--- _id: '5965' abstract: - lang: eng text: Relaxed concurrent data structures have become increasingly popular, due to their scalability in graph processing and machine learning applications (\citeNguyen13, gonzalez2012powergraph ). Despite considerable interest, there exist families of natural, high performing randomized relaxed concurrent data structures, such as the popular MultiQueue~\citeMQ pattern for implementing relaxed priority queue data structures, for which no guarantees are known in the concurrent setting~\citeAKLN17. Our main contribution is in showing for the first time that, under a set of analytic assumptions, a family of relaxed concurrent data structures, including variants of MultiQueues, but also a new approximate counting algorithm we call the MultiCounter, provides strong probabilistic guarantees on the degree of relaxation with respect to the sequential specification, in arbitrary concurrent executions. We formalize these guarantees via a new correctness condition called distributional linearizability, tailored to concurrent implementations with randomized relaxations. Our result is based on a new analysis of an asynchronous variant of the classic power-of-two-choices load balancing algorithm, in which placement choices can be based on inconsistent, outdated information (this result may be of independent interest). We validate our results empirically, showing that the MultiCounter algorithm can implement scalable relaxed timestamps. article_processing_charge: No arxiv: 1 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: Trevor A full_name: Brown, Trevor A id: 3569F0A0-F248-11E8-B48F-1D18A9856A87 last_name: Brown - first_name: Justin full_name: Kopinsky, Justin last_name: Kopinsky - first_name: Jerry Z. full_name: Li, Jerry Z. last_name: Li - first_name: Giorgi full_name: Nadiradze, Giorgi last_name: Nadiradze citation: ama: 'Alistarh D-A, Brown TA, Kopinsky J, Li JZ, Nadiradze G. Distributionally linearizable data structures. In: Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  - SPAA ’18. ACM Press; 2018:133-142. doi:10.1145/3210377.3210411' apa: 'Alistarh, D.-A., Brown, T. A., Kopinsky, J., Li, J. Z., & Nadiradze, G. (2018). Distributionally linearizable data structures. In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  - SPAA ’18 (pp. 133–142). Vienna, Austria: ACM Press. https://doi.org/10.1145/3210377.3210411' chicago: Alistarh, Dan-Adrian, Trevor A Brown, Justin Kopinsky, Jerry Z. Li, and Giorgi Nadiradze. “Distributionally Linearizable Data Structures.” In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  - SPAA ’18, 133–42. ACM Press, 2018. https://doi.org/10.1145/3210377.3210411. ieee: D.-A. Alistarh, T. A. Brown, J. Kopinsky, J. Z. Li, and G. Nadiradze, “Distributionally linearizable data structures,” in Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  - SPAA ’18, Vienna, Austria, 2018, pp. 133–142. ista: 'Alistarh D-A, Brown TA, Kopinsky J, Li JZ, Nadiradze G. 2018. Distributionally linearizable data structures. Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  - SPAA ’18. SPAA: Symposium on Parallelism in Algorithms and Architectures, 133–142.' mla: Alistarh, Dan-Adrian, et al. “Distributionally Linearizable Data Structures.” Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  - SPAA ’18, ACM Press, 2018, pp. 133–42, doi:10.1145/3210377.3210411. short: D.-A. Alistarh, T.A. Brown, J. Kopinsky, J.Z. Li, G. Nadiradze, in:, Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  - SPAA ’18, ACM Press, 2018, pp. 133–142. conference: end_date: 2018-07-18 location: Vienna, Austria name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures' start_date: 2018-07-16 date_created: 2019-02-13T10:17:19Z date_published: 2018-07-16T00:00:00Z date_updated: 2023-09-19T10:44:13Z day: '16' department: - _id: DaAl doi: 10.1145/3210377.3210411 external_id: arxiv: - '1804.01018' isi: - '000545269600016' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.01018 month: '07' oa: 1 oa_version: Preprint page: 133-142 publication: Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA '18 publication_identifier: isbn: - '9781450357999' publication_status: published publisher: ACM Press quality_controlled: '1' related_material: record: - id: '10429' relation: dissertation_contains status: public scopus_import: '1' status: public title: Distributionally linearizable data structures type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '5966' abstract: - lang: eng text: 'The transactional conflict problem arises in transactional systems whenever two or more concurrent transactions clash on a data item. While the standard solution to such conflicts is to immediately abort one of the transactions, some practical systems consider the alternative of delaying conflict resolution for a short interval, which may allow one of the transactions to commit. The challenge in the transactional conflict problem is to choose the optimal length of this delay interval so as to minimize the overall running time penalty for the conflicting transactions. In this paper, we propose a family of optimal online algorithms for the transactional conflict problem. Specifically, we consider variants of this problem which arise in different implementations of transactional systems, namely "requestor wins'''' and "requestor aborts'''' implementations: in the former, the recipient of a coherence request is aborted, whereas in the latter, it is the requestor which has to abort. Both strategies are implemented by real systems. We show that the requestor aborts case can be reduced to a classic instance of the ski rental problem, while the requestor wins case leads to a new version of this classical problem, for which we derive optimal deterministic and randomized algorithms. Moreover, we prove that, under a simplified adversarial model, our algorithms are constant-competitive with the offline optimum in terms of throughput. We validate our algorithmic results empirically through a hardware simulation of hardware transactional memory (HTM), showing that our algorithms can lead to non-trivial performance improvements for classic concurrent data structures.' article_processing_charge: No arxiv: 1 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: Syed Kamran full_name: Haider, Syed Kamran last_name: Haider - first_name: Raphael full_name: Kübler, Raphael last_name: Kübler - first_name: Giorgi full_name: Nadiradze, Giorgi last_name: Nadiradze citation: ama: 'Alistarh D-A, Haider SK, Kübler R, Nadiradze G. The transactional conflict problem. In: Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  - SPAA ’18. ACM Press; 2018:383-392. doi:10.1145/3210377.3210406' apa: 'Alistarh, D.-A., Haider, S. K., Kübler, R., & Nadiradze, G. (2018). The transactional conflict problem. In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  - SPAA ’18 (pp. 383–392). Vienna, Austria: ACM Press. https://doi.org/10.1145/3210377.3210406' chicago: Alistarh, Dan-Adrian, Syed Kamran Haider, Raphael Kübler, and Giorgi Nadiradze. “The Transactional Conflict Problem.” In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  - SPAA ’18, 383–92. ACM Press, 2018. https://doi.org/10.1145/3210377.3210406. ieee: D.-A. Alistarh, S. K. Haider, R. Kübler, and G. Nadiradze, “The transactional conflict problem,” in Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  - SPAA ’18, Vienna, Austria, 2018, pp. 383–392. ista: 'Alistarh D-A, Haider SK, Kübler R, Nadiradze G. 2018. The transactional conflict problem. Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  - SPAA ’18. SPAA: Symposium on Parallelism in Algorithms and Architectures, 383–392.' mla: Alistarh, Dan-Adrian, et al. “The Transactional Conflict Problem.” Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  - SPAA ’18, ACM Press, 2018, pp. 383–92, doi:10.1145/3210377.3210406. short: D.-A. Alistarh, S.K. Haider, R. Kübler, G. Nadiradze, in:, Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  - SPAA ’18, ACM Press, 2018, pp. 383–392. conference: end_date: 2018-07-18 location: Vienna, Austria name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures' start_date: 2018-07-16 date_created: 2019-02-13T10:26:07Z date_published: 2018-07-16T00:00:00Z date_updated: 2023-09-19T10:44:49Z day: '16' department: - _id: DaAl doi: 10.1145/3210377.3210406 external_id: arxiv: - '1804.00947' isi: - '000545269600046' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.00947 month: '07' oa: 1 oa_version: Preprint page: 383-392 publication: Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA '18 publication_identifier: isbn: - '9781450357999' publication_status: published publisher: ACM Press quality_controlled: '1' scopus_import: '1' status: public title: The transactional conflict problem type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '5967' abstract: - lang: eng text: "The Big Match is a multi-stage two-player game. In each stage Player 1 hides one or two pebbles in his hand, and his opponent has to guess that number; Player 1 loses a point if Player 2 is correct, and otherwise he wins a point. As soon as Player 1 hides one pebble, the players cannot change their choices in any future stage.\r\nBlackwell and Ferguson (1968) give an ε-optimal strategy for Player 1 that hides, in each stage, one pebble with a probability that depends on the entire past history. Any strategy that depends just on the clock or on a finite memory is worthless. The long-standing natural open problem has been whether every strategy that depends just on the clock and a finite memory is worthless. We prove that there is such a strategy that is ε-optimal. In fact, we show that just two states of memory are sufficient.