[{"author":[{"first_name":"Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"de Vladar, Harold","last_name":"de Vladar","orcid":"0000-0002-5985-7653"},{"first_name":"Julian","last_name":"Chela Flores","full_name":"Chela Flores, Julian"}],"status":"public","doi":"10.1007/978-94-007-4966-5_22","date_published":"2012-01-01T00:00:00Z","abstract":[{"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.","lang":"eng"}],"intvolume":"        24","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T07:42:20Z","volume":24,"day":"01","publication":"Life on Earth and other planetary bodies","title":"Can the evolution of multicellularity be anticipated in the exploration of the solar system?","department":[{"_id":"NiBa"}],"month":"01","year":"2012","page":"387 - 405","publist_id":"3369","_id":"3277","publication_status":"published","quality_controlled":"1","alternative_title":["Cellular Origin, Life in Extreme Habitats and Astrobiology"],"date_created":"2018-12-11T12:02:25Z","citation":{"ieee":"H. de Vladar and J. Chela Flores, “Can the evolution of multicellularity be anticipated in the exploration of the solar system?,” in <i>Life on Earth and other planetary bodies</i>, vol. 24, Springer, 2012, pp. 387–405.","short":"H. de Vladar, J. Chela Flores, in:, Life on Earth and Other Planetary Bodies, 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.","ama":"de Vladar H, Chela Flores J. Can the evolution of multicellularity be anticipated in the exploration of the solar system? In: <i>Life on Earth and Other Planetary Bodies</i>. Vol 24. Springer; 2012:387-405. doi:<a href=\"https://doi.org/10.1007/978-94-007-4966-5_22\">10.1007/978-94-007-4966-5_22</a>","mla":"de Vladar, Harold, and Julian Chela Flores. “Can the Evolution of Multicellularity Be Anticipated in the Exploration of the Solar System?” <i>Life on Earth and Other Planetary Bodies</i>, vol. 24, Springer, 2012, pp. 387–405, doi:<a href=\"https://doi.org/10.1007/978-94-007-4966-5_22\">10.1007/978-94-007-4966-5_22</a>.","chicago":"Vladar, Harold de, and Julian Chela Flores. “Can the Evolution of Multicellularity Be Anticipated in the Exploration of the Solar System?” In <i>Life on Earth and Other Planetary Bodies</i>, 24:387–405. Springer, 2012. <a href=\"https://doi.org/10.1007/978-94-007-4966-5_22\">https://doi.org/10.1007/978-94-007-4966-5_22</a>.","apa":"de Vladar, H., &#38; Chela Flores, J. (2012). Can the evolution of multicellularity be anticipated in the exploration of the solar system? In <i>Life on Earth and other planetary bodies</i> (Vol. 24, pp. 387–405). Springer. <a href=\"https://doi.org/10.1007/978-94-007-4966-5_22\">https://doi.org/10.1007/978-94-007-4966-5_22</a>"},"oa_version":"None","type":"book_chapter","publisher":"Springer"},{"quality_controlled":"1","conference":{"start_date":"2012-03-19","name":"TCC: Theory of Cryptography Conference","end_date":"2012-03-21","location":"Taormina, Sicily, Italy"},"citation":{"ista":"Jain A, Pietrzak KZ, Tentes A. 2012. Hardness preserving constructions of pseudorandom functions. TCC: Theory of Cryptography Conference, LNCS, vol. 7194, 369–382.","short":"A. Jain, K.Z. Pietrzak, A. Tentes, in:, Springer, 2012, pp. 369–382.","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.","ama":"Jain A, Pietrzak KZ, Tentes A. Hardness preserving constructions of pseudorandom functions. In: Vol 7194. Springer; 2012:369-382. doi:<a href=\"https://doi.org/10.1007/978-3-642-28914-9_21\">10.1007/978-3-642-28914-9_21</a>","chicago":"Jain, Abhishek, Krzysztof Z Pietrzak, and Aris Tentes. “Hardness Preserving Constructions of Pseudorandom Functions,” 7194:369–82. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-28914-9_21\">https://doi.org/10.1007/978-3-642-28914-9_21</a>.","apa":"Jain, A., Pietrzak, K. Z., &#38; 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. <a href=\"https://doi.org/10.1007/978-3-642-28914-9_21\">https://doi.org/10.1007/978-3-642-28914-9_21</a>","mla":"Jain, Abhishek, et al. <i>Hardness Preserving Constructions of Pseudorandom Functions</i>. Vol. 7194, Springer, 2012, pp. 369–82, doi:<a href=\"https://doi.org/10.1007/978-3-642-28914-9_21\">10.1007/978-3-642-28914-9_21</a>."},"date_created":"2018-12-11T12:02:25Z","publist_id":"3367","page":"369 - 382","title":"Hardness preserving constructions of pseudorandom functions","day":"04","acknowledgement":"Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC)","volume":7194,"date_published":"2012-05-04T00:00:00Z","intvolume":"      7194","doi":"10.1007/978-3-642-28914-9_21","ec_funded":1,"publisher":"Springer","publication_status":"published","alternative_title":["LNCS"],"_id":"3279","oa_version":"None","type":"conference","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668"}],"year":"2012","month":"05","department":[{"_id":"KrPi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T07:42:21Z","scopus_import":1,"main_file_link":[{"url":"http://www.iacr.org/archive/tcc2012/tcc2012-index.html"}],"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"}],"status":"public","author":[{"last_name":"Jain","full_name":"Jain, Abhishek","first_name":"Abhishek"},{"orcid":"0000-0002-9139-1654","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"first_name":"Aris","full_name":"Tentes, Aris","last_name":"Tentes"}]},{"oa_version":"Submitted Version","type":"conference","alternative_title":["LNCS"],"publication_status":"published","_id":"3280","publisher":"Springer","department":[{"_id":"KrPi"}],"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668"}],"month":"05","year":"2012","main_file_link":[{"open_access":"1","url":"http://www.iacr.org/archive/tcc2012/71940166/71940166.pdf"}],"abstract":[{"text":"The (decisional) learning with errors problem (LWE) asks to distinguish &quot;noisy&quot; 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 &quot;subspace LWE&quot; (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. ","lang":"eng"}],"date_updated":"2021-01-12T07:42:21Z","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","author":[{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"date_created":"2018-12-11T12:02:26Z","citation":{"ama":"Pietrzak KZ. Subspace LWE. In: Vol 7194. Springer; 2012:548-563. doi:<a href=\"https://doi.org/10.1007/978-3-642-28914-9_31\">10.1007/978-3-642-28914-9_31</a>","short":"K.Z. Pietrzak, in:, Springer, 2012, pp. 548–563.","ista":"Pietrzak KZ. 2012. Subspace LWE. TCC: Theory of Cryptography Conference, LNCS, vol. 7194, 548–563.","ieee":"K. Z. Pietrzak, “Subspace LWE,” presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy, 2012, vol. 7194, pp. 548–563.","mla":"Pietrzak, Krzysztof Z. <i>Subspace LWE</i>. Vol. 7194, Springer, 2012, pp. 548–63, doi:<a href=\"https://doi.org/10.1007/978-3-642-28914-9_31\">10.1007/978-3-642-28914-9_31</a>.","apa":"Pietrzak, K. Z. (2012). Subspace LWE (Vol. 7194, pp. 548–563). Presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy: Springer. <a href=\"https://doi.org/10.1007/978-3-642-28914-9_31\">https://doi.org/10.1007/978-3-642-28914-9_31</a>","chicago":"Pietrzak, Krzysztof Z. “Subspace LWE,” 7194:548–63. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-28914-9_31\">https://doi.org/10.1007/978-3-642-28914-9_31</a>."},"quality_controlled":"1","conference":{"start_date":"2012-03-19","name":"TCC: Theory of Cryptography Conference","location":"Taormina, Sicily, Italy","end_date":"2012-03-21"},"oa":1,"title":"Subspace LWE","publist_id":"3366","page":"548 - 563","intvolume":"      7194","date_published":"2012-05-04T00:00:00Z","day":"04","acknowledgement":"Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC).","volume":7194,"ec_funded":1,"doi":"10.1007/978-3-642-28914-9_31"},{"author":[{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"},{"last_name":"Rosen","full_name":"Rosen, Alon","first_name":"Alon"},{"first_name":"Gil","full_name":"Segev, Gil","last_name":"Segev"}],"status":"public","doi":"10.1007/978-3-642-28914-9_26","date_published":"2012-05-04T00:00:00Z","abstract":[{"lang":"eng","text":"We consider the problem of amplifying the &quot;lossiness&quot; 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 &quot;lossy functions,&quot; 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."