name: Brenner - first_name: Katharina full_name: Ribbeck, Katharina last_name: Ribbeck citation: ama: Goodrich CP, Brenner MP, Ribbeck K. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 2018;9. doi:10.1038/s41467-018-06851-5 apa: Goodrich, C. P., Brenner, M. P., & Ribbeck, K. (2018). Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-06851-5 chicago: Goodrich, Carl Peter, Michael P. Brenner, and Katharina Ribbeck. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-06851-5. ieee: C. P. Goodrich, M. P. Brenner, and K. Ribbeck, “Enhanced diffusion by binding to the crosslinks of a polymer gel,” Nature Communications, vol. 9. Springer Nature, 2018. ista: Goodrich CP, Brenner MP, Ribbeck K. 2018. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 9, 4348. mla: Goodrich, Carl Peter, et al. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” Nature Communications, vol. 9, 4348, Springer Nature, 2018, doi:10.1038/s41467-018-06851-5. short: C.P. Goodrich, M.P. Brenner, K. Ribbeck, Nature Communications 9 (2018). date_created: 2020-04-30T11:38:01Z date_published: 2018-10-19T00:00:00Z date_updated: 2021-01-12T08:15:18Z day: '19' doi: 10.1038/s41467-018-06851-5 extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-018-06851-5 month: '10' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Enhanced diffusion by binding to the crosslinks of a polymer gel type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '7783' abstract: - lang: eng text: The Drosophila Genetic Reference Panel (DGRP) serves as a valuable resource to better understand the genetic landscapes underlying quantitative traits. However, such DGRP studies have so far only focused on nuclear genetic variants. To address this, we sequenced the mitochondrial genomes of >170 DGRP lines, identifying 229 variants including 21 indels and 7 frameshifts. We used our mitochondrial variation data to identify 12 genetically distinct mitochondrial haplotypes, thus revealing important population structure at the mitochondrial level. We further examined whether this population structure was reflected on the nuclear genome by screening for the presence of potential mito-nuclear genetic incompatibilities in the form of significant genotype ratio distortions (GRDs) between mitochondrial and nuclear variants. In total, we detected a remarkable 1,845 mito-nuclear GRDs, with the highest enrichment observed in a 40 kb region around the gene Sex-lethal (Sxl). Intriguingly, downstream phenotypic analyses did not uncover major fitness effects associated with these GRDs, suggesting that a large number of mito-nuclear GRDs may reflect population structure at the mitochondrial level rather than actual genomic incompatibilities. This is further supported by the GRD landscape showing particular large genomic regions associated with a single mitochondrial haplotype. Next, we explored the functional relevance of the detected mitochondrial haplotypes through an association analysis on a set of 259 assembled, non-correlating DGRP phenotypes. We found multiple significant associations with stress- and metabolism-related phenotypes, including food intake in males. We validated the latter observation by reciprocal swapping of mitochondrial genomes from high food intake DGRP lines to low food intake ones. In conclusion, our study uncovered important mitochondrial population structure and haplotype-specific metabolic variation in the DGRP, thus demonstrating the significance of incorporating mitochondrial haplotypes in geno-phenotype relationship studies. article_processing_charge: No author: - first_name: Roel P.J. full_name: Bevers, Roel P.J. last_name: Bevers - first_name: Maria full_name: Litovchenko, Maria last_name: Litovchenko - first_name: Adamandia full_name: Kapopoulou, Adamandia last_name: Kapopoulou - first_name: Virginie S. full_name: Braman, Virginie S. last_name: Braman - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Johan full_name: Auwerx, Johan last_name: Auwerx - first_name: Brian full_name: Hollis, Brian last_name: Hollis - first_name: Bart full_name: Deplancke, Bart last_name: Deplancke citation: ama: Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv. 2018. apa: Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J., … Deplancke, B. (2018). Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv. Cold Spring Harbor Laboratory. chicago: Bevers, Roel P.J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S. Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke. “Extensive Mitochondrial Population Structure and Haplotype-Specific Phenotypic Variation in the Drosophila Genetic Reference Panel.” BioRxiv. Cold Spring Harbor Laboratory, 2018. ieee: R. P. J. Bevers et al., “Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel,” bioRxiv. Cold Spring Harbor Laboratory, 2018. ista: Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. 2018. Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel. bioRxiv, . mla: Bevers, Roel P. J., et al. “Extensive Mitochondrial Population Structure and Haplotype-Specific Phenotypic Variation in the Drosophila Genetic Reference Panel.” BioRxiv, Cold Spring Harbor Laboratory, 2018. short: R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson, J. Auwerx, B. Hollis, B. Deplancke, BioRxiv (2018). date_created: 2020-04-30T13:09:37Z date_published: 2018-11-09T00:00:00Z date_updated: 2021-01-12T08:15:30Z day: '09' extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/466771 ' month: '11' oa: 1 oa_version: Preprint page: '49' publication: bioRxiv publication_status: published publisher: Cold Spring Harbor Laboratory status: public title: Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '6001' abstract: - lang: eng text: "The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem; existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU are either prohibitively expensive or require significant programming expertise to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated.\r\nIn this article, we take a new approach to concurrent memory reclamation. Instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm, called ThreadScan, leverages operating system signaling to automatically detect which memory locations are being accessed by concurrent threads.\r\nInitial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free." article_number: '18' author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: William full_name: Leiserson, William last_name: Leiserson - first_name: Alexander full_name: Matveev, Alexander last_name: Matveev - first_name: Nir full_name: Shavit, Nir last_name: Shavit citation: ama: 'Alistarh D-A, Leiserson W, Matveev A, Shavit N. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 2018;4(4). doi:10.1145/3201897' apa: 'Alistarh, D.-A., Leiserson, W., Matveev, A., & Shavit, N. (2018). ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. Association for Computing Machinery. https://doi.org/10.1145/3201897' chicago: 'Alistarh, Dan-Adrian, William Leiserson, Alexander Matveev, and Nir Shavit. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing. Association for Computing Machinery, 2018. https://doi.org/10.1145/3201897.' ieee: 'D.-A. Alistarh, W. Leiserson, A. Matveev, and N. Shavit, “ThreadScan: Automatic and scalable memory reclamation,” ACM Transactions on Parallel Computing, vol. 4, no. 4. Association for Computing Machinery, 2018.' ista: 'Alistarh D-A, Leiserson W, Matveev A, Shavit N. 2018. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 4(4), 18.' mla: 'Alistarh, Dan-Adrian, et al. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing, vol. 4, no. 4, 18, Association for Computing Machinery, 2018, doi:10.1145/3201897.' short: D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, ACM Transactions on Parallel Computing 4 (2018). date_created: 2019-02-14T13:24:11Z date_published: 2018-09-01T00:00:00Z date_updated: 2023-02-23T13:17:54Z day: '01' department: - _id: DaAl doi: 10.1145/3201897 intvolume: ' 4' issue: '4' language: - iso: eng month: '09' oa_version: None publication: ACM Transactions on Parallel Computing publication_identifier: issn: - 2329-4949 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '779' relation: earlier_version status: public scopus_import: 1 status: public title: 'ThreadScan: Automatic and scalable memory reclamation' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2018' ... --- _id: '7812' abstract: - lang: eng text: Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method, differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model. We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices. article_processing_charge: No author: - first_name: Antonio full_name: Polino, Antonio last_name: Polino - first_name: Razvan full_name: Pascanu, Razvan last_name: Pascanu - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: 6th International Conference on Learning Representations. ; 2018.' apa: Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via distillation and quantization. In 6th International Conference on Learning Representations. Vancouver, Canada. chicago: Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In 6th International Conference on Learning Representations, 2018. ieee: A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018. ista: 'Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation and quantization. 