\r\n" article_processing_charge: No author: - first_name: Kristoffer Arnsfelt full_name: Hansen, Kristoffer Arnsfelt last_name: Hansen - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Abraham full_name: Neyman, Abraham last_name: Neyman citation: ama: 'Hansen KA, Ibsen-Jensen R, Neyman A. The Big Match with a clock and a bit of memory. In: Proceedings of the 2018 ACM Conference on Economics and Computation  - EC ’18. ACM Press; 2018:149-150. doi:10.1145/3219166.3219198' apa: 'Hansen, K. A., Ibsen-Jensen, R., & Neyman, A. (2018). The Big Match with a clock and a bit of memory. In Proceedings of the 2018 ACM Conference on Economics and Computation  - EC ’18 (pp. 149–150). Ithaca, NY, United States: ACM Press. https://doi.org/10.1145/3219166.3219198' chicago: Hansen, Kristoffer Arnsfelt, Rasmus Ibsen-Jensen, and Abraham Neyman. “The Big Match with a Clock and a Bit of Memory.” In Proceedings of the 2018 ACM Conference on Economics and Computation  - EC ’18, 149–50. ACM Press, 2018. https://doi.org/10.1145/3219166.3219198. ieee: K. A. Hansen, R. Ibsen-Jensen, and A. Neyman, “The Big Match with a clock and a bit of memory,” in Proceedings of the 2018 ACM Conference on Economics and Computation  - EC ’18, Ithaca, NY, United States, 2018, pp. 149–150. ista: 'Hansen KA, Ibsen-Jensen R, Neyman A. 2018. The Big Match with a clock and a bit of memory. Proceedings of the 2018 ACM Conference on Economics and Computation  - EC ’18. EC: Conference on Economics and Computation, 149–150.' mla: Hansen, Kristoffer Arnsfelt, et al. “The Big Match with a Clock and a Bit of Memory.” Proceedings of the 2018 ACM Conference on Economics and Computation  - EC ’18, ACM Press, 2018, pp. 149–50, doi:10.1145/3219166.3219198. short: K.A. Hansen, R. Ibsen-Jensen, A. Neyman, in:, Proceedings of the 2018 ACM Conference on Economics and Computation  - EC ’18, ACM Press, 2018, pp. 149–150. conference: end_date: 2018-06-22 location: Ithaca, NY, United States name: 'EC: Conference on Economics and Computation' start_date: 2018-06-18 date_created: 2019-02-13T10:31:41Z date_published: 2018-06-18T00:00:00Z date_updated: 2023-09-19T10:45:15Z day: '18' ddc: - '000' department: - _id: KrCh doi: 10.1145/3219166.3219198 external_id: isi: - '000492755100020' file: - access_level: open_access checksum: bb52683e349cfd864f4769a8f38f2798 content_type: application/pdf creator: dernst date_created: 2019-11-19T08:24:24Z date_updated: 2020-07-14T12:47:14Z file_id: '7054' file_name: 2018_EC18_Hansen.pdf file_size: 302539 relation: main_file file_date_updated: 2020-07-14T12:47:14Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 149-150 publication: Proceedings of the 2018 ACM Conference on Economics and Computation - EC '18 publication_identifier: isbn: - '9781450358293' publication_status: published publisher: ACM Press quality_controlled: '1' scopus_import: '1' status: public title: The Big Match with a clock and a bit of memory type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '5971' abstract: - lang: eng text: "We consider a Wigner-type ensemble, i.e. large hermitian N×N random matrices H=H∗ with centered independent entries and with a general matrix of variances Sxy=\U0001D53C∣∣Hxy∣∣2. The norm of H is asymptotically given by the maximum of the support of the self-consistent density of states. We establish a bound on this maximum in terms of norms of powers of S that substantially improves the earlier bound 2∥S∥1/2∞ given in [O. Ajanki, L. Erdős and T. Krüger, Universality for general Wigner-type matrices, Prob. Theor. Rel. Fields169 (2017) 667–727]. The key element of the proof is an effective Markov chain approximation for the contributions of the weighted Dyck paths appearing in the iterative solution of the corresponding Dyson equation." article_number: '1950009' article_processing_charge: No arxiv: 1 author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Peter full_name: Mühlbacher, Peter last_name: Mühlbacher citation: ama: 'Erdös L, Mühlbacher P. Bounds on the norm of Wigner-type random matrices. Random matrices: Theory and applications. 2018. doi:10.1142/s2010326319500096' apa: 'Erdös, L., & Mühlbacher, P. (2018). Bounds on the norm of Wigner-type random matrices. Random Matrices: Theory and Applications. World Scientific Publishing. https://doi.org/10.1142/s2010326319500096' chicago: 'Erdös, László, and Peter Mühlbacher. “Bounds on the Norm of Wigner-Type Random Matrices.” Random Matrices: Theory and Applications. World Scientific Publishing, 2018. https://doi.org/10.1142/s2010326319500096.' ieee: 'L. Erdös and P. Mühlbacher, “Bounds on the norm of Wigner-type random matrices,” Random matrices: Theory and applications. World Scientific Publishing, 2018.' ista: 'Erdös L, Mühlbacher P. 2018. Bounds on the norm of Wigner-type random matrices. Random matrices: Theory and applications., 1950009.' mla: 'Erdös, László, and Peter Mühlbacher. “Bounds on the Norm of Wigner-Type Random Matrices.” Random Matrices: Theory and Applications, 1950009, World Scientific Publishing, 2018, doi:10.1142/s2010326319500096.' short: 'L. Erdös, P. Mühlbacher, Random Matrices: Theory and Applications (2018).' date_created: 2019-02-13T10:40:54Z date_published: 2018-09-26T00:00:00Z date_updated: 2023-09-19T14:24:05Z day: '26' department: - _id: LaEr doi: 10.1142/s2010326319500096 ec_funded: 1 external_id: arxiv: - '1802.05175' isi: - '000477677200002' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.05175 month: '09' 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: 'Random matrices: Theory and applications' publication_identifier: eissn: - 2010-3271 issn: - 2010-3263 publication_status: published publisher: World Scientific Publishing quality_controlled: '1' scopus_import: '1' status: public title: Bounds on the norm of Wigner-type random matrices type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '5975' abstract: - lang: eng text: We consider the recent formulation of the algorithmic Lov ́asz Local Lemma [N. Har-vey and J. Vondr ́ak, inProceedings of FOCS, 2015, pp. 1327–1345; D. Achlioptas and F. Iliopoulos,inProceedings of SODA, 2016, pp. 2024–2038; D. Achlioptas, F. Iliopoulos, and V. Kolmogorov,ALocal Lemma for Focused Stochastic Algorithms, arXiv preprint, 2018] for finding objects that avoid“bad features,” or “flaws.” It extends the Moser–Tardos resampling algorithm [R. A. Moser andG. Tardos,J. ACM, 57 (2010), 11] to more general discrete spaces. At each step the method picks aflaw present in the current state and goes to a new state according to some prespecified probabilitydistribution (which depends on the current state and the selected flaw). However, the recent formu-lation is less flexible than the Moser–Tardos method since it requires a specific flaw selection rule,whereas the algorithm of Moser and Tardos allows an arbitrary rule (and thus can potentially beimplemented more efficiently). We formulate a new “commutativity” condition and prove that it issufficient for an arbitrary rule to work. It also enables an efficient parallelization under an additionalassumption. We then show that existing resampling oracles for perfect matchings and permutationsdo satisfy this condition. article_processing_charge: No arxiv: 1 author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Kolmogorov V. Commutativity in the algorithmic Lovász local lemma. SIAM Journal on Computing. 2018;47(6):2029-2056. doi:10.1137/16m1093306 apa: Kolmogorov, V. (2018). Commutativity in the algorithmic Lovász local lemma. SIAM Journal on Computing. Society for Industrial & Applied Mathematics (SIAM). https://doi.org/10.1137/16m1093306 chicago: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovász Local Lemma.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics (SIAM), 2018. https://doi.org/10.1137/16m1093306. ieee: V. Kolmogorov, “Commutativity in the algorithmic Lovász local lemma,” SIAM Journal on Computing, vol. 47, no. 6. Society for Industrial & Applied Mathematics (SIAM), pp. 2029–2056, 2018. ista: Kolmogorov V. 2018. Commutativity in the algorithmic Lovász local lemma. SIAM Journal on Computing. 47(6), 2029–2056. mla: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovász Local Lemma.” SIAM Journal on Computing, vol. 47, no. 6, Society for Industrial & Applied Mathematics (SIAM), 2018, pp. 2029–56, doi:10.1137/16m1093306. short: V. Kolmogorov, SIAM Journal on Computing 47 (2018) 2029–2056. date_created: 2019-02-13T12:59:33Z date_published: 2018-11-08T00:00:00Z date_updated: 2023-09-19T14:24:58Z day: '08' department: - _id: VlKo doi: 10.1137/16m1093306 ec_funded: 1 external_id: arxiv: - '1506.08547' isi: - '000453785100001' intvolume: ' 47' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1506.08547 month: '11' oa: 1 oa_version: Preprint page: 2029-2056 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: SIAM Journal on Computing publication_identifier: eissn: - 1095-7111 issn: - 0097-5397 publication_status: published publisher: Society for Industrial & Applied Mathematics (SIAM) quality_controlled: '1' related_material: record: - id: '1193' relation: earlier_version status: public scopus_import: '1' status: public title: Commutativity in the algorithmic Lovász local lemma type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 47 year: '2018' ... --- _id: '5976' abstract: - lang: eng text: We propose FlexMaps, a novel framework for fabricating smooth shapes out of flat, flexible panels with tailored mechanical properties. We start by mapping the 3D surface onto a 2D domain as in traditional UV mapping to design a set of deformable flat panels called FlexMaps. For these panels, we design and obtain specific mechanical properties such that, once they are assembled, the static equilibrium configuration matches the desired 3D shape. FlexMaps can be fabricated from an almost rigid material, such as wood or plastic, and are made flexible in a controlled way by using computationally designed spiraling microstructures. article_number: '241' article_processing_charge: No article_type: original author: - first_name: Luigi full_name: Malomo, Luigi last_name: Malomo - first_name: Jesus full_name: Perez Rodriguez, Jesus id: 2DC83906-F248-11E8-B48F-1D18A9856A87 last_name: Perez Rodriguez - first_name: Emmanuel full_name: Iarussi, Emmanuel id: 33F19F16-F248-11E8-B48F-1D18A9856A87 last_name: Iarussi - first_name: Nico full_name: Pietroni, Nico last_name: Pietroni - first_name: Eder full_name: Miguel, Eder last_name: Miguel - first_name: Paolo full_name: Cignoni, Paolo last_name: Cignoni - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: 'Malomo L, Perez Rodriguez J, Iarussi E, et al. FlexMaps: Computational design of flat flexible shells for shaping 3D objects. ACM Transactions on Graphics. 