}],"intvolume":"      7194","main_file_link":[{"url":"http://www.iacr.org/archive/tcc2012/tcc2012-index.html"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"volume":7194,"date_updated":"2021-01-12T07:42:22Z","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","day":"04","title":"Lossy functions do not amplify well","department":[{"_id":"KrPi"}],"month":"05","year":"2012","publist_id":"3365","page":"458 - 475","conference":{"start_date":"2012-03-19","name":"TCC: Theory of Cryptography Conference","location":"Taormina, Sicily, Italy","end_date":"2012-03-21"},"_id":"3281","quality_controlled":"1","alternative_title":["LNCS"],"publication_status":"published","date_created":"2018-12-11T12:02:26Z","citation":{"mla":"Pietrzak, Krzysztof Z., et al. <i>Lossy Functions Do Not Amplify Well</i>. Vol. 7194, Springer, 2012, pp. 458–75, doi:<a href=\"https://doi.org/10.1007/978-3-642-28914-9_26\">10.1007/978-3-642-28914-9_26</a>.","chicago":"Pietrzak, Krzysztof Z, Alon Rosen, and Gil Segev. “Lossy Functions Do Not Amplify Well,” 7194:458–75. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-28914-9_26\">https://doi.org/10.1007/978-3-642-28914-9_26</a>.","apa":"Pietrzak, K. Z., Rosen, A., &#38; 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. <a href=\"https://doi.org/10.1007/978-3-642-28914-9_26\">https://doi.org/10.1007/978-3-642-28914-9_26</a>","short":"K.Z. Pietrzak, A. Rosen, G. Segev, in:, Springer, 2012, 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.","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.","ama":"Pietrzak KZ, Rosen A, Segev G. Lossy functions do not amplify well. In: Vol 7194. Springer; 2012:458-475. doi:<a href=\"https://doi.org/10.1007/978-3-642-28914-9_26\">10.1007/978-3-642-28914-9_26</a>"},"type":"conference","oa_version":"None","publisher":"Springer"},{"file_date_updated":"2020-07-14T12:46:06Z","doi":"10.1007/978-3-642-29011-4_22","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"acknowledgement":"Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC)","day":"10","volume":7237,"date_published":"2012-03-10T00:00:00Z","intvolume":"      7237","has_accepted_license":"1","page":"355 - 374","publist_id":"3364","title":"Message authentication, revisited","oa":1,"quality_controlled":"1","conference":{"end_date":"2012-04-19","location":"Cambridge, UK","start_date":"2012-04-15","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"date_created":"2018-12-11T12:02:27Z","citation":{"mla":"Dodis, Yevgeniy, et al. <i>Message Authentication, Revisited</i>. Vol. 7237, Springer, 2012, pp. 355–74, doi:<a href=\"https://doi.org/10.1007/978-3-642-29011-4_22\">10.1007/978-3-642-29011-4_22</a>.","chicago":"Dodis, Yevgeniy, Krzysztof Z Pietrzak, Eike Kiltz, and Daniel Wichs. “Message Authentication, Revisited,” 7237:355–74. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-29011-4_22\">https://doi.org/10.1007/978-3-642-29011-4_22</a>.","apa":"Dodis, Y., Pietrzak, K. Z., Kiltz, E., &#38; Wichs, D. (2012). Message authentication, revisited (Vol. 7237, pp. 355–374). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Cambridge, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-642-29011-4_22\">https://doi.org/10.1007/978-3-642-29011-4_22</a>","short":"Y. Dodis, K.Z. Pietrzak, E. Kiltz, D. Wichs, in:, Springer, 2012, pp. 355–374.","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.","ama":"Dodis Y, Pietrzak KZ, Kiltz E, Wichs D. Message authentication, revisited. In: Vol 7237. Springer; 2012:355-374. doi:<a href=\"https://doi.org/10.1007/978-3-642-29011-4_22\">10.1007/978-3-642-29011-4_22</a>"},"status":"public","author":[{"full_name":"Dodis, Yevgeniy","last_name":"Dodis","first_name":"Yevgeniy"},{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"last_name":"Kiltz","full_name":"Kiltz, Eike","first_name":"Eike"},{"last_name":"Wichs","full_name":"Wichs, Daniel","first_name":"Daniel"}],"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:22Z","abstract":[{"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 &quot;message-hiding&quot; 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.","lang":"eng"}],"project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"}],"year":"2012","month":"03","department":[{"_id":"KrPi"}],"publisher":"Springer","pubrep_id":"686","publication_status":"published","alternative_title":["LNCS"],"_id":"3282","type":"conference","oa_version":"Submitted Version","ddc":["000","004"],"file":[{"file_name":"IST-2016-686-v1+1_059.pdf","file_id":"5074","creator":"system","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:46:06Z","file_size":372292,"checksum":"8557c17a8c2586d06ebfe62d934f5c5f","date_created":"2018-12-12T10:14:23Z"}]},{"publication_status":"published","external_id":{"pmid":["22031940"]},"_id":"3289","issue":"1","type":"journal_article","oa_version":"Submitted Version","publisher":"ASM","department":[{"_id":"JoBo"}],"month":"01","year":"2012","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255887/","open_access":"1"}],"abstract":[{"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","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T07:42:25Z","status":"public","author":[{"full_name":"Pereira, Anna","last_name":"Pereira","first_name":"Anna"},{"full_name":"Leite, Flávia","last_name":"Leite","first_name":"Flávia","id":"36705F98-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Brasil, Bruno","last_name":"Brasil","first_name":"Bruno"},{"full_name":"Soares Martins, Jamaria","last_name":"Soares Martins","first_name":"Jamaria"},{"first_name":"Alice","last_name":"Torres","full_name":"Torres, Alice"},{"full_name":"Pimenta, Paulo","last_name":"Pimenta","first_name":"Paulo"},{"last_name":"Souto Padrón","full_name":"Souto Padrón, Thais","first_name":"Thais"},{"full_name":"Tranktman, Paula","last_name":"Tranktman","first_name":"Paula"},{"last_name":"Ferreira","full_name":"Ferreira, Paulo","first_name":"Paulo"},{"last_name":"Kroon","full_name":"Kroon, Erna","first_name":"Erna"},{"last_name":"Bonjardim","full_name":"Bonjardim, Cláudio","first_name":"Cláudio"}],"quality_controlled":"1","citation":{"ieee":"A. Pereira <i>et al.</i>, “A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization,” <i>Journal of Virology</i>, vol. 86, no. 1. ASM, pp. 172–184, 2012.","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.","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.","ama":"Pereira A, Leite F, Brasil B, et al. A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization. <i>Journal of Virology</i>. 2012;86(1):172-184. doi:<a href=\"https://doi.org/10.1128/JVI.05638-11\">10.1128/JVI.05638-11</a>","mla":"Pereira, Anna, et al. “A Vaccinia Virus-Driven Interplay between the MKK4/7-JNK1/2 Pathway and Cytoskeleton Reorganization.” <i>Journal of Virology</i>, vol. 86, no. 1, ASM, 2012, pp. 172–84, doi:<a href=\"https://doi.org/10.1128/JVI.05638-11\">10.1128/JVI.05638-11</a>.","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.” <i>Journal of Virology</i>. ASM, 2012. <a href=\"https://doi.org/10.1128/JVI.05638-11\">https://doi.org/10.1128/JVI.05638-11</a>.","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. <i>Journal of Virology</i>. ASM. <a href=\"https://doi.org/10.1128/JVI.05638-11\">https://doi.org/10.1128/JVI.05638-11</a>"},"date_created":"2018-12-11T12:02:29Z","oa":1,"title":"A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization","page":"172 - 184","publist_id":"3356","date_published":"2012-01-01T00:00:00Z","intvolume":"        86","pmid":1,"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.","publication":"Journal of Virology","day":"01","volume":86,"doi":"10.1128/JVI.05638-11"},{"department":[{"_id":"HeEd"}],"year":"2012","month":"08","publication_status":"published","issue":"11","_id":"3310","type":"journal_article","ddc":["000"],"file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:06Z","file_size":280280,"checksum":"d65f79775b51258a604ca5ec741297cc","date_created":"2018-12-12T10:15:00Z","file_name":"IST-2016-542-v1+1_2012-J-01-Poinculus.pdf","creator":"system","file_id":"5116","relation":"main_file"}],"oa_version":"Submitted Version","publisher":"Elsevier","pubrep_id":"542","status":"public","author":[{"first_name":"Paul","id":"43F6EC54-F248-11E8-B48F-1D18A9856A87","last_name":"Bendich","full_name":"Bendich, Paul"},{"last_name":"Cabello","full_name":"Cabello, Sergio","first_name":"Sergio"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"}],"scopus_import":1,"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."}],"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:34Z","title":"A point calculus for interlevel set homology","page":"1436 - 1444","publist_id":"3330","quality_controlled":"1","citation":{"ama":"Bendich P, Cabello S, Edelsbrunner H. A point calculus for interlevel set homology. <i>Pattern Recognition Letters</i>. 