--- _id: '3282' abstract: - lang: eng text: 'Traditionally, symmetric-key message authentication codes (MACs) are easily built from pseudorandom functions (PRFs). In this work we propose a wide variety of other approaches to building efficient MACs, without going through a PRF first. In particular, unlike deterministic PRF-based MACs, where each message has a unique valid tag, we give a number of probabilistic MAC constructions from various other primitives/assumptions. Our main results are summarized as follows: We show several new probabilistic MAC constructions from a variety of general assumptions, including CCA-secure encryption, Hash Proof Systems and key-homomorphic weak PRFs. By instantiating these frameworks under concrete number theoretic assumptions, we get several schemes which are more efficient than just using a state-of-the-art PRF instantiation under the corresponding assumption. For probabilistic MACs, unlike deterministic ones, unforgeability against a chosen message attack (uf-cma ) alone does not imply security if the adversary can additionally make verification queries (uf-cmva ). We give an efficient generic transformation from any uf-cma secure MAC which is "message-hiding" into a uf-cmva secure MAC. This resolves the main open problem of Kiltz et al. from Eurocrypt''11; By using our transformation on their constructions, we get the first efficient MACs from the LPN assumption. While all our new MAC constructions immediately give efficient actively secure, two-round symmetric-key identification schemes, we also show a very simple, three-round actively secure identification protocol from any weak PRF. In particular, the resulting protocol is much more efficient than the trivial approach of building a regular PRF from a weak PRF. © 2012 International Association for Cryptologic Research.' acknowledgement: Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC) alternative_title: - LNCS author: - first_name: Yevgeniy full_name: Dodis, Yevgeniy last_name: Dodis - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Eike full_name: Kiltz, Eike last_name: Kiltz - first_name: Daniel full_name: Wichs, Daniel last_name: Wichs citation: ama: 'Dodis Y, Pietrzak KZ, Kiltz E, Wichs D. Message authentication, revisited. In: Vol 7237. Springer; 2012:355-374. doi:10.1007/978-3-642-29011-4_22' apa: 'Dodis, Y., Pietrzak, K. Z., Kiltz, E., & Wichs, D. (2012). Message authentication, revisited (Vol. 7237, pp. 355–374). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Cambridge, UK: Springer. https://doi.org/10.1007/978-3-642-29011-4_22' chicago: Dodis, Yevgeniy, Krzysztof Z Pietrzak, Eike Kiltz, and Daniel Wichs. “Message Authentication, Revisited,” 7237:355–74. Springer, 2012. https://doi.org/10.1007/978-3-642-29011-4_22. ieee: 'Y. Dodis, K. Z. Pietrzak, E. Kiltz, and D. Wichs, “Message authentication, revisited,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Cambridge, UK, 2012, vol. 7237, pp. 355–374.' ista: 'Dodis Y, Pietrzak KZ, Kiltz E, Wichs D. 2012. Message authentication, revisited. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 7237, 355–374.' mla: Dodis, Yevgeniy, et al. Message Authentication, Revisited. Vol. 7237, Springer, 2012, pp. 355–74, doi:10.1007/978-3-642-29011-4_22. short: Y. Dodis, K.Z. Pietrzak, E. Kiltz, D. Wichs, in:, Springer, 2012, pp. 355–374. conference: end_date: 2012-04-19 location: Cambridge, UK name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' start_date: 2012-04-15 date_created: 2018-12-11T12:02:27Z date_published: 2012-03-10T00:00:00Z date_updated: 2021-01-12T07:42:22Z day: '10' ddc: - '000' - '004' department: - _id: KrPi doi: 10.1007/978-3-642-29011-4_22 ec_funded: 1 file: - access_level: open_access checksum: 8557c17a8c2586d06ebfe62d934f5c5f content_type: application/pdf creator: system date_created: 2018-12-12T10:14:23Z date_updated: 2020-07-14T12:46:06Z file_id: '5074' file_name: IST-2016-686-v1+1_059.pdf file_size: 372292 relation: main_file file_date_updated: 2020-07-14T12:46:06Z has_accepted_license: '1' intvolume: ' 7237' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 355 - 374 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '3364' pubrep_id: '686' quality_controlled: '1' status: public title: Message authentication, revisited 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7237 year: '2012' ... --- _id: '3280' abstract: - lang: eng text: 'The (decisional) learning with errors problem (LWE) asks to distinguish "noisy" inner products of a secret vector with random vectors from uniform. The learning parities with noise problem (LPN) is the special case where the elements of the vectors are bits. In recent years, the LWE and LPN problems have found many applications in cryptography. In this paper we introduce a (seemingly) much stronger adaptive assumption, called "subspace LWE" (SLWE), where the adversary can learn the inner product of the secret and random vectors after they were projected into an adaptively and adversarially chosen subspace. We prove that, surprisingly, the SLWE problem mapping into subspaces of dimension d is almost as hard as LWE using secrets of length d (the other direction is trivial.) This result immediately implies that several existing cryptosystems whose security is based on the hardness of the LWE/LPN problems are provably secure in a much stronger sense than anticipated. As an illustrative example we show that the standard way of using LPN for symmetric CPA secure encryption is even secure against a very powerful class of related key attacks. ' acknowledgement: Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC). alternative_title: - LNCS 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. Subspace LWE. In: Vol 7194. Springer; 2012:548-563. doi:10.1007/978-3-642-28914-9_31' apa: 'Pietrzak, K. Z. (2012). Subspace LWE (Vol. 7194, pp. 548–563). Presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy: Springer. https://doi.org/10.1007/978-3-642-28914-9_31' chicago: Pietrzak, Krzysztof Z. “Subspace LWE,” 7194:548–63. Springer, 2012. https://doi.org/10.1007/978-3-642-28914-9_31. ieee: 'K. Z. Pietrzak, “Subspace LWE,” presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy, 2012, vol. 7194, pp. 548–563.' ista: 'Pietrzak KZ. 2012. Subspace LWE. TCC: Theory of Cryptography Conference, LNCS, vol. 7194, 548–563.' mla: Pietrzak, Krzysztof Z. Subspace LWE. Vol. 7194, Springer, 2012, pp. 548–63, doi:10.1007/978-3-642-28914-9_31. short: K.Z. Pietrzak, in:, Springer, 2012, pp. 548–563. conference: end_date: 2012-03-21 location: Taormina, Sicily, Italy name: 'TCC: Theory of Cryptography Conference' start_date: 2012-03-19 date_created: 2018-12-11T12:02:26Z date_published: 2012-05-04T00:00:00Z date_updated: 2021-01-12T07:42:21Z day: '04' department: - _id: KrPi doi: 10.1007/978-3-642-28914-9_31 ec_funded: 1 intvolume: ' 7194' language: - iso: eng main_file_link: - open_access: '1' url: http://www.iacr.org/archive/tcc2012/71940166/71940166.pdf month: '05' oa: 1 oa_version: Submitted Version page: 548 - 563 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '3366' quality_controlled: '1' status: public title: Subspace LWE type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7194 year: '2012' ... --- _id: '3281' abstract: - lang: eng text: 'We consider the problem of amplifying the "lossiness" of functions. We say that an oracle circuit C*: {0,1} m → {0,1}* amplifies relative lossiness from ℓ/n to L/m if for every function f:{0,1} n → {0,1} n it holds that 1 If f is injective then so is C f. 2 If f has image size of at most 2 n-ℓ, then C f has image size at most 2 m-L. The question is whether such C* exists for L/m ≫ ℓ/n. This problem arises naturally in the context of cryptographic "lossy functions," where the relative lossiness is the key parameter. We show that for every circuit C* that makes at most t queries to f, the relative lossiness of C f is at most L/m ≤ ℓ/n + O(log t)/n. In particular, no black-box method making a polynomial t = poly(n) number of queries can amplify relative lossiness by more than an O(logn)/n additive term. We show that this is tight by giving a simple construction (cascading with some randomization) that achieves such amplification.' acknowledgement: "We would like to thank Oded Goldreich and Omer Rein- gold for discussions at an early stage of this project, and Scott Aaronson for clarifications regarding the collision problem.\r\n" alternative_title: - LNCS author: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Alon full_name: Rosen, Alon last_name: Rosen - first_name: Gil full_name: Segev, Gil last_name: Segev citation: ama: 'Pietrzak KZ, Rosen A, Segev G. Lossy functions do not amplify well. In: Vol 7194. Springer; 2012:458-475. doi:10.1007/978-3-642-28914-9_26' apa: 'Pietrzak, K. Z., Rosen, A., & Segev, G. (2012). Lossy functions do not amplify well (Vol. 7194, pp. 458–475). Presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy: Springer. https://doi.org/10.1007/978-3-642-28914-9_26' chicago: Pietrzak, Krzysztof Z, Alon Rosen, and Gil Segev. “Lossy Functions Do Not Amplify Well,” 7194:458–75. Springer, 2012. https://doi.org/10.1007/978-3-642-28914-9_26. ieee: 'K. Z. Pietrzak, A. Rosen, and G. Segev, “Lossy functions do not amplify well,” presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy, 2012, vol. 7194, pp. 458–475.' ista: 'Pietrzak KZ, Rosen A, Segev G. 2012. Lossy functions do not amplify well. TCC: Theory of Cryptography Conference, LNCS, vol. 7194, 458–475.' mla: Pietrzak, Krzysztof Z., et al. Lossy Functions Do Not Amplify Well. Vol. 7194, Springer, 2012, pp. 458–75, doi:10.1007/978-3-642-28914-9_26. short: K.Z. Pietrzak, A. Rosen, G. Segev, in:, Springer, 2012, pp. 458–475. conference: end_date: 2012-03-21 location: Taormina, Sicily, Italy name: 'TCC: Theory of Cryptography Conference' start_date: 2012-03-19 date_created: 2018-12-11T12:02:26Z date_published: 2012-05-04T00:00:00Z date_updated: 2021-01-12T07:42:22Z day: '04' department: - _id: KrPi doi: 10.1007/978-3-642-28914-9_26 intvolume: ' 7194' language: - iso: eng main_file_link: - url: http://www.iacr.org/archive/tcc2012/tcc2012-index.html month: '05' oa_version: None page: 458 - 475 publication_status: published publisher: Springer publist_id: '3365' quality_controlled: '1' status: public title: Lossy functions do not amplify well type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7194 year: '2012' ... --- _id: '3284' abstract: - lang: eng text: |- We study the complexity of valued constraint satisfaction problems (VCSP). A problem from VCSP is characterised by a constraint language, a fixed set of cost functions over a finite domain. An instance of the problem is specified by a sum of cost functions from the language and the goal is to minimise the sum. Under the unique games conjecture, the approximability of finite-valued VCSPs is well-understood, see Raghavendra [FOCS’08]. However, there is no characterisation of finite-valued VCSPs, let alone general-valued VCSPs, that can be solved exactly in polynomial time, thus giving insights from a combinatorial optimisation perspective. We consider the case of languages containing all possible unary cost functions. In the case of languages consisting of only {0, ∞}-valued cost functions (i.e. relations), such languages have been called conservative and studied by Bulatov [LICS’03] and recently by Barto [LICS’11]. Since we study valued languages, we call a language conservative if it contains all finite-valued unary cost functions. The computational complexity of conservative valued languages has been studied by Cohen et al. [AIJ’06] for languages over Boolean domains, by Deineko et al. [JACM’08] for {0,1}-valued languages (a.k.a Max-CSP), and by Takhanov [STACS’10] for {0,∞}-valued languages containing all finite- valued unary cost functions (a.k.a. Min-Cost-Hom). We prove a Schaefer-like dichotomy theorem for conservative valued languages: if all cost functions in the language satisfy a certain condition (specified by a complementary combination of STP and MJN multimorphisms), then any instance can be solved in polynomial time (via a new algorithm developed in this paper), otherwise the language is NP-hard. This is the first complete complexity classification of general-valued constraint languages over non-Boolean domains. It is a common phenomenon that complexity classifications of problems over non-Boolean domains is significantly harder than the Boolean case. The polynomial-time algorithm we present for the tractable cases is a generalisation of the submodular minimisation problem and a result of Cohen et al. [TCS’08]. Our results generalise previous results by Takhanov [STACS’10] and (a subset of results) by Cohen et al. [AIJ’06] and Deineko et al. [JACM’08]. Moreover, our results do not rely on any computer-assisted search as in Deineko et al. [JACM’08], and provide a powerful tool for proving hardness of finite-valued and general-valued languages. acknowledgement: Vladimir Kolmogorov is supported by the Royal Academy of Eng ineering/EPSRC. author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Stanislav full_name: Živný, Stanislav last_name: Živný citation: ama: 'Kolmogorov V, Živný S. The complexity of conservative valued CSPs. In: SIAM; 2012:750-759.' apa: 'Kolmogorov, V., & Živný, S. (2012). The complexity of conservative valued CSPs (pp. 750–759). Presented at the SODA: Symposium on Discrete Algorithms, SIAM.' chicago: Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative Valued CSPs,” 750–59. SIAM, 2012. ieee: 'V. Kolmogorov and S. Živný, “The complexity of conservative valued CSPs,” presented at the SODA: Symposium on Discrete Algorithms, 2012, pp. 750–759.' ista: 'Kolmogorov V, Živný S. 2012. The complexity of conservative valued CSPs. SODA: Symposium on Discrete Algorithms, 750–759.' mla: Kolmogorov, Vladimir, and Stanislav Živný. The Complexity of Conservative Valued CSPs. SIAM, 2012, pp. 750–59. short: V. Kolmogorov, S. Živný, in:, SIAM, 2012, pp. 750–759. conference: name: 'SODA: Symposium on Discrete Algorithms' date_created: 2018-12-11T12:02:27Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T07:42:23Z day: '01' extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/1008.1555 month: '01' oa: 1 page: 750 - 759 publication_status: published publisher: SIAM publist_id: '3362' quality_controlled: 0 status: public title: The complexity of conservative valued CSPs type: conference year: '2012' ... --- _id: '330' abstract: - lang: eng text: 'A procedure for the continuous production of Cu 2ZnSnS 4 (CZTS) nanoparticles with controlled composition is presented. CZTS nanoparticles were prepared through the reaction of the metals'' amino complexes with elemental sulfur in a continuous-flow reactor at moderate temperatures (300-330 °C). High-resolution transmission electron microscopy and X-ray diffraction analysis showed the nanocrystals to have a crystallographic structure compatible with that of the kesterite. Chemical characterization of the materials showed the presence of the four elements in each individual nanocrystal. Composition control was achieved by adjusting the solution flow rate through the reactor and the proper choice of the nominal precursor concentration within the flowing solution. Single-particle analysis revealed a composition distribution within each sample, which was optimized at the highest synthesis temperatures used. ' article_processing_charge: No article_type: original author: - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Alex full_name: Carrete, Alex last_name: Carrete - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Shavel A, Cadavid D, Ibáñez M, Carrete A, Cabot A. Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. 2012;134(3):1438-1441. doi:10.1021/ja209688a apa: Shavel, A., Cadavid, D., Ibáñez, M., Carrete, A., & Cabot, A. (2012). Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja209688a chicago: Shavel, Alexey, Doris Cadavid, Maria Ibáñez, Alex Carrete, and Andreu Cabot. “Continuous Production of Cu Inf 2 Inf ZnSnS Inf 4 Inf Nanocrystals in a Flow Reactor.” Journal of the American Chemical Society. ACS, 2012. https://doi.org/10.1021/ja209688a. ieee: A. Shavel, D. Cadavid, M. Ibáñez, A. Carrete, and A. Cabot, “Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor,” Journal of the American Chemical Society, vol. 134, no. 3. ACS, pp. 1438–1441, 2012. ista: Shavel A, Cadavid D, Ibáñez M, Carrete A, Cabot A. 2012. Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. 134(3), 1438–1441. mla: Shavel, Alexey, et al. “Continuous Production of Cu Inf 2 Inf ZnSnS Inf 4 Inf Nanocrystals in a Flow Reactor.” Journal of the American Chemical Society, vol. 134, no. 3, ACS, 2012, pp. 1438–41, doi:10.1021/ja209688a. short: A. Shavel, D. Cadavid, M. Ibáñez, A. Carrete, A. Cabot, Journal of the American Chemical Society 134 (2012) 1438–1441. date_created: 2018-12-11T11:45:51Z date_published: 2012-01-02T00:00:00Z date_updated: 2021-01-12T07:42:29Z day: '02' doi: 10.1021/ja209688a extern: '1' intvolume: ' 134' issue: '3' language: - iso: eng month: '01' oa_version: None page: 1438 - 1441 publication: Journal of the American Chemical Society publication_status: published publisher: ACS publist_id: '7531' quality_controlled: '1' status: public title: Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2012' ... --- _id: '3317' abstract: - lang: eng text: The physical distance between presynaptic Ca2+ channels and the Ca2+ sensors that trigger exocytosis of neurotransmitter-containing vesicles is a key determinant of the signalling properties of synapses in the nervous system. Recent functional analysis indicates that in some fast central synapses, transmitter release is triggered by a small number of Ca2+ channels that are coupled to Ca2+ sensors at the nanometre scale. Molecular analysis suggests that this tight coupling is generated by protein–protein interactions involving Ca2+ channels, Ca2+ sensors and various other synaptic proteins. Nanodomain coupling has several functional advantages, as it increases the efficacy, speed and energy efficiency of synaptic transmission. acknowledgement: "Work of the authors was funded by grants of the Deutsche Forschungsgemeinschaft to P.J. (grants SFB 780/A5, TR 3/B10 and the Leibniz programme), a European Research Council Advanced grant to P.J. and a Swiss National Foundation fellowship to E.E.\r\nWe thank D. Tsien and E. Neher for their comments on this Review, J. Guzmán and A. Pernía-Andrade for reading earlier versions and E. Kramberger for perfect editorial support. We apologize that owing to space constraints, not all relevant papers could be cited.\r\n" author: - first_name: Emmanuel full_name: Eggermann, Emmanuel id: 34DACA34-E9AE-11E9-849C-D35BD8ADC20C last_name: Eggermann - first_name: Iancu full_name: Bucurenciu, Iancu id: 4BD1D872-E9AE-11E9-9EE9-8BF4597A9E2A last_name: Bucurenciu - first_name: Sarit full_name: Goswami, Sarit id: 3A578F32-F248-11E8-B48F-1D18A9856A87 last_name: Goswami - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Eggermann E, Bucurenciu I, Goswami S, Jonas PM. Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. Nature Reviews Neuroscience. 2012;13(1):7-21. doi:10.1038/nrn3125 apa: Eggermann, E., Bucurenciu, I., Goswami, S., & Jonas, P. M. (2012). Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. Nature Reviews Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nrn3125 chicago: Eggermann, Emmanuel, Iancu Bucurenciu, Sarit Goswami, and Peter M Jonas. “Nanodomain Coupling between Ca(2+) Channels and Sensors of Exocytosis at Fast Mammalian Synapses.” Nature Reviews Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nrn3125. ieee: E. Eggermann, I. Bucurenciu, S. Goswami, and P. M. Jonas, “Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses,” Nature Reviews Neuroscience, vol. 13, no. 1. Nature Publishing Group, pp. 7–21, 2012. ista: Eggermann E, Bucurenciu I, Goswami S, Jonas PM. 2012. Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. Nature Reviews Neuroscience. 13(1), 7–21. mla: Eggermann, Emmanuel, et al. “Nanodomain Coupling between Ca(2+) Channels and Sensors of Exocytosis at Fast Mammalian Synapses.” Nature Reviews Neuroscience, vol. 13, no. 1, Nature Publishing Group, 2012, pp. 7–21, doi:10.1038/nrn3125. short: E. Eggermann, I. Bucurenciu, S. Goswami, P.M. Jonas, Nature Reviews Neuroscience 13 (2012) 7–21. date_created: 2018-12-11T12:02:38Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T07:42:36Z day: '01' ddc: - '570' department: - _id: PeJo doi: 10.1038/nrn3125 file: - access_level: open_access checksum: 4c1c86b2f6e4e1562f5bb800b457ea9f content_type: application/pdf creator: system date_created: 2018-12-12T10:12:13Z date_updated: 2020-07-14T12:46:07Z file_id: '4931' file_name: IST-2017-820-v1+1_17463_3_art_file_109404_ltmxbw.pdf file_size: 314246 relation: main_file - access_level: open_access checksum: bceb2efdd49d115f4dde8486bc1be3f2 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:14Z date_updated: 2020-07-14T12:46:07Z file_id: '4932' file_name: IST-2017-820-v1+2_17463_3_figure_109402_ltmwlp.pdf file_size: 1840216 relation: main_file file_date_updated: 2020-07-14T12:46:07Z has_accepted_license: '1' intvolume: ' 13' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 7 - 21 project: - _id: 25BC64A8-B435-11E9-9278-68D0E5697425 grant_number: JO_780/A5 name: Synaptic Mechanisms of Neuronal Network Function - _id: 25BDE9A4-B435-11E9-9278-68D0E5697425 grant_number: SFB-TR3-TP10B name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen publication: Nature Reviews Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '3322' pubrep_id: '820' quality_controlled: '1' scopus_import: 1 status: public title: Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2012' ... --- _id: '3314' abstract: - lang: eng text: We introduce two-level discounted and mean-payoff games played by two players on a perfect-information stochastic game graph. The upper level game is a discounted or mean-payoff game and the lower level game is a (undiscounted) reachability game. Two-level games model hierarchical and sequential decision making under uncertainty across different time scales. For both discounted and mean-payoff two-level games, we show the existence of pure memoryless optimal strategies for both players and an ordered field property. We show that if there is only one player (Markov decision processes), then the values can be computed in polynomial time. It follows that whether the value of a player is equal to a given rational constant in two-level discounted or mean-payoff games can be decided in NP ∩ coNP. We also give an alternate strategy improvement algorithm to compute the value. © 2012 World Scientific Publishing Company. author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar citation: ama: Chatterjee K, Majumdar R. Discounting and averaging in games across time scales. International Journal of Foundations of Computer Science. 2012;23(3):609-625. doi:10.1142/S0129054112400308 apa: Chatterjee, K., & Majumdar, R. (2012). Discounting and averaging in games across time scales. International Journal of Foundations of Computer Science. World Scientific Publishing. https://doi.org/10.1142/S0129054112400308 chicago: Chatterjee, Krishnendu, and Ritankar Majumdar. “Discounting and Averaging in Games across Time Scales.” International Journal of Foundations of Computer Science. World Scientific Publishing, 2012. https://doi.org/10.1142/S0129054112400308. ieee: K. Chatterjee and R. Majumdar, “Discounting and averaging in games across time scales,” International Journal of Foundations of Computer Science, vol. 23, no. 3. World Scientific Publishing, pp. 609–625, 2012. ista: Chatterjee K, Majumdar R. 2012. Discounting and averaging in games across time scales. International Journal of Foundations of Computer Science. 23(3), 609–625. mla: Chatterjee, Krishnendu, and Ritankar Majumdar. “Discounting and Averaging in Games across Time Scales.” International Journal of Foundations of Computer Science, vol. 23, no. 3, World Scientific Publishing, 2012, pp. 609–25, doi:10.1142/S0129054112400308. short: K. Chatterjee, R. Majumdar, International Journal of Foundations of Computer Science 23 (2012) 609–625. date_created: 2018-12-11T12:02:37Z date_published: 2012-04-01T00:00:00Z date_updated: 2021-01-12T07:42:35Z day: '01' department: - _id: KrCh doi: 10.1142/S0129054112400308 intvolume: ' 23' issue: '3' language: - iso: eng month: '04' oa_version: None page: 609 - 625 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: International Journal of Foundations of Computer Science publication_status: published publisher: World Scientific Publishing publist_id: '3326' quality_controlled: '1' scopus_import: 1 status: public title: Discounting and averaging in games across time scales type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2012' ... --- _id: '3115' abstract: - lang: eng text: 'We consider the offset-deconstruction problem: Given a polygonal shape Q with n vertices, can it be expressed, up to a tolerance ε in Hausdorff distance, as the Minkowski sum of another polygonal shape P with a disk of fixed radius? If it does, we also seek a preferably simple-looking solution P; then, P''s offset constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We give an O(nlogn)-time exact decision algorithm that handles any polygonal shape, assuming the real-RAM model of computation. A variant of the algorithm, which we have implemented using the cgal library, is based on rational arithmetic and answers the same deconstruction problem up to an uncertainty parameter δ its running time additionally depends on δ. If the input shape is found to be approximable, this algorithm also computes an approximate solution for the problem. It also allows us to solve parameter-optimization problems induced by the offset-deconstruction problem. For convex shapes, the complexity of the exact decision algorithm drops to O(n), which is also the time required to compute a solution P with at most one more vertex than a vertex-minimal one.' acknowledgement: "We thank Eyal Flato (Plataine Ltd.) for raising the offset-deconstruction problem in connection with wood cutting. We also thank Tim Bretl (UIUC) for suggesting the digital-pen offset-deconstruction problem. This work has been supported in part by the Israel Science Foundation (grant no. 1102/11), by the German–Israeli Foundation (grant no. 969/07), by the Hermann Minkowski–Minerva Center for Geometry at Tel Aviv University, and by the EU Project under Contract No. 255827 (CGL—Computational Geometry Learning).\r\n" author: - first_name: Eric full_name: Berberich, Eric last_name: Berberich - first_name: Dan full_name: Halperin, Dan last_name: Halperin - first_name: Michael full_name: Kerber, Michael id: 36E4574A-F248-11E8-B48F-1D18A9856A87 last_name: Kerber orcid: 0000-0002-8030-9299 - first_name: Roza full_name: Pogalnikova, Roza last_name: Pogalnikova citation: ama: Berberich E, Halperin D, Kerber M, Pogalnikova R. Deconstructing approximate offsets. Discrete & Computational Geometry. 2012;48(4):964-989. doi:10.1007/s00454-012-9441-5 apa: Berberich, E., Halperin, D., Kerber, M., & Pogalnikova, R. (2012). Deconstructing approximate offsets. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-012-9441-5 chicago: Berberich, Eric, Dan Halperin, Michael Kerber, and Roza Pogalnikova. “Deconstructing Approximate Offsets.” Discrete & Computational Geometry. Springer, 2012. https://doi.org/10.1007/s00454-012-9441-5. ieee: E. Berberich, D. Halperin, M. Kerber, and R. Pogalnikova, “Deconstructing approximate offsets,” Discrete & Computational Geometry, vol. 48, no. 4. Springer, pp. 964–989, 2012. ista: Berberich E, Halperin D, Kerber M, Pogalnikova R. 2012. Deconstructing approximate offsets. Discrete & Computational Geometry. 48(4), 964–989. mla: Berberich, Eric, et al. “Deconstructing Approximate Offsets.” Discrete & Computational Geometry, vol. 48, no. 4, Springer, 2012, pp. 964–89, doi:10.1007/s00454-012-9441-5. short: E. Berberich, D. Halperin, M. Kerber, R. Pogalnikova, Discrete & Computational Geometry 48 (2012) 964–989. date_created: 2018-12-11T12:01:28Z date_published: 2012-12-01T00:00:00Z date_updated: 2023-02-23T11:22:30Z day: '01' department: - _id: HeEd doi: 10.1007/s00454-012-9441-5 external_id: arxiv: - '1109.2158' intvolume: ' 48' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1109.2158 month: '12' oa: 1 oa_version: Preprint page: 964 - 989 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '3584' quality_controlled: '1' related_material: record: - id: '3329' relation: earlier_version status: public scopus_import: 1 status: public title: Deconstructing approximate offsets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2012' ... --- _id: '3331' abstract: - lang: eng text: Computing the topology of an algebraic plane curve C means computing a combinatorial graph that is isotopic to C and thus represents its topology in R2. We prove that, for a polynomial of degree n with integer coefficients bounded by 2ρ, the topology of the induced curve can be computed with bit operations ( indicates that we omit logarithmic factors). Our analysis improves the previous best known complexity bounds by a factor of n2. The improvement is based on new techniques to compute and refine isolating intervals for the real roots of polynomials, and on the consequent amortized analysis of the critical fibers of the algebraic curve. author: - first_name: Michael full_name: Kerber, Michael id: 36E4574A-F248-11E8-B48F-1D18A9856A87 last_name: Kerber orcid: 0000-0002-8030-9299 - first_name: Michael full_name: Sagraloff, Michael last_name: Sagraloff citation: ama: Kerber M, Sagraloff M. A worst case bound for topology computation of algebraic curves. Journal of Symbolic Computation. 2012;47(3):239-258. doi:10.1016/j.jsc.2011.11.001 apa: Kerber, M., & Sagraloff, M. (2012). A worst case bound for topology computation of algebraic curves. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2011.11.001 chicago: Kerber, Michael, and Michael Sagraloff. “A Worst Case Bound for Topology Computation of Algebraic Curves.” Journal of Symbolic Computation. Elsevier, 2012. https://doi.org/10.1016/j.jsc.2011.11.001. ieee: M. Kerber and M. Sagraloff, “A worst case bound for topology computation of algebraic curves,” Journal of Symbolic Computation, vol. 47, no. 3. Elsevier, pp. 239–258, 2012. ista: Kerber M, Sagraloff M. 2012. A worst case bound for topology computation of algebraic curves. Journal of Symbolic Computation. 47(3), 239–258. mla: Kerber, Michael, and Michael Sagraloff. “A Worst Case Bound for Topology Computation of Algebraic Curves.” Journal of Symbolic Computation, vol. 47, no. 3, Elsevier, 2012, pp. 239–58, doi:10.1016/j.jsc.2011.11.001. short: M. Kerber, M. Sagraloff, Journal of Symbolic Computation 47 (2012) 239–258. date_created: 2018-12-11T12:02:43Z date_published: 2012-03-01T00:00:00Z date_updated: 2021-01-12T07:42:43Z day: '01' department: - _id: HeEd doi: 10.1016/j.jsc.2011.11.001 intvolume: ' 47' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1104.1510 month: '03' oa: 1 oa_version: Preprint page: 239 - 258 publication: ' Journal of Symbolic Computation' publication_status: published publisher: Elsevier publist_id: '3303' quality_controlled: '1' scopus_import: 1 status: public title: A worst case bound for topology computation of algebraic curves type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2012' ... --- _id: '346' abstract: - lang: eng text: Arrays of vertically aligned ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires (NWs) were prepared by means of the combination of two solution-growth processes. First, single-crystal ZnO NWs with controlled n-type doping were grown on conducting substrates by a low-cost, high-yield and seed-free electrochemical route. These NWs were covered by a titanium oxide shell of tunable thickness mediating successive adsorption-hydrolysis-condensation steps. Using this atomic-layer growth procedure, titania shells with controlled thickness and the anatase TiO2 phase were obtained after sintering at 450 °C. Higher sintering temperatures resulted in the formation of ZnO : Cl/ZnxTiOy/TiO2 core–shell NWs by the interdiffusion of Zn and Ti ions at the ZnO–TiO2 interface. The performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell NWs towards photoelectrochemical (PEC) water splitting was investigated as a function of the titania shell thickness. Furthermore, the performance of such core–shell NWs as photoelectrodes in dye-sensitized solar cells was also characterized. The TiO2 presence at the ZnO : Cl surface promoted a two-fold increase on the produced photocurrent densities, probing their potential for PEC and optoelectronic applications. Electrochemical impedance spectroscopy was used to corroborate the lower resistance for charge transfer between the NWs and the electrolyte in the presence of the TiO2 shell. acknowledgement: The research was supported by the European Regional Development Funds and the Spanish MICINN projects MAT2010-15138, MAT2010-21510 and CSD2009-00050. JF and AS thank the FI-DGR and BP grants from the Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR) from the Catalan Government. MI and AC thank the Spanish MICINN for the PhD grant and the financial support through the Ramóny Cajal program. article_processing_charge: No article_type: original author: - first_name: Jiandong full_name: Fan, Jiandong last_name: Fan - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Cristina full_name: Fábrega, Cristina last_name: Fábrega - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Cristina full_name: Flox, Cristina last_name: Flox - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Teresa full_name: Andreu, Teresa last_name: Andreu - first_name: Amtonio full_name: López, Amtonio last_name: López - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Joan full_name: Morante, Joan last_name: Morante - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Fan J, Zamani R, Fábrega C, et al. Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness. Journal of Physics D: Applied Physics. 2012;45(41). doi:10.1088/0022-3727/45/41/415301' apa: 'Fan, J., Zamani, R., Fábrega, C., Shavel, A., Flox, C., Ibáñez, M., … Cabot, A. (2012). Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness. Journal of Physics D: Applied Physics. IOP Publishing Ltd. https://doi.org/10.1088/0022-3727/45/41/415301' chicago: 'Fan, Jiandong, Reza Zamani, Cristina Fábrega, Alexey Shavel, Cristina Flox, Maria Ibáñez, Teresa Andreu, et al. “Solution-Growth and Optoelectronic Performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 Core–Shell Nanowires with Tunable Shell Thickness.” Journal of Physics D: Applied Physics. IOP Publishing Ltd., 2012. https://doi.org/10.1088/0022-3727/45/41/415301.' ieee: 'J. Fan et al., “Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness,” Journal of Physics D: Applied Physics, vol. 45, no. 41. IOP Publishing Ltd., 2012.' ista: 'Fan J, Zamani R, Fábrega C, Shavel A, Flox C, Ibáñez M, Andreu T, López A, Arbiol J, Morante J, Cabot A. 2012. Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness. Journal of Physics D: Applied Physics. 45(41).' mla: 'Fan, Jiandong, et al. “Solution-Growth and Optoelectronic Performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 Core–Shell Nanowires with Tunable Shell Thickness.” Journal of Physics D: Applied Physics, vol. 45, no. 41, IOP Publishing Ltd., 2012, doi:10.1088/0022-3727/45/41/415301.' short: 'J. Fan, R. Zamani, C. Fábrega, A. Shavel, C. Flox, M. Ibáñez, T. Andreu, A. López, J. Arbiol, J. Morante, A. Cabot, Journal of Physics D: Applied Physics 45 (2012).' date_created: 2018-12-11T11:45:56Z date_published: 2012-10-17T00:00:00Z date_updated: 2021-01-12T07:43:36Z day: '17' doi: 10.1088/0022-3727/45/41/415301 extern: '1' intvolume: ' 45' issue: '41' language: - iso: eng month: '10' oa_version: None publication: 'Journal of Physics D: Applied Physics' publication_status: published publisher: IOP Publishing Ltd. publist_id: '7486' quality_controlled: '1' status: public title: Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2012' ... --- _id: '3168' abstract: - lang: eng text: The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a mathematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the combinatorial complexity by quotienting the reachable set of molecular species into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently, we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper, we prove that this quotienting yields a sufficient condition for weak lumpability (that is to say that the quotient system is still Markovian for a given set of initial distributions) and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system (which means that the conditional probability of being in a given state in the original system knowing that we are in its equivalence class is an invariant of the system). We illustrate the framework on a case study of the epidermal growth factor (EGF)/insulin receptor crosstalk. acknowledgement: "We would like to thank the anonymous reviewers for their comments on the different versions of the paper. We would also like to thank Ferdinanda Camporesi for her careful reading and the useful insights that she gave us about the paper.\r\nJérôme Feret’s contribution was partially supported by the AbstractCell ANR-Chair of Excellence. Heinz Koeppl’s research is supported by the Swiss National Science Foundation, grant no. 200020-117975/1. Tatjana Petrov’s research is supported by SystemsX.ch (the Swiss Initiative in Systems Biology)." author: - first_name: Jérôme full_name: Feret, Jérôme last_name: Feret - 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: Heinz full_name: Koeppl, Heinz last_name: Koeppl - first_name: Tatjana full_name: Petrov, Tatjana id: 3D5811FC-F248-11E8-B48F-1D18A9856A87 last_name: Petrov orcid: 0000-0002-9041-0905 citation: ama: Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule based systems. Theoretical Computer Science. 2012;431:137-164. doi:10.1016/j.tcs.2011.12.059 apa: Feret, J., Henzinger, T. A., Koeppl, H., & Petrov, T. (2012). Lumpability abstractions of rule based systems. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2011.12.059 chicago: Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability Abstractions of Rule Based Systems.” Theoretical Computer Science. Elsevier, 2012. https://doi.org/10.1016/j.tcs.2011.12.059. ieee: J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions of rule based systems,” Theoretical Computer Science, vol. 431. Elsevier, pp. 137–164, 2012. ista: Feret J, Henzinger TA, Koeppl H, Petrov T. 2012. Lumpability abstractions of rule based systems. Theoretical Computer Science. 431, 137–164. mla: Feret, Jérôme, et al. “Lumpability Abstractions of Rule Based Systems.” Theoretical Computer Science, vol. 431, Elsevier, 2012, pp. 137–64, doi:10.1016/j.tcs.2011.12.059. short: J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, Theoretical Computer Science 431 (2012) 137–164. date_created: 2018-12-11T12:01:47Z date_published: 2012-05-04T00:00:00Z date_updated: 2023-02-23T11:39:40Z day: '04' department: - _id: ToHe doi: 10.1016/j.tcs.2011.12.059 intvolume: ' 431' language: - iso: eng month: '05' oa_version: None page: 137 - 164 publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '3515' pubrep_id: '73' quality_controlled: '1' related_material: record: - id: '3719' relation: earlier_version status: public scopus_import: 1 status: public title: Lumpability abstractions of rule based systems type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 431 year: '2012' ... --- _id: '377' abstract: - lang: eng text: The potential to control the composition and crystal phase at the nanometer scale enable the production of nanocrystalline materials with enhanced functionalities and new applications. In the present work, we detail a novel colloidal synthesis route to prepare nanoparticles of the ternary semiconductor Cu2GeSe3 (CGSe) with nanometer-scale control over their crystal phases. We also demonstrate the structural effect on the thermoelectric properties of bottom-up-prepared CGSe nanomaterials. By careful adjustment of the nucleation and growth temperatures, pure orthorhombic CGSe nanoparticles with cationic order or polytypic CGSe nanoparticles with disordered cation positions can be produced. In this second type of nanoparticle, a high density of twins can be created to periodically change the atomic plane stacking, forming a hexagonal wurtzite CGSe phase. The high yield of the synthetic routes reported here allows the production of single-phase and multiphase CGSe nanoparticles in the gram scale, which permits characterization of the thermoelectric properties of these materials. Reduced thermal conductivities and a related 2.5-fold increase of the thermoelectric figure of merit for multiphase nanomaterials compared to pure-phase CGSe are systematically obtained. These results are discussed in terms of the density and efficiency of phonon scattering centers in both types of materials. article_processing_charge: No author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Stéphane full_name: Gorse, Stéphane last_name: Gorse - first_name: Nebll full_name: Katchoi, Nebll last_name: Katchoi - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Antonioo full_name: López, Antonioo last_name: López - first_name: Joan full_name: Morante, Joan last_name: Morante - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Ibáñez M, Zamani R, Li W, et al. Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials. Chemistry of Materials. 2012;24(23):4615-4622. doi:10.1021/cm303252q' apa: 'Ibáñez, M., Zamani, R., Li, W., Cadavid, D., Gorse, S., Katchoi, N., … Cabot, A. (2012). Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/cm303252q' chicago: 'Ibáñez, Maria, Reza Zamani, Wenhua Li, Doris Cadavid, Stéphane Gorse, Nebll Katchoi, Alexey Shavel, et al. “Crystallographic Control at the Nanoscale to Enhance Functionality: Polytypic Cu2GeSe3 Nanoparticles as Thermoelectric Materials.” Chemistry of Materials. American Chemical Society, 2012. https://doi.org/10.1021/cm303252q.' ieee: 'M. Ibáñez et al., “Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials,” Chemistry of Materials, vol. 24, no. 23. American Chemical Society, pp. 4615–4622, 2012.' ista: 'Ibáñez M, Zamani R, Li W, Cadavid D, Gorse S, Katchoi N, Shavel A, López A, Morante J, Arbiol J, Cabot A. 2012. Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials. Chemistry of Materials. 24(23), 4615–4622.' mla: 'Ibáñez, Maria, et al. “Crystallographic Control at the Nanoscale to Enhance Functionality: Polytypic Cu2GeSe3 Nanoparticles as Thermoelectric Materials.” Chemistry of Materials, vol. 24, no. 23, American Chemical Society, 2012, pp. 4615–22, doi:10.1021/cm303252q.' short: M. Ibáñez, R. Zamani, W. Li, D. Cadavid, S. Gorse, N. Katchoi, A. Shavel, A. López, J. Morante, J. Arbiol, A. Cabot, Chemistry of Materials 24 (2012) 4615–4622. date_created: 2018-12-11T11:46:07Z date_published: 2012-11-14T00:00:00Z date_updated: 2021-01-12T07:52:04Z day: '14' doi: 10.1021/cm303252q extern: '1' intvolume: ' 24' issue: '23' language: - iso: eng month: '11' oa_version: None page: 4615 - 4622 publication: Chemistry of Materials publication_status: published publisher: American Chemical Society publist_id: '7452' status: public title: 'Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2012' ... --- _id: '3846' abstract: - lang: eng text: We summarize classical and recent results about two-player games played on graphs with ω-regular objectives. These games have applications in the verification and synthesis of reactive systems. Important distinctions are whether a graph game is turn-based or concurrent; deterministic or stochastic; zero-sum or not. We cluster known results and open problems according to these classifications. acknowledgement: This research was supported in part by the ONR grant N00014-02-1-0671, by the AFOSR MURI grant F49620-00-1-0327, and by the NSF grants CCR-9988172, CCR-0085949, and CCR-0225610. article_processing_charge: No article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: Chatterjee K, Henzinger TA. A survey of stochastic ω regular games. Journal of Computer and System Sciences. 