[{"doi":"10.6084/m9.figshare.6401390.v1","date_published":"2018-05-31T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.6401390.v1"}],"citation":{"ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401390.v1","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1.","mla":"Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018)."},"oa":1,"article_processing_charge":"No","month":"05","day":"31","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"279"}]},"author":[{"first_name":"Luis","last_name":"Zapata","full_name":"Zapata, Luis"},{"full_name":"Pich, Oriol","first_name":"Oriol","last_name":"Pich"},{"full_name":"Serrano, Luis","first_name":"Luis","last_name":"Serrano"},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"first_name":"Stephan","last_name":"Ossowski","full_name":"Ossowski, Stephan"},{"full_name":"Schaefer, Martin","first_name":"Martin","last_name":"Schaefer"}],"oa_version":"Preprint","date_updated":"2023-09-13T09:01:31Z","date_created":"2021-08-06T12:53:49Z","year":"2018","_id":"9811","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","status":"public","title":"Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","abstract":[{"lang":"eng","text":"This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb)"}],"type":"research_data_reference"},{"license":"https://creativecommons.org/licenses/by/4.0/","publist_id":"8035","file_date_updated":"2020-07-14T12:45:23Z","department":[{"_id":"SiHi"}],"publisher":"BioMed Central","publication_status":"published","acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19).","year":"2018","volume":19,"date_updated":"2023-09-13T09:10:47Z","date_created":"2018-12-11T11:44:12Z","related_material":{"record":[{"id":"9807","status":"public","relation":"research_data"},{"status":"public","relation":"research_data","id":"9808"}]},"author":[{"last_name":"Higareda Almaraz","first_name":"Juan","full_name":"Higareda Almaraz, Juan"},{"last_name":"Karbiener","first_name":"Michael","full_name":"Karbiener, Michael"},{"full_name":"Giroud, Maude","last_name":"Giroud","first_name":"Maude"},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian","last_name":"Pauler"},{"last_name":"Gerhalter","first_name":"Teresa","full_name":"Gerhalter, Teresa"},{"full_name":"Herzig, Stephan","first_name":"Stephan","last_name":"Herzig"},{"last_name":"Scheideler","first_name":"Marcel","full_name":"Scheideler, Marcel"}],"publication_identifier":{"issn":["1471-2164"]},"month":"11","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000450976700002"]},"language":[{"iso":"eng"}],"doi":"10.1186/s12864-018-5173-0","type":"journal_article","issue":"1","abstract":[{"text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.","lang":"eng"}],"intvolume":" 19","ddc":["570"],"status":"public","title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","_id":"20","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_size":4629784,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_BMCGenomics_Higareda.pdf","checksum":"a56516e734dab589dc7f3e1915973b4d","date_updated":"2020-07-14T12:45:23Z","date_created":"2018-12-17T14:52:57Z","relation":"main_file","file_id":"5712"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"03","article_type":"original","citation":{"chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0.","mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics, vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1).","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-018-5173-0","ieee":"J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” BMC Genomics, vol. 19, no. 1. BioMed Central, 2018.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0"},"publication":"BMC Genomics","date_published":"2018-11-03T00:00:00Z"},{"issue":"4","abstract":[{"lang":"eng","text":"We introduce the notion of “non-malleable codes” which relaxes the notion of error correction and error detection. Informally, a code is non-malleable if the message contained in a modified codeword is either the original message, or a completely unrelated value. In contrast to error correction and error detection, non-malleability can be achieved for very rich classes of modifications. We construct an efficient code that is non-malleable with respect to modifications that affect each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set it to either 0 or 1), but independently of the value of the other bits of the codeword. Using the probabilistic method, we also show a very strong and general statement: there exists a non-malleable code for every “small enough” family F of functions via which codewords can be modified. Although this probabilistic method argument does not directly yield efficient constructions, it gives us efficient non-malleable codes in the random-oracle model for very general classes of tampering functions—e.g., functions where every bit in the tampered codeword can depend arbitrarily on any 99% of the bits in the original codeword. As an application of non-malleable codes, we show that they provide an elegant algorithmic solution to the task of protecting functionalities implemented in hardware (e.g., signature cards) against “tampering attacks.” In such attacks, the secret state of a physical system is tampered, in the hopes that future interaction with the modified system will reveal some secret information. This problem was previously studied in the work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security” (ATP). We show that non-malleable codes can be used to achieve important improvements over the prior work. In particular, we show that any functionality can be made secure against a large class of tampering attacks, simply by encoding the secret state with a non-malleable code while it is stored in memory."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 65","status":"public","title":"Non-malleable codes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"107","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-08-01T00:00:00Z","article_type":"original","citation":{"ista":"Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of the ACM. 65(4), 20.","apa":"Dziembowski, S., Pietrzak, K. Z., & Wichs, D. (2018). Non-malleable codes. Journal of the ACM. ACM. https://doi.org/10.1145/3178432","ieee":"S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” Journal of the ACM, vol. 65, no. 4. ACM, 2018.","ama":"Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. Journal of the ACM. 2018;65(4). doi:10.1145/3178432","chicago":"Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable Codes.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3178432.","mla":"Dziembowski, Stefan, et al. “Non-Malleable Codes.” Journal of the ACM, vol. 65, no. 4, 20, ACM, 2018, doi:10.1145/3178432.","short":"S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018)."},"publication":"Journal of the ACM","publist_id":"7947","ec_funded":1,"article_number":"20","volume":65,"date_updated":"2023-09-13T09:05:17Z","date_created":"2018-12-11T11:44:40Z","author":[{"full_name":"Dziembowski, Stefan","last_name":"Dziembowski","first_name":"Stefan"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"},{"last_name":"Wichs","first_name":"Daniel","full_name":"Wichs, Daniel"}],"department":[{"_id":"KrPi"}],"publisher":"ACM","publication_status":"published","year":"2018","month":"08","language":[{"iso":"eng"}],"doi":"10.1145/3178432","project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"},{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000442938200004"]},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2009/608"}]},{"page":"4267-4283","publication":"Journal of Cell Biology","citation":{"short":"L. Carvalho, P. Patricio, S. Ponte, C.