2012;33(11):1436-1444. doi:<a href=\"https://doi.org/10.1016/j.patrec.2011.10.007\">10.1016/j.patrec.2011.10.007</a>","short":"P. Bendich, S. Cabello, H. Edelsbrunner, Pattern Recognition Letters 33 (2012) 1436–1444.","ieee":"P. Bendich, S. Cabello, and H. Edelsbrunner, “A point calculus for interlevel set homology,” <i>Pattern Recognition Letters</i>, 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.” <i>Pattern Recognition Letters</i>, vol. 33, no. 11, Elsevier, 2012, pp. 1436–44, doi:<a href=\"https://doi.org/10.1016/j.patrec.2011.10.007\">10.1016/j.patrec.2011.10.007</a>.","apa":"Bendich, P., Cabello, S., &#38; Edelsbrunner, H. (2012). A point calculus for interlevel set homology. <i>Pattern Recognition Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.patrec.2011.10.007\">https://doi.org/10.1016/j.patrec.2011.10.007</a>","chicago":"Bendich, Paul, Sergio Cabello, and Herbert Edelsbrunner. “A Point Calculus for Interlevel Set Homology.” <i>Pattern Recognition Letters</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.patrec.2011.10.007\">https://doi.org/10.1016/j.patrec.2011.10.007</a>."},"date_created":"2018-12-11T12:02:36Z","oa":1,"file_date_updated":"2020-07-14T12:46:06Z","doi":"10.1016/j.patrec.2011.10.007","date_published":"2012-08-01T00:00:00Z","has_accepted_license":"1","intvolume":"        33","acknowledgement":"Research by the third author is partially supported by the National Science Foundation (NSF) under grant DBI-0820624.","day":"01","publication":"Pattern Recognition Letters","volume":33},{"scopus_import":1,"date_published":"2012-04-01T00:00:00Z","intvolume":"        23","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"International Journal of Foundations of Computer Science","day":"01","date_updated":"2021-01-12T07:42:35Z","volume":23,"status":"public","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Majumdar, Ritankar","last_name":"Majumdar","first_name":"Ritankar"}],"doi":"10.1142/S0129054112400308","publication_status":"published","quality_controlled":"1","_id":"3314","issue":"3","oa_version":"None","type":"journal_article","citation":{"ama":"Chatterjee K, Majumdar R. Discounting and averaging in games across time scales. <i>International Journal of Foundations of Computer Science</i>. 2012;23(3):609-625. doi:<a href=\"https://doi.org/10.1142/S0129054112400308\">10.1142/S0129054112400308</a>","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.","short":"K. Chatterjee, R. Majumdar, International Journal of Foundations of Computer Science 23 (2012) 609–625.","ieee":"K. Chatterjee and R. Majumdar, “Discounting and averaging in games across time scales,” <i>International Journal of Foundations of Computer Science</i>, vol. 23, no. 3. World Scientific Publishing, pp. 609–625, 2012.","mla":"Chatterjee, Krishnendu, and Ritankar Majumdar. “Discounting and Averaging in Games across Time Scales.” <i>International Journal of Foundations of Computer Science</i>, vol. 23, no. 3, World Scientific Publishing, 2012, pp. 609–25, doi:<a href=\"https://doi.org/10.1142/S0129054112400308\">10.1142/S0129054112400308</a>.","apa":"Chatterjee, K., &#38; Majumdar, R. (2012). Discounting and averaging in games across time scales. <i>International Journal of Foundations of Computer Science</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129054112400308\">https://doi.org/10.1142/S0129054112400308</a>","chicago":"Chatterjee, Krishnendu, and Ritankar Majumdar. “Discounting and Averaging in Games across Time Scales.” <i>International Journal of Foundations of Computer Science</i>. World Scientific Publishing, 2012. <a href=\"https://doi.org/10.1142/S0129054112400308\">https://doi.org/10.1142/S0129054112400308</a>."},"date_created":"2018-12-11T12:02:37Z","publisher":"World Scientific Publishing","department":[{"_id":"KrCh"}],"title":"Discounting and averaging in games across time scales","publist_id":"3326","page":"609 - 625","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"year":"2012","month":"04"},{"publisher":"Nature Publishing Group","pubrep_id":"820","publication_status":"published","issue":"1","_id":"3317","type":"journal_article","oa_version":"Submitted Version","ddc":["570"],"file":[{"checksum":"4c1c86b2f6e4e1562f5bb800b457ea9f","file_size":314246,"date_created":"2018-12-12T10:12:13Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:07Z","creator":"system","file_id":"4931","relation":"main_file","file_name":"IST-2017-820-v1+1_17463_3_art_file_109404_ltmxbw.pdf"},{"date_updated":"2020-07-14T12:46:07Z","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:12:14Z","file_size":1840216,"checksum":"bceb2efdd49d115f4dde8486bc1be3f2","file_name":"IST-2017-820-v1+2_17463_3_figure_109402_ltmwlp.pdf","relation":"main_file","creator":"system","file_id":"4932"}],"project":[{"name":"Synaptic Mechanisms of Neuronal Network Function","_id":"25BC64A8-B435-11E9-9278-68D0E5697425","grant_number":"JO_780/A5"},{"grant_number":"SFB-TR3-TP10B","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen"}],"year":"2012","month":"01","department":[{"_id":"PeJo"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:36Z","scopus_import":1,"abstract":[{"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.","lang":"eng"}],"status":"public","author":[{"id":"34DACA34-E9AE-11E9-849C-D35BD8ADC20C","first_name":"Emmanuel","last_name":"Eggermann","full_name":"Eggermann, Emmanuel"},{"full_name":"Bucurenciu, Iancu","last_name":"Bucurenciu","id":"4BD1D872-E9AE-11E9-9EE9-8BF4597A9E2A","first_name":"Iancu"},{"last_name":"Goswami","full_name":"Goswami, Sarit","first_name":"Sarit","id":"3A578F32-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"quality_controlled":"1","date_created":"2018-12-11T12:02:38Z","citation":{"mla":"Eggermann, Emmanuel, et al. “Nanodomain Coupling between Ca(2+) Channels and Sensors of Exocytosis at Fast Mammalian Synapses.” <i>Nature Reviews Neuroscience</i>, vol. 13, no. 1, Nature Publishing Group, 2012, pp. 7–21, doi:<a href=\"https://doi.org/10.1038/nrn3125\">10.1038/nrn3125</a>.","apa":"Eggermann, E., Bucurenciu, I., Goswami, S., &#38; Jonas, P. M. (2012). Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. <i>Nature Reviews Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nrn3125\">https://doi.org/10.1038/nrn3125</a>","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.” <i>Nature Reviews Neuroscience</i>. Nature Publishing Group, 2012. <a href=\"https://doi.org/10.1038/nrn3125\">https://doi.org/10.1038/nrn3125</a>.","ama":"Eggermann E, Bucurenciu I, Goswami S, Jonas PM. Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. <i>Nature Reviews Neuroscience</i>. 2012;13(1):7-21. doi:<a href=\"https://doi.org/10.1038/nrn3125\">10.1038/nrn3125</a>","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,” <i>Nature Reviews Neuroscience</i>, 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.","short":"E. Eggermann, I. Bucurenciu, S. Goswami, P.M. Jonas, Nature Reviews Neuroscience 13 (2012) 7–21."},"page":"7 - 21","publist_id":"3322","title":"Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses","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","day":"01","publication":"Nature Reviews Neuroscience","volume":13,"date_published":"2012-01-01T00:00:00Z","intvolume":"        13","has_accepted_license":"1","file_date_updated":"2020-07-14T12:46:07Z","doi":"10.1038/nrn3125"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T07:42:43Z","volume":47,"day":"01","publication":" Journal of Symbolic Computation","scopus_import":1,"date_published":"2012-03-01T00:00:00Z","abstract":[{"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.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1104.1510"}],"intvolume":"        47","doi":"10.1016/j.jsc.2011.11.001","author":[{"last_name":"Kerber","full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"},{"last_name":"Sagraloff","full_name":"Sagraloff, Michael","first_name":"Michael"}],"status":"public","oa":1,"publisher":"Elsevier","issue":"3","_id":"3331","publication_status":"published","quality_controlled":"1","date_created":"2018-12-11T12:02:43Z","citation":{"ista":"Kerber M, Sagraloff M. 2012. A worst case bound for topology computation of algebraic curves.  Journal of Symbolic Computation. 47(3), 239–258.","short":"M. Kerber, M. Sagraloff,  Journal of Symbolic Computation 47 (2012) 239–258.","ieee":"M. Kerber and M. Sagraloff, “A worst case bound for topology computation of algebraic curves,” <i> Journal of Symbolic Computation</i>, vol. 47, no. 3. Elsevier, pp. 239–258, 2012.","ama":"Kerber M, Sagraloff M. A worst case bound for topology computation of algebraic curves. <i> Journal of Symbolic Computation</i>. 