2012;78(2):394-413. doi:10.1016/j.jcss.2011.05.002 apa: Chatterjee, K., & Henzinger, T. A. (2012). A survey of stochastic ω regular games. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2011.05.002 chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “A Survey of Stochastic ω Regular Games.” Journal of Computer and System Sciences. Elsevier, 2012. https://doi.org/10.1016/j.jcss.2011.05.002. ieee: K. Chatterjee and T. A. Henzinger, “A survey of stochastic ω regular games,” Journal of Computer and System Sciences, vol. 78, no. 2. Elsevier, pp. 394–413, 2012. ista: Chatterjee K, Henzinger TA. 2012. A survey of stochastic ω regular games. Journal of Computer and System Sciences. 78(2), 394–413. mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. “A Survey of Stochastic ω Regular Games.” Journal of Computer and System Sciences, vol. 78, no. 2, Elsevier, 2012, pp. 394–413, doi:10.1016/j.jcss.2011.05.002. short: K. Chatterjee, T.A. Henzinger, Journal of Computer and System Sciences 78 (2012) 394–413. date_created: 2018-12-11T12:05:29Z date_published: 2012-03-02T00:00:00Z date_updated: 2022-05-24T08:00:54Z day: '02' ddc: - '000' department: - _id: KrCh - _id: ToHe doi: 10.1016/j.jcss.2011.05.002 file: - access_level: open_access checksum: 241b939deb4517cdd4426d49c67e3fa2 content_type: application/pdf creator: kschuh date_created: 2019-01-29T10:54:28Z date_updated: 2020-07-14T12:46:17Z file_id: '5897' file_name: a_survey_of_stochastic_omega-regular_games.pdf file_size: 336450 relation: main_file file_date_updated: 2020-07-14T12:46:17Z has_accepted_license: '1' intvolume: ' 78' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.jcss.2011.05.002 month: '03' oa: 1 oa_version: Submitted Version page: 394 - 413 publication: Journal of Computer and System Sciences publication_status: published publisher: Elsevier publist_id: '2341' quality_controlled: '1' scopus_import: '1' status: public title: A survey of stochastic ω regular games type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 78 year: '2012' ... --- _id: '387' abstract: - lang: eng text: In this Letter we present detailed study of the density of states near defects in Bi 2Se 3. In particular, we present data on the commonly found triangular defects in this system. While we do not find any measurable quasiparticle scattering interference effects, we do find localized resonances, which can be well fitted by theory once the potential is taken to be extended to properly account for the observed defects. The data together with the fits confirm that while the local density of states around the Dirac point of the electronic spectrum at the surface is significantly disrupted near the impurity by the creation of low-energy resonance state, the Dirac point is not locally destroyed. We discuss our results in terms of the expected protected surface state of topological insulators. © 2012 American Physical Society. author: - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 - first_name: Rudro full_name: Biswas, Rudro last_name: Biswas - first_name: Alexander full_name: Balatsky, Alexander last_name: Balatsky - first_name: James full_name: Analytis, James last_name: Analytis - first_name: Jiunhaw full_name: Chu, Jiunhaw last_name: Chu - first_name: Ian full_name: Fisher, Ian last_name: Fisher - first_name: Aharon full_name: Kapitulnik, Aharon last_name: Kapitulnik citation: ama: Alpichshev Z, Biswas R, Balatsky A, et al. STM imaging of impurity resonances on Bi 2Se 3. Physical Review Letters. 2012;108(20). doi:10.1103/PhysRevLett.108.206402 apa: Alpichshev, Z., Biswas, R., Balatsky, A., Analytis, J., Chu, J., Fisher, I., & Kapitulnik, A. (2012). STM imaging of impurity resonances on Bi 2Se 3. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.108.206402 chicago: Alpichshev, Zhanybek, Rudro Biswas, Alexander Balatsky, James Analytis, Jiunhaw Chu, Ian Fisher, and Aharon Kapitulnik. “STM Imaging of Impurity Resonances on Bi 2Se 3.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.108.206402. ieee: Z. Alpichshev et al., “STM imaging of impurity resonances on Bi 2Se 3,” Physical Review Letters, vol. 108, no. 20. American Physical Society, 2012. ista: Alpichshev Z, Biswas R, Balatsky A, Analytis J, Chu J, Fisher I, Kapitulnik A. 2012. STM imaging of impurity resonances on Bi 2Se 3. Physical Review Letters. 108(20). mla: Alpichshev, Zhanybek, et al. “STM Imaging of Impurity Resonances on Bi 2Se 3.” Physical Review Letters, vol. 108, no. 20, American Physical Society, 2012, doi:10.1103/PhysRevLett.108.206402. short: Z. Alpichshev, R. Biswas, A. Balatsky, J. Analytis, J. Chu, I. Fisher, A. Kapitulnik, Physical Review Letters 108 (2012). date_created: 2018-12-11T11:46:11Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T07:52:49Z day: '01' doi: 10.1103/PhysRevLett.108.206402 extern: '1' intvolume: ' 108' issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1108.0022 month: '01' oa: 1 oa_version: None publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7442' status: public title: STM imaging of impurity resonances on Bi 2Se 3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2012' ... --- _id: '3110' abstract: - lang: eng text: 'The directional transport of the phytohormone auxin depends on the phosphorylation status and polar localization of PIN-FORMED (PIN) auxin efflux proteins. While PINIOD (PID) kinase is directly involved in the phosphorylation of PIN proteins, the phosphatase holoenzyme complexes that dephosphorylate PIN proteins remain elusive. Here, we demonstrate that mutations simultaneously disrupting the function of Arabidopsis thaliana FyPP1 (for Phytochrome-associated serine/threonine protein phosphatase1) and FyPP3, two homologous genes encoding the catalytic subunits of protein phosphatase6 (PP6), cause elevated accumulation of phosphorylated PIN proteins, correlating with a basal-to-apical shift in subcellular PIN localization. The changes in PIN polarity result in increased root basipetal auxin transport and severe defects, including shorter roots, fewer lateral roots, defective columella cells, root meristem collapse, abnormal cotyledons (small, cup-shaped, or fused cotyledons), and altered leaf venation. Our molecular, biochemical, and genetic data support the notion that FyPP1/3, SAL (for SAPS DOMAIN-LIKE), and PP2AA proteins (RCN1 [for ROOTS CURL IN NAPHTHYLPHTHALAMIC ACID1] or PP2AA1, PP2AA2, and PP2AA3) physically interact to form a novel PP6-type heterotrimeric holoenzyme complex. We also show that FyPP1/3, SAL, and PP2AA interact with a subset of PIN proteins and that for SAL the strength of the interaction depends on the PIN phosphorylation status. Thus, an Arabidopsis PP6-type phosphatase holoenzyme acts antagonistically with PID to direct auxin transport polarity and plant development by directly regulating PIN phosphorylation. ' author: - first_name: Mingqiu full_name: Dai, Mingqiu last_name: Dai - first_name: Chen full_name: Zhang, Chen last_name: Zhang - first_name: Urszula full_name: Urszula Kania id: 4AE5C486-F248-11E8-B48F-1D18A9856A87 last_name: Kania - first_name: Fang full_name: Chen, Fang last_name: Chen - first_name: Qin full_name: Xue, Qin last_name: Xue - first_name: Tyra full_name: McCray, Tyra last_name: Mccray - first_name: Gang full_name: Li, Gang last_name: Li - first_name: Genji full_name: Qin, Genji last_name: Qin - first_name: Michelle full_name: Wakeley, Michelle last_name: Wakeley - first_name: William full_name: Terzaghi, William last_name: Terzaghi - first_name: Jianmin full_name: Wan, Jianmin last_name: Wan - first_name: Yunde full_name: Zhao, Yunde last_name: Zhao - first_name: Jian full_name: Xu, Jian last_name: Xu - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Xing full_name: Deng, Xing W last_name: Deng - first_name: Haiyang full_name: Wang, Haiyang last_name: Wang citation: ama: Dai M, Zhang C, Kania U, et al. A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell. 2012;24(6):2497-2514. doi:10.1105/tpc.112.098905 apa: Dai, M., Zhang, C., Kania, U., Chen, F., Xue, Q., Mccray, T., … Wang, H. (2012). A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.112.098905 chicago: Dai, Mingqiu, Chen Zhang, Urszula Kania, Fang Chen, Qin Xue, Tyra Mccray, Gang Li, et al. “A PP6 Type Phosphatase Holoenzyme Directly Regulates PIN Phosphorylation and Auxin Efflux in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2012. https://doi.org/10.1105/tpc.112.098905. ieee: M. Dai et al., “A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis,” Plant Cell, vol. 24, no. 6. American Society of Plant Biologists, pp. 2497–2514, 2012. ista: Dai M, Zhang C, Kania U, Chen F, Xue Q, Mccray T, Li G, Qin G, Wakeley M, Terzaghi W, Wan J, Zhao Y, Xu J, Friml J, Deng X, Wang H. 2012. A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell. 24(6), 2497–2514. mla: Dai, Mingqiu, et al. “A PP6 Type Phosphatase Holoenzyme Directly Regulates PIN Phosphorylation and Auxin Efflux in Arabidopsis.” Plant Cell, vol. 24, no. 6, American Society of Plant Biologists, 2012, pp. 2497–514, doi:10.1105/tpc.112.098905. short: M. Dai, C. Zhang, U. Kania, F. Chen, Q. Xue, T. Mccray, G. Li, G. Qin, M. Wakeley, W. Terzaghi, J. Wan, Y. Zhao, J. Xu, J. Friml, X. Deng, H. Wang, Plant Cell 24 (2012) 2497–2514. date_created: 2018-12-11T12:01:27Z date_published: 2012-06-01T00:00:00Z date_updated: 2021-01-12T07:41:08Z day: '01' doi: 10.1105/tpc.112.098905 extern: 1 intvolume: ' 24' issue: '6' month: '06' page: 2497 - 2514 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3589' quality_controlled: 0 status: public title: A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis type: journal_article volume: 24 year: '2012' ... --- _id: '3113' abstract: - lang: eng text: A cell membrane can be considered a liquid-phase plane in which lipids and proteins theoretically are free to diffuse. Numerous reports,however, describe retarded diffusion ofmembrane proteins in animal cells. This anomalous diffusion results from a combination of structuring factors including protein-protein interactions, cytoskeleton corralling, and lipid organization into microdomains. In plant cells, plasma-membrane (PM) proteins have been described as relatively immobile, but the control mechanisms that structure the PM have not been studied. Here, we use fluorescence recovery after photobleaching to estimate mobility of a set of minimal PM proteins. These proteins consist only of a PM-anchoring domain fused to a fluorescent protein, but their mobilities remained limited, as is the case for many full-length proteins. Neither the cytoskeleton nor membrane microdomain structure was involved in constraining the diffusion of these proteins. The cell wall, however, was shown to have a crucial role in immobilizing PM proteins. In addition, by single-molecule fluorescence imaging we confirmed that the pattern of cellulose deposition in the cell wall affects the trajectory and speed ofPMprotein diffusion. Regulation ofPMprotein dynamics by the plant cell wall can be interpreted as a mechanism for regulating protein interactions in processes such as trafficking and signal transduction. author: - first_name: Alexandre full_name: Martinière, Alexandre last_name: Martinière - first_name: Irene full_name: Lavagi, Irene last_name: Lavagi - first_name: Gayathri full_name: Nageswaran, Gayathri last_name: Nageswaran - first_name: Daniel full_name: Rolfe, Daniel J last_name: Rolfe - first_name: Lilly full_name: Maneta-Peyret, Lilly last_name: Maneta Peyret - first_name: Doan full_name: Luu, Doan-Trung last_name: Luu - first_name: Stanley full_name: Botchway, Stanley W last_name: Botchway - first_name: Stephen full_name: Webb, Stephen E last_name: Webb - first_name: Sebastien full_name: Mongrand, Sebastien last_name: Mongrand - first_name: Christophe full_name: Maurel, Christophe last_name: Maurel - first_name: Marisa full_name: Martin-Fernandez, Marisa L last_name: Martin Fernandez - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Patrick full_name: Moreau, Patrick last_name: Moreau - first_name: John full_name: Runions, John last_name: Runions citation: ama: Martinière A, Lavagi I, Nageswaran G, et al. Cell wall constrains lateral diffusion of plant plasma membrane proteins. PNAS. 2012;109(31):12805-12810. doi:10.1073/pnas.1202040109 apa: Martinière, A., Lavagi, I., Nageswaran, G., Rolfe, D., Maneta Peyret, L., Luu, D., … Runions, J. (2012). Cell wall constrains lateral diffusion of plant plasma membrane proteins. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1202040109 chicago: Martinière, Alexandre, Irene Lavagi, Gayathri Nageswaran, Daniel Rolfe, Lilly Maneta Peyret, Doan Luu, Stanley Botchway, et al. “Cell Wall Constrains Lateral Diffusion of Plant Plasma Membrane Proteins.” PNAS. National Academy of Sciences, 2012. https://doi.org/10.1073/pnas.1202040109. ieee: A. Martinière et al., “Cell wall constrains lateral diffusion of plant plasma membrane proteins,” PNAS, vol. 109, no. 31. National Academy of Sciences, pp. 12805–12810, 2012. ista: Martinière A, Lavagi I, Nageswaran G, Rolfe D, Maneta Peyret L, Luu D, Botchway S, Webb S, Mongrand S, Maurel C, Martin Fernandez M, Kleine Vehn J, Friml J, Moreau P, Runions J. 2012. Cell wall constrains lateral diffusion of plant plasma membrane proteins. PNAS. 109(31), 12805–12810. mla: Martinière, Alexandre, et al. “Cell Wall Constrains Lateral Diffusion of Plant Plasma Membrane Proteins.” PNAS, vol. 109, no. 31, National Academy of Sciences, 2012, pp. 12805–10, doi:10.1073/pnas.1202040109. short: A. Martinière, I. Lavagi, G. Nageswaran, D. Rolfe, L. Maneta Peyret, D. Luu, S. Botchway, S. Webb, S. Mongrand, C. Maurel, M. Martin Fernandez, J. Kleine Vehn, J. Friml, P. Moreau, J. Runions, PNAS 109 (2012) 12805–12810. date_created: 2018-12-11T12:01:28Z date_published: 2012-07-31T00:00:00Z date_updated: 2021-01-12T07:41:09Z day: '31' doi: 10.1073/pnas.1202040109 extern: 1 intvolume: ' 109' issue: '31' month: '07' page: 12805 - 12810 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3586' quality_controlled: 0 status: public title: Cell wall constrains lateral diffusion of plant plasma membrane proteins type: journal_article volume: 109 year: '2012' ... --- _id: '3114' abstract: - lang: eng text: Auxin is a key coordinative signal required for many aspects of plant development and its levels are controlled by auxin metabolism and intercellular auxin transport. Here we find that a member of PIN auxin transporter family, PIN8 is expressed in male gametophyte of Arabidopsis thaliana and has a crucial role in pollen development and functionality. Ectopic expression in sporophytic tissues establishes a role of PIN8 in regulating auxin homoeostasis and metabolism. PIN8 co-localizes with PIN5 to the endoplasmic reticulum (ER) where it acts as an auxin transporter. Genetic analyses reveal an antagonistic action of PIN5 and PIN8 in the regulation of intracellular auxin homoeostasis and gametophyte as well as sporophyte development. Our results reveal a role of the auxin transport in male gametophyte development in which the distinct actions of ER-localized PIN transporters regulate cellular auxin homoeostasis and maintain the auxin levels optimal for pollen development and pollen tube growth. author: - first_name: Zhaojun full_name: Ding, Zhaojun last_name: Ding - first_name: Bangjun full_name: Wang, Bangjun last_name: Wang - first_name: Ignacio full_name: Moreno, Ignacio last_name: Moreno - first_name: Nikoleta full_name: Dupláková, Nikoleta last_name: Dupláková - first_name: Sibu full_name: Sibu Simon id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Nicola full_name: Carraro, Nicola last_name: Carraro - first_name: Jesica full_name: Reemmer, Jesica last_name: Reemmer - first_name: Aleš full_name: Pěnčík, Aleš last_name: Pěnčík - first_name: Xu full_name: Xu Chen id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Ricardo full_name: Tejos, Ricardo I last_name: Tejos - first_name: Petr full_name: Skůpa, Petr last_name: Skůpa - first_name: Stephan full_name: Pollmann, Stephan last_name: Pollmann - first_name: Jozef full_name: Mravec, Jozef last_name: Mravec - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: David full_name: Honys, David last_name: Honys - first_name: Jakub full_name: Rolčík, Jakub last_name: Rolčík - first_name: Angus full_name: Murphy, Angus S last_name: Murphy - first_name: Ariel full_name: Orellana, Ariel last_name: Orellana - first_name: Markus full_name: Geisler, Markus last_name: Geisler - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Ding Z, Wang B, Moreno I, et al. ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. Nature Communications. 2012;3(AN 941). doi:10.1038/ncomms1941 apa: Ding, Z., Wang, B., Moreno, I., Dupláková, N., Simon, S., Carraro, N., … Friml, J. (2012). ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms1941 chicago: Ding, Zhaojun, Bangjun Wang, Ignacio Moreno, Nikoleta Dupláková, Sibu Simon, Nicola Carraro, Jesica Reemmer, et al. “ER-Localized Auxin Transporter PIN8 Regulates Auxin Homeostasis and Male Gametophyte Development in Arabidopsis.” Nature Communications. Nature Publishing Group, 2012. https://doi.org/10.1038/ncomms1941. ieee: Z. Ding et al., “ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis,” Nature Communications, vol. 3, no. AN 941. Nature Publishing Group, 2012. ista: Ding Z, Wang B, Moreno I, Dupláková N, Simon S, Carraro N, Reemmer J, Pěnčík A, Chen X, Tejos R, Skůpa P, Pollmann S, Mravec J, Petrášek J, Zažímalová E, Honys D, Rolčík J, Murphy A, Orellana A, Geisler M, Friml J. 2012. ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. Nature Communications. 3(AN 941). mla: Ding, Zhaojun, et al. “ER-Localized Auxin Transporter PIN8 Regulates Auxin Homeostasis and Male Gametophyte Development in Arabidopsis.” Nature Communications, vol. 3, no. AN 941, Nature Publishing Group, 2012, doi:10.1038/ncomms1941. short: Z. Ding, B. Wang, I. Moreno, N. Dupláková, S. Simon, N. Carraro, J. Reemmer, A. Pěnčík, X. Chen, R. Tejos, P. Skůpa, S. Pollmann, J. Mravec, J. Petrášek, E. Zažímalová, D. Honys, J. Rolčík, A. Murphy, A. Orellana, M. Geisler, J. Friml, Nature Communications 3 (2012). date_created: 2018-12-11T12:01:28Z date_published: 2012-07-03T00:00:00Z date_updated: 2021-01-12T07:41:09Z day: '03' doi: 10.1038/ncomms1941 extern: 1 intvolume: ' 3' issue: AN 941 month: '07' publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '3585' quality_controlled: 0 status: public title: ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis type: journal_article volume: 3 year: '2012' ... --- _id: '3111' abstract: - lang: eng text: PIN-FORMED (PIN) protein-mediated auxin polar transport is critically important for development, pattern formation, and morphogenesis in plants. Auxin has been implicated in the regulation of polar auxin transport by inhibiting PIN endocytosis [1, 2], but how auxin regulates this process is poorly understood. Our genetic screen identified the Arabidopsis SPIKE1 (SPK1) gene whose loss-of-function mutations increased lateral root density and retarded gravitropic responses, as do pin2 knockout mutations [3]. SPK1 belongs to the conserved DHR2-Dock family of Rho guanine nucleotide exchange factors [4-6]. The spk1 mutations induced PIN2 internalization that was not suppressed by auxin, as did the loss-of-function mutations for Rho-like GTPase from Plants 6 (ROP6)-GTPase or its effector RIC1. Furthermore, SPK1 was required for auxin induction of ROP6 activation. Our results have established a Rho GTPase-based auxin signaling pathway that maintains PIN2 polar distribution to the plasma membrane via inhibition of its internalization in Arabidopsis roots. Our findings provide new insights into signaling mechanisms that underlie the regulation of the dynamic trafficking of PINs required for long-distance auxin transport and that link auxin signaling to PIN-mediated pattern formation and morphogenesis. author: - first_name: Deshu full_name: Lin, Deshu last_name: Lin - first_name: Shingo full_name: Nagawa, Shingo last_name: Nagawa - first_name: Jisheng full_name: Chen, Jisheng last_name: Chen - first_name: Lingyan full_name: Cao, Lingyan last_name: Cao - first_name: Xu full_name: Xu Chen id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Tongda full_name: Xu, Tongda last_name: Xu - first_name: Hongjiang full_name: Hongjiang Li id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Pankaj full_name: Dhonukshe, Pankaj last_name: Dhonukshe - first_name: Chizuko full_name: Yamamuro, Chizuko last_name: Yamamuro - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Ben full_name: Scheres, Ben last_name: Scheres - first_name: Ying full_name: Fu, Ying last_name: Fu - first_name: Zhenbiao full_name: Yang, Zhenbiao last_name: Yang citation: ama: Lin D, Nagawa S, Chen J, et al. A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. Current Biology. 2012;22(14):1319-1325. doi:10.1016/j.cub.2012.05.019 apa: Lin, D., Nagawa, S., Chen, J., Cao, L., Chen, X., Xu, T., … Yang, Z. (2012). A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2012.05.019 chicago: Lin, Deshu, Shingo Nagawa, Jisheng Chen, Lingyan Cao, Xu Chen, Tongda Xu, Hongjiang Li, et al. “A ROP GTPase Dependent Auxin Signaling Pathway Regulates the Subcellular Distribution of PIN2 in Arabidopsis Roots.” Current Biology. Cell Press, 2012. https://doi.org/10.1016/j.cub.2012.05.019. ieee: D. Lin et al., “A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots,” Current Biology, vol. 22, no. 14. Cell Press, pp. 1319–1325, 2012. ista: Lin D, Nagawa S, Chen J, Cao L, Chen X, Xu T, Li H, Dhonukshe P, Yamamuro C, Friml J, Scheres B, Fu Y, Yang Z. 2012. A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. Current Biology. 22(14), 1319–1325. mla: Lin, Deshu, et al. “A ROP GTPase Dependent Auxin Signaling Pathway Regulates the Subcellular Distribution of PIN2 in Arabidopsis Roots.” Current Biology, vol. 22, no. 14, Cell Press, 2012, pp. 1319–25, doi:10.1016/j.cub.2012.05.019. short: D. Lin, S. Nagawa, J. Chen, L. Cao, X. Chen, T. Xu, H. Li, P. Dhonukshe, C. Yamamuro, J. Friml, B. Scheres, Y. Fu, Z. Yang, Current Biology 22 (2012) 1319–1325. date_created: 2018-12-11T12:01:27Z date_published: 2012-07-24T00:00:00Z date_updated: 2021-01-12T07:41:08Z day: '24' doi: 10.1016/j.cub.2012.05.019 extern: 1 intvolume: ' 22' issue: '14' month: '07' page: 1319 - 1325 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '3588' quality_controlled: 0 status: public title: A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots type: journal_article volume: 22 year: '2012' ... --- _id: '3112' abstract: - lang: eng text: The dynamic spatial and temporal distribution of the crucial plant signaling molecule auxin is achieved by feedback coordination of auxin signaling and intercellular auxin transport pathways [1, 2]. Developmental roles of auxin have been attributed predominantly to its effect on transcription; however, an alternative pathway involving AUXIN BINDING PROTEIN1 (ABP1) has been proposed to regulate clathrin-mediated endocytosis in roots and Rho-like GTPase (ROP)-dependent pavement cell interdigitation in leaves [3, 4]. In this study, we show that ROP6 and its downstream effector RIC1 regulate clathrin association with the plasma membrane for clathrin-mediated endocytosis, as well as for its feedback regulation by auxin. Genetic analysis revealed that ROP6/RIC1 acts downstream of ABP1 to regulate endocytosis. This signaling circuit is also involved in the feedback regulation of PIN-FORMED 1 (PIN1) and PIN2 auxin transporters activity (via its constitutive endocytosis) and corresponding auxin transport-mediated processes, including root gravitropism and leave vascular tissue patterning. Our findings suggest that the signaling module auxin-ABP1-ROP6/RIC1-clathrin-PIN1/PIN2 is a shared component of the feedback regulation of auxin transport during both root and aerial development. author: - first_name: Xu full_name: Xu Chen id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Satoshi full_name: Naramoto, Satoshi last_name: Naramoto - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Christian full_name: Löfke, Christian last_name: Löfke - first_name: Deshu full_name: Lin, Deshu last_name: Lin - first_name: Zhenbiao full_name: Yang, Zhenbiao last_name: Yang - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Chen X, Naramoto S, Robert S, et al. ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots. Current Biology. 2012;22(14):1326-1332. doi:10.1016/j.cub.2012.05.020 apa: Chen, X., Naramoto, S., Robert, S., Tejos, R., Löfke, C., Lin, D., … Friml, J. (2012). ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2012.05.020 chicago: Chen, Xu, Satoshi Naramoto, Stéphanie Robert, Ricardo Tejos, Christian Löfke, Deshu Lin, Zhenbiao Yang, and Jiří Friml. “ABP1 and ROP6 GTPase Signaling Regulate Clathrin Mediated Endocytosis in Arabidopsis Roots.” Current Biology. Cell Press, 2012. https://doi.org/10.1016/j.cub.2012.05.020. ieee: X. Chen et al., “ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots,” Current Biology, vol. 22, no. 14. Cell Press, pp. 1326–1332, 2012. ista: Chen X, Naramoto S, Robert S, Tejos R, Löfke C, Lin D, Yang Z, Friml J. 2012. ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots. Current Biology. 22(14), 1326–1332. mla: Chen, Xu, et al. “ABP1 and ROP6 GTPase Signaling Regulate Clathrin Mediated Endocytosis in Arabidopsis Roots.” Current Biology, vol. 22, no. 14, Cell Press, 2012, pp. 1326–32, doi:10.1016/j.cub.2012.05.020. short: X. Chen, S. Naramoto, S. Robert, R. Tejos, C. Löfke, D. Lin, Z. Yang, J. Friml, Current Biology 22 (2012) 1326–1332. date_created: 2018-12-11T12:01:27Z date_published: 2012-07-24T00:00:00Z date_updated: 2021-01-12T07:41:08Z day: '24' doi: 10.1016/j.cub.2012.05.020 extern: 1 intvolume: ' 22' issue: '14' month: '07' page: 1326 - 1332 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '3587' quality_controlled: 0 status: public title: ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots type: journal_article volume: 22 year: '2012' ... --- _id: '3128' abstract: - lang: eng text: 'We consider two-player zero-sum stochastic games on graphs with ω-regular winning conditions specified as parity objectives. These games have applications in the design and control of reactive systems. We survey the complexity results for the problem of deciding the winner in such games, and in classes of interest obtained as special cases, based on the information and the power of randomization available to the players, on the class of objectives and on the winning mode. On the basis of information, these games can be classified as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided partial-observation (one player has partial-observation and the other player has complete-observation); and (c) complete-observation (both players have complete view of the game). The one-sided partial-observation games have two important subclasses: the one-player games, known as partial-observation Markov decision processes (POMDPs), and the blind one-player games, known as probabilistic automata. On the basis of randomization, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization. Finally, various classes of games are obtained by restricting the parity objective to a reachability, safety, Büchi, or coBüchi condition. We also consider several winning modes, such as sure-winning (i.e., all outcomes of a strategy have to satisfy the winning condition), almost-sure winning (i.e., winning with probability 1), limit-sure winning (i.e., winning with probability arbitrarily close to 1), and value-threshold winning (i.e., winning with probability at least ν, where ν is a given rational). ' acknowledgement: 'The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification, FWF NFN Grant No. S11407-N23(RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, ERC Advanced grant QUAREM, and FWF Grant No. S11403-N23 (RiSE).' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: Chatterjee K, Doyen L, Henzinger TA. A survey of partial-observation stochastic parity games. Formal Methods in System Design. 2012;43(2):268-284. doi:10.1007/s10703-012-0164-2 apa: Chatterjee, K., Doyen, L., & Henzinger, T. A. (2012). A survey of partial-observation stochastic parity games. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-012-0164-2 chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “A Survey of Partial-Observation Stochastic Parity Games.” Formal Methods in System Design. Springer, 2012. https://doi.org/10.1007/s10703-012-0164-2. ieee: K. Chatterjee, L. Doyen, and T. A. Henzinger, “A survey of partial-observation stochastic parity games,” Formal Methods in System Design, vol. 43, no. 2. Springer, pp. 268–284, 2012. ista: Chatterjee K, Doyen L, Henzinger TA. 2012. A survey of partial-observation stochastic parity games. Formal Methods in System Design. 43(2), 268–284. mla: Chatterjee, Krishnendu, et al. “A Survey of Partial-Observation Stochastic Parity Games.” Formal Methods in System Design, vol. 43, no. 2, Springer, 2012, pp. 268–84, doi:10.1007/s10703-012-0164-2. short: K. Chatterjee, L. Doyen, T.A. Henzinger, Formal Methods in System Design 43 (2012) 268–284. date_created: 2018-12-11T12:01:33Z date_published: 2012-10-01T00:00:00Z date_updated: 2021-01-12T07:41:15Z day: '01' ddc: - '005' department: - _id: KrCh - _id: ToHe doi: 10.1007/s10703-012-0164-2 ec_funded: 1 file: - access_level: open_access checksum: dd3d590f383bb2ac6cfda1489ac1c42a content_type: application/pdf creator: system date_created: 2018-12-12T10:11:27Z date_updated: 2020-07-14T12:46:00Z file_id: '4882' file_name: IST-2014-303-v1+1_Survey_Partial-Observation_Stochastic_Parity_Games.pdf file_size: 163983 relation: main_file file_date_updated: 2020-07-14T12:46:00Z has_accepted_license: '1' intvolume: ' 43' issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 268 - 284 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Formal Methods in System Design publication_status: published publisher: Springer publist_id: '3570' pubrep_id: '303' quality_controlled: '1' scopus_import: 1 status: public title: A survey of partial-observation stochastic parity games type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2012' ... --- _id: '3125' abstract: - lang: eng text: We propose a new learning method to infer a mid-level feature representation that combines the advantage of semantic attribute representations with the higher expressive power of non-semantic features. The idea lies in augmenting an existing attribute-based representation with additional dimensions for which an autoencoder model is coupled with a large-margin principle. This construction allows a smooth transition between the zero-shot regime with no training example, the unsupervised regime with training examples but without class labels, and the supervised regime with training examples and with class labels. The resulting optimization problem can be solved efficiently, because several of the necessity steps have closed-form solutions. Through extensive experiments we show that the augmented representation achieves better results in terms of object categorization accuracy than the semantic representation alone. alternative_title: - LNCS article_processing_charge: No author: - first_name: Viktoriia full_name: Sharmanska, Viktoriia id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87 last_name: Sharmanska orcid: 0000-0003-0192-9308 - first_name: Novi full_name: Quadrianto, Novi last_name: Quadrianto - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Sharmanska V, Quadrianto N, Lampert C. Augmented attribute representations. In: Vol 7576. Springer; 2012:242-255. doi:10.1007/978-3-642-33715-4_18' apa: 'Sharmanska, V., Quadrianto, N., & Lampert, C. (2012). Augmented attribute representations (Vol. 7576, pp. 242–255). Presented at the ECCV: European Conference on Computer Vision, Florence, Italy: Springer. https://doi.org/10.1007/978-3-642-33715-4_18' chicago: Sharmanska, Viktoriia, Novi Quadrianto, and Christoph Lampert. “Augmented Attribute Representations,” 7576:242–55. Springer, 2012. https://doi.org/10.1007/978-3-642-33715-4_18. ieee: 'V. Sharmanska, N. Quadrianto, and C. Lampert, “Augmented attribute representations,” presented at the ECCV: European Conference on Computer Vision, Florence, Italy, 2012, vol. 7576, no. PART 5, pp. 242–255.' ista: 'Sharmanska V, Quadrianto N, Lampert C. 2012. Augmented attribute representations. ECCV: European Conference on Computer Vision, LNCS, vol. 7576, 242–255.' mla: Sharmanska, Viktoriia, et al. Augmented Attribute Representations. Vol. 7576, no. PART 5, Springer, 2012, pp. 242–55, doi:10.1007/978-3-642-33715-4_18. short: V. Sharmanska, N. Quadrianto, C. Lampert, in:, Springer, 2012, pp. 242–255. conference: end_date: 2012-10-13 location: Florence, Italy name: 'ECCV: European Conference on Computer Vision' start_date: 2012-10-07 date_created: 2018-12-11T12:01:32Z date_published: 2012-10-01T00:00:00Z date_updated: 2023-02-23T11:13:25Z day: '01' ddc: - '000' department: - _id: ChLa doi: 10.1007/978-3-642-33715-4_18 file: - access_level: open_access checksum: bccdbe0663780d25a1e0524002b2d896 content_type: application/pdf creator: dernst date_created: 2020-05-15T12:29:04Z date_updated: 2020-07-14T12:46:00Z file_id: '7861' file_name: 2012_ECCV_Sharmanska.pdf file_size: 6073897 relation: main_file file_date_updated: 2020-07-14T12:46:00Z has_accepted_license: '1' intvolume: ' 7576' issue: PART 5 language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 242 - 255 publication_status: published publisher: Springer publist_id: '3574' quality_controlled: '1' scopus_import: 1 status: public title: Augmented attribute representations type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7576 year: '2012' ... --- _id: '3129' abstract: - lang: eng text: "Let K be a simplicial complex and g the rank of its p-th homology group Hp(K) defined with ℤ2 coefficients. We show that we can compute a basis H of Hp(K) and annotate each p-simplex of K with a binary vector of length g with the following property: the annotations, summed over all p-simplices in any p-cycle z, provide the coordinate vector of the homology class [z] in the basis H. The basis and the annotations for all simplices can be computed in O(n ω ) time, where n is the size of K and ω < 2.376 is a quantity so that two n×n matrices can be multiplied in O(n ω ) time. The precomputed annotations permit answering queries about the independence or the triviality of p-cycles efficiently.\r\n\r\nUsing annotations of edges in 2-complexes, we derive better algorithms for computing optimal basis and optimal homologous cycles in 1 - dimensional homology. Specifically, for computing an optimal basis of H1(K) , we improve the previously known time complexity from O(n 4) to O(n ω  + n 2 g ω − 1). Here n denotes the size of the 2-skeleton of K and g the rank of H1(K) . Computing an optimal cycle homologous to a given 1-cycle is NP-hard even for surfaces and an algorithm taking 2 O(g) nlogn time is known for surfaces. We extend this algorithm to work with arbitrary 2-complexes in O(n ω ) + 2 O(g) n 2logn time using annotations.\r\n" alternative_title: - LNCS author: - first_name: Oleksiy full_name: Busaryev, Oleksiy last_name: Busaryev - first_name: Sergio full_name: Cabello, Sergio last_name: Cabello - first_name: Chao full_name: Chen, Chao id: 3E92416E-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Tamal full_name: Dey, Tamal last_name: Dey - first_name: Yusu full_name: Wang, Yusu last_name: Wang citation: ama: 'Busaryev O, Cabello S, Chen C, Dey T, Wang Y. Annotating simplices with a homology basis and its applications. In: Vol 7357. Springer; 2012:189-200. doi:10.1007/978-3-642-31155-0_17' apa: 'Busaryev, O., Cabello, S., Chen, C., Dey, T., & Wang, Y. (2012). Annotating simplices with a homology basis and its applications (Vol. 7357, pp. 189–200). Presented at the SWAT: Symposium and Workshops on Algorithm Theory, Helsinki, Finland: Springer. https://doi.org/10.1007/978-3-642-31155-0_17' chicago: Busaryev, Oleksiy, Sergio Cabello, Chao Chen, Tamal Dey, and Yusu Wang. “Annotating Simplices with a Homology Basis and Its Applications,” 7357:189–200. Springer, 2012. https://doi.org/10.1007/978-3-642-31155-0_17. ieee: 'O. Busaryev, S. Cabello, C. Chen, T. Dey, and Y. Wang, “Annotating simplices with a homology basis and its applications,” presented at the SWAT: Symposium and Workshops on Algorithm Theory, Helsinki, Finland, 2012, vol. 7357, pp. 189–200.' ista: 'Busaryev O, Cabello S, Chen C, Dey T, Wang Y. 2012. Annotating simplices with a homology basis and its applications. SWAT: Symposium and Workshops on Algorithm Theory, LNCS, vol. 7357, 189–200.' mla: Busaryev, Oleksiy, et al. Annotating Simplices with a Homology Basis and Its Applications. Vol. 7357, Springer, 2012, pp. 189–200, doi:10.1007/978-3-642-31155-0_17. short: O. Busaryev, S. Cabello, C. Chen, T. Dey, Y. Wang, in:, Springer, 2012, pp. 189–200. conference: end_date: 2012-07-06 location: Helsinki, Finland name: 'SWAT: Symposium and Workshops on Algorithm Theory' start_date: 2012-07-04 date_created: 2018-12-11T12:01:33Z date_published: 2012-06-19T00:00:00Z date_updated: 2021-01-12T07:41:15Z day: '19' department: - _id: HeEd doi: 10.1007/978-3-642-31155-0_17 external_id: arxiv: - '1107.3793' intvolume: ' 7357' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1107.3793 month: '06' oa: 1 oa_version: Preprint page: 189 - 200 publication_status: published publisher: Springer publist_id: '3569' quality_controlled: '1' scopus_import: 1 status: public title: Annotating simplices with a homology basis and its applications type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7357 year: '2012' ... --- _id: '3126' abstract: - lang: eng text: "In this work we propose a new information-theoretic clustering algorithm that infers cluster memberships by direct optimization of a non-parametric mutual information estimate between data distribution and cluster assignment. Although the optimization objective has a solid theoretical foundation it is hard to optimize. We propose an approximate optimization formulation that leads to an efficient algorithm with low runtime complexity. The algorithm has a single free parameter, the number of clusters to find. We demonstrate superior performance on several synthetic and real datasets.\r\n" alternative_title: - LNCS author: - first_name: Andreas full_name: Müller, Andreas last_name: Müller - first_name: Sebastian full_name: Nowozin, Sebastian last_name: Nowozin - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Müller A, Nowozin S, Lampert C. Information theoretic clustering using minimal spanning trees. In: Vol 7476. Springer; 2012:205-215. doi:10.1007/978-3-642-32717-9_21' apa: 'Müller, A., Nowozin, S., & Lampert, C. (2012). Information theoretic clustering using minimal spanning trees (Vol. 7476, pp. 205–215). Presented at the DAGM: German Association For Pattern Recognition, Graz, Austria: Springer. https://doi.org/10.1007/978-3-642-32717-9_21' chicago: Müller, Andreas, Sebastian Nowozin, and Christoph Lampert. “Information Theoretic Clustering Using Minimal Spanning Trees,” 7476:205–15. Springer, 2012. https://doi.org/10.1007/978-3-642-32717-9_21. ieee: 'A. Müller, S. Nowozin, and C. Lampert, “Information theoretic clustering using minimal spanning trees,” presented at the DAGM: German Association For Pattern Recognition, Graz, Austria, 2012, vol. 7476, pp. 205–215.' ista: 'Müller A, Nowozin S, Lampert C. 2012. Information theoretic clustering using minimal spanning trees. DAGM: German Association For Pattern Recognition, LNCS, vol. 7476, 205–215.' mla: Müller, Andreas, et al. Information Theoretic Clustering Using Minimal Spanning Trees. Vol. 7476, Springer, 2012, pp. 205–15, doi:10.1007/978-3-642-32717-9_21. short: A. Müller, S. Nowozin, C. Lampert, in:, Springer, 2012, pp. 205–215. conference: end_date: 2012-08-31 location: Graz, Austria name: 'DAGM: German Association For Pattern Recognition' start_date: 2012-08-28 date_created: 2018-12-11T12:01:32Z date_published: 2012-08-14T00:00:00Z date_updated: 2021-01-12T07:41:14Z day: '14' department: - _id: ChLa doi: 10.1007/978-3-642-32717-9_21 intvolume: ' 7476' language: - iso: eng month: '08' oa_version: None page: 205 - 215 publication_status: published publisher: Springer publist_id: '3573' quality_controlled: '1' scopus_import: 1 status: public title: Information theoretic clustering using minimal spanning trees type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7476 year: '2012' ... --- _id: '3155' abstract: - lang: eng text: 'We propose synchronous interfaces, a new interface theory for discrete-time systems. We use an application to time-triggered scheduling to drive the design choices for our formalism; in particular, additionally to deriving useful mathematical properties, we focus on providing a syntax which is adapted to natural high-level system modeling. As a result, we develop an interface model that relies on a guarded-command based language and is equipped with shared variables and explicit discrete-time clocks. We define all standard interface operations: compatibility checking, composition, refinement, and shared refinement. Apart from the synchronous interface model, the contribution of this paper is the establishment of a formal relation between interface theories and real-time scheduling, where we demonstrate a fully automatic framework for the incremental computation of time-triggered schedules.' acknowledgement: Research partially supported by the Danish-Chinese Center for Cyber Physical Systems (Grant No.61061130541) and VKR Center of Excellence MT-LAB. alternative_title: - LNCS author: - first_name: Benoît full_name: Delahaye, Benoît last_name: Delahaye - first_name: Uli full_name: Fahrenberg, Uli last_name: Fahrenberg - 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: Axel full_name: Legay, Axel last_name: Legay - first_name: Dejan full_name: Nickovic, Dejan id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic citation: ama: 'Delahaye B, Fahrenberg U, Henzinger TA, Legay A, Nickovic D. Synchronous interface theories and time triggered scheduling. In: Vol 7273. Springer; 2012:203-218. doi:10.1007/978-3-642-30793-5_13' apa: 'Delahaye, B., Fahrenberg, U., Henzinger, T. A., Legay, A., & Nickovic, D. (2012). Synchronous interface theories and time triggered scheduling (Vol. 7273, pp. 203–218). Presented at the FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed Systems , Stockholm, Sweden: Springer. https://doi.org/10.1007/978-3-642-30793-5_13' chicago: Delahaye, Benoît, Uli Fahrenberg, Thomas A Henzinger, Axel Legay, and Dejan Nickovic. “Synchronous Interface Theories and Time Triggered Scheduling,” 7273:203–18. Springer, 2012. https://doi.org/10.1007/978-3-642-30793-5_13. ieee: 'B. Delahaye, U. Fahrenberg, T. A. Henzinger, A. Legay, and D. Nickovic, “Synchronous interface theories and time triggered scheduling,” presented at the FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed Systems , Stockholm, Sweden, 2012, vol. 7273, pp. 203–218.' ista: 'Delahaye B, Fahrenberg U, Henzinger TA, Legay A, Nickovic D. 2012. Synchronous interface theories and time triggered scheduling. FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed Systems , LNCS, vol. 7273, 203–218.' mla: Delahaye, Benoît, et al. Synchronous Interface Theories and Time Triggered Scheduling. Vol. 7273, Springer, 2012, pp. 203–18, doi:10.1007/978-3-642-30793-5_13. short: B. Delahaye, U. Fahrenberg, T.A. Henzinger, A. Legay, D. Nickovic, in:, Springer, 2012, pp. 203–218. conference: end_date: 2012-06-16 location: Stockholm, Sweden name: 'FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed Systems ' start_date: 2012-06-13 date_created: 2018-12-11T12:01:43Z date_published: 2012-06-01T00:00:00Z date_updated: 2021-01-12T07:41:26Z day: '01' ddc: - '004' department: - _id: ToHe doi: 10.1007/978-3-642-30793-5_13 file: - access_level: open_access checksum: feae2e07f2d9a59843f8ddabf25d179f content_type: application/pdf creator: system date_created: 2018-12-12T10:11:25Z date_updated: 2020-07-14T12:46:01Z file_id: '4879' file_name: IST-2012-88-v1+1_Synchronous_interface_theories_and_time_triggered_scheduling.pdf file_size: 493198 relation: main_file file_date_updated: 2020-07-14T12:46:01Z has_accepted_license: '1' intvolume: ' 7273' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 203 - 218 publication_status: published publisher: Springer publist_id: '3539' pubrep_id: '88' quality_controlled: '1' scopus_import: 1 status: public title: Synchronous interface theories and time triggered scheduling type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7273 year: '2012' ... --- _id: '3159' abstract: - lang: eng text: The structure of hierarchical networks in biological and physical systems has long been characterized using the Horton-Strahler ordering scheme. The scheme assigns an integer order to each edge in the network based on the topology of branching such that the order increases from distal parts of the network (e.g., mountain streams or capillaries) to the "root" of the network (e.g., the river outlet or the aorta). However, Horton-Strahler ordering cannot be applied to networks with loops because they they create a contradiction in the edge ordering in terms of which edge precedes another in the hierarchy. Here, we present a generalization of the Horton-Strahler order to weighted planar reticular networks, where weights are assumed to correlate with the importance of network edges, e.g., weights estimated from edge widths may correlate to flow capacity. Our method assigns hierarchical levels not only to edges of the network, but also to its loops, and classifies the edges into reticular edges, which are responsible for loop formation, and tree edges. In addition, we perform a detailed and rigorous theoretical analysis of the sensitivity of the hierarchical levels to weight perturbations. In doing so, we show that the ordering of the reticular edges is more robust to noise in weight estimation than is the ordering of the tree edges. We discuss applications of this generalized Horton-Strahler ordering to the study of leaf venation and other biological networks. acknowledgement: "his work was supported by the National Science Foundation Plant Genome Research Program (grant 0820624 to H.E. and J.S.W.), the Defense Advanced Projects Research Agency (grant HR0011-09-1-0055 to H.E. and J.S.W.), and the European Science Foundation (under the Research Networking Programme on “Applied and Computational Algebraic Topology” run by H.E.). Joshua S. Weitz, Ph.D., holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund.\r\n\r\n\r\n\r\nDuring preparation of this manuscript the authors became aware of a related work by Katifori and Magnasco (arXiv:1110.1412v1), concurrently submitted and accepted for publication in PLoS ONE." article_number: e36715 author: - first_name: Yuriy full_name: Mileyko, Yuriy last_name: Mileyko - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Charles full_name: Price, Charles last_name: Price - first_name: Joshua full_name: Weitz, Joshua last_name: Weitz citation: ama: Mileyko Y, Edelsbrunner H, Price C, Weitz J. Hierarchical ordering of reticular networks. PLoS One. 2012;7(6). doi:10.1371/journal.pone.0036715 apa: Mileyko, Y., Edelsbrunner, H., Price, C., & Weitz, J. (2012). Hierarchical ordering of reticular networks. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0036715 chicago: Mileyko, Yuriy, Herbert Edelsbrunner, Charles Price, and Joshua Weitz. “Hierarchical Ordering of Reticular Networks.” PLoS One. Public Library of Science, 2012. https://doi.org/10.1371/journal.pone.0036715. ieee: Y. Mileyko, H. Edelsbrunner, C. Price, and J. Weitz, “Hierarchical ordering of reticular networks,” PLoS One, vol. 7, no. 6. Public Library of Science, 2012. ista: Mileyko Y, Edelsbrunner H, Price C, Weitz J. 2012. Hierarchical ordering of reticular networks. PLoS One. 7(6), e36715. mla: Mileyko, Yuriy, et al. “Hierarchical Ordering of Reticular Networks.” PLoS One, vol. 7, no. 6, e36715, Public Library of Science, 2012, doi:10.1371/journal.pone.0036715. short: Y. Mileyko, H. Edelsbrunner, C. Price, J. Weitz, PLoS One 7 (2012). date_created: 2018-12-11T12:01:44Z date_published: 2012-06-06T00:00:00Z date_updated: 2021-01-12T07:41:28Z day: '06' ddc: - '510' department: - _id: HeEd doi: 10.1371/journal.pone.0036715 file: - access_level: open_access checksum: 515a98ad72e470752f03f13663dcaff8 content_type: application/pdf creator: kschuh date_created: 2019-02-05T12:38:43Z date_updated: 2020-07-14T12:46:01Z file_id: '5922' file_name: 2012_PLoS_Mileyko.PDF file_size: 541583 relation: main_file file_date_updated: 2020-07-14T12:46:01Z has_accepted_license: '1' intvolume: ' 7' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '3530' pubrep_id: '385' quality_controlled: '1' scopus_import: 1 status: public title: Hierarchical ordering of reticular networks 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: 7 year: '2012' ... --- _id: '3156' abstract: - lang: eng text: Dispersal is crucial for gene flow and often determines the long-term stability of meta-populations, particularly in rare species with specialized life cycles. Such species are often foci of conservation efforts because they suffer disproportionally from degradation and fragmentation of their habitat. However, detailed knowledge of effective gene flow through dispersal is often missing, so that conservation strategies have to be based on mark-recapture observations that are suspected to be poor predictors of long-distance dispersal. These constraints have been especially severe in the study of butterfly populations, where microsatellite markers have been difficult to develop. We used eight microsatellite markers to analyse genetic population structure of the Large Blue butterfly Maculinea arion in Sweden. During recent decades, this species has become an icon of insect conservation after massive decline throughout Europe and extinction in Britain followed by reintroduction of a seed population from the Swedish island of Öland. We find that populations are highly structured genetically, but that gene flow occurs over distances 15 times longer than the maximum distance recorded from mark-recapture studies, which can only be explained by maximum dispersal distances at least twice as large as previously accepted. However, we also find evidence that gaps between sites with suitable habitat exceeding ∼ 20 km induce genetic erosion that can be detected from bottleneck analyses. Although further work is needed, our results suggest that M. arion can maintain fully functional metapopulations when they consist of optimal habitat patches that are no further apart than ∼10 km. acknowledgement: "The work was financed by the Danish National Science Research Foundation via a grant to the Centre for Social Evolution.\r\nWe thank four anonymous reviewers for useful comments on the manuscript, J. Bergsten, P. Bina, B. Carlsson, M. Johannesson and A.E. Lomborg for providing additional wingtip samples, A. Illum for assistance in the field, and in particular P.S. Nielsen for mediating the contact to the collectors and the Swedish authorities. Collection was made possible through a permit by the Åtgärdsprogrammet, supported by the Swedish Environmental Protection Agency." author: - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Anne full_name: Andersen, Anne last_name: Andersen - first_name: Jacobus full_name: Boomsma, Jacobus last_name: Boomsma - first_name: David full_name: Nash, David last_name: Nash citation: ama: Ugelvig LV, Andersen A, Boomsma J, Nash D. Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. 2012;21(13):3224-3236. doi:10.1111/j.1365-294X.2012.05592.x apa: Ugelvig, L. V., Andersen, A., Boomsma, J., & Nash, D. (2012). Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05592.x chicago: Ugelvig, Line V, Anne Andersen, Jacobus Boomsma, and David Nash. “Dispersal and Gene Flow in the Rare Parasitic Large Blue Butterfly Maculinea Arion.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05592.x. ieee: L. V. Ugelvig, A. Andersen, J. Boomsma, and D. Nash, “Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion,” Molecular Ecology, vol. 21, no. 13. Wiley-Blackwell, pp. 3224–3236, 2012. ista: Ugelvig LV, Andersen A, Boomsma J, Nash D. 2012. Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. 21(13), 3224–3236. mla: Ugelvig, Line V., et al. “Dispersal and Gene Flow in the Rare Parasitic Large Blue Butterfly Maculinea Arion.” Molecular Ecology, vol. 21, no. 13, Wiley-Blackwell, 2012, pp. 3224–36, doi:10.1111/j.1365-294X.2012.05592.x. short: L.V. Ugelvig, A. Andersen, J. Boomsma, D. Nash, Molecular Ecology 21 (2012) 3224–3236. date_created: 2018-12-11T12:01:43Z date_published: 2012-07-01T00:00:00Z date_updated: 2021-01-12T07:41:27Z day: '01' department: - _id: SyCr doi: 10.1111/j.1365-294X.2012.05592.x intvolume: ' 21' issue: '13' language: - iso: eng month: '07' oa_version: None page: 3224 - 3236 publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3538' quality_controlled: '1' scopus_import: 1 status: public title: Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2012' ... --- _id: '3158' abstract: - lang: eng text: We describe here the development and characterization of a conditionally inducible mouse model expressing Lifeact-GFP, a peptide that reports the dynamics of filamentous actin. We have used this model to study platelets, megakaryocytes and melanoblasts and we provide evidence that Lifeact-GFP is a useful reporter in these cell types ex vivo. In the case of platelets and megakaryocytes, these cells are not transfectable by traditional methods, so conditional activation of Lifeact allows the study of actin dynamics in these cells live. We studied melanoblasts in native skin explants from embryos, allowing the visualization of live actin dynamics during cytokinesis and migration. Our study revealed that melanoblasts lacking the small GTPase Rac1 show a delay in the formation of new pseudopodia following cytokinesis that accounts for the previously reported cytokinesis delay in these cells. Thus, through use of this mouse model, we were able to gain insights into the actin dynamics of cells that could only previously be studied using fixed specimens or following isolation from their native tissue environment. author: - first_name: Hannah full_name: Schachtner, Hannah last_name: Schachtner - first_name: Ang full_name: Li, Ang last_name: Li - first_name: David full_name: Stevenson, David last_name: Stevenson - first_name: Simon full_name: Calaminus, Simon last_name: Calaminus - first_name: Steven full_name: Thomas, Steven last_name: Thomas - first_name: Steve full_name: Watson, Steve last_name: Watson - 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: Roland full_name: Wedlich Söldner, Roland last_name: Wedlich Söldner - first_name: Douglas full_name: Strathdee, Douglas last_name: Strathdee - first_name: Laura full_name: Machesky, Laura last_name: Machesky citation: ama: Schachtner H, Li A, Stevenson D, et al. Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. European Journal of Cell Biology. 2012;91(11-12):923-929. doi:10.1016/j.ejcb.2012.04.002 apa: Schachtner, H., Li, A., Stevenson, D., Calaminus, S., Thomas, S., Watson, S., … Machesky, L. (2012). Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2012.04.002 chicago: Schachtner, Hannah, Ang Li, David Stevenson, Simon Calaminus, Steven Thomas, Steve Watson, Michael K Sixt, Roland Wedlich Söldner, Douglas Strathdee, and Laura Machesky. “Tissue Inducible Lifeact Expression Allows Visualization of Actin Dynamics in Vivo and Ex Vivo.” European Journal of Cell Biology. Elsevier, 2012. https://doi.org/10.1016/j.ejcb.2012.04.002. ieee: H. Schachtner et al., “Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo,” European Journal of Cell Biology, vol. 91, no. 11–12. Elsevier, pp. 923–929, 2012. ista: Schachtner H, Li A, Stevenson D, Calaminus S, Thomas S, Watson S, Sixt MK, Wedlich Söldner R, Strathdee D, Machesky L. 2012. Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. European Journal of Cell Biology. 91(11–12), 923–929. mla: Schachtner, Hannah, et al. “Tissue Inducible Lifeact Expression Allows Visualization of Actin Dynamics in Vivo and Ex Vivo.” European Journal of Cell Biology, vol. 91, no. 11–12, Elsevier, 2012, pp. 923–29, doi:10.1016/j.ejcb.2012.04.002. short: H. Schachtner, A. Li, D. Stevenson, S. Calaminus, S. Thomas, S. Watson, M.K. Sixt, R. Wedlich Söldner, D. Strathdee, L. Machesky, European Journal of Cell Biology 91 (2012) 923–929. date_created: 2018-12-11T12:01:44Z date_published: 2012-11-01T00:00:00Z date_updated: 2021-01-12T07:41:27Z day: '01' department: - _id: MiSi doi: 10.1016/j.ejcb.2012.04.002 external_id: pmid: - '22658956' intvolume: ' 91' issue: 11-12 language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930012/ month: '11' oa: 1 oa_version: Submitted Version page: 923 - 929 pmid: 1 publication: European Journal of Cell Biology publication_status: published publisher: Elsevier publist_id: '3534' quality_controlled: '1' scopus_import: 1 status: public title: Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 91 year: '2012' ... --- _id: '3248' abstract: - lang: eng text: We describe RTblob, a high speed vision system that detects objects in cluttered scenes based on their color and shape at a speed of over 800 frames/s. Because the system is available as open-source software and relies only on off-the-shelf PC hardware components, it can provide the basis for multiple application scenarios. As an illustrative example, we show how RTblob can be used in a robotic table tennis scenario to estimate ball trajectories through 3D space simultaneously from four cameras images at a speed of 200 Hz. article_processing_charge: No article_type: original author: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Jan full_name: Peters, Jan last_name: Peters citation: ama: Lampert C, Peters J. Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. Journal of Real-Time Image Processing. 2012;7(1):31-41. doi:10.1007/s11554-010-0168-3 apa: Lampert, C., & Peters, J. (2012). Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. Journal of Real-Time Image Processing. Springer. https://doi.org/10.1007/s11554-010-0168-3 chicago: Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects in Multiple Camera Streams with off-the-Shelf Hardware Components.” Journal of Real-Time Image Processing. Springer, 2012. https://doi.org/10.1007/s11554-010-0168-3. ieee: C. Lampert and J. Peters, “Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components,” Journal of Real-Time Image Processing, vol. 7, no. 1. Springer, pp. 31–41, 2012. ista: Lampert C, Peters J. 2012. Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. Journal of Real-Time Image Processing. 7(1), 31–41. mla: Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects in Multiple Camera Streams with off-the-Shelf Hardware Components.” Journal of Real-Time Image Processing, vol. 7, no. 1, Springer, 2012, pp. 31–41, doi:10.1007/s11554-010-0168-3. short: C. Lampert, J. Peters, Journal of Real-Time Image Processing 7 (2012) 31–41. date_created: 2018-12-11T12:02:15Z date_published: 2012-03-01T00:00:00Z date_updated: 2022-05-24T08:05:40Z day: '01' ddc: - '000' department: - _id: ChLa doi: 10.1007/s11554-010-0168-3 file: - access_level: open_access checksum: 241be47ea50e81a283bcf4c45b07e8cc content_type: application/pdf creator: kschuh date_created: 2019-02-12T10:52:25Z date_updated: 2020-07-14T12:46:04Z file_id: '5958' file_name: 2012_Springer_Lampert.pdf file_size: 2933187 relation: main_file file_date_updated: 2020-07-14T12:46:04Z has_accepted_license: '1' intvolume: ' 7' issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 31 - 41 publication: Journal of Real-Time Image Processing publication_identifier: eissn: - 1861-8219 issn: - 1861-8200 publication_status: published publisher: Springer publist_id: '3417' quality_controlled: '1' scopus_import: '1' status: public title: Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2012' ... --- _id: '3247' abstract: - lang: eng text: The Brazilian Merganser is a very rare and threatened species that nowadays inhabits only a few protected areas and their surroundings in the Brazilian territory. In order to estimate the remaining genetic diversity and population structure in this species, two mitochondrial genes were sequenced in 39 individuals belonging to two populations and in one individual collected in Argentina in 1950. We found a highly significant divergence between two major remaining populations of Mergus octosetaceus, which suggests a historical population structure in this species. Furthermore, two deeply divergent lineages were found in a single location, which could due to current or historical secondary contact. Based on the available genetic data, we point out future directions which would contribute to design strategies for conservation and management of this threatened species. acknowledgement: "The present study received grants from FAPEMIG, CNPq, Petrobras Ambiental and Fundação O Boticário de Conservação da Natureza, and followed all ethical guidelines and legal requirements of Brazil for sampling and studying an endangered species.\r\nWe thank the Specialist Work Group for the Conservation of Brazilian Merganser for valuable discussions and opinions on this manuscript. We also thank all the staff from Instituto Terra Brasilis and Funatura (Vivian S. Braz and Gislaine Disconzi) for collecting the samples at Serra da Canastra and Chapada dos Veadeiros, respectively; Dario A. Lijtmaerand and Pablo Tubaro for providing the samples from Argentina, Bradley C. Livezey for sending copies of his papers, and Geoff M. Hilton and Paulo de Tarso Z. Antas for useful suggestions that greatly improved this manuscript." author: - first_name: Sibelle full_name: Vilaça, Sibelle last_name: Vilaça - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Lívia full_name: Lins, Lívia last_name: Lins - first_name: Fabrício full_name: Santos, Fabrício last_name: Santos citation: ama: Vilaça S, Fernandes Redondo RA, Lins L, Santos F. Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. 2012;13(1):293-298. doi:10.1007/s10592-011-0262-5 apa: Vilaça, S., Fernandes Redondo, R. A., Lins, L., & Santos, F. (2012). Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. Springer. https://doi.org/10.1007/s10592-011-0262-5 chicago: Vilaça, Sibelle, Rodrigo A Fernandes Redondo, Lívia Lins, and Fabrício Santos. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” Conservation Genetics. Springer, 2012. https://doi.org/10.1007/s10592-011-0262-5. ieee: S. Vilaça, R. A. Fernandes Redondo, L. Lins, and F. Santos, “Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus),” Conservation Genetics, vol. 13, no. 1. Springer, pp. 293–298, 2012. ista: Vilaça S, Fernandes Redondo RA, Lins L, Santos F. 2012. Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. 13(1), 293–298. mla: Vilaça, Sibelle, et al. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” Conservation Genetics, vol. 13, no. 1, Springer, 2012, pp. 293–98, doi:10.1007/s10592-011-0262-5. short: S. Vilaça, R.A. Fernandes Redondo, L. Lins, F. Santos, Conservation Genetics 13 (2012) 293–298. date_created: 2018-12-11T12:02:15Z date_published: 2012-02-01T00:00:00Z date_updated: 2021-01-12T07:42:05Z day: '01' department: - _id: JoBo doi: 10.1007/s10592-011-0262-5 intvolume: ' 13' issue: '1' language: - iso: eng month: '02' oa_version: None page: 293 - 298 publication: Conservation Genetics publication_status: published publisher: Springer publist_id: '3420' quality_controlled: '1' scopus_import: 1 status: public title: Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2012' ... --- _id: '3245' abstract: - lang: eng text: How cells orchestrate their behavior during collective migration is a long-standing question. Using magnetic tweezers to apply mechanical stimuli to Xenopus mesendoderm cells, Weber etal. (2012) now reveal, in this issue of Developmental Cell, a cadherin-mediated mechanosensitive response that promotes cell polarization and movement persistence during the collective mesendoderm migration in gastrulation. author: - first_name: Martin full_name: Behrndt, Martin id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87 last_name: Behrndt - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Behrndt M, Heisenberg C-PJ. Spurred by resistance mechanosensation in collective migration. Developmental Cell. 2012;22(1):3-4. doi:10.1016/j.devcel.2011.12.018 apa: Behrndt, M., & Heisenberg, C.-P. J. (2012). Spurred by resistance mechanosensation in collective migration. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2011.12.018 chicago: Behrndt, Martin, and Carl-Philipp J Heisenberg. “Spurred by Resistance Mechanosensation in Collective Migration.” Developmental Cell. Cell Press, 2012. https://doi.org/10.1016/j.devcel.2011.12.018. ieee: M. Behrndt and C.-P. J. Heisenberg, “Spurred by resistance mechanosensation in collective migration,” Developmental Cell, vol. 22, no. 1. Cell Press, pp. 3–4, 2012. ista: Behrndt M, Heisenberg C-PJ. 2012. Spurred by resistance mechanosensation in collective migration. Developmental Cell. 22(1), 3–4. mla: Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Spurred by Resistance Mechanosensation in Collective Migration.” Developmental Cell, vol. 22, no. 1, Cell Press, 2012, pp. 3–4, doi:10.1016/j.devcel.2011.12.018. short: M. Behrndt, C.-P.J. Heisenberg, Developmental Cell 22 (2012) 3–4. date_created: 2018-12-11T12:02:14Z date_published: 2012-01-17T00:00:00Z date_updated: 2021-01-12T07:42:05Z day: '17' department: - _id: CaHe doi: 10.1016/j.devcel.2011.12.018 intvolume: ' 22' issue: '1' language: - iso: eng month: '01' oa_version: None page: 3 - 4 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '3426' quality_controlled: '1' scopus_import: 1 status: public title: Spurred by resistance mechanosensation in collective migration type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2012' ... --- _id: '3262' abstract: - lang: eng text: Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of nearby genes. But the expression of transcription factor proteins is itself regulated, and many transcription factors regulate their own expression in addition to responding to other input signals. Here we analyze the simplest of such self-regulatory circuits, asking how parameters can be chosen to optimize information transmission from inputs to outputs in the steady state. Some nonzero level of self-regulation is almost always optimal, with self-activation dominant when transcription factor concentrations are low and self-repression dominant when concentrations are high. In steady state the optimal self-activation is never strong enough to induce bistability, although there is a limit in which the optimal parameters are very close to the critical point. acknowledgement: "We thank T. Gregor, E. F. Wieschaus, and, especially, C. G. Callan for helpful discussions.\r\nWork at Princeton was supported in part by NSF Grants No. PHY–0957573 and No. CCF–0939370, by NIH Grant No. R01 GM077599, and by the W. M. Keck Foundation. For part of this work, G.T. was supported in part by NSF Grant No. EF–0928048 and by the Vice Provost for Research at the University of Pennsylvania." article_number: '041903' author: - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Aleksandra full_name: Walczak, Aleksandra last_name: Walczak - first_name: William full_name: Bialek, William last_name: Bialek citation: ama: Tkačik G, Walczak A, Bialek W. Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E statistical nonlinear and soft matter physics . 2012;85(4). doi:10.1103/PhysRevE.85.041903 apa: Tkačik, G., Walczak, A., & Bialek, W. (2012). Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.85.041903 chicago: Tkačik, Gašper, Aleksandra Walczak, and William Bialek. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2012. https://doi.org/10.1103/PhysRevE.85.041903. ieee: G. Tkačik, A. Walczak, and W. Bialek, “Optimizing information flow in small genetic networks. III. A self-interacting gene,” Physical Review E statistical nonlinear and soft matter physics , vol. 85, no. 4. American Institute of Physics, 2012. ista: Tkačik G, Walczak A, Bialek W. 2012. Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E statistical nonlinear and soft matter physics . 85(4), 041903. mla: Tkačik, Gašper, et al. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 85, no. 4, 041903, American Institute of Physics, 2012, doi:10.1103/PhysRevE.85.041903. short: G. Tkačik, A. Walczak, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 85 (2012). date_created: 2018-12-11T12:02:20Z date_published: 2012-04-01T00:00:00Z date_updated: 2021-01-12T07:42:14Z day: '01' department: - _id: GaTk doi: 10.1103/PhysRevE.85.041903 intvolume: ' 85' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1112.5026 month: '04' oa: 1 oa_version: Preprint publication: ' Physical Review E statistical nonlinear and soft matter physics ' publication_status: published publisher: American Institute of Physics publist_id: '3386' quality_controlled: '1' scopus_import: 1 status: public title: Optimizing information flow in small genetic networks. III. A self-interacting gene type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 85 year: '2012' ... --- _id: '3257' abstract: - lang: eng text: Consider a convex relaxation f̂ of a pseudo-Boolean function f. We say that the relaxation is totally half-integral if f̂(x) is a polyhedral function with half-integral extreme points x, and this property is preserved after adding an arbitrary combination of constraints of the form x i=x j, x i=1-x j, and x i=γ where γ∈{0,1,1/2} is a constant. A well-known example is the roof duality relaxation for quadratic pseudo-Boolean functions f. We argue that total half-integrality is a natural requirement for generalizations of roof duality to arbitrary pseudo-Boolean functions. Our contributions are as follows. First, we provide a complete characterization of totally half-integral relaxations f̂ by establishing a one-to-one correspondence with bisubmodular functions. Second, we give a new characterization of bisubmodular functions. Finally, we show some relationships between general totally half-integral relaxations and relaxations based on the roof duality. On the conceptual level, our results show that bisubmodular functions provide a natural generalization of the roof duality approach to higher-order terms. This can be viewed as a non-submodular analogue of the fact that submodular functions generalize the s-t minimum cut problem with non-negative weights to higher-order terms. author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Kolmogorov V. Generalized roof duality and bisubmodular functions. Discrete Applied Mathematics. 2012;160(4-5):416-426. doi:10.1016/j.dam.2011.10.026 apa: Kolmogorov, V. (2012). Generalized roof duality and bisubmodular functions. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2011.10.026 chicago: Kolmogorov, Vladimir. “Generalized Roof Duality and Bisubmodular Functions.” Discrete Applied Mathematics. Elsevier, 2012. https://doi.org/10.1016/j.dam.2011.10.026. ieee: V. Kolmogorov, “Generalized roof duality and bisubmodular functions,” Discrete Applied Mathematics, vol. 160, no. 4–5. Elsevier, pp. 416–426, 2012. ista: Kolmogorov V. 2012. Generalized roof duality and bisubmodular functions. Discrete Applied Mathematics. 160(4–5), 416–426. mla: Kolmogorov, Vladimir. “Generalized Roof Duality and Bisubmodular Functions.” Discrete Applied Mathematics, vol. 160, no. 4–5, Elsevier, 2012, pp. 416–26, doi:10.1016/j.dam.2011.10.026. short: V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 416–426. date_created: 2018-12-11T12:02:18Z date_published: 2012-03-01T00:00:00Z date_updated: 2023-02-23T11:04:49Z day: '01' department: - _id: VlKo doi: 10.1016/j.dam.2011.10.026 external_id: arxiv: - '1005.2305' intvolume: ' 160' issue: 4-5 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1005.2305 month: '03' oa: 1 oa_version: Preprint page: 416 - 426 publication: Discrete Applied Mathematics publication_status: published publisher: Elsevier publist_id: '3397' quality_controlled: '1' related_material: record: - id: '2934' relation: earlier_version status: public scopus_import: 1 status: public title: Generalized roof duality and bisubmodular functions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 160 year: '2012' ... --- _id: '3277' abstract: - lang: eng text: The problem of the origin of metazoa is becoming more urgent in the context of astrobiology. By now it is clear that clues to the understanding of this crucial transition in the evolution of life can arise in a fourth pathway besides the three possibilities in the quest for simplicity outlined by Bonner in his classical book. In other words, solar system exploration seems to be one way in the long-term to elucidate the simplicity of evolutionary development. We place these ideas in the context of different inheritance systems, namely the genotypic and phenotypic replicators with limited or unlimited heredity, and ask which of these can support multicellular development, and to which degree of complexity. However, the quest for evidence on the evolution of biotas from planets around other stars does not seem to be feasible with present technology with direct visualization of living organisms on exoplanets. But this may be attempted on the Galilean moons of Jupiter where there is a possibility of detecting reliable biomarkers in the next decade with the Europa Jupiter System Mission, in view of recent progress by landing micropenetrators on planetary, or satellite surfaces. Mars is a second possibility in the inner Solar System, in spite of the multiple difficulties faced by the fleet of past, present and future missions. We discuss a series of preliminary ideas for elucidating the origin of metazoan analogues with available instrumentation in potential payloads of feasible space missions to the Galilean moons. alternative_title: - Cellular Origin, Life in Extreme Habitats and Astrobiology author: - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 - first_name: Julian full_name: Chela Flores, Julian last_name: Chela Flores citation: ama: 'de Vladar H, Chela Flores J. Can the evolution of multicellularity be anticipated in the exploration of the solar system? In: Life on Earth and Other Planetary Bodies. Vol 24. Springer; 2012:387-405. doi:10.1007/978-94-007-4966-5_22' apa: de Vladar, H., & Chela Flores, J. (2012). Can the evolution of multicellularity be anticipated in the exploration of the solar system? In Life on Earth and other planetary bodies (Vol. 24, pp. 387–405). Springer. https://doi.org/10.1007/978-94-007-4966-5_22 chicago: Vladar, Harold de, and Julian Chela Flores. “Can the Evolution of Multicellularity Be Anticipated in the Exploration of the Solar System?” In Life on Earth and Other Planetary Bodies, 24:387–405. Springer, 2012. https://doi.org/10.1007/978-94-007-4966-5_22. ieee: H. de Vladar and J. Chela Flores, “Can the evolution of multicellularity be anticipated in the exploration of the solar system?,” in Life on Earth and other planetary bodies, vol. 24, Springer, 2012, pp. 387–405. ista: 'de Vladar H, Chela Flores J. 2012.Can the evolution of multicellularity be anticipated in the exploration of the solar system? In: Life on Earth and other planetary bodies. Cellular Origin, Life in Extreme Habitats and Astrobiology, vol. 24, 387–405.' mla: de Vladar, Harold, and Julian Chela Flores. “Can the Evolution of Multicellularity Be Anticipated in the Exploration of the Solar System?” Life on Earth and Other Planetary Bodies, vol. 24, Springer, 2012, pp. 387–405, doi:10.1007/978-94-007-4966-5_22. short: H. de Vladar, J. Chela Flores, in:, Life on Earth and Other Planetary Bodies, Springer, 2012, pp. 387–405. date_created: 2018-12-11T12:02:25Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T07:42:20Z day: '01' department: - _id: NiBa doi: 10.1007/978-94-007-4966-5_22 intvolume: ' 24' language: - iso: eng month: '01' oa_version: None page: 387 - 405 publication: Life on Earth and other planetary bodies publication_status: published publisher: Springer publist_id: '3369' quality_controlled: '1' status: public title: Can the evolution of multicellularity be anticipated in the exploration of the solar system? type: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2012' ... --- _id: '3279' abstract: - lang: eng text: "We show a hardness-preserving construction of a PRF from any length doubling PRG which improves upon known constructions whenever we can put a non-trivial upper bound q on the number of queries to the PRF. Our construction requires only O(logq) invocations to the underlying PRG with each query. In comparison, the number of invocations by the best previous hardness-preserving construction (GGM using Levin's trick) is logarithmic in the hardness of the PRG. For example, starting from an exponentially secure PRG {0,1} n → {0,1} 2n, we get a PRF which is exponentially secure if queried at most q = exp(√n)times and where each invocation of the PRF requires Θ(√n) queries to the underlying PRG. This is much less than the Θ(n) required by known constructions. \r\n" acknowledgement: Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC) alternative_title: - LNCS author: - first_name: Abhishek full_name: Jain, Abhishek last_name: Jain - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Aris full_name: Tentes, Aris last_name: Tentes citation: ama: 'Jain A, Pietrzak KZ, Tentes A. Hardness preserving constructions of pseudorandom functions. In: Vol 7194. Springer; 2012:369-382. doi:10.1007/978-3-642-28914-9_21' apa: 'Jain, A., Pietrzak, K. Z., & Tentes, A. (2012). Hardness preserving constructions of pseudorandom functions (Vol. 7194, pp. 369–382). Presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy: Springer. https://doi.org/10.1007/978-3-642-28914-9_21' chicago: Jain, Abhishek, Krzysztof Z Pietrzak, and Aris Tentes. “Hardness Preserving Constructions of Pseudorandom Functions,” 7194:369–82. Springer, 2012. https://doi.org/10.1007/978-3-642-28914-9_21. ieee: 'A. Jain, K. Z. Pietrzak, and A. Tentes, “Hardness preserving constructions of pseudorandom functions,” presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy, 2012, vol. 7194, pp. 369–382.' ista: 'Jain A, Pietrzak KZ, Tentes A. 2012. Hardness preserving constructions of pseudorandom functions. TCC: Theory of Cryptography Conference, LNCS, vol. 7194, 369–382.' mla: Jain, Abhishek, et al. Hardness Preserving Constructions of Pseudorandom Functions. Vol. 7194, Springer, 2012, pp. 369–82, doi:10.1007/978-3-642-28914-9_21. short: A. Jain, K.Z. Pietrzak, A. Tentes, in:, Springer, 2012, pp. 369–382. conference: end_date: 2012-03-21 location: Taormina, Sicily, Italy name: 'TCC: Theory of Cryptography Conference' start_date: 2012-03-19 date_created: 2018-12-11T12:02:25Z date_published: 2012-05-04T00:00:00Z date_updated: 2021-01-12T07:42:21Z day: '04' department: - _id: KrPi doi: 10.1007/978-3-642-28914-9_21 ec_funded: 1 intvolume: ' 7194' language: - iso: eng main_file_link: - url: http://www.iacr.org/archive/tcc2012/tcc2012-index.html month: '05' oa_version: None page: 369 - 382 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '3367' quality_controlled: '1' scopus_import: 1 status: public title: Hardness preserving constructions of pseudorandom functions type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7194 year: '2012' ... --- _id: '3274' abstract: - lang: eng text: A boundary element model of a tunnel running through horizontally layered soil with anisotropic material properties is presented. Since there is no analytical fundamental solution for wave propagation inside a layered orthotropic medium in 3D, the fundamental displacements and stresses have to be calculated numerically. In our model this is done in the Fourier domain with respect to space and time. The assumption of a straight tunnel with infinite extension in the x direction makes it possible to decouple the system for every wave number kx, leading to a 2.5D-problem, which is suited for parallel computation. The special form of the fundamental solution, resulting from our Fourier ansatz, and the fact, that the calculation of the boundary integral equation is performed in the Fourier domain, enhances the stability and efficiency of the numerical calculations. acknowledgement: This work was supported by the Austrian Federal Ministry of Transport, Innovation and Technology under the Grant Bmvit-isb2 and the FFG under the project Pr. Nr. 809089. author: - first_name: Georg full_name: Rieckh, Georg id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87 last_name: Rieckh - first_name: Wolfgang full_name: Kreuzer, Wolfgang last_name: Kreuzer - first_name: Holger full_name: Waubke, Holger last_name: Waubke - first_name: Peter full_name: Balazs, Peter last_name: Balazs citation: ama: Rieckh G, Kreuzer W, Waubke H, Balazs P. A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil. Engineering Analysis with Boundary Elements. 2012;36(6):960-967. doi:10.1016/j.enganabound.2011.12.014 apa: Rieckh, G., Kreuzer, W., Waubke, H., & Balazs, P. (2012). A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil. Engineering Analysis with Boundary Elements. Elsevier. https://doi.org/10.1016/j.enganabound.2011.12.014 chicago: Rieckh, Georg, Wolfgang Kreuzer, Holger Waubke, and Peter Balazs. “A 2.5D-Fourier-BEM Model for Vibrations in a Tunnel Running through Layered Anisotropic Soil.” Engineering Analysis with Boundary Elements. Elsevier, 2012. https://doi.org/10.1016/j.enganabound.2011.12.014. ieee: G. Rieckh, W. Kreuzer, H. Waubke, and P. Balazs, “A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil,” Engineering Analysis with Boundary Elements, vol. 36, no. 6. Elsevier, pp. 960–967, 2012. ista: Rieckh G, Kreuzer W, Waubke H, Balazs P. 2012. A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil. Engineering Analysis with Boundary Elements. 36(6), 960–967. mla: Rieckh, Georg, et al. “A 2.5D-Fourier-BEM Model for Vibrations in a Tunnel Running through Layered Anisotropic Soil.” Engineering Analysis with Boundary Elements, vol. 36, no. 6, Elsevier, 2012, pp. 960–67, doi:10.1016/j.enganabound.2011.12.014. short: G. Rieckh, W. Kreuzer, H. Waubke, P. Balazs, Engineering Analysis with Boundary Elements 36 (2012) 960–967. date_created: 2018-12-11T12:02:24Z date_published: 2012-06-01T00:00:00Z date_updated: 2021-01-12T07:42:19Z day: '01' department: - _id: GaTk doi: 10.1016/j.enganabound.2011.12.014 intvolume: ' 36' issue: '6' language: - iso: eng month: '06' oa_version: None page: 960 - 967 publication: ' Engineering Analysis with Boundary Elements' publication_status: published publisher: Elsevier publist_id: '3372' quality_controlled: '1' scopus_import: 1 status: public title: A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2012' ... --- _id: '3289' abstract: - lang: eng text: "Viral manipulation of transduction pathways associated with key cellular functions such as survival, response to microbial infection, and cytoskeleton reorganization can provide the supportive milieu for a productive infection. Here, we demonstrate that vaccinia virus (VACV) infection leads to activation of the stress-activated protein kinase (SAPK)/extracellular signal-regulated kinase (ERK) 4/7 (MKK4/7)-c-Jun N-terminal protein kinase 1/2 (JNK1/2) pathway; further, the stimulation of this pathway requires postpenetration, prereplicative events in the viral replication cycle. Although the formation of intracellular mature virus (IMV) was not affected in MKK4/7- or JNK1/2-knockout (KO) cells, we did note an accentuated deregulation of microtubule and actin network organization in infected JNK1/2-KO cells. This was followed by deregulated viral trafficking to the periphery and enhanced enveloped particle release. Furthermore, VACV infection induced alterations in the cell contractility and morphology, and cell migration was reduced in the JNK-KO cells. In addition, phosphorylation of proteins implicated with early cell contractility and cell migration, such as microtubule-associated protein 1B and paxillin, respectively, was not detected in the VACV-infected KO cells. In sum, our findings uncover a regulatory role played by the MKK4/7-JNK1/2 pathway in cytoskeleton reorganization during VACV infection.\r\n" acknowledgement: "This work was supported by grants from Fundação de Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG), the Brazilian Federal Agency for Support and Evaluation of Graduate Education (CAPES), and the National Council for Scientific and Technological Development (CNPq). A.C.T.C.P., B.S.A.F.B., F.G.G.L., and J.A.P.S.-M. were recipients of predoctoral fellowships from CNPq. C.A.B., E.G.K., T.S.-P., P.F.P.P., and P.C.P.F. are recipients of research fellowships from CNPq. \r\n\r\n\r\nWe are grateful to Angela S. Lopes, Ilda M. V. Gama, João R. dos Santos, and Andreza A. Carvalho for their secretarial/technical assistance and to Fernanda Gambogi for help with immunofluorescence microscopy. We also thank M. C. Sogayar (Department of Biochemistry, University of São Paulo, São Paulo, Brazil), who kindly provided us with the A31 cell line, and R. Davis (Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA) for the WT and JNK1/2-, MKK4-, MKK7-, and MKK4/7-KO cells. VACV WR was from C. Jungwirth (Universität Würzburg, Würzburg, Germany). The recombinant VACV vF13L-GFP and the rabbit polyclonal antibodies against viral proteins, B5R, D8L, L1R, and A36R, were from B. Moss (NIAID, Bethesda, MD). The pcDNA3-Myc-JNK2-MKK7 WT plasmid was from Eugen Kerkhoff (Universität Würzburg, Würzburg, Germany). We also thank Flávio G. da Fonseca (UFMG, Belo Horizonte, MG, Brazil) and Kathleen A. Boyle (Medical College of Wisconsin, Milwaukee, WI) for critically reading the manuscript." author: - first_name: Anna full_name: Pereira, Anna last_name: Pereira - first_name: Flávia full_name: Leite, Flávia id: 36705F98-F248-11E8-B48F-1D18A9856A87 last_name: Leite - first_name: Bruno full_name: Brasil, Bruno last_name: Brasil - first_name: Jamaria full_name: Soares Martins, Jamaria last_name: Soares Martins - first_name: Alice full_name: Torres, Alice last_name: Torres - first_name: Paulo full_name: Pimenta, Paulo last_name: Pimenta - first_name: Thais full_name: Souto Padrón, Thais last_name: Souto Padrón - first_name: Paula full_name: Tranktman, Paula last_name: Tranktman - first_name: Paulo full_name: Ferreira, Paulo last_name: Ferreira - first_name: Erna full_name: Kroon, Erna last_name: Kroon - first_name: Cláudio full_name: Bonjardim, Cláudio last_name: Bonjardim citation: ama: Pereira A, Leite F, Brasil B, et al. A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization. Journal of Virology. 