-P.J. Heisenberg, L. Almeida, A.S. Nunes, N.A.M. Araújo, A. Jacinto, Journal of Cell Biology 217 (2018) 4267–4283.","mla":"Carvalho, Lara, et al. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology, vol. 217, no. 12, Rockefeller University Press, 2018, pp. 4267–83, doi:10.1083/jcb.201804048.","chicago":"Carvalho, Lara, Pedro Patricio, Susana Ponte, Carl-Philipp J Heisenberg, Luis Almeida, André S. Nunes, Nuno A.M. Araújo, and Antonio Jacinto. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201804048.","ama":"Carvalho L, Patricio P, Ponte S, et al. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 2018;217(12):4267-4283. doi:10.1083/jcb.201804048","ieee":"L. Carvalho et al., “Occluding junctions as novel regulators of tissue mechanics during wound repair,” Journal of Cell Biology, vol. 217, no. 12. Rockefeller University Press, pp. 4267–4283, 2018.","apa":"Carvalho, L., Patricio, P., Ponte, S., Heisenberg, C.-P. J., Almeida, L., Nunes, A. S., … Jacinto, A. (2018). Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201804048","ista":"Carvalho L, Patricio P, Ponte S, Heisenberg C-PJ, Almeida L, Nunes AS, Araújo NAM, Jacinto A. 2018. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 217(12), 4267–4283."},"date_published":"2018-12-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Occluding junctions as novel regulators of tissue mechanics during wound repair","intvolume":" 217","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5676","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"In epithelial tissues, cells tightly connect to each other through cell–cell junctions, but they also present the remarkable capacity of reorganizing themselves without compromising tissue integrity. Upon injury, simple epithelia efficiently resolve small lesions through the action of actin cytoskeleton contractile structures at the wound edge and cellular rearrangements. However, the underlying mechanisms and how they cooperate are still poorly understood. In this study, we combine live imaging and theoretical modeling to reveal a novel and indispensable role for occluding junctions (OJs) in this process. We demonstrate that OJ loss of function leads to defects in wound-closure dynamics: instead of contracting, wounds dramatically increase their area. OJ mutants exhibit phenotypes in cell shape, cellular rearrangements, and mechanical properties as well as in actin cytoskeleton dynamics at the wound edge. We propose that OJs are essential for wound closure by impacting on epithelial mechanics at the tissue level, which in turn is crucial for correct regulation of the cellular events occurring at the wound edge."}],"issue":"12","quality_controlled":"1","isi":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"external_id":{"pmid":["30228162 "],"isi":["000451960800018"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30228162"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1083/jcb.201804048","month":"12","publication_identifier":{"issn":["00219525"]},"publication_status":"published","publisher":"Rockefeller University Press","department":[{"_id":"CaHe"}],"year":"2018","pmid":1,"date_created":"2018-12-16T22:59:19Z","date_updated":"2023-09-13T09:11:17Z","volume":217,"author":[{"last_name":"Carvalho","first_name":"Lara","full_name":"Carvalho, Lara"},{"full_name":"Patricio, Pedro","first_name":"Pedro","last_name":"Patricio"},{"first_name":"Susana","last_name":"Ponte","full_name":"Ponte, Susana"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Almeida, Luis","first_name":"Luis","last_name":"Almeida"},{"full_name":"Nunes, André S.","last_name":"Nunes","first_name":"André S."},{"full_name":"Araújo, Nuno A.M.","first_name":"Nuno A.M.","last_name":"Araújo"},{"full_name":"Jacinto, Antonio","last_name":"Jacinto","first_name":"Antonio"}],"ec_funded":1},{"_id":"9807","year":"2018","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Springer Nature","department":[{"_id":"SiHi"}],"title":"Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","status":"public","related_material":{"record":[{"id":"20","relation":"used_in_publication","status":"public"}]},"author":[{"first_name":"Juan","last_name":"Higareda Almaraz","full_name":"Higareda Almaraz, Juan"},{"first_name":"Michael","last_name":"Karbiener","full_name":"Karbiener, Michael"},{"last_name":"Giroud","first_name":"Maude","full_name":"Giroud, Maude"},{"orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","first_name":"Florian","full_name":"Pauler, Florian"},{"full_name":"Gerhalter, Teresa","first_name":"Teresa","last_name":"Gerhalter"},{"full_name":"Herzig, Stephan","last_name":"Herzig","first_name":"Stephan"},{"last_name":"Scheideler","first_name":"Marcel","full_name":"Scheideler, Marcel"}],"oa_version":"Published Version","date_updated":"2023-09-13T09:10:47Z","date_created":"2021-08-06T12:26:53Z","type":"research_data_reference","abstract":[{"text":"Table S1. Genes with highest betweenness. Table S2. Local and Master regulators up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb).","lang":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7295339.v1"}],"citation":{"apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295339.v1","ieee":"J. Higareda Almaraz et al., “Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295339.v1.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295339.v1","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295339.v1.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","mla":"Higareda Almaraz, Juan, et al. Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295339.v1."},"date_published":"2018-11-03T00:00:00Z","doi":"10.6084/m9.figshare.7295339.v1","article_processing_charge":"No","day":"03","month":"11"},{"_id":"9808","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2018","publisher":"Springer Nature","department":[{"_id":"SiHi"}],"status":"public","title":"Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","related_material":{"record":[{"id":"20","relation":"used_in_publication","status":"public"}]},"author":[{"last_name":"Higareda Almaraz","first_name":"Juan","full_name":"Higareda Almaraz, Juan"},{"last_name":"Karbiener","first_name":"Michael","full_name":"Karbiener, Michael"},{"full_name":"Giroud, Maude","first_name":"Maude","last_name":"Giroud"},{"full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","first_name":"Florian"},{"full_name":"Gerhalter, Teresa","last_name":"Gerhalter","first_name":"Teresa"},{"full_name":"Herzig, Stephan","last_name":"Herzig","first_name":"Stephan"},{"full_name":"Scheideler, Marcel","first_name":"Marcel","last_name":"Scheideler"}],"oa_version":"Published Version","date_updated":"2023-09-13T09:10:47Z","date_created":"2021-08-06T12:31:57Z","type":"research_data_reference","abstract":[{"text":"Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb).","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7295369.v1","open_access":"1"}],"citation":{"ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295369.v1.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295369.v1","ieee":"J. Higareda Almaraz et al., “Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295369.v1","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295369.v1.","mla":"Higareda Almaraz, Juan, et al. Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295369.v1.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018)."