2018;37(6). doi:10.1145/3272127.3275076' apa: 'Malomo, L., Perez Rodriguez, J., Iarussi, E., Pietroni, N., Miguel, E., Cignoni, P., & Bickel, B. (2018). FlexMaps: Computational design of flat flexible shells for shaping 3D objects. ACM Transactions on Graphics. Association for Computing Machinery (ACM). https://doi.org/10.1145/3272127.3275076' chicago: 'Malomo, Luigi, Jesus Perez Rodriguez, Emmanuel Iarussi, Nico Pietroni, Eder Miguel, Paolo Cignoni, and Bernd Bickel. “FlexMaps: Computational Design of Flat Flexible Shells for Shaping 3D Objects.” ACM Transactions on Graphics. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3272127.3275076.' ieee: 'L. Malomo et al., “FlexMaps: Computational design of flat flexible shells for shaping 3D objects,” ACM Transactions on Graphics, vol. 37, no. 6. Association for Computing Machinery (ACM), 2018.' ista: 'Malomo L, Perez Rodriguez J, Iarussi E, Pietroni N, Miguel E, Cignoni P, Bickel B. 2018. FlexMaps: Computational design of flat flexible shells for shaping 3D objects. ACM Transactions on Graphics. 37(6), 241.' mla: 'Malomo, Luigi, et al. “FlexMaps: Computational Design of Flat Flexible Shells for Shaping 3D Objects.” ACM Transactions on Graphics, vol. 37, no. 6, 241, Association for Computing Machinery (ACM), 2018, doi:10.1145/3272127.3275076.' short: L. Malomo, J. Perez Rodriguez, E. Iarussi, N. Pietroni, E. Miguel, P. Cignoni, B. Bickel, ACM Transactions on Graphics 37 (2018). date_created: 2019-02-13T13:12:53Z date_published: 2018-11-01T00:00:00Z date_updated: 2023-09-19T14:25:30Z day: '01' ddc: - '000' department: - _id: BeBi doi: 10.1145/3272127.3275076 ec_funded: 1 external_id: isi: - '000455953100064' file: - access_level: open_access checksum: d0529a41c78b37ab8840685579fb33b4 content_type: application/pdf creator: bbickel date_created: 2019-09-23T12:48:52Z date_updated: 2020-07-14T12:47:14Z file_id: '6901' file_name: flexmaps_author_version.pdf file_size: 100109811 relation: main_file file_date_updated: 2020-07-14T12:47:14Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' - _id: 25082902-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '645599' name: Soft-bodied intelligence for Manipulation - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: ACM Transactions on Graphics publication_identifier: issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery (ACM) pubrep_id: '1068' quality_controlled: '1' scopus_import: '1' status: public title: 'FlexMaps: Computational design of flat flexible shells for shaping 3D objects' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 37 year: '2018' ... --- _id: '5977' abstract: - lang: eng text: 'We consider the stochastic shortest path (SSP)problem for succinct Markov decision processes(MDPs), where the MDP consists of a set of vari-ables, and a set of nondeterministic rules that up-date the variables. First, we show that several ex-amples from the AI literature can be modeled assuccinct MDPs. Then we present computationalapproaches for upper and lower bounds for theSSP problem: (a) for computing upper bounds, ourmethod is polynomial-time in the implicit descrip-tion of the MDP; (b) for lower bounds, we present apolynomial-time (in the size of the implicit descrip-tion) reduction to quadratic programming. Our ap-proach is applicable even to infinite-state MDPs.Finally, we present experimental results to demon-strate the effectiveness of our approach on severalclassical examples from the AI literature.' article_processing_charge: No arxiv: 1 author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Hongfei full_name: Fu, Hongfei id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87 last_name: Fu - first_name: Amir full_name: Goharshady, Amir id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Nastaran full_name: Okati, Nastaran last_name: Okati citation: ama: 'Chatterjee K, Fu H, Goharshady AK, Okati N. Computational approaches for stochastic shortest path on succinct MDPs. In: Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. Vol 2018. IJCAI; 2018:4700-4707. doi:10.24963/ijcai.2018/653' apa: 'Chatterjee, K., Fu, H., Goharshady, A. K., & Okati, N. (2018). Computational approaches for stochastic shortest path on succinct MDPs. In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence (Vol. 2018, pp. 4700–4707). Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/653' chicago: Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Nastaran Okati. “Computational Approaches for Stochastic Shortest Path on Succinct MDPs.” In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018:4700–4707. IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/653. ieee: K. Chatterjee, H. Fu, A. K. Goharshady, and N. Okati, “Computational approaches for stochastic shortest path on succinct MDPs,” in Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol. 2018, pp. 4700–4707. ista: 'Chatterjee K, Fu H, Goharshady AK, Okati N. 2018. Computational approaches for stochastic shortest path on succinct MDPs. Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018, 4700–4707.' mla: Chatterjee, Krishnendu, et al. “Computational Approaches for Stochastic Shortest Path on Succinct MDPs.” Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, vol. 2018, IJCAI, 2018, pp. 4700–07, doi:10.24963/ijcai.2018/653. short: K. Chatterjee, H. Fu, A.K. Goharshady, N. Okati, in:, Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4700–4707. conference: end_date: 2018-07-19 location: Stockholm, Sweden name: 'IJCAI: International Joint Conference on Artificial Intelligence' start_date: 2018-07-13 date_created: 2019-02-13T13:26:27Z date_published: 2018-07-17T00:00:00Z date_updated: 2025-06-02T08:53:44Z day: '17' department: - _id: KrCh doi: 10.24963/ijcai.2018/653 ec_funded: 1 external_id: arxiv: - '1804.08984' isi: - '000764175404118' intvolume: ' 2018' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.08984 month: '07' oa: 1 oa_version: Preprint page: 4700-4707 project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence publication_identifier: isbn: - 978-099924112-7 issn: - '10450823' publication_status: published publisher: IJCAI quality_controlled: '1' related_material: record: - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: Computational approaches for stochastic shortest path on succinct MDPs type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2018 year: '2018' ... --- _id: '5978' abstract: - lang: eng text: 'We consider the MAP-inference problem for graphical models,which is a valued constraint satisfaction problem defined onreal numbers with a natural summation operation. We proposea family of relaxations (different from the famous Sherali-Adams hierarchy), which naturally define lower bounds for itsoptimum. This family always contains a tight relaxation andwe give an algorithm able to find it and therefore, solve theinitial non-relaxed NP-hard problem.The relaxations we consider decompose the original probleminto two non-overlapping parts: an easy LP-tight part and adifficult one. For the latter part a combinatorial solver must beused. As we show in our experiments, in a number of applica-tions the second, difficult part constitutes only a small fractionof the whole problem. This property allows to significantlyreduce the computational time of the combinatorial solver andtherefore solve problems which were out of reach before.' article_processing_charge: No arxiv: 1 author: - first_name: Stefan full_name: Haller, Stefan last_name: Haller - 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: 'Haller S, Swoboda P, Savchynskyy B. Exact MAP-inference by confining combinatorial search with LP relaxation. In: Proceedings of the 32st AAAI Conference on Artificial Intelligence. AAAI Press; 2018:6581-6588.' apa: 'Haller, S., Swoboda, P., & Savchynskyy, B. (2018). Exact MAP-inference by confining combinatorial search with LP relaxation. In Proceedings of the 32st AAAI Conference on Artificial Intelligence (pp. 6581–6588). New Orleans, LU, United States: AAAI Press.' chicago: Haller, Stefan, Paul Swoboda, and Bogdan Savchynskyy. “Exact MAP-Inference by Confining Combinatorial Search with LP Relaxation.” In Proceedings of the 32st AAAI Conference on Artificial Intelligence, 6581–88. AAAI Press, 2018. ieee: S. Haller, P. Swoboda, and B. Savchynskyy, “Exact MAP-inference by confining combinatorial search with LP relaxation,” in Proceedings of the 32st AAAI Conference on Artificial Intelligence, New Orleans, LU, United States, 2018, pp. 6581–6588. ista: 'Haller S, Swoboda P, Savchynskyy B. 2018. Exact MAP-inference by confining combinatorial search with LP relaxation. Proceedings of the 32st AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence, 6581–6588.' mla: Haller, Stefan, et al. “Exact MAP-Inference by Confining Combinatorial Search with LP Relaxation.” Proceedings of the 32st AAAI Conference on Artificial Intelligence, AAAI Press, 2018, pp. 6581–88. short: S. Haller, P. Swoboda, B. Savchynskyy, in:, Proceedings of the 32st AAAI Conference on Artificial Intelligence, AAAI Press, 2018, pp. 6581–6588. conference: end_date: 2018-02-07 location: New Orleans, LU, United States name: 'AAAI: Conference on Artificial Intelligence' start_date: 2018-02-02 date_created: 2019-02-13T13:32:48Z date_published: 2018-02-01T00:00:00Z date_updated: 2023-09-19T14:26:52Z day: '01' department: - _id: VlKo external_id: arxiv: - '2004.06370' isi: - '000485488906082' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2004.06370 month: '02' oa: 1 oa_version: Preprint page: 6581-6588 publication: Proceedings of the 32st AAAI Conference on Artificial Intelligence publication_status: published publisher: AAAI Press quality_controlled: '1' scopus_import: '1' status: public title: Exact MAP-inference by confining combinatorial search with LP relaxation type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '5980' abstract: - lang: eng text: The problem of private set-intersection (PSI) has been traditionally treated as an instance of the more general problem of multi-party computation (MPC). Consequently, in order to argue security, or compose these protocols one has to rely on the general theory that was developed for the purpose of MPC. The pursuit of efficient protocols, however, has resulted in designs that exploit properties pertaining to PSI. In almost all practical applications where a PSI protocol is deployed, it is expected to be executed multiple times, possibly on related inputs. In this work we initiate a dedicated study of PSI in the multi-interaction (MI) setting. In this model a server sets up the common system parameters and executes set-intersection multiple times with potentially different clients. We discuss a few attacks that arise when protocols are naïvely composed in this manner and, accordingly, craft security definitions for the MI setting and study their inter-relation. Finally, we suggest a set of protocols that are MI-secure, at the same time almost as efficient as their parent, stand-alone, protocols. article_processing_charge: No author: - first_name: Sanjit full_name: Chatterjee, Sanjit last_name: Chatterjee - first_name: Chethan full_name: Kamath Hosdurg, Chethan id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87 last_name: Kamath Hosdurg - first_name: Vikas full_name: Kumar, Vikas last_name: Kumar citation: ama: Chatterjee S, Kamath Hosdurg C, Kumar V. Private set-intersection with common set-up. American Institute of Mathematical Sciences. 2018;12(1):17-47. doi:10.3934/amc.2018002 apa: Chatterjee, S., Kamath Hosdurg, C., & Kumar, V. (2018). Private set-intersection with common set-up. American Institute of Mathematical Sciences. AIMS. https://doi.org/10.3934/amc.2018002 chicago: Chatterjee, Sanjit, Chethan Kamath Hosdurg, and Vikas Kumar. “Private Set-Intersection with Common Set-Up.” American Institute of Mathematical Sciences. AIMS, 2018. https://doi.org/10.3934/amc.2018002. ieee: S. Chatterjee, C. Kamath Hosdurg, and V. Kumar, “Private set-intersection with common set-up,” American Institute of Mathematical Sciences, vol. 12, no. 1. AIMS, pp. 17–47, 2018. ista: Chatterjee S, Kamath Hosdurg C, Kumar V. 2018. Private set-intersection with common set-up. American Institute of Mathematical Sciences. 12(1), 17–47. mla: Chatterjee, Sanjit, et al. “Private Set-Intersection with Common Set-Up.” American Institute of Mathematical Sciences, vol. 12, no. 1, AIMS, 2018, pp. 17–47, doi:10.3934/amc.2018002. short: S. Chatterjee, C. Kamath Hosdurg, V. Kumar, American Institute of Mathematical Sciences 12 (2018) 17–47. date_created: 2019-02-13T13:49:41Z date_published: 2018-02-01T00:00:00Z date_updated: 2023-09-19T14:27:59Z day: '01' department: - _id: KrPi doi: 10.3934/amc.2018002 external_id: isi: - '000430950400002' intvolume: ' 12' isi: 1 issue: '1' language: - iso: eng month: '02' oa_version: None page: 17-47 publication: American Institute of Mathematical Sciences publication_status: published publisher: AIMS quality_controlled: '1' scopus_import: '1' status: public title: Private set-intersection with common set-up type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 12 year: '2018' ... --- _id: '5982' abstract: - lang: eng text: In the present work, we detail a fast and simple solution-based method to synthesize hexagonal SnSe2 nanoplates (NPLs) and their use to produce crystallographically textured SnSe2 nanomaterials. We also demonstrate that the same strategy can be used to produce orthorhombic SnSe nanostructures and nanomaterials. NPLs are grown through a screw dislocation-driven mechanism. This mechanism typically results in pyramidal structures, but we demonstrate here that the growth from multiple dislocations results in flower-like structures. Crystallographically textured SnSe2 bulk nanomaterials obtained from the hot pressing of these SnSe2 structures display highly anisotropic charge and heat transport properties and thermoelectric (TE) figures of merit limited by relatively low electrical conductivities. To improve this parameter, SnSe2 NPLs are blended here with metal nanoparticles. The electrical conductivities of the blends are significantly improved with respect to bare SnSe2 NPLs, what translates into a three-fold increase of the TE Figure of merit, reaching unprecedented ZT values up to 0.65. article_processing_charge: No article_type: original author: - first_name: Yu full_name: Zhang, Yu last_name: Zhang - first_name: Yu full_name: Liu, Yu last_name: Liu - first_name: Khak Ho full_name: Lim, Khak Ho last_name: Lim - first_name: Congcong full_name: Xing, Congcong last_name: Xing - first_name: Mengyao full_name: Li, Mengyao last_name: Li - first_name: Ting full_name: Zhang, Ting last_name: Zhang - first_name: Pengyi full_name: Tang, Pengyi last_name: Tang - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Jordi full_name: Llorca, Jordi last_name: Llorca - first_name: Ka Ming full_name: Ng, Ka Ming last_name: Ng - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Pablo full_name: Guardia, Pablo last_name: Guardia - first_name: Mirko full_name: Prato, Mirko last_name: Prato - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Zhang Y, Liu Y, Lim KH, et al. Tin diselenide molecular precursor for solution-processable thermoelectric materials. Angewandte Chemie International Edition. 2018;57(52):17063-17068. doi:10.1002/anie.201809847 apa: Zhang, Y., Liu, Y., Lim, K. H., Xing, C., Li, M., Zhang, T., … Cabot, A. (2018). Tin diselenide molecular precursor for solution-processable thermoelectric materials. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201809847 chicago: Zhang, Yu, Yu Liu, Khak Ho Lim, Congcong Xing, Mengyao Li, Ting Zhang, Pengyi Tang, et al. “Tin Diselenide Molecular Precursor for Solution-Processable Thermoelectric Materials.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201809847. ieee: Y. Zhang et al., “Tin diselenide molecular precursor for solution-processable thermoelectric materials,” Angewandte Chemie International Edition, vol. 57, no. 52. Wiley, pp. 17063–17068, 2018. ista: Zhang Y, Liu Y, Lim KH, Xing C, Li M, Zhang T, Tang P, Arbiol J, Llorca J, Ng KM, Ibáñez M, Guardia P, Prato M, Cadavid D, Cabot A. 2018. Tin diselenide molecular precursor for solution-processable thermoelectric materials. Angewandte Chemie International Edition. 57(52), 17063–17068. mla: Zhang, Yu, et al. “Tin Diselenide Molecular Precursor for Solution-Processable Thermoelectric Materials.” Angewandte Chemie International Edition, vol. 57, no. 52, Wiley, 2018, pp. 17063–68, doi:10.1002/anie.201809847. short: Y. Zhang, Y. Liu, K.H. Lim, C. Xing, M. Li, T. Zhang, P. Tang, J. Arbiol, J. Llorca, K.M. Ng, M. Ibáñez, P. Guardia, M. Prato, D. Cadavid, A. Cabot, Angewandte Chemie International Edition 57 (2018) 17063–17068. date_created: 2019-02-14T10:23:27Z date_published: 2018-12-21T00:00:00Z date_updated: 2023-09-19T14:28:31Z day: '21' department: - _id: MaIb doi: 10.1002/anie.201809847 external_id: isi: - '000454575500020' intvolume: ' 57' isi: 1 issue: '52' language: - iso: eng main_file_link: - open_access: '1' url: https://upcommons.upc.edu/bitstream/2117/130444/1/Zhang%20preprint.pdf month: '12' oa: 1 oa_version: Submitted Version page: 17063-17068 publication: Angewandte Chemie International Edition publication_identifier: issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Tin diselenide molecular precursor for solution-processable thermoelectric materials type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 57 year: '2018' ... --- _id: '5983' abstract: - lang: eng text: We study a quantum impurity possessing both translational and internal rotational degrees of freedom interacting with a bosonic bath. Such a system corresponds to a “rotating polaron,” which can be used to model, e.g., a rotating molecule immersed in an ultracold Bose gas or superfluid helium. We derive the Hamiltonian of the rotating polaron and study its spectrum in the weak- and strong-coupling regimes using a combination of variational, diagrammatic, and mean-field approaches. We reveal how the coupling between linear and angular momenta affects stable quasiparticle states, and demonstrate that internal rotation leads to an enhanced self-localization in the translational degrees of freedom. article_number: '224506' article_processing_charge: No arxiv: 1 author: - first_name: Enderalp full_name: Yakaboylu, Enderalp id: 38CB71F6-F248-11E8-B48F-1D18A9856A87 last_name: Yakaboylu orcid: 0000-0001-5973-0874 - first_name: Bikashkali full_name: Midya, Bikashkali id: 456187FC-F248-11E8-B48F-1D18A9856A87 last_name: Midya - first_name: Andreas full_name: Deuchert, Andreas id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87 last_name: Deuchert orcid: 0000-0003-3146-6746 - first_name: Nikolai K full_name: Leopold, Nikolai K id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87 last_name: Leopold orcid: 0000-0002-0495-6822 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: 'Yakaboylu E, Midya B, Deuchert A, Leopold NK, Lemeshko M. Theory of the rotating polaron: Spectrum and self-localization. Physical Review B. 2018;98(22). doi:10.1103/physrevb.98.224506' apa: 'Yakaboylu, E., Midya, B., Deuchert, A., Leopold, N. K., & Lemeshko, M. (2018). Theory of the rotating polaron: Spectrum and self-localization. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.98.224506' chicago: 'Yakaboylu, Enderalp, Bikashkali Midya, Andreas Deuchert, Nikolai K Leopold, and Mikhail Lemeshko. “Theory of the Rotating Polaron: Spectrum and Self-Localization.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.98.224506.' ieee: 'E. Yakaboylu, B. Midya, A. Deuchert, N. K. Leopold, and M. Lemeshko, “Theory of the rotating polaron: Spectrum and self-localization,” Physical Review B, vol. 98, no. 22. American Physical Society, 2018.' ista: 'Yakaboylu E, Midya B, Deuchert A, Leopold NK, Lemeshko M. 2018. Theory of the rotating polaron: Spectrum and self-localization. Physical Review B. 98(22), 224506.' mla: 'Yakaboylu, Enderalp, et al. “Theory of the Rotating Polaron: Spectrum and Self-Localization.” Physical Review B, vol. 98, no. 22, 224506, American Physical Society, 2018, doi:10.1103/physrevb.98.224506.' short: E. Yakaboylu, B. Midya, A. Deuchert, N.K. Leopold, M. Lemeshko, Physical Review B 98 (2018). date_created: 2019-02-14T10:37:09Z date_published: 2018-12-12T00:00:00Z date_updated: 2023-09-19T14:29:03Z day: '12' department: - _id: MiLe - _id: RoSe doi: 10.1103/physrevb.98.224506 ec_funded: 1 external_id: arxiv: - '1809.01204' isi: - '000452992700008' intvolume: ' 98' isi: 1 issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.01204 month: '12' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Theory of the rotating polaron: Spectrum and self-localization' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 98 year: '2018' ... --- _id: '5984' abstract: - lang: eng text: G-protein-coupled receptors (GPCRs) form the largest receptor family, relay environmental stimuli to changes in cell behavior and represent prime drug targets. Many GPCRs are classified as orphan receptors because of the limited knowledge on their ligands and coupling to cellular signaling machineries. Here, we engineer a library of 63 chimeric receptors that contain the signaling domains of human orphan and understudied GPCRs functionally linked to the light-sensing domain of rhodopsin. Upon stimulation with visible light, we identify activation of canonical cell signaling pathways, including cAMP-, Ca2+-, MAPK/ERK-, and Rho-dependent pathways, downstream of the engineered receptors. For the human pseudogene GPR33, we resurrect a signaling function that supports its hypothesized role as a pathogen entry site. These results demonstrate that substituting unknown chemical activators with a light switch can reveal information about protein function and provide an optically controlled protein library for exploring the physiology and therapeutic potential of understudied GPCRs. article_number: '1950' article_processing_charge: No author: - first_name: Maurizio full_name: Morri, Maurizio id: 4863116E-F248-11E8-B48F-1D18A9856A87 last_name: Morri - first_name: Inmaculada full_name: Sanchez-Romero, Inmaculada id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87 last_name: Sanchez-Romero - first_name: Alexandra-Madelaine full_name: Tichy, Alexandra-Madelaine id: 29D8BB2C-F248-11E8-B48F-1D18A9856A87 last_name: Tichy - first_name: Stephanie full_name: Kainrath, Stephanie id: 32CFBA64-F248-11E8-B48F-1D18A9856A87 last_name: Kainrath - first_name: Elliot J. full_name: Gerrard, Elliot J. last_name: Gerrard - first_name: Priscila full_name: Hirschfeld, Priscila id: 435ACB3A-F248-11E8-B48F-1D18A9856A87 last_name: Hirschfeld - first_name: Jan full_name: Schwarz, Jan id: 346C1EC6-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 citation: ama: Morri M, Sanchez-Romero I, Tichy A-M, et al. Optical functionalization of human class A orphan G-protein-coupled receptors. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-04342-1 apa: Morri, M., Sanchez-Romero, I., Tichy, A.-M., Kainrath, S., Gerrard, E. J., Hirschfeld, P., … Janovjak, H. L. (2018). Optical functionalization of human class A orphan G-protein-coupled receptors. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04342-1 chicago: Morri, Maurizio, Inmaculada Sanchez-Romero, Alexandra-Madelaine Tichy, Stephanie Kainrath, Elliot J. Gerrard, Priscila Hirschfeld, Jan Schwarz, and Harald L Janovjak. “Optical Functionalization of Human Class A Orphan G-Protein-Coupled Receptors.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04342-1. ieee: M. Morri et al., “Optical functionalization of human class A orphan G-protein-coupled receptors,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018. ista: Morri M, Sanchez-Romero I, Tichy A-M, Kainrath S, Gerrard EJ, Hirschfeld P, Schwarz J, Janovjak HL. 2018. Optical functionalization of human class A orphan G-protein-coupled receptors. Nature Communications. 9(1), 1950. mla: Morri, Maurizio, et al. “Optical Functionalization of Human Class A Orphan G-Protein-Coupled Receptors.” Nature Communications, vol. 9, no. 1, 1950, Springer Nature, 2018, doi:10.1038/s41467-018-04342-1. short: M. Morri, I. Sanchez-Romero, A.-M. Tichy, S. Kainrath, E.J. Gerrard, P. Hirschfeld, J. Schwarz, H.L. Janovjak, Nature Communications 9 (2018). date_created: 2019-02-14T10:50:24Z date_published: 2018-12-01T00:00:00Z date_updated: 2023-09-19T14:29:32Z day: '01' ddc: - '570' department: - _id: HaJa - _id: CaGu - _id: MiSi doi: 10.1038/s41467-018-04342-1 ec_funded: 1 external_id: isi: - '000432280000006' file: - access_level: open_access checksum: 8325fcc194264af4749e662a73bf66b5 content_type: application/pdf creator: kschuh date_created: 2019-02-14T10:58:29Z date_updated: 2020-07-14T12:47:14Z file_id: '5985' file_name: 2018_Springer_Morri.pdf file_size: 1349914 relation: main_file file_date_updated: 2020-07-14T12:47:14Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 25548C20-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303564' name: Microbial Ion Channels for Synthetic Neurobiology - _id: 255A6082-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Optical functionalization of human class A orphan G-protein-coupled receptors 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 9 year: '2018' ... --- _id: '5989' abstract: - lang: eng text: Schistosomes are the causative agents of schistosomiasis, a neglected tropical disease affecting over 230 million people worldwide.Additionally to their major impact on human health, they are also models of choice in evolutionary biology. These parasitic flatwormsare unique among the common hermaphroditic trematodes as they have separate sexes. This so-called “evolutionary scandal”displays a female heterogametic genetic sex-determination system (ZZ males and ZW females), as well as a pronounced adult sexualdimorphism. These phenotypic differences are determined by a shared set of genes in both sexes, potentially leading to intralocussexual conflicts. To resolve these conflicts in sexually selected traits, molecular mechanisms such as sex-biased gene expression couldoccur, but parent-of-origin gene expression also provides an alternative. In this work we investigated the latter mechanism, that is,genes expressed preferentially from either the maternal or the paternal allele, inSchistosoma mansonispecies. To this end, tran-scriptomes from male and female hybrid adults obtained by strain crosses were sequenced. Strain-specific single nucleotide poly-morphism (SNP) markers allowed us to discriminate the parental origin, while reciprocal crosses helped to differentiate parentalexpression from strain-specific expression. We identified genes containing SNPs expressed in a parent-of-origin manner consistentwith paternal and maternal imprints. Although the majority of the SNPs was identified in mitochondrial and Z-specific loci, theremaining SNPs found in male and female transcriptomes were situated in genes that have the potential to explain sexual differencesin schistosome parasites. Furthermore, we identified and validated four new Z-specific scaffolds. article_processing_charge: No author: - first_name: Julien full_name: Kincaid-Smith, Julien last_name: Kincaid-Smith - first_name: Marion A L full_name: Picard, Marion A L id: 2C921A7A-F248-11E8-B48F-1D18A9856A87 last_name: Picard orcid: 0000-0002-8101-2518 - first_name: Céline full_name: Cosseau, Céline last_name: Cosseau - first_name: Jérôme full_name: Boissier, Jérôme last_name: Boissier - first_name: Dany full_name: Severac, Dany last_name: Severac - first_name: Christoph full_name: Grunau, Christoph last_name: Grunau - first_name: Eve full_name: Toulza, Eve last_name: Toulza citation: ama: Kincaid-Smith J, Picard MAL, Cosseau C, et al. Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. Genome Biology and Evolution. 2018;10(3):840-856. doi:10.1093/gbe/evy037 apa: Kincaid-Smith, J., Picard, M. A. L., Cosseau, C., Boissier, J., Severac, D., Grunau, C., & Toulza, E. (2018). Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evy037 chicago: Kincaid-Smith, Julien, Marion A L Picard, Céline Cosseau, Jérôme Boissier, Dany Severac, Christoph Grunau, and Eve Toulza. “Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites.” Genome Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy037. ieee: J. Kincaid-Smith et al., “Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University Press, pp. 840–856, 2018. ista: Kincaid-Smith J, Picard MAL, Cosseau C, Boissier J, Severac D, Grunau C, Toulza E. 2018. Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. Genome Biology and Evolution. 