6th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.' mla: Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” 6th International Conference on Learning Representations, 2018. short: A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018. conference: end_date: 2018-05-03 location: Vancouver, Canada name: 'ICLR: International Conference on Learning Representations' start_date: 2018-04-30 date_created: 2020-05-10T22:00:51Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-02-23T13:18:41Z day: '01' ddc: - '000' department: - _id: DaAl external_id: arxiv: - '1802.05668' file: - access_level: open_access checksum: a4336c167978e81891970e4e4517a8c3 content_type: application/pdf creator: dernst date_created: 2020-05-26T13:02:00Z date_updated: 2020-07-14T12:48:03Z file_id: '7894' file_name: 2018_ICLR_Polino.pdf file_size: 308339 relation: main_file file_date_updated: 2020-07-14T12:48:03Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: 6th International Conference on Learning Representations publication_status: published quality_controlled: '1' scopus_import: 1 status: public title: Model compression via distillation and quantization type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '7983' abstract: - lang: ger text: 'Feste Alkalicarbonate sind universelle Bestandteile von Passivierungsschichten an Materialien für Interkalationsbatterien, übliche Nebenprodukte in Metall‐O2‐Batterien, und es wird angenommen, dass sie sich reversibel in Metall‐O2 /CO2‐Zellen bilden und zersetzen. In all diesen Kathoden zersetzt sich Li2CO3 zu CO2, sobald es Spannungen >3.8 V vs. Li/Li+ ausgesetzt wird. Beachtenswert ist, dass keine O2‐Entwicklung detektiert wird, wie gemäß der Zersetzungsreaktion 2 Li2CO3 → 4 Li+ + 4 e− + 2 CO2 + O2 zu erwarten wäre. Deswegen war der Verbleib eines der O‐Atome ungeklärt und wurde nicht identifizierten parasitären Reaktionen zugerechnet. Hier zeigen wir, dass hochreaktiver Singulett‐Sauerstoff (1O2) bei der Oxidation von Li2CO3 in einem aprotischen Elektrolyten gebildet und daher nicht als O2 freigesetzt wird. Diese Ergebnisse haben weitreichende Auswirkungen auf die langfristige Zyklisierbarkeit von Batterien: sie untermauern die Wichtigkeit, 1O2 in Metall‐O2‐Batterien zu verhindern, stellen die Möglichkeit einer reversiblen Metall‐O2 /CO2‐Batterie basierend auf einem Carbonat‐Entladeprodukt in Frage und helfen, Grenzflächenreaktivität von Übergangsmetallkathoden mit Li2CO3‐Resten zu erklären.' article_processing_charge: No article_type: original author: - first_name: Nika full_name: Mahne, Nika last_name: Mahne - first_name: Sara E. full_name: Renfrew, Sara E. last_name: Renfrew - first_name: Bryan D. full_name: McCloskey, Bryan D. last_name: McCloskey - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. 2018;130(19):5627-5631. doi:10.1002/ange.201802277 apa: Mahne, N., Renfrew, S. E., McCloskey, B. D., & Freunberger, S. A. (2018). Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201802277 chicago: Mahne, Nika, Sara E. Renfrew, Bryan D. McCloskey, and Stefan Alexander Freunberger. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.” Angewandte Chemie. Wiley, 2018. https://doi.org/10.1002/ange.201802277. ieee: N. Mahne, S. E. Renfrew, B. D. McCloskey, and S. A. Freunberger, “Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff,” Angewandte Chemie, vol. 130, no. 19. Wiley, pp. 5627–5631, 2018. ista: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. 2018. Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie. 130(19), 5627–5631. mla: Mahne, Nika, et al. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.” Angewandte Chemie, vol. 130, no. 19, Wiley, 2018, pp. 5627–31, doi:10.1002/ange.201802277. short: N. Mahne, S.E. Renfrew, B.D. McCloskey, S.A. Freunberger, Angewandte Chemie 130 (2018) 5627–5631. date_created: 2020-06-19T08:33:24Z date_published: 2018-05-04T00:00:00Z date_updated: 2021-01-12T08:16:21Z day: '04' ddc: - '540' doi: 10.1002/ange.201802277 extern: '1' file: - access_level: open_access checksum: 81506e0f7079e1e3591f3cd9f626bf67 content_type: application/pdf creator: dernst date_created: 2020-06-19T11:58:06Z date_updated: 2020-07-14T12:48:06Z file_id: '7988' file_name: 2018_AngChemieDT_Mahne.pdf file_size: 674789 relation: main_file file_date_updated: 2020-07-14T12:48:06Z has_accepted_license: '1' intvolume: ' 130' issue: '19' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 5627-5631 publication: Angewandte Chemie publication_identifier: issn: - 0044-8249 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 130 year: '2018' ... --- _id: '8015' abstract: - lang: eng text: 'The neural code of cortical processing remains uncracked; however, it must necessarily rely on faithful signal propagation between cortical areas. In this issue of Neuron, Joglekar et al. (2018) show that strong inter-areal excitation balanced by local inhibition can enable reliable signal propagation in data-constrained network models of macaque cortex. ' article_processing_charge: No article_type: original author: - first_name: Jake P. full_name: Stroud, Jake P. last_name: Stroud - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: 'Stroud JP, Vogels TP. Cortical signal propagation: Balance, amplify, transmit. Neuron. 2018;98(1):8-9. doi:10.1016/j.neuron.2018.03.028' apa: 'Stroud, J. P., & Vogels, T. P. (2018). Cortical signal propagation: Balance, amplify, transmit. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.03.028' chicago: 'Stroud, Jake P., and Tim P Vogels. “Cortical Signal Propagation: Balance, Amplify, Transmit.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2018.03.028.' ieee: 'J. P. Stroud and T. P. Vogels, “Cortical signal propagation: Balance, amplify, transmit,” Neuron, vol. 98, no. 1. Elsevier, pp. 8–9, 2018.' ista: 'Stroud JP, Vogels TP. 2018. Cortical signal propagation: Balance, amplify, transmit. Neuron. 98(1), 8–9.' mla: 'Stroud, Jake P., and Tim P. Vogels. “Cortical Signal Propagation: Balance, Amplify, Transmit.” Neuron, vol. 98, no. 1, Elsevier, 2018, pp. 8–9, doi:10.1016/j.neuron.2018.03.028.' short: J.P. Stroud, T.P. Vogels, Neuron 98 (2018) 8–9. date_created: 2020-06-25T12:53:39Z date_published: 2018-04-04T00:00:00Z date_updated: 2021-01-12T08:16:31Z day: '04' doi: 10.1016/j.neuron.2018.03.028 extern: '1' external_id: pmid: - '29621492' intvolume: ' 98' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.neuron.2018.03.028 month: '04' oa: 1 oa_version: Published Version page: 8-9 pmid: 1 publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'Cortical signal propagation: Balance, amplify, transmit' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 98 year: '2018' ... --- _id: '8073' abstract: - lang: eng text: Motor cortex (M1) exhibits a rich repertoire of neuronal activities to support the generation of complex movements. Although recent neuronal-network models capture many qualitative aspects of M1 dynamics, they can generate only a few distinct movements. Additionally, it is unclear how M1 efficiently controls movements over a wide range of shapes and speeds. We demonstrate that modulation of neuronal input–output gains in recurrent neuronal-network models with a fixed architecture can dramatically reorganize neuronal activity and thus downstream muscle outputs. Consistent with the observation of diffuse neuromodulatory projections to M1, a relatively small number of modulatory control units provide sufficient flexibility to adjust high-dimensional network activity using a simple reward-based learning rule. Furthermore, it is possible to assemble novel movements from previously learned primitives, and one can separately change movement speed while preserving movement shape. Our results provide a new perspective on the role of modulatory systems in controlling recurrent cortical activity. article_processing_charge: No article_type: original author: - first_name: Jake P. full_name: Stroud, Jake P. last_name: Stroud - first_name: Mason A. full_name: Porter, Mason A. last_name: Porter - first_name: Guillaume full_name: Hennequin, Guillaume last_name: Hennequin - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: Stroud JP, Porter MA, Hennequin G, Vogels TP. Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. 2018;21(12):1774-1783. doi:10.1038/s41593-018-0276-0 apa: Stroud, J. P., Porter, M. A., Hennequin, G., & Vogels, T. P. (2018). Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-018-0276-0 chicago: Stroud, Jake P., Mason A. Porter, Guillaume Hennequin, and Tim P Vogels. “Motor Primitives in Space and Time via Targeted Gain Modulation in Cortical Networks.” Nature Neuroscience. Springer Nature, 2018. https://doi.org/10.1038/s41593-018-0276-0. ieee: J. P. Stroud, M. A. Porter, G. Hennequin, and T. P. Vogels, “Motor primitives in space and time via targeted gain modulation in cortical networks,” Nature Neuroscience, vol. 21, no. 12. Springer Nature, pp. 1774–1783, 2018. ista: Stroud JP, Porter MA, Hennequin G, Vogels TP. 2018. Motor primitives in space and time via targeted gain modulation in cortical networks. Nature Neuroscience. 21(12), 1774–1783. mla: Stroud, Jake P., et al. “Motor Primitives in Space and Time via Targeted Gain Modulation in Cortical Networks.” Nature Neuroscience, vol. 21, no. 12, Springer Nature, 2018, pp. 1774–83, doi:10.1038/s41593-018-0276-0. short: J.P. Stroud, M.A. Porter, G. Hennequin, T.P. Vogels, Nature Neuroscience 21 (2018) 1774–1783. date_created: 2020-06-30T13:18:02Z date_published: 2018-12-01T00:00:00Z date_updated: 2021-01-12T08:16:46Z day: '01' doi: 10.1038/s41593-018-0276-0 extern: '1' external_id: pmid: - '30482949' intvolume: ' 21' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276991/ month: '12' oa: 1 oa_version: Submitted Version page: 1774-1783 pmid: 1 publication: Nature Neuroscience publication_identifier: issn: - 1097-6256 - 1546-1726 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41593-018-0307-x status: public title: Motor primitives in space and time via targeted gain modulation in cortical networks type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 21 year: '2018' ... --- _id: '8231' article_processing_charge: No article_type: letter_note author: - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Josef full_name: Singer, Josef last_name: Singer - first_name: Kristina M. full_name: Ilieva, Kristina M. last_name: Ilieva - first_name: Miroslawa full_name: Matz, Miroslawa last_name: Matz - first_name: Ina full_name: Herrmann, Ina last_name: Herrmann - first_name: Edzard full_name: Spillner, Edzard last_name: Spillner - first_name: Sophia N. full_name: Karagiannis, Sophia N. last_name: Karagiannis - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim citation: ama: 'Singer J, Singer J, Ilieva KM, et al. AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. 2018;142(3):973-976.e11. doi:10.1016/j.jaci.2018.04.021' apa: 'Singer, J., Singer, J., Ilieva, K. M., Matz, M., Herrmann, I., Spillner, E., … Jensen-Jarolim, E. (2018). AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. Elsevier. https://doi.org/10.1016/j.jaci.2018.04.021' chicago: 'Singer, Judit, Josef Singer, Kristina M. Ilieva, Miroslawa Matz, Ina Herrmann, Edzard Spillner, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology: Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.” Journal of Allergy and Clinical Immunology. Elsevier, 2018. https://doi.org/10.1016/j.jaci.2018.04.021.' ieee: 'J. Singer et al., “AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor,” Journal of Allergy and Clinical Immunology, vol. 142, no. 3. Elsevier, p. 973–976.e11, 2018.' ista: 'Singer J, Singer J, Ilieva KM, Matz M, Herrmann I, Spillner E, Karagiannis SN, Jensen-Jarolim E. 2018. AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. 142(3), 973–976.e11.' mla: 'Singer, Judit, et al. “AllergoOncology: Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.” Journal of Allergy and Clinical Immunology, vol. 142, no. 3, Elsevier, 2018, p. 973–976.e11, doi:10.1016/j.jaci.2018.04.021.' short: J. Singer, J. Singer, K.M. Ilieva, M. Matz, I. Herrmann, E. Spillner, S.N. Karagiannis, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology 142 (2018) 973–976.e11. date_created: 2020-08-10T11:51:36Z date_published: 2018-09-01T00:00:00Z date_updated: 2021-01-12T08:17:37Z day: '01' doi: 10.1016/j.jaci.2018.04.021 extern: '1' intvolume: ' 142' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.jaci.2018.04.021 month: '09' oa: 1 oa_version: Published Version page: 973-976.e11 publication: Journal of Allergy and Clinical Immunology publication_identifier: issn: - 0091-6749 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 142 year: '2018' ... --- _id: '8234' abstract: - lang: eng text: Molecular imaging probes such as PET-tracers have the potential to improve the accuracy of tumor characterization by directly visualizing the biochemical situation. Thus, molecular changes can be detected early before morphological manifestation. The A3 adenosine receptor (A3AR) is described to be highly expressed in colon cancer cell lines and human colorectal cancer (CRC), suggesting this receptor as a tumor marker. The aim of this preclinical study was the evaluation of FE@SUPPY as a PET-tracer for CRC using in vitro imaging and in vivo PET imaging. First, affinity and selectivity of FE@SUPPY and its metabolites were determined, proving the favorable binding profile of FE@SUPPY. The human adenocarcinoma cell line HT-29 was characterized regarding its hA3AR expression and was subsequently chosen as tumor graft. Promising results regarding the potential of FE@SUPPY as a PET-tracer for CRC imaging were obtained by autoradiography as ≥2.3-fold higher accumulation of FE@SUPPY was found in CRC tissue compared to adjacent healthy colon tissue from the same patient. Nevertheless, first in vivo studies using HT-29 xenografts showed insufficient tumor uptake due to (1) poor conservation of target expression in xenografts and (2) unfavorable pharmacokinetics of FE@SUPPY in mice. We therefore conclude that HT-29 xenografts are not adequate to visualize hA3ARs using FE@SUPPY. article_number: '1269830' article_processing_charge: No article_type: original author: - first_name: T. full_name: Balber, T. last_name: Balber - first_name: Judit full_name: Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Singer orcid: 0000-0002-8777-3502 - first_name: N. full_name: Berroterán-Infante, N. last_name: Berroterán-Infante - first_name: M. full_name: Dumanic, M. last_name: Dumanic - first_name: L. full_name: Fetty, L. last_name: Fetty - first_name: J. full_name: Fazekas-Singer, J. last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: C. full_name: Vraka, C. last_name: Vraka - first_name: L. full_name: Nics, L. last_name: Nics - first_name: M. full_name: Bergmann, M. last_name: Bergmann - first_name: K. full_name: Pallitsch, K. last_name: Pallitsch - first_name: H. full_name: Spreitzer, H. last_name: Spreitzer - first_name: W. full_name: Wadsak, W. last_name: Wadsak orcid: 0000-0003-4479-8053 - first_name: M. full_name: Hacker, M. last_name: Hacker - first_name: E. full_name: Jensen-Jarolim, E. last_name: Jensen-Jarolim - first_name: H. full_name: Viernstein, H. last_name: Viernstein - first_name: M. full_name: Mitterhauser, M. last_name: Mitterhauser orcid: 0000-0003-3173-5272 citation: ama: 'Balber T, Singer J, Berroterán-Infante N, et al. Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. 2018;2018. doi:10.1155/2018/1269830' apa: 'Balber, T., Singer, J., Berroterán-Infante, N., Dumanic, M., Fetty, L., Fazekas-Singer, J., … Mitterhauser, M. (2018). Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. Hindawi. https://doi.org/10.1155/2018/1269830' chicago: 'Balber, T., Judit Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer, C. Vraka, et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.” Contrast Media & Molecular Imaging. Hindawi, 2018. https://doi.org/10.1155/2018/1269830.' ieee: 'T. Balber et al., “Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer,” Contrast Media & Molecular Imaging, vol. 2018. Hindawi, 2018.' ista: 'Balber T, Singer J, Berroterán-Infante N, Dumanic M, Fetty L, Fazekas-Singer J, Vraka C, Nics L, Bergmann M, Pallitsch K, Spreitzer H, Wadsak W, Hacker M, Jensen-Jarolim E, Viernstein H, Mitterhauser M. 2018. Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. 2018, 1269830.' mla: 'Balber, T., et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.” Contrast Media & Molecular Imaging, vol. 2018, 1269830, Hindawi, 2018, doi:10.1155/2018/1269830.' short: T. Balber, J. Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer, C. Vraka, L. Nics, M. Bergmann, K. Pallitsch, H. Spreitzer, W. Wadsak, M. Hacker, E. Jensen-Jarolim, H. Viernstein, M. Mitterhauser, Contrast Media & Molecular Imaging 2018 (2018). date_created: 2020-08-10T11:53:07Z date_published: 2018-02-13T00:00:00Z date_updated: 2021-01-12T08:17:38Z day: '13' doi: 10.1155/2018/1269830 extern: '1' intvolume: ' 2018' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1155/2018/1269830 month: '02' oa: 1 oa_version: Published Version publication: Contrast Media & Molecular Imaging publication_identifier: issn: - 1555-4309 - 1555-4317 publication_status: published publisher: Hindawi quality_controlled: '1' status: public title: 'Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2018 year: '2018' ... --- _id: '8232' abstract: - lang: eng text: 'Anti-epidermal growth factor receptor (EGFR) antibody therapy is used in EGFR expressing cancers including lung, colon, head and neck, and bladder cancers, however results have been modest. Near infrared photoimmunotherapy (NIR-PIT) is a highly selective tumor treatment that employs an antibody-photo-absorber conjugate which is activated by NIR light. NIR-PIT is in clinical trials in patients with recurrent head and neck cancers using cetuximab-IR700 as the conjugate. However, its use has otherwise been restricted to mouse models. This is an effort to explore larger animal models with NIR-PIT. We describe the use of a recombinant canine anti-EGFR monoclonal antibody (mAb), can225IgG, conjugated to the photo-absorber, IR700DX, in three EGFR expressing canine transitional cell carcinoma (TCC) cell lines as a prelude to possible canine clinical studies. Can225-IR700 conjugate showed specific binding and cell-specific killing after NIR-PIT on EGFR expressing cells in vitro. In the in vivo study, can225-IR700 conjugate demonstrated accumulation of the fluorescent conjugate with high tumor-to-background ratio. Tumor-bearing mice were separated into 4 groups: (1) no treatment; (2) 100 μg of can225-IR700 i.v. only; (3) NIR light exposure only; (4) 100 μg of can225-IR700 i.v., NIR light exposure. Tumor growth was significantly inhibited by NIR-PIT treatment compared with the other groups (p < 0.001), and significantly prolonged survival was achieved (p < 0.001 vs. other groups) in the treatment groups. In conclusion, NIR-PIT with can225-IR700 is a promising treatment for canine EGFR-expressing cancers, including invasive transitional cell carcinoma in pet dogs, that could provide a pathway to translation to humans.' article_processing_charge: No article_type: original author: - first_name: Tadanobu full_name: Nagaya, Tadanobu last_name: Nagaya - first_name: Shuhei full_name: Okuyama, Shuhei last_name: Okuyama - first_name: Fusa full_name: Ogata, Fusa last_name: Ogata - first_name: Yasuhiro full_name: Maruoka, Yasuhiro last_name: Maruoka - first_name: Deborah W. full_name: Knapp, Deborah W. last_name: Knapp - first_name: Sophia N. full_name: Karagiannis, Sophia N. last_name: Karagiannis - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Peter L. full_name: Choyke, Peter L. last_name: Choyke - first_name: Amy K. full_name: LeBlanc, Amy K. last_name: LeBlanc - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim - first_name: Hisataka full_name: Kobayashi, Hisataka last_name: Kobayashi citation: ama: Nagaya T, Okuyama S, Ogata F, et al. Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. 2018;9:19026-19038. doi:10.18632/oncotarget.24876 apa: Nagaya, T., Okuyama, S., Ogata, F., Maruoka, Y., Knapp, D. W., Karagiannis, S. N., … Kobayashi, H. (2018). Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. Impact Journals. https://doi.org/10.18632/oncotarget.24876 chicago: Nagaya, Tadanobu, Shuhei Okuyama, Fusa Ogata, Yasuhiro Maruoka, Deborah W. Knapp, Sophia N. Karagiannis, Judit Singer, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” Oncotarget. Impact Journals, 2018. https://doi.org/10.18632/oncotarget.24876. ieee: T. Nagaya et al., “Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody,” Oncotarget, vol. 9. Impact Journals, pp. 19026–19038, 2018. ista: Nagaya T, Okuyama S, Ogata F, Maruoka Y, Knapp DW, Karagiannis SN, Singer J, Choyke PL, LeBlanc AK, Jensen-Jarolim E, Kobayashi H. 2018. Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. 9, 19026–19038. mla: Nagaya, Tadanobu, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” Oncotarget, vol. 9, Impact Journals, 2018, pp. 19026–38, doi:10.18632/oncotarget.24876. short: T. Nagaya, S. Okuyama, F. Ogata, Y. Maruoka, D.W. Knapp, S.N. Karagiannis, J. Singer, P.L. Choyke, A.K. LeBlanc, E. Jensen-Jarolim, H. Kobayashi, Oncotarget 9 (2018) 19026–19038. date_created: 2020-08-10T11:52:54Z date_published: 2018-04-10T00:00:00Z date_updated: 2021-01-12T08:17:37Z day: '10' doi: 10.18632/oncotarget.24876 extern: '1' intvolume: ' 9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.18632/oncotarget.24876 month: '04' oa: 1 oa_version: Published Version page: 19026-19038 publication: Oncotarget publication_identifier: eissn: - 1949-2553 publication_status: published publisher: Impact Journals quality_controlled: '1' status: public title: Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '8233' abstract: - lang: eng text: The M2a subtype of macrophages plays an important role in human immunoglobulin E (IgE-mediated allergies) and other Th2 type immune reactions. In contrast, very little is known about these cells in the dog. Here we describe an in vitro method to activate canine histiocytic DH82 cells and primary canine monocyte-derived macrophages (MDMs) toward the M2a macrophages using human cytokines. For a side-by-side comparison, we compared the canine cells to human MDMs, and the human monocytic cell line U937 activated towards M1 and M2a cells on the cellular and molecular level. In analogy to activated human M2a cells, canine M2a, differentiated from both DH82 and MDMs, showed an increase in CD206 surface receptor expression compared to M1. Interestingly, canine M2a, but not M1 derived from MDM, upregulated the high-affinity IgE receptor (FcεRI). Transcription levels of M2a-associated genes (IL10, CCL22, TGFβ, CD163) showed a diverse pattern between the human and dog species, whereas M1 genes (IDO1, CXCL11, IL6, TNF-α) were similarly upregulated in canine and human M1 cells (cell lines and MDMs). We suggest that our novel in vitro method will be suitable in comparative allergology studies focussing on macrophages. article_processing_charge: No article_type: original author: - first_name: Ina full_name: Herrmann, Ina last_name: Herrmann - first_name: Jelena full_name: Gotovina, Jelena last_name: Gotovina - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Michael B. full_name: Fischer, Michael B. last_name: Fischer - first_name: Karin full_name: Hufnagl, Karin last_name: Hufnagl - first_name: Rodolfo full_name: Bianchini, Rodolfo last_name: Bianchini - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim citation: ama: Herrmann I, Gotovina J, Singer J, et al. Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. 2018;82(5):118-127. doi:10.1016/j.dci.2018.01.005 apa: Herrmann, I., Gotovina, J., Singer, J., Fischer, M. B., Hufnagl, K., Bianchini, R., & Jensen-Jarolim, E. (2018). Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. Elsevier. https://doi.org/10.1016/j.dci.2018.01.005 chicago: Herrmann, Ina, Jelena Gotovina, Judit Singer, Michael B. Fischer, Karin Hufnagl, Rodolfo Bianchini, and Erika Jensen-Jarolim. “Canine Macrophages Can like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in Allergy.” Developmental & Comparative Immunology. Elsevier, 2018. https://doi.org/10.1016/j.dci.2018.01.005. ieee: I. Herrmann et al., “Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy,” Developmental & Comparative Immunology, vol. 82, no. 5. Elsevier, pp. 118–127, 2018. ista: Herrmann I, Gotovina J, Singer J, Fischer MB, Hufnagl K, Bianchini R, Jensen-Jarolim E. 2018. Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. 82(5), 118–127. mla: Herrmann, Ina, et al. “Canine Macrophages Can like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in Allergy.” Developmental & Comparative Immunology, vol. 82, no. 5, Elsevier, 2018, pp. 118–27, doi:10.1016/j.dci.2018.01.005. short: I. Herrmann, J. Gotovina, J. Singer, M.B. Fischer, K. Hufnagl, R. Bianchini, E. Jensen-Jarolim, Developmental & Comparative Immunology 82 (2018) 118–127. date_created: 2020-08-10T11:53:01Z date_published: 2018-05-01T00:00:00Z date_updated: 2021-01-12T08:17:38Z day: '01' doi: 10.1016/j.dci.2018.01.005 extern: '1' intvolume: ' 82' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.dci.2018.01.005 month: '05' oa: 1 oa_version: Published Version page: 118-127 publication: Developmental & Comparative Immunology publication_identifier: issn: - 0145-305X publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 82 year: '2018' ... --- _id: '8262' abstract: - lang: eng text: "Background: The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes.\r\n\r\nResults: We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.\r\n\r\nConclusions: This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei." article_number: '965' article_processing_charge: No article_type: original author: - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Elena V. full_name: Moroz, Elena V. last_name: Moroz - first_name: Iakov I. full_name: Davydov, Iakov I. last_name: Davydov - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Bochkareva O, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 2018;19. doi:10.1186/s12864-018-5245-1 apa: Bochkareva, O., Moroz, E. V., Davydov, I. I., & Gelfand, M. S. (2018). Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. Springer Nature. https://doi.org/10.1186/s12864-018-5245-1 chicago: Bochkareva, Olga, Elena V. Moroz, Iakov I. Davydov, and Mikhail S. Gelfand. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” BMC Genomics. Springer Nature, 2018. https://doi.org/10.1186/s12864-018-5245-1. ieee: O. Bochkareva, E. V. Moroz, I. I. Davydov, and M. S. Gelfand, “Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.,” BMC Genomics, vol. 19. Springer Nature, 2018. ista: Bochkareva O, Moroz EV, Davydov II, Gelfand MS. 2018. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 19, 965. mla: Bochkareva, Olga, et al. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” BMC Genomics, vol. 19, 965, Springer Nature, 2018, doi:10.1186/s12864-018-5245-1. short: O. Bochkareva, E.V. Moroz, I.I. Davydov, M.S. Gelfand, BMC Genomics 19 (2018). date_created: 2020-08-15T11:02:08Z date_published: 2018-12-27T00:00:00Z date_updated: 2023-02-23T13:28:52Z day: '27' doi: 10.1186/s12864-018-5245-1 extern: '1' intvolume: ' 19' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1186/s12864-018-5245-1 month: '12' oa: 1 oa_version: Published Version publication: BMC Genomics publication_identifier: issn: - 1471-2164 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2018' ... --- _id: '8265' abstract: - lang: eng text: Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements by inversions. We also reconciled phylogenetic trees for each of the three CRISPR loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis of contradictions between the obtained evolutionary trees yielded numerous parallel inversions and gain/loss events. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content. article_number: e4545 article_processing_charge: No article_type: original author: - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Natalia O. full_name: Dranenko, Natalia O. last_name: Dranenko - first_name: Elena S. full_name: Ocheredko, Elena S. last_name: Ocheredko - first_name: German M. full_name: Kanevsky, German M. last_name: Kanevsky - first_name: Yaroslav N. full_name: Lozinsky, Yaroslav N. last_name: Lozinsky - first_name: Vera A. full_name: Khalaycheva, Vera A. last_name: Khalaycheva - first_name: Irena I. full_name: Artamonova, Irena I. last_name: Artamonova - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Bochkareva O, Dranenko NO, Ocheredko ES, et al. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. 2018;6. doi:10.7717/peerj.4545 apa: Bochkareva, O., Dranenko, N. O., Ocheredko, E. S., Kanevsky, G. M., Lozinsky, Y. N., Khalaycheva, V. A., … Gelfand, M. S. (2018). Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. PeerJ. https://doi.org/10.7717/peerj.4545 chicago: Bochkareva, Olga, Natalia O. Dranenko, Elena S. Ocheredko, German M. Kanevsky, Yaroslav N. Lozinsky, Vera A. Khalaycheva, Irena I. Artamonova, and Mikhail S. Gelfand. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.4545. ieee: O. Bochkareva et al., “Genome rearrangements and phylogeny reconstruction in Yersinia pestis,” PeerJ, vol. 6. PeerJ, 2018. ista: Bochkareva O, Dranenko NO, Ocheredko ES, Kanevsky GM, Lozinsky YN, Khalaycheva VA, Artamonova II, Gelfand MS. 2018. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. 6, e4545. mla: Bochkareva, Olga, et al. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.” PeerJ, vol. 6, e4545, PeerJ, 2018, doi:10.7717/peerj.4545. short: O. Bochkareva, N.O. Dranenko, E.S. Ocheredko, G.M. Kanevsky, Y.N. Lozinsky, V.A. Khalaycheva, I.I. Artamonova, M.S. Gelfand, PeerJ 6 (2018). date_created: 2020-08-15T11:08:23Z date_published: 2018-03-27T00:00:00Z date_updated: 2023-02-23T13:28:57Z day: '27' doi: 10.7717/peerj.4545 extern: '1' external_id: pmid: - '29607260' intvolume: ' 6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.7717/peerj.4545 month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: PeerJ publication_identifier: issn: - 2167-8359 publication_status: published publisher: PeerJ quality_controlled: '1' status: public title: Genome rearrangements and phylogeny reconstruction in Yersinia pestis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2018' ... --- _id: '8274' abstract: - lang: eng text: 'Background/Aim: Our aim was to investigate the crosstalk between tumor and immune cells (M2 macrophages) and its effects on cyclo-oxygenase-2 (COX2) regulation in canine mammary tumors (CMT). Materials and Methods: Sh1b CMT cells and human BT474 mammary or HT29 colon cancer cells were co-cultured with canine peripheral blood mononuclear cells (PBMCs) or with macrophage-like differentiated THP1 monocytes (dTHP1). Intracellular COX2 expression by PBMCs, dTHP1 and cancer cells was evaluated by flow cytometry. Results: Co-culturing of Sh1b and canine PBMCs induced COX2 overexpression in CMT cells. In turn, COX2 expression by PBMCs, mostly CD68+ macrophages, was attenuated by co-culture with Sh1b (p=0.0001). In accordance, co-culture with dTHP1 prompted intracellular production of COX2 in both Sh1b CMT cells and HT29 human colon cancer cells and reduced production of COX2 in BT474 human mammary cancer cells. The intracellular COX2 expression from dTHP1 decreased when treated with conditioned medium from cultured Sh1b and HT29 cancer cells. Conclusion: Bidirectional COX2 regulation between cancer and monocytes/macrophages might shape a tolerogenic tumor microenvironment in CMT.' article_processing_charge: No article_type: original author: - first_name: Maria Isabel full_name: Carvalho, Maria Isabel last_name: Carvalho - first_name: Rodolfo full_name: Bianchini, Rodolfo last_name: Bianchini - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Ina full_name: Herrmann, Ina last_name: Herrmann - first_name: Irene full_name: Flickinger, Irene last_name: Flickinger - first_name: Johann G. full_name: Thalhammer, Johann G. last_name: Thalhammer - first_name: Isabel full_name: Pires, Isabel last_name: Pires - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim - first_name: Felisbina L. full_name: Queiroga, Felisbina L. last_name: Queiroga citation: ama: Carvalho MI, Bianchini R, Singer J, et al. Bidirectional regulation of COX-2 expression between cancer cells and macrophages. Anticancer Research. 2018;38(5):2811-2817. doi:10.21873/anticanres.12525 apa: Carvalho, M. I., Bianchini, R., Singer, J., Herrmann, I., Flickinger, I., Thalhammer, J. G., … Queiroga, F. L. (2018). Bidirectional regulation of COX-2 expression between cancer cells and macrophages. Anticancer Research. International Institute of Anticancer Research. https://doi.org/10.21873/anticanres.12525 chicago: Carvalho, Maria Isabel, Rodolfo Bianchini, Judit Singer, Ina Herrmann, Irene Flickinger, Johann G. Thalhammer, Isabel Pires, Erika Jensen-Jarolim, and Felisbina L. Queiroga. “Bidirectional Regulation of COX-2 Expression between Cancer Cells and Macrophages.” Anticancer Research. International Institute of Anticancer Research, 2018. https://doi.org/10.21873/anticanres.12525. ieee: M. I. Carvalho et al., “Bidirectional regulation of COX-2 expression between cancer cells and macrophages,” Anticancer Research, vol. 38, no. 5. International Institute of Anticancer Research, pp. 2811–2817, 2018. ista: Carvalho MI, Bianchini R, Singer J, Herrmann I, Flickinger I, Thalhammer JG, Pires I, Jensen-Jarolim E, Queiroga FL. 2018. Bidirectional regulation of COX-2 expression between cancer cells and macrophages. Anticancer Research. 38(5), 2811–2817. mla: Carvalho, Maria Isabel, et al. “Bidirectional Regulation of COX-2 Expression between Cancer Cells and Macrophages.” Anticancer Research, vol. 38, no. 5, International Institute of Anticancer Research, 2018, pp. 2811–17, doi:10.21873/anticanres.12525. short: M.I. Carvalho, R. Bianchini, J. Singer, I. Herrmann, I. Flickinger, J.G. Thalhammer, I. Pires, E. Jensen-Jarolim, F.L. Queiroga, Anticancer Research 38 (2018) 2811–2817. date_created: 2020-08-17T07:13:55Z date_published: 2018-05-01T00:00:00Z date_updated: 2021-01-12T08:17:52Z day: '01' doi: 10.21873/anticanres.12525 extern: '1' intvolume: ' 38' issue: '5' language: - iso: eng month: '05' oa_version: None page: 2811-2817 publication: Anticancer Research publication_identifier: eissn: - 1791-7530 issn: - 0250-7005 publication_status: published publisher: International Institute of Anticancer Research quality_controlled: '1' status: public title: Bidirectional regulation of COX-2 expression between cancer cells and macrophages type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2018' ... --- _id: '8298' abstract: - lang: eng text: Sharding, or partitioning the system’s state so that different subsets of participants handle it, is a proven approach to building distributed systems whose total capacity scales horizontally with the number of participants. Many distributed ledgers have adopted this approach to increase their