2012;86(1):172-184. doi:10.1128/JVI.05638-11 apa: Pereira, A., Leite, F., Brasil, B., Soares Martins, J., Torres, A., Pimenta, P., … Bonjardim, C. (2012). A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization. Journal of Virology. ASM. https://doi.org/10.1128/JVI.05638-11 chicago: Pereira, Anna, Flávia Leite, Bruno Brasil, Jamaria Soares Martins, Alice Torres, Paulo Pimenta, Thais Souto Padrón, et al. “A Vaccinia Virus-Driven Interplay between the MKK4/7-JNK1/2 Pathway and Cytoskeleton Reorganization.” Journal of Virology. ASM, 2012. https://doi.org/10.1128/JVI.05638-11. ieee: A. Pereira et al., “A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization,” Journal of Virology, vol. 86, no. 1. ASM, pp. 172–184, 2012. ista: Pereira A, Leite F, Brasil B, Soares Martins J, Torres A, Pimenta P, Souto Padrón T, Tranktman P, Ferreira P, Kroon E, Bonjardim C. 2012. A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization. Journal of Virology. 86(1), 172–184. mla: Pereira, Anna, et al. “A Vaccinia Virus-Driven Interplay between the MKK4/7-JNK1/2 Pathway and Cytoskeleton Reorganization.” Journal of Virology, vol. 86, no. 1, ASM, 2012, pp. 172–84, doi:10.1128/JVI.05638-11. short: A. Pereira, F. Leite, B. Brasil, J. Soares Martins, A. Torres, P. Pimenta, T. Souto Padrón, P. Tranktman, P. Ferreira, E. Kroon, C. Bonjardim, Journal of Virology 86 (2012) 172–184. date_created: 2018-12-11T12:02:29Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T07:42:25Z day: '01' department: - _id: JoBo doi: 10.1128/JVI.05638-11 external_id: pmid: - '22031940' intvolume: ' 86' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255887/ month: '01' oa: 1 oa_version: Submitted Version page: 172 - 184 pmid: 1 publication: Journal of Virology publication_status: published publisher: ASM publist_id: '3356' quality_controlled: '1' scopus_import: 1 status: public title: A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 86 year: '2012' ... --- _id: '3310' abstract: - lang: eng text: The theory of persistent homology opens up the possibility to reason about topological features of a space or a function quantitatively and in combinatorial terms. We refer to this new angle at a classical subject within algebraic topology as a point calculus, which we present for the family of interlevel sets of a real-valued function. Our account of the subject is expository, devoid of proofs, and written for non-experts in algebraic topology. acknowledgement: Research by the third author is partially supported by the National Science Foundation (NSF) under grant DBI-0820624. author: - first_name: Paul full_name: Bendich, Paul id: 43F6EC54-F248-11E8-B48F-1D18A9856A87 last_name: Bendich - first_name: Sergio full_name: Cabello, Sergio last_name: Cabello - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: Bendich P, Cabello S, Edelsbrunner H. A point calculus for interlevel set homology. Pattern Recognition Letters. 2012;33(11):1436-1444. doi:10.1016/j.patrec.2011.10.007 apa: Bendich, P., Cabello, S., & Edelsbrunner, H. (2012). A point calculus for interlevel set homology. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2011.10.007 chicago: Bendich, Paul, Sergio Cabello, and Herbert Edelsbrunner. “A Point Calculus for Interlevel Set Homology.” Pattern Recognition Letters. Elsevier, 2012. https://doi.org/10.1016/j.patrec.2011.10.007. ieee: P. Bendich, S. Cabello, and H. Edelsbrunner, “A point calculus for interlevel set homology,” Pattern Recognition Letters, vol. 33, no. 11. Elsevier, pp. 1436–1444, 2012. ista: Bendich P, Cabello S, Edelsbrunner H. 2012. A point calculus for interlevel set homology. Pattern Recognition Letters. 33(11), 1436–1444. mla: Bendich, Paul, et al. “A Point Calculus for Interlevel Set Homology.” Pattern Recognition Letters, vol. 33, no. 11, Elsevier, 2012, pp. 1436–44, doi:10.1016/j.patrec.2011.10.007. short: P. Bendich, S. Cabello, H. Edelsbrunner, Pattern Recognition Letters 33 (2012) 1436–1444. date_created: 2018-12-11T12:02:36Z date_published: 2012-08-01T00:00:00Z date_updated: 2021-01-12T07:42:34Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1016/j.patrec.2011.10.007 file: - access_level: open_access checksum: d65f79775b51258a604ca5ec741297cc content_type: application/pdf creator: system date_created: 2018-12-12T10:15:00Z date_updated: 2020-07-14T12:46:06Z file_id: '5116' file_name: IST-2016-542-v1+1_2012-J-01-Poinculus.pdf file_size: 280280 relation: main_file file_date_updated: 2020-07-14T12:46:06Z has_accepted_license: '1' intvolume: ' 33' issue: '11' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 1436 - 1444 publication: Pattern Recognition Letters publication_status: published publisher: Elsevier publist_id: '3330' pubrep_id: '542' quality_controlled: '1' scopus_import: 1 status: public title: A point calculus for interlevel set homology type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2012' ... --- _id: '338' abstract: - lang: eng text: The ample chemical and structural freedom of quaternary compounds permits engineering materials that fulfill the requirements of a wide variety of applications. In this work, the mechanisms to achieve unprecedented size, shape, and composition control in quaternary nanocrystals are detailed. The described procedure allows obtaining tetrahedral and penta-tetrahedral quaternary nanocrystals with tuned size distributions and controlled compositions from a plethora of I 2-II-IV-VI 4 semiconductors. acknowledgement: "This work was supported by the Spanish MICINN Projects MAT2008-05779, MAT2008-03400-E/MAT, MAT2010-15138, ENE2008-03277-E/CON, CSD2009-00050, and CSD2009-00013. M.I. thanks the Spanish MICINN for her Ph.D. grant. J.A. and R.Z. also acknowledge Generalitat de Catalunya 2009-SGR-770 and XaRMAE. A.C. is grateful for financial support through the Ramon y Cajal program of the Spanish MICINN.\r\n\r\n" article_processing_charge: No article_type: original author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Joan full_name: Morante, Joan last_name: Morante - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Ibáñez M, Zamani R, Li W, et al. Extending the nanocrystal synthesis control to quaternary compositions. Crystal Growth and Design . 2012;12(3):1085-1090. doi:10.1021/cg201709c apa: Ibáñez, M., Zamani, R., Li, W., Shavel, A., Arbiol, J., Morante, J., & Cabot, A. (2012). Extending the nanocrystal synthesis control to quaternary compositions. Crystal Growth and Design . American Chemical Society (ACS). https://doi.org/10.1021/cg201709c chicago: Ibáñez, Maria, Reza Zamani, Wenhua Li, Alexey Shavel, Jordi Arbiol, Joan Morante, and Andreu Cabot. “Extending the Nanocrystal Synthesis Control to Quaternary Compositions.” Crystal Growth and Design . American Chemical Society (ACS), 2012. https://doi.org/10.1021/cg201709c. ieee: M. Ibáñez et al., “Extending the nanocrystal synthesis control to quaternary compositions,” Crystal Growth and Design , vol. 12, no. 3. American Chemical Society (ACS), pp. 1085–1090, 2012. ista: Ibáñez M, Zamani R, Li W, Shavel A, Arbiol J, Morante J, Cabot A. 2012. Extending the nanocrystal synthesis control to quaternary compositions. Crystal Growth and Design . 12(3), 1085–1090. mla: Ibáñez, Maria, et al. “Extending the Nanocrystal Synthesis Control to Quaternary Compositions.” Crystal Growth and Design , vol. 12, no. 3, American Chemical Society (ACS), 2012, pp. 1085–90, doi:10.1021/cg201709c. short: M. Ibáñez, R. Zamani, W. Li, A. Shavel, J. Arbiol, J. Morante, A. Cabot, Crystal Growth and Design 12 (2012) 1085–1090. date_created: 2018-12-11T11:45:54Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T07:43:05Z day: '01' doi: 10.1021/cg201709c extern: '1' intvolume: ' 12' issue: '3' language: - iso: eng month: '01' oa_version: None page: 1085 - 1090 publication: 'Crystal Growth and Design ' publication_status: published publisher: American Chemical Society (ACS) publist_id: '7488' quality_controlled: '1' status: public title: Extending the nanocrystal synthesis control to quaternary compositions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2012' ... --- _id: '339' abstract: - lang: eng text: A high-yield and upscalable colloidal synthesis route for the production of quaternary I 2-II-IV-VI 4 nanocrystals, particularly stannite Cu 2+xCd 1-xSnSe 4, with narrow size distribution and precisely controlled composition is presented. It is also shown here how the diversity of valences in the constituent elements allows an effective control of their electrical conductivity through the adjustment of the cation ratios. At the same time, while the crystallographic complexity of quaternary chalcogenides is associated with intrinsically low thermal conductivities, the reduction of the lattice dimensions to the nanoscale further reduces the materials thermal conductivity. In the specific case of the stannite crystal structure, a convenient slab distribution of the valence band maximum states permits a partial decoupling of the p-type electrical conductivity from both the Seebeck coefficient and the thermal conductivity. Combining these features, we demonstrate how an initial optimization of the nanocrystals Cd/Cu ratio allowed us to obtain low-temperature solution-processed materials with ZT values up to 0.71 at 685 K. acknowledgement: This work was supported by the Spanish MICINN Projects MAT2008-05779, MAT2008-03400-E/MAT, MAT2010-15138, ENE2008-03277-E/CON, CSD2009-00050. and CSD2009-00013. M.I. and N.G.-C. thank the Spanish MICINN for the PhD grant. J.A. and R.Z. also acknowledge Generalitat de Catalunya 2009-SGR-770 and XaRMAE. A.C. is thankful for financial support through the Ramon y Cajal program of the Spanish MICINN. N.G.-C. and J.D.P. are thankful for the computer resources, technical expertise and assistance provided by the Barcelona Supercomputing Center - Centro Nacional de Supercomputación. article_processing_charge: No article_type: original author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Nuria full_name: García Castelló, Nuria last_name: García Castelló - first_name: Victora full_name: Izquierdo Roca, Victora last_name: Izquierdo Roca - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Andrew full_name: Fairbrother, Andrew last_name: Fairbrother - first_name: Joan full_name: Prades, Joan last_name: Prades - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Alejandro full_name: Pérez Rodríguez, Alejandro last_name: Pérez Rodríguez - first_name: Joan full_name: Morante, Joan last_name: Morante - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Ibáñez M, Cadavid D, Zamani R, et al. Composition control and thermoelectric properties of quaternary chalcogenide nanocrystals: The case of stannite Cu2CdSnSe4. Chemistry of Materials. 2012;24(3):562-570. doi:10.1021/cm2031812' apa: 'Ibáñez, M., Cadavid, D., Zamani, R., García Castelló, N., Izquierdo Roca, V., Li, W., … Cabot, A. (2012). Composition control and thermoelectric properties of quaternary chalcogenide nanocrystals: The case of stannite Cu2CdSnSe4. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/cm2031812' chicago: 'Ibáñez, Maria, Doris Cadavid, Reza Zamani, Nuria García Castelló, Victora Izquierdo Roca, Wenhua Li, Andrew Fairbrother, et al. “Composition Control and Thermoelectric Properties of Quaternary Chalcogenide Nanocrystals: The Case of Stannite Cu2CdSnSe4.” Chemistry of Materials. American Chemical Society, 2012. https://doi.org/10.1021/cm2031812.' ieee: 'M. Ibáñez et al., “Composition control and thermoelectric properties of quaternary chalcogenide nanocrystals: The case of stannite Cu2CdSnSe4,” Chemistry of Materials, vol. 24, no. 3. American Chemical Society, pp. 562–570, 2012.' ista: 'Ibáñez M, Cadavid D, Zamani R, García Castelló N, Izquierdo Roca V, Li W, Fairbrother A, Prades J, Shavel A, Arbiol J, Pérez Rodríguez A, Morante J, Cabot A. 2012. Composition control and thermoelectric properties of quaternary chalcogenide nanocrystals: The case of stannite Cu2CdSnSe4. Chemistry of Materials. 24(3), 562–570.' mla: 'Ibáñez, Maria, et al. “Composition Control and Thermoelectric Properties of Quaternary Chalcogenide Nanocrystals: The Case of Stannite Cu2CdSnSe4.” Chemistry of Materials, vol. 24, no. 3, American Chemical Society, 2012, pp. 562–70, doi:10.1021/cm2031812.' short: M. Ibáñez, D. Cadavid, R. Zamani, N. García Castelló, V. Izquierdo Roca, W. Li, A. Fairbrother, J. Prades, A. Shavel, J. Arbiol, A. Pérez Rodríguez, J. Morante, A. Cabot, Chemistry of Materials 24 (2012) 562–570. date_created: 2018-12-11T11:45:54Z date_published: 2012-01-31T00:00:00Z date_updated: 2021-01-12T07:43:09Z day: '31' doi: 10.1021/cm2031812 extern: '1' intvolume: ' 24' issue: '3' language: - iso: eng month: '01' oa_version: None page: 562 - 570 publication: Chemistry of Materials publication_status: published publisher: American Chemical Society publist_id: '7489' quality_controlled: '1' status: public title: 'Composition control and thermoelectric properties of quaternary chalcogenide nanocrystals: The case of stannite Cu2CdSnSe4' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2012' ... --- _id: '340' abstract: - lang: eng text: 'A procedure for the continuous production of Cu 2ZnSnS 4 (CZTS) nanoparticles with controlled composition is presented. CZTS nanoparticles were prepared through the reaction of the metals'' amino complexes with elemental sulfur in a continuous-flow reactor at moderate temperatures (300-330 °C). High-resolution transmission electron microscopy and X-ray diffraction analysis showed the nanocrystals to have a crystallographic structure compatible with that of the kesterite. Chemical characterization of the materials showed the presence of the four elements in each individual nanocrystal. Composition control was achieved by adjusting the solution flow rate through the reactor and the proper choice of the nominal precursor concentration within the flowing solution. Single-particle analysis revealed a composition distribution within each sample, which was optimized at the highest synthesis temperatures used. ' acknowledgement: This work was supported by the Spanish MICINN Projects MAT2008-05779, MAT2008-03400-E/MAT, CDS2009-00050, CSD2009-00013, and ENE2008-03277-E/CON. M.I. thanks the Spanish MICINN for her Ph.D. grant. A.C. is thankful for financial support through the Ramón y Cajal Program. article_processing_charge: No article_type: original author: - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Alex full_name: Carrete, Alex last_name: Carrete - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Shavel A, Cadavid D, Ibáñez M, Carrete A, Cabot A. Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. 2012;134(3):1438-1441. doi:10.1021/ja209688a apa: Shavel, A., Cadavid, D., Ibáñez, M., Carrete, A., & Cabot, A. (2012). Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja209688a chicago: Shavel, Alexey, Doris Cadavid, Maria Ibáñez, Alex Carrete, and Andreu Cabot. “Continuous Production of Cu Inf 2 Inf ZnSnS Inf 4 Inf Nanocrystals in a Flow Reactor.” Journal of the American Chemical Society. ACS, 2012. https://doi.org/10.1021/ja209688a. ieee: A. Shavel, D. Cadavid, M. Ibáñez, A. Carrete, and A. Cabot, “Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor,” Journal of the American Chemical Society, vol. 134, no. 3. ACS, pp. 1438–1441, 2012. ista: Shavel A, Cadavid D, Ibáñez M, Carrete A, Cabot A. 2012. Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. 134(3), 1438–1441. mla: Shavel, Alexey, et al. “Continuous Production of Cu Inf 2 Inf ZnSnS Inf 4 Inf Nanocrystals in a Flow Reactor.” Journal of the American Chemical Society, vol. 134, no. 3, ACS, 2012, pp. 1438–41, doi:10.1021/ja209688a. short: A. Shavel, D. Cadavid, M. Ibáñez, A. Carrete, A. Cabot, Journal of the American Chemical Society 134 (2012) 1438–1441. date_created: 2018-12-11T11:45:54Z date_published: 2012-01-02T00:00:00Z date_updated: 2021-01-12T07:43:13Z day: '02' doi: 10.1021/ja209688a extern: '1' intvolume: ' 134' issue: '3' language: - iso: eng month: '01' oa_version: None page: 1438 - 1441 publication: Journal of the American Chemical Society publication_status: published publisher: ACS publist_id: '7490' quality_controlled: '1' status: public title: Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2012' ... --- _id: '345' abstract: - lang: eng text: 'Nanocomposites are highly promising materials to enhance the efficiency of current thermoelectric devices. A straightforward and at the same time highly versatile and controllable approach to produce nanocomposites is the assembly of solution-processed nanocrystal building blocks. The convenience of this bottom-up approach to produce nanocomposites with homogeneous phase distributions and adjustable composition is demonstrated here by blending Ag2Te and PbTe colloidal nanocrystals to form Ag2Te–PbTe bulk nanocomposites. The thermoelectric properties of these nanocomposites are analyzed in the temperature range from 300 to 700 K. The evolution of their electrical conductivity and Seebeck coefficient is discussed in terms of the blend composition and the characteristics of the constituent materials. ' acknowledgement: Acknowledgments The research was supported by the European Regional Development Funds and the Spanish MICINN Projects MAT2008-05779, MAT2008-03400-E/MAT, MAT2010-15138, MAT2010-21510, CSD2009-00050, and ENE2008-03277-E/CON. M.I. is grateful to the Spanish MIC-INN for her PhD grant. A. Cirera acknowledges support from ICREA Academia program. A. Cabot is grateful to the Spanish MICINN for financial support through the Ramón y Cajal program. article_processing_charge: No article_type: original author: - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Stéphane full_name: Gorsse, Stéphane last_name: Gorsse - first_name: Antonio full_name: López, Antonio last_name: López - first_name: Albert full_name: Cirera, Albert last_name: Cirera - first_name: Joan full_name: Morante, Joan last_name: Morante - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Cadavid D, Ibáñez M, Gorsse S, et al. Bottom-up processing of thermoelectric nanocomposites from colloidal nanocrystal building blocks: The case of Ag2Te–PbTe. Journal of Nanoparticle Research. 2012;14(12). doi:10.1007/s11051-012-1328-0' apa: 'Cadavid, D., Ibáñez, M., Gorsse, S., López, A., Cirera, A., Morante, J., & Cabot, A. (2012). Bottom-up processing of thermoelectric nanocomposites from colloidal nanocrystal building blocks: The case of Ag2Te–PbTe. Journal of Nanoparticle Research. Kluwer. https://doi.org/10.1007/s11051-012-1328-0' chicago: 'Cadavid, Doris, Maria Ibáñez, Stéphane Gorsse, Antonio López, Albert Cirera, Joan Morante, and Andreu Cabot. “Bottom-up Processing of Thermoelectric Nanocomposites from Colloidal Nanocrystal Building Blocks: The Case of Ag2Te–PbTe.” Journal of Nanoparticle Research. Kluwer, 2012. https://doi.org/10.1007/s11051-012-1328-0.' ieee: 'D. Cadavid et al., “Bottom-up processing of thermoelectric nanocomposites from colloidal nanocrystal building blocks: The case of Ag2Te–PbTe,” Journal of Nanoparticle Research, vol. 14, no. 12. Kluwer, 2012.' ista: 'Cadavid D, Ibáñez M, Gorsse S, López A, Cirera A, Morante J, Cabot A. 2012. Bottom-up processing of thermoelectric nanocomposites from colloidal nanocrystal building blocks: The case of Ag2Te–PbTe. Journal of Nanoparticle Research. 14(12).' mla: 'Cadavid, Doris, et al. “Bottom-up Processing of Thermoelectric Nanocomposites from Colloidal Nanocrystal Building Blocks: The Case of Ag2Te–PbTe.” Journal of Nanoparticle Research, vol. 14, no. 12, Kluwer, 2012, doi:10.1007/s11051-012-1328-0.' short: D. Cadavid, M. Ibáñez, S. Gorsse, A. López, A. Cirera, J. Morante, A. Cabot, Journal of Nanoparticle Research 14 (2012). date_created: 2018-12-11T11:45:56Z date_published: 2012-12-01T00:00:00Z date_updated: 2021-01-12T07:43:32Z day: '01' doi: 10.1007/s11051-012-1328-0 extern: '1' intvolume: ' 14' issue: '12' language: - iso: eng month: '12' oa_version: None publication: Journal of Nanoparticle Research publication_status: published publisher: Kluwer publist_id: '7485' quality_controlled: '1' status: public title: 'Bottom-up processing of thermoelectric nanocomposites from colloidal nanocrystal building blocks: The case of Ag2Te–PbTe' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2012' ... --- _id: '347' abstract: - lang: eng text: 'A synthetic route for producing Cu 2ZnGeSe 4 nanocrystals with narrow size distributions and controlled composition is presented. These nanocrystals were used to produce densely packed nanomaterials by hot-pressing. From the characterization of the thermoelectric properties of these nanomaterials, Cu 2ZnGeSe 4 is demonstrated to show excellent thermoelectric properties. A very preliminary adjustment of the nanocrystal composition has already resulted in a figure of merit of up to 0.55 at 450°C. ' acknowledgement: This work was supported by the Spanish MICINN Projects MAT2008-05779, MAT2008-03400-E/MAT, MAT2010-15138, ENE2008-03277-E/CON, CSD2009-00050, and CSD2009-00013. M.I. thanks the Spanish MICINN for her Ph.D. Grant. J.A. and R.Z. also acknowledge Generalitat de Catalunya 2009-SGR-770 and XaRMAE. A.C. is thankful for financial support through the Ramon y Cajal Program of the Spanish MICINN. article_processing_charge: No article_type: original author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Aaron full_name: Lalonde, Aaron last_name: Lalonde - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Joan full_name: Morante, Joan last_name: Morante - first_name: Stéphane full_name: Gorsse, Stéphane last_name: Gorsse - first_name: G Jeffrey full_name: Snyder, G Jeffrey last_name: Snyder - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Ibáñez M, Zamani R, Lalonde A, et al. Cu 2ZnGeSe 4 nanocrystals: Synthesis and thermoelectric properties. Journal of the American Chemical Society. 2012;134(9):4060-4063. doi:10.1021/ja211952z' apa: 'Ibáñez, M., Zamani, R., Lalonde, A., Cadavid, D., Li, W., Shavel, A., … Cabot, A. (2012). Cu 2ZnGeSe 4 nanocrystals: Synthesis and thermoelectric properties. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja211952z' chicago: 'Ibáñez, Maria, Reza Zamani, Aaron Lalonde, Doris Cadavid, Wenhua Li, Alexey Shavel, Jordi Arbiol, et al. “Cu 2ZnGeSe 4 Nanocrystals: Synthesis and Thermoelectric Properties.” Journal of the American Chemical Society. ACS, 2012. https://doi.org/10.1021/ja211952z.' ieee: 'M. Ibáñez et al., “Cu 2ZnGeSe 4 nanocrystals: Synthesis and thermoelectric properties,” Journal of the American Chemical Society, vol. 134, no. 9. ACS, pp. 4060–4063, 2012.' ista: 'Ibáñez M, Zamani R, Lalonde A, Cadavid D, Li W, Shavel A, Arbiol J, Morante J, Gorsse S, Snyder GJ, Cabot A. 2012. Cu 2ZnGeSe 4 nanocrystals: Synthesis and thermoelectric properties. Journal of the American Chemical Society. 134(9), 4060–4063.' mla: 'Ibáñez, Maria, et al. “Cu 2ZnGeSe 4 Nanocrystals: Synthesis and Thermoelectric Properties.” Journal of the American Chemical Society, vol. 134, no. 9, ACS, 2012, pp. 4060–63, doi:10.1021/ja211952z.' short: M. Ibáñez, R. Zamani, A. Lalonde, D. Cadavid, W. Li, A. Shavel, J. Arbiol, J. Morante, S. Gorsse, G.J. Snyder, A. Cabot, Journal of the American Chemical Society 134 (2012) 4060–4063. date_created: 2018-12-11T11:45:57Z date_published: 2012-03-07T00:00:00Z date_updated: 2021-01-12T07:43:40Z day: '07' doi: 10.1021/ja211952z extern: '1' intvolume: ' 134' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://authors.library.caltech.edu/30261/ month: '03' oa: 1 oa_version: None page: 4060 - 4063 publication: Journal of the American Chemical Society publication_status: published publisher: ACS publist_id: '7487' quality_controlled: '1' status: public title: 'Cu 2ZnGeSe 4 nanocrystals: Synthesis and thermoelectric properties' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2012' ... --- _id: '3836' abstract: - lang: eng text: Hierarchical Timing Language (HTL) is a coordination language for distributed, hard real-time applications. HTL is a hierarchical extension of Giotto and, like its predecessor, based on the logical execution time (LET) paradigm of real-time programming. Giotto is compiled into code for a virtual machine, called the EmbeddedMachine (or E machine). If HTL is targeted to the E machine, then the hierarchicalprogram structure needs to be flattened; the flattening makes separatecompilation difficult, and may result in E machinecode of exponential size. In this paper, we propose a generalization of the E machine, which supports a hierarchicalprogram structure at runtime through real-time trigger mechanisms that are arranged in a tree. We present the generalized E machine, and a modular compiler for HTL that generates code of linear size. The compiler may generate code for any part of a given HTL program separately in any order. author: - first_name: Arkadeb full_name: Ghosal, Arkadeb last_name: Ghosal - first_name: Daniel full_name: Iercan, Daniel last_name: Iercan - first_name: Christoph full_name: Kirsch, Christoph last_name: Kirsch - 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: Alberto full_name: Sangiovanni Vincentelli, Alberto last_name: Sangiovanni Vincentelli citation: ama: Ghosal A, Iercan D, Kirsch C, Henzinger TA, Sangiovanni Vincentelli A. Separate compilation of hierarchical real-time programs into linear-bounded embedded machine code. Science of Computer Programming. 2012;77(2):96-112. doi:10.1016/j.scico.2010.06.004 apa: Ghosal, A., Iercan, D., Kirsch, C., Henzinger, T. A., & Sangiovanni Vincentelli, A. (2012). Separate compilation of hierarchical real-time programs into linear-bounded embedded machine code. Science of Computer Programming. Elsevier. https://doi.org/10.1016/j.scico.2010.06.004 chicago: Ghosal, Arkadeb, Daniel Iercan, Christoph Kirsch, Thomas A Henzinger, and Alberto Sangiovanni Vincentelli. “Separate Compilation of Hierarchical Real-Time Programs into Linear-Bounded Embedded Machine Code.” Science of Computer Programming. Elsevier, 2012. https://doi.org/10.1016/j.scico.2010.06.004. ieee: A. Ghosal, D. Iercan, C. Kirsch, T. A. Henzinger, and A. Sangiovanni Vincentelli, “Separate compilation of hierarchical real-time programs into linear-bounded embedded machine code,” Science of Computer Programming, vol. 77, no. 2. Elsevier, pp. 96–112, 2012. ista: Ghosal A, Iercan D, Kirsch C, Henzinger TA, Sangiovanni Vincentelli A. 2012. Separate compilation of hierarchical real-time programs into linear-bounded embedded machine code. Science of Computer Programming. 77(2), 96–112. mla: Ghosal, Arkadeb, et al. “Separate Compilation of Hierarchical Real-Time Programs into Linear-Bounded Embedded Machine Code.” Science of Computer Programming, vol. 77, no. 2, Elsevier, 2012, pp. 96–112, doi:10.1016/j.scico.2010.06.004. short: A. Ghosal, D. Iercan, C. Kirsch, T.A. Henzinger, A. Sangiovanni Vincentelli, Science of Computer Programming 77 (2012) 96–112. date_created: 2018-12-11T12:05:26Z date_published: 2012-02-01T00:00:00Z date_updated: 2021-01-12T07:52:32Z day: '01' department: - _id: ToHe doi: 10.1016/j.scico.2010.06.004 intvolume: ' 77' issue: '2' language: - iso: eng month: '02' oa_version: None page: 96 - 112 publication: Science of Computer Programming publication_status: published publisher: Elsevier publist_id: '2370' quality_controlled: '1' scopus_import: 1 status: public title: Separate compilation of hierarchical real-time programs into linear-bounded embedded machine code type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 77 year: '2012' ... --- _id: '2972' abstract: - lang: eng text: 'Energy parity games are infinite two-player turn-based games played on weighted graphs. The objective of the game combines a (qualitative) parity condition with the (quantitative) requirement that the sum of the weights (i.e., the level of energy in the game) must remain positive. Beside their own interest in the design and synthesis of resource-constrained omega-regular specifications, energy parity games provide one of the simplest model of games with combined qualitative and quantitative objectives. Our main results are as follows: (a) exponential memory is sufficient and may be necessary for winning strategies in energy parity games; (b) the problem of deciding the winner in energy parity games can be solved in NP ∩ coNP; and (c) we give an algorithm to solve energy parity by reduction to energy games. We also show that the problem of deciding the winner in energy parity games is logspace-equivalent to the problem of deciding the winner in mean-payoff parity games, which can thus be solved in NP ∩ coNP. As a consequence we also obtain a conceptually simple algorithm to solve mean-payoff parity games.' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen citation: ama: Chatterjee K, Doyen L. Energy parity games. Theoretical Computer Science. 2012;458:49-60. doi:10.1016/j.tcs.2012.07.038 apa: Chatterjee, K., & Doyen, L. (2012). Energy parity games. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2012.07.038 chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Energy Parity Games.” Theoretical Computer Science. Elsevier, 2012. https://doi.org/10.1016/j.tcs.2012.07.038. ieee: K. Chatterjee and L. Doyen, “Energy parity games,” Theoretical Computer Science, vol. 458. Elsevier, pp. 49–60, 2012. ista: Chatterjee K, Doyen L. 2012. Energy parity games. Theoretical Computer Science. 458, 49–60. mla: Chatterjee, Krishnendu, and Laurent Doyen. “Energy Parity Games.” Theoretical Computer Science, vol. 458, Elsevier, 2012, pp. 49–60, doi:10.1016/j.tcs.2012.07.038. short: K. Chatterjee, L. Doyen, Theoretical Computer Science 458 (2012) 49–60. date_created: 2018-12-11T12:00:37Z date_published: 2012-11-02T00:00:00Z date_updated: 2023-02-23T11:45:29Z day: '02' ddc: - '004' department: - _id: KrCh doi: 10.1016/j.tcs.2012.07.038 ec_funded: 1 external_id: arxiv: - '1001.5183' file: - access_level: open_access checksum: 719e4a5af5a01ad3f2f7f7f05b3c2b09 content_type: application/pdf creator: kschuh date_created: 2019-02-06T11:56:22Z date_updated: 2020-07-14T12:45:57Z file_id: '5935' file_name: 2012_Elsevier_Chatterjee.pdf file_size: 351271 relation: main_file file_date_updated: 2020-07-14T12:45:57Z has_accepted_license: '1' intvolume: ' 458' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 49 - 60 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: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '3736' pubrep_id: '935' quality_controlled: '1' related_material: record: - id: '3851' relation: earlier_version status: public scopus_import: 1 status: public title: Energy parity games 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: 458 year: '2012' ... --- _id: '2967' abstract: - lang: eng text: For programs whose data variables range over Boolean or finite domains, program verification is decidable, and this forms the basis of recent tools for software model checking. In this article, we consider algorithmic verification of programs that use Boolean variables, and in addition, access a single read-only array whose length is potentially unbounded, and whose elements range over an unbounded data domain. We show that the reachability problem, while undecidable in general, is (1) PSPACE-complete for programs in which the array-accessing for-loops are not nested, (2) decidable for a restricted class of programs with doubly nested loops. The second result establishes connections to automata and logics defining languages over data words. acknowledgement: This research was supported in part by the NSF Cybertrust award CNS 0524059, by the European Research Council (ERC) Advanced Investigator Grant QUAREM, and by the Austrian Science Fund (FWF) project S11402-N23. article_number: '27' author: - first_name: Rajeev full_name: Alur, Rajeev last_name: Alur - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Scott full_name: Weinstein, Scott last_name: Weinstein citation: ama: Alur R, Cerny P, Weinstein S. Algorithmic analysis of array-accessing programs. ACM Transactions on Computational Logic (TOCL). 2012;13(3). doi:10.1145/2287718.2287727 apa: Alur, R., Cerny, P., & Weinstein, S. (2012). Algorithmic analysis of array-accessing programs. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/2287718.2287727 chicago: Alur, Rajeev, Pavol Cerny, and Scott Weinstein. “Algorithmic Analysis of Array-Accessing Programs.” ACM Transactions on Computational Logic (TOCL). ACM, 2012. https://doi.org/10.1145/2287718.2287727. ieee: R. Alur, P. Cerny, and S. Weinstein, “Algorithmic analysis of array-accessing programs,” ACM Transactions on Computational Logic (TOCL), vol. 13, no. 3. ACM, 2012. ista: Alur R, Cerny P, Weinstein S. 2012. Algorithmic analysis of array-accessing programs. ACM Transactions on Computational Logic (TOCL). 13(3), 27. mla: Alur, Rajeev, et al. “Algorithmic Analysis of Array-Accessing Programs.” ACM Transactions on Computational Logic (TOCL), vol. 13, no. 3, 27, ACM, 2012, doi:10.1145/2287718.2287727. short: R. Alur, P. Cerny, S. Weinstein, ACM Transactions on Computational Logic (TOCL) 13 (2012). date_created: 2018-12-11T12:00:36Z date_published: 2012-08-01T00:00:00Z date_updated: 2023-02-23T12:09:43Z day: '01' department: - _id: ToHe doi: 10.1145/2287718.2287727 ec_funded: 1 intvolume: ' 13' issue: '3' language: - iso: eng month: '08' oa_version: None project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: ACM Transactions on Computational Logic (TOCL) publication_status: published publisher: ACM publist_id: '3748' quality_controlled: '1' related_material: record: - id: '4403' relation: earlier_version status: public scopus_import: 1 status: public title: Algorithmic analysis of array-accessing programs type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2012' ... --- _id: '492' abstract: - lang: eng text: 'Background: Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks.Results: We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user.Conclusions: We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis.' article_number: '116' article_processing_charge: No author: - first_name: Taras full_name: Galkovskyi, Taras last_name: Galkovskyi - first_name: Yuriy full_name: Mileyko, Yuriy last_name: Mileyko - first_name: Alexander full_name: Bucksch, Alexander last_name: Bucksch - first_name: Brad full_name: Moore, Brad last_name: Moore - first_name: Olga full_name: Symonova, Olga id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87 last_name: Symonova - first_name: Charles full_name: Price, Charles last_name: Price - first_name: Chrostopher full_name: Topp, Chrostopher last_name: Topp - first_name: Anjali full_name: Iyer Pascuzzi, Anjali last_name: Iyer Pascuzzi - first_name: Paul full_name: Zurek, Paul last_name: Zurek - first_name: Suqin full_name: Fang, Suqin last_name: Fang - first_name: John full_name: Harer, John last_name: Harer - first_name: Philip full_name: Benfey, Philip last_name: Benfey - first_name: Joshua full_name: Weitz, Joshua last_name: Weitz citation: ama: 'Galkovskyi T, Mileyko Y, Bucksch A, et al. GiA Roots: Software for the high throughput analysis of plant root system architecture. BMC Plant Biology. 2012;12. doi:10.1186/1471-2229-12-116' apa: 'Galkovskyi, T., Mileyko, Y., Bucksch, A., Moore, B., Symonova, O., Price, C., … Weitz, J. (2012). GiA Roots: Software for the high throughput analysis of plant root system architecture. BMC Plant Biology. BioMed Central. https://doi.org/10.1186/1471-2229-12-116' chicago: 'Galkovskyi, Taras, Yuriy Mileyko, Alexander Bucksch, Brad Moore, Olga Symonova, Charles Price, Chrostopher Topp, et al. “GiA Roots: Software for the High Throughput Analysis of Plant Root System Architecture.” BMC Plant Biology. BioMed Central, 2012. https://doi.org/10.1186/1471-2229-12-116.' ieee: 'T. Galkovskyi et al., “GiA Roots: Software for the high throughput analysis of plant root system architecture,” BMC Plant Biology, vol. 12. BioMed Central, 2012.' ista: 'Galkovskyi T, Mileyko Y, Bucksch A, Moore B, Symonova O, Price C, Topp C, Iyer Pascuzzi A, Zurek P, Fang S, Harer J, Benfey P, Weitz J. 2012. GiA Roots: Software for the high throughput analysis of plant root system architecture. BMC Plant Biology. 12, 116.' mla: 'Galkovskyi, Taras, et al. “GiA Roots: Software for the High Throughput Analysis of Plant Root System Architecture.” BMC Plant Biology, vol. 12, 116, BioMed Central, 2012, doi:10.1186/1471-2229-12-116.' short: T. Galkovskyi, Y. Mileyko, A. Bucksch, B. Moore, O. Symonova, C. Price, C. Topp, A. Iyer Pascuzzi, P. Zurek, S. Fang, J. Harer, P. Benfey, J. Weitz, BMC Plant Biology 12 (2012). date_created: 2018-12-11T11:46:46Z date_published: 2012-07-26T00:00:00Z date_updated: 2022-08-25T14:59:17Z day: '26' ddc: - '005' - '514' - '516' doi: 10.1186/1471-2229-12-116 extern: '1' file: - access_level: open_access checksum: 0c629e36acd5f2878ff7dd088d67d494 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:35Z date_updated: 2020-07-14T12:46:35Z file_id: '4953' file_name: IST-2018-946-v1+1_2012_Symonova_GiA_Roots.pdf file_size: 1691436 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 12' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: BMC Plant Biology publication_status: published publisher: BioMed Central publist_id: '7328' pubrep_id: '946' quality_controlled: '1' scopus_import: '1' status: public title: 'GiA Roots: Software for the high throughput analysis of plant root system architecture' 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: 12 year: '2012' ... --- _id: '493' abstract: - lang: eng text: 'The BCI competition IV stands in the tradition of prior BCI competitions that aim to provide high quality neuroscientific data for open access to the scientific community. As experienced already in prior competitions not only scientists from the narrow field of BCI compete, but scholars with a broad variety of backgrounds and nationalities. They include high specialists as well as students.The goals of all BCI competitions have always been to challenge with respect to novel paradigms and complex data. We report on the following challenges: (1) asynchronous data, (2) synthetic, (3) multi-class continuous data, (4) sessionto-session transfer, (5) directionally modulated MEG, (6) finger movements recorded by ECoG. As after past competitions, our hope is that winning entries may enhance the analysis methods of future BCIs.' acknowledgement: "The studies were in part or completely supported by the Bundesministerium für Bildung und Forschung (BMBF), Fkz 01IB001A, 01GQ0850, by the German Science Foundation (DFG, contract MU 987/3-2), by the European ICT Programme Projects FP7-224631 and 216886, the World Class University Program through the National Research Foundation of Korea funded by the Ministry of Education, Science, and Technology (Grant R31-10008), the US Army Research Office [W911NF-08-1-0216 (Gerwin Schalk) and W911NF-07-1-0415 (Gerwin Schalk)] and the NIH [EB006356 (Gerwin Schalk) and EB000856 (Gerwin Schalk), the WIN-Kolleg of the Heidelberg Academy of Sciences and Humanities, German Federal Ministry of Education and Research grants 01GQ0420, 01GQ0761, 01GQ0762, and 01GQ0830, German Research Foundation grants 550/B5 and C6, and by a scholarship from the German National Academic Foundation. This paper only reflects the authors’ views and funding agencies are not liable for any use that may be made of the information contained herein.\r\n" article_number: '55' author: - first_name: Michael full_name: Tangermann, Michael last_name: Tangermann - first_name: Klaus full_name: Müller, Klaus last_name: Müller - first_name: Ad full_name: Aertsen, Ad last_name: Aertsen - first_name: Niels full_name: Birbaumer, Niels last_name: Birbaumer - first_name: Christoph full_name: Braun, Christoph last_name: Braun - first_name: Clemens full_name: Brunner, Clemens last_name: Brunner - first_name: Robert full_name: Leeb, Robert last_name: Leeb - first_name: Carsten full_name: Mehring, Carsten last_name: Mehring - first_name: Kai full_name: Miller, Kai last_name: Miller - first_name: Gernot full_name: Müller Putz, Gernot last_name: Müller Putz - first_name: Guido full_name: Nolte, Guido last_name: Nolte - first_name: Gert full_name: Pfurtscheller, Gert last_name: Pfurtscheller - first_name: Hubert full_name: Preissl, Hubert last_name: Preissl - first_name: Gerwin full_name: Schalk, Gerwin last_name: Schalk - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Carmen full_name: Vidaurre, Carmen last_name: Vidaurre - first_name: Stephan full_name: Waldert, Stephan last_name: Waldert - first_name: Benjamin full_name: Blankertz, Benjamin last_name: Blankertz citation: ama: Tangermann M, Müller K, Aertsen A, et al. Review of the BCI competition IV. Frontiers in Neuroscience. 2012;6. doi:10.3389/fnins.2012.00055 apa: Tangermann, M., Müller, K., Aertsen, A., Birbaumer, N., Braun, C., Brunner, C., … Blankertz, B. (2012). Review of the BCI competition IV. Frontiers in Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fnins.2012.00055 chicago: Tangermann, Michael, Klaus Müller, Ad Aertsen, Niels Birbaumer, Christoph Braun, Clemens Brunner, Robert Leeb, et al. “Review of the BCI Competition IV.” Frontiers in Neuroscience. Frontiers Research Foundation, 2012. https://doi.org/10.3389/fnins.2012.00055. ieee: M. Tangermann et al., “Review of the BCI competition IV,” Frontiers in Neuroscience, vol. 6. Frontiers Research Foundation, 2012. ista: Tangermann M, Müller K, Aertsen A, Birbaumer N, Braun C, Brunner C, Leeb R, Mehring C, Miller K, Müller Putz G, Nolte G, Pfurtscheller G, Preissl H, Schalk G, Schlögl A, Vidaurre C, Waldert S, Blankertz B. 2012. Review of the BCI competition IV. Frontiers in Neuroscience. 