[{"doi":"10.1109/ISIT.2018.8437654","date_published":"2018-08-16T00:00:00Z","date_created":"2018-12-11T11:44:40Z","isi":1,"year":"2018","day":"16","publisher":"IEEE","quality_controlled":"1","oa":1,"author":[{"full_name":"Obremski, Marciej","last_name":"Obremski","first_name":"Marciej"},{"last_name":"Skorski","full_name":"Skorski, Maciej","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"}],"publist_id":"7946","article_processing_charge":"No","external_id":{"isi":["000448139300368"]},"title":"Inverted leftover hash lemma","citation":{"apa":"Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol. 2018). Presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654","ama":"Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:10.1109/ISIT.2018.8437654","ieee":"M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018, vol. 2018.","short":"M. Obremski, M. Skórski, in:, IEEE, 2018.","mla":"Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma. Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654.","ista":"Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International Symposium on Information Theory, ISIT Proceedings, vol. 2018.","chicago":"Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":2018,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","alternative_title":["ISIT Proceedings"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/507"}],"month":"08","intvolume":" 2018","abstract":[{"lang":"eng","text":"Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \\'collision graph\\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes."}],"oa_version":"Submitted Version","department":[{"_id":"KrPi"}],"date_updated":"2023-09-13T08:23:18Z","type":"conference","conference":{"location":"Vail, CO, USA","end_date":"2018-06-22","start_date":"2018-06-17 ","name":"ISIT: International Symposium on Information Theory"},"status":"public","_id":"108"},{"oa":1,"publisher":"Springer","quality_controlled":"1","date_created":"2018-12-11T11:44:57Z","doi":"10.1007/978-3-319-96145-3_5","date_published":"2018-07-18T00:00:00Z","page":"79 - 102","day":"18","year":"2018","has_accepted_license":"1","isi":1,"project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Layered Concurrent Programs","article_processing_charge":"No","external_id":{"isi":["000491481600005"]},"publist_id":"7761","author":[{"last_name":"Kragl","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.","chicago":"Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_5.","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","apa":"Kragl, B., & Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-96145-3_5","ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:10.1007/978-3-319-96145-3_5","mla":"Kragl, Bernhard, and Shaz Qadeer. Layered Concurrent Programs. Vol. 10981, Springer, 2018, pp. 79–102, doi:10.1007/978-3-319-96145-3_5."},"intvolume":" 10981","month":"07","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs.","lang":"eng"}],"related_material":{"record":[{"id":"8332","status":"public","relation":"dissertation_contains"}]},"volume":10981,"language":[{"iso":"eng"}],"file":[{"file_name":"2018_LNCS_Kragl.pdf","date_created":"2018-12-17T12:52:12Z","creator":"dernst","file_size":1603844,"date_updated":"2020-07-14T12:45:04Z","file_id":"5705","checksum":"c64fff560fe5a7532ec10626ad1c215e","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"location":"Oxford, UK","end_date":"2018-07-17","start_date":"2018-07-14","name":"CAV: Computer Aided Verification"},"type":"conference","_id":"160","file_date_updated":"2020-07-14T12:45:04Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-09-13T08:45:09Z"},{"title":"KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis","external_id":{"isi":["000435571000017"]},"article_processing_charge":"No","author":[{"full_name":"Gao, Zhen","last_name":"Gao","first_name":"Zhen"},{"first_name":"Anna","full_name":"Daneva, Anna","last_name":"Daneva"},{"last_name":"Salanenka","full_name":"Salanenka, Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","first_name":"Yuliya"},{"first_name":"Matthias","last_name":"Van Durme","full_name":"Van Durme, Matthias"},{"full_name":"Huysmans, Marlies","last_name":"Huysmans","first_name":"Marlies"},{"last_name":"Lin","full_name":"Lin, Zongcheng","first_name":"Zongcheng"},{"full_name":"De Winter, Freya","last_name":"De Winter","first_name":"Freya"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"first_name":"Mansour","full_name":"Karimi, Mansour","last_name":"Karimi"},{"last_name":"Van De Velde","full_name":"Van De Velde, Jan","first_name":"Jan"},{"full_name":"Vandepoele, Klaas","last_name":"Vandepoele","first_name":"Klaas"},{"first_name":"Davy","last_name":"Van De Walle","full_name":"Van De Walle, Davy"},{"first_name":"Koen","last_name":"Dewettinck","full_name":"Dewettinck, Koen"},{"full_name":"Lambrecht, Bart","last_name":"Lambrecht","first_name":"Bart"},{"full_name":"Nowack, Moritz","last_name":"Nowack","first_name":"Moritz"}],"publist_id":"7619","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375.","chicago":"Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans, Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0160-7.","apa":"Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., … Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0160-7","ama":"Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 2018;4(6):365-375. doi:10.1038/s41477-018-0160-7","ieee":"Z. Gao et al., “KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis,” Nature Plants, vol. 4, no. 6. Nature Publishing Group, pp. 365–375, 2018.","short":"Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle, K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375.","mla":"Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants, vol. 4, no. 6, Nature Publishing Group, 2018, pp. 365–75, doi:10.1038/s41477-018-0160-7."