performance, however, they focus on the permissionless setting that assumes the existence of a strong adversary. In this paper, we deploy channels for permissioned blockchains. Our first contribution is to adapt sharding on asset-management applications for the permissioned setting, while preserving liveness and safety even on transactions spanning across-channels. Our second contribution is to leverage channels as a confidentiality boundary, enabling different organizations and consortia to preserve their privacy within their channels and still be part of a bigger collaborative ecosystem. To make our system concrete we map it on top of Hyperledger Fabric. alternative_title: - LNCS article_processing_charge: No author: - first_name: Elli full_name: Androulaki, Elli last_name: Androulaki - first_name: Christian full_name: Cachin, Christian last_name: Cachin - first_name: Angelo full_name: De Caro, Angelo last_name: De Caro - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias citation: ama: 'Androulaki E, Cachin C, De Caro A, Kokoris Kogias E. Channels: Horizontal scaling and confidentiality on permissioned blockchains. In: Computer Security. Vol 11098. Springer Nature; 2018:111-131. doi:10.1007/978-3-319-99073-6_6' apa: 'Androulaki, E., Cachin, C., De Caro, A., & Kokoris Kogias, E. (2018). Channels: Horizontal scaling and confidentiality on permissioned blockchains. In Computer Security (Vol. 11098, pp. 111–131). Barcelona, Spain: Springer Nature. https://doi.org/10.1007/978-3-319-99073-6_6' chicago: 'Androulaki, Elli, Christian Cachin, Angelo De Caro, and Eleftherios Kokoris Kogias. “Channels: Horizontal Scaling and Confidentiality on Permissioned Blockchains.” In Computer Security, 11098:111–31. Springer Nature, 2018. https://doi.org/10.1007/978-3-319-99073-6_6.' ieee: 'E. Androulaki, C. Cachin, A. De Caro, and E. Kokoris Kogias, “Channels: Horizontal scaling and confidentiality on permissioned blockchains,” in Computer Security, Barcelona, Spain, 2018, vol. 11098, pp. 111–131.' ista: 'Androulaki E, Cachin C, De Caro A, Kokoris Kogias E. 2018. Channels: Horizontal scaling and confidentiality on permissioned blockchains. Computer Security. ESORICS: European Symposium on Research in Computer Security, LNCS, vol. 11098, 111–131.' mla: 'Androulaki, Elli, et al. “Channels: Horizontal Scaling and Confidentiality on Permissioned Blockchains.” Computer Security, vol. 11098, Springer Nature, 2018, pp. 111–31, doi:10.1007/978-3-319-99073-6_6.' short: E. Androulaki, C. Cachin, A. De Caro, E. Kokoris Kogias, in:, Computer Security, Springer Nature, 2018, pp. 111–131. conference: end_date: 2018-09-07 location: Barcelona, Spain name: 'ESORICS: European Symposium on Research in Computer Security' start_date: 2018-09-03 date_created: 2020-08-26T11:47:34Z date_published: 2018-08-08T00:00:00Z date_updated: 2021-01-12T08:17:57Z day: '08' doi: 10.1007/978-3-319-99073-6_6 extern: '1' intvolume: ' 11098' language: - iso: eng month: '08' oa_version: None page: 111-131 publication: Computer Security publication_identifier: eisbn: - '9783319990736' isbn: - '9783319990729' issn: - 0302-9743 - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'Channels: Horizontal scaling and confidentiality on permissioned blockchains' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11098 year: '2018' ... --- _id: '8297' abstract: - lang: eng text: "Designing a secure permissionless distributed ledger (blockchain) that performs on par with centralized payment\r\nprocessors, such as Visa, is a challenging task. Most existing distributed ledgers are unable to scale-out, i.e., to grow their totalprocessing capacity with the number of validators; and those that do, compromise security or decentralization. We present OmniLedger, a novel scale-out distributed ledger that preserves longterm security under permissionless operation. It ensures security and correctness by using a bias-resistant public-randomness protocol for choosing large, statistically representative shards that process transactions, and by introducing an efficient crossshard commit protocol that atomically handles transactions affecting multiple shards. OmniLedger also optimizes performance via parallel intra-shard transaction processing, ledger pruning via collectively-signed state blocks, and low-latency “trust-butverify” \r\nvalidation for low-value transactions. An evaluation ofour experimental prototype shows that OmniLedger’s throughput\r\nscales linearly in the number of active validators, supporting Visa-level workloads and beyond, while confirming typical transactions in under two seconds." article_processing_charge: No author: - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Philipp full_name: Jovanovic, Philipp last_name: Jovanovic - first_name: Linus full_name: Gasser, Linus last_name: Gasser - first_name: Nicolas full_name: Gailly, Nicolas last_name: Gailly - first_name: Ewa full_name: Syta, Ewa last_name: Syta - first_name: Bryan full_name: Ford, Bryan last_name: Ford citation: ama: 'Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. OmniLedger: A secure, scale-out, decentralized ledger via sharding. In: 2018 IEEE Symposium on Security and Privacy. IEEE; 2018:583-598. doi:10.1109/sp.2018.000-5' apa: 'Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Syta, E., & Ford, B. (2018). OmniLedger: A secure, scale-out, decentralized ledger via sharding. In 2018 IEEE Symposium on Security and Privacy (pp. 583–598). San Francisco, CA, United States: IEEE. https://doi.org/10.1109/sp.2018.000-5' chicago: 'Kokoris Kogias, Eleftherios, Philipp Jovanovic, Linus Gasser, Nicolas Gailly, Ewa Syta, and Bryan Ford. “OmniLedger: A Secure, Scale-out, Decentralized Ledger via Sharding.” In 2018 IEEE Symposium on Security and Privacy, 583–98. IEEE, 2018. https://doi.org/10.1109/sp.2018.000-5.' ieee: 'E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, and B. Ford, “OmniLedger: A secure, scale-out, decentralized ledger via sharding,” in 2018 IEEE Symposium on Security and Privacy, San Francisco, CA, United States, 2018, pp. 583–598.' ista: 'Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. 2018. OmniLedger: A secure, scale-out, decentralized ledger via sharding. 2018 IEEE Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 583–598.' mla: 'Kokoris Kogias, Eleftherios, et al. “OmniLedger: A Secure, Scale-out, Decentralized Ledger via Sharding.” 2018 IEEE Symposium on Security and Privacy, IEEE, 2018, pp. 583–98, doi:10.1109/sp.2018.000-5.' short: E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, B. Ford, in:, 2018 IEEE Symposium on Security and Privacy, IEEE, 2018, pp. 583–598. conference: end_date: 2018-05-24 location: San Francisco, CA, United States name: 'SP: Symposium on Security and Privacy' start_date: 2018-05-20 date_created: 2020-08-26T11:46:35Z date_published: 2018-07-26T00:00:00Z date_updated: 2021-01-12T08:17:56Z day: '26' doi: 10.1109/sp.2018.000-5 extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2017/406 month: '07' oa: 1 oa_version: Preprint page: 583-598 publication: 2018 IEEE Symposium on Security and Privacy publication_identifier: isbn: - '9781538643532' issn: - 2375-1207 publication_status: published publisher: IEEE quality_controlled: '1' status: public title: 'OmniLedger: A secure, scale-out, decentralized ledger via sharding' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '8443' abstract: - lang: eng text: Characterizing the structure of membrane proteins (MPs) generally requires extraction from their native environment, most commonly with detergents. Yet, the physicochemical properties of detergent micelles and lipid bilayers differ markedly and could alter the structural organization of MPs, albeit without general rules. Dodecylphosphocholine (DPC) is the most widely used detergent for MP structure determination by NMR, but the physiological relevance of several prominent structures has been questioned, though indirectly, by other biophysical techniques, e.g., functional/thermostability assay (TSA) and molecular dynamics (MD) simulations. Here, we resolve unambiguously this controversy by probing the functional relevance of three different mitochondrial carriers (MCs) in DPC at the atomic level, using an exhaustive set of solution-NMR experiments, complemented by functional/TSA and MD data. Our results provide atomic-level insight into the structure, substrate interaction and dynamics of the detergent–membrane protein complexes and demonstrates cogently that, while high-resolution NMR signals can be obtained for MCs in DPC, they systematically correspond to nonfunctional states. article_processing_charge: No article_type: original author: - first_name: Vilius full_name: Kurauskas, Vilius last_name: Kurauskas - first_name: Audrey full_name: Hessel, Audrey last_name: Hessel - first_name: Peixiang full_name: Ma, Peixiang last_name: Ma - first_name: Paola full_name: Lunetti, Paola last_name: Lunetti - first_name: Katharina full_name: Weinhäupl, Katharina last_name: Weinhäupl - first_name: Lionel full_name: Imbert, Lionel last_name: Imbert - first_name: Bernhard full_name: Brutscher, Bernhard last_name: Brutscher - first_name: Martin S. full_name: King, Martin S. last_name: King - first_name: Rémy full_name: Sounier, Rémy last_name: Sounier - first_name: Vincenza full_name: Dolce, Vincenza last_name: Dolce - first_name: Edmund R. S. full_name: Kunji, Edmund R. S. last_name: Kunji - first_name: Loredana full_name: Capobianco, Loredana last_name: Capobianco - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: François full_name: Dehez, François last_name: Dehez - first_name: Beate full_name: Bersch, Beate last_name: Bersch - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: 'Kurauskas V, Hessel A, Ma P, et al. How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry Letters. 