2012;47(3):239-258. doi:<a href=\"https://doi.org/10.1016/j.jsc.2011.11.001\">10.1016/j.jsc.2011.11.001</a>","chicago":"Kerber, Michael, and Michael Sagraloff. “A Worst Case Bound for Topology Computation of Algebraic Curves.” <i> Journal of Symbolic Computation</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.jsc.2011.11.001\">https://doi.org/10.1016/j.jsc.2011.11.001</a>.","apa":"Kerber, M., &#38; Sagraloff, M. (2012). A worst case bound for topology computation of algebraic curves. <i> Journal of Symbolic Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsc.2011.11.001\">https://doi.org/10.1016/j.jsc.2011.11.001</a>","mla":"Kerber, Michael, and Michael Sagraloff. “A Worst Case Bound for Topology Computation of Algebraic Curves.” <i> Journal of Symbolic Computation</i>, vol. 47, no. 3, Elsevier, 2012, pp. 239–58, doi:<a href=\"https://doi.org/10.1016/j.jsc.2011.11.001\">10.1016/j.jsc.2011.11.001</a>."},"oa_version":"Preprint","type":"journal_article","year":"2012","month":"03","publist_id":"3303","page":"239 - 258","title":"A worst case bound for topology computation of algebraic curves","department":[{"_id":"HeEd"}]},{"citation":{"ama":"Chatterjee K. Robustness of structurally equivalent concurrent parity games. In: Vol 7213. Springer; 2012:270-285. doi:<a href=\"https://doi.org/10.1007/978-3-642-28729-9_18\">10.1007/978-3-642-28729-9_18</a>","ista":"Chatterjee K. 2012. Robustness of structurally equivalent concurrent parity games. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 7213, 270–285.","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.","short":"K. Chatterjee, in:, Springer, 2012, pp. 270–285.","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. <a href=\"https://doi.org/10.1007/978-3-642-28729-9_18\">https://doi.org/10.1007/978-3-642-28729-9_18</a>","chicago":"Chatterjee, Krishnendu. “Robustness of Structurally Equivalent Concurrent Parity Games,” 7213:270–85. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-28729-9_18\">https://doi.org/10.1007/978-3-642-28729-9_18</a>.","mla":"Chatterjee, Krishnendu. <i>Robustness of Structurally Equivalent Concurrent Parity Games</i>. Vol. 7213, Springer, 2012, pp. 270–85, doi:<a href=\"https://doi.org/10.1007/978-3-642-28729-9_18\">10.1007/978-3-642-28729-9_18</a>."},"date_created":"2018-12-11T12:02:46Z","conference":{"location":"Tallinn, Estonia","end_date":"2012-04-01","start_date":"2012-03-24","name":"FoSSaCS: Foundations of Software Science and Computation Structures"},"quality_controlled":"1","arxiv":1,"oa":1,"title":"Robustness of structurally equivalent concurrent parity games","page":"270 - 285","publist_id":"3284","intvolume":"      7213","date_published":"2012-03-22T00:00:00Z","volume":7213,"day":"22","ec_funded":1,"doi":"10.1007/978-3-642-28729-9_18","oa_version":"Preprint","type":"conference","_id":"3341","publication_status":"published","external_id":{"arxiv":["1107.2009"]},"alternative_title":["LNCS"],"publisher":"Springer","department":[{"_id":"KrCh"}],"month":"03","year":"2012","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"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)."}],"related_material":{"record":[{"id":"5382","status":"public","relation":"earlier_version"}]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1107.2009"}],"scopus_import":1,"date_updated":"2023-02-23T12:23:46Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"status":"public"},{"doi":"10.1007/978-1-4614-3903-5_6","article_processing_charge":"No","author":[{"id":"3C77F464-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","last_name":"zur Nedden","full_name":"zur Nedden, Stephanie"},{"last_name":"Doney","full_name":"Doney, Alexander S.","first_name":"Alexander S."},{"first_name":"Bruno G.","last_name":"Frenguelli","full_name":"Frenguelli, Bruno G."}],"status":"public","date_updated":"2022-06-21T11:51:58Z","acknowledgement":"We are grateful to Research into Ageing/Ageing UK and The Dunhill Trust for funding SzN’s graduate studies, and to Prof Nicholas Dale for his valuable input.","publication":"Adenosine","day":"23","place":"New York","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Under physiological conditions the brain, via the purine salvage pathway, reuses the preformed purine bases hypoxanthine, derived from ATP degradation, and adenine (Ade), derived from polyamine synthesis, to restore its ATP pool. However, the massive degradation of ATP during ischemia, although providing valuable neuroprotective adenosine, results in the accumulation and loss of diffusible purine metabolites and thereby leads to a protracted reduction in the post-ischemic ATP pool size. In vivo, this may both limit the ability to deploy ATP-dependent reparative mechanisms and reduce the subsequent availability of adenosine, whilst in brain slices results in tissue with substantially lower levels of ATP than in vivo. In the present review, we describe the mechanisms by which brain tissue replenishes its ATP, how this can be improved with the clinically tolerated chemicals D-ribose and adenine, and the functional, and potential therapeutic, implications of doing so."}],"editor":[{"first_name":"Susan","full_name":"Masino, Susan","last_name":"Masino"},{"full_name":"Boison, Detlev","last_name":"Boison","first_name":"Detlev"}],"scopus_import":"1","date_published":"2012-07-23T00:00:00Z","publication_identifier":{"eisbn":["9781461439035"],"isbn":["9781461439028"]},"month":"07","year":"2012","page":"109-129","title":"The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books","department":[{"_id":"HaJa"}],"edition":"1","publisher":"Springer","date_created":"2022-03-21T07:16:12Z","citation":{"ama":"zur Nedden S, Doney AS, Frenguelli BG. The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In: Masino S, Boison D, eds. <i>Adenosine</i>. 1st ed. New York: Springer; 2012:109-129. doi:<a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">10.1007/978-1-4614-3903-5_6</a>","ieee":"S. zur Nedden, A. S. Doney, and B. G. Frenguelli, “The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books,” in <i>Adenosine</i>, 1st ed., S. Masino and D. Boison, Eds. New York: Springer, 2012, pp. 109–129.","short":"S. zur Nedden, A.S. Doney, B.G. Frenguelli, in:, S. Masino, D. Boison (Eds.), Adenosine, 1st ed., Springer, New York, 2012, pp. 109–129.","ista":"zur Nedden S, Doney AS, Frenguelli BG. 2012.The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In: Adenosine. , 109–129.","mla":"zur Nedden, Stephanie, et al. “The Double-Edged Sword: Gaining Adenosine at the Expense of ATP. How to Balance the Books.” <i>Adenosine</i>, edited by Susan Masino and Detlev Boison, 1st ed., Springer, 2012, pp. 109–29, doi:<a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">10.1007/978-1-4614-3903-5_6</a>.","apa":"zur Nedden, S., Doney, A. S., &#38; Frenguelli, B. G. (2012). The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In S. Masino &#38; D. Boison (Eds.), <i>Adenosine</i> (1st ed., pp. 109–129). New York: Springer. <a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">https://doi.org/10.1007/978-1-4614-3903-5_6</a>","chicago":"Nedden, Stephanie zur, Alexander S. Doney, and Bruno G. Frenguelli. “The Double-Edged Sword: Gaining Adenosine at the Expense of ATP. How to Balance the Books.” In <i>Adenosine</i>, edited by Susan Masino and Detlev Boison, 1st ed., 109–29. New York: Springer, 2012. <a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">https://doi.org/10.1007/978-1-4614-3903-5_6</a>."},"oa_version":"None","type":"book_chapter","_id":"10896","quality_controlled":"1","publication_status":"published"},{"article_processing_charge":"No","doi":"10.1007/978-3-642-33386-6_14","intvolume":"      7561","date_published":"2012-10-15T00:00:00Z","volume":7561,"acknowledgement":"This work has been partially supported by the French ANR project Veridyc","publication":"Automated Technology for Verification and Analysis","day":"15","place":"Berlin, Heidelberg","title":"Accurate invariant checking for programs manipulating lists and arrays with infinite data","page":"167-182","citation":{"mla":"Bouajjani, Ahmed, et al. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” <i>Automated Technology for Verification and Analysis</i>, vol. 7561, Springer, 2012, pp. 167–82, doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">10.1007/978-3-642-33386-6_14</a>.","apa":"Bouajjani, A., Dragoi, C., Enea, C., &#38; Sighireanu, M. (2012). Accurate invariant checking for programs manipulating lists and arrays with infinite data. In <i>Automated Technology for Verification and Analysis</i> (Vol. 7561, pp. 167–182). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">https://doi.org/10.1007/978-3-642-33386-6_14</a>","chicago":"Bouajjani, Ahmed, Cezara Dragoi, Constantin Enea, and Mihaela Sighireanu. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” In <i>Automated Technology for Verification and Analysis</i>, 7561:167–82. LNCS. Berlin, Heidelberg: Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">https://doi.org/10.1007/978-3-642-33386-6_14</a>.","ama":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. Accurate invariant checking for programs manipulating lists and arrays with infinite data. In: <i>Automated Technology for Verification and Analysis</i>. Vol 7561. LNCS. Berlin, Heidelberg: Springer; 2012:167-182. doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">10.1007/978-3-642-33386-6_14</a>","short":"A. Bouajjani, C. Dragoi, C. Enea, M. Sighireanu, in:, Automated Technology for Verification and Analysis, Springer, Berlin, Heidelberg, 2012, pp. 167–182.","ista":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. 2012. Accurate invariant checking for programs manipulating lists and arrays with infinite data. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and AnalysisLNCS, LNCS, vol. 7561, 167–182.","ieee":"A. Bouajjani, C. Dragoi, C. Enea, and M. Sighireanu, “Accurate invariant checking for programs manipulating lists and arrays with infinite data,” in <i>Automated Technology for Verification and Analysis</i>, Thiruvananthapuram, India, 2012, vol. 7561, pp. 167–182."},"date_created":"2022-03-21T07:58:39Z","conference":{"start_date":"2012-10-03","name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2012-10-06","location":"Thiruvananthapuram, India"},"quality_controlled":"1","author":[{"full_name":"Bouajjani, Ahmed","last_name":"Bouajjani","first_name":"Ahmed"},{"first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","full_name":"Dragoi, Cezara","last_name":"Dragoi"},{"full_name":"Enea, Constantin","last_name":"Enea","first_name":"Constantin"},{"first_name":"Mihaela","full_name":"Sighireanu, Mihaela","last_name":"Sighireanu"}],"status":"public","abstract":[{"text":"We propose a logic-based framework for automated reasoning about sequential programs manipulating singly-linked lists and arrays with unbounded data. We introduce the logic SLAD, which allows combining shape constraints, written in a fragment of Separation Logic, with data and size constraints. We address the problem of checking the entailment between SLAD formulas, which is crucial in performing pre-post condition reasoning. Although this problem is undecidable in general for SLAD, we propose a sound and powerful procedure that is able to solve this problem for a large class of formulas, beyond the capabilities of existing techniques and tools. We prove that this procedure is complete, i.e., it is actually a decision procedure for this problem, for an important fragment of SLAD including known decidable logics. We implemented this procedure and shown its preciseness and its efficiency on a significant benchmark of formulas.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-09-05T14:07:24Z","series_title":"LNCS","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"publication_identifier":{"eisbn":["9783642333866"],"eissn":["1611-3349"],"isbn":["9783642333859"],"issn":["0302-9743"]},"month":"10","year":"2012","type":"conference","oa_version":"None","_id":"10903","publication_status":"published","alternative_title":["LNCS"],"publisher":"Springer"},{"doi":"10.1007/978-3-642-32940-1_10","article_processing_charge":"No","ec_funded":1,"acknowledgement":"Author supported by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407 (RiSE), ERC Start Grant (279307: Graph Games), Microsoft faculty fellowship.","day":"15","publication":"CONCUR 2012 - Concurrency Theory","volume":7454,"place":"Berlin, Heidelberg","editor":[{"first_name":"Maciej","last_name":"Koutny","full_name":"Koutny, Maciej"},{"first_name":"Irek","full_name":"Ulidowski, Irek","last_name":"Ulidowski"}],"intvolume":"      7454","date_published":"2012-09-15T00:00:00Z","page":"115-131","title":"Strategy synthesis for multi-dimensional quantitative objectives","date_created":"2022-03-21T08:00:21Z","citation":{"short":"K. Chatterjee, M. Randour, J.-F. Raskin, in:, M. Koutny, I. Ulidowski (Eds.), CONCUR 2012 - Concurrency Theory, Springer, Berlin, Heidelberg, 2012, pp. 115–131.","ieee":"K. Chatterjee, M. Randour, and J.-F. Raskin, “Strategy synthesis for multi-dimensional quantitative objectives,” in <i>CONCUR 2012 - Concurrency Theory</i>, Newcastle upon Tyne, United Kingdom, 2012, vol. 7454, pp. 115–131.","ista":"Chatterjee K, Randour M, Raskin J-F. 2012. Strategy synthesis for multi-dimensional quantitative objectives. CONCUR 2012 - Concurrency Theory. CONCUR: Conference on Concurrency Theory, LNCS, vol. 7454, 115–131.","ama":"Chatterjee K, Randour M, Raskin J-F. Strategy synthesis for multi-dimensional quantitative objectives. In: Koutny M, Ulidowski I, eds. <i>CONCUR 2012 - Concurrency Theory</i>. Vol 7454. Berlin, Heidelberg: Springer; 2012:115-131. doi:<a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">10.1007/978-3-642-32940-1_10</a>","mla":"Chatterjee, Krishnendu, et al. “Strategy Synthesis for Multi-Dimensional Quantitative Objectives.” <i>CONCUR 2012 - Concurrency Theory</i>, edited by Maciej Koutny and Irek Ulidowski, vol. 7454, Springer, 2012, pp. 115–31, doi:<a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">10.1007/978-3-642-32940-1_10</a>.","chicago":"Chatterjee, Krishnendu, Mickael Randour, and Jean-François Raskin. “Strategy Synthesis for Multi-Dimensional Quantitative Objectives.” In <i>CONCUR 2012 - Concurrency Theory</i>, edited by Maciej Koutny and Irek Ulidowski, 7454:115–31. Berlin, Heidelberg: Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">https://doi.org/10.1007/978-3-642-32940-1_10</a>.","apa":"Chatterjee, K., Randour, M., &#38; Raskin, J.-F. (2012). Strategy synthesis for multi-dimensional quantitative objectives. In M. Koutny &#38; I. Ulidowski (Eds.), <i>CONCUR 2012 - Concurrency Theory</i> (Vol. 7454, pp. 115–131). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">https://doi.org/10.1007/978-3-642-32940-1_10</a>"},"arxiv":1,"quality_controlled":"1","conference":{"location":"Newcastle upon Tyne, United Kingdom","end_date":"2012-09-07","name":"CONCUR: Conference on Concurrency Theory","start_date":"2012-09-04"},"status":"public","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Randour, Mickael","last_name":"Randour","first_name":"Mickael"},{"first_name":"Jean-François","full_name":"Raskin, Jean-François","last_name":"Raskin"}],"date_updated":"2023-02-23T10:55:06Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"later_version","id":"2716"}]},"abstract":[{"lang":"eng","text":"Multi-dimensional mean-payoff and energy games provide the mathematical foundation for the quantitative study of reactive systems, and play a central role in the emerging quantitative theory of verification and synthesis. In this work, we study the strategy synthesis problem for games with such multi-dimensional objectives along with a parity condition, a canonical way to express ω-regular conditions. While in general, the winning strategies in such games may require infinite memory, for synthesis the most relevant problem is the construction of a finite-memory winning strategy (if one exists). Our main contributions are as follows. First, we show a tight exponential bound (matching upper and lower bounds) on the memory required for finite-memory winning strategies in both multi-dimensional mean-payoff and energy games along with parity objectives. This significantly improves the triple exponential upper bound for multi energy games (without parity) that could be derived from results in literature for games on VASS (vector addition systems with states). Second, we present an optimal symbolic and incremental algorithm to compute a finite-memory winning strategy (if one exists) in such games. Finally, we give a complete characterization of when finite memory of strategies can be traded off for randomness. In particular, we show that for one-dimension mean-payoff parity games, randomized memoryless strategies are as powerful as their pure finite-memory counterparts."