},"date_created":"2018-12-11T11:45:35Z","doi":"10.1038/s41477-018-0160-7","date_published":"2018-05-28T00:00:00Z","page":"365 - 375","publication":"Nature Plants","day":"28","year":"2018","isi":1,"quality_controlled":"1","publisher":"Nature Publishing Group","acknowledgement":"We gratefully acknowledge funding from the Chinese Scholarship Council (CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek (FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.), the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH (project number 639234 to M.K.N.).","department":[{"_id":"JiFr"}],"date_updated":"2023-09-13T08:24:17Z","status":"public","type":"journal_article","_id":"280","issue":"6","volume":4,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 4","month":"05","scopus_import":"1","oa_version":"None","abstract":[{"text":"Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span.","lang":"eng"}]},{"date_published":"2018-02-20T00:00:00Z","doi":"10.1016/j.jbiotec.2018.01.008","date_created":"2018-12-11T11:46:50Z","page":"40 - 52","day":"20","publication":"Journal of Biotechnology","isi":1,"year":"2018","publisher":"Elsevier","quality_controlled":"1","acknowledgement":"We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1 and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all members of the Guet lab for critically reading the manuscript. We also thank the Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n","title":"Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains","author":[{"last_name":"Tomasek","orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"publist_id":"7317","external_id":{"isi":["000425715100006"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology, vol. 268, Elsevier, 2018, pp. 40–52, doi:10.1016/j.jbiotec.2018.01.008.","ieee":"K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” Journal of Biotechnology, vol. 268. Elsevier, pp. 40–52, 2018.","short":"K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52.","ama":"Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 2018;268:40-52. doi:10.1016/j.jbiotec.2018.01.008","apa":"Tomasek, K., Bergmiller, T., & Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. Elsevier. https://doi.org/10.1016/j.jbiotec.2018.01.008","chicago":"Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology. Elsevier, 2018. https://doi.org/10.1016/j.jbiotec.2018.01.008.","ista":"Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 268, 40–52."},"volume":268,"language":[{"iso":"eng"}],"publication_status":"published","month":"02","intvolume":" 268","scopus_import":"1","oa_version":"None","abstract":[{"text":"Buffers are essential for diluting bacterial cultures for flow cytometry analysis in order to study bacterial physiology and gene expression parameters based on fluorescence signals. Using a variety of constitutively expressed fluorescent proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes in fluorescence levels after dilution into the commonly used flow cytometry buffer phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9 salts. These changes appeared very rapidly after dilution, and were linked to increased membrane permeability and loss in cell viability. We observed buffer-related effects in several different E. coli strains, K-12, C and W, but not E. coli B, which can be partially explained by differences in lipopolysaccharide (LPS) and outer membrane composition. Supplementing the buffers with divalent cations responsible for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane is essential for precise and unbiased measurements of fluorescence parameters using flow cytometry.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"department":[{"_id":"CaGu"}],"date_updated":"2023-09-13T08:24:51Z","status":"public","type":"journal_article","_id":"503"},{"related_material":{"record":[{"relation":"research_data","id":"9810","status":"public"}]},"volume":16,"issue":"8","file":[{"creator":"dernst","file_size":4007095,"date_updated":"2020-07-14T12:48:10Z","file_name":"2018_Plos_Chaudhry.pdf","date_created":"2018-12-17T12:55:31Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"527076f78265cd4ea192cd1569851587","file_id":"5706"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"08","intvolume":" 16","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term "leaky resistance." We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”.","lang":"eng"}],"department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:48:10Z","ddc":["570"],"date_updated":"2023-09-13T08:45:41Z","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"82","date_published":"2018-08-16T00:00:00Z","doi":"10.1371/journal.pbio.2005971","date_created":"2018-12-11T11:44:32Z","day":"16","publication":"PLoS Biology","has_accepted_license":"1","isi":1,"year":"2018","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","publist_id":"7972","author":[{"first_name":"Waqas","last_name":"Chaudhry","full_name":"Chaudhry, Waqas"},{"last_name":"Pleska","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shah, Nilang","last_name":"Shah","first_name":"Nilang"},{"first_name":"Howard","last_name":"Weiss","full_name":"Weiss, Howard"},{"first_name":"Ingrid","last_name":"Mccall","full_name":"Mccall, Ingrid"},{"last_name":"Meyer","full_name":"Meyer, Justin","first_name":"Justin"},{"first_name":"Animesh","last_name":"Gupta","full_name":"Gupta, Animesh"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"},{"first_name":"Bruce","last_name":"Levin","full_name":"Levin, Bruce"}],"article_processing_charge":"Yes","external_id":{"isi":["000443383300024"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971.","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","ieee":"W. Chaudhry et al., “Leaky resistance and the conditions for the existence of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8. Public Library of Science, 2018.","ama":"Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 2018;16(8). doi:10.1371/journal.pbio.2005971","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971","mla":"Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971."},"article_number":"2005971"}]