[{"year":"2016","acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG-20101109-PSDP to JF). JM internship was supported by the grant “Action Austria – Slovakia”. MG was supported by the scholarship \"Stipendien der Stipendienstiftung der Republik Österreich\". Work by EH and CPR were supported by ANR blanc ANR-14-CE11-0018. We would like to thank Mark Estelle and Yunde Zhao for provid\r\n-\r\ning \r\nabp1-c1\r\n, \r\nabp1-TD1 \r\nand \r\nabp1-WTc1 \r\nseeds. We thank Emeline \r\nHuault for technical assistance.","article_number":"86","month":"01","intvolume":"         5","date_published":"2016-01-20T00:00:00Z","oa":1,"date_updated":"2025-05-07T11:12:30Z","doi":"10.12688/f1000research.7654.1","publication":"F1000 Research ","ec_funded":1,"oa_version":"Published Version","volume":5,"day":"20","status":"public","ddc":["581"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:50:47Z","publist_id":"6113","department":[{"_id":"JiFr"}],"article_processing_charge":"No","pubrep_id":"711","article_type":"original","language":[{"iso":"eng"}],"publisher":"F1000 Research","has_accepted_license":"1","file":[{"content_type":"application/pdf","file_id":"5154","creator":"system","file_size":2990459,"relation":"main_file","access_level":"open_access","checksum":"c9e50bb6096a7ba4a832969935820f19","file_name":"IST-2016-711-v1+1_770cf1e0-612f-4e85-a500-54b6349fbbab_7654_-_jaroslav_michalko.pdf","date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-12T10:15:33Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","last_name":"Michalko","full_name":"Michalko, Jaroslav"},{"orcid":"0000-0003-0619-7783","last_name":"Glanc","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","full_name":"Glanc, Matous"},{"full_name":"Perrot Rechenmann, Catherine","first_name":"Catherine","last_name":"Perrot Rechenmann"},{"full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"title":"Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein","publication_status":"published","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7"}],"file_date_updated":"2020-07-14T12:44:39Z","type":"journal_article","abstract":[{"text":"The Auxin Binding Protein 1 (ABP1) is one of the most studied proteins in plants. Since decades ago, it has been the prime receptor candidate for the plant hormone auxin with a plethora of described functions in auxin signaling and development. The developmental importance of ABP1 has recently been questioned by identification of Arabidopsis thaliana abp1 knock-out alleles that show no obvious phenotypes under normal growth conditions. In this study, we examined the contradiction between the normal growth and development of the abp1 knock-outs and the strong morphological defects observed in three different ethanol-inducible abp1 knock-down mutants ( abp1-AS, SS12K, SS12S). By analyzing segregating populations of abp1 knock-out vs. abp1 knock-down crosses we show that the strong morphological defects that were believed to be the result of conditional down-regulation of ABP1 can be reproduced also in the absence of the functional ABP1 protein. This data suggests that the phenotypes in abp1 knock-down lines are due to the off-target effects and asks for further reflections on the biological function of ABP1 or alternative explanations for the missing phenotypic defects in the abp1 loss-of-function alleles.","lang":"eng"}],"scopus_import":"1","citation":{"chicago":"Michalko, Jaroslav, Matous Glanc, Catherine Perrot Rechenmann, and Jiří Friml. “Strong Morphological Defects in Conditional Arabidopsis Abp1 Knock-down Mutants Generated in Absence of Functional ABP1 Protein.” <i>F1000 Research </i>. F1000 Research, 2016. <a href=\"https://doi.org/10.12688/f1000research.7654.1\">https://doi.org/10.12688/f1000research.7654.1</a>.","ama":"Michalko J, Glanc M, Perrot Rechenmann C, Friml J. Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein. <i>F1000 Research </i>. 2016;5. doi:<a href=\"https://doi.org/10.12688/f1000research.7654.1\">10.12688/f1000research.7654.1</a>","short":"J. Michalko, M. Glanc, C. Perrot Rechenmann, J. Friml, F1000 Research  5 (2016).","ieee":"J. Michalko, M. Glanc, C. Perrot Rechenmann, and J. Friml, “Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein,” <i>F1000 Research </i>, vol. 5. F1000 Research, 2016.","ista":"Michalko J, Glanc M, Perrot Rechenmann C, Friml J. 2016. Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein. F1000 Research . 5, 86.","mla":"Michalko, Jaroslav, et al. “Strong Morphological Defects in Conditional Arabidopsis Abp1 Knock-down Mutants Generated in Absence of Functional ABP1 Protein.” <i>F1000 Research </i>, vol. 5, 86, F1000 Research, 2016, doi:<a href=\"https://doi.org/10.12688/f1000research.7654.1\">10.12688/f1000research.7654.1</a>.","apa":"Michalko, J., Glanc, M., Perrot Rechenmann, C., &#38; Friml, J. (2016). Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein. <i>F1000 Research </i>. F1000 Research. <a href=\"https://doi.org/10.12688/f1000research.7654.1\">https://doi.org/10.12688/f1000research.7654.1</a>"},"quality_controlled":"1","_id":"1221"},{"title":"Optimal packings of congruent circles on a square flat torus","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Musin, Oleg","last_name":"Musin","first_name":"Oleg"},{"id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","first_name":"Anton","last_name":"Nikitenko","full_name":"Nikitenko, Anton"}],"publisher":"Springer","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"publist_id":"6111","_id":"1222","quality_controlled":"1","citation":{"apa":"Musin, O., &#38; Nikitenko, A. (2016). Optimal packings of congruent circles on a square flat torus. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-015-9742-6\">https://doi.org/10.1007/s00454-015-9742-6</a>","mla":"Musin, Oleg, and Anton Nikitenko. “Optimal Packings of Congruent Circles on a Square Flat Torus.” <i>Discrete &#38; Computational Geometry</i>, vol. 55, no. 1, Springer, 2016, pp. 1–20, doi:<a href=\"https://doi.org/10.1007/s00454-015-9742-6\">10.1007/s00454-015-9742-6</a>.","short":"O. Musin, A. Nikitenko, Discrete &#38; Computational Geometry 55 (2016) 1–20.","ieee":"O. Musin and A. Nikitenko, “Optimal packings of congruent circles on a square flat torus,” <i>Discrete &#38; Computational Geometry</i>, vol. 55, no. 1. Springer, pp. 1–20, 2016.","ista":"Musin O, Nikitenko A. 2016. Optimal packings of congruent circles on a square flat torus. Discrete &#38; Computational Geometry. 55(1), 1–20.","ama":"Musin O, Nikitenko A. Optimal packings of congruent circles on a square flat torus. <i>Discrete &#38; Computational Geometry</i>. 2016;55(1):1-20. doi:<a href=\"https://doi.org/10.1007/s00454-015-9742-6\">10.1007/s00454-015-9742-6</a>","chicago":"Musin, Oleg, and Anton Nikitenko. “Optimal Packings of Congruent Circles on a Square Flat Torus.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00454-015-9742-6\">https://doi.org/10.1007/s00454-015-9742-6</a>."},"abstract":[{"text":"We consider packings of congruent circles on a square flat torus, i.e., periodic (w.r.t. a square lattice) planar circle packings, with the maximal circle radius. This problem is interesting due to a practical reason—the problem of “super resolution of images.” We have found optimal arrangements for N=6, 7 and 8 circles. Surprisingly, for the case N=7 there are three different optimal arrangements. Our proof is based on a computer enumeration of toroidal irreducible contact graphs.","lang":"eng"}],"scopus_import":1,"type":"journal_article","publication_status":"published","date_updated":"2021-01-12T06:49:11Z","oa":1,"issue":"1","date_published":"2016-01-01T00:00:00Z","intvolume":"        55","month":"01","acknowledgement":"We wish to thank Alexey Tarasov, Vladislav Volkov and Brittany Fasy for some useful comments and remarks, and especially Thom Sulanke for modifying surftri to suit our purposes. Oleg R. Musin was partially supported by the NSF Grant DMS-1400876 and by the RFBR Grant 15-01-99563. Anton V. Nikitenko was supported by the Chebyshev Laboratory (Department of Mathematics and Mechanics, St. Petersburg State University) under RF Government Grant 11.G34.31.0026.","year":"2016","page":"1 - 20","date_created":"2018-12-11T11:50:48Z","status":"public","day":"01","volume":55,"oa_version":"Preprint","publication":"Discrete & Computational Geometry","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1212.0649"}],"doi":"10.1007/s00454-015-9742-6"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1408.3961"}],"publication_status":"published","doi":"10.4171/JST/132","publication":"Journal of Spectral Theory","oa_version":"Preprint","citation":{"ista":"Froese R, Lee D, Sadel C, Spitzer W, Stolz G. 2016. Localization for transversally periodic random potentials on binary trees. Journal of Spectral Theory. 6(3), 557–600.","short":"R. Froese, D. Lee, C. Sadel, W. Spitzer, G. Stolz, Journal of Spectral Theory 6 (2016) 557–600.","ieee":"R. Froese, D. Lee, C. Sadel, W. Spitzer, and G. Stolz, “Localization for transversally periodic random potentials on binary trees,” <i>Journal of Spectral Theory</i>, vol. 6, no. 3. European Mathematical Society, pp. 557–600, 2016.","ama":"Froese R, Lee D, Sadel C, Spitzer W, Stolz G. Localization for transversally periodic random potentials on binary trees. <i>Journal of Spectral Theory</i>. 2016;6(3):557-600. doi:<a href=\"https://doi.org/10.4171/JST/132\">10.4171/JST/132</a>","chicago":"Froese, Richard, Darrick Lee, Christian Sadel, Wolfgang Spitzer, and Günter Stolz. “Localization for Transversally Periodic Random Potentials on Binary Trees.” <i>Journal of Spectral Theory</i>. European Mathematical Society, 2016. <a href=\"https://doi.org/10.4171/JST/132\">https://doi.org/10.4171/JST/132</a>.","apa":"Froese, R., Lee, D., Sadel, C., Spitzer, W., &#38; Stolz, G. (2016). Localization for transversally periodic random potentials on binary trees. <i>Journal of Spectral Theory</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/JST/132\">https://doi.org/10.4171/JST/132</a>","mla":"Froese, Richard, et al. “Localization for Transversally Periodic Random Potentials on Binary Trees.” <i>Journal of Spectral Theory</i>, vol. 6, no. 3, European Mathematical Society, 2016, pp. 557–600, doi:<a href=\"https://doi.org/10.4171/JST/132\">10.4171/JST/132</a>."