10(3), 840–856. mla: Kincaid-Smith, Julien, et al. “Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites.” Genome Biology and Evolution, vol. 10, no. 3, Oxford University Press, 2018, pp. 840–56, doi:10.1093/gbe/evy037. short: J. Kincaid-Smith, M.A.L. Picard, C. Cosseau, J. Boissier, D. Severac, C. Grunau, E. Toulza, Genome Biology and Evolution 10 (2018) 840–856. date_created: 2019-02-14T12:13:52Z date_published: 2018-03-01T00:00:00Z date_updated: 2023-09-19T14:39:08Z day: '01' ddc: - '570' department: - _id: BeVi doi: 10.1093/gbe/evy037 external_id: isi: - '000429483700013' file: - access_level: open_access checksum: 736a459cb77de5824354466bb0331caf content_type: application/pdf creator: dernst date_created: 2019-02-14T12:20:01Z date_updated: 2020-07-14T12:47:15Z file_id: '5991' file_name: 2018_GBE_Kincaid_Smith.pdf file_size: 529755 relation: main_file file_date_updated: 2020-07-14T12:47:15Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '03' oa: 1 oa_version: Published Version page: 840-856 publication: Genome Biology and Evolution publication_identifier: issn: - 1759-6653 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10 year: '2018' ... --- _id: '5990' abstract: - lang: eng text: 'A Ge–Si core–shell nanowire is used to realize a Josephson field‐effect transistor with highly transparent contacts to superconducting leads. By changing the electric field, access to two distinct regimes, not combined before in a single device, is gained: in the accumulation mode the device is highly transparent and the supercurrent is carried by multiple subbands, while near depletion, the supercurrent is carried by single‐particle levels of a strongly coupled quantum dot operating in the few‐hole regime. These results establish Ge–Si nanowires as an important platform for hybrid superconductor–semiconductor physics and Majorana fermions.' article_number: '1802257' article_processing_charge: No arxiv: 1 author: - first_name: Joost full_name: Ridderbos, Joost last_name: Ridderbos - first_name: Matthias full_name: Brauns, Matthias id: 33F94E3C-F248-11E8-B48F-1D18A9856A87 last_name: Brauns - first_name: Jie full_name: Shen, Jie last_name: Shen - first_name: Folkert K. full_name: de Vries, Folkert K. last_name: de Vries - first_name: Ang full_name: Li, Ang last_name: Li - first_name: Erik P. A. M. full_name: Bakkers, Erik P. A. M. last_name: Bakkers - first_name: Alexander full_name: Brinkman, Alexander last_name: Brinkman - first_name: Floris A. full_name: Zwanenburg, Floris A. last_name: Zwanenburg citation: ama: Ridderbos J, Brauns M, Shen J, et al. Josephson effect in a few-hole quantum dot. Advanced Materials. 2018;30(44). doi:10.1002/adma.201802257 apa: Ridderbos, J., Brauns, M., Shen, J., de Vries, F. K., Li, A., Bakkers, E. P. A. M., … Zwanenburg, F. A. (2018). Josephson effect in a few-hole quantum dot. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201802257 chicago: Ridderbos, Joost, Matthias Brauns, Jie Shen, Folkert K. de Vries, Ang Li, Erik P. A. M. Bakkers, Alexander Brinkman, and Floris A. Zwanenburg. “Josephson Effect in a Few-Hole Quantum Dot.” Advanced Materials. Wiley, 2018. https://doi.org/10.1002/adma.201802257. ieee: J. Ridderbos et al., “Josephson effect in a few-hole quantum dot,” Advanced Materials, vol. 30, no. 44. Wiley, 2018. ista: Ridderbos J, Brauns M, Shen J, de Vries FK, Li A, Bakkers EPAM, Brinkman A, Zwanenburg FA. 2018. Josephson effect in a few-hole quantum dot. Advanced Materials. 30(44), 1802257. mla: Ridderbos, Joost, et al. “Josephson Effect in a Few-Hole Quantum Dot.” Advanced Materials, vol. 30, no. 44, 1802257, Wiley, 2018, doi:10.1002/adma.201802257. short: J. Ridderbos, M. Brauns, J. Shen, F.K. de Vries, A. Li, E.P.A.M. Bakkers, A. Brinkman, F.A. Zwanenburg, Advanced Materials 30 (2018). date_created: 2019-02-14T12:14:26Z date_published: 2018-11-02T00:00:00Z date_updated: 2023-09-19T14:29:58Z day: '02' department: - _id: GeKa doi: 10.1002/adma.201802257 external_id: arxiv: - '1809.08487' isi: - '000450232800015' intvolume: ' 30' isi: 1 issue: '44' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.08487 month: '11' oa: 1 oa_version: Preprint publication: Advanced Materials publication_identifier: issn: - 0935-9648 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Josephson effect in a few-hole quantum dot type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 30 year: '2018' ... --- _id: '5992' abstract: - lang: eng text: Lamellipodia are flat membrane protrusions formed during mesenchymal motion. Polymerization at the leading edge assembles the actin filament network and generates protrusion force. How this force is supported by the network and how the assembly rate is shared between protrusion and network retrograde flow determines the protrusion rate. We use mathematical modeling to understand experiments changing the F-actin density in lamellipodia of B16-F1 melanoma cells by modulation of Arp2/3 complex activity or knockout of the formins FMNL2 and FMNL3. Cells respond to a reduction of density with a decrease of protrusion velocity, an increase in the ratio of force to filament number, but constant network assembly rate. The relation between protrusion force and tension gradient in the F-actin network and the density dependency of friction, elasticity, and viscosity of the network explain the experimental observations. The formins act as filament nucleators and elongators with differential rates. Modulation of their activity suggests an effect on network assembly rate. Contrary to these expectations, the effect of changes in elongator composition is much weaker than the consequences of the density change. We conclude that the force acting on the leading edge membrane is the force required to drive F-actin network retrograde flow. article_processing_charge: No author: - first_name: Setareh full_name: Dolati, Setareh last_name: Dolati - first_name: Frieda full_name: Kage, Frieda last_name: Kage - first_name: Jan full_name: Mueller, Jan last_name: Mueller - first_name: Mathias full_name: Müsken, Mathias last_name: Müsken - first_name: Marieluise full_name: Kirchner, Marieluise last_name: Kirchner - first_name: Gunnar full_name: Dittmar, Gunnar last_name: Dittmar - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner - first_name: Martin full_name: Falcke, Martin last_name: Falcke citation: ama: Dolati S, Kage F, Mueller J, et al. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 2018;29(22):2674-2686. doi:10.1091/mbc.e18-02-0082 apa: Dolati, S., Kage, F., Mueller, J., Müsken, M., Kirchner, M., Dittmar, G., … Falcke, M. (2018). On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. American Society for Cell Biology . https://doi.org/10.1091/mbc.e18-02-0082 chicago: Dolati, Setareh, Frieda Kage, Jan Mueller, Mathias Müsken, Marieluise Kirchner, Gunnar Dittmar, Michael K Sixt, Klemens Rottner, and Martin Falcke. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” Molecular Biology of the Cell. American Society for Cell Biology , 2018. https://doi.org/10.1091/mbc.e18-02-0082. ieee: S. Dolati et al., “On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility,” Molecular Biology of the Cell, vol. 29, no. 22. American Society for Cell Biology , pp. 2674–2686, 2018. ista: Dolati S, Kage F, Mueller J, Müsken M, Kirchner M, Dittmar G, Sixt MK, Rottner K, Falcke M. 2018. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 29(22), 2674–2686. mla: Dolati, Setareh, et al. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” Molecular Biology of the Cell, vol. 29, no. 22, American Society for Cell Biology , 2018, pp. 2674–86, doi:10.1091/mbc.e18-02-0082. short: S. Dolati, F. Kage, J. Mueller, M. Müsken, M. Kirchner, G. Dittmar, M.K. Sixt, K. Rottner, M. Falcke, Molecular Biology of the Cell 29 (2018) 2674–2686. date_created: 2019-02-14T12:25:47Z date_published: 2018-11-01T00:00:00Z date_updated: 2023-09-19T14:30:23Z day: '01' ddc: - '570' department: - _id: MiSi doi: 10.1091/mbc.e18-02-0082 external_id: isi: - '000455641000011' pmid: - '30156465' file: - access_level: open_access checksum: e98465b4416b3e804c47f40086932af2 content_type: application/pdf creator: kschuh date_created: 2019-02-14T12:34:29Z date_updated: 2020-07-14T12:47:15Z file_id: '5994' file_name: 2018_ASCB_Dolati.pdf file_size: 6668971 relation: main_file file_date_updated: 2020-07-14T12:47:15Z has_accepted_license: '1' intvolume: ' 29' isi: 1 issue: '22' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '11' oa: 1 oa_version: Published Version page: 2674-2686 pmid: 1 publication: Molecular Biology of the Cell publication_identifier: eissn: - 1939-4586 publication_status: published publisher: 'American Society for Cell Biology ' quality_controlled: '1' scopus_import: '1' status: public title: On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 29 year: '2018' ... --- _id: '5993' abstract: - lang: eng text: 'In this article, we consider the termination problem of probabilistic programs with real-valued variables. Thequestions concerned are: qualitative ones that ask (i) whether the program terminates with probability 1(almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); andquantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) tocompute a boundBsuch that the probability not to terminate afterBsteps decreases exponentially (con-centration problem). To solve these questions, we utilize the notion of ranking supermartingales, which isa powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmicsynthesis of linear ranking-supermartingales over affine probabilistic programs (Apps) with both angelic anddemonic non-determinism. An important subclass of Apps is LRApp which is defined as the class of all Appsover which a linear ranking-supermartingale exists.Our main contributions are as follows. Firstly, we show that the membership problem of LRApp (i) canbe decided in polynomial time for Apps with at most demonic non-determinism, and (ii) isNP-hard and inPSPACEfor Apps with angelic non-determinism. Moreover, theNP-hardness result holds already for Appswithout probability and demonic non-determinism. Secondly, we show that the concentration problem overLRApp can be solved in the same complexity as for the membership problem of LRApp. Finally, we show thatthe expectation problem over LRApp can be solved in2EXPTIMEand isPSPACE-hard even for Apps withoutprobability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate theeffectiveness of our approach to answer the qualitative and quantitative questions over Apps with at mostdemonic non-determinism.' article_number: '7' article_processing_charge: No arxiv: 1 author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Hongfei full_name: Fu, Hongfei id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87 last_name: Fu - first_name: Petr full_name: Novotný, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotný - first_name: Rouzbeh full_name: Hasheminezhad, Rouzbeh last_name: Hasheminezhad citation: ama: Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. 