},"oa":1,"date_published":"2018-11-03T00:00:00Z","doi":"10.6084/m9.figshare.7295369.v1","article_processing_charge":"No","month":"11","day":"03"},{"publist_id":"7723","ec_funded":1,"date_updated":"2023-09-13T09:13:12Z","date_created":"2018-12-11T11:45:07Z","author":[{"full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","first_name":"Joel F"},{"first_name":"Peter","last_name":"Gazi","full_name":"Gazi, Peter"},{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Klein"},{"full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","first_name":"Georg F"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Reyzin","first_name":"Lenoid","full_name":"Reyzin, Lenoid"},{"full_name":"Rolinek, Michal","first_name":"Michal","last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michal","last_name":"Rybar","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","full_name":"Rybar, Michal"}],"publication_status":"published","publisher":"ACM","department":[{"_id":"KrPi"},{"_id":"HeEd"},{"_id":"VlKo"}],"acknowledgement":"Leonid Reyzin was supported in part by IST Austria and by US NSF grants 1012910, 1012798, and 1422965; this research was performed while he was visiting IST Austria.","year":"2018","month":"06","language":[{"iso":"eng"}],"conference":{"name":"ASIACCS: Asia Conference on Computer and Communications Security ","start_date":"2018-06-04","location":"Incheon, Republic of Korea","end_date":"2018-06-08"},"doi":"10.1145/3196494.3196534","quality_controlled":"1","isi":1,"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"},{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"oa":1,"external_id":{"isi":["000516620100005"]},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/783"}],"abstract":[{"lang":"eng","text":"We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki'16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block'16] for analyzing the hardware costs of an iMHF."}],"type":"conference","oa_version":"Submitted Version","title":"On the memory hardness of data independent password hashing functions","status":"public","_id":"193","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-06-01T00:00:00Z","page":"51 - 65","publication":"Proceedings of the 2018 on Asia Conference on Computer and Communication Security","citation":{"chicago":"Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar. “On the Memory Hardness of Data Independent Password Hashing Functions.” In Proceedings of the 2018 on Asia Conference on Computer and Communication Security, 51–65. ACM, 2018. https://doi.org/10.1145/3196494.3196534.","mla":"Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password Hashing Functions.” Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65, doi:10.1145/3196494.3196534.","short":"J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak, L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65.","ista":"Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password hashing functions. Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ASIACCS: Asia Conference on Computer and Communications Security , 51–65.","ieee":"J. F. Alwen et al., “On the memory hardness of data independent password hashing functions,” in Proceedings of the 2018 on Asia Conference on Computer and Communication Security, Incheon, Republic of Korea, 2018, pp. 51–65.","apa":"Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak, K. Z., … Rybar, M. (2018). On the memory hardness of data independent password hashing functions. In Proceedings of the 2018 on Asia Conference on Computer and Communication Security (pp. 51–65). Incheon, Republic of Korea: ACM. https://doi.org/10.1145/3196494.3196534","ama":"Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data independent password hashing functions. In: Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ACM; 2018:51-65. doi:10.1145/3196494.3196534"}},{"day":"31","article_processing_charge":"No","scopus_import":"1","date_published":"2018-03-31T00:00:00Z","page":"3 - 28","citation":{"ista":"Micciancio D, Walter M. 2018. On the bit security of cryptographic primitives. Eurocrypt: Advances in Cryptology, LNCS, vol. 10820, 3–28.","ieee":"D. Micciancio and M. Walter, “On the bit security of cryptographic primitives,” presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10820, pp. 3–28.","apa":"Micciancio, D., & Walter, M. (2018). On the bit security of cryptographic primitives (Vol. 10820, pp. 3–28). Presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78381-9_1","ama":"Micciancio D, Walter M. On the bit security of cryptographic primitives. In: Vol 10820. Springer; 2018:3-28. doi:10.1007/978-3-319-78381-9_1","chicago":"Micciancio, Daniele, and Michael Walter. “On the Bit Security of Cryptographic Primitives,” 10820:3–28. Springer, 2018. https://doi.org/10.1007/978-3-319-78381-9_1.","mla":"Micciancio, Daniele, and Michael Walter. On the Bit Security of Cryptographic Primitives. Vol. 10820, Springer, 2018, pp. 3–28, doi:10.1007/978-3-319-78381-9_1.","short":"D. Micciancio, M. Walter, in:, Springer, 2018, pp. 3–28."},"abstract":[{"lang":"eng","text":"We introduce a formal quantitative notion of “bit security” for a general type of cryptographic games (capturing both decision and search problems), aimed at capturing the intuition that a cryptographic primitive with k-bit security is as hard to break as an ideal cryptographic function requiring a brute force attack on a k-bit key space. Our new definition matches the notion of bit security commonly used by cryptographers and cryptanalysts when studying search (e.g., key recovery) problems, where the use of the traditional definition is well established. However, it produces a quantitatively different metric in the case of decision (indistinguishability) problems, where the use of (a straightforward generalization of) the traditional definition is more problematic and leads to a number of paradoxical situations or mismatches between theoretical/provable security and practical/common sense intuition. Key to our new definition is to consider adversaries that may explicitly declare failure of the attack. We support and justify the new definition by proving a number of technical results, including tight reductions between several standard cryptographic problems, a new hybrid theorem that preserves bit security, and an application to the security analysis of indistinguishability primitives making use of (approximate) floating point numbers. This is the first result showing that (standard precision) 53-bit floating point numbers can be used to achieve 100-bit security in the context of cryptographic primitives with general indistinguishability-based security definitions. Previous results of this type applied only to search problems, or special types of decision problems."