},"volume":6,"type":"journal_article","abstract":[{"text":"We consider a random Schrödinger operator on the binary tree with a random potential which is the sum of a random radially symmetric potential, Qr, and a random transversally periodic potential, κQt, with coupling constant κ. Using a new one-dimensional dynamical systems approach combined with Jensen's inequality in hyperbolic space (our key estimate) we obtain a fractional moment estimate proving localization for small and large κ. Together with a previous result we therefore obtain a model with two Anderson transitions, from localization to delocalization and back to localization, when increasing κ. As a by-product we also have a partially new proof of one-dimensional Anderson localization at any disorder.","lang":"eng"}],"scopus_import":1,"date_created":"2018-12-11T11:50:48Z","_id":"1223","status":"public","quality_controlled":"1","day":"01","page":"557 - 600","department":[{"_id":"LaEr"}],"publist_id":"6112","language":[{"iso":"eng"}],"year":"2016","intvolume":"         6","month":"01","date_published":"2016-01-01T00:00:00Z","publisher":"European Mathematical Society","date_updated":"2021-01-12T06:49:12Z","issue":"3","oa":1,"title":"Localization for transversally periodic random potentials on binary trees","author":[{"full_name":"Froese, Richard","first_name":"Richard","last_name":"Froese"},{"first_name":"Darrick","last_name":"Lee","full_name":"Lee, Darrick"},{"full_name":"Sadel, Christian","last_name":"Sadel","orcid":"0000-0001-8255-3968","first_name":"Christian","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Spitzer, Wolfgang","last_name":"Spitzer","first_name":"Wolfgang"},{"first_name":"Günter","last_name":"Stolz","full_name":"Stolz, Günter"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Sexual dimorphism in resource allocation is expected to change during the life cycle of dioecious plants because of temporal differences between the sexes in reproductive investment. Given the potential for sex-specific differences in reproductive costs, resource availability may contribute to variation in reproductive allocation in females and males. Here, we used Rumex hastatulus, a dioecious, wind-pollinated annual plant, to investigate whether sexual dimorphism varies with life-history stage and nutrient availability, and determine whether allocation patterns differ depending on reproductive commitment. To examine if the costs of reproduction varied between the sexes, reproduction was either allowed or prevented through bud removal, and biomass allocation was measured at maturity. In a second experiment to assess variation in sexual dimorphism across the life cycle, and whether this varied with resource availability, plants were grown in high and low nutrients and allocation to roots, aboveground vegetative growth and reproduction were measured at three developmental stages. Males prevented from reproducing compensated with increased above- and belowground allocation to a much larger degree than females, suggesting that male reproductive costs reduce vegetative growth. The proportional allocation to roots, reproductive structures and aboveground vegetative growth varied between the sexes and among life-cycle stages, but not with nutrient treatment. Females allocated proportionally more resources to roots than males at peak flowering, but this pattern was reversed at reproductive maturity under low-nutrient conditions. Our study illustrates the importance of temporal dynamics in sex-specific resource allocation and provides support for high male reproductive costs in wind-pollinated plants."}],"scopus_import":1,"citation":{"chicago":"Teitel, Zachary, Melinda Pickup, David Field, and Spencer Barrett. “The Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” <i>Plant Biology</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1111/plb.12336\">https://doi.org/10.1111/plb.12336</a>.","ama":"Teitel Z, Pickup M, Field D, Barrett S. The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. <i>Plant Biology</i>. 2016;18(1):98-103. doi:<a href=\"https://doi.org/10.1111/plb.12336\">10.1111/plb.12336</a>","short":"Z. Teitel, M. Pickup, D. Field, S. Barrett, Plant Biology 18 (2016) 98–103.","ieee":"Z. Teitel, M. Pickup, D. Field, and S. Barrett, “The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant,” <i>Plant Biology</i>, vol. 18, no. 1. Wiley-Blackwell, pp. 98–103, 2016.","ista":"Teitel Z, Pickup M, Field D, Barrett S. 2016. The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. Plant Biology. 18(1), 98–103.","mla":"Teitel, Zachary, et al. “The Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” <i>Plant Biology</i>, vol. 18, no. 1, Wiley-Blackwell, 2016, pp. 98–103, doi:<a href=\"https://doi.org/10.1111/plb.12336\">10.1111/plb.12336</a>.","apa":"Teitel, Z., Pickup, M., Field, D., &#38; Barrett, S. (2016). The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. <i>Plant Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/plb.12336\">https://doi.org/10.1111/plb.12336</a>"},"volume":18,"status":"public","quality_controlled":"1","day":"01","date_created":"2018-12-11T11:50:48Z","_id":"1224","publication_status":"published","doi":"10.1111/plb.12336","publication":"Plant Biology","oa_version":"None","publisher":"Wiley-Blackwell","month":"01","intvolume":"        18","date_published":"2016-01-01T00:00:00Z","issue":"1","author":[{"full_name":"Teitel, Zachary","last_name":"Teitel","first_name":"Zachary"},{"full_name":"Pickup, Melinda","last_name":"Pickup","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda"},{"last_name":"Field","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Field, David"},{"last_name":"Barrett","first_name":"Spencer","full_name":"Barrett, Spencer"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant","date_updated":"2021-01-12T06:49:12Z","department":[{"_id":"NiBa"}],"publist_id":"6110","page":"98 - 103","year":"2016","language":[{"iso":"eng"}]},{"ec_funded":1,"oa_version":"Submitted Version","related_material":{"record":[{"id":"1647","relation":"earlier_version","status":"public"}]},"doi":"10.1007/978-3-319-44618-9_21","main_file_link":[{"url":"https://eprint.iacr.org/2016/662","open_access":"1"}],"day":"11","status":"public","date_created":"2018-12-11T11:50:49Z","volume":9841,"year":"2016","conference":{"start_date":"2016-08-31","end_date":"2016-09-02","name":"SCN: Security and Cryptography for Networks","location":"Amalfi, Italy"},"page":"391 - 408","oa":1,"date_updated":"2023-02-23T10:08:16Z","intvolume":"      9841","month":"08","date_published":"2016-08-11T00:00:00Z","alternative_title":["LNCS"],"publication_status":"published","project":[{"grant_number":"259668","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography"},{"grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","_id":"1225","type":"conference","abstract":[{"lang":"eng","text":"At Crypto 2015 Fuchsbauer, Hanser and Slamanig (FHS) presented the first standard-model construction of efficient roundoptimal blind signatures that does not require complexity leveraging. It is conceptually simple and builds on the primitive of structure-preserving signatures on equivalence classes (SPS-EQ). FHS prove the unforgeability of their scheme assuming EUF-CMA security of the SPS-EQ scheme and hardness of a version of the DH inversion problem. Blindness under adversarially chosen keys is proven under an interactive variant of the DDH assumption. We propose a variant of their scheme whose blindness can be proven under a non-interactive assumption, namely a variant of the bilinear DDH assumption. We moreover prove its unforgeability assuming only unforgeability of the underlying SPS-EQ but no additional assumptions as needed for the FHS scheme."}],"scopus_import":1,"citation":{"chicago":"Fuchsbauer, Georg, Christian Hanser, Chethan Kamath Hosdurg, and Daniel Slamanig. “Practical Round-Optimal Blind Signatures in the Standard Model from Weaker Assumptions,” 9841:391–408. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-44618-9_21\">https://doi.org/10.1007/978-3-319-44618-9_21</a>.","ama":"Fuchsbauer G, Hanser C, Kamath Hosdurg C, Slamanig D. Practical round-optimal blind signatures in the standard model from weaker assumptions. In: Vol 9841. Springer; 2016:391-408. doi:<a href=\"https://doi.org/10.1007/978-3-319-44618-9_21\">10.1007/978-3-319-44618-9_21</a>","ista":"Fuchsbauer G, Hanser C, Kamath Hosdurg C, Slamanig D. 2016. Practical round-optimal blind signatures in the standard model from weaker assumptions. SCN: Security and Cryptography for Networks, LNCS, vol. 9841, 391–408.","ieee":"G. Fuchsbauer, C. Hanser, C. Kamath Hosdurg, and D. Slamanig, “Practical round-optimal blind signatures in the standard model from weaker assumptions,” presented at the SCN: Security and Cryptography for Networks, Amalfi, Italy, 2016, vol. 9841, pp. 391–408.","short":"G. Fuchsbauer, C. Hanser, C. Kamath Hosdurg, D. Slamanig, in:, Springer, 2016, pp. 391–408.","mla":"Fuchsbauer, Georg, et al. <i>Practical Round-Optimal Blind Signatures in the Standard Model from Weaker Assumptions</i>. Vol. 9841, Springer, 2016, pp. 391–408, doi:<a href=\"https://doi.org/10.1007/978-3-319-44618-9_21\">10.1007/978-3-319-44618-9_21</a>.","apa":"Fuchsbauer, G., Hanser, C., Kamath Hosdurg, C., &#38; Slamanig, D. (2016). Practical round-optimal blind signatures in the standard model from weaker assumptions (Vol. 9841, pp. 391–408). Presented at the SCN: Security and Cryptography for Networks, Amalfi, Italy: Springer. <a href=\"https://doi.org/10.1007/978-3-319-44618-9_21\">https://doi.org/10.1007/978-3-319-44618-9_21</a>"},"language":[{"iso":"eng"}],"department":[{"_id":"KrPi"}],"publist_id":"6109","title":"Practical round-optimal blind signatures in the standard model from weaker assumptions","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"},{"full_name":"Hanser, Christian","first_name":"Christian","last_name":"Hanser"},{"first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Slamanig, Daniel","last_name":"Slamanig","first_name":"Daniel"}],"publisher":"Springer"},{"publisher":"Nature Publishing Group","author":[{"full_name":"Fiedorczuk, Karol","last_name":"Fiedorczuk","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","first_name":"Karol"},{"last_name":"Letts","orcid":"0000-0002-9864-3586","id":"322DA418-F248-11E8-B48F-1D18A9856A87","first_name":"James A","full_name":"Letts, James A"},{"full_name":"Degliesposti, Gianluca","first_name":"Gianluca","last_name":"Degliesposti"},{"full_name":"Kaszuba, Karol","last_name":"Kaszuba","first_name":"Karol","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Skehel, Mark","last_name":"Skehel","first_name":"Mark"},{"orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Atomic structure of the entire mammalian mitochondrial complex i","department":[{"_id":"LeSa"}],"publist_id":"6108","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"scopus_import":1,"abstract":[{"lang":"eng","text":"Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) contributes to cellular energy production by transferring electrons from NADH to ubiquinone coupled to proton translocation across the membrane. It is the largest protein assembly of the respiratory chain with a total mass of 970 kilodaltons. Here we present a nearly complete atomic structure of ovine (Ovis aries) mitochondrial complex I at 3.9 Å resolution, solved by cryo-electron microscopy with cross-linking and mass-spectrometry mapping experiments. All 14 conserved core subunits and 31 mitochondria-specific supernumerary subunits are resolved within the L-shaped molecule. The hydrophilic matrix arm comprises flavin mononucleotide and 8 iron-sulfur clusters involved in electron transfer, and the membrane arm contains 78 transmembrane helices, mostly contributed by antiporter-like subunits involved in proton translocation. Supernumerary subunits form an interlinked, stabilizing shell around the conserved core. Tightly bound lipids (including cardiolipins) further stabilize interactions between the hydrophobic subunits. Subunits with possible regulatory roles contain additional cofactors, NADPH and two phosphopantetheine molecules, which are shown to be involved in inter-subunit interactions. We observe two different conformations of the complex, which may be related to the conformationally driven coupling mechanism and to the active-deactive transition of the enzyme. Our structure provides insight into the mechanism, assembly, maturation and dysfunction of mitochondrial complex I, and allows detailed molecular analysis of disease-causing mutations."