2018;9(5):933-938. doi:10.1021/acs.jpclett.8b00269' apa: 'Kurauskas, V., Hessel, A., Ma, P., Lunetti, P., Weinhäupl, K., Imbert, L., … Schanda, P. (2018). How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.8b00269' chicago: 'Kurauskas, Vilius, Audrey Hessel, Peixiang Ma, Paola Lunetti, Katharina Weinhäupl, Lionel Imbert, Bernhard Brutscher, et al. “How Detergent Impacts Membrane Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine.” The Journal of Physical Chemistry Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.jpclett.8b00269.' ieee: 'V. Kurauskas et al., “How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine,” The Journal of Physical Chemistry Letters, vol. 9, no. 5. American Chemical Society, pp. 933–938, 2018.' ista: 'Kurauskas V, Hessel A, Ma P, Lunetti P, Weinhäupl K, Imbert L, Brutscher B, King MS, Sounier R, Dolce V, Kunji ERS, Capobianco L, Chipot C, Dehez F, Bersch B, Schanda P. 2018. How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry Letters. 9(5), 933–938.' mla: 'Kurauskas, Vilius, et al. “How Detergent Impacts Membrane Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine.” The Journal of Physical Chemistry Letters, vol. 9, no. 5, American Chemical Society, 2018, pp. 933–38, doi:10.1021/acs.jpclett.8b00269.' short: V. Kurauskas, A. Hessel, P. Ma, P. Lunetti, K. Weinhäupl, L. Imbert, B. Brutscher, M.S. King, R. Sounier, V. Dolce, E.R.S. Kunji, L. Capobianco, C. Chipot, F. Dehez, B. Bersch, P. Schanda, The Journal of Physical Chemistry Letters 9 (2018) 933–938. date_created: 2020-09-18T10:05:45Z date_published: 2018-02-03T00:00:00Z date_updated: 2021-01-12T08:19:18Z day: '03' doi: 10.1021/acs.jpclett.8b00269 extern: '1' intvolume: ' 9' issue: '5' keyword: - General Materials Science language: - iso: eng month: '02' oa_version: None page: 933-938 publication: The Journal of Physical Chemistry Letters publication_identifier: issn: - 1948-7185 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: 'How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2018' ... --- _id: '8440' abstract: - lang: eng text: Mycobacterium tuberculosis can remain dormant in the host, an ability that explains the failure of many current tuberculosis treatments. Recently, the natural products cyclomarin, ecumicin, and lassomycin have been shown to efficiently kill Mycobacterium tuberculosis persisters. Their target is the N-terminal domain of the hexameric AAA+ ATPase ClpC1, which recognizes, unfolds, and translocates protein substrates, such as proteins containing phosphorylated arginine residues, to the ClpP1P2 protease for degradation. Surprisingly, these antibiotics do not inhibit ClpC1 ATPase activity, and how they cause cell death is still unclear. Here, using NMR and small-angle X-ray scattering, we demonstrate that arginine-phosphate binding to the ClpC1 N-terminal domain induces millisecond dynamics. We show that these dynamics are caused by conformational changes and do not result from unfolding or oligomerization of this domain. Cyclomarin binding to this domain specifically blocked these N-terminal dynamics. On the basis of these results, we propose a mechanism of action involving cyclomarin-induced restriction of ClpC1 dynamics, which modulates the chaperone enzymatic activity leading eventually to cell death. article_processing_charge: No article_type: original author: - first_name: Katharina full_name: Weinhäupl, Katharina last_name: Weinhäupl - first_name: Martha full_name: Brennich, Martha last_name: Brennich - first_name: Uli full_name: Kazmaier, Uli last_name: Kazmaier - first_name: Joel full_name: Lelievre, Joel last_name: Lelievre - first_name: Lluis full_name: Ballell, Lluis last_name: Ballell - first_name: Alfred full_name: Goldberg, Alfred last_name: Goldberg - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Hugo full_name: Fraga, Hugo last_name: Fraga citation: ama: Weinhäupl K, Brennich M, Kazmaier U, et al. The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. Journal of Biological Chemistry. 2018;293(22):8379-8393. doi:10.1074/jbc.ra118.002251 apa: Weinhäupl, K., Brennich, M., Kazmaier, U., Lelievre, J., Ballell, L., Goldberg, A., … Fraga, H. (2018). The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. Journal of Biological Chemistry. American Society for Biochemistry & Molecular Biology. https://doi.org/10.1074/jbc.ra118.002251 chicago: Weinhäupl, Katharina, Martha Brennich, Uli Kazmaier, Joel Lelievre, Lluis Ballell, Alfred Goldberg, Paul Schanda, and Hugo Fraga. “The Antibiotic Cyclomarin Blocks Arginine-Phosphate–Induced Millisecond Dynamics in the N-Terminal Domain of ClpC1 from Mycobacterium Tuberculosis.” Journal of Biological Chemistry. American Society for Biochemistry & Molecular Biology, 2018. https://doi.org/10.1074/jbc.ra118.002251. ieee: K. Weinhäupl et al., “The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis,” Journal of Biological Chemistry, vol. 293, no. 22. American Society for Biochemistry & Molecular Biology, pp. 8379–8393, 2018. ista: Weinhäupl K, Brennich M, Kazmaier U, Lelievre J, Ballell L, Goldberg A, Schanda P, Fraga H. 2018. The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. Journal of Biological Chemistry. 293(22), 8379–8393. mla: Weinhäupl, Katharina, et al. “The Antibiotic Cyclomarin Blocks Arginine-Phosphate–Induced Millisecond Dynamics in the N-Terminal Domain of ClpC1 from Mycobacterium Tuberculosis.” Journal of Biological Chemistry, vol. 293, no. 22, American Society for Biochemistry & Molecular Biology, 2018, pp. 8379–93, doi:10.1074/jbc.ra118.002251. short: K. Weinhäupl, M. Brennich, U. Kazmaier, J. Lelievre, L. Ballell, A. Goldberg, P. Schanda, H. Fraga, Journal of Biological Chemistry 293 (2018) 8379–8393. date_created: 2020-09-18T10:05:18Z date_published: 2018-06-01T00:00:00Z date_updated: 2021-01-12T08:19:17Z day: '01' doi: 10.1074/jbc.ra118.002251 extern: '1' intvolume: ' 293' issue: '22' keyword: - Cell Biology - Biochemistry - Molecular Biology language: - iso: eng month: '06' oa_version: None page: 8379-8393 publication: Journal of Biological Chemistry publication_identifier: issn: - 0021-9258 - 1083-351X publication_status: published publisher: American Society for Biochemistry & Molecular Biology quality_controlled: '1' status: public title: The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 293 year: '2018' ... --- _id: '8442' abstract: - lang: eng text: Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents. article_processing_charge: No article_type: original author: - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: François full_name: Dehez, François last_name: Dehez - first_name: Jason R. full_name: Schnell, Jason R. last_name: Schnell - first_name: Nicole full_name: Zitzmann, Nicole last_name: Zitzmann - first_name: Eva full_name: Pebay-Peyroula, Eva last_name: Pebay-Peyroula - first_name: Laurent J. full_name: Catoire, Laurent J. last_name: Catoire - first_name: Bruno full_name: Miroux, Bruno last_name: Miroux - first_name: Edmund R. S. full_name: Kunji, Edmund R. S. last_name: Kunji - first_name: Gianluigi full_name: Veglia, Gianluigi last_name: Veglia - first_name: Timothy A. full_name: Cross, Timothy A. last_name: Cross - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: 'Chipot C, Dehez F, Schnell JR, et al. Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies. Chemical Reviews. 2018;118(7):3559-3607. doi:10.1021/acs.chemrev.7b00570' apa: 'Chipot, C., Dehez, F., Schnell, J. R., Zitzmann, N., Pebay-Peyroula, E., Catoire, L. J., … Schanda, P. (2018). Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies. Chemical Reviews. American Chemical Society. https://doi.org/10.1021/acs.chemrev.7b00570' chicago: 'Chipot, Christophe, François Dehez, Jason R. Schnell, Nicole Zitzmann, Eva Pebay-Peyroula, Laurent J. Catoire, Bruno Miroux, et al. “Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.” Chemical Reviews. American Chemical Society, 2018. https://doi.org/10.1021/acs.chemrev.7b00570.' ieee: 'C. Chipot et al., “Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies,” Chemical Reviews, vol. 118, no. 7. American Chemical Society, pp. 3559–3607, 2018.' ista: 'Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. 