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","status":"public","title":"On the bit security of cryptographic primitives","intvolume":" 10820","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"300","month":"03","language":[{"iso":"eng"}],"conference":{"name":"Eurocrypt: Advances in Cryptology","location":"Tel Aviv, Israel","start_date":"2018-04-29","end_date":"2018-05-03"},"doi":"10.1007/978-3-319-78381-9_1","isi":1,"quality_controlled":"1","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000517097500001"]},"main_file_link":[{"url":"https://eprint.iacr.org/2018/077","open_access":"1"}],"oa":1,"publist_id":"7581","ec_funded":1,"date_updated":"2023-09-13T09:12:04Z","date_created":"2018-12-11T11:45:42Z","volume":10820,"author":[{"last_name":"Micciancio","first_name":"Daniele","full_name":"Micciancio, Daniele"},{"last_name":"Walter","first_name":"Michael","orcid":"0000-0003-3186-2482","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","full_name":"Walter, Michael"}],"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer","acknowledgement":"Research supported in part by the Defense Advanced Research Projects Agency (DARPA) and the U.S. Army Research Office under the SafeWare program. Opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views, position or policy of the Government. The second author was also supported by the European Research Council, ERC consolidator grant (682815 - TOCNeT).","year":"2018"},{"scopus_import":"1","article_processing_charge":"No","day":"29","page":"750 - 782","article_type":"original","citation":{"mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math, vol. 32, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 750–82, doi:10.1137/16M1097201.","short":"H. Edelsbrunner, M. Iglesias Ham, SIAM J Discrete Math 32 (2018) 750–782.","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1097201.","ama":"Edelsbrunner H, Iglesias Ham M. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 2018;32(1):750-782. doi:10.1137/16M1097201","ista":"Edelsbrunner H, Iglesias Ham M. 2018. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 32(1), 750–782.","apa":"Edelsbrunner, H., & Iglesias Ham, M. (2018). On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1097201","ieee":"H. Edelsbrunner and M. Iglesias Ham, “On the optimality of the FCC lattice for soft sphere packing,” SIAM J Discrete Math, vol. 32, no. 1. Society for Industrial and Applied Mathematics , pp. 750–782, 2018."},"publication":"SIAM J Discrete Math","date_published":"2018-03-29T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Motivated by biological questions, we study configurations of equal spheres that neither pack nor cover. Placing their centers on a lattice, we define the soft density of the configuration by penalizing multiple overlaps. Considering the 1-parameter family of diagonally distorted 3-dimensional integer lattices, we show that the soft density is maximized at the FCC lattice."}],"intvolume":" 32","title":"On the optimality of the FCC lattice for soft sphere packing","status":"public","_id":"312","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","publication_identifier":{"issn":["08954801"]},"month":"03","project":[{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000428958900038"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://pdfs.semanticscholar.org/d2d5/6da00fbc674e6a8b1bb9d857167e54200dc6.pdf"}],"language":[{"iso":"eng"}],"doi":"10.1137/16M1097201","publist_id":"7553","department":[{"_id":"HeEd"}],"publisher":"Society for Industrial and Applied Mathematics ","publication_status":"published","year":"2018","acknowledgement":"This work was partially supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics,” through grant I02979-N35 of the Austrian Science Fund (FWF).","volume":32,"date_created":"2018-12-11T11:45:46Z","date_updated":"2023-09-13T09:34:38Z","author":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Iglesias Ham, Mabel","last_name":"Iglesias Ham","first_name":"Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87"}]},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-04-01T00:00:00Z","publication":"Comptes Rendus Mathematique","citation":{"chicago":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique. Elsevier, 2018. https://doi.org/10.1016/j.crma.2018.03.005.","mla":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique, vol. 356, no. 4, Elsevier, 2018, pp. 412–14, doi:10.1016/j.crma.2018.03.005.","short":"A. Akopyan, Comptes Rendus Mathematique 356 (2018) 412–414.","ista":"Akopyan A. 2018. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 356(4), 412–414.","ieee":"A. Akopyan, “On the number of non-hexagons in a planar tiling,” Comptes Rendus Mathematique, vol. 356, no. 4. Elsevier, pp. 412–414, 2018.","apa":"Akopyan, A. (2018). On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. Elsevier. https://doi.org/10.1016/j.crma.2018.03.005","ama":"Akopyan A. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 2018;356(4):412-414. doi:10.1016/j.crma.2018.03.005"},"article_type":"original","page":"412-414","abstract":[{"lang":"eng","text":"We give a simple proof of T. Stehling's result [4], whereby in any normal tiling of the plane with convex polygons with number of sides not less than six, all tiles except a finite number are hexagons."}],"issue":"4","type":"journal_article","oa_version":"Preprint","_id":"409","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"On the number of non-hexagons in a planar tiling","status":"public","intvolume":" 356","month":"04","publication_identifier":{"issn":["1631073X"]},"doi":"10.1016/j.crma.2018.03.005","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000430402700009"],"arxiv":["1805.01652"]},"main_file_link":[{"url":"https://arxiv.org/abs/1805.01652","open_access":"1"}],"isi":1,"quality_controlled":"1","publist_id":"7420","author":[{"full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan"}],"date_updated":"2023-09-13T09:34:12Z","date_created":"2018-12-11T11:46:19Z","volume":356,"year":"2018","publication_status":"published","publisher":"Elsevier","department":[{"_id":"HeEd"}]},{"related_material":{"link":[{"url":"http://doi.org/10.1038/s41562-018-0342-3","relation":"erratum"}]},"author":[{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"volume":2,"date_created":"2018-12-11T11:46:22Z","date_updated":"2023-09-13T09:38:54Z","year":"2018","publisher":"Nature Publishing Group","department":[{"_id":"KrCh"}],"publication_status":"published","publist_id":"7404","ec_funded":1,"file_date_updated":"2020-07-14T12:46:25Z","doi":"10.1038/s41562-018-0320-9","language":[{"iso":"eng"}],"external_id":{"isi":["000446612000016"]},"oa":1,"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"month":"03","file":[{"file_name":"2018_NatureHumanBeh_Hilbe.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":598033,"file_id":"7052","relation":"main_file","date_created":"2019-11-19T08:19:51Z","date_updated":"2020-07-14T12:46:25Z","checksum":"571b8cc0ba14e8d5d8b18e439a9835eb"}],"oa_version":"Submitted Version","_id":"419","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 2","status":"public","ddc":["000"],"title":"Partners and rivals in direct reciprocity","abstract":[{"text":"Reciprocity is a major factor in human social life and accounts for a large part of cooperation in our communities. Direct reciprocity arises when repeated interactions occur between the same individuals. The framework of iterated games formalizes this phenomenon. Despite being introduced more than five decades ago, the concept keeps offering beautiful surprises. Recent theoretical research driven by new mathematical tools has proposed a remarkable dichotomy among the crucial strategies: successful individuals either act as partners or as rivals. Rivals strive for unilateral advantages by applying selfish or extortionate strategies. Partners aim to share the payoff for mutual cooperation, but are ready to fight back when being exploited. Which of these behaviours evolves depends on the environment. Whereas small population sizes and a limited number of rounds favour rivalry, partner strategies are selected when populations are large and relationships stable. Only partners allow for evolution of cooperation, while the rivals’ attempt to put themselves first leads to defection. Hilbe et al. synthesize recent theoretical work on zero-determinant and ‘rival’ versus ‘partner’ strategies in social dilemmas. They describe the environments under which these contrasting selfish or cooperative strategies emerge in evolution.","lang":"eng"}],"type":"journal_article","date_published":"2018-03-19T00:00:00Z","citation":{"ama":"Hilbe C, Chatterjee K, Nowak M. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2018;2:469–477. doi:10.1038/s41562-018-0320-9","apa":"Hilbe, C., Chatterjee, K., & Nowak, M. (2018). Partners and rivals in direct reciprocity. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0320-9","ieee":"C. Hilbe, K. Chatterjee, and M. Nowak, “Partners and rivals in direct reciprocity,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 469–477, 2018.","ista":"Hilbe C, Chatterjee K, Nowak M. 2018. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2, 469–477.","short":"C. Hilbe, K. Chatterjee, M. Nowak, Nature Human Behaviour 2 (2018) 469–477.","mla":"Hilbe, Christian, et al. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 469–477, doi:10.1038/s41562-018-0320-9.","chicago":"Hilbe, Christian, Krishnendu Chatterjee, and Martin Nowak. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0320-9."},"publication":"Nature Human Behaviour","page":"469–477","article_type":"review","has_accepted_license":"1","article_processing_charge":"No","day":"19","scopus_import":"1"},{"year":"2018","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","author":[{"first_name":"Alexey","last_name":"Bakhirkin","full_name":"Bakhirkin, Alexey"},{"first_name":"Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"},{"full_name":"Nickovic, Dejan","first_name":"Dejan","last_name":"Nickovic"},{"full_name":"Maler, Oded","first_name":"Oded","last_name":"Maler"},{"last_name":"Asarin","first_name":"Eugene","full_name":"Asarin, Eugene"}],"date_updated":"2023-09-13T09:35:46Z","date_created":"2018-12-11T11:44:31Z","volume":11022,"file_date_updated":"2020-07-14T12:48:03Z","publist_id":"7976","oa":1,"external_id":{"isi":["000884993200013"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","start_date":"2018-09-04","location":"Bejing, China","end_date":"2018-09-06"},"doi":"10.1007/978-3-030-00151-3_13","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"isbn":["978-3-030-00150-6"]},"_id":"78","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"title":"Online timed pattern matching using automata","status":"public","intvolume":" 11022","oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":374851,"creator":"dernst","file_name":"2018_LNCS_Bakhirkin.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-14T11:34:34Z","checksum":"436b7574934324cfa7d1d3986fddc65b","relation":"main_file","file_id":"7831"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by ϕ and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads ω, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated."}],"citation":{"apa":"Bakhirkin, A., Ferrere, T., Nickovic, D., Maler, O., & Asarin, E. (2018). Online timed pattern matching using automata (Vol. 11022, pp. 215–232). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_13","ieee":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, and E. Asarin, “Online timed pattern matching using automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China, 2018, vol. 11022, pp. 215–232.","ista":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. 2018. Online timed pattern matching using automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 215–232.","ama":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. Online timed pattern matching using automata. In: Vol 11022. Springer; 2018:215-232. doi:10.1007/978-3-030-00151-3_13","chicago":"Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_13.","short":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer, 2018, pp. 215–232.","mla":"Bakhirkin, Alexey, et al. Online Timed Pattern Matching Using Automata. Vol. 11022, Springer, 2018, pp. 215–32, doi:10.1007/978-3-030-00151-3_13."},"page":"215 - 232","date_published":"2018-08-26T00:00:00Z","scopus_import":"1","day":"26","has_accepted_license":"1","article_processing_charge":"No"},{"publication":"Scientific Reports","citation":{"chicago":"Brauns, Matthias, Sergey Amitonov, Paul Spruijtenburg, and Floris Zwanenburg. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-24004-y.","short":"M. Brauns, S. Amitonov, P. Spruijtenburg, F. Zwanenburg, Scientific Reports 8 (2018).","mla":"Brauns, Matthias, et al. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports, vol. 8, no. 1, 5690, Nature Publishing Group, 2018, doi:10.1038/s41598-018-24004-y.","apa":"Brauns, M., Amitonov, S., Spruijtenburg, P., & Zwanenburg, F. (2018). Palladium gates for reproducible quantum dots in silicon. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-24004-y","ieee":"M. Brauns, S. Amitonov, P. Spruijtenburg, and F. Zwanenburg, “Palladium gates for reproducible quantum dots in silicon,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","ista":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. 2018. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 8(1), 5690.","ama":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-24004-y"},"date_published":"2018-04-09T00:00:00Z","scopus_import":"1","day":"09","article_processing_charge":"No","has_accepted_license":"1","_id":"317","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Palladium gates for reproducible quantum dots in silicon","status":"public","ddc":["539"],"intvolume":" 8","pubrep_id":"1016","oa_version":"Published Version","file":[{"file_id":"5256","relation":"main_file","checksum":"20af238ca4ba6491b77270be8d826bf5","date_updated":"2020-07-14T12:46:02Z","date_created":"2018-12-12T10:17:04Z","access_level":"open_access","file_name":"IST-2018-1016-v1+1_2018_Brauns_Palladium_gates.pdf","creator":"system","content_type":"application/pdf","file_size":1850530}],"type":"journal_article","abstract":[{"text":"We replace the established aluminium gates for the formation of quantum dots in silicon with gates made from palladium. We study the morphology of both aluminium and palladium gates with transmission electron microscopy. The native aluminium oxide is found to be formed all around the aluminium gates, which could lead to the formation of unintentional dots. Therefore, we report on a novel fabrication route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined quantum dots, which are reproducibly fabricated. Furthermore, palladium enables us to further shrink the gate design, allowing us to perform electron transport measurements in the few-electron regime in devices comprising only two gate layers, a major technological advancement. It remains to be seen, whether the introduction of palladium gates can improve the excellent results on electron and nuclear spin qubits defined with an aluminium gate stack.","lang":"eng"}],"issue":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000429404300013"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41598-018-24004-y","language":[{"iso":"eng"}],"month":"04","year":"2018","publication_status":"published","department":[{"_id":"GeKa"}],"publisher":"Nature Publishing