}],"type":"journal_article","citation":{"mla":"Fiedorczuk, Karol, et al. “Atomic Structure of the Entire Mammalian Mitochondrial Complex I.” <i>Nature</i>, vol. 538, no. 7625, Nature Publishing Group, 2016, pp. 406–10, doi:<a href=\"https://doi.org/10.1038/nature19794\">10.1038/nature19794</a>.","apa":"Fiedorczuk, K., Letts, J. A., Degliesposti, G., Kaszuba, K., Skehel, M., &#38; Sazanov, L. A. (2016). Atomic structure of the entire mammalian mitochondrial complex i. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature19794\">https://doi.org/10.1038/nature19794</a>","chicago":"Fiedorczuk, Karol, James A Letts, Gianluca Degliesposti, Karol Kaszuba, Mark Skehel, and Leonid A Sazanov. “Atomic Structure of the Entire Mammalian Mitochondrial Complex I.” <i>Nature</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nature19794\">https://doi.org/10.1038/nature19794</a>.","ieee":"K. Fiedorczuk, J. A. Letts, G. Degliesposti, K. Kaszuba, M. Skehel, and L. A. Sazanov, “Atomic structure of the entire mammalian mitochondrial complex i,” <i>Nature</i>, vol. 538, no. 7625. Nature Publishing Group, pp. 406–410, 2016.","ista":"Fiedorczuk K, Letts JA, Degliesposti G, Kaszuba K, Skehel M, Sazanov LA. 2016. Atomic structure of the entire mammalian mitochondrial complex i. Nature. 538(7625), 406–410.","short":"K. Fiedorczuk, J.A. Letts, G. Degliesposti, K. Kaszuba, M. Skehel, L.A. Sazanov, Nature 538 (2016) 406–410.","ama":"Fiedorczuk K, Letts JA, Degliesposti G, Kaszuba K, Skehel M, Sazanov LA. Atomic structure of the entire mammalian mitochondrial complex i. <i>Nature</i>. 2016;538(7625):406-410. doi:<a href=\"https://doi.org/10.1038/nature19794\">10.1038/nature19794</a>"},"quality_controlled":"1","_id":"1226","publication_status":"published","project":[{"name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (FEBS)","_id":"2593EBD6-B435-11E9-9278-68D0E5697425"},{"name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","_id":"2590DB08-B435-11E9-9278-68D0E5697425","grant_number":"701309","call_identifier":"H2020"}],"date_published":"2016-10-20T00:00:00Z","intvolume":"       538","month":"10","oa":1,"issue":"7625","date_updated":"2021-01-12T06:49:13Z","external_id":{"pmid":["27595392"]},"page":"406 - 410","year":"2016","volume":538,"pmid":1,"status":"public","day":"20","date_created":"2018-12-11T11:50:49Z","publication":"Nature","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5164932/"}],"doi":"10.1038/nature19794","oa_version":"Submitted Version","ec_funded":1},{"pubrep_id":"781","language":[{"iso":"eng"}],"publist_id":"6107","department":[{"_id":"ToHe"}],"title":"Discrete abstraction of multiaffine systems","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Kong","orcid":"0000-0002-3066-6941","first_name":"Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","full_name":"Kong, Hui"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","last_name":"Bogomolov","orcid":"0000-0002-0686-0365"},{"full_name":"Grosu, Radu","first_name":"Radu","last_name":"Grosu"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Yu","last_name":"Jiang","full_name":"Jiang, Yu"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0003-3658-1065","last_name":"Schilling","full_name":"Schilling, Christian"}],"file":[{"content_type":"application/pdf","file_id":"4840","file_size":683955,"creator":"system","relation":"main_file","access_level":"open_access","checksum":"994e164b558c47bacf8dc066dd27c8fc","file_name":"IST-2017-781-v1+1_main.pdf","date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-12T10:10:49Z"}],"publisher":"Springer","has_accepted_license":"1","publication_status":"published","project":[{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"}],"quality_controlled":"1","_id":"1227","abstract":[{"lang":"eng","text":"Many biological systems can be modeled as multiaffine hybrid systems. Due to the nonlinearity of multiaffine systems, it is difficult to verify their properties of interest directly. A common strategy to tackle this problem is to construct and analyze a discrete overapproximation of the original system. However, the conservativeness of a discrete abstraction significantly determines the level of confidence we can have in the properties of the original system. In this paper, in order to reduce the conservativeness of a discrete abstraction, we propose a new method based on a sufficient and necessary decision condition for computing discrete transitions between states in the abstract system. We assume the state space partition of a multiaffine system to be based on a set of multivariate polynomials. Hence, a rectangular partition defined in terms of polynomials of the form (xi − c) is just a simple case of multivariate polynomial partition, and the new decision condition applies naturally. We analyze and demonstrate the improvement of our method over the existing methods using some examples."}],"scopus_import":1,"type":"conference","file_date_updated":"2020-07-14T12:44:39Z","citation":{"mla":"Kong, Hui, et al. <i>Discrete Abstraction of Multiaffine Systems</i>. Vol. 9957, Springer, 2016, pp. 128–44, doi:<a href=\"https://doi.org/10.1007/978-3-319-47151-8_9\">10.1007/978-3-319-47151-8_9</a>.","apa":"Kong, H., Bartocci, E., Bogomolov, S., Grosu, R., Henzinger, T. A., Jiang, Y., &#38; Schilling, C. (2016). Discrete abstraction of multiaffine systems (Vol. 9957, pp. 128–144). Presented at the HSB: Hybrid Systems Biology, Grenoble, France: Springer. <a href=\"https://doi.org/10.1007/978-3-319-47151-8_9\">https://doi.org/10.1007/978-3-319-47151-8_9</a>","chicago":"Kong, Hui, Ezio Bartocci, Sergiy Bogomolov, Radu Grosu, Thomas A Henzinger, Yu Jiang, and Christian Schilling. “Discrete Abstraction of Multiaffine Systems,” 9957:128–44. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-47151-8_9\">https://doi.org/10.1007/978-3-319-47151-8_9</a>.","ista":"Kong H, Bartocci E, Bogomolov S, Grosu R, Henzinger TA, Jiang Y, Schilling C. 2016. Discrete abstraction of multiaffine systems. HSB: Hybrid Systems Biology, LNCS, vol. 9957, 128–144.","short":"H. Kong, E. Bartocci, S. Bogomolov, R. Grosu, T.A. Henzinger, Y. Jiang, C. Schilling, in:, Springer, 2016, pp. 128–144.","ieee":"H. Kong <i>et al.</i>, “Discrete abstraction of multiaffine systems,” presented at the HSB: Hybrid Systems Biology, Grenoble, France, 2016, vol. 9957, pp. 128–144.","ama":"Kong H, Bartocci E, Bogomolov S, et al. Discrete abstraction of multiaffine systems. In: Vol 9957. Springer; 2016:128-144. doi:<a href=\"https://doi.org/10.1007/978-3-319-47151-8_9\">10.1007/978-3-319-47151-8_9</a>"},"year":"2016","conference":{"location":"Grenoble, France","start_date":"2016-10-20","end_date":"2016-10-21","name":"HSB: Hybrid Systems Biology"},"page":"128 - 144","oa":1,"date_updated":"2021-01-12T06:49:13Z","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","date_published":"2016-09-25T00:00:00Z","alternative_title":["LNCS"],"month":"09","intvolume":"      9957","oa_version":"Submitted Version","doi":"10.1007/978-3-319-47151-8_9","day":"25","status":"public","date_created":"2018-12-11T11:50:49Z","ddc":["005"],"volume":9957},{"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"83"}]},"ec_funded":1,"oa_version":"Submitted Version","doi":"10.1007/978-3-319-39555-5_16","ddc":["005","600"],"date_created":"2018-12-11T11:50:50Z","day":"09","status":"public","volume":9696,"year":"2016","page":"285 - 303","conference":{"location":"Guildford, UK","name":"ACNS: Applied Cryptography and Network Security","start_date":"2016-06-19","end_date":"2016-06-22"},"date_updated":"2023-09-07T12:30:22Z","oa":1,"intvolume":"      9696","month":"06","date_published":"2016-06-09T00:00:00Z","alternative_title":["LNCS"],"acknowledgement":"Research  supported  by  the  European  Research  Council,  ERC  starting  grant (259668-PSPC) and ERC consolidator grant (682815 - TOCNeT).","project":[{"name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7"},{"call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks"}],"publication_status":"published","_id":"1229","quality_controlled":"1","citation":{"apa":"Abusalah, H. M., Fuchsbauer, G., &#38; Pietrzak, K. Z. (2016). Offline witness encryption (Vol. 9696, pp. 285–303). Presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">https://doi.org/10.1007/978-3-319-39555-5_16</a>","mla":"Abusalah, Hamza M., et al. <i>Offline Witness Encryption</i>. Vol. 9696, Springer, 2016, pp. 285–303, doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">10.1007/978-3-319-39555-5_16</a>.","ista":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Offline witness encryption. ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696, 285–303.","short":"H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 285–303.","ieee":"H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Offline witness encryption,” presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK, 2016, vol. 9696, pp. 285–303.","ama":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. Offline witness encryption. In: Vol 9696. Springer; 2016:285-303. doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">10.1007/978-3-319-39555-5_16</a>","chicago":"Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Offline Witness Encryption,” 9696:285–303. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">https://doi.org/10.1007/978-3-319-39555-5_16</a>."