6, 55. mla: Tangermann, Michael, et al. “Review of the BCI Competition IV.” Frontiers in Neuroscience, vol. 6, 55, Frontiers Research Foundation, 2012, doi:10.3389/fnins.2012.00055. short: M. Tangermann, K. Müller, A. Aertsen, N. Birbaumer, C. Braun, C. Brunner, R. Leeb, C. Mehring, K. Miller, G. Müller Putz, G. Nolte, G. Pfurtscheller, H. Preissl, G. Schalk, A. Schlögl, C. Vidaurre, S. Waldert, B. Blankertz, Frontiers in Neuroscience 6 (2012). date_created: 2018-12-11T11:46:46Z date_published: 2012-07-13T00:00:00Z date_updated: 2021-01-12T08:01:03Z day: '13' ddc: - '004' department: - _id: ScienComp - _id: PeJo doi: 10.3389/fnins.2012.00055 file: - access_level: open_access checksum: 195238221c4b0b0f4035f6f6c16ea17c content_type: application/pdf creator: system date_created: 2018-12-12T10:18:34Z date_updated: 2020-07-14T12:46:35Z file_id: '5356' file_name: IST-2018-945-v1+1_2012_Schloegl_Review_of.pdf file_size: 2693701 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Frontiers in Neuroscience publication_status: published publisher: Frontiers Research Foundation publist_id: '7327' pubrep_id: '945' quality_controlled: '1' scopus_import: 1 status: public title: Review of the BCI competition IV 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: 6 year: '2012' ... --- _id: '495' abstract: - lang: eng text: An automaton with advice is a finite state automaton which has access to an additional fixed infinite string called an advice tape. We refine the Myhill-Nerode theorem to characterize the languages of finite strings that are accepted by automata with advice. We do the same for tree automata with advice. alternative_title: - EPTCS author: - first_name: Alex full_name: Kruckman, Alex last_name: Kruckman - first_name: Sasha full_name: Rubin, Sasha id: 2EC51194-F248-11E8-B48F-1D18A9856A87 last_name: Rubin - first_name: John full_name: Sheridan, John last_name: Sheridan - first_name: Ben full_name: Zax, Ben last_name: Zax citation: ama: 'Kruckman A, Rubin S, Sheridan J, Zax B. A Myhill Nerode theorem for automata with advice. In: Proceedings GandALF 2012. Vol 96. Open Publishing Association; 2012:238-246. doi:10.4204/EPTCS.96.18' apa: 'Kruckman, A., Rubin, S., Sheridan, J., & Zax, B. (2012). A Myhill Nerode theorem for automata with advice. In Proceedings GandALF 2012 (Vol. 96, pp. 238–246). Napoli, Italy: Open Publishing Association. https://doi.org/10.4204/EPTCS.96.18' chicago: Kruckman, Alex, Sasha Rubin, John Sheridan, and Ben Zax. “A Myhill Nerode Theorem for Automata with Advice.” In Proceedings GandALF 2012, 96:238–46. Open Publishing Association, 2012. https://doi.org/10.4204/EPTCS.96.18. ieee: A. Kruckman, S. Rubin, J. Sheridan, and B. Zax, “A Myhill Nerode theorem for automata with advice,” in Proceedings GandALF 2012, Napoli, Italy, 2012, vol. 96, pp. 238–246. ista: 'Kruckman A, Rubin S, Sheridan J, Zax B. 2012. A Myhill Nerode theorem for automata with advice. Proceedings GandALF 2012. GandALF: Games, Automata, Logics and Formal Verification, EPTCS, vol. 96, 238–246.' mla: Kruckman, Alex, et al. “A Myhill Nerode Theorem for Automata with Advice.” Proceedings GandALF 2012, vol. 96, Open Publishing Association, 2012, pp. 238–46, doi:10.4204/EPTCS.96.18. short: A. Kruckman, S. Rubin, J. Sheridan, B. Zax, in:, Proceedings GandALF 2012, Open Publishing Association, 2012, pp. 238–246. conference: end_date: 2012-09-08 location: Napoli, Italy name: 'GandALF: Games, Automata, Logics and Formal Verification' start_date: 2012-09-06 date_created: 2018-12-11T11:46:47Z date_published: 2012-10-07T00:00:00Z date_updated: 2021-01-12T08:01:04Z day: '07' ddc: - '004' department: - _id: KrCh doi: 10.4204/EPTCS.96.18 ec_funded: 1 file: - access_level: open_access checksum: 56277f95edc9d531fa3bdc5f9579fda8 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:31Z date_updated: 2020-07-14T12:46:35Z file_id: '5152' file_name: IST-2018-944-v1+1_2012_Rubin_A_Myhill.pdf file_size: 97736 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 96' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 238 - 246 project: - _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 GandALF 2012 publication_status: published publisher: Open Publishing Association publist_id: '7325' pubrep_id: '944' quality_controlled: '1' scopus_import: 1 status: public title: A Myhill Nerode theorem for automata with advice 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 96 year: '2012' ... --- _id: '498' abstract: - lang: eng text: Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration. acknowledgement: "We thank Graham Pickup, David Steer, Linda Broadhurst, Lan Li and Carole Elliott for technical assistance. The New\r\nSouth Wales Department of Environment and Climate Change, ACT Parks, Conservation and Lands and the\r\nDepartment of Sustainability and Environment in Victoria provided permits for seed and soil collection. We thank\r\nSpencer C. H. Barrett for comments that improved the quality of the manuscript.\r\n" author: - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: David full_name: Rowell, David last_name: Rowell - first_name: Andrew full_name: Young, Andrew last_name: Young citation: ama: 'Pickup M, Field D, Rowell D, Young A. Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. Evolutionary Applications. 2012;5(8):913-924. doi:10.1111/j.1752-4571.2012.00284.x' apa: 'Pickup, M., Field, D., Rowell, D., & Young, A. (2012). Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. Evolutionary Applications. Wiley-Blackwell. https://doi.org/10.1111/j.1752-4571.2012.00284.x' chicago: 'Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Predicting Local Adaptation in Fragmented Plant Populations: Implications for Restoration Genetics.” Evolutionary Applications. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1752-4571.2012.00284.x.' ieee: 'M. Pickup, D. Field, D. Rowell, and A. Young, “Predicting local adaptation in fragmented plant populations: Implications for restoration genetics,” Evolutionary Applications, vol. 5, no. 8. Wiley-Blackwell, pp. 913–924, 2012.' ista: 'Pickup M, Field D, Rowell D, Young A. 2012. Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. Evolutionary Applications. 5(8), 913–924.' mla: 'Pickup, Melinda, et al. “Predicting Local Adaptation in Fragmented Plant Populations: Implications for Restoration Genetics.” Evolutionary Applications, vol. 5, no. 8, Wiley-Blackwell, 2012, pp. 913–24, doi:10.1111/j.1752-4571.2012.00284.x.' short: M. Pickup, D. Field, D. Rowell, A. Young, Evolutionary Applications 5 (2012) 913–924. date_created: 2018-12-11T11:46:48Z date_published: 2012-12-01T00:00:00Z date_updated: 2021-01-12T08:01:06Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1111/j.1752-4571.2012.00284.x file: - access_level: open_access checksum: 233007138606aca5a2f75f7ae1742f43 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:33Z date_updated: 2020-07-14T12:46:35Z file_id: '4821' file_name: IST-2018-942-v1+1_Pickup_et_al-2012-Evolutionary_Applications.pdf file_size: 396136 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 5' issue: '8' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 913 - 924 publication: Evolutionary Applications publication_status: published publisher: Wiley-Blackwell publist_id: '7322' pubrep_id: '942' quality_controlled: '1' status: public title: 'Predicting local adaptation in fragmented plant populations: Implications for restoration genetics' 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2012' ... --- _id: '496' abstract: - lang: eng text: 'We study the expressive power of logical interpretations on the class of scattered trees, namely those with countably many infinite branches. Scattered trees can be thought of as the tree analogue of scattered linear orders. Every scattered tree has an ordinal rank that reflects the structure of its infinite branches. We prove, roughly, that trees and orders of large rank cannot be interpreted in scattered trees of small rank. We consider a quite general notion of interpretation: each element of the interpreted structure is represented by a set of tuples of subsets of the interpreting tree. Our trees are countable, not necessarily finitely branching, and may have finitely many unary predicates as labellings. We also show how to replace injective set-interpretations in (not necessarily scattered) trees by ''finitary'' set-interpretations.' alternative_title: - LICS article_number: '6280474' author: - first_name: Alexander full_name: Rabinovich, Alexander last_name: Rabinovich - first_name: Sasha full_name: Rubin, Sasha id: 2EC51194-F248-11E8-B48F-1D18A9856A87 last_name: Rubin citation: ama: 'Rabinovich A, Rubin S. Interpretations in trees with countably many branches. In: IEEE; 2012. doi:10.1109/LICS.2012.65' apa: 'Rabinovich, A., & Rubin, S. (2012). Interpretations in trees with countably many branches. Presented at the LICS: Symposium on Logic in Computer Science, Dubrovnik, Croatia: IEEE. https://doi.org/10.1109/LICS.2012.65' chicago: Rabinovich, Alexander, and Sasha Rubin. “Interpretations in Trees with Countably Many Branches.” IEEE, 2012. https://doi.org/10.1109/LICS.2012.65. ieee: 'A. Rabinovich and S. Rubin, “Interpretations in trees with countably many branches,” presented at the LICS: Symposium on Logic in Computer Science, Dubrovnik, Croatia, 2012.' ista: 'Rabinovich A, Rubin S. 2012. Interpretations in trees with countably many branches. LICS: Symposium on Logic in Computer Science, LICS, , 6280474.' mla: Rabinovich, Alexander, and Sasha Rubin. Interpretations in Trees with Countably Many Branches. 6280474, IEEE, 2012, doi:10.1109/LICS.2012.65. short: A. Rabinovich, S. Rubin, in:, IEEE, 2012. conference: end_date: 2012-06-28 location: Dubrovnik, Croatia name: 'LICS: Symposium on Logic in Computer Science' start_date: 2012-06-25 date_created: 2018-12-11T11:46:47Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T08:01:05Z day: '01' department: - _id: KrCh doi: 10.1109/LICS.2012.65 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arise.or.at/pubpdf/Interpretations_in_Trees_with_Countably_Many_Branches.pdf month: '01' oa: 1 oa_version: Preprint project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: IEEE publist_id: '7324' quality_controlled: '1' scopus_import: 1 status: public title: Interpretations in trees with countably many branches type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '494' abstract: - lang: eng text: We solve the longstanding open problems of the blow-up involved in the translations, when possible, of a nondeterministic Büchi word automaton (NBW) to a nondeterministic co-Büchi word automaton (NCW) and to a deterministic co-Büchi word automaton (DCW). For the NBW to NCW translation, the currently known upper bound is 2o(nlog n) and the lower bound is 1.5n. We improve the upper bound to n2n and describe a matching lower bound of 2ω(n). For the NBW to DCW translation, the currently known upper bound is 2o(nlog n). We improve it to 2 o(n), which is asymptotically tight. Both of our upper-bound constructions are based on a simple subset construction, do not involve intermediate automata with richer acceptance conditions, and can be implemented symbolically. We continue and solve the open problems of translating nondeterministic Streett, Rabin, Muller, and parity word automata to NCW and to DCW. Going via an intermediate NBW is not optimal and we describe direct, simple, and asymptotically tight constructions, involving a 2o(n) blow-up. The constructions are variants of the subset construction, providing a unified approach for translating all common classes of automata to NCW and DCW. Beyond the theoretical importance of the results, we point to numerous applications of the new constructions. In particular, they imply a simple subset-construction based translation, when possible, of LTL to deterministic Büchi word automata. article_number: '29' author: - first_name: Udi full_name: Boker, Udi id: 31E297B6-F248-11E8-B48F-1D18A9856A87 last_name: Boker - first_name: Orna full_name: Kupferman, Orna last_name: Kupferman citation: ama: Boker U, Kupferman O. Translating to Co-Büchi made tight, unified, and useful. ACM Transactions on Computational Logic (TOCL). 2012;13(4). doi:10.1145/2362355.2362357 apa: Boker, U., & Kupferman, O. (2012). Translating to Co-Büchi made tight, unified, and useful. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/2362355.2362357 chicago: Boker, Udi, and Orna Kupferman. “Translating to Co-Büchi Made Tight, Unified, and Useful.” ACM Transactions on Computational Logic (TOCL). ACM, 2012. https://doi.org/10.1145/2362355.2362357. ieee: U. Boker and O. Kupferman, “Translating to Co-Büchi made tight, unified, and useful,” ACM Transactions on Computational Logic (TOCL), vol. 13, no. 4. ACM, 2012. ista: Boker U, Kupferman O. 2012. Translating to Co-Büchi made tight, unified, and useful. ACM Transactions on Computational Logic (TOCL). 13(4), 29. mla: Boker, Udi, and Orna Kupferman. “Translating to Co-Büchi Made Tight, Unified, and Useful.” ACM Transactions on Computational Logic (TOCL), vol. 13, no. 4, 29, ACM, 2012, doi:10.1145/2362355.2362357. short: U. Boker, O. Kupferman, ACM Transactions on Computational Logic (TOCL) 13 (2012). date_created: 2018-12-11T11:46:47Z date_published: 2012-10-01T00:00:00Z date_updated: 2021-01-12T08:01:03Z day: '01' department: - _id: ToHe doi: 10.1145/2362355.2362357 intvolume: ' 13' issue: '4' language: - iso: eng month: '10' oa_version: None publication: ACM Transactions on Computational Logic (TOCL) publication_status: published publisher: ACM publist_id: '7326' quality_controlled: '1' scopus_import: 1 status: public title: Translating to Co-Büchi made tight, unified, and useful type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2012' ... --- _id: '506' article_processing_charge: No article_type: original author: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: 'Sixt MK. Cell migration: Fibroblasts find a new way to get ahead. Journal of Cell Biology. 2012;197(3):347-349. doi:10.1083/jcb.201204039' apa: 'Sixt, M. K. (2012). Cell migration: Fibroblasts find a new way to get ahead. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201204039' chicago: 'Sixt, Michael K. “Cell Migration: Fibroblasts Find a New Way to Get Ahead.” Journal of Cell Biology. Rockefeller University Press, 2012. https://doi.org/10.1083/jcb.201204039.' ieee: 'M. K. Sixt, “Cell migration: Fibroblasts find a new way to get ahead,” Journal of Cell Biology, vol. 197, no. 3. Rockefeller University Press, pp. 347–349, 2012.' ista: 'Sixt MK. 2012. Cell migration: Fibroblasts find a new way to get ahead. Journal of Cell Biology. 197(3), 347–349.' mla: 'Sixt, Michael K. “Cell Migration: Fibroblasts Find a New Way to Get Ahead.” Journal of Cell Biology, vol. 197, no. 3, Rockefeller University Press, 2012, pp. 347–49, doi:10.1083/jcb.201204039.' short: M.K. Sixt, Journal of Cell Biology 197 (2012) 347–349. date_created: 2018-12-11T11:46:51Z date_published: 2012-04-30T00:00:00Z date_updated: 2021-01-12T08:01:11Z day: '30' ddc: - '570' department: - _id: MiSi doi: 10.1083/jcb.201204039 file: - access_level: open_access checksum: 45c02be33ebd99fc3077d60b9c90bdfa content_type: application/pdf creator: kschuh date_created: 2019-02-12T09:03:09Z date_updated: 2020-07-14T12:46:36Z file_id: '5957' file_name: 2012_CellBiology_Sixt.pdf file_size: 986566 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 197' issue: '3' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 347 - 349 publication: Journal of Cell Biology publication_status: published publisher: Rockefeller University Press publist_id: '7314' quality_controlled: '1' scopus_import: 1 status: public title: 'Cell migration: Fibroblasts find a new way to get ahead' 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 197 year: '2012' ... --- _id: '497' abstract: - lang: eng text: 'One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n 3·m) time as compared to the previous known O(n 6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n·m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm. © Krishnendu Chatterjee, Siddhesh Chaubal, and Pritish Kamath.' alternative_title: - LIPIcs author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Siddhesh full_name: Chaubal, Siddhesh last_name: Chaubal - first_name: Pritish full_name: Kamath, Pritish last_name: Kamath citation: ama: 'Chatterjee K, Chaubal S, Kamath P. Faster algorithms for alternating refinement relations. In: Vol 16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2012:167-182. doi:10.4230/LIPIcs.CSL.2012.167' apa: 'Chatterjee, K., Chaubal, S., & Kamath, P. (2012). Faster algorithms for alternating refinement relations (Vol. 16, pp. 167–182). Presented at the EACSL: European Association for Computer Science Logic, Fontainebleau, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CSL.2012.167' chicago: Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. “Faster Algorithms for Alternating Refinement Relations,” 16:167–82. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012. https://doi.org/10.4230/LIPIcs.CSL.2012.167. ieee: 'K. Chatterjee, S. Chaubal, and P. Kamath, “Faster algorithms for alternating refinement relations,” presented at the EACSL: European Association for Computer Science Logic, Fontainebleau, France, 2012, vol. 16, pp. 167–182.' ista: 'Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating refinement relations. EACSL: European Association for Computer Science Logic, LIPIcs, vol. 16, 167–182.' mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Alternating Refinement Relations. Vol. 16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 167–82, doi:10.4230/LIPIcs.CSL.2012.167. short: K. Chatterjee, S. Chaubal, P. Kamath, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 167–182. conference: end_date: 2012-09-06 location: Fontainebleau, France name: 'EACSL: European Association for Computer Science Logic' start_date: 2012-09-03 date_created: 2018-12-11T11:46:48Z date_published: 2012-09-01T00:00:00Z date_updated: 2023-02-23T12:23:32Z day: '01' ddc: - '004' department: - _id: KrCh doi: 10.4230/LIPIcs.CSL.2012.167 ec_funded: 1 file: - access_level: open_access checksum: f1b0dd99240800db2d7dbf9b5131fe5e content_type: application/pdf creator: system date_created: 2018-12-12T10:08:50Z date_updated: 2020-07-14T12:46:35Z file_id: '4712' file_name: IST-2018-943-v1+1_2012_Chatterjee_Faster_Algorithms.pdf file_size: 471236 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 16' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 167 - 182 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: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7323' pubrep_id: '943' quality_controlled: '1' related_material: record: - id: '5378' relation: earlier_version status: public scopus_import: 1 status: public title: Faster algorithms for alternating refinement relations 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2012' ... --- _id: '3165' abstract: - lang: eng text: Computing the winning set for Büchi objectives in alternating games on graphs is a central problem in computer aided verification with a large number of applications. The long standing best known upper bound for solving the problem is Õ(n·m), where n is the number of vertices and m is the number of edges in the graph. We are the first to break the Õ(n·m) boundary by presenting a new technique that reduces the running time to O(n 2). This bound also leads to O(n 2) time algorithms for computing the set of almost-sure winning vertices for Büchi objectives (1) in alternating games with probabilistic transitions (improving an earlier bound of Õ(n·m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n 3)), and (3) in Markov decision processes (improving for m > n 4/3 an earlier bound of O(min(m 1.5, m·n 2/3)). We also show that the same technique can be used to compute the maximal end-component decomposition of a graph in time O(n 2), which is an improvement over earlier bounds for m > n 4/3. Finally, we show how to maintain the winning set for Büchi objectives in alternating games under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per operation. This is the first dynamic algorithm for this problem. acknowledgement: 'The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification, Vienna Science and Technology Fund (WWTF) Grant ICT10-002, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 citation: ama: 'Chatterjee K, Henzinger MH. An O(n2) time algorithm for alternating Büchi games. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SIAM; 2012:1386-1399. doi:10.1137/1.9781611973099.109' apa: 'Chatterjee, K., & Henzinger, M. H. (2012). An O(n2) time algorithm for alternating Büchi games. In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1386–1399). Kyoto, Japan: SIAM. https://doi.org/10.1137/1.9781611973099.109' chicago: Chatterjee, Krishnendu, and Monika H Henzinger. “An O(N2) Time Algorithm for Alternating Büchi Games.” In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, 1386–99. SIAM, 2012. https://doi.org/10.1137/1.9781611973099.109. ieee: K. Chatterjee and M. H. Henzinger, “An O(n2) time algorithm for alternating Büchi games,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Kyoto, Japan, 2012, pp. 1386–1399. ista: 'Chatterjee K, Henzinger MH. 2012. An O(n2) time algorithm for alternating Büchi games. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1386–1399.' mla: Chatterjee, Krishnendu, and Monika H. Henzinger. “An O(N2) Time Algorithm for Alternating Büchi Games.” Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2012, pp. 1386–99, doi:10.1137/1.9781611973099.109. short: K. Chatterjee, M.H. Henzinger, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2012, pp. 1386–1399. conference: end_date: 2012-01-19 location: Kyoto, Japan name: 'SODA: Symposium on Discrete Algorithms' start_date: 2012-01-17 date_created: 2018-12-11T12:01:46Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-02-23T12:23:35Z day: '01' department: - _id: KrCh doi: 10.1137/1.9781611973099.109 ec_funded: 1 external_id: arxiv: - '1109.5018' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1109.5018 month: '01' oa: 1 oa_version: None page: 1386 - 1399 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms publication_status: published publisher: SIAM publist_id: '3519' pubrep_id: '15' quality_controlled: '1' related_material: record: - id: '2141' relation: later_version status: public - id: '5379' relation: earlier_version status: public status: public title: An O(n2) time algorithm for alternating Büchi games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '2956' abstract: - lang: eng text: 'Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work we consider solving recursive game graphs (or pushdown game graphs) that can model the control flow of sequential programs with recursion. While pushdown games have been studied before with qualitative objectives, such as reachability and parity objectives, in this work we study for the first time such games with the most well-studied quantitative objective, namely, mean payoff objectives. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation, but only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games; and memoryless modular strategies are sufficient in two-player pushdown games. Finally we also show that all the problems have the same computational complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.' acknowledgement: "The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the Israeli Centers of Research Excellence (ICORE) program, (Center No. 4/11), the RICH Model Toolkit (ICT COST Action IC0901), and was carried out in partial fulfillment of the requirements for the Ph.D. degree of the second author.\r\nA Technical Report of this paper is available via internal link." article_number: '6280438' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: ama: 'Chatterjee K, Velner Y. Mean payoff pushdown games. In: Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE; 2012. doi:10.1109/LICS.2012.30' apa: 'Chatterjee, K., & Velner, Y. (2012). Mean payoff pushdown games. In Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. Dubrovnik, Croatia : IEEE. https://doi.org/10.1109/LICS.2012.30' chicago: Chatterjee, Krishnendu, and Yaron Velner. “Mean Payoff Pushdown Games.” In Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE, 2012. https://doi.org/10.1109/LICS.2012.30. ieee: K. Chatterjee and Y. Velner, “Mean payoff pushdown games,” in Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, Dubrovnik, Croatia , 2012. ista: 'Chatterjee K, Velner Y. 2012. Mean payoff pushdown games. Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, 6280438.' mla: Chatterjee, Krishnendu, and Yaron Velner. “Mean Payoff Pushdown Games.” Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, 6280438, IEEE, 2012, doi:10.1109/LICS.2012.30. short: K. Chatterjee, Y. Velner, in:, Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2012. conference: end_date: 2012-06-28 location: 'Dubrovnik, Croatia ' name: 'LICS: Logic in Computer Science' start_date: 2012-06-25 date_created: 2018-12-11T12:00:32Z date_published: 2012-08-23T00:00:00Z date_updated: 2023-02-23T12:23:30Z day: '23' department: - _id: KrCh doi: 10.1109/LICS.2012.30 ec_funded: 1 language: - iso: eng month: '08' oa_version: None 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: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science publication_status: published publisher: IEEE publist_id: '3770' quality_controlled: '1' related_material: record: - id: '5377' relation: earlier_version status: public scopus_import: 1 status: public title: Mean payoff pushdown games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '5377' abstract: - lang: eng text: 'Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work we consider solving recursive game graphs (or pushdown game graphs) that can model the control flow of sequential programs with recursion. While pushdown games have been studied before with qualitative objectives, such as reachability and ω-regular objectives, in this work we study for the first time such games with the most well-studied quantitative objective, namely, mean-payoff objectives. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation, but only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two- player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP- hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games; and memoryless modular strategies are sufficient in two- player pushdown games. Finally we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.' alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: ama: Chatterjee K, Velner Y. Mean-Payoff Pushdown Games. IST Austria; 2012. doi:10.15479/AT:IST-2012-0002 apa: Chatterjee, K., & Velner, Y. (2012). Mean-payoff pushdown games. IST Austria. https://doi.org/10.15479/AT:IST-2012-0002 chicago: Chatterjee, Krishnendu, and Yaron Velner. Mean-Payoff Pushdown Games. IST Austria, 2012. https://doi.org/10.15479/AT:IST-2012-0002. ieee: K. Chatterjee and Y. Velner, Mean-payoff pushdown games. IST Austria, 2012. ista: Chatterjee K, Velner Y. 2012. Mean-payoff pushdown games, IST Austria, 33p. mla: Chatterjee, Krishnendu, and Yaron Velner. Mean-Payoff Pushdown Games. IST Austria, 2012, doi:10.15479/AT:IST-2012-0002. short: K. Chatterjee, Y. Velner, Mean-Payoff Pushdown Games, IST Austria, 2012. date_created: 2018-12-12T11:38:59Z date_published: 2012-07-02T00:00:00Z date_updated: 2023-02-23T11:05:50Z day: '02' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2012-0002 file: - access_level: open_access checksum: a03c08c1589dbb0c96183a8bcf3ab240 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:00Z date_updated: 2020-07-14T12:46:38Z file_id: '5522' file_name: IST-2012-002_IST-2012-0002.pdf file_size: 592098 relation: main_file file_date_updated: 2020-07-14T12:46:38Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '33' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '10' related_material: record: - id: '2956' relation: later_version status: public status: public title: Mean-payoff pushdown games type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '5378' abstract: - lang: eng text: 'One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n3 · m) time as compared to the previous known O(n6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n · m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm.' alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Siddhesh full_name: Chaubal, Siddhesh last_name: Chaubal - first_name: Pritish full_name: Kamath, Pritish last_name: Kamath citation: ama: Chatterjee K, Chaubal S, Kamath P. Faster Algorithms for Alternating Refinement Relations. IST Austria; 2012. doi:10.15479/AT:IST-2012-0001 apa: Chatterjee, K., Chaubal, S., & Kamath, P. (2012). Faster algorithms for alternating refinement relations. IST Austria. https://doi.org/10.15479/AT:IST-2012-0001 chicago: Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. Faster Algorithms for Alternating Refinement Relations. IST Austria, 2012. https://doi.org/10.15479/AT:IST-2012-0001. ieee: K. Chatterjee, S. Chaubal, and P. Kamath, Faster algorithms for alternating refinement relations. IST Austria, 2012. ista: Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating refinement relations, IST Austria, 21p. mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Alternating Refinement Relations. IST Austria, 2012, doi:10.15479/AT:IST-2012-0001. short: K. Chatterjee, S. Chaubal, P. Kamath, Faster Algorithms for Alternating Refinement Relations, IST Austria, 2012. date_created: 2018-12-12T11:38:59Z date_published: 2012-07-04T00:00:00Z date_updated: 2023-02-23T12:21:38Z day: '04' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2012-0001 file: - access_level: open_access checksum: ec8d1857cc7095d3de5107a0162ced37 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:28Z date_updated: 2020-07-14T12:46:39Z file_id: '5489' file_name: IST-2012-0001_IST-2012-0001.pdf file_size: 394256 relation: main_file file_date_updated: 2020-07-14T12:46:39Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '21' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '14' related_material: record: - id: '497' relation: later_version status: public status: public title: Faster algorithms for alternating refinement relations type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '2955' abstract: - lang: eng text: 'We consider two-player stochastic games played on finite graphs with reachability objectives where the first player tries to ensure a target state to be visited almost-surely (i.e., with probability 1), or positively (i.e., with positive probability), no matter the strategy of the second player. We classify such games according to the information and the power of randomization available to the players. On the basis of information, the game can be one-sided with either (a) player 1, or (b) player 2 having partial observation (and the other player has perfect observation), or two-sided with (c) both players having partial observation. On the basis of randomization, the players (a) may not be allowed to use randomization (pure strategies), or (b) may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) may use full randomization. Our main results for pure strategies are as follows. (1) For one-sided games with player 1 having partial observation we show that (in contrast to full randomized strategies) belief-based (subset-construction based) strategies are not sufficient, and we present an exponential upper bound on memory both for almostsure and positive winning strategies; we show that the problem of deciding the existence of almost-sure and positive winning strategies for player 1 is EXPTIME-complete. (2) For one-sided games with player 2 having partial observation we show that non-elementary memory is both necessary and sufficient for both almost-sure and positive winning strategies. (3) We show that for the general (two-sided) case finite-memory strategies are sufficient for both positive and almost-sure winning, and at least non-elementary memory is required. We establish the equivalence of the almost-sure winning problems for pure strategies and for randomized strategies with actions invisible. Our equivalence result exhibits serious flaws in previous results of the literature: we show a non-elementary memory lower bound for almost-sure winning whereas an exponential upper bound was previously claimed.' acknowledgement: 'This work was partially supported by FWF Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.' article_number: '6280436' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen citation: ama: 'Chatterjee K, Doyen L. Partial-observation stochastic games: How to win when belief fails. In: Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE; 2012. doi:10.1109/LICS.2012.28' apa: 'Chatterjee, K., & Doyen, L. (2012). Partial-observation stochastic games: How to win when belief fails. In Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. Dubrovnik, Croatia: IEEE. https://doi.org/10.1109/LICS.2012.28' chicago: 'Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic Games: How to Win When Belief Fails.” In Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE, 2012. https://doi.org/10.1109/LICS.2012.28.' ieee: 'K. Chatterjee and L. Doyen, “Partial-observation stochastic games: How to win when belief fails,” in Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, Dubrovnik, Croatia, 2012.' ista: 'Chatterjee K, Doyen L. 2012. Partial-observation stochastic games: How to win when belief fails. Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, 6280436.' mla: 'Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic Games: How to Win When Belief Fails.” Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, 6280436, IEEE, 2012, doi:10.1109/LICS.2012.28.' short: K. Chatterjee, L. Doyen, in:, Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2012. conference: end_date: 2012-06-28 location: Dubrovnik, Croatia name: 'LICS: Logic in Computer Science' start_date: 2012-06-25 date_created: 2018-12-11T12:00:32Z date_published: 2012-08-23T00:00:00Z date_updated: 2023-02-23T12:23:43Z day: '23' department: - _id: KrCh doi: 10.1109/LICS.2012.28 ec_funded: 1 external_id: arxiv: - '1107.2141' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1107.2141 month: '08' oa: 1 oa_version: Preprint 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: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science publication_status: published publisher: IEEE publist_id: '3771' quality_controlled: '1' related_material: record: - id: '2211' relation: later_version status: public - id: '5381' relation: earlier_version status: public scopus_import: 1 status: public title: 'Partial-observation stochastic games: How to win when belief fails' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '3341' abstract: - lang: eng text: 'We consider two-player stochastic games played on a finite state space for an infinite number of rounds. The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine a probability distribution over the successor states. We also consider the important special case of turn-based stochastic games where players make moves in turns, rather than concurrently. We study concurrent games with \omega-regular winning conditions specified as parity objectives. The value for player 1 for a parity objective is the maximal probability with which the player can guarantee the satisfaction of the objective against all strategies of the opponent. We study the problem of continuity and robustness of the value function in concurrent and turn-based stochastic parity gameswith respect to imprecision in the transition probabilities. We present quantitative bounds on the difference of the value function (in terms of the imprecision of the transition probabilities) and show the value continuity for structurally equivalent concurrent games (two games are structurally equivalent if the support of the transition function is same and the probabilities differ). We also show robustness of optimal strategies for structurally equivalent turn-based stochastic parity games. Finally we show that the value continuity property breaks without the structurally equivalent assumption (even for Markov chains) and show that our quantitative bound is asymptotically optimal. Hence our results are tight (the assumption is both necessary and sufficient) and optimal (our quantitative bound is asymptotically optimal).' alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Chatterjee K. Robustness of structurally equivalent concurrent parity games. In: Vol 7213. Springer; 2012:270-285. doi:10.1007/978-3-642-28729-9_18' apa: 'Chatterjee, K. (2012). Robustness of structurally equivalent concurrent parity games (Vol. 7213, pp. 270–285). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Tallinn, Estonia: Springer. https://doi.org/10.1007/978-3-642-28729-9_18' chicago: Chatterjee, Krishnendu. “Robustness of Structurally Equivalent Concurrent Parity Games,” 7213:270–85. Springer, 2012. https://doi.org/10.1007/978-3-642-28729-9_18. ieee: 'K. Chatterjee, “Robustness of structurally equivalent concurrent parity games,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Tallinn, Estonia, 2012, vol. 7213, pp. 270–285.' ista: 'Chatterjee K. 2012. Robustness of structurally equivalent concurrent parity games. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 7213, 270–285.' mla: Chatterjee, Krishnendu. Robustness of Structurally Equivalent Concurrent Parity Games. Vol. 7213, Springer, 2012, pp. 270–85, doi:10.1007/978-3-642-28729-9_18. short: K. Chatterjee, in:, Springer, 2012, pp. 270–285. conference: end_date: 2012-04-01 location: Tallinn, Estonia name: 'FoSSaCS: Foundations of Software Science and Computation Structures' start_date: 2012-03-24 date_created: 2018-12-11T12:02:46Z date_published: 2012-03-22T00:00:00Z date_updated: 2023-02-23T12:23:46Z day: '22' department: - _id: KrCh doi: 10.1007/978-3-642-28729-9_18 ec_funded: 1 external_id: arxiv: - '1107.2009' intvolume: ' 7213' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1107.2009 month: '03' oa: 1 oa_version: Preprint page: 270 - 285 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: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '3284' quality_controlled: '1' related_material: record: - id: '5382' relation: earlier_version status: public scopus_import: 1 status: public title: Robustness of structurally equivalent concurrent parity games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7213 year: '2012' ... --- _id: '2957' abstract: - lang: eng text: 'We consider probabilistic automata on infinite words with acceptance defined by parity conditions. We consider three qualitative decision problems: (i) the positive decision problem asks whether there is a word that is accepted with positive probability; (ii) the almost decision problem asks whether there is a word that is accepted with probability 1; and (iii) the limit decision problem asks whether words are accepted with probability arbitrarily close to 1. We unify and generalize several decidability results for probabilistic automata over infinite words, and identify a robust (closed under union and intersection) subclass of probabilistic automata for which all the qualitative decision problems are decidable for parity conditions. We also show that if the input words are restricted to lasso shape (regular) words, then the positive and almost problems are decidable for all probabilistic automata with parity conditions. For most decidable problems we show an optimal PSPACE-complete complexity bound.' article_number: '6280437' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Mathieu full_name: Tracol, Mathieu id: 3F54FA38-F248-11E8-B48F-1D18A9856A87 last_name: Tracol citation: ama: 'Chatterjee K, Tracol M. Decidable problems for probabilistic automata on infinite words. In: Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE; 2012. doi:10.1109/LICS.2012.29' apa: 'Chatterjee, K., & Tracol, M. (2012). Decidable problems for probabilistic automata on infinite words. In Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. Dubrovnik, Croatia : IEEE. https://doi.org/10.1109/LICS.2012.29' chicago: Chatterjee, Krishnendu, and Mathieu Tracol. “Decidable Problems for Probabilistic Automata on Infinite Words.” In Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE, 2012. https://doi.org/10.1109/LICS.2012.29. ieee: K. Chatterjee and M. Tracol, “Decidable problems for probabilistic automata on infinite words,” in Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, Dubrovnik, Croatia , 2012. ista: 'Chatterjee K, Tracol M. 2012. Decidable problems for probabilistic automata on infinite words. Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, 6280437.' mla: Chatterjee, Krishnendu, and Mathieu Tracol. “Decidable Problems for Probabilistic Automata on Infinite Words.” Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, 6280437, IEEE, 2012, doi:10.1109/LICS.2012.29. short: K. Chatterjee, M. Tracol, in:, Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2012. conference: end_date: 2012-06-28 location: 'Dubrovnik, Croatia ' name: 'LICS: Logic in Computer Science' start_date: 2012-06-25 date_created: 2018-12-11T12:00:33Z date_published: 2012-08-23T00:00:00Z date_updated: 2023-02-23T12:23:51Z day: '23' department: - _id: KrCh doi: 10.1109/LICS.2012.29 ec_funded: 1 external_id: arxiv: - '1107.2091' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1107.2091 month: '08' oa: 1 oa_version: Preprint 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: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science publication_status: published publisher: IEEE publist_id: '3769' quality_controlled: '1' related_material: record: - id: '5384' relation: earlier_version status: public scopus_import: 1 status: public title: Decidable problems for probabilistic automata on infinite words type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '3249' abstract: - lang: eng text: Boolean notions of correctness are formalized by preorders on systems. Quantitative measures of correctness can be formalized by real-valued distance functions between systems, where the distance between implementation and specification provides a measure of "fit" or "desirability". We extend the simulation preorder to the quantitative setting by making each player of a simulation game pay a certain price for her choices. We use the resulting games with quantitative objectives to define three different simulation distances. The correctness distance measures how much the specification must be changed in order to be satisfied by the implementation. The coverage distance measures how much the implementation restricts the degrees of freedom offered by the specification. The robustness distance measures how much a system can deviate from the implementation description without violating the specification. We consider these distances for safety as well as liveness specifications. The distances can be computed in polynomial time for safety specifications, and for liveness specifications given by weak fairness constraints. We show that the distance functions satisfy the triangle inequality, that the distance between two systems does not increase under parallel composition with a third system, and that the distance between two systems can be bounded from above and below by distances between abstractions of the two systems. These properties suggest that our simulation distances provide an appropriate basis for a quantitative theory of discrete systems. We also demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes. acknowledgement: This work was partially supported by the ERC Advanced Grant QUAREM, the FWF NFN Grant S11402-N23 (RiSE), the European Union project COMBEST and the European Network of Excellence Artist Design. author: - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - 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: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna citation: ama: Cerny P, Henzinger TA, Radhakrishna A. Simulation distances. Theoretical Computer Science. 2012;413(1):21-35. doi:10.1016/j.tcs.2011.08.002 apa: Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2012). Simulation distances. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2011.08.002 chicago: Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Simulation Distances.” Theoretical Computer Science. Elsevier, 2012. https://doi.org/10.1016/j.tcs.2011.08.002. ieee: P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Simulation distances,” Theoretical Computer Science, vol. 413, no. 1. Elsevier, pp. 21–35, 2012. ista: Cerny P, Henzinger TA, Radhakrishna A. 2012. Simulation distances. Theoretical Computer Science. 413(1), 21–35. mla: Cerny, Pavol, et al. “Simulation Distances.” Theoretical Computer Science, vol. 413, no. 1, Elsevier, 2012, pp. 21–35, doi:10.1016/j.tcs.2011.08.002. short: P. Cerny, T.A. Henzinger, A. Radhakrishna, Theoretical Computer Science 413 (2012) 21–35. date_created: 2018-12-11T12:02:15Z date_published: 2012-01-06T00:00:00Z date_updated: 2023-02-23T12:24:04Z day: '06' department: - _id: ToHe doi: 10.1016/j.tcs.2011.08.002 ec_funded: 1 intvolume: ' 413' issue: '1' language: - iso: eng month: '01' oa_version: None page: 21 - 35 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25EFB36C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '215543' name: COMponent-Based Embedded Systems design Techniques - _id: 25F1337C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '214373' name: Design for Embedded Systems publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '3408' pubrep_id: '42' quality_controlled: '1' related_material: record: - id: '4393' relation: earlier_version status: public - id: '5389' relation: earlier_version status: public scopus_import: 1 status: public title: Simulation distances type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 413 year: '2012' ... --- _id: '3124' abstract: - lang: eng text: "We consider the problem of inference in a graphical model with binary variables. While in theory it is arguably preferable to compute marginal probabilities, in practice researchers often use MAP inference due to the availability of efficient discrete optimization algorithms. We bridge the gap between the two approaches by introducing the Discrete Marginals technique in which approximate marginals are obtained by minimizing an objective function with unary and pairwise terms over a discretized domain. This allows the use of techniques originally developed for MAP-MRF inference and learning. We explore two ways to set up the objective function - by discretizing the Bethe free energy and by learning it from training data. Experimental results show that for certain types of graphs a learned function can outperform the Bethe approximation. We also establish a link between the Bethe free energy and submodular functions.