2018;40(2). doi:10.1145/3174800 apa: Chatterjee, K., Fu, H., Novotný, P., & Hasheminezhad, R. (2018). Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM). https://doi.org/10.1145/3174800 chicago: Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs.” ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3174800. ieee: K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs,” ACM Transactions on Programming Languages and Systems, vol. 40, no. 2. Association for Computing Machinery (ACM), 2018. ista: Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2018. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. 40(2), 7. mla: Chatterjee, Krishnendu, et al. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs.” ACM Transactions on Programming Languages and Systems, vol. 40, no. 2, 7, Association for Computing Machinery (ACM), 2018, doi:10.1145/3174800. short: K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, ACM Transactions on Programming Languages and Systems 40 (2018). date_created: 2019-02-14T12:29:10Z date_published: 2018-06-01T00:00:00Z date_updated: 2023-09-19T14:38:42Z day: '01' department: - _id: KrCh doi: 10.1145/3174800 ec_funded: 1 external_id: arxiv: - '1510.08517' isi: - '000434634500003' intvolume: ' 40' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1510.08517 month: '06' oa: 1 oa_version: Submitted Version project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ACM Transactions on Programming Languages and Systems publication_identifier: issn: - 0164-0925 publication_status: published publisher: Association for Computing Machinery (ACM) quality_controlled: '1' related_material: record: - id: '1438' relation: earlier_version status: public scopus_import: '1' status: public title: Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 40 year: '2018' ... --- _id: '5995' abstract: - lang: eng text: "Motivation\r\nComputational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations.\r\n\r\nResults\r\nHere we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a self-consistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. Authors using algorithms for predicting effects of mutations should be aware of the bias described here." article_processing_charge: No author: - first_name: Dinara R full_name: Usmanova, Dinara R last_name: Usmanova - first_name: Natalya S full_name: Bogatyreva, Natalya S last_name: Bogatyreva - first_name: Joan full_name: Ariño Bernad, Joan last_name: Ariño Bernad - first_name: Aleksandra A full_name: Eremina, Aleksandra A last_name: Eremina - first_name: Anastasiya A full_name: Gorshkova, Anastasiya A last_name: Gorshkova - first_name: German M full_name: Kanevskiy, German M last_name: Kanevskiy - first_name: Lyubov R full_name: Lonishin, Lyubov R last_name: Lonishin - first_name: Alexander V full_name: Meister, Alexander V last_name: Meister - first_name: Alisa G full_name: Yakupova, Alisa G last_name: Yakupova - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Dmitry full_name: Ivankov, Dmitry id: 49FF1036-F248-11E8-B48F-1D18A9856A87 last_name: Ivankov citation: ama: Usmanova DR, Bogatyreva NS, Ariño Bernad J, et al. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 2018;34(21):3653-3658. doi:10.1093/bioinformatics/bty340 apa: Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova, A. A., Kanevskiy, G. M., … Ivankov, D. (2018). Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. Oxford University Press . https://doi.org/10.1093/bioinformatics/bty340 chicago: Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics. Oxford University Press , 2018. https://doi.org/10.1093/bioinformatics/bty340. ieee: D. R. Usmanova et al., “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” Bioinformatics, vol. 34, no. 21. Oxford University Press , pp. 3653–3658, 2018. ista: Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov F, Ivankov D. 2018. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 34(21), 3653–3658. mla: Usmanova, Dinara R., et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics, vol. 34, no. 21, Oxford University Press , 2018, pp. 3653–58, doi:10.1093/bioinformatics/bty340. short: D.R. Usmanova, N.S. Bogatyreva, J. Ariño Bernad, A.A. Eremina, A.A. Gorshkova, G.M. Kanevskiy, L.R. Lonishin, A.V. Meister, A.G. Yakupova, F. Kondrashov, D. Ivankov, Bioinformatics 34 (2018) 3653–3658. date_created: 2019-02-14T12:48:00Z date_published: 2018-11-01T00:00:00Z date_updated: 2023-09-19T14:31:13Z day: '01' ddc: - '570' department: - _id: FyKo doi: 10.1093/bioinformatics/bty340 ec_funded: 1 external_id: isi: - '000450038900008' pmid: - '29722803' file: - access_level: open_access checksum: 7e0495153f44211479674601d7f6ee03 content_type: application/pdf creator: kschuh date_created: 2019-02-14T13:00:55Z date_updated: 2020-07-14T12:47:15Z file_id: '5997' file_name: 2018_Oxford_Usmanova.pdf file_size: 291969 relation: main_file file_date_updated: 2020-07-14T12:47:15Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '21' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 3653-3658 pmid: 1 project: - _id: 26120F5C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '335980' name: Systematic investigation of epistasis in molecular evolution publication: Bioinformatics publication_identifier: issn: - 1367-4803 - 1460-2059 publication_status: published publisher: 'Oxford University Press ' quality_controlled: '1' scopus_import: '1' status: public title: Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 34 year: '2018' ... --- _id: '5996' abstract: - lang: eng text: 'In pipes, turbulence sets in despite the linear stability of the laminar Hagen–Poiseuille flow. The Reynolds number ( ) for which turbulence first appears in a given experiment – the ‘natural transition point’ – depends on imperfections of the set-up, or, more precisely, on the magnitude of finite amplitude perturbations. At onset, turbulence typically only occupies a certain fraction of the flow, and this fraction equally is found to differ from experiment to experiment. Despite these findings, Reynolds proposed that after sufficiently long times, flows may settle to steady conditions: below a critical velocity, flows should (regardless of initial conditions) always return to laminar, while above this velocity, eddying motion should persist. As will be shown, even in pipes several thousand diameters long, the spatio-temporal intermittent flow patterns observed at the end of the pipe strongly depend on the initial conditions, and there is no indication that different flow patterns would eventually settle to a (statistical) steady state. Exploiting the fact that turbulent puffs do not age (i.e. they are memoryless), we continuously recreate the puff sequence exiting the pipe at the pipe entrance, and in doing so introduce periodic boundary conditions for the puff pattern. This procedure allows us to study the evolution of the flow patterns for arbitrary long times, and we find that after times in excess of advective time units, indeed a statistical steady state is reached. Although the resulting flows remain spatio-temporally intermittent, puff splitting and decay rates eventually reach a balance, so that the turbulent fraction fluctuates around a well-defined level which only depends on . In accordance with Reynolds’ proposition, we find that at lower (here 2020), flows eventually always resume to laminar, while for higher ( ), turbulence persists. The critical point for pipe flow hence falls in the interval of $2020 , which is in very good agreement with the recently proposed value of . The latter estimate was based on single-puff statistics and entirely neglected puff interactions. Unlike in typical contact processes where such interactions strongly affect the percolation threshold, in pipe flow, the critical point is only marginally influenced. Interactions, on the other hand, are responsible for the approach to the statistical steady state. As shown, they strongly affect the resulting flow patterns, where they cause ‘puff clustering’, and these regions of large puff densities are observed to travel across the puff pattern in a wave-like fashion.' acknowledgement: ' We also thank Philipp Maier and the IST Austria workshop for theirdedicated technical support' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Mukund full_name: Vasudevan, Mukund id: 3C5A959A-F248-11E8-B48F-1D18A9856A87 last_name: Vasudevan - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Vasudevan M, Hof B. The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. 2018;839:76-94. doi:10.1017/jfm.2017.923 apa: Vasudevan, M., & Hof, B. (2018). The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.923 chicago: Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to Turbulence in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2018. https://doi.org/10.1017/jfm.2017.923. ieee: M. Vasudevan and B. Hof, “The critical point of the transition to turbulence in pipe flow,” Journal of Fluid Mechanics, vol. 839. Cambridge University Press, pp. 76–94, 2018. ista: Vasudevan M, Hof B. 2018. The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. 