},"type":"conference","file_date_updated":"2020-07-14T12:44:39Z","scopus_import":1,"abstract":[{"lang":"eng","text":"Witness encryption (WE) was introduced by Garg et al. [GGSW13]. A WE scheme is defined for some NP language L and lets a sender encrypt messages relative to instances x. A ciphertext for x can be decrypted using w witnessing x ∈ L, but hides the message if x ∈ L. Garg et al. construct WE from multilinear maps and give another construction [GGH+13b] using indistinguishability obfuscation (iO) for circuits. Due to the reliance on such heavy tools, WE can cur- rently hardly be implemented on powerful hardware and will unlikely be realizable on constrained devices like smart cards any time soon. We construct a WE scheme where encryption is done by simply computing a Naor-Yung ciphertext (two CPA encryptions and a NIZK proof). To achieve this, our scheme has a setup phase, which outputs public parameters containing an obfuscated circuit (only required for decryption), two encryption keys and a common reference string (used for encryption). This setup need only be run once, and the parame- ters can be used for arbitrary many encryptions. Our scheme can also be turned into a functional WE scheme, where a message is encrypted w.r.t. a statement and a function f, and decryption with a witness w yields f (m, w). Our construction is inspired by the functional encryption scheme by Garg et al. and we prove (selective) security assuming iO and statistically simulation-sound NIZK. We give a construction of the latter in bilinear groups and combining it with ElGamal encryption, our ciphertexts are of size 1.3 kB at a 128-bit security level and can be computed on a smart card."}],"language":[{"iso":"eng"}],"pubrep_id":"765","publist_id":"6105","department":[{"_id":"KrPi"}],"file":[{"file_name":"IST-2017-765-v1+1_838.pdf","date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-12T10:17:20Z","file_id":"5273","content_type":"application/pdf","creator":"system","file_size":515000,"access_level":"open_access","checksum":"34fa9ce681da845a1ba945ba3dc57867","relation":"main_file"}],"author":[{"id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M","last_name":"Abusalah","full_name":"Abusalah, Hamza M"},{"last_name":"Fuchsbauer","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","full_name":"Fuchsbauer, Georg"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"title":"Offline witness encryption","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","publisher":"Springer"},{"doi":"10.1007/978-3-662-49122-5_16","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.02615"}],"ec_funded":1,"oa_version":"Preprint","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1155"}]},"volume":9583,"status":"public","day":"01","date_created":"2018-12-11T11:50:50Z","conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation","start_date":"2016-01-17","end_date":"2016-01-19","location":"St. Petersburg, FL, USA"},"page":"328 - 347","year":"2016","acknowledgement":"We thank Andrey Kupriyanov for feedback on the manuscript,\r\nand Michael Tautschnig for help with preparing the experiments. This research was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award).","month":"01","intvolume":"      9583","date_published":"2016-01-01T00:00:00Z","alternative_title":["LNCS"],"oa":1,"date_updated":"2023-09-07T11:58:33Z","publication_status":"published","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"type":"conference","abstract":[{"text":"Concolic testing is a promising method for generating test suites for large programs. However, it suffers from the path-explosion problem and often fails to find tests that cover difficult-to-reach parts of programs. In contrast, model checkers based on counterexample-guided abstraction refinement explore programs exhaustively, while failing to scale on large programs with precision. In this paper, we present a novel method that iteratively combines concolic testing and model checking to find a test suite for a given coverage criterion. If concolic testing fails to cover some test goals, then the model checker refines its program abstraction to prove more paths infeasible, which reduces the search space for concolic testing. We have implemented our method on top of the concolictesting tool Crest and the model checker CpaChecker. We evaluated our tool on a collection of programs and a category of SvComp benchmarks. In our experiments, we observed an improvement in branch coverage compared to Crest from 48% to 63% in the best case, and from 66% to 71% on average.","lang":"eng"}],"scopus_import":1,"citation":{"ama":"Daca P, Gupta A, Henzinger TA. Abstraction-driven concolic testing. In: Vol 9583. Springer; 2016:328-347. doi:<a href=\"https://doi.org/10.1007/978-3-662-49122-5_16\">10.1007/978-3-662-49122-5_16</a>","short":"P. Daca, A. Gupta, T.A. Henzinger, in:, Springer, 2016, pp. 328–347.","ieee":"P. Daca, A. Gupta, and T. A. Henzinger, “Abstraction-driven concolic testing,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, St. Petersburg, FL, USA, 2016, vol. 9583, pp. 328–347.","ista":"Daca P, Gupta A, Henzinger TA. 2016. Abstraction-driven concolic testing. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 9583, 328–347.","chicago":"Daca, Przemyslaw, Ashutosh Gupta, and Thomas A Henzinger. “Abstraction-Driven Concolic Testing,” 9583:328–47. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-49122-5_16\">https://doi.org/10.1007/978-3-662-49122-5_16</a>.","apa":"Daca, P., Gupta, A., &#38; Henzinger, T. A. (2016). Abstraction-driven concolic testing (Vol. 9583, pp. 328–347). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, St. Petersburg, FL, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-662-49122-5_16\">https://doi.org/10.1007/978-3-662-49122-5_16</a>","mla":"Daca, Przemyslaw, et al. <i>Abstraction-Driven Concolic Testing</i>. Vol. 9583, Springer, 2016, pp. 328–47, doi:<a href=\"https://doi.org/10.1007/978-3-662-49122-5_16\">10.1007/978-3-662-49122-5_16</a>."},"quality_controlled":"1","_id":"1230","publist_id":"6104","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Abstraction-driven concolic testing","author":[{"last_name":"Daca","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw"},{"full_name":"Gupta, Ashutosh","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724"}]},{"volume":9666,"status":"public","day":"28","date_created":"2018-12-11T11:50:51Z","doi":"10.1007/978-3-662-49896-5_13","main_file_link":[{"url":"https://eprint.iacr.org/2016/100","open_access":"1"}],"ec_funded":1,"oa_version":"Submitted Version","acknowledgement":"Joël Alwen, Chethan Kamath, and Krzysztof Pietrzak’s research is partially supported by an ERC starting grant (259668-PSPC). Vladimir Kolmogorov is partially supported by an ERC consolidator grant (616160-DOICV). Binyi Chen was partially supported by NSF grants CNS-1423566 and CNS-1514526, and a gift from the Gareatis Foundation. Stefano Tessaro was partially supported by NSF grants CNS-1423566, CNS-1528178, a Hellman Fellowship, and the Glen and Susanne Culler Chair.\r\n\r\nThis work was done in part while the authors were visiting the Simons Institute for the Theory of Computing, supported by the Simons Foundation and by the DIMACS/Simons Collaboration in Cryptography through NSF grant CNS-1523467.","month":"04","intvolume":"      9666","date_published":"2016-04-28T00:00:00Z","alternative_title":["LNCS"],"oa":1,"date_updated":"2021-01-12T06:49:15Z","conference":{"location":"Vienna, Austria","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","start_date":"2016-05-08","end_date":"2016-05-12"},"page":"358 - 387","year":"2016","type":"conference","abstract":[{"lang":"eng","text":"We study the time-and memory-complexities of the problem of computing labels of (multiple) randomly selected challenge-nodes in a directed acyclic graph. The w-bit label of a node is the hash of the labels of its parents, and the hash function is modeled as a random oracle. Specific instances of this problem underlie both proofs of space [Dziembowski et al. CRYPTO’15] as well as popular memory-hard functions like scrypt. As our main tool, we introduce the new notion of a probabilistic parallel entangled pebbling game, a new type of combinatorial pebbling game on a graph, which is closely related to the labeling game on the same graph. As a first application of our framework, we prove that for scrypt, when the underlying hash function is invoked n times, the cumulative memory complexity (CMC) (a notion recently introduced by Alwen and Serbinenko (STOC’15) to capture amortized memory-hardness for parallel adversaries) is at least Ω(w · (n/ log(n))2). This bound holds for adversaries that can store many natural functions of the labels (e.g., linear combinations), but still not arbitrary functions thereof. We then introduce and study a combinatorial quantity, and show how a sufficiently small upper bound on it (which we conjecture) extends our CMC bound for scrypt to hold against arbitrary adversaries. We also show that such an upper bound solves the main open problem for proofs-of-space protocols: namely, establishing that the time complexity of computing the label of a random node in a graph on n nodes (given an initial kw-bit state) reduces tightly to the time complexity for black pebbling on the same graph (given an initial k-node pebbling)."}],"scopus_import":1,"citation":{"mla":"Alwen, Joel F., et al. <i>On the Complexity of Scrypt and Proofs of Space in the Parallel Random Oracle Model</i>. Vol. 9666, Springer, 2016, pp. 358–87, doi:<a href=\"https://doi.org/10.1007/978-3-662-49896-5_13\">10.1007/978-3-662-49896-5_13</a>.","apa":"Alwen, J. F., Chen, B., Kamath Hosdurg, C., Kolmogorov, V., Pietrzak, K. Z., &#38; Tessaro, S. (2016). On the complexity of scrypt and proofs of space in the parallel random oracle model (Vol. 9666, pp. 358–387). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-662-49896-5_13\">https://doi.org/10.1007/978-3-662-49896-5_13</a>","chicago":"Alwen, Joel F, Binyi Chen, Chethan Kamath Hosdurg, Vladimir Kolmogorov, Krzysztof Z Pietrzak, and Stefano Tessaro. “On the Complexity of Scrypt and Proofs of Space in the Parallel Random Oracle Model,” 9666:358–87. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-49896-5_13\">https://doi.org/10.1007/978-3-662-49896-5_13</a>.","ama":"Alwen JF, Chen B, Kamath Hosdurg C, Kolmogorov V, Pietrzak KZ, Tessaro S. On the complexity of scrypt and proofs of space in the parallel random oracle model. In: Vol 9666. Springer; 2016:358-387. doi:<a href=\"https://doi.org/10.1007/978-3-662-49896-5_13\">10.1007/978-3-662-49896-5_13</a>","short":"J.F. Alwen, B. Chen, C. Kamath Hosdurg, V. Kolmogorov, K.Z. Pietrzak, S. Tessaro, in:, Springer, 2016, pp. 358–387.","ieee":"J. F. Alwen, B. Chen, C. Kamath Hosdurg, V. Kolmogorov, K. Z. Pietrzak, and S. Tessaro, “On the complexity of scrypt and proofs of space in the parallel random oracle model,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria, 2016, vol. 9666, pp. 358–387.","ista":"Alwen JF, Chen B, Kamath Hosdurg C, Kolmogorov V, Pietrzak KZ, Tessaro S. 2016. On the complexity of scrypt and proofs of space in the parallel random oracle model. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 9666, 358–387."