\r\n" alternative_title: - Inferning 2012 author: - first_name: Filip full_name: Korc, Filip id: 476A2FD6-F248-11E8-B48F-1D18A9856A87 last_name: Korc - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Korc F, Kolmogorov V, Lampert C. Approximating marginals using discrete energy minimization. In: ICML; 2012.' apa: 'Korc, F., Kolmogorov, V., & Lampert, C. (2012). Approximating marginals using discrete energy minimization. Presented at the ICML: International Conference on Machine Learning, Edinburgh, Scotland: ICML.' chicago: Korc, Filip, Vladimir Kolmogorov, and Christoph Lampert. “Approximating Marginals Using Discrete Energy Minimization.” ICML, 2012. ieee: 'F. Korc, V. Kolmogorov, and C. Lampert, “Approximating marginals using discrete energy minimization,” presented at the ICML: International Conference on Machine Learning, Edinburgh, Scotland, 2012.' ista: 'Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete energy minimization. ICML: International Conference on Machine Learning, Inferning 2012, .' mla: Korc, Filip, et al. Approximating Marginals Using Discrete Energy Minimization. ICML, 2012. short: F. Korc, V. Kolmogorov, C. Lampert, in:, ICML, 2012. conference: end_date: 2012-07-01 location: Edinburgh, Scotland name: 'ICML: International Conference on Machine Learning' start_date: 2012-06-26 date_created: 2018-12-11T12:01:31Z date_published: 2012-06-30T00:00:00Z date_updated: 2023-02-23T12:24:24Z day: '30' ddc: - '000' department: - _id: ChLa - _id: VlKo file: - access_level: open_access checksum: 3d0d4246548c736857302aadb2ff5d15 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:34Z date_updated: 2020-07-14T12:46:00Z file_id: '4889' file_name: IST-2016-565-v1+1_DM-inferning2012.pdf file_size: 305836 relation: main_file file_date_updated: 2020-07-14T12:46:00Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version publication_status: published publisher: ICML publist_id: '3575' pubrep_id: '565' quality_controlled: '1' related_material: record: - id: '5396' relation: later_version status: public status: public title: Approximating marginals using discrete energy minimization type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '5396' abstract: - lang: eng text: We consider the problem of inference in agraphical model with binary variables. While in theory it is arguably preferable to compute marginal probabilities, in practice researchers often use MAP inference due to the availability of efficient discrete optimization algorithms. We bridge the gap between the two approaches by introducing the Discrete Marginals technique in which approximate marginals are obtained by minimizing an objective function with unary and pair-wise terms over a discretized domain. This allows the use of techniques originally devel-oped for MAP-MRF inference and learning. We explore two ways to set up the objective function - by discretizing the Bethe free energy and by learning it from training data. Experimental results show that for certain types of graphs a learned function can out-perform the Bethe approximation. We also establish a link between the Bethe free energy and submodular functions. alternative_title: - IST Austria Technical Report author: - first_name: Filip full_name: Korc, Filip id: 476A2FD6-F248-11E8-B48F-1D18A9856A87 last_name: Korc - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: Korc F, Kolmogorov V, Lampert C. Approximating Marginals Using Discrete Energy Minimization. IST Austria; 2012. doi:10.15479/AT:IST-2012-0003 apa: Korc, F., Kolmogorov, V., & Lampert, C. (2012). Approximating marginals using discrete energy minimization. IST Austria. https://doi.org/10.15479/AT:IST-2012-0003 chicago: Korc, Filip, Vladimir Kolmogorov, and Christoph Lampert. Approximating Marginals Using Discrete Energy Minimization. IST Austria, 2012. https://doi.org/10.15479/AT:IST-2012-0003. ieee: F. Korc, V. Kolmogorov, and C. Lampert, Approximating marginals using discrete energy minimization. IST Austria, 2012. ista: Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete energy minimization, IST Austria, 13p. mla: Korc, Filip, et al. Approximating Marginals Using Discrete Energy Minimization. IST Austria, 2012, doi:10.15479/AT:IST-2012-0003. short: F. Korc, V. Kolmogorov, C. Lampert, Approximating Marginals Using Discrete Energy Minimization, IST Austria, 2012. date_created: 2018-12-12T11:39:06Z date_published: 2012-07-23T00:00:00Z date_updated: 2023-02-23T11:13:22Z day: '23' ddc: - '000' department: - _id: VlKo - _id: ChLa doi: 10.15479/AT:IST-2012-0003 file: - access_level: open_access checksum: 7e0ba85ad123b13223aaf6cdde2d288c content_type: application/pdf creator: system date_created: 2018-12-12T11:53:29Z date_updated: 2020-07-14T12:46:44Z file_id: '5490' file_name: IST-2012-0003_IST-2012-0003.pdf file_size: 618744 relation: main_file file_date_updated: 2020-07-14T12:46:44Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '13' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '36' related_material: record: - id: '3124' relation: earlier_version status: public status: public title: Approximating marginals using discrete energy minimization type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '5398' abstract: - lang: eng text: This document is created as a part of the project “Repository for Research Data on IST Austria”. It summarises the actual state of research data at IST Austria, based on survey results. It supports the choice of appropriate software, which would best fit the requirements of their users, the researchers. author: - first_name: Jana full_name: Porsche, Jana id: 3252EDC2-F248-11E8-B48F-1D18A9856A87 last_name: Porsche citation: ama: Porsche J. Actual State of Research Data @ ISTAustria. IST Austria; 2012. apa: Porsche, J. (2012). Actual state of research data @ ISTAustria. IST Austria. chicago: Porsche, Jana. Actual State of Research Data @ ISTAustria. IST Austria, 2012. ieee: J. Porsche, Actual state of research data @ ISTAustria. IST Austria, 2012. ista: Porsche J. 2012. Actual state of research data @ ISTAustria, IST Austria,p. mla: Porsche, Jana. Actual State of Research Data @ ISTAustria. IST Austria, 2012. short: J. Porsche, Actual State of Research Data @ ISTAustria, IST Austria, 2012. date_created: 2018-12-12T11:39:06Z date_published: 2012-11-12T00:00:00Z date_updated: 2020-07-14T23:04:49Z day: '12' ddc: - '020' department: - _id: E-Lib file: - access_level: open_access checksum: e0a7c041eea1ca4b70ab6f9ec5177f4e content_type: application/pdf creator: system date_created: 2018-12-12T11:53:11Z date_updated: 2020-07-14T12:46:44Z file_id: '5472' file_name: IST-2012-103-v1+1_Actual_state_of_research_data_@_IST_Austria.pdf file_size: 238544 relation: main_file file_date_updated: 2020-07-14T12:46:44Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication_status: published publisher: IST Austria pubrep_id: '103' status: public title: Actual state of research data @ ISTAustria type: report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '5839' abstract: - lang: eng text: "Canny's edge detection algorithm is a classical and robust method for edge detection in gray-scale images. The two \r\nsignificant features of this method are introduction of NMS (Non-Maximum Suppression) and double thresholding of \r\nthe \ gradient image. Due to poor illumination, the region boundaries in \ an image may become vague, creating \r\nuncertainties in the gradient \ image. In this paper, we have proposed an algorithm based on the \ concept of type-2 fuzzy sets to handle uncertainties that automatically \ selects the threshold values needed to segment the gradient image using classical Canny’s edge detection algorithm. The results show that our algorithm works significantly well on different benchmark images as well as medical images (hand radiography images). " author: - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Jaya full_name: Sil, Jaya last_name: Sil citation: ama: Biswas R, Sil J. An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. Procedia Technology. 2012;4:820-824. doi:10.1016/j.protcy.2012.05.134 apa: Biswas, R., & Sil, J. (2012). An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. Procedia Technology. Elsevier. https://doi.org/10.1016/j.protcy.2012.05.134 chicago: Biswas, Ranita, and Jaya Sil. “An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets.” Procedia Technology. Elsevier, 2012. https://doi.org/10.1016/j.protcy.2012.05.134. ieee: R. Biswas and J. Sil, “An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets,” Procedia Technology, vol. 4. Elsevier, pp. 820–824, 2012. ista: Biswas R, Sil J. 2012. An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. Procedia Technology. 4, 820–824. mla: Biswas, Ranita, and Jaya Sil. “An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets.” Procedia Technology, vol. 4, Elsevier, 2012, pp. 820–24, doi:10.1016/j.protcy.2012.05.134. short: R. Biswas, J. Sil, Procedia Technology 4 (2012) 820–824. date_created: 2019-01-17T11:54:21Z date_published: 2012-05-01T00:00:00Z date_updated: 2021-01-12T08:03:43Z day: '01' ddc: - '000' doi: 10.1016/j.protcy.2012.05.134 extern: '1' file: - access_level: open_access checksum: ba0185986b151d8c11201f48cd505ceb content_type: application/pdf creator: dernst date_created: 2019-01-21T07:28:06Z date_updated: 2020-07-14T12:47:12Z file_id: '5863' file_name: 2012_Procedia_Biswas.pdf file_size: 305426 relation: main_file file_date_updated: 2020-07-14T12:47:12Z has_accepted_license: '1' intvolume: ' 4' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 820-824 publication: Procedia Technology publication_identifier: issn: - 2212-0173 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets 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: 4 year: '2012' ... --- _id: '596' abstract: - lang: eng text: The human Mediator complex controls RNA polymerase II (pol II) function in ways that remain incompletely understood. Activator-Mediator binding alters Mediator structure, and these activator-induced structural shifts appear to play key roles in regulating transcription. A recent cryo-electron microscopy (EM) analysis revealed that pol II adopted a stable orientation within a Mediator-pol II-TFIIF assembly in which Mediator was bound to the activation domain of viral protein 16 (VP16). Whereas TFIIF was shown to be important for orienting pol II within this assembly, the potential role of the activator was not assessed. To determine how activator binding might affect pol II orientation, we isolated human Mediator-pol II-TFIIF complexes in which Mediator was not bound to an activator. Cryo-EM analysis of this assembly, coupled with pol II crystal structure docking, revealed that pol II binds Mediator at the same general location; however, in contrast to VP16-bound Mediator, pol II does not appear to stably orient in the absence of an activator. Variability in pol II orientation might be important mechanistically, perhaps to enable sense and antisense transcription at human promoters. Because Mediator interacts extensively with pol II, these results suggest that Mediator structural shifts induced by activator binding help stably orient pol II prior to transcription initiation. article_processing_charge: No author: - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 - first_name: Dylan full_name: Taatjes, Dylan last_name: Taatjes citation: ama: Bernecky C, Taatjes D. Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. Journal of Molecular Biology. 2012;417(5):387-394. doi:10.1016/j.jmb.2012.02.014 apa: Bernecky, C., & Taatjes, D. (2012). Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2012.02.014 chicago: Bernecky, Carrie, and Dylan Taatjes. “Activator-Mediator Binding Stabilizes RNA Polymerase II Orientation within the Human Mediator-RNA Polymerase II-TFIIF Assembly.” Journal of Molecular Biology. Elsevier, 2012. https://doi.org/10.1016/j.jmb.2012.02.014. ieee: C. Bernecky and D. Taatjes, “Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly,” Journal of Molecular Biology, vol. 417, no. 5. Elsevier, pp. 387–394, 2012. ista: Bernecky C, Taatjes D. 2012. Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. Journal of Molecular Biology. 417(5), 387–394. mla: Bernecky, Carrie, and Dylan Taatjes. “Activator-Mediator Binding Stabilizes RNA Polymerase II Orientation within the Human Mediator-RNA Polymerase II-TFIIF Assembly.” Journal of Molecular Biology, vol. 417, no. 5, Elsevier, 2012, pp. 387–94, doi:10.1016/j.jmb.2012.02.014. short: C. Bernecky, D. Taatjes, Journal of Molecular Biology 417 (2012) 387–394. date_created: 2018-12-11T11:47:24Z date_published: 2012-04-13T00:00:00Z date_updated: 2021-01-12T08:05:21Z day: '13' doi: 10.1016/j.jmb.2012.02.014 extern: '1' intvolume: ' 417' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4582759/ month: '04' oa: 1 oa_version: None page: 387 - 394 publication: Journal of Molecular Biology publication_status: published publisher: Elsevier publist_id: '7208' status: public title: Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 417 year: '2012' ... --- _id: '6136' abstract: - lang: eng text: Tonic receptors convey stimulus duration and intensity and are implicated in homeostatic control. However, how tonic homeostatic signals are generated and how they reconfigure neural circuits and modify animal behavior is poorly understood. Here we show that Caenorhabditis elegans O2-sensing neurons are tonic receptors that continuously signal ambient [O2] to set the animal's behavioral state. Sustained signaling relied on a Ca2+ relay involving L-type voltage-gated Ca2+ channels, the ryanodine and the inositol-1,4,5-trisphosphate receptors. Tonic activity evoked continuous neuropeptide release, which helps elicit the enduring behavioral state associated with high [O2]. Sustained O2 receptor signaling was propagated to downstream neural circuits, including the hub interneuron RMG. O2 receptors evoked similar locomotory states at particular O2 concentrations, regardless of previous d[O2]/dt. However, a phasic component of the URX receptors' response to high d[O2]/dt, as well as tonic-to-phasic transformations in downstream interneurons, enabled transient reorientation movements shaped by d[O2]/dt. Our results highlight how tonic homeostatic signals can generate both transient and enduring behavioral change. author: - first_name: Karl Emanuel full_name: Busch, Karl Emanuel last_name: Busch - first_name: Patrick full_name: Laurent, Patrick last_name: Laurent - first_name: Zoltan full_name: Soltesz, Zoltan last_name: Soltesz - first_name: Robin Joseph full_name: Murphy, Robin Joseph last_name: Murphy - first_name: Olivier full_name: Faivre, Olivier last_name: Faivre - first_name: Berthold full_name: Hedwig, Berthold last_name: Hedwig - first_name: Martin full_name: Thomas, Martin last_name: Thomas - first_name: Heather L full_name: Smith, Heather L last_name: Smith - 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: Busch KE, Laurent P, Soltesz Z, et al. Tonic signaling from O2 sensors sets neural circuit activity and behavioral state. Nature Neuroscience. 2012;15(4):581-591. doi:10.1038/nn.3061 apa: Busch, K. E., Laurent, P., Soltesz, Z., Murphy, R. J., Faivre, O., Hedwig, B., … de Bono, M. (2012). Tonic signaling from O2 sensors sets neural circuit activity and behavioral state. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/nn.3061 chicago: Busch, Karl Emanuel, Patrick Laurent, Zoltan Soltesz, Robin Joseph Murphy, Olivier Faivre, Berthold Hedwig, Martin Thomas, Heather L Smith, and Mario de Bono. “Tonic Signaling from O2 Sensors Sets Neural Circuit Activity and Behavioral State.” Nature Neuroscience. Springer Nature, 2012. https://doi.org/10.1038/nn.3061. ieee: K. E. Busch et al., “Tonic signaling from O2 sensors sets neural circuit activity and behavioral state,” Nature Neuroscience, vol. 15, no. 4. Springer Nature, pp. 581–591, 2012. ista: Busch KE, Laurent P, Soltesz Z, Murphy RJ, Faivre O, Hedwig B, Thomas M, Smith HL, de Bono M. 2012. Tonic signaling from O2 sensors sets neural circuit activity and behavioral state. Nature Neuroscience. 15(4), 581–591. mla: Busch, Karl Emanuel, et al. “Tonic Signaling from O2 Sensors Sets Neural Circuit Activity and Behavioral State.” Nature Neuroscience, vol. 15, no. 4, Springer Nature, 2012, pp. 581–91, doi:10.1038/nn.3061. short: K.E. Busch, P. Laurent, Z. Soltesz, R.J. Murphy, O. Faivre, B. Hedwig, M. Thomas, H.L. Smith, M. de Bono, Nature Neuroscience 15 (2012) 581–591. date_created: 2019-03-20T14:23:30Z date_published: 2012-03-04T00:00:00Z date_updated: 2021-01-12T08:06:17Z day: '04' doi: 10.1038/nn.3061 extern: '1' external_id: pmid: - '22388961' intvolume: ' 15' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564487/ month: '03' oa: 1 oa_version: Submitted Version page: 581-591 pmid: 1 publication: Nature Neuroscience publication_identifier: issn: - 1097-6256 - 1546-1726 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Tonic signaling from O2 sensors sets neural circuit activity and behavioral state type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2012' ... --- _id: '6746' abstract: - lang: eng text: This paper proposes a novel cooperative approach for two-hop amplify-and-forward (A&F) relaying that exploits both the signal forwarded by the relay and the one directly transmitted by the source in impulse-radio ultra-wideband (IR-UWB) systems. Specifically, we focus on a non-coherent setup employing a double-differential encoding scheme at the source node and a single differential demodulation at the relay and destination. The log-likelihood ratio based decision rule is derived at the destination node. A semi-analytical power allocation strategy is presented by evaluating a closed-form expression for the effective signal to noise ratio (SNR) at the destination, which is maximized by exhaustive search. Numerical simulations show that the proposed system outperforms both the direct transmission with single differential encoding and the non-cooperative multi-hop approach in different scenarios. author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Qi full_name: Zhou, Qi last_name: Zhou - first_name: Xiaoli full_name: Ma, Xiaoli last_name: Ma - first_name: Vincenzo full_name: Lottici, Vincenzo last_name: Lottici citation: ama: 'Mondelli M, Zhou Q, Ma X, Lottici V. A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems. In: 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). IEEE; 2012:2905-2908. doi:10.1109/icassp.2012.6288524' apa: 'Mondelli, M., Zhou, Q., Ma, X., & Lottici, V. (2012). A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems. In 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) (pp. 2905–2908). Kyoto, Japan: IEEE. https://doi.org/10.1109/icassp.2012.6288524' chicago: Mondelli, Marco, Qi Zhou, Xiaoli Ma, and Vincenzo Lottici. “A Cooperative Approach for Amplify-and-Forward Differential Transmitted Reference IR-UWB Relay Systems.” In 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2905–8. IEEE, 2012. https://doi.org/10.1109/icassp.2012.6288524. ieee: M. Mondelli, Q. Zhou, X. Ma, and V. Lottici, “A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems,” in 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Kyoto, Japan, 2012, pp. 2905–2908. ista: 'Mondelli M, Zhou Q, Ma X, Lottici V. 2012. A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems. 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). ICASSP: International Conference on Acoustics, Speech and Signal Processing, 2905–2908.' mla: Mondelli, Marco, et al. “A Cooperative Approach for Amplify-and-Forward Differential Transmitted Reference IR-UWB Relay Systems.” 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), IEEE, 2012, pp. 2905–08, doi:10.1109/icassp.2012.6288524. short: M. Mondelli, Q. Zhou, X. Ma, V. Lottici, in:, 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), IEEE, 2012, pp. 2905–2908. conference: end_date: 2012-03-30 location: Kyoto, Japan name: 'ICASSP: International Conference on Acoustics, Speech and Signal Processing' start_date: 2012-03-25 date_created: 2019-07-31T09:14:48Z date_published: 2012-07-31T00:00:00Z date_updated: 2021-01-12T08:08:49Z day: '31' doi: 10.1109/icassp.2012.6288524 extern: '1' language: - iso: eng month: '07' oa_version: None page: 2905-2908 publication: 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) publication_identifier: issn: - 1520-6149 publication_status: published publisher: IEEE quality_controlled: '1' status: public title: A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '7074' abstract: - lang: eng text: The Seebeck coefficients, electrical resistivities, total thermal conductivities, and magnetization are reported for temperatures between 5 and 350 K for n-type Bi0.88Sb0.12 nano-composite alloys made by Ho-doping at the 0, 1, and 3 % atomic levels. The alloys were prepared using a dc hot-pressing method, and are shown to be single phase for both Ho contents with grain sizes on the average of 900 nm. We find the parent compound has a maximum of ZT = 0.28 at 231 K, while doping 1 % Ho increases the maximum ZT to 0.31 at 221 K and the 3 % doped sample suppresses the maximum ZT = 0.24 at a temperature of 260 K. article_processing_charge: No article_type: original author: - first_name: K. C. full_name: Lukas, K. C. last_name: Lukas - first_name: G. full_name: Joshi, G. last_name: Joshi - 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: Z. F. full_name: Ren, Z. F. last_name: Ren - first_name: C. P. full_name: Opeil, C. P. last_name: Opeil citation: ama: Lukas KC, Joshi G, Modic KA, Ren ZF, Opeil CP. Thermoelectric properties of Ho-doped Bi0.88Sb0.12. Journal of Materials Science. 2012;47(15):5729-5734. doi:10.1007/s10853-012-6463-6 apa: Lukas, K. C., Joshi, G., Modic, K. A., Ren, Z. F., & Opeil, C. P. (2012). Thermoelectric properties of Ho-doped Bi0.88Sb0.12. Journal of Materials Science. Springer Nature. https://doi.org/10.1007/s10853-012-6463-6 chicago: Lukas, K. C., G. Joshi, Kimberly A Modic, Z. F. Ren, and C. P. Opeil. “Thermoelectric Properties of Ho-Doped Bi0.88Sb0.12.” Journal of Materials Science. Springer Nature, 2012. https://doi.org/10.1007/s10853-012-6463-6. ieee: K. C. Lukas, G. Joshi, K. A. Modic, Z. F. Ren, and C. P. Opeil, “Thermoelectric properties of Ho-doped Bi0.88Sb0.12,” Journal of Materials Science, vol. 47, no. 15. Springer Nature, pp. 5729–5734, 2012. ista: Lukas KC, Joshi G, Modic KA, Ren ZF, Opeil CP. 2012. Thermoelectric properties of Ho-doped Bi0.88Sb0.12. Journal of Materials Science. 47(15), 5729–5734. mla: Lukas, K. C., et al. “Thermoelectric Properties of Ho-Doped Bi0.88Sb0.12.” Journal of Materials Science, vol. 47, no. 15, Springer Nature, 2012, pp. 5729–34, doi:10.1007/s10853-012-6463-6. short: K.C. Lukas, G. Joshi, K.A. Modic, Z.F. Ren, C.P. Opeil, Journal of Materials Science 47 (2012) 5729–5734. date_created: 2019-11-19T13:36:54Z date_published: 2012-08-01T00:00:00Z date_updated: 2021-01-12T08:11:43Z day: '01' doi: 10.1007/s10853-012-6463-6 extern: '1' intvolume: ' 47' issue: '15' language: - iso: eng month: '08' oa_version: None page: 5729-5734 publication: Journal of Materials Science publication_identifier: eissn: - 1573-4803 issn: - 0022-2461 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Thermoelectric properties of Ho-doped Bi0.88Sb0.12 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2012' ... --- _id: '7308' abstract: - lang: eng text: 'Carbon has been used widely as the basis of porous cathodes for nonaqueous Li–O2 cells. However, the stability of carbon and the effect of carbon on electrolyte decomposition in such cells are complex and depend on the hydrophobicity/hydrophilicity of the carbon surface. Analyzing carbon cathodes, cycled in Li–O2 cells between 2 and 4 V, using acid treatment and Fenton’s reagent, and combined with differential electrochemical mass spectrometry and FTIR, demonstrates the following: Carbon is relatively stable below 3.5 V (vs Li/Li+) on discharge or charge, especially so for hydrophobic carbon, but is unstable on charging above 3.5 V (in the presence of Li2O2), oxidatively decomposing to form Li2CO3. Direct chemical reaction with Li2O2 accounts for only a small proportion of the total carbon decomposition on cycling. Carbon promotes electrolyte decomposition during discharge and charge in a Li–O2 cell, giving rise to Li2CO3 and Li carboxylates (DMSO and tetraglyme electrolytes). The Li2CO3 and Li carboxylates present at the end of discharge and those that form on charge result in polarization on the subsequent charge. Li2CO3 (derived from carbon and from the electrolyte) as well as the Li carboxylates (derived from the electrolyte) decompose and form on charging. Oxidation of Li2CO3 on charging to ∼4 V is incomplete; Li2CO3 accumulates on cycling resulting in electrode passivation and capacity fading. Hydrophilic carbon is less stable and more catalytically active toward electrolyte decomposition than carbon with a hydrophobic surface. If the Li–O2 cell could be charged at or below 3.5 V, then carbon may be relatively stable, however, its ability to promote electrolyte decomposition, presenting problems for its use in a practical Li–O2 battery. The results emphasize that stable cycling of Li2O2 at the cathode in a Li–O2 cell depends on the synergy between electrolyte and electrode; the stability of the electrode and the electrolyte cannot be considered in isolation.' article_processing_charge: No article_type: original author: - first_name: Muhammed M. full_name: Ottakam Thotiyl, Muhammed M. last_name: Ottakam Thotiyl - 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: Zhangquan full_name: Peng, Zhangquan last_name: Peng - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce citation: ama: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Bruce PG. The carbon electrode in nonaqueous Li–O2 cells. Journal of the American Chemical Society. 2012;135(1):494-500. doi:10.1021/ja310258x apa: Ottakam Thotiyl, M. M., Freunberger, S. A., Peng, Z., & Bruce, P. G. (2012). The carbon electrode in nonaqueous Li–O2 cells. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja310258x chicago: Ottakam Thotiyl, Muhammed M., Stefan Alexander Freunberger, Zhangquan Peng, and Peter G. Bruce. “The Carbon Electrode in Nonaqueous Li–O2 Cells.” Journal of the American Chemical Society. ACS, 2012. https://doi.org/10.1021/ja310258x. ieee: M. M. Ottakam Thotiyl, S. A. Freunberger, Z. Peng, and P. G. Bruce, “The carbon electrode in nonaqueous Li–O2 cells,” Journal of the American Chemical Society, vol. 135, no. 1. ACS, pp. 494–500, 2012. ista: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Bruce PG. 2012. The carbon electrode in nonaqueous Li–O2 cells. Journal of the American Chemical Society. 135(1), 494–500. mla: Ottakam Thotiyl, Muhammed M., et al. “The Carbon Electrode in Nonaqueous Li–O2 Cells.” Journal of the American Chemical Society, vol. 135, no. 1, ACS, 2012, pp. 494–500, doi:10.1021/ja310258x. short: M.M. Ottakam Thotiyl, S.A. Freunberger, Z. Peng, P.G. Bruce, Journal of the American Chemical Society 135 (2012) 494–500. date_created: 2020-01-15T12:18:57Z date_published: 2012-11-28T00:00:00Z date_updated: 2021-01-12T08:12:56Z day: '28' doi: 10.1021/ja310258x extern: '1' intvolume: ' 135' issue: '1' language: - iso: eng month: '11' oa_version: None page: 494-500 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: ACS quality_controlled: '1' status: public title: The carbon electrode in nonaqueous Li–O2 cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2012' ... --- _id: '7309' abstract: - lang: eng text: Energy‐storage technologies, including electrical double‐layer capacitors and rechargeable batteries, have attracted significant attention for applications in portable electronic devices, electric vehicles, bulk electricity storage at power stations, and “load leveling” of renewable sources, such as solar energy and wind power. Transforming lithium batteries and electric double‐layer capacitors requires a step change in the science underpinning these devices, including the discovery of new materials, new electrochemistry, and an increased understanding of the processes on which the devices depend. The Review will consider some of the current scientific issues underpinning lithium batteries and electric double‐layer capacitors. article_processing_charge: No article_type: original author: - first_name: Nam-Soon full_name: Choi, Nam-Soon last_name: Choi - first_name: Zonghai full_name: Chen, Zonghai last_name: Chen - 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: Xiulei full_name: Ji, Xiulei last_name: Ji - first_name: Yang-Kook full_name: Sun, Yang-Kook last_name: Sun - first_name: Khalil full_name: Amine, Khalil last_name: Amine - first_name: Gleb full_name: Yushin, Gleb last_name: Yushin - first_name: Linda F. full_name: Nazar, Linda F. last_name: Nazar - first_name: Jaephil full_name: Cho, Jaephil last_name: Cho - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce citation: ama: Choi N-S, Chen Z, Freunberger SA, et al. Challenges facing Lithium batteries and electrical double-layer capacitors. Angewandte Chemie International Edition. 2012;51(40):9994-10024. doi:10.1002/anie.201201429 apa: Choi, N.-S., Chen, Z., Freunberger, S. A., Ji, X., Sun, Y.-K., Amine, K., … Bruce, P. G. (2012). Challenges facing Lithium batteries and electrical double-layer capacitors. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201201429 chicago: Choi, Nam-Soon, Zonghai Chen, Stefan Alexander Freunberger, Xiulei Ji, Yang-Kook Sun, Khalil Amine, Gleb Yushin, Linda F. Nazar, Jaephil Cho, and Peter G. Bruce. “Challenges Facing Lithium Batteries and Electrical Double-Layer Capacitors.” Angewandte Chemie International Edition. Wiley, 2012. https://doi.org/10.1002/anie.201201429. ieee: N.-S. Choi et al., “Challenges facing Lithium batteries and electrical double-layer capacitors,” Angewandte Chemie International Edition, vol. 51, no. 40. Wiley, pp. 9994–10024, 2012. ista: Choi N-S, Chen Z, Freunberger SA, Ji X, Sun Y-K, Amine K, Yushin G, Nazar LF, Cho J, Bruce PG. 2012. Challenges facing Lithium batteries and electrical double-layer capacitors. Angewandte Chemie International Edition. 51(40), 9994–10024. mla: Choi, Nam-Soon, et al. “Challenges Facing Lithium Batteries and Electrical Double-Layer Capacitors.” Angewandte Chemie International Edition, vol. 51, no. 40, Wiley, 2012, pp. 9994–10024, doi:10.1002/anie.201201429. short: N.-S. Choi, Z. Chen, S.A. Freunberger, X. Ji, Y.-K. Sun, K. Amine, G. Yushin, L.F. Nazar, J. Cho, P.G. Bruce, Angewandte Chemie International Edition 51 (2012) 9994–10024. date_created: 2020-01-15T12:19:11Z date_published: 2012-10-01T00:00:00Z date_updated: 2021-01-12T08:12:56Z day: '01' doi: 10.1002/anie.201201429 extern: '1' intvolume: ' 51' issue: '40' language: - iso: eng month: '10' oa_version: None page: 9994-10024 publication: Angewandte Chemie International Edition publication_identifier: issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Challenges facing Lithium batteries and electrical double-layer capacitors type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2012' ... --- _id: '7310' abstract: - lang: eng text: The rechargeable nonaqueous lithium-air (Li-O2) battery is receiving a great deal of interest because, theoretically, its specific energy far exceeds the best that can be achieved with lithium-ion cells. Operation of the rechargeable Li-O2 battery depends critically on repeated and highly reversible formation/decomposition of lithium peroxide (Li2O2) at the cathode upon cycling. Here, we show that this process is possible with the use of a dimethyl sulfoxide electrolyte and a porous gold electrode (95% capacity retention from cycles 1 to 100), whereas previously only partial Li2O2 formation/decomposition and limited cycling could occur. Furthermore, we present data indicating that the kinetics of Li2O2 oxidation on charge is approximately 10 times faster than on carbon electrodes. article_processing_charge: No article_type: original author: - first_name: Z. full_name: Peng, Z. last_name: Peng - 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: Y. full_name: Chen, Y. last_name: Chen - first_name: P. G. full_name: Bruce, P. G. last_name: Bruce citation: ama: Peng Z, Freunberger SA, Chen Y, Bruce PG. A reversible and higher-rate Li-O2 battery. Science. 2012;337(6094):563-566. doi:10.1126/science.1223985 apa: Peng, Z., Freunberger, S. A., Chen, Y., & Bruce, P. G. (2012). A reversible and higher-rate Li-O2 battery. Science. AAAS. https://doi.org/10.1126/science.1223985 chicago: Peng, Z., Stefan Alexander Freunberger, Y. Chen, and P. G. Bruce. “A Reversible and Higher-Rate Li-O2 Battery.” Science. AAAS, 2012. https://doi.org/10.1126/science.1223985. ieee: Z. Peng, S. A. Freunberger, Y. Chen, and P. G. Bruce, “A reversible and higher-rate Li-O2 battery,” Science, vol. 337, no. 6094. AAAS, pp. 563–566, 2012. ista: Peng Z, Freunberger SA, Chen Y, Bruce PG. 2012. A reversible and higher-rate Li-O2 battery. Science. 337(6094), 563–566. mla: Peng, Z., et al. “A Reversible and Higher-Rate Li-O2 Battery.” Science, vol. 337, no. 6094, AAAS, 2012, pp. 563–66, doi:10.1126/science.1223985. short: Z. Peng, S.A. Freunberger, Y. Chen, P.G. Bruce, Science 337 (2012) 563–566. date_created: 2020-01-15T12:19:23Z date_published: 2012-08-03T00:00:00Z date_updated: 2021-01-12T08:12:57Z day: '03' doi: 10.1126/science.1223985 extern: '1' intvolume: ' 337' issue: '6094' language: - iso: eng month: '08' oa_version: None page: 563-566 publication: Science publication_identifier: issn: - 0036-8075 - 1095-9203 publication_status: published publisher: AAAS quality_controlled: '1' status: public title: A reversible and higher-rate Li-O2 battery type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 337 year: '2012' ... --- _id: '7311' abstract: - lang: eng text: Stability of the electrolyte toward reduced oxygen species generated at the cathode is a crucial challenge for the rechargeable nonaqueous Li–O2 battery. Here, we investigate dimethylformamide as the basis of an electrolyte. Although reactions at the O2 cathode on the first discharge–charge cycle are dominated by reversible Li2O2 formation/decomposition, there is also electrolyte decomposition, which increases on cycling. The products of decomposition at the cathode on discharge are Li2O2, Li2CO3, HCO2Li, CH3CO2Li, NO, H2O, and CO2. Li2CO3 accumulates in the electrode with cycling. The stability of dimethylformamide toward reduced oxygen species is insufficient for its use in the rechargeable nonaqueous Li–O2 battery. article_processing_charge: No article_type: original author: - first_name: Yuhui full_name: Chen, Yuhui last_name: Chen - 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: Zhangquan full_name: Peng, Zhangquan last_name: Peng - first_name: Fanny full_name: Bardé, Fanny last_name: Bardé - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce citation: ama: Chen Y, Freunberger SA, Peng Z, Bardé F, Bruce PG. Li–O2 battery with a dimethylformamide electrolyte. Journal of the American Chemical Society. 2012;134(18):7952-7957. doi:10.1021/ja302178w apa: Chen, Y., Freunberger, S. A., Peng, Z., Bardé, F., & Bruce, P. G. (2012). Li–O2 battery with a dimethylformamide electrolyte. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja302178w chicago: Chen, Yuhui, Stefan Alexander Freunberger, Zhangquan Peng, Fanny Bardé, and Peter G. Bruce. “Li–O2 Battery with a Dimethylformamide Electrolyte.” Journal of the American Chemical Society. ACS, 2012. https://doi.org/10.1021/ja302178w. ieee: Y. Chen, S. A. Freunberger, Z. Peng, F. Bardé, and P. G. Bruce, “Li–O2 battery with a dimethylformamide electrolyte,” Journal of the American Chemical Society, vol. 134, no. 18. ACS, pp. 7952–7957, 2012. ista: Chen Y, Freunberger SA, Peng Z, Bardé F, Bruce PG. 2012. Li–O2 battery with a dimethylformamide electrolyte. Journal of the American Chemical Society. 134(18), 7952–7957. mla: Chen, Yuhui, et al. “Li–O2 Battery with a Dimethylformamide Electrolyte.” Journal of the American Chemical Society, vol. 134, no. 18, ACS, 2012, pp. 7952–57, doi:10.1021/ja302178w. short: Y. Chen, S.A. Freunberger, Z. Peng, F. Bardé, P.G. Bruce, Journal of the American Chemical Society 134 (2012) 7952–7957. date_created: 2020-01-15T12:19:36Z date_published: 2012-04-19T00:00:00Z date_updated: 2021-01-12T08:12:58Z day: '19' doi: 10.1021/ja302178w extern: '1' intvolume: ' 134' issue: '18' language: - iso: eng month: '04' oa_version: None page: 7952-7957 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: ACS quality_controlled: '1' status: public title: Li–O2 battery with a dimethylformamide electrolyte type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2012' ... --- _id: '762' abstract: - lang: eng text: Decades of research in distributed computing have led to a variety of perspectives on what it means for a concurrent algorithm to be efficient, depending on model assumptions, progress guarantees, and complexity metrics. It is therefore natural to ask whether one could compose algorithms that perform efficiently under different conditions, so that the composition preserves the performance of the original components when their conditions are met. In this paper, we evaluate the cost of composing shared-memory algorithms. First, we formally define the notion of safely composable algorithms and we show that every sequential type has a safely composable implementation, as long as enough state is transferred between modules. Since such generic implementations are inherently expensive, we present a more general light-weight specification that allows the designer to transfer very little state between modules, by taking advantage of the semantics of the implemented object. Using this framework, we implement a composed longlived test-and-set object, with the property that each of its modules is asymptotically optimal with respect to the progress condition it ensures, while the entire implementation only uses objects with consensus number at most two. Thus, we show that the overhead of composition can be negligible in the case of some important shared-memory abstractions. article_processing_charge: No 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: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Petr full_name: Kuznetsov, Petr last_name: Kuznetsov - first_name: Giuliano full_name: Losa, Giuliano last_name: Losa citation: ama: 'Alistarh D-A, Guerraoui R, Kuznetsov P, Losa G. On the cost of composing shared-memory algorithms. In: ACM; 2012:298-307. doi:10.1145/2312005.2312057' apa: 'Alistarh, D.-A., Guerraoui, R., Kuznetsov, P., & Losa, G. (2012). On the cost of composing shared-memory algorithms (pp. 298–307). Presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, ACM. https://doi.org/10.1145/2312005.2312057' chicago: Alistarh, Dan-Adrian, Rachid Guerraoui, Petr Kuznetsov, and Giuliano Losa. “On the Cost of Composing Shared-Memory Algorithms,” 298–307. ACM, 2012. https://doi.org/10.1145/2312005.2312057. ieee: 'D.-A. Alistarh, R. Guerraoui, P. Kuznetsov, and G. Losa, “On the cost of composing shared-memory algorithms,” presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, 2012, pp. 298–307.' ista: 'Alistarh D-A, Guerraoui R, Kuznetsov P, Losa G. 2012. On the cost of composing shared-memory algorithms. SPAA: Symposium on Parallelism in Algorithms and Architectures, 298–307.' mla: Alistarh, Dan-Adrian, et al. On the Cost of Composing Shared-Memory Algorithms. ACM, 2012, pp. 298–307, doi:10.1145/2312005.2312057. short: D.-A. Alistarh, R. Guerraoui, P. Kuznetsov, G. Losa, in:, ACM, 2012, pp. 298–307. conference: name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures' date_created: 2018-12-11T11:48:22Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-02-23T13:12:27Z day: '01' doi: 10.1145/2312005.2312057 extern: '1' language: - iso: eng month: '01' oa_version: None page: 298 - 307 publication_status: published publisher: ACM publist_id: '6892' status: public title: On the cost of composing shared-memory algorithms type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '763' abstract: - lang: eng text: Renaming is a fundamental problem in distributed computing, in which a set of n processes need to pick unique names from a namespace of limited size. In this paper, we present the first early-deciding upper bounds for synchronous renaming, in which the running time adapts to the actual number of failures f in the execution. We show that, surprisingly, renaming can be solved in constant time if the number of failures f is limited to O(√n), while for general f ≤ n - 1 renaming can always be solved in O(log f) communication rounds. In the wait-free case, i.e. for f = n - 1, our upper bounds match the Ω(log n) lower bound of Chaudhuri et al. [13]. acknowledgement: "Hagit Attiya - Supported in party by Israel Science Foundation (grant number 1227/10).\r\nCorentin Travers - Additional supports from the ANR projects ALADDIN and DISPLEXITY\r\n" alternative_title: - LNCS article_processing_charge: No 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: Hagit full_name: Attiya, Hagit last_name: Attiya - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Corentin full_name: Travers, Corentin last_name: Travers citation: ama: 'Alistarh D-A, Attiya H, Guerraoui R, Travers C. Early deciding synchronous renaming in O(log f) rounds or less. In: Vol 7355 LNCS. Springer; 2012:195-206. doi:10.1007/978-3-642-31104-8_17' apa: 'Alistarh, D.-A., Attiya, H., Guerraoui, R., & Travers, C. (2012). Early deciding synchronous renaming in O(log f) rounds or less (Vol. 7355 LNCS, pp. 195–206). Presented at the SIROCCO: Structural Information and Communication Complexity, Springer. https://doi.org/10.1007/978-3-642-31104-8_17' chicago: Alistarh, Dan-Adrian, Hagit Attiya, Rachid Guerraoui, and Corentin Travers. “Early Deciding Synchronous Renaming in O(Log f) Rounds or Less,” 7355 LNCS:195–206. Springer, 2012. https://doi.org/10.1007/978-3-642-31104-8_17. ieee: 'D.-A. Alistarh, H. Attiya, R. Guerraoui, and C. Travers, “Early deciding synchronous renaming in O(log f) rounds or less,” presented at the SIROCCO: Structural Information and Communication Complexity, 2012, vol. 7355 LNCS, pp. 195–206.' ista: 'Alistarh D-A, Attiya H, Guerraoui R, Travers C. 2012. Early deciding synchronous renaming in O(log f) rounds or less. SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 7355 LNCS, 195–206.' mla: Alistarh, Dan-Adrian, et al. Early Deciding Synchronous Renaming in O(Log f) Rounds or Less. Vol. 7355 LNCS, Springer, 2012, pp. 195–206, doi:10.1007/978-3-642-31104-8_17. short: D.