839, 76–94. mla: Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to Turbulence in Pipe Flow.” Journal of Fluid Mechanics, vol. 839, Cambridge University Press, 2018, pp. 76–94, doi:10.1017/jfm.2017.923. short: M. Vasudevan, B. Hof, Journal of Fluid Mechanics 839 (2018) 76–94. date_created: 2019-02-14T12:50:50Z date_published: 2018-03-25T00:00:00Z date_updated: 2023-09-19T14:37:49Z day: '25' department: - _id: BjHo doi: 10.1017/jfm.2017.923 ec_funded: 1 external_id: arxiv: - '1709.06372' isi: - '000437858300003' intvolume: ' 839' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1709.06372 month: '03' oa: 1 oa_version: Preprint page: 76-94 project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Journal of Fluid Mechanics publication_identifier: eissn: - 1469-7645 issn: - 0022-1120 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: The critical point of the transition to turbulence in pipe flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 839 year: '2018' ... --- _id: '5998' abstract: - lang: eng text: Genome amplification and cellular senescence are commonly associated with pathological processes. While physiological roles for polyploidization and senescence have been described in mouse development, controversy exists over their significance in humans. Here, we describe tetraploidization and senescence as phenomena of normal human placenta development. During pregnancy, placental extravillous trophoblasts (EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted microenvironment required for the developing embryo. This process is critically dependent on continuous cell proliferation and differentiation, which is thought to follow the classical model of cell cycle arrest prior to terminal differentiation. Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied with a genome-wide polyploidization, independent of mitotic cycles. DNA replication in these cells was analysed by a fluorescent cell-cycle indicator reporter system, cell cycle marker expression and EdU incorporation. Upon invasion into the decidua, EVTs widely lose their replicative potential and enter a senescent state characterized by high senescence-associated (SA) β-galactosidase activity, induction of a SA secretory phenotype as well as typical metabolic alterations. Furthermore, we show that the shift from endocycle-dependent genome amplification to growth arrest is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy disorder associated with increased risk of developing choriocarinoma. Senescence is decreased in CHM-EVTs, accompanied by exacerbated endoreduplication and hyperploidy. We propose induction of cellular senescence as a ploidy-limiting mechanism during normal human placentation and unravel a link between excessive polyploidization and reduced senescence in CHM. article_number: e1007698 article_processing_charge: No author: - first_name: Philipp full_name: Velicky, Philipp id: 39BDC62C-F248-11E8-B48F-1D18A9856A87 last_name: Velicky orcid: 0000-0002-2340-7431 - first_name: Gudrun full_name: Meinhardt, Gudrun last_name: Meinhardt - first_name: Kerstin full_name: Plessl, Kerstin last_name: Plessl - first_name: Sigrid full_name: Vondra, Sigrid last_name: Vondra - first_name: Tamara full_name: Weiss, Tamara last_name: Weiss - first_name: Peter full_name: Haslinger, Peter last_name: Haslinger - first_name: Thomas full_name: Lendl, Thomas last_name: Lendl - first_name: Karin full_name: Aumayr, Karin last_name: Aumayr - first_name: Mario full_name: Mairhofer, Mario last_name: Mairhofer - first_name: Xiaowei full_name: Zhu, Xiaowei last_name: Zhu - first_name: Birgit full_name: Schütz, Birgit last_name: Schütz - first_name: Roberta L. full_name: Hannibal, Roberta L. last_name: Hannibal - first_name: Robert full_name: Lindau, Robert last_name: Lindau - first_name: Beatrix full_name: Weil, Beatrix last_name: Weil - first_name: Jan full_name: Ernerudh, Jan last_name: Ernerudh - first_name: Jürgen full_name: Neesen, Jürgen last_name: Neesen - first_name: Gerda full_name: Egger, Gerda last_name: Egger - first_name: Mario full_name: Mikula, Mario last_name: Mikula - first_name: Clemens full_name: Röhrl, Clemens last_name: Röhrl - first_name: Alexander E. full_name: Urban, Alexander E. last_name: Urban - first_name: Julie full_name: Baker, Julie last_name: Baker - first_name: Martin full_name: Knöfler, Martin last_name: Knöfler - first_name: Jürgen full_name: Pollheimer, Jürgen last_name: Pollheimer citation: ama: Velicky P, Meinhardt G, Plessl K, et al. Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. 2018;14(10). doi:10.1371/journal.pgen.1007698 apa: Velicky, P., Meinhardt, G., Plessl, K., Vondra, S., Weiss, T., Haslinger, P., … Pollheimer, J. (2018). Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007698 chicago: Velicky, Philipp, Gudrun Meinhardt, Kerstin Plessl, Sigrid Vondra, Tamara Weiss, Peter Haslinger, Thomas Lendl, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” PLOS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007698. ieee: P. Velicky et al., “Genome amplification and cellular senescence are hallmarks of human placenta development,” PLOS Genetics, vol. 14, no. 10. Public Library of Science, 2018. ista: Velicky P, Meinhardt G, Plessl K, Vondra S, Weiss T, Haslinger P, Lendl T, Aumayr K, Mairhofer M, Zhu X, Schütz B, Hannibal RL, Lindau R, Weil B, Ernerudh J, Neesen J, Egger G, Mikula M, Röhrl C, Urban AE, Baker J, Knöfler M, Pollheimer J. 2018. Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. 14(10), e1007698. mla: Velicky, Philipp, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” PLOS Genetics, vol. 14, no. 10, e1007698, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007698. short: P. Velicky, G. Meinhardt, K. Plessl, S. Vondra, T. Weiss, P. Haslinger, T. Lendl, K. Aumayr, M. Mairhofer, X. Zhu, B. Schütz, R.L. Hannibal, R. Lindau, B. Weil, J. Ernerudh, J. Neesen, G. Egger, M. Mikula, C. Röhrl, A.E. Urban, J. Baker, M. Knöfler, J. Pollheimer, PLOS Genetics 14 (2018). date_created: 2019-02-14T13:07:45Z date_published: 2018-10-12T00:00:00Z date_updated: 2023-09-19T14:31:43Z day: '12' ddc: - '570' department: - _id: JoDa doi: 10.1371/journal.pgen.1007698 external_id: isi: - '000449328500025' file: - access_level: open_access checksum: 34aa9a5972f61889c19f18be8ee787a0 content_type: application/pdf creator: kschuh date_created: 2019-02-14T13:14:35Z date_updated: 2020-07-14T12:47:15Z file_id: '6000' file_name: 2018_PLOS_Velicky.pdf file_size: 4592947 relation: main_file file_date_updated: 2020-07-14T12:47:15Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: PLOS Genetics publication_identifier: issn: - 1553-7404 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Genome amplification and cellular senescence are hallmarks of human placenta development 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2018' ... --- _id: '5999' abstract: - lang: eng text: "We introduce for each quiver Q and each algebraic oriented cohomology theory A, the cohomological Hall algebra (CoHA) of Q, as the A-homology of the moduli of representations of the preprojective algebra of Q. This generalizes the K-theoretic Hall algebra of commuting varieties defined by Schiffmann-Vasserot. When A is the Morava K-theory, we show evidence that this algebra is a candidate for Lusztig's reformulated conjecture on modular representations of algebraic groups.\r\nWe construct an action of the preprojective CoHA on the A-homology of Nakajima quiver varieties. We compare this with the action of the Borel subalgebra of Yangian when A is the intersection theory. We also give a shuffle algebra description of this CoHA in terms of the underlying formal group law of A. As applications, we obtain a shuffle description of the Yangian. " article_processing_charge: No arxiv: 1 author: - first_name: Yaping full_name: Yang, Yaping last_name: Yang - first_name: Gufang full_name: Zhao, Gufang id: 2BC2AC5E-F248-11E8-B48F-1D18A9856A87 last_name: Zhao citation: ama: Yang Y, Zhao G. The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. 2018;116(5):1029-1074. doi:10.1112/plms.12111 apa: Yang, Y., & Zhao, G. (2018). The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. Oxford University Press. https://doi.org/10.1112/plms.12111 chicago: Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective Algebra.” Proceedings of the London Mathematical Society. Oxford University Press, 2018. https://doi.org/10.1112/plms.12111. ieee: Y. Yang and G. Zhao, “The cohomological Hall algebra of a preprojective algebra,” Proceedings of the London Mathematical Society, vol. 116, no. 5. Oxford University Press, pp. 1029–1074, 2018. ista: Yang Y, Zhao G. 2018. The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. 116(5), 1029–1074. mla: Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective Algebra.” Proceedings of the London Mathematical Society, vol. 116, no. 5, Oxford University Press, 2018, pp. 1029–74, doi:10.1112/plms.12111. short: Y. Yang, G. Zhao, Proceedings of the London Mathematical Society 116 (2018) 1029–1074. date_created: 2019-02-14T13:14:22Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-09-19T14:37:19Z day: '01' department: - _id: TaHa doi: 10.1112/plms.12111 external_id: arxiv: - '1407.7994' isi: - '000431506400001' intvolume: ' 116' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1407.7994 month: '05' oa: 1 oa_version: Preprint page: 1029-1074 publication: Proceedings of the London Mathematical Society publication_identifier: issn: - 0024-6115 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: The cohomological Hall algebra of a preprojective algebra type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 116 year: '2018' ...