},"quality_controlled":"1","_id":"1231","publication_status":"published","project":[{"grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425"},{"name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7"}],"publisher":"Springer","title":"On the complexity of scrypt and proofs of space in the parallel random oracle model","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Alwen, Joel F","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen"},{"last_name":"Chen","first_name":"Binyi","full_name":"Chen, Binyi"},{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg"},{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Tessaro, Stefano","last_name":"Tessaro","first_name":"Stefano"}],"publist_id":"6103","department":[{"_id":"KrPi"},{"_id":"VlKo"}],"language":[{"iso":"eng"}]},{"volume":537,"citation":{"mla":"Letts, James A., et al. “The Architecture of Respiratory Supercomplexes.” <i>Nature</i>, vol. 537, no. 7622, Nature Publishing Group, 2016, pp. 644–48, doi:<a href=\"https://doi.org/10.1038/nature19774\">10.1038/nature19774</a>.","apa":"Letts, J. A., Fiedorczuk, K., &#38; Sazanov, L. A. (2016). The architecture of respiratory supercomplexes. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature19774\">https://doi.org/10.1038/nature19774</a>","chicago":"Letts, James A, Karol Fiedorczuk, and Leonid A Sazanov. “The Architecture of Respiratory Supercomplexes.” <i>Nature</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nature19774\">https://doi.org/10.1038/nature19774</a>.","short":"J.A. Letts, K. Fiedorczuk, L.A. Sazanov, Nature 537 (2016) 644–648.","ieee":"J. A. Letts, K. Fiedorczuk, and L. A. Sazanov, “The architecture of respiratory supercomplexes,” <i>Nature</i>, vol. 537, no. 7622. Nature Publishing Group, pp. 644–648, 2016.","ista":"Letts JA, Fiedorczuk K, Sazanov LA. 2016. The architecture of respiratory supercomplexes. Nature. 537(7622), 644–648.","ama":"Letts JA, Fiedorczuk K, Sazanov LA. The architecture of respiratory supercomplexes. <i>Nature</i>. 2016;537(7622):644-648. doi:<a href=\"https://doi.org/10.1038/nature19774\">10.1038/nature19774</a>"},"scopus_import":1,"abstract":[{"text":"Mitochondrial electron transport chain complexes are organized into supercomplexes responsible for carrying out cellular respiration. Here we present three architectures of mammalian (ovine) supercomplexes determined by cryo-electron microscopy. We identify two distinct arrangements of supercomplex CICIII 2 CIV (the respirasome) - a major 'tight' form and a minor 'loose' form (resolved at the resolution of 5.8 Å and 6.7 Å, respectively), which may represent different stages in supercomplex assembly or disassembly. We have also determined an architecture of supercomplex CICIII 2 at 7.8 Å resolution. All observed density can be attributed to the known 80 subunits of the individual complexes, including 132 transmembrane helices. The individual complexes form tight interactions that vary between the architectures, with complex IV subunit COX7a switching contact from complex III to complex I. The arrangement of active sites within the supercomplex may help control reactive oxygen species production. To our knowledge, these are the first complete architectures of the dominant, physiologically relevant state of the electron transport chain.","lang":"eng"}],"type":"journal_article","date_created":"2018-12-11T11:50:51Z","_id":"1232","status":"public","quality_controlled":"1","day":"29","project":[{"_id":"2593EBD6-B435-11E9-9278-68D0E5697425","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (FEBS)"}],"publication":"Nature","doi":"10.1038/nature19774","publication_status":"published","oa_version":"None","date_published":"2016-09-29T00:00:00Z","month":"09","intvolume":"       537","acknowledgement":"We thank the MRC LMB Cambridge for the use of the Titan Krios microscope. Data processing was performed using the IST high-performance computer cluster. J.A.L. holds a long-term fellowship from FEBS. K.F. is partially funded by a MRC UK PhD fellowship.","publisher":"Nature Publishing Group","date_updated":"2021-01-12T06:49:16Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"The architecture of respiratory supercomplexes","author":[{"full_name":"Letts, James A","orcid":"0000-0002-9864-3586","last_name":"Letts","first_name":"James A","id":"322DA418-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","last_name":"Fiedorczuk","full_name":"Fiedorczuk, Karol"},{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov"}],"issue":"7622","page":"644 - 648","department":[{"_id":"LeSa"}],"publist_id":"6102","language":[{"iso":"eng"}],"year":"2016"},{"department":[{"_id":"KrPi"}],"publist_id":"6100","language":[{"iso":"eng"}],"publisher":"Springer","title":"Standard security does imply security against selective opening for markov distributions","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heuer","first_name":"Felix","full_name":"Heuer, Felix"},{"full_name":"Kiltz, Eike","last_name":"Kiltz","first_name":"Eike"},{"orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"}],"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7","grant_number":"259668"}],"publication_status":"published","citation":{"mla":"Fuchsbauer, Georg, et al. <i>Standard Security Does Imply Security against Selective Opening for Markov Distributions</i>. Vol. 9562, Springer, 2016, pp. 282–305, doi:<a href=\"https://doi.org/10.1007/978-3-662-49096-9_12\">10.1007/978-3-662-49096-9_12</a>.","apa":"Fuchsbauer, G., Heuer, F., Kiltz, E., &#38; Pietrzak, K. Z. (2016). Standard security does imply security against selective opening for markov distributions (Vol. 9562, pp. 282–305). Presented at the TCC: Theory of Cryptography Conference, Tel Aviv, Israel: Springer. <a href=\"https://doi.org/10.1007/978-3-662-49096-9_12\">https://doi.org/10.1007/978-3-662-49096-9_12</a>","chicago":"Fuchsbauer, Georg, Felix Heuer, Eike Kiltz, and Krzysztof Z Pietrzak. “Standard Security Does Imply Security against Selective Opening for Markov Distributions,” 9562:282–305. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-49096-9_12\">https://doi.org/10.1007/978-3-662-49096-9_12</a>.","ama":"Fuchsbauer G, Heuer F, Kiltz E, Pietrzak KZ. Standard security does imply security against selective opening for markov distributions. In: Vol 9562. Springer; 2016:282-305. doi:<a href=\"https://doi.org/10.1007/978-3-662-49096-9_12\">10.1007/978-3-662-49096-9_12</a>","short":"G. Fuchsbauer, F. Heuer, E. Kiltz, K.Z. Pietrzak, in:, Springer, 2016, pp. 282–305.","ista":"Fuchsbauer G, Heuer F, Kiltz E, Pietrzak KZ. 2016. Standard security does imply security against selective opening for markov distributions. TCC: Theory of Cryptography Conference, LNCS, vol. 9562, 282–305.","ieee":"G. Fuchsbauer, F. Heuer, E. Kiltz, and K. Z. Pietrzak, “Standard security does imply security against selective opening for markov distributions,” presented at the TCC: Theory of Cryptography Conference, Tel Aviv, Israel, 2016, vol. 9562, pp. 282–305."},"abstract":[{"lang":"eng","text":"About three decades ago it was realized that implementing private channels between parties which can be adaptively corrupted requires an encryption scheme that is secure against selective opening attacks. Whether standard (IND-CPA) security implies security against selective opening attacks has been a major open question since. The only known reduction from selective opening to IND-CPA security loses an exponential factor. A polynomial reduction is only known for the very special case where the distribution considered in the selective opening security experiment is a product distribution, i.e., the messages are sampled independently from each other. In this paper we give a reduction whose loss is quantified via the dependence graph (where message dependencies correspond to edges) of the underlying message distribution. In particular, for some concrete distributions including Markov distributions, our reduction is polynomial."}],"scopus_import":1,"type":"conference","_id":"1233","quality_controlled":"1","page":"282 - 305","conference":{"location":"Tel Aviv, Israel","name":"TCC: Theory of Cryptography Conference","end_date":"2016-01-13","start_date":"2016-01-10"},"year":"2016","alternative_title":["LNCS"],"date_published":"2016-01-01T00:00:00Z","intvolume":"      9562","month":"01","acknowledgement":"G. Fuchsbauer and K. Pietrzak are supported by the European Research Council, ERC Starting Grant (259668-PSPC). F. Heuer is funded by a Sofja Kovalevskaja Award of the Alexander von Humboldt Foundation and DFG SPP 1736, Algorithms for BIG DATA. E. Kiltz is supported by a Sofja Kovalevskaja Award of the Alexander von Humboldt Foundation, the German Israel Foundation, and ERC Project ERCC (FP7/615074).","date_updated":"2021-01-12T06:49:16Z","oa":1,"doi":"10.1007/978-3-662-49096-9_12","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2015/853"}],"ec_funded":1,"oa_version":"Submitted Version","volume":9562,"date_created":"2018-12-11T11:50:51Z","day":"01","status":"public"},{"volume":9636,"date_created":"2018-12-11T11:50:51Z","status":"public","day":"01","main_file_link":[{"url":"https://arxiv.org/abs/1504.05739","open_access":"1"}],"doi":"10.1007/978-3-662-49674-9_7","related_material":{"record":[{"status":"public","relation":"later_version","id":"471"},{"status":"public","relation":"dissertation_contains","id":"1155"}]},"ec_funded":1,"oa_version":"Preprint","intvolume":"      9636","month":"01","date_published":"2016-01-01T00:00:00Z","alternative_title":["LNCS"],"acknowledgement":"This research was funded in part by the European Research Council (ERC) under\r\ngrant  agreement  267989  (QUAREM),  the  Austrian  Science  Fund  (FWF)  under\r\ngrants project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), the Peo-\r\nple Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734, the SNSF Advanced Postdoc.\r\nMobility Fellowship – grant number P300P2\r\n161067, and the Czech Science Foun-\r\ndation under grant agreement P202/12/G061.","date_updated":"2023-09-07T11:58:33Z","oa":1,"page":"112 - 129","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2016-04-02","end_date":"2016-04-08","location":"Eindhoven, The Netherlands"},"year":"2016","citation":{"short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Springer, 2016, pp. 112–129.","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Faster statistical model checking for unbounded temporal properties. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 9636, 112–129.","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical model checking for unbounded temporal properties,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands, 2016, vol. 9636, pp. 112–129.","ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking for unbounded temporal properties. In: Vol 9636. Springer; 2016:112-129. doi:<a href=\"https://doi.org/10.1007/978-3-662-49674-9_7\">10.1007/978-3-662-49674-9_7</a>","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Faster Statistical Model Checking for Unbounded Temporal Properties,” 9636:112–29. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-49674-9_7\">https://doi.org/10.1007/978-3-662-49674-9_7</a>.","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., &#38; Petrov, T. (2016). Faster statistical model checking for unbounded temporal properties (Vol. 9636, pp. 112–129). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands: Springer. <a href=\"https://doi.org/10.1007/978-3-662-49674-9_7\">https://doi.org/10.1007/978-3-662-49674-9_7</a>","mla":"Daca, Przemyslaw, et al. <i>Faster Statistical Model Checking for Unbounded Temporal Properties</i>. Vol. 9636, Springer, 2016, pp. 112–29, doi:<a href=\"https://doi.org/10.1007/978-3-662-49674-9_7\">10.1007/978-3-662-49674-9_7</a>."},"type":"conference","scopus_import":1,"abstract":[{"text":"We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds.","lang":"eng"}],"_id":"1234","quality_controlled":"1","project":[{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"},{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"publication_status":"published","publisher":"Springer","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","full_name":"Daca, Przemyslaw"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8122-2881","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Kretinsky, Jan"},{"full_name":"Petrov, Tatjana","last_name":"Petrov","orcid":"0000-0002-9041-0905","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"}],"title":"Faster statistical model checking for unbounded temporal properties","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"publist_id":"6099","language":[{"iso":"eng"}]},{"acknowledgement":"H. Abusalah—Research supported by the European Research Council, ERC starting grant (259668-PSPC) and ERC consolidator grant (682815 - TOCNeT).","intvolume":"      9696","month":"01","alternative_title":["LNCS"],"date_published":"2016-01-01T00:00:00Z","oa":1,"date_updated":"2023-09-07T12:30:22Z","conference":{"location":"Guildford, UK","name":"ACNS: Applied Cryptography and Network Security","start_date":"2016-06-19","end_date":"2016-06-22"},"page":"445 - 463","year":"2016","volume":9696,"day":"01","status":"public","date_created":"2018-12-11T11:50:52Z","doi":"10.1007/978-3-319-39555-5_24","main_file_link":[{"url":"https://eprint.iacr.org/2016/279.pdf","open_access":"1"}],"ec_funded":1,"oa_version":"Submitted Version","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"83"}]},"publisher":"Springer","author":[{"last_name":"Abusalah","first_name":"Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M"},{"full_name":"Fuchsbauer, Georg","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer"}],"title":"Constrained PRFs for unbounded inputs with short keys","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrPi"}],"publist_id":"6098","language":[{"iso":"eng"}],"type":"conference","scopus_import":1,"abstract":[{"lang":"eng","text":"A constrained pseudorandom function (CPRF) F: K×X → Y for a family T of subsets of χ is a function where for any key k ∈ K and set S ∈ T one can efficiently compute a short constrained key kS, which allows to evaluate F(k, ·) on all inputs x ∈ S, while the outputs on all inputs x /∈ S look random even given kS. Abusalah et al. recently constructed the first constrained PRF for inputs of arbitrary length whose sets S are decided by Turing machines. They use their CPRF to build broadcast encryption and the first ID-based non-interactive key exchange for an unbounded number of users. Their constrained keys are obfuscated circuits and are therefore large. In this work we drastically reduce the key size and define a constrained key for a Turing machine M as a short signature on M. For this, we introduce a new signature primitive with constrained signing keys that let one only sign certain messages, while forging a signature on others is hard even when knowing the coins for key generation."}],"citation":{"mla":"Abusalah, Hamza M., and Georg Fuchsbauer. <i>Constrained PRFs for Unbounded Inputs with Short Keys</i>. Vol. 9696, Springer, 2016, pp. 445–63, doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">10.1007/978-3-319-39555-5_24</a>.","apa":"Abusalah, H. M., &#38; Fuchsbauer, G. (2016). Constrained PRFs for unbounded inputs with short keys (Vol. 9696, pp. 445–463). Presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">https://doi.org/10.1007/978-3-319-39555-5_24</a>","chicago":"Abusalah, Hamza M, and Georg Fuchsbauer. “Constrained PRFs for Unbounded Inputs with Short Keys,” 9696:445–63. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">https://doi.org/10.1007/978-3-319-39555-5_24</a>.","ama":"Abusalah HM, Fuchsbauer G. Constrained PRFs for unbounded inputs with short keys. In: Vol 9696. Springer; 2016:445-463. doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">10.1007/978-3-319-39555-5_24</a>","ieee":"H. M. Abusalah and G. Fuchsbauer, “Constrained PRFs for unbounded inputs with short keys,” presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK, 2016, vol. 9696, pp. 445–463.","short":"H.M. Abusalah, G. Fuchsbauer, in:, Springer, 2016, pp. 445–463.","ista":"Abusalah HM, Fuchsbauer G. 2016. Constrained PRFs for unbounded inputs with short keys. ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696, 445–463."},"quality_controlled":"1","_id":"1235","publication_status":"published","project":[{"grant_number":"259668","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography"},{"call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}]},{"scopus_import":1,"abstract":[{"lang":"eng","text":"A constrained pseudorandom function F: K × X → Y for a family T ⊆ 2X of subsets of X is a function where for any key k ∈ K and set S ∈ T one can efficiently compute a constrained key kS which allows to evaluate F (k, ·) on all inputs x ∈ S, while even given this key, the outputs on all inputs x ∉ S look random. At Asiacrypt’13 Boneh and Waters gave a construction which supports the most general set family so far. Its keys kc are defined for sets decided by boolean circuits C and enable evaluation of the PRF on any x ∈ X where C(x) = 1. In their construction the PRF input length and the size of the circuits C for which constrained keys can be computed must be fixed beforehand during key generation. We construct a constrained PRF that has an unbounded input length and whose constrained keys can be defined for any set recognized by a Turing machine. The only a priori bound we make is on the description size of the machines. We prove our construction secure assuming publiccoin differing-input obfuscation. As applications of our constrained PRF we build a broadcast encryption scheme where the number of potential receivers need not be fixed at setup (in particular, the length of the keys is independent of the number of parties) and the first identity-based non-interactive key exchange protocol with no bound on the number of parties that can agree on a shared key."}],"file_date_updated":"2020-07-14T12:44:41Z","type":"conference","citation":{"apa":"Abusalah, H. M., Fuchsbauer, G., &#38; Pietrzak, K. Z. (2016). Constrained PRFs for unbounded inputs (Vol. 9610, pp. 413–428). Presented at the CT-RSA: Topics in Cryptology, San Francisco, CA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">https://doi.org/10.1007/978-3-319-29485-8_24</a>","mla":"Abusalah, Hamza M., et al. <i>Constrained PRFs for Unbounded Inputs</i>. Vol. 9610, Springer, 2016, pp. 413–28, doi:<a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">10.1007/978-3-319-29485-8_24</a>.","ama":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. Constrained PRFs for unbounded inputs. In: Vol 9610. Springer; 2016:413-428. doi:<a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">10.1007/978-3-319-29485-8_24</a>","short":"H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 413–428.","ieee":"H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Constrained PRFs for unbounded inputs,” presented at the CT-RSA: Topics in Cryptology, San Francisco, CA, USA, 2016, vol. 9610, pp. 413–428.","ista":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Constrained PRFs for unbounded inputs. CT-RSA: Topics in Cryptology, LNCS, vol. 9610, 413–428.","chicago":"Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Constrained PRFs for Unbounded Inputs,” 9610:413–28. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">https://doi.org/10.1007/978-3-319-29485-8_24</a>."},"quality_controlled":"1","_id":"1236","publication_status":"published","project":[{"grant_number":"259668","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography"}],"publisher":"Springer","has_accepted_license":"1","title":"Constrained PRFs for unbounded inputs","author":[{"full_name":"Abusalah, Hamza M","first_name":"Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","last_name":"Abusalah"},{"full_name":"Fuchsbauer, Georg","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer"},{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_id":"4664","creator":"system","file_size":495176,"relation":"main_file","checksum":"3851cee49933ae13b1272e516f213e13","access_level":"open_access","file_name":"IST-2017-764-v1+1_279.pdf","date_updated":"2020-07-14T12:44:41Z","date_created":"2018-12-12T10:08:05Z"}],"department":[{"_id":"KrPi"}],"publist_id":"6097","pubrep_id":"764","language":[{"iso":"eng"}],"volume":9610,"day":"02","status":"public","ddc":["005","600"],"date_created":"2018-12-11T11:50:52Z","doi":"10.1007/978-3-319-29485-8_24","ec_funded":1,"oa_version":"Submitted Version","related_material":{"record":[{"id":"83","status":"public","relation":"dissertation_contains"}]},"acknowledgement":"Supported by the European Research Council, ERC Starting Grant (259668-PSPC).","date_published":"2016-02-02T00:00:00Z","alternative_title":["LNCS"],"intvolume":"      9610","month":"02","oa":1,"date_updated":"2023-09-07T12:30:22Z","conference":{"name":"CT-RSA: Topics in Cryptology","end_date":"2016-03-04","start_date":"2016-02-29","location":"San Francisco, CA, USA"},"page":"413 - 428","year":"2016"},{"publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"name":"Persistent Homology - Images, Data and Maps","_id":"255F06BE-B435-11E9-9278-68D0E5697425","grant_number":"622033","call_identifier":"FP7"}],"quality_controlled":"1","_id":"1237","scopus_import":1,"abstract":[{"text":"Bitmap images of arbitrary dimension may be formally perceived as unions of m-dimensional boxes aligned with respect to a rectangular grid in ℝm. Cohomology and homology groups are well known topological invariants of such sets. Cohomological operations, such as the cup product, provide higher-order algebraic topological invariants, especially important for digital images of dimension higher than 3. If such an operation is determined at the level of simplicial chains [see e.g. González-Díaz, Real, Homology, Homotopy Appl, 2003, 83-93], then it is effectively computable. However, decomposing a cubical complex into a simplicial one deleteriously affects the efficiency of such an approach. In order to avoid this overhead, a direct cubical approach was applied in [Pilarczyk, Real, Adv. Comput. Math., 2015, 253-275] for the cup product in cohomology, and implemented in the ChainCon software package [http://www.pawelpilarczyk.com/chaincon/]. We establish a formula for the Steenrod square operations [see Steenrod, Annals of Mathematics. Second Series, 1947, 290-320] directly at the level of cubical chains, and we prove the correctness of this formula. An implementation of this formula is programmed in C++ within the ChainCon software framework. We provide a few examples and discuss the effectiveness of this approach. One specific application follows from the fact that Steenrod squares yield tests for the topological extension problem: Can a given map A → Sd to a sphere Sd be extended to a given super-complex X of A? In particular, the ROB-SAT problem, which is to decide for a given function f: X → ℝm and a value r &gt; 0 whether every g: X → ℝm with ∥g - f ∥∞ ≤ r has a root, reduces to the extension problem.","lang":"eng"}],"type":"conference","citation":{"ista":"Krcál M, Pilarczyk P. 2016. Computation of cubical Steenrod squares. CTIC: Computational Topology in Image Context, LNCS, vol. 9667, 140–151.","ieee":"M. Krcál and P. Pilarczyk, “Computation of cubical Steenrod squares,” presented at the CTIC: Computational Topology in Image Context, Marseille, France, 2016, vol. 9667, pp. 140–151.","short":"M. Krcál, P. Pilarczyk, in:, Springer, 2016, pp. 140–151.","ama":"Krcál M, Pilarczyk P. Computation of cubical Steenrod squares. In: Vol 9667. Springer; 2016:140-151. doi:<a href=\"https://doi.org/10.1007/978-3-319-39441-1_13\">10.1007/978-3-319-39441-1_13</a>","chicago":"Krcál, Marek, and Pawel Pilarczyk. “Computation of Cubical Steenrod Squares,” 9667:140–51. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39441-1_13\">https://doi.org/10.1007/978-3-319-39441-1_13</a>.","apa":"Krcál, M., &#38; Pilarczyk, P. (2016). Computation of cubical Steenrod squares (Vol. 9667, pp. 140–151). Presented at the CTIC: Computational Topology in Image Context, Marseille, France: Springer. <a href=\"https://doi.org/10.1007/978-3-319-39441-1_13\">https://doi.org/10.1007/978-3-319-39441-1_13</a>","mla":"Krcál, Marek, and Pawel Pilarczyk. <i>Computation of Cubical Steenrod Squares</i>. Vol. 9667, Springer, 2016, pp. 140–51, doi:<a href=\"https://doi.org/10.1007/978-3-319-39441-1_13\">10.1007/978-3-319-39441-1_13</a>."},"language":[{"iso":"eng"}],"publist_id":"6096","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Krcál, Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek","last_name":"Krcál"},{"full_name":"Pilarczyk, Pawel","first_name":"Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","last_name":"Pilarczyk"}],"title":"Computation of cubical Steenrod squares","publisher":"Springer","ec_funded":1,"oa_version":"None","doi":"10.1007/978-3-319-39441-1_13","status":"public","day":"02","date_created":"2018-12-11T11:50:52Z","volume":9667,"year":"2016","conference":{"end_date":"2016-06-17","start_date":"2016-06-15","name":"CTIC: Computational Topology in Image Context","location":"Marseille, France"},"page":"140 - 151","date_updated":"2021-01-12T06:49:18Z","acknowledgement":"The research conducted by both authors has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreements no. 291734 (for M. K.) and no. 622033 (for P. P.).","alternative_title":["LNCS"],"date_published":"2016-06-02T00:00:00Z","intvolume":"      9667","month":"06"},{"publication_status":"published","quality_controlled":"1","_id":"1238","abstract":[{"lang":"eng","text":"The dynamic localization of endosomal compartments labeled with targeted fluorescent protein tags is routinely followed by time lapse fluorescence microscopy approaches and single particle tracking algorithms. In this way trajectories of individual endosomes can be mapped and linked to physiological processes as cell growth. However, other aspects of dynamic behavior including endosomal interactions are difficult to follow in this manner. Therefore, we characterized the localization and dynamic properties of early and late endosomes throughout the entire course of root hair formation by means of spinning disc time lapse imaging and post-acquisition automated multitracking and quantitative analysis. Our results show differential motile behavior of early and late endosomes and interactions of late endosomes that may be specified to particular root hair domains. Detailed data analysis revealed a particular transient interaction between late endosomes—termed herein as dancing-endosomes—which is not concluding to vesicular fusion. Endosomes preferentially located in the root hair tip interacted as dancing-endosomes and traveled short distances during this interaction. Finally, sizes of early and late endosomes were addressed by means of super-resolution structured illumination microscopy (SIM) to corroborate measurements on the spinning disc. This is a first study providing quantitative microscopic data on dynamic spatio-temporal interactions of endosomes during root hair tip growth."}],"scopus_import":1,"type":"journal_article","file_date_updated":"2020-07-14T12:44:41Z","citation":{"short":"D. von Wangenheim, A. Rosero, G. Komis, O. Šamajová, M. Ovečka, B. Voigt, J. Šamaj, Frontiers in Plant Science 6 (2016).","ista":"von Wangenheim D, Rosero A, Komis G, Šamajová O, Ovečka M, Voigt B, Šamaj J. 2016. Endosomal interactions during root hair growth. Frontiers in Plant Science. 6(JAN2016), 1262.","ieee":"D. von Wangenheim <i>et al.</i>, “Endosomal interactions during root hair growth,” <i>Frontiers in Plant Science</i>, vol. 6, no. JAN2016. Frontiers Research Foundation, 2016.","ama":"von Wangenheim D, Rosero A, Komis G, et al. Endosomal interactions during root hair growth. <i>Frontiers in Plant Science</i>. 2016;6(JAN2016). doi:<a href=\"https://doi.org/10.3389/fpls.2015.01262\">10.3389/fpls.2015.01262</a>","chicago":"Wangenheim, Daniel von, Amparo Rosero, George Komis, Olga Šamajová, Miroslav Ovečka, Boris Voigt, and Jozef Šamaj. “Endosomal Interactions during Root Hair Growth.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2016. <a href=\"https://doi.org/10.3389/fpls.2015.01262\">https://doi.org/10.3389/fpls.2015.01262</a>.","apa":"von Wangenheim, D., Rosero, A., Komis, G., Šamajová, O., Ovečka, M., Voigt, B., &#38; Šamaj, J. (2016). Endosomal interactions during root hair growth. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2015.01262\">https://doi.org/10.3389/fpls.2015.01262</a>","mla":"von Wangenheim, Daniel, et al. “Endosomal Interactions during Root Hair Growth.” <i>Frontiers in Plant Science</i>, vol. 6, no. JAN2016, 1262, Frontiers Research Foundation, 2016, doi:<a href=\"https://doi.org/10.3389/fpls.2015.01262\">10.3389/fpls.2015.01262</a>."},"pubrep_id":"710","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"publist_id":"6094","title":"Endosomal interactions during root hair growth","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","last_name":"Von Wangenheim","full_name":"Von Wangenheim, Daniel"},{"last_name":"Rosero","first_name":"Amparo","full_name":"Rosero, Amparo"},{"last_name":"Komis","first_name":"George","full_name":"Komis, George"},{"first_name":"Olga","last_name":"Šamajová","full_name":"Šamajová, Olga"},{"full_name":"Ovečka, Miroslav","first_name":"Miroslav","last_name":"Ovečka"},{"full_name":"Voigt, Boris","last_name":"Voigt","first_name":"Boris"},{"last_name":"Šamaj","first_name":"Jozef","full_name":"Šamaj, Jozef"}],"file":[{"file_id":"4760","content_type":"application/pdf","creator":"system","file_size":1640550,"relation":"main_file","checksum":"3127eab844d53564bf47e2b6b42f1ca0","access_level":"open_access","file_name":"IST-2016-710-v1+1_fpls-06-01262.pdf","date_updated":"2020-07-14T12:44:41Z","date_created":"2018-12-12T10:09:36Z"}],"publisher":"Frontiers Research Foundation","has_accepted_license":"1","oa_version":"Published Version","publication":"Frontiers in Plant Science","doi":"10.3389/fpls.2015.01262","status":"public","day":"29","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["581"],"date_created":"2018-12-11T11:50:53Z","volume":6,"year":"2016","oa":1,"issue":"JAN2016","date_updated":"2021-01-12T06:49:18Z","acknowledgement":"This work was supported by National Program for Sustainability I (grant no. LO1204) provided by the Czech Ministry of Education and by Institutional Fund of Palacký University Olomouc (GK and OŠ).\r\nWe thank Sabine Fischer for help with the statistics.","article_number":"1262","date_published":"2016-01-29T00:00:00Z","month":"01","intvolume":"         6"},{"volume":116,"citation":{"mla":"Callan Jones, Andrew, et al. “Cortical Flow-Driven Shapes of Nonadherent Cells.” <i>Physical Review Letters</i>, vol. 116, no. 2, 028102, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.116.028102\">10.1103/PhysRevLett.116.028102</a>.","apa":"Callan Jones, A., Ruprecht, V., Wieser, S., Heisenberg, C.-P. J., &#38; Voituriez, R. (2016). Cortical flow-driven shapes of nonadherent cells. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.116.028102\">https://doi.org/10.1103/PhysRevLett.116.028102</a>","chicago":"Callan Jones, Andrew, Verena Ruprecht, Stefan Wieser, Carl-Philipp J Heisenberg, and Raphaël Voituriez. “Cortical Flow-Driven Shapes of Nonadherent Cells.” <i>Physical Review Letters</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevLett.116.028102\">https://doi.org/10.1103/PhysRevLett.116.028102</a>.","ista":"Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. 2016. Cortical flow-driven shapes of nonadherent cells. Physical Review Letters. 116(2), 028102.","ieee":"A. Callan Jones, V. Ruprecht, S. Wieser, C.-P. J. Heisenberg, and R. Voituriez, “Cortical flow-driven shapes of nonadherent cells,” <i>Physical Review Letters</i>, vol. 116, no. 2. American Physical Society, 2016.","short":"A. Callan Jones, V. Ruprecht, S. Wieser, C.-P.J. Heisenberg, R. Voituriez, Physical Review Letters 116 (2016).","ama":"Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. Cortical flow-driven shapes of nonadherent cells. <i>Physical Review Letters</i>. 2016;116(2). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.116.028102\">10.1103/PhysRevLett.116.028102</a>"},"scopus_import":1,"abstract":[{"text":"Nonadherent polarized cells have been observed to have a pearlike, elongated shape. Using a minimal model that describes the cell cortex as a thin layer of contractile active gel, we show that the anisotropy of active stresses, controlled by cortical viscosity and filament ordering, can account for this morphology. The predicted shapes can be determined from the flow pattern only; they prove to be independent of the mechanism at the origin of the cortical flow, and are only weakly sensitive to the cytoplasmic rheology. In the case of actin flows resulting from a contractile instability, we propose a phase diagram of three-dimensional cell shapes that encompasses nonpolarized spherical, elongated, as well as oblate shapes, all of which have been observed in experiment.","lang":"eng"}],"type":"journal_article","_id":"1239","date_created":"2018-12-11T11:50:53Z","quality_controlled":"1","day":"15","status":"public","project":[{"_id":"2529486C-B435-11E9-9278-68D0E5697425","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","call_identifier":"FWF","grant_number":"T 560-B17"}],"publication":"Physical Review Letters","doi":"10.1103/PhysRevLett.116.028102","publication_status":"published","oa_version":"None","date_published":"2016-01-15T00:00:00Z","intvolume":"       116","month":"01","publisher":"American Physical Society","article_number":"028102","acknowledgement":"V. R. acknowledges support by the Austrian Science Fund (FWF): (Grant No. T560-B17).","date_updated":"2021-01-12T06:49:19Z","title":"Cortical flow-driven shapes of nonadherent cells","author":[{"full_name":"Callan Jones, Andrew","last_name":"Callan Jones","first_name":"Andrew"},{"last_name":"Ruprecht","orcid":"0000-0003-4088-8633","first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","full_name":"Ruprecht, Verena"},{"full_name":"Wieser, Stefan","last_name":"Wieser","orcid":"0000-0002-2670-2217","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Voituriez","first_name":"Raphaël","full_name":"Voituriez, Raphaël"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"2","publist_id":"6095","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"year":"2016"},{"has_accepted_license":"1","publisher":"BioMed Central","title":"Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kornienko, Aleksandra","first_name":"Aleksandra","last_name":"Kornienko"},{"last_name":"Dotter","first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph"},{"first_name":"Philipp","last_name":"Guenzl","full_name":"Guenzl, Philipp"},{"last_name":"Gisslinger","first_name":"Heinz","full_name":"Gisslinger, Heinz"},{"first_name":"Bettina","last_name":"Gisslinger","full_name":"Gisslinger, Bettina"},{"full_name":"Cleary, Ciara","first_name":"Ciara","last_name":"Cleary"},{"last_name":"Kralovics","first_name":"Robert","full_name":"Kralovics, Robert"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian"},{"first_name":"Denise","last_name":"Barlow","full_name":"Barlow, Denise"}],"file":[{"file_size":2914601,"creator":"system","file_id":"4789","content_type":"application/pdf","checksum":"a268beee1a690801c83ec6729f9ebc5b","relation":"main_file","access_level":"open_access","file_name":"IST-2016-709-v1+1_s13059-016-0873-8.pdf","date_updated":"2020-07-14T12:44:41Z","date_created":"2018-12-12T10:10:05Z"}],"department":[{"_id":"GaNo"}],"publist_id":"6093","language":[{"iso":"eng"}],"pubrep_id":"709","citation":{"mla":"Kornienko, Aleksandra, et al. “Long Non-Coding RNAs Display Higher Natural Expression Variation than Protein-Coding Genes in Healthy Humans.” <i>Genome Biology</i>, vol. 17, no. 1, 14, BioMed Central, 2016, doi:<a href=\"https://doi.org/10.1186/s13059-016-0873-8\">10.1186/s13059-016-0873-8</a>.","apa":"Kornienko, A., Dotter, C., Guenzl, P., Gisslinger, H., Gisslinger, B., Cleary, C., … Barlow, D. (2016). Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-016-0873-8\">https://doi.org/10.1186/s13059-016-0873-8</a>","chicago":"Kornienko, Aleksandra, Christoph Dotter, Philipp Guenzl, Heinz Gisslinger, Bettina Gisslinger, Ciara Cleary, Robert Kralovics, Florian Pauler, and Denise Barlow. “Long Non-Coding RNAs Display Higher Natural Expression Variation than Protein-Coding Genes in Healthy Humans.” <i>Genome Biology</i>. BioMed Central, 2016. <a href=\"https://doi.org/10.1186/s13059-016-0873-8\">https://doi.org/10.1186/s13059-016-0873-8</a>.","short":"A. Kornienko, C. Dotter, P. Guenzl, H. Gisslinger, B. Gisslinger, C. Cleary, R. Kralovics, F. Pauler, D. Barlow, Genome Biology 17 (2016).","ista":"Kornienko A, Dotter C, Guenzl P, Gisslinger H, Gisslinger B, Cleary C, Kralovics R, Pauler F, Barlow D. 2016. Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. Genome Biology. 17(1), 14.","ieee":"A. Kornienko <i>et al.</i>, “Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans,” <i>Genome Biology</i>, vol. 17, no. 1. BioMed Central, 2016.","ama":"Kornienko A, Dotter C, Guenzl P, et al. Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. <i>Genome Biology</i>. 2016;17(1). doi:<a href=\"https://doi.org/10.1186/s13059-016-0873-8\">10.1186/s13059-016-0873-8</a>"},"scopus_import":1,"abstract":[{"lang":"eng","text":"Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ultimately be more numerous than protein-coding genes in the human genome. Despite large numbers of reported lncRNAs, reference annotations are likely incomplete due to their lower and tighter tissue-specific expression compared to mRNAs. An unexplored factor potentially confounding lncRNA identification is inter-individual expression variability. Here, we characterize lncRNA natural expression variability in human primary granulocytes. Results: We annotate granulocyte lncRNAs and mRNAs in RNA-seq data from 10 healthy individuals, identifying multiple lncRNAs absent from reference annotations, and use this to investigate three known features (higher tissue-specificity, lower expression, and reduced splicing efficiency) of lncRNAs relative to mRNAs. Expression variability was examined in seven individuals sampled three times at 1- or more than 1-month intervals. We show that lncRNAs display significantly more inter-individual expression variability compared to mRNAs. We confirm this finding in two independent human datasets by analyzing multiple tissues from the GTEx project and lymphoblastoid cell lines from the GEUVADIS project. Using the latter dataset we also show that including more human donors into the transcriptome annotation pipeline allows identification of an increasing number of lncRNAs, but minimally affects mRNA gene number. Conclusions: A comprehensive annotation of lncRNAs is known to require an approach that is sensitive to low and tight tissue-specific expression. Here we show that increased inter-individual expression variability is an additional general lncRNA feature to consider when creating a comprehensive annotation of human lncRNAs or proposing their use as prognostic or disease markers."}],"file_date_updated":"2020-07-14T12:44:41Z","type":"journal_article","_id":"1240","quality_controlled":"1","publication_status":"published","date_published":"2016-01-29T00:00:00Z","intvolume":"        17","month":"01","article_number":"14","acknowledgement":"This study was partly funded by the Austrian Science Fund (FWF F43-B09, FWF W1207-B09). PMG is a recipient of a DOC Fellowship of the Austrian Academy of Sciences.\r\nWe thank Ruth Klement, Tomasz Kulinski, Elisangela Valente, Elisabeth Salzer,\r\nand Roland Jäger for technical/bioinformatic assistance and advice, the CeMM\r\nIT department and José Manuel Molero for help and advice on software usage,\r\nthe Biomedical Sequencing Facility (http://biomedical-sequencing.at/) for\r\nsequencing and advice, Jacques Colinge, Daniel Andergassen, and Tomasz\r\nKulinski for discussions, Quanah Hudson and Jörg Menche for reading and\r\ncommenting on the manuscript.","date_updated":"2021-01-12T06:49:20Z","oa":1,"issue":"1","year":"2016","volume":17,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["576"],"date_created":"2018-12-11T11:50:53Z","status":"public","day":"29","publication":"Genome Biology","doi":"10.1186/s13059-016-0873-8","oa_version":"Published Version"},{"oa_version":"Preprint","ec_funded":1,"main_file_link":[{"open_access":"1","url":"http://biorxiv.org/content/early/2015/07/06/022020.abstract"}],"doi":"10.1534/genetics.115.180299","publication":"Genetics","status":"public","day":"01","date_created":"2018-12-11T11:50:54Z","volume":202,"year":"2016","page":"721 - 732","issue":"2","oa":1,"date_updated":"2023-02-21T10:24:19Z","acknowledgement":"This work was made possible by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria) and European Research Council grant 250152 (to Nick Barton).","intvolume":"       202","month":"02","date_published":"2016-02-01T00:00:00Z","publication_status":"published","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"},{"name":"L'OREAL Fellowship","_id":"25B67606-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","_id":"1241","type":"journal_article","scopus_import":1,"abstract":[{"text":"How likely is it that a population escapes extinction through adaptive evolution? The answer to this question is of great relevance in conservation biology, where we aim at species’ rescue and the maintenance of biodiversity, and in agriculture and medicine, where we seek to hamper the emergence of pesticide or drug resistance. By reshuffling the genome, recombination has two antagonistic effects on the probability of evolutionary rescue: It generates and it breaks up favorable gene combinations. Which of the two effects prevails depends on the fitness effects of mutations and on the impact of stochasticity on the allele frequencies. In this article, we analyze a mathematical model for rescue after a sudden environmental change when adaptation is contingent on mutations at two loci. The analysis reveals a complex nonlinear dependence of population survival on recombination. We moreover find that, counterintuitively, a fast eradication of the wild type can promote rescue in the presence of recombination. The model also shows that two-step rescue is not unlikely to happen and can even be more likely than single-step rescue (where adaptation relies on a single mutation), depending on the circumstances.","lang":"eng"}],"citation":{"short":"H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.","ieee":"H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,” <i>Genetics</i>, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016.","ista":"Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 721–732.","ama":"Uecker H, Hermisson J. The role of recombination in evolutionary rescue. <i>Genetics</i>. 2016;202(2):721-732. doi:<a href=\"https://doi.org/10.1534/genetics.115.180299\">10.1534/genetics.115.180299</a>","chicago":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.180299\">https://doi.org/10.1534/genetics.115.180299</a>.","apa":"Uecker, H., &#38; Hermisson, J. (2016). The role of recombination in evolutionary rescue. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.180299\">https://doi.org/10.1534/genetics.115.180299</a>","mla":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” <i>Genetics</i>, vol. 202, no. 2, Genetics Society of America, 2016, pp. 721–32, doi:<a href=\"https://doi.org/10.1534/genetics.115.180299\">10.1534/genetics.115.180299</a>."},"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"publist_id":"6091","author":[{"full_name":"Uecker, Hildegard","orcid":"0000-0001-9435-2813","last_name":"Uecker","first_name":"Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hermisson","first_name":"Joachim","full_name":"Hermisson, Joachim"}],"title":"The role of recombination in evolutionary rescue","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Genetics Society of America"}]