-A. Alistarh, H. Attiya, R. Guerraoui, C. Travers, in:, Springer, 2012, pp. 195–206. conference: name: 'SIROCCO: Structural Information and Communication Complexity' date_created: 2018-12-11T11:48:22Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-02-23T13:12:41Z day: '01' doi: 10.1007/978-3-642-31104-8_17 extern: '1' language: - iso: eng month: '01' oa_version: None page: 195 - 206 publication_status: published publisher: Springer publist_id: '6893' status: public title: Early deciding synchronous renaming in O(log f) rounds or less type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7355 LNCS year: '2012' ... --- _id: '764' abstract: - lang: eng text: Set agreement is a fundamental problem in distributed computing in which processes collectively choose a small subset of values from a larger set of proposals. The impossibility of fault-tolerant set agreement in asynchronous networks is one of the seminal results in distributed computing. In synchronous networks, too, the complexity of set agreement has been a significant research challenge that has now been resolved. Real systems, however, are neither purely synchronous nor purely asynchronous. Rather, they tend to alternate between periods of synchrony and periods of asynchrony. Nothing specific is known about the complexity of set agreement in such a "partially synchronous" setting. In this paper, we address this challenge, presenting the first (asymptotically) tight bound on the complexity of set agreement in such systems. We introduce a novel technique for simulating, in a fault-prone asynchronous shared memory, executions of an asynchronous and failure-prone message-passing system in which some fragments appear synchronous to some processes. We use this simulation technique to derive a lower bound on the round complexity of set agreement in a partially synchronous system by a reduction from asynchronous wait-free set agreement. Specifically, we show that every set agreement protocol requires at least $\lfloor\frac t k \rfloor + 2$ synchronous rounds to decide. We present an (asymptotically) matching algorithm that relies on a distributed asynchrony detection mechanism to decide as soon as possible during periods of synchrony. From these two results, we derive the size of the minimal window of synchrony needed to solve set agreement. By relating synchronous, asynchronous and partially synchronous environments, our simulation technique is of independent interest. In particular, it allows us to obtain a new lower bound on the complexity of early deciding k-set agreement complementary to that of Gafni et al. (in SIAM J. Comput. 40(1):63-78, 2011), and to re-derive the combinatorial topology lower bound of Guerraoui et al. (in Theor. Comput. Sci. 410(6-7):570-580, 2009) in an algorithmic way. acknowledgement: "We would like to thank Hagit Attiya, Keren Censor-Hillel, and the anonymous\r\nreviewers for their feedback on drafts of this paper.\r\nPart of the work was performed as C. Travers was a Post-Doctoral Fellow at the Technion, Haifa,\r\nsupported by the “Sam & Cecilia Neaman” Fellowship. Part of the work was performed as S. Gilbert was\r\na Post-Doctoral Fellow at the Swiss Federal Institute of Technology, Lausanne, Switzerland." article_processing_charge: No 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: Seth full_name: Gilbert, Seth last_name: Gilbert - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Corentin full_name: Travers, Corentin last_name: Travers citation: ama: 'Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Of choices, failures and asynchrony: the many faces of set agreement. Algorithmica (New York). 2012;62(1-2):595-629. doi:10.1007/s00453-011-9581-7' apa: 'Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2012). Of choices, failures and asynchrony: the many faces of set agreement. Algorithmica (New York). Springer. https://doi.org/10.1007/s00453-011-9581-7' chicago: 'Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers. “Of Choices, Failures and Asynchrony: The Many Faces of Set Agreement.” Algorithmica (New York). Springer, 2012. https://doi.org/10.1007/s00453-011-9581-7.' ieee: 'D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Of choices, failures and asynchrony: the many faces of set agreement,” Algorithmica (New York), vol. 62, no. 1–2. Springer, pp. 595–629, 2012.' ista: 'Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2012. Of choices, failures and asynchrony: the many faces of set agreement. Algorithmica (New York). 62(1–2), 595–629.' mla: 'Alistarh, Dan-Adrian, et al. “Of Choices, Failures and Asynchrony: The Many Faces of Set Agreement.” Algorithmica (New York), vol. 62, no. 1–2, Springer, 2012, pp. 595–629, doi:10.1007/s00453-011-9581-7.' short: D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, Algorithmica (New York) 62 (2012) 595–629. date_created: 2018-12-11T11:48:23Z date_published: 2012-02-01T00:00:00Z date_updated: 2023-02-23T13:13:02Z day: '01' doi: 10.1007/s00453-011-9581-7 extern: '1' intvolume: ' 62' issue: 1-2 language: - iso: eng month: '02' oa_version: None page: 595 - 629 publication: Algorithmica (New York) publication_status: published publisher: Springer publist_id: '6894' status: public title: 'Of choices, failures and asynchrony: the many faces of set agreement' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2012' ... --- _id: '766' abstract: - lang: eng text: 'Asynchronous task allocation is a fundamental problem in distributed computing in which p asynchronous processes must execute a set of m tasks. Also known as write-all or do-all, this problem been studied extensively, both independently and as a key building block for various distributed algorithms. In this paper, we break new ground on this classic problem: we introduce the To-Do Tree concurrent data structure, which improves on the best known randomized and deterministic upper bounds. In the presence of an adaptive adversary, the randomized To-Do Tree algorithm has O(m + p log p log2 m) work complexity. We then show that there exists a deterministic variant of the To-Do Tree algorithm with work complexity O(m + p log5 m log2 max(m, p)). For all values of m and p, our algorithms are within log factors of the Ω(m + p log p) lower bound for this problem. The key technical ingredient in our results is a new approach for analyzing concurrent executions against a strong adaptive scheduler. This technique allows us to handle the complex dependencies between the processes'' coin flips and their scheduling, and to tightly bound the work needed to perform subsets of the tasks.' article_processing_charge: No 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: Michael full_name: Bender, Michael last_name: Bender - first_name: Seth full_name: Gilbert, Seth last_name: Gilbert - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui citation: ama: 'Alistarh D-A, Bender M, Gilbert S, Guerraoui R. How to allocate tasks asynchronously. In: IEEE; 2012:331-340. doi:10.1109/FOCS.2012.41' apa: 'Alistarh, D.-A., Bender, M., Gilbert, S., & Guerraoui, R. (2012). How to allocate tasks asynchronously (pp. 331–340). Presented at the FOCS: Foundations of Computer Science, IEEE. https://doi.org/10.1109/FOCS.2012.41' chicago: Alistarh, Dan-Adrian, Michael Bender, Seth Gilbert, and Rachid Guerraoui. “How to Allocate Tasks Asynchronously,” 331–40. IEEE, 2012. https://doi.org/10.1109/FOCS.2012.41. ieee: 'D.-A. Alistarh, M. Bender, S. Gilbert, and R. Guerraoui, “How to allocate tasks asynchronously,” presented at the FOCS: Foundations of Computer Science, 2012, pp. 331–340.' ista: 'Alistarh D-A, Bender M, Gilbert S, Guerraoui R. 2012. How to allocate tasks asynchronously. FOCS: Foundations of Computer Science, 331–340.' mla: Alistarh, Dan-Adrian, et al. How to Allocate Tasks Asynchronously. IEEE, 2012, pp. 331–40, doi:10.1109/FOCS.2012.41. short: D.-A. Alistarh, M. Bender, S. Gilbert, R. Guerraoui, in:, IEEE, 2012, pp. 331–340. conference: name: 'FOCS: Foundations of Computer Science' date_created: 2018-12-11T11:48:23Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-02-23T13:13:27Z day: '01' doi: 10.1109/FOCS.2012.41 extern: '1' language: - iso: eng month: '01' oa_version: None page: 331 - 340 publication_status: published publisher: IEEE publist_id: '6890' status: public title: How to allocate tasks asynchronously type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '767' abstract: - lang: eng text: Synchronous distributed algorithms are easier to design and prove correct than algorithms that tolerate asynchrony. Yet, in the real world, networks experience asynchrony and other timing anomalies. In this paper, we address the question of how to efficiently transform an algorithm that relies on synchronous timing into an algorithm that tolerates asynchronous executions. We introduce a transformation technique from synchronous algorithms to indulgent algorithms (Guerraoui, in PODC, pp. 289-297, 2000), which induces only a constant overhead in terms of time complexity in well-behaved executions. Our technique is based on a new abstraction we call an asynchrony detector, which the participating processes implement collectively. The resulting transformation works for the class of colorless distributed tasks, including consensus and set agreement. Interestingly, we also show that our technique is relevant for colored tasks, by applying it to the renaming problem, to obtain the first indulgent renaming algorithm. acknowledgement: "Dan Alistarh was supported by the NCCR MICS Project. Corentin Travers had additional support from INRIA team REGAL and ANR project SPREADS.\r\nThe authors would like to thank Hagit Attiya and Nikola Kneževi\r\n ́\r\nc for their feed-\r\nback on previous drafts of this paper, and the anonymous reviewers for their useful comments." article_processing_charge: No 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: Seth full_name: Gilbert, Seth last_name: Gilbert - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Corentin full_name: Travers, Corentin last_name: Travers citation: ama: Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Generating Fast Indulgent Algorithms. Theory of Computing Systems. 2012;51(4):404-424. doi:10.1007/s00224-012-9407-2 apa: Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2012). Generating Fast Indulgent Algorithms. Theory of Computing Systems. Elsevier. https://doi.org/10.1007/s00224-012-9407-2 chicago: Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers. “Generating Fast Indulgent Algorithms.” Theory of Computing Systems. Elsevier, 2012. https://doi.org/10.1007/s00224-012-9407-2. ieee: D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Generating Fast Indulgent Algorithms,” Theory of Computing Systems, vol. 51, no. 4. Elsevier, pp. 404–424, 2012. ista: Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2012. Generating Fast Indulgent Algorithms. Theory of Computing Systems. 51(4), 404–424. mla: Alistarh, Dan-Adrian, et al. “Generating Fast Indulgent Algorithms.” Theory of Computing Systems, vol. 51, no. 4, Elsevier, 2012, pp. 404–24, doi:10.1007/s00224-012-9407-2. short: D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, Theory of Computing Systems 51 (2012) 404–424. date_created: 2018-12-11T11:48:23Z date_published: 2012-01-01T00:00:00Z date_updated: 2023-02-23T13:13:40Z day: '01' doi: 10.1007/s00224-012-9407-2 extern: '1' intvolume: ' 51' issue: '4' language: - iso: eng month: '01' oa_version: None page: 404 - 424 publication: Theory of Computing Systems publication_status: published publisher: Elsevier publist_id: '6891' status: public title: Generating Fast Indulgent Algorithms type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2012' ... --- _id: '7749' abstract: - lang: eng text: Although studies on laboratory species and natural populations of vertebrates have shown reproduction to impair later performance, little is known of the age‐specific associations between reproduction and survival, and how such findings apply to the ageing of large, long‐lived species. Herein we develop a framework to examine population‐level patterns of reproduction and survival across lifespan in long‐lived organisms, and decompose those changes into individual‐level effects, and the effects of age‐specific trade‐offs between fitness components. We apply this to an extensive longitudinal dataset on female semi‐captive Asian timber elephants (Elephas maximus) and report the first evidence of age‐specific fitness declines that are driven by age‐specific associations between fitness components in a long‐lived mammal. Associations between reproduction and survival are positive in early life, but negative in later life with up to 71% of later‐life survival declines associated with investing in the production of offspring within this population of this critically endangered species. article_processing_charge: No article_type: original author: - 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: Khyne U full_name: Mar, Khyne U last_name: Mar - first_name: Virpi full_name: Lummaa, Virpi last_name: Lummaa citation: ama: Robinson MR, Mar KU, Lummaa V. Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants. Ecology Letters. 2012;15(3):260-266. doi:10.1111/j.1461-0248.2011.01735.x apa: Robinson, M. R., Mar, K. U., & Lummaa, V. (2012). Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants. Ecology Letters. Wiley. https://doi.org/10.1111/j.1461-0248.2011.01735.x chicago: Robinson, Matthew Richard, Khyne U Mar, and Virpi Lummaa. “Senescence and Age-Specific Trade-Offs between Reproduction and Survival in Female Asian Elephants.” Ecology Letters. Wiley, 2012. https://doi.org/10.1111/j.1461-0248.2011.01735.x. ieee: M. R. Robinson, K. U. Mar, and V. Lummaa, “Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants,” Ecology Letters, vol. 15, no. 3. Wiley, pp. 260–266, 2012. ista: Robinson MR, Mar KU, Lummaa V. 2012. Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants. Ecology Letters. 15(3), 260–266. mla: Robinson, Matthew Richard, et al. “Senescence and Age-Specific Trade-Offs between Reproduction and Survival in Female Asian Elephants.” Ecology Letters, vol. 15, no. 3, Wiley, 2012, pp. 260–66, doi:10.1111/j.1461-0248.2011.01735.x. short: M.R. Robinson, K.U. Mar, V. Lummaa, Ecology Letters 15 (2012) 260–266. date_created: 2020-04-30T11:01:26Z date_published: 2012-03-01T00:00:00Z date_updated: 2021-01-12T08:15:16Z day: '01' doi: 10.1111/j.1461-0248.2011.01735.x extern: '1' intvolume: ' 15' issue: '3' language: - iso: eng month: '03' oa_version: None page: 260-266 publication: Ecology Letters publication_identifier: issn: - 1461-023X publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2012' ... --- _id: '7748' abstract: - lang: eng text: Female mate choice acts as an important evolutionary force, yet the influence of the environment on both its expression and the selective pressures acting upon it remains unknown. We found consistent heritable differences between females in their choice of mate based on ornament size during a 25‐year study of a population of collared flycatchers. However, the fitness consequences of mate choice were dependent on environmental conditions experienced whilst breeding. Females breeding with highly ornamented males experienced high relative fitness during dry summer conditions, but low relative fitness during wetter years. Our results imply that sexual selection within a population can be highly variable and dependent upon the prevailing weather conditions experienced by individuals. article_processing_charge: No article_type: original author: - 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: G. full_name: Sander van Doorn, G. last_name: Sander van Doorn - first_name: Lars full_name: Gustafsson, Lars last_name: Gustafsson - first_name: Anna full_name: Qvarnström, Anna last_name: Qvarnström citation: ama: Robinson MR, Sander van Doorn G, Gustafsson L, Qvarnström A. Environment-dependent selection on mate choice in a natural population of birds. Ecology Letters. 2012;15(6):611-618. doi:10.1111/j.1461-0248.2012.01780.x apa: Robinson, M. R., Sander van Doorn, G., Gustafsson, L., & Qvarnström, A. (2012). Environment-dependent selection on mate choice in a natural population of birds. Ecology Letters. Wiley. https://doi.org/10.1111/j.1461-0248.2012.01780.x chicago: Robinson, Matthew Richard, G. Sander van Doorn, Lars Gustafsson, and Anna Qvarnström. “Environment-Dependent Selection on Mate Choice in a Natural Population of Birds.” Ecology Letters. Wiley, 2012. https://doi.org/10.1111/j.1461-0248.2012.01780.x. ieee: M. R. Robinson, G. Sander van Doorn, L. Gustafsson, and A. Qvarnström, “Environment-dependent selection on mate choice in a natural population of birds,” Ecology Letters, vol. 15, no. 6. Wiley, pp. 611–618, 2012. ista: Robinson MR, Sander van Doorn G, Gustafsson L, Qvarnström A. 2012. Environment-dependent selection on mate choice in a natural population of birds. Ecology Letters. 15(6), 611–618. mla: Robinson, Matthew Richard, et al. “Environment-Dependent Selection on Mate Choice in a Natural Population of Birds.” Ecology Letters, vol. 15, no. 6, Wiley, 2012, pp. 611–18, doi:10.1111/j.1461-0248.2012.01780.x. short: M.R. Robinson, G. Sander van Doorn, L. Gustafsson, A. Qvarnström, Ecology Letters 15 (2012) 611–618. date_created: 2020-04-30T11:01:07Z date_published: 2012-06-01T00:00:00Z date_updated: 2021-01-12T08:15:15Z day: '01' doi: 10.1111/j.1461-0248.2012.01780.x extern: '1' intvolume: ' 15' issue: '6' language: - iso: eng month: '06' oa_version: None page: 611-618 publication: Ecology Letters publication_identifier: issn: - 1461-023X publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Environment-dependent selection on mate choice in a natural population of birds type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2012' ... --- _id: '7776' abstract: - lang: eng text: We present an analysis of finite-size effects in jammed packings of N soft, frictionless spheres at zero temperature. There is a 1/N correction to the discrete jump in the contact number at the transition so that jammed packings exist only above isostaticity. As a result, the canonical power-law scalings of the contact number and elastic moduli break down at low pressure. These quantities exhibit scaling collapse with a nontrivial scaling function, demonstrating that the jamming transition can be considered a phase transition. Scaling is achieved as a function of N in both two and three dimensions, indicating an upper critical dimension of 2. article_number: '095704' 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: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel citation: ama: Goodrich CP, Liu AJ, Nagel SR. Finite-size scaling at the jamming transition. Physical Review Letters. 2012;109(9). doi:10.1103/physrevlett.109.095704 apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2012). Finite-size scaling at the jamming transition. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.109.095704 chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Finite-Size Scaling at the Jamming Transition.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/physrevlett.109.095704. ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Finite-size scaling at the jamming transition,” Physical Review Letters, vol. 109, no. 9. American Physical Society, 2012. ista: Goodrich CP, Liu AJ, Nagel SR. 2012. Finite-size scaling at the jamming transition. Physical Review Letters. 109(9), 095704. mla: Goodrich, Carl Peter, et al. “Finite-Size Scaling at the Jamming Transition.” Physical Review Letters, vol. 109, no. 9, 095704, American Physical Society, 2012, doi:10.1103/physrevlett.109.095704. short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 109 (2012). date_created: 2020-04-30T11:44:12Z date_published: 2012-08-27T00:00:00Z date_updated: 2021-01-12T08:15:27Z day: '27' doi: 10.1103/physrevlett.109.095704 extern: '1' intvolume: ' 109' issue: '9' language: - iso: eng month: '08' oa_version: None publication: Physical Review Letters publication_identifier: issn: - 0031-9007 - 1079-7114 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Finite-size scaling at the jamming transition type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 109 year: '2012' ... --- _id: '801' abstract: - lang: eng text: Fungal cell walls frequently contain a polymer of mannose and galactose called galactomannan. In the pathogenic filamentous fungus Aspergillus fumigatus, this polysaccharide is made of a linear mannan backbone with side chains of galactofuran and is anchored to the plasma membrane via a glycosylphosphatidylinositol or is covalently linked to the cell wall. To date, the biosynthesis and significance of this polysaccharide are unknown. The present data demonstrate that deletion of the Golgi UDP-galactofuranose transporter GlfB or the GDP-mannose transporter GmtA leads to the absence of galactofuran or galactomannan, respectively. This indicates that the biosynthesis of galactomannan probably occurs in the lumen of the Golgi apparatus and thus contrasts with the biosynthesis of other fungal cell wall polysaccharides studied to date that takes place at the plasma membrane. Transglycosylation of galactomannan from the membrane to the cell wall is hypothesized because both the cell wall-bound and membrane-bound polysaccharide forms are affected in the generated mutants. Considering the severe growth defect of the A. fumigatus GmtA-deficient mutant, proving this paradigm might provide new targets for antifungal therapy. acknowledgement: This work was supported by the Deutsche Forschungsgemeinschaft. article_processing_charge: No article_type: original author: - first_name: Jakob full_name: Engel, Jakob last_name: Engel - first_name: Philipp S full_name: Schmalhorst, Philipp S id: 309D50DA-F248-11E8-B48F-1D18A9856A87 last_name: Schmalhorst orcid: 0000-0002-5795-0133 - first_name: Françoise full_name: Routier, Françoise last_name: Routier citation: ama: Engel J, Schmalhorst PS, Routier F. Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose. Journal of Biological Chemistry. 2012;287(53):44418-44424. doi:10.1074/jbc.M112.398321 apa: Engel, J., Schmalhorst, P. S., & Routier, F. (2012). Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M112.398321 chicago: Engel, Jakob, Philipp S Schmalhorst, and Françoise Routier. “Biosynthesis of the Fungal Cell Wall Polysaccharide Galactomannan Requires Intraluminal GDP-Mannose.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2012. https://doi.org/10.1074/jbc.M112.398321. ieee: J. Engel, P. S. Schmalhorst, and F. Routier, “Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose,” Journal of Biological Chemistry, vol. 287, no. 53. American Society for Biochemistry and Molecular Biology, pp. 44418–44424, 2012. ista: Engel J, Schmalhorst PS, Routier F. 2012. Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose. Journal of Biological Chemistry. 287(53), 44418–44424. mla: Engel, Jakob, et al. “Biosynthesis of the Fungal Cell Wall Polysaccharide Galactomannan Requires Intraluminal GDP-Mannose.” Journal of Biological Chemistry, vol. 287, no. 53, American Society for Biochemistry and Molecular Biology, 2012, pp. 44418–24, doi:10.1074/jbc.M112.398321. short: J. Engel, P.S. Schmalhorst, F. Routier, Journal of Biological Chemistry 287 (2012) 44418–44424. date_created: 2018-12-11T11:48:34Z date_published: 2012-12-28T00:00:00Z date_updated: 2022-03-21T07:57:14Z day: '28' doi: 10.1074/jbc.M112.398321 extern: '1' external_id: pmid: - '23139423' intvolume: ' 287' issue: '53' language: - iso: eng month: '12' oa_version: None page: 44418 - 44424 pmid: 1 publication: Journal of Biological Chemistry publication_status: published publisher: American Society for Biochemistry and Molecular Biology publist_id: '6852' quality_controlled: '1' scopus_import: '1' status: public title: Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 287 year: '2012' ... --- _id: '8024' abstract: - lang: eng text: In dynamical models of cortical networks, the recurrent connectivity can amplify the input given to the network in two distinct ways. One is induced by the presence of near-critical eigenvalues in the connectivity matrix W, producing large but slow activity fluctuations along the corresponding eigenvectors (dynamical slowing). The other relies on W not being normal, which allows the network activity to make large but fast excursions along specific directions. Here we investigate the trade-off between non-normal amplification and dynamical slowing in the spontaneous activity of large random neuronal networks composed of excitatory and inhibitory neurons. We use a Schur decomposition of W to separate the two amplification mechanisms. Assuming linear stochastic dynamics, we derive an exact expression for the expected amount of purely non-normal amplification. We find that amplification is very limited if dynamical slowing must be kept weak. We conclude that, to achieve strong transient amplification with little slowing, the connectivity must be structured. We show that unidirectional connections between neurons of the same type together with reciprocal connections between neurons of different types, allow for amplification already in the fast dynamical regime. Finally, our results also shed light on the differences between balanced networks in which inhibition exactly cancels excitation and those where inhibition dominates. article_number: '011909' article_processing_charge: No article_type: original author: - 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 - first_name: Wulfram full_name: Gerstner, Wulfram last_name: Gerstner citation: ama: Hennequin G, Vogels TP, Gerstner W. Non-normal amplification in random balanced neuronal networks. Physical Review E. 2012;86(1). doi:10.1103/physreve.86.011909 apa: Hennequin, G., Vogels, T. P., & Gerstner, W. (2012). Non-normal amplification in random balanced neuronal networks. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.86.011909 chicago: Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Non-Normal Amplification in Random Balanced Neuronal Networks.” Physical Review E. American Physical Society, 2012. https://doi.org/10.1103/physreve.86.011909. ieee: G. Hennequin, T. P. Vogels, and W. Gerstner, “Non-normal amplification in random balanced neuronal networks,” Physical Review E, vol. 86, no. 1. American Physical Society, 2012. ista: Hennequin G, Vogels TP, Gerstner W. 2012. Non-normal amplification in random balanced neuronal networks. Physical Review E. 86(1), 011909. mla: Hennequin, Guillaume, et al. “Non-Normal Amplification in Random Balanced Neuronal Networks.” Physical Review E, vol. 86, no. 1, 011909, American Physical Society, 2012, doi:10.1103/physreve.86.011909. short: G. Hennequin, T.P. Vogels, W. Gerstner, Physical Review E 86 (2012). date_created: 2020-06-25T13:09:06Z date_published: 2012-06-11T00:00:00Z date_updated: 2021-01-12T08:16:35Z day: '11' doi: 10.1103/physreve.86.011909 extern: '1' external_id: pmid: - '23005454' intvolume: ' 86' issue: '1' language: - iso: eng month: '06' oa_version: None pmid: 1 publication: Physical Review E publication_identifier: eisbn: - 1550-2376 issn: - 1539-3755 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Non-normal amplification in random balanced neuronal networks type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 86 year: '2012' ... --- _id: '808' abstract: - lang: eng text: Using correlated live-cell imaging and electron tomography we found that actin branch junctions in protruding and treadmilling lamellipodia are not concentrated at the front as previously supposed, but link actin filament subsets in which there is a continuum of distances from a junction to the filament plus ends, for up to at least 1 mm. When branch sites were observed closely spaced on the same filament their separation was commonly a multiple of the actin helical repeat of 36 nm. Image averaging of branch junctions in the tomograms yielded a model for the in vivo branch at 2.9 nm resolution, which was comparable with that derived for the in vitro actin- Arp2/3 complex. Lamellipodium initiation was monitored in an intracellular wound-healing model and was found to involve branching from the sides of actin filaments oriented parallel to the plasmalemma. Many filament plus ends, presumably capped, terminated behind the lamellipodium tip and localized on the dorsal and ventral surfaces of the actin network. These findings reveal how branching events initiate and maintain a network of actin filaments of variable length, and provide the first structural model of the branch junction in vivo. A possible role of filament capping in generating the lamellipodium leaflet is discussed and a mathematical model of protrusion is also presented. acknowledgement: This work was supported by the Austrian Science Fund [projects FWF I516-B09 and FWF P21292-B09 to J.V.S.]; the Vienna Science and Technology Fund [WWTF-grant numbers MA 09-004 to J.V.S. and C.S], ZIT - The Technology Agency of the City of Vienna [VSOE, CMCN to J.V.S. and G.P.R.]; the Deutsche Forschungsgemeinschaft [grant number RO 2414/1-2 to K.R.]; the Daiko research foundation [grant number 9134 to A.N.]; and a Grant-in-Aid for Scientific Research [S, grant number 20227008 to Y.M.] and a Grant-in-Aid for Young Scientists [B, grant number 22770145 to A.N.] (B) from The Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government. Deposited in PMC for immediate release. We thank Tibor Kulcsar for assistance with graphics. author: - first_name: Marlene full_name: Vinzenz, Marlene last_name: Vinzenz - first_name: Maria full_name: Nemethova, Maria id: 34E27F1C-F248-11E8-B48F-1D18A9856A87 last_name: Nemethova - first_name: Florian full_name: Schur, Florian id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Jan full_name: Mueller, Jan last_name: Mueller - first_name: Akihiro full_name: Narita, Akihiro last_name: Narita - first_name: Edit full_name: Urban, Edit last_name: Urban - first_name: Christoph full_name: Winkler, Christoph last_name: Winkler - first_name: Christian full_name: Schmeiser, Christian last_name: Schmeiser - first_name: Stefan full_name: Koestler, Stefan last_name: Koestler - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner - first_name: Guenter full_name: Resch, Guenter last_name: Resch - first_name: Yuichiro full_name: Maéda, Yuichiro last_name: Maéda - first_name: John full_name: Small, John last_name: Small citation: ama: Vinzenz M, Nemethova M, Schur FK, et al. Actin branching in the initiation and maintenance of lamellipodia. Journal of Cell Science. 2012;125(11):2775-2785. doi:10.1242/jcs.107623 apa: Vinzenz, M., Nemethova, M., Schur, F. K., Mueller, J., Narita, A., Urban, E., … Small, J. (2012). Actin branching in the initiation and maintenance of lamellipodia. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.107623 chicago: Vinzenz, Marlene, Maria Nemethova, Florian KM Schur, Jan Mueller, Akihiro Narita, Edit Urban, Christoph Winkler, et al. “Actin Branching in the Initiation and Maintenance of Lamellipodia.” Journal of Cell Science. Company of Biologists, 2012. https://doi.org/10.1242/jcs.107623. ieee: M. Vinzenz et al., “Actin branching in the initiation and maintenance of lamellipodia,” Journal of Cell Science, vol. 125, no. 11. Company of Biologists, pp. 2775–2785, 2012. ista: Vinzenz M, Nemethova M, Schur FK, Mueller J, Narita A, Urban E, Winkler C, Schmeiser C, Koestler S, Rottner K, Resch G, Maéda Y, Small J. 2012. Actin branching in the initiation and maintenance of lamellipodia. Journal of Cell Science. 125(11), 2775–2785. mla: Vinzenz, Marlene, et al. “Actin Branching in the Initiation and Maintenance of Lamellipodia.” Journal of Cell Science, vol. 125, no. 11, Company of Biologists, 2012, pp. 2775–85, doi:10.1242/jcs.107623. short: M. Vinzenz, M. Nemethova, F.K. Schur, J. Mueller, A. Narita, E. Urban, C. Winkler, C. Schmeiser, S. Koestler, K. Rottner, G. Resch, Y. Maéda, J. Small, Journal of Cell Science 125 (2012) 2775–2785. date_created: 2018-12-11T11:48:37Z date_published: 2012-06-01T00:00:00Z date_updated: 2021-01-12T08:16:47Z day: '01' ddc: - '570' doi: 10.1242/jcs.107623 extern: '1' file: - access_level: open_access checksum: 2f59e15cc3a85bb500a9887cef2aab67 content_type: application/pdf creator: kschuh date_created: 2019-02-12T08:54:51Z date_updated: 2020-07-14T12:48:09Z file_id: '5956' file_name: 2012_Biologists_Vinzenz.pdf file_size: 3326073 relation: main_file file_date_updated: 2020-07-14T12:48:09Z has_accepted_license: '1' intvolume: ' 125' issue: '11' language: - iso: eng month: '06' oa: 1 oa_version: None page: 2775 - 2785 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '6842' quality_controlled: '1' status: public title: Actin branching in the initiation and maintenance of lamellipodia 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 125 year: '2012' ... --- _id: '8246' abstract: - lang: eng text: The Staphylococcus aureus cell wall stress stimulon (CWSS) is activated by cell envelope-targeting antibiotics or depletion of essential cell wall biosynthesis enzymes. The functionally uncharacterized S. aureus LytR-CpsA-Psr (LCP) proteins, MsrR, SA0908 and SA2103, all belong to the CWSS. Although not essential, deletion of all three LCP proteins severely impairs cell division. We show here that VraSR-dependent CWSS expression was up to 250-fold higher in single, double and triple LCP mutants than in wild type S. aureus in the absence of external stress. The LCP triple mutant was virtually depleted of wall teichoic acids (WTA), which could be restored to different degrees by any of the single LCP proteins. Subinhibitory concentrations of tunicamycin, which inhibits the first WTA synthesis enzyme TarO (TagO), could partially complement the severe growth defect of the LCP triple mutant. Both of the latter findings support a role for S. aureus LCP proteins in late WTA synthesis, as in Bacillus subtilis where LCP proteins were recently proposed to transfer WTA from lipid carriers to the cell wall peptidoglycan. Intrinsic activation of the CWSS upon LCP deletion and the fact that LCP proteins were essential for WTA-loading of the cell wall, highlight their important role(s) in S. aureus cell envelope biogenesis. article_processing_charge: No article_type: original author: - first_name: Vanina full_name: Dengler, Vanina last_name: Dengler - first_name: Patricia Stutzmann full_name: Meier, Patricia Stutzmann last_name: Meier - first_name: Ronald full_name: Heusser, Ronald last_name: Heusser - first_name: Peter full_name: Kupferschmied, Peter last_name: Kupferschmied - first_name: Judit full_name: Fazekas, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas orcid: 0000-0002-8777-3502 - first_name: Sarah full_name: Friebe, Sarah last_name: Friebe - first_name: Sibylle Burger full_name: Staufer, Sibylle Burger last_name: Staufer - first_name: Paul A. full_name: Majcherczyk, Paul A. last_name: Majcherczyk - first_name: Philippe full_name: Moreillon, Philippe last_name: Moreillon - first_name: Brigitte full_name: Berger-Bächi, Brigitte last_name: Berger-Bächi - first_name: Nadine full_name: McCallum, Nadine last_name: McCallum citation: ama: Dengler V, Meier PS, Heusser R, et al. Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response. FEMS Microbiology Letters. 2012;333(2):109-120. doi:10.1111/j.1574-6968.2012.02603.x apa: Dengler, V., Meier, P. S., Heusser, R., Kupferschmied, P., Singer, J., Friebe, S., … McCallum, N. (2012). Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response. FEMS Microbiology Letters. Oxford University Press. https://doi.org/10.1111/j.1574-6968.2012.02603.x chicago: Dengler, Vanina, Patricia Stutzmann Meier, Ronald Heusser, Peter Kupferschmied, Judit Singer, Sarah Friebe, Sibylle Burger Staufer, et al. “Deletion of Hypothetical Wall Teichoic Acid Ligases in Staphylococcus Aureus Activates the Cell Wall Stress Response.” FEMS Microbiology Letters. Oxford University Press, 2012. https://doi.org/10.1111/j.1574-6968.2012.02603.x. ieee: V. Dengler et al., “Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response,” FEMS Microbiology Letters, vol. 333, no. 2. Oxford University Press, pp. 109–120, 2012. ista: Dengler V, Meier PS, Heusser R, Kupferschmied P, Singer J, Friebe S, Staufer SB, Majcherczyk PA, Moreillon P, Berger-Bächi B, McCallum N. 2012. Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response. FEMS Microbiology Letters. 333(2), 109–120. mla: Dengler, Vanina, et al. “Deletion of Hypothetical Wall Teichoic Acid Ligases in Staphylococcus Aureus Activates the Cell Wall Stress Response.” FEMS Microbiology Letters, vol. 333, no. 2, Oxford University Press, 2012, pp. 109–20, doi:10.1111/j.1574-6968.2012.02603.x. short: V. Dengler, P.S. Meier, R. Heusser, P. Kupferschmied, J. Singer, S. Friebe, S.B. Staufer, P.A. Majcherczyk, P. Moreillon, B. Berger-Bächi, N. McCallum, FEMS Microbiology Letters 333 (2012) 109–120. date_created: 2020-08-10T11:54:47Z date_published: 2012-08-01T00:00:00Z date_updated: 2021-01-12T08:17:43Z day: '01' doi: 10.1111/j.1574-6968.2012.02603.x extern: '1' external_id: pmid: - '22640011' intvolume: ' 333' issue: '2' language: - iso: eng month: '08' oa_version: None page: 109-120 pmid: 1 publication: FEMS Microbiology Letters publication_identifier: issn: - 0378-1097 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 333 year: '2012' ... --- _id: '826' abstract: - lang: eng text: Plants exhibit a unique developmental flexibility to ever-changing environmental conditions. To achieve their profound adaptability, plants are able to maintain permanent stem cell populations and form new organs during the entire plant life cycle. Signaling substances, called plant hormones, such as auxin, cytokinin, abscisic acid, brassinosteroid, ethylene, gibberellin, jasmonic acid, and strigolactone, govern and coordinate these developmental processes. Physiological and genetic studies have dissected the molecular components of signal perception and transduction of the individual hormonal pathways. However, over recent years it has become evident that hormones do not act only in a linear pathway. Hormonal pathways are interconnected by a complex network of interactions and feedback circuits that determines the final outcome of the individual hormone actions. This raises questions about the molecular mechanisms underlying hormonal cross talk and about how these hormonal networks are established, maintained, and modulated throughout plant development. acknowledgement: We would like to thank Annick Bleys for help in preparing the manuscript. This work was supported by the European Research Council with a Starting Independent Research grant (ERC-2007-Stg-207362-HCPO) and the project CZ.1.07/2.3.00/20.0043 (to the Central European Institute of Technology, CEITEC) to E.B. M.V. is a postdoctoral fellow of the Research Foundation Flanders. We apologize that, because of space restrictions, the scientific contributions of only a limited number of original articles could be cited and discussed. author: - first_name: Marleen full_name: Vanstraelen, Marleen last_name: Vanstraelen - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Vanstraelen M, Benková E. Hormonal interactions in the regulation of plant development. Annual Review of Cell and Developmental Biology. 2012;28:463-487. doi:10.1146/annurev-cellbio-101011-155741 apa: Vanstraelen, M., & Benková, E. (2012). Hormonal interactions in the regulation of plant development. Annual Review of Cell and Developmental Biology. Annual Reviews. https://doi.org/10.1146/annurev-cellbio-101011-155741 chicago: Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation of Plant Development.” Annual Review of Cell and Developmental Biology. Annual Reviews, 2012. https://doi.org/10.1146/annurev-cellbio-101011-155741. ieee: M. Vanstraelen and E. Benková, “Hormonal interactions in the regulation of plant development,” Annual Review of Cell and Developmental Biology, vol. 28. Annual Reviews, pp. 463–487, 2012. ista: Vanstraelen M, Benková E. 2012. Hormonal interactions in the regulation of plant development. Annual Review of Cell and Developmental Biology. 28, 463–487. mla: Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation of Plant Development.” Annual Review of Cell and Developmental Biology, vol. 28, Annual Reviews, 2012, pp. 463–87, doi:10.1146/annurev-cellbio-101011-155741. short: M. Vanstraelen, E. Benková, Annual Review of Cell and Developmental Biology 28 (2012) 463–487. date_created: 2018-12-11T11:48:43Z date_published: 2012-11-01T00:00:00Z date_updated: 2021-01-12T08:17:46Z day: '01' doi: 10.1146/annurev-cellbio-101011-155741 extern: 1 intvolume: ' 28' month: '11' page: 463 - 487 publication: Annual Review of Cell and Developmental Biology publication_status: published publisher: Annual Reviews publist_id: '6822' quality_controlled: 0 status: public title: Hormonal interactions in the regulation of plant development type: journal_article volume: 28 year: '2012' ... --- _id: '829' abstract: - lang: eng text: The architecture of a plant's root system, established postembryonically, results from both coordinated root growth and lateral root branching. The plant hormones auxin and cytokinin are central endogenous signaling molecules that regulate lateral root organogenesis positively and negatively, respectively. Tight control and mutual balance of their antagonistic activities are particularly important during the early phases of lateral root organogenesis to ensure continuous lateral root initiation (LRI) and proper development of lateral root primordia (LRP). Here, we show that the early phases of lateral root organogenesis, including priming and initiation, take place in root zones with a repressed cytokinin response. Accordingly, ectopic overproduction of cytokinin in the root basal meristem most efficiently inhibits LRI. Enhanced cytokinin responses in pericycle cells between existing LRP might restrict LRI near existing LRP and, when compromised, ectopic LRI occurs. Furthermore, our results demonstrate that young LRP are more sensitive to perturbations in the cytokinin activity than are developmentally more advanced primordia. We hypothesize that the effect of cytokinin on the development of primordia possibly depends on the robustness and stability of the auxin gradient. acknowledgement: We thank Jen Sheen, Dolf Weijers, Tatsuo Kakimoto, Stephen Depuydt, and Laurent Laplaze for sharing published material, Jiri Friml for discussions, and Martine De Cock and Annick Bleys for help in preparing the manuscript. This work was supported by a Starting Independent Research grant from the European Research Council (ERC-2007-Stg-207362-HCPO) and the project CZ.1.07/2.3.00/20.0043 to the Central European Institute of Technology to E.B. and grants from the Ministry of Education, Youth, and Sports of the Czech Republic (MSM 6198959216) and the Centre of the Region Haná for Biotechnological and Agricultural Research (ED0007/01/01) to P.T. author: - first_name: Agnieszka full_name: Bielach, Agnieszka last_name: Bielach - first_name: Katerina full_name: Podlesakova, Katerina last_name: Podlesakova - first_name: Peter full_name: Peter Marhavy id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Jérôme full_name: Duclercq, Jérôme last_name: Duclercq - first_name: Candela full_name: Candela Cuesta id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: Bruno full_name: Muller, Bruno last_name: Muller - first_name: Wim full_name: Grunewald, Wim last_name: Grunewald - first_name: Petr full_name: Tarkowski, Petr last_name: Tarkowski - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Bielach A, Podlesakova K, Marhavý P, et al. Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin. The Plant Cell. 2012;24(10):3967-3981. doi:10.1105/tpc.112.103044 apa: Bielach, A., Podlesakova, K., Marhavý, P., Duclercq, J., Cuesta, C., Muller, B., … Benková, E. (2012). Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.112.103044 chicago: Bielach, Agnieszka, Katerina Podlesakova, Peter Marhavý, Jérôme Duclercq, Candela Cuesta, Bruno Muller, Wim Grunewald, Petr Tarkowski, and Eva Benková. “Spatiotemporal Regulation of Lateral Root Organogenesis in Arabidopsis by Cytokinin.” The Plant Cell. American Society of Plant Biologists, 2012. https://doi.org/10.1105/tpc.112.103044. ieee: A. Bielach et al., “Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin,” The Plant Cell, vol. 24, no. 10. American Society of Plant Biologists, pp. 3967–3981, 2012. ista: Bielach A, Podlesakova K, Marhavý P, Duclercq J, Cuesta C, Muller B, Grunewald W, Tarkowski P, Benková E. 2012. Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin. The Plant Cell. 24(10), 3967–3981. mla: Bielach, Agnieszka, et al. “Spatiotemporal Regulation of Lateral Root Organogenesis in Arabidopsis by Cytokinin.” The Plant Cell, vol. 24, no. 10, American Society of Plant Biologists, 2012, pp. 3967–81, doi:10.1105/tpc.112.103044. short: A. Bielach, K. Podlesakova, P. Marhavý, J. Duclercq, C. Cuesta, B. Muller, W. Grunewald, P. Tarkowski, E. Benková, The Plant Cell 24 (2012) 3967–3981. date_created: 2018-12-11T11:48:43Z date_published: 2012-10-01T00:00:00Z date_updated: 2021-01-12T08:17:55Z day: '01' doi: 10.1105/tpc.112.103044 extern: 1 intvolume: ' 24' issue: '10' month: '10' page: 3967 - 3981 publication: The Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '6819' quality_controlled: 0 status: public title: Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin type: journal_article volume: 24 year: '2012' ... --- _id: '846' abstract: - lang: eng text: Whether or not evolutionary change is inherently irreversible remains a controversial topic. Some examples of evolutionary irreversibility are known; however, this question has not been comprehensively addressed at the molecular level. Here, we use data from 221 human genes with known pathogenic mutations to estimate the rate of irreversibility in protein evolution. For these genes, we reconstruct ancestral amino acid sequences along the mammalian phylogeny and identify ancestral amino acid states that match known pathogenic mutations. Such cases represent inherent evolutionary irreversibility because, at the present moment, reversals to these ancestral amino acid states are impossible for the human lineage. We estimate that approximately 10% of all amino acid substitutions along the mammalian phylogeny are irreversible, such that a return to the ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes with high rates of irreversibility, as much as 40% of all amino acid evolution was estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes, the molecular nature of the high rate of irreversibility in proteins is best explained by evolution with a high prevalence of compensatory, epistatic interactions between amino acid sites. Under such mode of protein evolution, once an amino acid substitution is fixed, the probability of its reversal declines as the protein sequence accumulates changes that affect the phenotypic manifestation of the ancestral state. The prevalence of epistasis in evolution indicates that the observed high rate of irreversibility in protein evolution is an inherent property of protein structure and function. acknowledgement: This work was supported by Plan Nacional grant BFU2009-09271 from the Spanish Ministry of Science and Innovation and by FPU (Formación del Profesorado Universitario) program grant AP2008-01888 from the Spanish Ministry of Education to O.S. F.A.K. is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist. author: - first_name: Onuralp full_name: Soylemez, Onuralp last_name: Soylemez - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Soylemez O, Kondrashov F. Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. 2012;4(12):1213-1222. doi:10.1093/gbe/evs096 apa: Soylemez, O., & Kondrashov, F. (2012). Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evs096 chicago: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility in Protein Evolution.” Genome Biology and Evolution. Oxford University Press, 2012. https://doi.org/10.1093/gbe/evs096. ieee: O. Soylemez and F. Kondrashov, “Estimating the rate of irreversibility in protein evolution,” Genome Biology and Evolution, vol. 4, no. 12. Oxford University Press, pp. 1213–1222, 2012. ista: Soylemez O, Kondrashov F. 2012. Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. 4(12), 1213–1222. mla: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility in Protein Evolution.” Genome Biology and Evolution, vol. 4, no. 12, Oxford University Press, 2012, pp. 1213–22, doi:10.1093/gbe/evs096. short: O. Soylemez, F. Kondrashov, Genome Biology and Evolution 4 (2012) 1213–1222. date_created: 2018-12-11T11:48:49Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T08:19:25Z day: '01' doi: 10.1093/gbe/evs096 extern: 1 intvolume: ' 4' issue: '12' month: '01' page: 1213 - 1222 publication: Genome Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '6802' quality_controlled: 0 status: public title: Estimating the rate of irreversibility in protein evolution 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 volume: 4 year: '2012' ... --- _id: '8463' abstract: - lang: eng text: The 1H dipolar network, which is the major obstacle for applying proton detection in the solid-state, can be reduced by deuteration, employing the RAP (Reduced Adjoining Protonation) labeling scheme, which yields random protonation at non-exchangeable sites. We present here a systematic study on the optimal degree of random sidechain protonation in RAP samples as a function of the MAS (magic angle spinning) frequency. In particular, we compare 1H sensitivity and linewidth of a microcrystalline protein, the SH3 domain of chicken α-spectrin, for samples, prepared with 5–25 % H2O in the E. coli growth medium, in the MAS frequency range of 20–60 kHz. At an external field of 19.96 T (850 MHz), we find that using a proton concentration between 15 and 25 % in the M9 medium yields the best compromise in terms of sensitivity and resolution, with an achievable average 1H linewidth on the order of 40–50 Hz. Comparing sensitivities at a MAS frequency of 60 versus 20 kHz, a gain in sensitivity by a factor of 4–4.5 is observed in INEPT-based 1H detected 1D 1H,13C correlation experiments. In total, we find that spectra recorded with a 1.3 mm rotor at 60 kHz have almost the same sensitivity as spectra recorded with a fully packed 3.2 mm rotor at 20 kHz, even though ~20× less material is employed. The improved sensitivity is attributed to 1H line narrowing due to fast MAS and to the increased efficiency of the 1.3 mm coil. article_processing_charge: No article_type: original author: - first_name: Sam full_name: Asami, Sam last_name: Asami - first_name: Kathrin full_name: Szekely, Kathrin last_name: Szekely - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Beat H. full_name: Meier, Beat H. last_name: Meier - first_name: Bernd full_name: Reif, Bernd last_name: Reif citation: ama: Asami S, Szekely K, Schanda P, Meier BH, Reif B. Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency. Journal of Biomolecular NMR. 2012;54(2):155-168. doi:10.1007/s10858-012-9659-9 apa: Asami, S., Szekely, K., Schanda, P., Meier, B. H., & Reif, B. (2012). Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-012-9659-9 chicago: Asami, Sam, Kathrin Szekely, Paul Schanda, Beat H. Meier, and Bernd Reif. “Optimal Degree of Protonation for 1H Detection of Aliphatic Sites in Randomly Deuterated Proteins as a Function of the MAS Frequency.” Journal of Biomolecular NMR. Springer Nature, 2012. https://doi.org/10.1007/s10858-012-9659-9. ieee: S. Asami, K. Szekely, P. Schanda, B. H. Meier, and B. Reif, “Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency,” Journal of Biomolecular NMR, vol. 54, no. 2. Springer Nature, pp. 155–168, 2012. ista: Asami S, Szekely K, Schanda P, Meier BH, Reif B. 2012. Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency. Journal of Biomolecular NMR. 54(2), 155–168. mla: Asami, Sam, et al. “Optimal Degree of Protonation for 1H Detection of Aliphatic Sites in Randomly Deuterated Proteins as a Function of the MAS Frequency.” Journal of Biomolecular NMR, vol. 54, no. 2, Springer Nature, 2012, pp. 155–68, doi:10.1007/s10858-012-9659-9. short: S. Asami, K. Szekely, P. Schanda, B.H. Meier, B. Reif, Journal of Biomolecular NMR 54 (2012) 155–168. date_created: 2020-09-18T10:09:18Z date_published: 2012-08-23T00:00:00Z date_updated: 2021-01-12T08:19:27Z day: '23' doi: 10.1007/s10858-012-9659-9 extern: '1' intvolume: ' 54' issue: '2' language: - iso: eng month: '08' oa_version: None page: 155-168 publication: Journal of Biomolecular NMR publication_identifier: issn: - 0925-2738 - 1573-5001 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2012' ... --- _id: '8465' abstract: - lang: eng text: We demonstrate that conformational exchange processes in proteins on microsecond-to-millisecond time scales can be detected and quantified by solid-state NMR spectroscopy. We show two independent approaches that measure the effect of conformational exchange on transverse relaxation parameters, namely Carr–Purcell–Meiboom–Gill relaxation-dispersion experiments and measurement of differential multiple-quantum coherence decay. Long coherence lifetimes, as required for these experiments, are achieved by the use of highly deuterated samples and fast magic-angle spinning. The usefulness of the approaches is demonstrated by application to microcrystalline ubiquitin. We detect a conformational exchange process in a region of the protein for which dynamics have also been observed in solution. Interestingly, quantitative analysis of the data reveals that the exchange process is more than 1 order of magnitude slower than in solution, and this points to the impact of the crystalline environment on free energy barriers. article_processing_charge: No article_type: original author: - first_name: Martin full_name: Tollinger, Martin last_name: Tollinger - first_name: Astrid C. full_name: Sivertsen, Astrid C. last_name: Sivertsen - first_name: Beat H. full_name: Meier, Beat H. last_name: Meier - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. Journal of the American Chemical Society. 2012;134(36):14800-14807. doi:10.1021/ja303591y apa: Tollinger, M., Sivertsen, A. C., Meier, B. H., Ernst, M., & Schanda, P. (2012). Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja303591y chicago: Tollinger, Martin, Astrid C. Sivertsen, Beat H. Meier, Matthias Ernst, and Paul Schanda. “Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy.” Journal of the American Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja303591y. ieee: M. Tollinger, A. C. Sivertsen, B. H. Meier, M. Ernst, and P. Schanda, “Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy,” Journal of the American Chemical Society, vol. 134, no. 36. American Chemical Society, pp. 14800–14807, 2012. ista: Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. 2012. Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. Journal of the American Chemical Society. 134(36), 14800–14807. mla: Tollinger, Martin, et al. “Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy.” Journal of the American Chemical Society, vol. 134, no. 36, American Chemical Society, 2012, pp. 14800–07, doi:10.1021/ja303591y. short: M. Tollinger, A.C. Sivertsen, B.H. Meier, M. Ernst, P. Schanda, Journal of the American Chemical Society 134 (2012) 14800–14807. date_created: 2020-09-18T10:10:20Z date_published: 2012-08-21T00:00:00Z date_updated: 2021-01-12T08:19:27Z day: '21' doi: 10.1021/ja303591y extern: '1' intvolume: ' 134' issue: '36' language: - iso: eng month: '08' oa_version: None page: 14800-14807 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2012' ... --- _id: '8466' abstract: - lang: eng text: Recent advances in NMR spectroscopy and the availability of high magnetic field strengths now offer the possibility to record real-time 3D NMR spectra of short-lived protein states, e.g., states that become transiently populated during protein folding. Here we present a strategy for obtaining sequential NMR assignments as well as atom-resolved information on structural and dynamic features within a folding intermediate of the amyloidogenic protein β2-microglobulin that has a half-lifetime of only 20 min. article_processing_charge: No article_type: original author: - first_name: Enrico full_name: Rennella, Enrico last_name: Rennella - first_name: Thomas full_name: Cutuil, Thomas last_name: Cutuil - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Vincent full_name: Forge, Vincent last_name: Forge - first_name: Bernhard full_name: Brutscher, Bernhard last_name: Brutscher citation: ama: Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. Journal of the American Chemical Society. 2012;134(19):8066-8069. doi:10.1021/ja302598j apa: Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Forge, V., & Brutscher, B. (2012). Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja302598j chicago: Rennella, Enrico, Thomas Cutuil, Paul Schanda, Isabel Ayala, Vincent Forge, and Bernhard Brutscher. “Real-Time NMR Characterization of Structure and Dynamics in a Transiently Populated Protein Folding Intermediate.” Journal of the American Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja302598j. ieee: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, and B. Brutscher, “Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate,” Journal of the American Chemical Society, vol. 134, no. 19. American Chemical Society, pp. 8066–8069, 2012. ista: Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. 2012. Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. Journal of the American Chemical Society. 134(19), 8066–8069. mla: Rennella, Enrico, et al. “Real-Time NMR Characterization of Structure and Dynamics in a Transiently Populated Protein Folding Intermediate.” Journal of the American Chemical Society, vol. 134, no. 19, American Chemical Society, 2012, pp. 8066–69, doi:10.1021/ja302598j. short: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, B. Brutscher, Journal of the American Chemical Society 134 (2012) 8066–8069. date_created: 2020-09-18T10:10:28Z date_published: 2012-05-03T00:00:00Z date_updated: 2021-01-12T08:19:28Z day: '03' doi: 10.1021/ja302598j extern: '1' intvolume: ' 134' issue: '19' language: - iso: eng month: '05' oa_version: None page: 8066-8069 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 134 year: '2012' ... --- _id: '8467' abstract: - lang: eng text: Partial deuteration is a powerful tool to increase coherence life times and spectral resolution in proton solid-state NMR. The J coupling to deuterium needs, however, to be decoupled to maintain the good resolution in the (usually indirect) 13C dimension(s). We present a simple and reversible way to expand a commercial 1.3 mm HCN MAS probe with a 2H channel with sufficient field strength for J-decoupling of deuterium, namely 2–3 kHz. The coil is placed at the outside of the stator and requires no significant modifications to the probe. The performance and the realizable gains in sensitivity and resolution are demonstrated using perdeuterated ubiquitin, with selectively CHD2-labeled methyl groups. article_processing_charge: No article_type: original author: - first_name: Matthias full_name: Huber, Matthias last_name: Huber - first_name: Oliver full_name: With, Oliver last_name: With - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: René full_name: Verel, René last_name: Verel - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Beat H. full_name: Meier, Beat H. last_name: Meier citation: ama: Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. A supplementary coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance. 2012;214:76-80. doi:10.1016/j.jmr.2011.10.010 apa: Huber, M., With, O., Schanda, P., Verel, R., Ernst, M., & Meier, B. H. (2012). A supplementary coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2011.10.010 chicago: Huber, Matthias, Oliver With, Paul Schanda, René Verel, Matthias Ernst, and Beat H. Meier. “A Supplementary Coil for 2H Decoupling with Commercial HCN MAS Probes.” Journal of Magnetic Resonance. Elsevier, 2012. https://doi.org/10.1016/j.jmr.2011.10.010. ieee: M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, and B. H. Meier, “A supplementary coil for 2H decoupling with commercial HCN MAS probes,” Journal of Magnetic Resonance, vol. 214. Elsevier, pp. 76–80, 2012. ista: Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. 2012. A supplementary coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance. 214, 76–80. mla: Huber, Matthias, et al. “A Supplementary Coil for 2H Decoupling with Commercial HCN MAS Probes.” Journal of Magnetic Resonance, vol. 214, Elsevier, 2012, pp. 76–80, doi:10.1016/j.jmr.2011.10.010. short: M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, B.H. Meier, Journal of Magnetic Resonance 214 (2012) 76–80. date_created: 2020-09-18T10:10:36Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T08:19:28Z day: '01' doi: 10.1016/j.jmr.2011.10.010 extern: '1' intvolume: ' 214' language: - iso: eng month: '01' oa_version: None page: 76-80 publication: Journal of Magnetic Resonance publication_identifier: issn: - 1090-7807 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: A supplementary coil for 2H decoupling with commercial HCN MAS probes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 214 year: '2012' ... --- _id: '8502' abstract: - lang: eng text: 'The famous ergodic hypothesis suggests that for a typical Hamiltonian on a typical energy surface nearly all trajectories are dense. KAM theory disproves it. Ehrenfest (The Conceptual Foundations of the Statistical Approach in Mechanics. Ithaca, NY: Cornell University Press, 1959) and Birkhoff (Collected Math Papers. Vol 2, New York: Dover, pp 462–465, 1968) stated the quasi-ergodic hypothesis claiming that a typical Hamiltonian on a typical energy surface has a dense orbit. This question is wide open. Herman (Proceedings of the International Congress of Mathematicians, Vol II (Berlin, 1998). Doc Math 1998, Extra Vol II, Berlin: Int Math Union, pp 797–808, 1998) proposed to look for an example of a Hamiltonian near H0(I)=⟨I,I⟩2 with a dense orbit on the unit energy surface. In this paper we construct a Hamiltonian H0(I)+εH1(θ,I,ε) which has an orbit dense in a set of maximal Hausdorff dimension equal to 5 on the unit energy surface.' article_processing_charge: No article_type: original author: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Maria full_name: Saprykina, Maria last_name: Saprykina citation: ama: Kaloshin V, Saprykina M. An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. Communications in Mathematical Physics. 2012;315(3):643-697. doi:10.1007/s00220-012-1532-x apa: Kaloshin, V., & Saprykina, M. (2012). An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-012-1532-x chicago: Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable Hamiltonian System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.” Communications in Mathematical Physics. Springer Nature, 2012. https://doi.org/10.1007/s00220-012-1532-x. ieee: V. Kaloshin and M. Saprykina, “An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension,” Communications in Mathematical Physics, vol. 315, no. 3. Springer Nature, pp. 643–697, 2012. ista: Kaloshin V, Saprykina M. 2012. An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. Communications in Mathematical Physics. 315(3), 643–697. mla: Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable Hamiltonian System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.” Communications in Mathematical Physics, vol. 315, no. 3, Springer Nature, 2012, pp. 643–97, doi:10.1007/s00220-012-1532-x. short: V. Kaloshin, M. Saprykina, Communications in Mathematical Physics 315 (2012) 643–697. date_created: 2020-09-18T10:47:16Z date_published: 2012-11-01T00:00:00Z date_updated: 2021-01-12T08:19:44Z day: '01' doi: 10.1007/s00220-012-1532-x extern: '1' intvolume: ' 315' issue: '3' keyword: - Mathematical Physics - Statistical and Nonlinear Physics language: - iso: eng month: '11' oa_version: None page: 643-697 publication: Communications in Mathematical Physics publication_identifier: issn: - 0010-3616 - 1432-0916 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 315 year: '2012' ... --- _id: '858' abstract: - lang: eng text: 'ackground: The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of stop codons in bacterial genomes.Results: We show that in bacteria stop codons evolve slower than synonymous sites, suggesting the action of weak negative selection. However, the frequency of stop codons relative to genomic nucleotide content indicated that this selection regime is not straightforward. The frequency of TAA and TGA stop codons is GC-content dependent, with TAA decreasing and TGA increasing with GC-content, while TAG frequency is independent of GC-content. Applying a formal, analytical model to these data we found that the relationship between stop codon frequencies and nucleotide content cannot be explained by mutational biases or selection on nucleotide content. However, with weak nucleotide content-dependent selection on TAG, -0.5 < Nes < 1.5, the model fits all of the data and recapitulates the relationship between TAG and nucleotide content. For biologically plausible rates of mutations we show that, in bacteria, TAG stop codon is universally associated with lower fitness, with TAA being the optimal for G-content < 16% while for G-content > 16% TGA has a higher fitness than TAG.Conclusions: Our data indicate that TAG codon is universally suboptimal in the bacterial lineage, such that TAA is likely to be the preferred stop codon for low GC content while the TGA is the preferred stop codon for high GC content. The optimization of stop codon usage may therefore be useful in genome engineering or gene expression optimization applications.Reviewers: This article was reviewed by Michail Gelfand, Arcady Mushegian and Shamil Sunyaev. For the full reviews, please go to the Reviewers'' Comments section.' acknowledgement: | We thank Elena Alkalaeva and Peter Kolosov for insightful discussion and Brian Charlesworth for a critical reading of our manuscript. The work has been supported by a Plan Nacional grant from the Spanish Ministry of Science and Innovation, EMBO Young Investigator and Howard Hughes Medical Institute International Early Career Scientist awards. author: - first_name: Inna full_name: Povolotskaya, Inna last_name: Povolotskaya - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Alice full_name: Ledda, Alice last_name: Ledda - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov citation: ama: Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. Stop codons in bacteria are not selectively equivalent. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-30 apa: Povolotskaya, I., Kondrashov, F., Ledda, A., & Vlasov, P. (2012). Stop codons in bacteria are not selectively equivalent. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-30 chicago: Povolotskaya, Inna, Fyodor Kondrashov, Alice Ledda, and Peter Vlasov. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-30. ieee: I. Povolotskaya, F. Kondrashov, A. Ledda, and P. Vlasov, “Stop codons in bacteria are not selectively equivalent,” Biology Direct, vol. 7. BioMed Central, 2012. ista: Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. 2012. Stop codons in bacteria are not selectively equivalent. Biology Direct. 7. mla: Povolotskaya, Inna, et al. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct, vol. 7, BioMed Central, 2012, doi:10.1186/1745-6150-7-30. short: I. Povolotskaya, F. Kondrashov, A. Ledda, P. Vlasov, Biology Direct 7 (2012). date_created: 2018-12-11T11:48:52Z date_published: 2012-09-01T00:00:00Z date_updated: 2021-01-12T08:20:08Z day: '01' doi: 10.1186/1745-6150-7-30 extern: 1 intvolume: ' 7' month: '09' publication: Biology Direct publication_status: published publisher: BioMed Central publist_id: '6792' quality_controlled: 0 status: public title: Stop codons in bacteria are not selectively equivalent 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 volume: 7 year: '2012' ... --- _id: '900' abstract: - lang: eng text: 'The main forces directing long-term molecular evolution remain obscure. A sizable fraction of amino-acid substitutions seem to be fixed by positive selection, but it is unclear to what degree long-term protein evolution is constrained by epistasis, that is, instances when substitutions that are accepted in one genotype are deleterious in another. Here we obtain a quantitative estimate of the prevalence of epistasis in long-term protein evolution by relating data on amino-acid usage in 14 organelle proteins and 2 nuclear-encoded proteins to their rates of short-term evolution. We studied multiple alignments of at least 1,000 orthologues for each of these 16 proteins from species from a diverse phylogenetic background and found that an average site contained approximately eight different amino acids. Thus, without epistasis an average site should accept two-fifths of all possible amino acids, and the average rate of amino-acid substitutions should therefore be about three-fifths lower than the rate of neutral evolution. However, we found that the measured rate of amino-acid substitution in recent evolution is 20 times lower than the rate of neutral evolution and an order of magnitude lower than that expected in the absence of epistasis. These data indicate that epistasis is pervasive throughout protein evolution: about 90 per cent of all amino-acid substitutions have a neutral or beneficial impact only in the genetic backgrounds in which they occur, and must therefore be deleterious in a different background of other species. Our findings show that most amino-acid substitutions have different fitness effects in different species and that epistasis provides the primary conceptual framework to describe the tempo and mode of long-term protein evolution.' acknowledgement: | The work was supported by Plan Nacional grants from the Spanish Ministry of Science and Innovation, to F.A.K. and C.N. C.K. was supported by the European Union FP7 project Quantomics (KBBE2A222664). F.A.K. is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist. We thank B. Lehner and T. Warnecke for input and a critical reading of the manuscript. author: - first_name: Michael full_name: Breen, Michael S last_name: Breen - first_name: Carsten full_name: Kemena, Carsten last_name: Kemena - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov - first_name: Cédric full_name: Notredame, Cédric last_name: Notredame - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Epistasis as the primary factor in molecular evolution. Nature. 2012;490(7421):535-538. doi:10.1038/nature11510 apa: Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2012). Epistasis as the primary factor in molecular evolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11510 chicago: Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Epistasis as the Primary Factor in Molecular Evolution.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11510. ieee: M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Epistasis as the primary factor in molecular evolution,” Nature, vol. 490, no. 7421. Nature Publishing Group, pp. 535–538, 2012. ista: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2012. Epistasis as the primary factor in molecular evolution. Nature. 490(7421), 535–538. mla: Breen, Michael, et al. “Epistasis as the Primary Factor in Molecular Evolution.” Nature, vol. 490, no. 7421, Nature Publishing Group, 2012, pp. 535–38, doi:10.1038/nature11510. short: M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 490 (2012) 535–538. date_created: 2018-12-11T11:49:06Z date_published: 2012-10-25T00:00:00Z date_updated: 2021-01-12T08:21:45Z day: '25' doi: 10.1038/nature11510 extern: 1 intvolume: ' 490' issue: '7421' month: '10' page: 535 - 538 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6748' quality_controlled: 0 status: public title: Epistasis as the primary factor in molecular evolution type: journal_article volume: 490 year: '2012' ... --- _id: '9014' abstract: - lang: eng text: In this Letter, we explore experimentally the phase behavior of a dense active suspension of self-propelled colloids. In addition to a solidlike and gaslike phase observed for high and low densities, a novel cluster phase is reported at intermediate densities. This takes the form of a stationary assembly of dense aggregates—resulting from a permanent dynamical merging and separation of active colloids—whose average size grows with activity as a linear function of the self-propelling velocity. While different possible scenarios can be considered to account for these observations—such as a generic velocity weakening instability recently put forward—we show that the experimental results are reproduced mathematically by a chemotactic aggregation mechanism, originally introduced to account for bacterial aggregation and accounting here for diffusiophoretic chemical interaction between colloidal swimmers. article_number: '268303' article_processing_charge: No article_type: letter_note author: - first_name: I. full_name: Theurkauff, I. last_name: Theurkauff - first_name: C. full_name: Cottin-Bizonne, C. last_name: Cottin-Bizonne - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: C. full_name: Ybert, C. last_name: Ybert - first_name: L. full_name: Bocquet, L. last_name: Bocquet citation: ama: Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. 2012;108(26). doi:10.1103/physrevlett.108.268303 apa: Theurkauff, I., Cottin-Bizonne, C., Palacci, J. A., Ybert, C., & Bocquet, L. (2012). Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. American Physical Society . https://doi.org/10.1103/physrevlett.108.268303 chicago: Theurkauff, I., C. Cottin-Bizonne, Jérémie A Palacci, C. Ybert, and L. Bocquet. “Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling.” Physical Review Letters. American Physical Society , 2012. https://doi.org/10.1103/physrevlett.108.268303. ieee: I. Theurkauff, C. Cottin-Bizonne, J. A. Palacci, C. Ybert, and L. Bocquet, “Dynamic clustering in active colloidal suspensions with chemical signaling,” Physical Review Letters, vol. 108, no. 26. American Physical Society , 2012. ista: Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. 2012. Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. 108(26), 268303. mla: Theurkauff, I., et al. “Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling.” Physical Review Letters, vol. 108, no. 26, 268303, American Physical Society , 2012, doi:10.1103/physrevlett.108.268303. short: I. Theurkauff, C. Cottin-Bizonne, J.A. Palacci, C. Ybert, L. Bocquet, Physical Review Letters 108 (2012). date_created: 2021-01-19T10:26:59Z date_published: 2012-06-29T00:00:00Z date_updated: 2023-02-23T13:46:45Z day: '29' doi: 10.1103/physrevlett.108.268303 extern: '1' external_id: arxiv: - '1202.6264' pmid: - '23005020' intvolume: ' 108' issue: '26' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1202.6264 month: '06' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - '10797114' issn: - '00319007' publication_status: published publisher: 'American Physical Society ' quality_controlled: '1' scopus_import: '1' status: public title: Dynamic clustering in active colloidal suspensions with chemical signaling type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 108 year: '2012' ... --- _id: '91' abstract: - lang: eng text: 'We demonstrate how to appropriately estimate the zero-frequency (static) hyperpolarizability of an organic molecule from its charge distribution, and we explore applications of these estimates for identifying and evaluating new organic nonlinear optical (NLO) materials. First, we calculate hyperpolarizabilities from Hartree-Fock-derived charge distributions and find order-of-magnitude agreement with experimental values. We show that these simple arithmetic calculations will enable systematic searches for new organic NLO molecules. Second, we derive hyperpolarizabilities from crystallographic data using a multipolar charge-density analysis and find good agreement with empirical calculations. This demonstrates an experimental determination of the full static hyperpolarizability tensor in a solid-state sample. ' acknowledgement: This work was supported by The Winston Churchill Foundation of the United States (A.P.H., M.A.B.F., D.D.H.), The Royal Society via a University Research Fellowship (J.M.C.), and the University of New Brunswick via The Vice-Chancellor’s Research Chair (J.M.C.). article_number: '033512' 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: Jacqueline full_name: Cole, Jacqueline last_name: Cole - first_name: Martin full_name: Blood Forsythe, Martin last_name: Blood Forsythe - first_name: Daniel full_name: Hickstein, Daniel last_name: Hickstein citation: ama: Higginbotham AP, Cole J, Blood Forsythe M, Hickstein D. Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. 2012;111(3). doi:10.1063/1.3678593 apa: Higginbotham, A. P., Cole, J., Blood Forsythe, M., & Hickstein, D. (2012). Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. American Institute of Physics. https://doi.org/10.1063/1.3678593 chicago: Higginbotham, Andrew P, Jacqueline Cole, Martin Blood Forsythe, and Daniel Hickstein. “Identifying and Evaluating Organic Nonlinear Optical Materials via Molecular Moments.” Journal of Applied Physics. American Institute of Physics, 2012. https://doi.org/10.1063/1.3678593. ieee: A. P. Higginbotham, J. Cole, M. Blood Forsythe, and D. Hickstein, “Identifying and evaluating organic nonlinear optical materials via molecular moments,” Journal of Applied Physics, vol. 111, no. 3. American Institute of Physics, 2012. ista: Higginbotham AP, Cole J, Blood Forsythe M, Hickstein D. 2012. Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. 111(3), 033512. mla: Higginbotham, Andrew P., et al. “Identifying and Evaluating Organic Nonlinear Optical Materials via Molecular Moments.” Journal of Applied Physics, vol. 111, no. 3, 033512, American Institute of Physics, 2012, doi:10.1063/1.3678593. short: A.P. Higginbotham, J. Cole, M. Blood Forsythe, D. Hickstein, Journal of Applied Physics 111 (2012). date_created: 2018-12-11T11:44:35Z date_published: 2012-02-07T00:00:00Z date_updated: 2021-01-12T08:21:50Z day: '07' doi: 10.1063/1.3678593 extern: '1' intvolume: ' 111' issue: '3' language: - iso: eng month: '02' oa_version: None publication: Journal of Applied Physics publication_status: published publisher: American Institute of Physics publist_id: '7963' quality_controlled: '1' status: public title: Identifying and evaluating organic nonlinear optical materials via molecular moments type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2012' ... --- _id: '9142' abstract: - lang: eng text: "In models of radiative–convective equilibrium it is known that convection can spontaneously aggregate into one single localized moist region if the domain is large enough. The large changes in the mean climate state and radiative fluxes accompanying this self-aggregation raise questions as to what simulations at lower resolutions with parameterized convection, in similar homogeneous geometries, should be expected to produce to be considered successful in mimicking a cloud-resolving model.\r\nThe authors investigate this self-aggregation in a nonrotating, three-dimensional cloud-resolving model on a square domain without large-scale forcing. It is found that self-aggregation is sensitive not only to the domain size, but also to the horizontal resolution. With horizontally homogeneous initial conditions, convective aggregation only occurs on domains larger than about 200km and with resolutions coarser than about 2km in the model examined. The system exhibits hysteresis, so that with aggregated initial conditions, convection remains aggregated even at our finest resolution, 500m, as long as the domain is greater than 200–300km.\r\nThe sensitivity of self-aggregation to resolution and domain size in this model is due to the sensitivity of the distribution of low clouds to these two parameters. Indeed, the mechanism responsible for the aggregation of convection is the dynamical response to the longwave radiative cooling from low clouds. Strong longwave cooling near cloud top in dry regions forces downward motion, which by continuity generates inflow near cloud top and near-surface outflow from dry regions. This circulation results in the net export of moist static energy from regions with low moist static energy, yielding a positive feedback." article_processing_charge: No article_type: original author: - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Isaac M. full_name: Held, Isaac M. last_name: Held citation: ama: Muller CJ, Held IM. Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. 2012;69(8):2551-2565. doi:10.1175/jas-d-11-0257.1 apa: Muller, C. J., & Held, I. M. (2012). Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. American Meteorological Society. https://doi.org/10.1175/jas-d-11-0257.1 chicago: Muller, Caroline J, and Isaac M. Held. “Detailed Investigation of the Self-Aggregation of Convection in Cloud-Resolving Simulations.” Journal of the Atmospheric Sciences. American Meteorological Society, 2012. https://doi.org/10.1175/jas-d-11-0257.1. ieee: C. J. Muller and I. M. Held, “Detailed investigation of the self-aggregation of convection in cloud-resolving simulations,” Journal of the Atmospheric Sciences, vol. 69, no. 8. American Meteorological Society, pp. 2551–2565, 2012. ista: Muller CJ, Held IM. 2012. Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. 69(8), 2551–2565. mla: Muller, Caroline J., and Isaac M. Held. “Detailed Investigation of the Self-Aggregation of Convection in Cloud-Resolving Simulations.” Journal of the Atmospheric Sciences, vol. 69, no. 8, American Meteorological Society, 2012, pp. 2551–65, doi:10.1175/jas-d-11-0257.1. short: C.J. Muller, I.M. Held, Journal of the Atmospheric Sciences 69 (2012) 2551–2565. date_created: 2021-02-15T14:39:03Z date_published: 2012-08-01T00:00:00Z date_updated: 2022-01-24T13:49:41Z day: '01' doi: 10.1175/jas-d-11-0257.1 extern: '1' intvolume: ' 69' issue: '8' keyword: - Atmospheric Science language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1175/JAS-D-11-0257.1 month: '08' oa: 1 oa_version: Published Version page: 2551-2565 publication: Journal of the Atmospheric Sciences publication_identifier: issn: - 0022-4928 - 1520-0469 publication_status: published publisher: American Meteorological Society quality_controlled: '1' status: public title: Detailed investigation of the self-aggregation of convection in cloud-resolving simulations type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 69 year: '2012' ... --- _id: '9451' abstract: - lang: eng text: The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations. article_processing_charge: No article_type: original author: - first_name: Christian A. full_name: Ibarra, Christian A. last_name: Ibarra - first_name: Xiaoqi full_name: Feng, Xiaoqi last_name: Feng - first_name: Vera K. full_name: Schoft, Vera K. last_name: Schoft - first_name: Tzung-Fu full_name: Hsieh, Tzung-Fu last_name: Hsieh - first_name: Rie full_name: Uzawa, Rie last_name: Uzawa - first_name: Jessica A. full_name: Rodrigues, Jessica A. last_name: Rodrigues - first_name: Assaf full_name: Zemach, Assaf last_name: Zemach - first_name: Nina full_name: Chumak, Nina last_name: Chumak - first_name: Adriana full_name: Machlicova, Adriana last_name: Machlicova - first_name: Toshiro full_name: Nishimura, Toshiro last_name: Nishimura - first_name: Denisse full_name: Rojas, Denisse last_name: Rojas - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer - first_name: Hisashi full_name: Tamaru, Hisashi last_name: Tamaru - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364. doi:10.1126/science.1224839 apa: Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1224839 chicago: Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839. ieee: C. A. Ibarra et al., “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100. American Association for the Advancement of Science, pp. 1360–1364, 2012. ista: Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 337(6100), 1360–1364. mla: Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science, vol. 337, no. 6100, American Association for the Advancement of Science, 2012, pp. 1360–64, doi:10.1126/science.1224839. short: C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H. Tamaru, D. Zilberman, Science 337 (2012) 1360–1364. date_created: 2021-06-04T07:51:31Z date_published: 2012-09-14T00:00:00Z date_updated: 2021-12-14T08:28:51Z day: '14' ddc: - '580' department: - _id: DaZi doi: 10.1126/science.1224839 extern: '1' external_id: pmid: - '22984074' has_accepted_license: '1' intvolume: ' 337' issue: '6100' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/ month: '09' oa: 1 oa_version: Published Version page: 1360-1364 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 337 year: '2012' ... --- _id: '9535' abstract: - lang: eng text: The most well-studied function of DNA methylation in eukaryotic cells is the transcriptional silencing of genes and transposons. More recent results showed that many eukaryotes methylate the bodies of genes as well and that this methylation correlates with transcriptional activity rather than repression. The purpose of gene body methylation remains mysterious, but is potentially related to the histone variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and other investigators have shown that this relationship is likely to be the result of an ancient but unknown mechanism by which DNA methylation prevents the incorporation of H2A.Z. Recently, we discovered strong correlations between the presence of H2A.Z within gene bodies, the degree to which a gene's expression varies across tissue types or environmental conditions, and transcriptional misregulation in an h2a.z mutant. We propose that one basal function of gene body methylation is the establishment of constitutive expression patterns within housekeeping genes by excluding H2A.Z from their bodies. article_processing_charge: No article_type: review author: - first_name: D. full_name: Coleman-Derr, D. last_name: Coleman-Derr - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 2012;77:147-154. doi:10.1101/sqb.2012.77.014944 apa: Coleman-Derr, D., & Zilberman, D. (2012). DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/sqb.2012.77.014944 chicago: Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Laboratory Press, 2012. https://doi.org/10.1101/sqb.2012.77.014944. ieee: D. Coleman-Derr and D. Zilberman, “DNA methylation, H2A.Z, and the regulation of constitutive expression,” Cold Spring Harbor Symposia on Quantitative Biology, vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012. ista: Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 77, 147–154. mla: Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology, vol. 77, Cold Spring Harbor Laboratory Press, 2012, pp. 147–54, doi:10.1101/sqb.2012.77.014944. short: D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative Biology 77 (2012) 147–154. date_created: 2021-06-08T13:01:23Z date_published: 2012-12-18T00:00:00Z date_updated: 2021-12-14T08:33:09Z day: '18' department: - _id: DaZi doi: 10.1101/sqb.2012.77.014944 extern: '1' external_id: pmid: - '23250988' intvolume: ' 77' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/sqb.2012.77.014944 month: '12' oa: 1 oa_version: Published Version page: 147-154 pmid: 1 publication: Cold Spring Harbor Symposia on Quantitative Biology publication_identifier: eissn: - 1943-4456 issn: - 0091-7451 publication_status: published publisher: Cold Spring Harbor Laboratory Press quality_controlled: '1' scopus_import: '1' status: public title: DNA methylation, H2A.Z, and the regulation of constitutive expression type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 77 year: '2012' ...