}],"scopus_import":"1","publication_identifier":{"eisbn":["9783642329401"],"issn":["0302-9743","1611-3349"],"isbn":["9783642329395"]},"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"year":"2012","month":"09","department":[{"_id":"KrCh"}],"publisher":"Springer","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"publication_status":"published","external_id":{"arxiv":["1201.5073"]},"_id":"10904"},{"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530"},{"first_name":"Sebastian","last_name":"Krinninger","full_name":"Krinninger, Sebastian"},{"last_name":"Nanongkai","full_name":"Nanongkai, Danupon","first_name":"Danupon"}],"status":"public","abstract":[{"text":"Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP ∩ co−NP, but are not known to be in P. While the existence of polynomial-time algorithms has been a major open problem for decades, there is no algorithm that solves any non-trivial subclass in polynomial time.\r\nIn this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several counter examples that show that many previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting graph structures need not help.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.08234"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"535"}]},"scopus_import":"1","date_updated":"2023-09-05T14:09:30Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"KrCh"}],"publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783642330902"],"issn":["0302-9743"],"isbn":["9783642330896"]},"month":"10","year":"2012","project":[{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"type":"conference","oa_version":"Preprint","_id":"10905","publication_status":"published","alternative_title":["LNCS"],"external_id":{"arxiv":["1604.08234"]},"publisher":"Springer","article_processing_charge":"No","ec_funded":1,"doi":"10.1007/978-3-642-33090-2_27","intvolume":"      7501","date_published":"2012-10-01T00:00:00Z","volume":7501,"acknowledgement":"Supported by the Austrian Science Fund (FWF): P23499-N23, the Austrian Science Fund (FWF): S11407-N23 (RiSE), an ERC Start Grant (279307: Graph Games), and a Microsoft Faculty Fellows Award","publication":"Algorithms – ESA 2012","day":"01","title":"Polynomial-time algorithms for energy games with special weight structures","page":"301-312","citation":{"mla":"Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” <i>Algorithms – ESA 2012</i>, vol. 7501, Springer, 2012, pp. 301–12, doi:<a href=\"https://doi.org/10.1007/978-3-642-33090-2_27\">10.1007/978-3-642-33090-2_27</a>.","apa":"Chatterjee, K., Henzinger, M. H., Krinninger, S., &#38; Nanongkai, D. (2012). Polynomial-time algorithms for energy games with special weight structures. In <i>Algorithms – ESA 2012</i> (Vol. 7501, pp. 301–312). Ljubljana, Slovenia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-33090-2_27\">https://doi.org/10.1007/978-3-642-33090-2_27</a>","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, and Danupon Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” In <i>Algorithms – ESA 2012</i>, 7501:301–12. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33090-2_27\">https://doi.org/10.1007/978-3-642-33090-2_27</a>.","ama":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. Polynomial-time algorithms for energy games with special weight structures. In: <i>Algorithms – ESA 2012</i>. Vol 7501. Springer; 2012:301-312. doi:<a href=\"https://doi.org/10.1007/978-3-642-33090-2_27\">10.1007/978-3-642-33090-2_27</a>","ista":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. 2012. Polynomial-time algorithms for energy games with special weight structures. Algorithms – ESA 2012. ESA: European Symposium on Algorithms, LNCS, vol. 7501, 301–312.","ieee":"K. Chatterjee, M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time algorithms for energy games with special weight structures,” in <i>Algorithms – ESA 2012</i>, Ljubljana, Slovenia, 2012, vol. 7501, pp. 301–312.","short":"K. Chatterjee, M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, Algorithms – ESA 2012, Springer, 2012, pp. 301–312."},"date_created":"2022-03-21T08:01:45Z","conference":{"name":"ESA: European Symposium on Algorithms","start_date":"2012-09-10","end_date":"2012-09-12","location":"Ljubljana, Slovenia"},"quality_controlled":"1","arxiv":1,"oa":1},{"place":"Berlin, Heidelberg","volume":7214,"publication":"Tools and Algorithms for the Construction and Analysis of Systems","day":"01","date_published":"2012-04-01T00:00:00Z","intvolume":"      7214","editor":[{"full_name":"Flanagan, Cormac","last_name":"Flanagan","first_name":"Cormac"},{"first_name":"Barbara","last_name":"König","full_name":"König, Barbara"}],"doi":"10.1007/978-3-642-28756-5_46","article_processing_charge":"No","oa":1,"conference":{"end_date":"2012-04-01","location":"Tallinn, Estonia","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2012-03-24"},"quality_controlled":"1","citation":{"chicago":"Grebenshchikov, Sergey, Ashutosh Gupta, Nuno P. Lopes, Corneliu Popeea, and Andrey Rybalchenko. “HSF(C): A Software Verifier Based on Horn Clauses.” In <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, edited by Cormac Flanagan and Barbara König, 7214:549–51. LNCS. Berlin, Heidelberg: Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">https://doi.org/10.1007/978-3-642-28756-5_46</a>.","apa":"Grebenshchikov, S., Gupta, A., Lopes, N. P., Popeea, C., &#38; Rybalchenko, A. (2012). HSF(C): A software verifier based on Horn clauses. In C. Flanagan &#38; B. König (Eds.), <i>Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 7214, pp. 549–551). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">https://doi.org/10.1007/978-3-642-28756-5_46</a>","mla":"Grebenshchikov, Sergey, et al. “HSF(C): A Software Verifier Based on Horn Clauses.” <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, edited by Cormac Flanagan and Barbara König, vol. 7214, Springer, 2012, pp. 549–51, doi:<a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">10.1007/978-3-642-28756-5_46</a>.","ieee":"S. Grebenshchikov, A. Gupta, N. P. Lopes, C. Popeea, and A. Rybalchenko, “HSF(C): A software verifier based on Horn clauses,” in <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, Tallinn, Estonia, 2012, vol. 7214, pp. 549–551.","ista":"Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. 2012. HSF(C): A software verifier based on Horn clauses. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of SystemsLNCS, LNCS, vol. 7214, 549–551.","short":"S. Grebenshchikov, A. Gupta, N.P. Lopes, C. Popeea, A. Rybalchenko, in:, C. Flanagan, B. König (Eds.), Tools and Algorithms for the Construction and Analysis of Systems, Springer, Berlin, Heidelberg, 2012, pp. 549–551.","ama":"Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. HSF(C): A software verifier based on Horn clauses. In: Flanagan C, König B, eds. <i>Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 7214. LNCS. Berlin, Heidelberg: Springer; 2012:549-551. doi:<a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">10.1007/978-3-642-28756-5_46</a>"},"date_created":"2022-03-21T08:03:30Z","page":"549-551","title":"HSF(C): A software verifier based on Horn clauses","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"series_title":"LNCS","date_updated":"2023-09-05T14:09:54Z","scopus_import":"1","abstract":[{"text":"HSF(C) is a tool that automates verification of safety and liveness properties for C programs. This paper describes the verification approach taken by HSF(C) and provides instructions on how to install and use the tool.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/978-3-642-28756-5_46"}],"author":[{"full_name":"Grebenshchikov, Sergey","last_name":"Grebenshchikov","first_name":"Sergey"},{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","last_name":"Gupta","full_name":"Gupta, Ashutosh"},{"last_name":"Lopes","full_name":"Lopes, Nuno P.","first_name":"Nuno P."},{"first_name":"Corneliu","full_name":"Popeea, Corneliu","last_name":"Popeea"},{"full_name":"Rybalchenko, Andrey","last_name":"Rybalchenko","first_name":"Andrey"}],"status":"public","publisher":"Springer","_id":"10906","publication_status":"published","alternative_title":["LNCS"],"oa_version":"Published Version","type":"conference","year":"2012","month":"04","publication_identifier":{"issn":["0302-9743"],"isbn":["9783642287558"],"eissn":["1611-3349"],"eisbn":["9783642287565"]},"department":[{"_id":"ToHe"}]},{"title":"Practical leakage-resilient symmetric cryptography","publist_id":"5003","page":"213 - 232","conference":{"end_date":"2012-09-12","location":"Leuven, Belgium","name":"CHES: Cryptographic Hardware and Embedded Systems","start_date":"2012-09-09"},"quality_controlled":"1","date_created":"2018-12-11T11:55:25Z","citation":{"ama":"Faust S, Pietrzak KZ, Schipper J. Practical leakage-resilient symmetric cryptography. In: <i> Conference Proceedings CHES 2012</i>. Vol 7428. Springer; 2012:213-232. doi:<a href=\"https://doi.org/10.1007/978-3-642-33027-8_13\">10.1007/978-3-642-33027-8_13</a>","ista":"Faust S, Pietrzak KZ, Schipper J. 2012. Practical leakage-resilient symmetric cryptography.  