2018. Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies. Chemical Reviews. 118(7), 3559–3607.' mla: 'Chipot, Christophe, et al. “Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.” Chemical Reviews, vol. 118, no. 7, American Chemical Society, 2018, pp. 3559–607, doi:10.1021/acs.chemrev.7b00570.' short: C. Chipot, F. Dehez, J.R. Schnell, N. Zitzmann, E. Pebay-Peyroula, L.J. Catoire, B. Miroux, E.R.S. Kunji, G. Veglia, T.A. Cross, P. Schanda, Chemical Reviews 118 (2018) 3559–3607. date_created: 2020-09-18T10:05:35Z date_published: 2018-02-28T00:00:00Z date_updated: 2021-01-12T08:19:18Z day: '28' doi: 10.1021/acs.chemrev.7b00570 extern: '1' intvolume: ' 118' issue: '7' keyword: - General Chemistry language: - iso: eng month: '02' oa_version: None page: 3559-3607 publication: Chemical Reviews publication_identifier: issn: - 0009-2665 - 1520-6890 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: 'Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 118 year: '2018' ... --- _id: '8441' abstract: - lang: eng text: Solid-state near-rotary-resonance measurements of the spin–lattice relaxation rate in the rotating frame (R1ρ) is a powerful NMR technique for studying molecular dynamics in the microsecond time scale. The small difference between the spin-lock (SL) and magic-angle-spinning (MAS) frequencies allows sampling very slow motions, at the same time it brings up some methodological challenges. In this work, several issues affecting correct measurements and analysis of 15N R1ρ data are considered in detail. Among them are signal amplitude as a function of the difference between SL and MAS frequencies, “dead time” in the initial part of the relaxation decay caused by transient spin-dynamic oscillations, measurements under HORROR condition and proper treatment of the multi-exponential relaxation decays. The multiple 15N R1ρ measurements at different SL fields and temperatures have been conducted in 1D mode (i.e. without site-specific resolution) for a set of four different microcrystalline protein samples (GB1, SH3, MPD-ubiquitin and cubic-PEG-ubiquitin) to study the overall protein rocking in a crystal. While the amplitude of this motion varies very significantly, its correlation time for all four sample is practically the same, 30–50 μs. The amplitude of the rocking motion correlates with the packing density of a protein crystal. It has been suggested that the rocking motion is not diffusive but likely a jump-like dynamic process. article_processing_charge: No article_type: original author: - first_name: Alexey full_name: Krushelnitsky, Alexey last_name: Krushelnitsky - first_name: Diego full_name: Gauto, Diego last_name: Gauto - first_name: Diana C. full_name: Rodriguez Camargo, Diana C. last_name: Rodriguez Camargo - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Kay full_name: Saalwächter, Kay last_name: Saalwächter citation: ama: 'Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K. Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals. Journal of Biomolecular NMR. 2018;71(1):53-67. doi:10.1007/s10858-018-0191-4' apa: 'Krushelnitsky, A., Gauto, D., Rodriguez Camargo, D. C., Schanda, P., & Saalwächter, K. (2018). Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-018-0191-4' chicago: 'Krushelnitsky, Alexey, Diego Gauto, Diana C. Rodriguez Camargo, Paul Schanda, and Kay Saalwächter. “Microsecond Motions Probed by Near-Rotary-Resonance R1ρ 15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.” Journal of Biomolecular NMR. Springer Nature, 2018. https://doi.org/10.1007/s10858-018-0191-4.' ieee: 'A. Krushelnitsky, D. Gauto, D. C. Rodriguez Camargo, P. Schanda, and K. Saalwächter, “Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals,” Journal of Biomolecular NMR, vol. 71, no. 1. Springer Nature, pp. 53–67, 2018.' ista: 'Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K. 2018. Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals. Journal of Biomolecular NMR. 71(1), 53–67.' mla: 'Krushelnitsky, Alexey, et al. “Microsecond Motions Probed by Near-Rotary-Resonance R1ρ 15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.” Journal of Biomolecular NMR, vol. 71, no. 1, Springer Nature, 2018, pp. 53–67, doi:10.1007/s10858-018-0191-4.' short: A. Krushelnitsky, D. Gauto, D.C. Rodriguez Camargo, P. Schanda, K. Saalwächter, Journal of Biomolecular NMR 71 (2018) 53–67. date_created: 2020-09-18T10:05:28Z date_published: 2018-05-30T00:00:00Z date_updated: 2021-01-12T08:19:17Z day: '30' doi: 10.1007/s10858-018-0191-4 extern: '1' intvolume: ' 71' issue: '1' language: - iso: eng month: '05' oa_version: Published Version page: 53-67 publication: Journal of Biomolecular NMR publication_identifier: issn: - 0925-2738 - 1573-5001 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 71 year: '2018' ... --- _id: '8439' abstract: - lang: eng text: Lipopolysaccharides (LPS) are complex glycolipids forming the outside layer of Gram-negative bacteria. Their hydrophobic and heterogeneous nature greatly hampers their structural study in an environment similar to the bacterial surface. We have studied LPS purified from E. coli and pathogenic P. aeruginosa with long O-antigen polysaccharides assembled in solution as vesicles or elongated micelles. Solid-state NMR with magic-angle spinning permitted the identification of NMR signals arising from regions with different flexibilities in the LPS, from the lipid components to the O-antigen polysaccharides. Atomic scale data on the LPS enabled the study of the interaction of gentamicin antibiotic bound to P. aeruginosa LPS, for which we could confirm that a specific oligosaccharide is involved in the antibiotic binding. The possibility to study LPS alone and bound to a ligand when it is assembled in membrane-like structures opens great prospects for the investigation of proteins and antibiotics that specifically target such an important molecule at the surface of Gram-negative bacteria. article_processing_charge: No article_type: original author: - first_name: Cedric full_name: Laguri, Cedric last_name: Laguri - first_name: Alba full_name: Silipo, Alba last_name: Silipo - first_name: Alessandra M. full_name: Martorana, Alessandra M. last_name: Martorana - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Roberta full_name: Marchetti, Roberta last_name: Marchetti - first_name: Alessandra full_name: Polissi, Alessandra last_name: Polissi - first_name: Antonio full_name: Molinaro, Antonio last_name: Molinaro - first_name: Jean-Pierre full_name: Simorre, Jean-Pierre last_name: Simorre citation: ama: Laguri C, Silipo A, Martorana AM, et al. Solid state NMR studies of intact lipopolysaccharide endotoxin. ACS Chemical Biology. 2018;13(8):2106-2113. doi:10.1021/acschembio.8b00271 apa: Laguri, C., Silipo, A., Martorana, A. M., Schanda, P., Marchetti, R., Polissi, A., … Simorre, J.-P. (2018). Solid state NMR studies of intact lipopolysaccharide endotoxin. ACS Chemical Biology. American Chemical Society. https://doi.org/10.1021/acschembio.8b00271 chicago: Laguri, Cedric, Alba Silipo, Alessandra M. Martorana, Paul Schanda, Roberta Marchetti, Alessandra Polissi, Antonio Molinaro, and Jean-Pierre Simorre. “Solid State NMR Studies of Intact Lipopolysaccharide Endotoxin.” ACS Chemical Biology. American Chemical Society, 2018. https://doi.org/10.1021/acschembio.8b00271. ieee: C. Laguri et al., “Solid state NMR studies of intact lipopolysaccharide endotoxin,” ACS Chemical Biology, vol. 13, no. 8. American Chemical Society, pp. 2106–2113, 2018. ista: Laguri C, Silipo A, Martorana AM, Schanda P, Marchetti R, Polissi A, Molinaro A, Simorre J-P. 2018. Solid state NMR studies of intact lipopolysaccharide endotoxin. ACS Chemical Biology. 13(8), 2106–2113. mla: Laguri, Cedric, et al. “Solid State NMR Studies of Intact Lipopolysaccharide Endotoxin.” ACS Chemical Biology, vol. 13, no. 8, American Chemical Society, 2018, pp. 2106–13, doi:10.1021/acschembio.8b00271. short: C. Laguri, A. Silipo, A.M. Martorana, P. Schanda, R. Marchetti, A. Polissi, A. Molinaro, J.-P. Simorre, ACS Chemical Biology 13 (2018) 2106–2113. date_created: 2020-09-18T10:05:09Z date_published: 2018-07-02T00:00:00Z date_updated: 2021-01-12T08:19:16Z day: '02' doi: 10.1021/acschembio.8b00271 extern: '1' intvolume: ' 13' issue: '8' keyword: - Molecular Medicine - Biochemistry - General Medicine language: - iso: eng month: '07' oa_version: None page: 2106-2113 publication: ACS Chemical Biology publication_identifier: issn: - 1554-8929 - 1554-8937 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Solid state NMR studies of intact lipopolysaccharide endotoxin type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2018' ...