Conference proceedings CHES 2012. CHES: Cryptographic Hardware and Embedded Systems, LNCS, vol. 7428, 213–232.","ieee":"S. Faust, K. Z. Pietrzak, and J. Schipper, “Practical leakage-resilient symmetric cryptography,” in <i> Conference proceedings CHES 2012</i>, Leuven, Belgium, 2012, vol. 7428, pp. 213–232.","short":"S. Faust, K.Z. Pietrzak, J. Schipper, in:,  Conference Proceedings CHES 2012, Springer, 2012, pp. 213–232.","apa":"Faust, S., Pietrzak, K. Z., &#38; Schipper, J. (2012). Practical leakage-resilient symmetric cryptography. In <i> Conference proceedings CHES 2012</i> (Vol. 7428, pp. 213–232). Leuven, Belgium: Springer. <a href=\"https://doi.org/10.1007/978-3-642-33027-8_13\">https://doi.org/10.1007/978-3-642-33027-8_13</a>","chicago":"Faust, Sebastian, Krzysztof Z Pietrzak, and Joachim Schipper. “Practical Leakage-Resilient Symmetric Cryptography.” In <i> Conference Proceedings CHES 2012</i>, 7428:213–32. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33027-8_13\">https://doi.org/10.1007/978-3-642-33027-8_13</a>.","mla":"Faust, Sebastian, et al. “Practical Leakage-Resilient Symmetric Cryptography.” <i> Conference Proceedings CHES 2012</i>, vol. 7428, Springer, 2012, pp. 213–32, doi:<a href=\"https://doi.org/10.1007/978-3-642-33027-8_13\">10.1007/978-3-642-33027-8_13</a>."},"oa":1,"ec_funded":1,"doi":"10.1007/978-3-642-33027-8_13","date_published":"2012-09-01T00:00:00Z","intvolume":"      7428","volume":7428,"day":"01","acknowledgement":"Sebastian Faust acknowledges support from the Danish National Research Foundation and The National Science Foundation of China (under the grant 61061130540) for the Sino-Danish Center for the Theory of Interactive Computation, within part of this work was performed; and from the CFEM research center, supported by the Danish Strategic Research Council. \r\nSupported by the European Research Council/ERC Starting Grant 259668-PSPC.\r\n","publication":" Conference proceedings CHES 2012","department":[{"_id":"KrPi"}],"year":"2012","month":"09","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7","grant_number":"259668"}],"_id":"2048","alternative_title":["LNCS"],"publication_status":"published","type":"conference","oa_version":"Preprint","publisher":"Springer","author":[{"first_name":"Sebastian","full_name":"Faust, Sebastian","last_name":"Faust"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654"},{"first_name":"Joachim","id":"7BE863D4-E9CF-11E9-9EDB-90527418172C","full_name":"Schipper, Joachim","last_name":"Schipper"}],"status":"public","scopus_import":1,"abstract":[{"lang":"eng","text":"Leakage resilient cryptography attempts to incorporate side-channel leakage into the black-box security model and designs cryptographic schemes that are provably secure within it. Informally, a scheme is leakage-resilient if it remains secure even if an adversary learns a bounded amount of arbitrary information about the schemes internal state. Unfortunately, most leakage resilient schemes are unnecessarily complicated in order to achieve strong provable security guarantees. As advocated by Yu et al. [CCS’10], this mostly is an artefact of the security proof and in practice much simpler construction may already suffice to protect against realistic side-channel attacks. In this paper, we show that indeed for simpler constructions leakage-resilience can be obtained when we aim for relaxed security notions where the leakage-functions and/or the inputs to the primitive are chosen non-adaptively. For example, we show that a three round Feistel network instantiated with a leakage resilient PRF yields a leakage resilient PRP if the inputs are chosen non-adaptively (This complements the result of Dodis and Pietrzak [CRYPTO’10] who show that if a adaptive queries are allowed, a superlogarithmic number of rounds is necessary.) We also show that a minor variation of the classical GGM construction gives a leakage resilient PRF if both, the leakage-function and the inputs, are chosen non-adaptively."}],"main_file_link":[{"open_access":"1","url":"http://www.iacr.org/archive/ches2012/74280211/74280211.pdf"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:58Z"},{"date_updated":"2021-01-12T06:54:58Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"We propose a new authentication protocol that is provably secure based on a ring variant of the learning parity with noise (LPN) problem. The protocol follows the design principle of the LPN-based protocol from Eurocrypt’11 (Kiltz et al.), and like it, is a two round protocol secure against active attacks. Moreover, our protocol has small communication complexity and a very small footprint which makes it applicable in scenarios that involve low-cost, resource-constrained devices.\r\n\r\nPerformance-wise, our protocol is more efficient than previous LPN-based schemes, such as the many variants of the Hopper-Blum (HB) protocol and the aforementioned protocol from Eurocrypt’11. Our implementation results show that it is even comparable to the standard challenge-and-response protocols based on the AES block-cipher. Our basic protocol is roughly 20 times slower than AES, but with the advantage of having 10 times smaller code size. Furthermore, if a few hundred bytes of non-volatile memory are available to allow the storage of some off-line pre-computations, then the online phase of our protocols is only twice as slow as AES.\r\n","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.iacr.org/archive/fse2012/75490350/75490350.pdf"}],"scopus_import":1,"author":[{"full_name":"Heyse, Stefan","last_name":"Heyse","first_name":"Stefan"},{"first_name":"Eike","full_name":"Kiltz, Eike","last_name":"Kiltz"},{"full_name":"Lyubashevsky, Vadim","last_name":"Lyubashevsky","first_name":"Vadim"},{"first_name":"Christof","full_name":"Paar, Christof","last_name":"Paar"},{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"status":"public","publisher":"Springer","type":"conference","oa_version":"Preprint","_id":"2049","alternative_title":["LNCS"],"publication_status":"published","year":"2012","month":"03","project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"department":[{"_id":"KrPi"}],"volume":7549,"publication":" Conference proceedings FSE 2012","acknowledgement":"Supported by the European Research Council / ERC Starting Grant (259668- PSPC)\r\nWe would like to thank the anonymous referees of this confer- ence and those of the ECRYPT Workshop on Lightweight Cryptography for very useful comments, and in particular for the suggestion that the scheme is somewhat vulnerable to a man-in-the-middle attack whenever an adversary observes two reader challenges that are the same. We hope that the attack we described in Appendix A corresponds to what the reviewer had in mind. We also thank Tanja Lange for pointing us to the pa- per of [Kir11] and for discussions of some of her recent work. ","day":"01","intvolume":"      7549","date_published":"2012-03-01T00:00:00Z","doi":"10.1007/978-3-642-34047-5_20","ec_funded":1,"oa":1,"citation":{"ama":"Heyse S, Kiltz E, Lyubashevsky V, Paar C, Pietrzak KZ. Lapin: An efficient authentication protocol based on ring-LPN. In: <i> Conference Proceedings FSE 2012</i>. Vol 7549. Springer; 2012:346-365. doi:<a href=\"https://doi.org/10.1007/978-3-642-34047-5_20\">10.1007/978-3-642-34047-5_20</a>","ieee":"S. Heyse, E. Kiltz, V. Lyubashevsky, C. Paar, and K. Z. Pietrzak, “Lapin: An efficient authentication protocol based on ring-LPN,” in <i> Conference proceedings FSE 2012</i>, Washington, DC, USA, 2012, vol. 7549, pp. 346–365.","short":"S. Heyse, E. Kiltz, V. Lyubashevsky, C. Paar, K.Z. Pietrzak, in:,  Conference Proceedings FSE 2012, Springer, 2012, pp. 346–365.","ista":"Heyse S, Kiltz E, Lyubashevsky V, Paar C, Pietrzak KZ. 2012. Lapin: An efficient authentication protocol based on ring-LPN.  Conference proceedings FSE 2012. FSE: Fast Software Encryption, LNCS, vol. 7549, 346–365.","apa":"Heyse, S., Kiltz, E., Lyubashevsky, V., Paar, C., &#38; Pietrzak, K. Z. (2012). Lapin: An efficient authentication protocol based on ring-LPN. In <i> Conference proceedings FSE 2012</i> (Vol. 7549, pp. 346–365). Washington, DC, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-34047-5_20\">https://doi.org/10.1007/978-3-642-34047-5_20</a>","chicago":"Heyse, Stefan, Eike Kiltz, Vadim Lyubashevsky, Christof Paar, and Krzysztof Z Pietrzak. “Lapin: An Efficient Authentication Protocol Based on Ring-LPN.” In <i> Conference Proceedings FSE 2012</i>, 7549:346–65. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-34047-5_20\">https://doi.org/10.1007/978-3-642-34047-5_20</a>.","mla":"Heyse, Stefan, et al. “Lapin: An Efficient Authentication Protocol Based on Ring-LPN.” <i> Conference Proceedings FSE 2012</i>, vol. 7549, Springer, 2012, pp. 346–65, doi:<a href=\"https://doi.org/10.1007/978-3-642-34047-5_20\">10.1007/978-3-642-34047-5_20</a>."},"date_created":"2018-12-11T11:55:25Z","conference":{"start_date":"2012-03-19","name":"FSE: Fast Software Encryption","location":"Washington, DC, USA","end_date":"2012-03-21"},"quality_controlled":"1","page":"346 - 365","publist_id":"5002","title":"Lapin: An efficient authentication protocol based on ring-LPN"},{"pubrep_id":"387","publisher":"The Company of Biologists","type":"journal_article","ddc":["576"],"oa_version":"Published Version","file":[{"file_id":"4990","creator":"system","relation":"main_file","file_name":"IST-2015-387-v1+1_1200.full.pdf","file_size":726695,"checksum":"605a1800b81227848c361fd6ba7d22ba","date_created":"2018-12-12T10:13:09Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:35Z"}],"_id":"2263","issue":"12","publication_status":"published","month":"12","year":"2012","department":[{"_id":"SiHi"}],"date_updated":"2021-01-12T06:56:23Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"Nestin-cre transgenic mice have been widely used to direct recombination to neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs). Here we report that a readily utilized, and the only commercially available, Nestin-cre line is insufficient for directing recombination in early embryonic NSCs and NPCs. Analysis of recombination efficiency in multiple cre-dependent reporters and a genetic mosaic line revealed consistent temporal and spatial patterns of recombination in NSCs and NPCs. For comparison we utilized a knock-in Emx1cre line and found robust recombination in NSCs and NPCs in ventricular and subventricular zones of the cerebral cortices as early as embryonic day 12.5. In addition we found that the rate of Nestin-cre driven recombination only reaches sufficiently high levels in NSCs and NPCs during late embryonic and early postnatal periods. These findings are important when commercially available cre lines are considered for directing recombination to embryonic NSCs and NPCs.","lang":"eng"}],"scopus_import":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","author":[{"first_name":"Huixuan","full_name":"Liang, Huixuan","last_name":"Liang"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ghashghaei","full_name":"Ghashghaei, H.","first_name":"H."}],"status":"public","oa":1,"date_created":"2018-12-11T11:56:38Z","citation":{"mla":"Liang, Huixuan, et al. “A Nestin-Cre Transgenic Mouse Is Insufficient for Recombination in Early Embryonic Neural Progenitors.” <i>Biology Open</i>, vol. 1, no. 12, The Company of Biologists, 2012, pp. 1200–03, doi:<a href=\"https://doi.org/10.1242/bio.20122287\">10.1242/bio.20122287</a>.","chicago":"Liang, Huixuan, Simon Hippenmeyer, and H. Ghashghaei. “A Nestin-Cre Transgenic Mouse Is Insufficient for Recombination in Early Embryonic Neural Progenitors.” <i>Biology Open</i>. The Company of Biologists, 2012. <a href=\"https://doi.org/10.1242/bio.20122287\">https://doi.org/10.1242/bio.20122287</a>.","apa":"Liang, H., Hippenmeyer, S., &#38; Ghashghaei, H. (2012). A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. <i>Biology Open</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/bio.20122287\">https://doi.org/10.1242/bio.20122287</a>","short":"H. Liang, S. Hippenmeyer, H. Ghashghaei, Biology Open 1 (2012) 1200–1203.","ista":"Liang H, Hippenmeyer S, Ghashghaei H. 2012. A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. Biology open. 1(12), 1200–1203.","ieee":"H. Liang, S. Hippenmeyer, and H. Ghashghaei, “A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors,” <i>Biology open</i>, vol. 1, no. 12. The Company of Biologists, pp. 1200–1203, 2012.","ama":"Liang H, Hippenmeyer S, Ghashghaei H. A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. <i>Biology open</i>. 2012;1(12):1200-1203. doi:<a href=\"https://doi.org/10.1242/bio.20122287\">10.1242/bio.20122287</a>"},"quality_controlled":"1","publist_id":"4682","page":"1200 - 1203","title":"A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors","volume":1,"day":"15","publication":"Biology open","has_accepted_license":"1","intvolume":"         1","date_published":"2012-12-15T00:00:00Z","doi":"10.1242/bio.20122287","file_date_updated":"2020-07-14T12:45:35Z","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"}},{"publisher":"IEEE","type":"journal_article","oa_version":"None","_id":"2302","issue":"2","external_id":{"pmid":["22778152"]},"publication_status":"published","month":"07","year":"2012","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"department":[{"_id":"ToHe"},{"_id":"CaGu"}],"date_updated":"2021-01-12T06:56:38Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We introduce propagation models (PMs), a formalism able to express several kinds of equations that describe the behavior of biochemical reaction networks. Furthermore, we introduce the propagation abstract data type (PADT), which separates concerns regarding different numerical algorithms for the transient analysis of biochemical reaction networks from concerns regarding their implementation, thus allowing for portable and efficient solutions. The state of a propagation abstract data type is given by a vector that assigns mass values to a set of nodes, and its (next) operator propagates mass values through this set of nodes. We propose an approximate implementation of the (next) operator, based on threshold abstraction, which propagates only &quot;significant&quot; mass values and thus achieves a compromise between efficiency and accuracy. Finally, we give three use cases for propagation models: the chemical master equation (CME), the reaction rate equation (RRE), and a hybrid method that combines these two equations. These three applications use propagation models in order to propagate probabilities and/or expected values and variances of the model's variables."}],"scopus_import":1,"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"id":"3B43276C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Mateescu, Maria","last_name":"Mateescu"}],"status":"public","date_created":"2018-12-11T11:56:52Z","citation":{"chicago":"Henzinger, Thomas A, and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. IEEE, 2012. <a href=\"https://doi.org/10.1109/TCBB.2012.91\">https://doi.org/10.1109/TCBB.2012.91</a>.","apa":"Henzinger, T. A., &#38; Mateescu, M. (2012). The propagation approach for computing biochemical reaction networks. <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. IEEE. <a href=\"https://doi.org/10.1109/TCBB.2012.91\">https://doi.org/10.1109/TCBB.2012.91</a>","mla":"Henzinger, Thomas A., and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>, vol. 10, no. 2, IEEE, 2012, pp. 310–22, doi:<a href=\"https://doi.org/10.1109/TCBB.2012.91\">10.1109/TCBB.2012.91</a>.","ista":"Henzinger TA, Mateescu M. 2012. The propagation approach for computing biochemical reaction networks. IEEE ACM Transactions on Computational Biology and Bioinformatics. 10(2), 310–322.","short":"T.A. Henzinger, M. Mateescu, IEEE ACM Transactions on Computational Biology and Bioinformatics 10 (2012) 310–322.","ieee":"T. A. Henzinger and M. Mateescu, “The propagation approach for computing biochemical reaction networks,” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>, vol. 10, no. 2. IEEE, pp. 310–322, 2012.","ama":"Henzinger TA, Mateescu M. The propagation approach for computing biochemical reaction networks. <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. 2012;10(2):310-322. doi:<a href=\"https://doi.org/10.1109/TCBB.2012.91\">10.1109/TCBB.2012.91</a>"},"quality_controlled":"1","publist_id":"4625","page":"310 - 322","title":"The propagation approach for computing biochemical reaction networks","volume":10,"publication":"IEEE ACM Transactions on Computational Biology and Bioinformatics","day":"03","pmid":1,"intvolume":"        10","date_published":"2012-07-03T00:00:00Z","doi":"10.1109/TCBB.2012.91","ec_funded":1}]