Group","author":[{"full_name":"Brauns, Matthias","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","last_name":"Brauns","first_name":"Matthias"},{"full_name":"Amitonov, Sergey","first_name":"Sergey","last_name":"Amitonov"},{"full_name":"Spruijtenburg, Paul","first_name":"Paul","last_name":"Spruijtenburg"},{"full_name":"Zwanenburg, Floris","first_name":"Floris","last_name":"Zwanenburg"}],"date_created":"2018-12-11T11:45:47Z","date_updated":"2023-09-13T09:38:00Z","volume":8,"article_number":"5690","file_date_updated":"2020-07-14T12:46:02Z","publist_id":"7548"},{"author":[{"last_name":"Liutkeviciute","first_name":"Zita","full_name":"Liutkeviciute, Zita"},{"last_name":"Gil Mansilla","first_name":"Esther","full_name":"Gil Mansilla, Esther"},{"first_name":"Thomas","last_name":"Eder","full_name":"Eder, Thomas"},{"full_name":"Casillas Perez, Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","last_name":"Casillas Perez","first_name":"Barbara E"},{"full_name":"Giulia Di Giglio, Maria","last_name":"Giulia Di Giglio","first_name":"Maria"},{"full_name":"Muratspahić, Edin","first_name":"Edin","last_name":"Muratspahić"},{"full_name":"Grebien, Florian","first_name":"Florian","last_name":"Grebien"},{"full_name":"Rattei, Thomas","first_name":"Thomas","last_name":"Rattei"},{"last_name":"Muttenthaler","first_name":"Markus","full_name":"Muttenthaler, Markus"},{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia"},{"last_name":"Gruber","first_name":"Christian","full_name":"Gruber, Christian"}],"volume":32,"date_created":"2018-12-11T11:45:08Z","date_updated":"2023-09-13T09:37:32Z","pmid":1,"year":"2018","department":[{"_id":"SyCr"}],"publisher":"FASEB","publication_status":"published","publist_id":"7721","doi":"10.1096/fj.201800443","language":[{"iso":"eng"}],"external_id":{"isi":["000449359700035"],"pmid":["29939785"]},"oa":1,"main_file_link":[{"url":" https://doi.org/10.1096/fj.201800443","open_access":"1"}],"project":[{"_id":"25E3D34E-B435-11E9-9278-68D0E5697425","name":"Individual function and social role of oxytocin-like neuropeptides in ants"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["08926638"]},"month":"11","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"194","intvolume":" 32","title":"Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity","status":"public","issue":"12","abstract":[{"text":"Ants are emerging model systems to study cellular signaling because distinct castes possess different physiologic phenotypes within the same colony. Here we studied the functionality of inotocin signaling, an insect ortholog of mammalian oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined that specialization within the colony, seasonal factors, and physiologic conditions down-regulated the expression of the OT-like signaling system. Given this natural variation, we interrogated its function using RNAi knockdowns. Next-generation RNA sequencing of OT-like precursor knock-down ants highlighted its role in the regulation of genes involved in metabolism. Knock-down ants exhibited higher walking activity and increased self-grooming in the brood chamber. We propose that OT-like signaling in ants is important for regulating metabolic processes and locomotion.","lang":"eng"}],"type":"journal_article","date_published":"2018-11-29T00:00:00Z","citation":{"short":"Z. Liutkeviciute, E. Gil Mansilla, T. Eder, B.E. Casillas Perez, M. Giulia Di Giglio, E. Muratspahić, F. Grebien, T. Rattei, M. Muttenthaler, S. Cremer, C. Gruber, The FASEB Journal 32 (2018) 6808–6821.","mla":"Liutkeviciute, Zita, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal, vol. 32, no. 12, FASEB, 2018, pp. 6808–21, doi:10.1096/fj.201800443.","chicago":"Liutkeviciute, Zita, Esther Gil Mansilla, Thomas Eder, Barbara E Casillas Perez, Maria Giulia Di Giglio, Edin Muratspahić, Florian Grebien, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal. FASEB, 2018. https://doi.org/10.1096/fj.201800443.","ama":"Liutkeviciute Z, Gil Mansilla E, Eder T, et al. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 2018;32(12):6808-6821. doi:10.1096/fj.201800443","ieee":"Z. Liutkeviciute et al., “Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity,” The FASEB Journal, vol. 32, no. 12. FASEB, pp. 6808–6821, 2018.","apa":"Liutkeviciute, Z., Gil Mansilla, E., Eder, T., Casillas Perez, B. E., Giulia Di Giglio, M., Muratspahić, E., … Gruber, C. (2018). Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. FASEB. https://doi.org/10.1096/fj.201800443","ista":"Liutkeviciute Z, Gil Mansilla E, Eder T, Casillas Perez BE, Giulia Di Giglio M, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber C. 2018. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 32(12), 6808–6821."},"publication":"The FASEB Journal","page":"6808-6821","article_type":"original","article_processing_charge":"No","day":"29","scopus_import":"1"},{"publist_id":"7762","file_date_updated":"2020-07-14T12:45:03Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41589-021-00744-3"}]},"author":[{"last_name":"Fehrentz","first_name":"Timm","full_name":"Fehrentz, Timm"},{"last_name":"Huber","first_name":"Florian","full_name":"Huber, Florian"},{"full_name":"Hartrampf, Nina","first_name":"Nina","last_name":"Hartrampf"},{"full_name":"Bruegmann, Tobias","last_name":"Bruegmann","first_name":"Tobias"},{"full_name":"Frank, James","last_name":"Frank","first_name":"James"},{"last_name":"Fine","first_name":"Nicholas","full_name":"Fine, Nicholas"},{"full_name":"Malan, Daniela","last_name":"Malan","first_name":"Daniela"},{"orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G"},{"first_name":"Denis","last_name":"Tikhonov","full_name":"Tikhonov, Denis"},{"full_name":"Sumser, Maritn","first_name":"Maritn","last_name":"Sumser"},{"last_name":"Sasse","first_name":"Philipp","full_name":"Sasse, Philipp"},{"full_name":"Hodson, David","first_name":"David","last_name":"Hodson"},{"first_name":"Boris","last_name":"Zhorov","full_name":"Zhorov, Boris"},{"first_name":"Nikolaj","last_name":"Klocker","full_name":"Klocker, Nikolaj"},{"full_name":"Trauner, Dirk","first_name":"Dirk","last_name":"Trauner"}],"volume":14,"date_updated":"2023-09-13T09:36:35Z","date_created":"2018-12-11T11:44:56Z","year":"2018","department":[{"_id":"JoDa"}],"publisher":"Nature Publishing Group","publication_status":"published","month":"07","doi":"10.1038/s41589-018-0090-8","language":[{"iso":"eng"}],"external_id":{"isi":["000438970200010"]},"oa":1,"isi":1,"quality_controlled":"1","issue":"8","abstract":[{"text":"L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction coupling and release of hormones from secretory cells. They are targets of antihypertensive and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell function and cardiac activity under optical control.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"7832","date_created":"2020-05-14T12:14:09Z","date_updated":"2020-07-14T12:45:03Z","checksum":"d42935094ec845f54a0688bf12986d62","file_name":"2018_NatureChemicalBiology_Fehrentz.pdf","access_level":"open_access","file_size":6321000,"content_type":"application/pdf","creator":"dernst"}],"_id":"159","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 14","status":"public","title":"Optical control of L-type Ca2+ channels using a diltiazem photoswitch","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","day":"16","scopus_import":"1","date_published":"2018-07-16T00:00:00Z","citation":{"ama":"Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 2018;14(8):764-767. doi:10.1038/s41589-018-0090-8","apa":"Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N., … Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0090-8","ieee":"T. Fehrentz et al., “Optical control of L-type Ca2+ channels using a diltiazem photoswitch,” Nature Chemical Biology, vol. 14, no. 8. Nature Publishing Group, pp. 764–767, 2018.","ista":"Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 14(8), 764–767.","short":"T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D. Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N. Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767.","mla":"Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 764–67, doi:10.1038/s41589-018-0090-8.","chicago":"Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0090-8."},"publication":"Nature Chemical Biology","page":"764 - 767","article_type":"original"},{"day":"15","article_processing_charge":"No","scopus_import":"1","date_published":"2018-08-15T00:00:00Z","page":"53-70","citation":{"short":"S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer, 2018, pp. 53–70.","mla":"Arming, Sebastian, et al. Parameter-Independent Strategies for PMDPs via POMDPs. Vol. 11024, Springer, 2018, pp. 53–70, doi:10.1007/978-3-319-99154-2_4.","chicago":"Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen, and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70. Springer, 2018. https://doi.org/10.1007/978-3-319-99154-2_4.","ama":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:10.1007/978-3-319-99154-2_4","apa":"Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., & Sokolova, A. (2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp. 53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-319-99154-2_4","ieee":"S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70.","ista":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11024, 53–70."},"abstract":[{"lang":"eng","text":"Markov Decision Processes (MDPs) are a popular class of models suitable for solving control decision problems in probabilistic reactive systems. We consider parametric MDPs (pMDPs) that include parameters in some of the transition probabilities to account for stochastic uncertainties of the environment such as noise or input disturbances. We study pMDPs with reachability objectives where the parameter values are unknown and impossible to measure directly during execution, but there is a probability distribution known over the parameter values. We study for the first time computing parameter-independent strategies that are expectation optimal, i.e., optimize the expected reachability probability under the probability distribution over the parameters. We present an encoding of our problem to partially observable MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating (repeated) learner model; a series of benchmarks of varying configurations of a robot moving on a grid; and a consensus protocol."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","title":"Parameter-independent strategies for pMDPs via POMDPs","status":"public","intvolume":" 11024","_id":"79","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"08","language":[{"iso":"eng"}],"conference":{"location":"Beijing, China","start_date":"2018-09-04","end_date":"2018-09-07","name":"QEST: Quantitative Evaluation of Systems"},"doi":"10.1007/978-3-319-99154-2_4","quality_controlled":"1","isi":1,"oa":1,"external_id":{"arxiv":["1806.05126"],"isi":["000548912200004"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.05126"}],"publist_id":"7975","date_updated":"2023-09-13T09:38:28Z","date_created":"2018-12-11T11:44:31Z","volume":11024,"author":[{"first_name":"Sebastian","last_name":"Arming","full_name":"Arming, Sebastian"},{"full_name":"Bartocci, Ezio","first_name":"Ezio","last_name":"Bartocci"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Katoen","first_name":"Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","full_name":"Katoen, Joost P"},{"full_name":"Sokolova, Ana","last_name":"Sokolova","first_name":"Ana"}],"publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"year":"2018"},{"publication_status":"published","publisher":"Springer","department":[{"_id":"RoSe"}],"year":"2018","date_updated":"2023-09-15T12:04:15Z","date_created":"2018-12-11T11:46:15Z","volume":19,"author":[{"orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","last_name":"Deuchert","first_name":"Andreas","full_name":"Deuchert, Andreas"},{"full_name":"Geisinge, Alissa","last_name":"Geisinge","first_name":"Alissa"},{"first_name":"Christian","last_name":"Hainzl","full_name":"Hainzl, Christian"},{"first_name":"Michael","last_name":"Loss","full_name":"Loss, Michael"}],"file_date_updated":"2020-07-14T12:46:22Z","publist_id":"7429","ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000429799900008"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00023-018-0665-7","month":"05","ddc":["510"],"title":"Persistence of translational symmetry in the BCS model with radial pair interaction","status":"public","intvolume":" 19","_id":"400","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2018-1011-v1+1_2018_Deuchert_Persistence.pdf","creator":"system","file_size":582680,"content_type":"application/pdf","file_id":"4966","relation":"main_file","checksum":"04d2c9bd7cbf3ca1d7acaaf4e7dca3e5","date_updated":"2020-07-14T12:46:22Z","date_created":"2018-12-12T10:12:47Z"}],"pubrep_id":"1011","type":"journal_article","abstract":[{"lang":"eng","text":"We consider the two-dimensional BCS functional with a radial pair interaction. We show that the translational symmetry is not broken in a certain temperature interval below the critical temperature. In the case of vanishing angular momentum, our results carry over to the three-dimensional case."}],"issue":"5","page":"1507 - 1527","publication":"Annales Henri Poincare","citation":{"ieee":"A. Deuchert, A. Geisinge, C. Hainzl, and M. Loss, “Persistence of translational symmetry in the BCS model with radial pair interaction,” Annales Henri Poincare, vol. 19, no. 5. Springer, pp. 1507–1527, 2018.","apa":"Deuchert, A., Geisinge, A., Hainzl, C., & Loss, M. (2018). Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-0665-7","ista":"Deuchert A, Geisinge A, Hainzl C, Loss M. 2018. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 19(5), 1507–1527.","ama":"Deuchert A, Geisinge A, Hainzl C, Loss M. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 2018;19(5):1507-1527. doi:10.1007/s00023-018-0665-7","chicago":"Deuchert, Andreas, Alissa Geisinge, Christian Hainzl, and Michael Loss. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare. Springer, 2018. https://doi.org/10.1007/s00023-018-0665-7.","short":"A. Deuchert, A. Geisinge, C. Hainzl, M. Loss, Annales Henri Poincare 19 (2018) 1507–1527.","mla":"Deuchert, Andreas, et al. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare, vol. 19, no. 5, Springer, 2018, pp. 1507–27, doi:10.1007/s00023-018-0665-7."},"date_published":"2018-05-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)"},{"citation":{"chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.","mla":"Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018).","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic models of individual and collective animal behavior. PLoS One. 13(3).","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Probabilistic models of individual and collective animal behavior. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3. Public Library of Science, 2018.","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049"},"publication":"PLoS One","date_published":"2018-03-07T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"07","intvolume":" 13","ddc":["530","571"],"status":"public","title":"Probabilistic models of individual and collective animal behavior","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"406","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf","file_size":6887358,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5165","checksum":"684229493db75b43e98a46cd922da497","date_created":"2018-12-12T10:15:43Z","date_updated":"2020-07-14T12:46:22Z"}],"pubrep_id":"995","type":"journal_article","issue":"3","abstract":[{"text":"Recent developments in automated tracking allow uninterrupted, high-resolution recording of animal trajectories, sometimes coupled with the identification of stereotyped changes of body pose or other behaviors of interest. Analysis and interpretation of such data represents a challenge: the timing of animal behaviors may be stochastic and modulated by kinematic variables, by the interaction with the environment or with the conspecifics within the animal group, and dependent on internal cognitive or behavioral state of the individual. Existing models for collective motion typically fail to incorporate the discrete, stochastic, and internal-state-dependent aspects of behavior, while models focusing on individual animal behavior typically ignore the spatial aspects of the problem. Here we propose a probabilistic modeling framework to address this gap. Each animal can switch stochastically between different behavioral states, with each state resulting in a possibly different law of motion through space. Switching rates for behavioral transitions can depend in a very general way, which we seek to identify from data, on the effects of the environment as well as the interaction between the animals. We represent the switching dynamics as a Generalized Linear Model and show that: (i) forward simulation of multiple interacting animals is possible using a variant of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly, the maximum likelihood inference of switching rate functions is tractably solvable by gradient descent; (iii) model selection can be used to identify factors that modulate behavioral state switching and to appropriately adjust model complexity to data. To illustrate our framework, we apply it to two synthetic models of animal motion and to real zebrafish tracking data. ","lang":"eng"}],"project":[{"name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000426896800032"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0193049","month":"03","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publication_status":"published","year":"2018","acknowledgement":"This work was supported by the Human Frontier Science Program RGP0065/2012 (GT, ES).","volume":13,"date_updated":"2023-09-15T12:06:19Z","date_created":"2018-12-11T11:46:18Z","related_material":{"record":[{"id":"9831","status":"public","relation":"research_data"}]},"author":[{"full_name":"Bod’Ová, Katarína","last_name":"Bod’Ová","first_name":"Katarína"},{"full_name":"Mitchell, Gabriel","first_name":"Gabriel","last_name":"Mitchell","id":"315BCD80-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Harpaz, Roy","first_name":"Roy","last_name":"Harpaz"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"}],"publist_id":"7423","file_date_updated":"2020-07-14T12:46:22Z"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to self-medicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation."}],"issue":"19","title":"Protection against the lethal side effects of social immunity in ants","status":"public","intvolume":" 28","_id":"55","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","scopus_import":"1","day":"08","article_processing_charge":"No","article_type":"original","page":"R1139 - R1140","publication":"Current Biology","citation":{"short":"C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140.","mla":"Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology, vol. 28, no. 19, Cell Press, 2018, pp. R1139–40, doi:10.1016/j.cub.2018.08.063.","chicago":"Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology. Cell Press, 2018. https://doi.org/10.1016/j.cub.2018.08.063.","ama":"Pull C, Metzler S, Naderlinger E, Cremer S. Protection against the lethal side effects of social immunity in ants. Current Biology. 2018;28(19):R1139-R1140. doi:10.1016/j.cub.2018.08.063","apa":"Pull, C., Metzler, S., Naderlinger, E., & Cremer, S. (2018). Protection against the lethal side effects of social immunity in ants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2018.08.063","ieee":"C. Pull, S. Metzler, E. Naderlinger, and S. Cremer, “Protection against the lethal side effects of social immunity in ants,” Current Biology, vol. 28, no. 19. Cell Press, pp. R1139–R1140, 2018.","ista":"Pull C, Metzler S, Naderlinger E, Cremer S. 2018. Protection against the lethal side effects of social immunity in ants. Current Biology. 28(19), R1139–R1140."},"date_published":"2018-10-08T00:00:00Z","publist_id":"7999","publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"Cell Press","year":"2018","date_updated":"2023-09-15T12:06:46Z","date_created":"2018-12-11T11:44:23Z","volume":28,"author":[{"last_name":"Pull","first_name":"Christopher","orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","full_name":"Pull, Christopher"},{"full_name":"Metzler, Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9547-2494","first_name":"Sina","last_name":"Metzler"},{"id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth","last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"}],"month":"10","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2018.08.063","open_access":"1"}],"external_id":{"isi":["000446693400008"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2018.08.063"},{"month":"01","quality_controlled":"1","isi":1,"project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"},{"name":"Structured Non-Hermitian Random Matrices","call_identifier":"FWF","grant_number":"M02080","_id":"258F40A4-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01546"}],"oa":1,"external_id":{"arxiv":["1708.01546"],"isi":["000437018500032"]},"language":[{"iso":"eng"}],"doi":"10.1137/17M1143125","publist_id":"7740","ec_funded":1,"publication_status":"published","publisher":"Society for Industrial and Applied Mathematics ","department":[{"_id":"LaEr"}],"year":"2018","acknowledgement":"The work of the second author was also partially supported by the Hausdorff Center of Mathematics.","date_updated":"2023-09-15T12:05:52Z","date_created":"2018-12-11T11:45:03Z","volume":50,"author":[{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","first_name":"Torben H","full_name":"Krüger, Torben H"},{"full_name":"Renfrew, David T","last_name":"Renfrew","first_name":"David T","orcid":"0000-0003-3493-121X","id":"4845BF6A-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","day":"01","article_processing_charge":"No","page":"3271 - 3290","publication":"SIAM Journal on Mathematical Analysis","citation":{"ista":"Erdös L, Krüger TH, Renfrew DT. 2018. Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. 50(3), 3271–3290.","ieee":"L. Erdös, T. H. Krüger, and D. T. Renfrew, “Power law decay for systems of randomly coupled differential equations,” SIAM Journal on Mathematical Analysis, vol. 50, no. 3. Society for Industrial and Applied Mathematics , pp. 3271–3290, 2018.","apa":"Erdös, L., Krüger, T. H., & Renfrew, D. T. (2018). Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/17M1143125","ama":"Erdös L, Krüger TH, Renfrew DT. Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. 2018;50(3):3271-3290. doi:10.1137/17M1143125","chicago":"Erdös, László, Torben H Krüger, and David T Renfrew. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/17M1143125.","mla":"Erdös, László, et al. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 3271–90, doi:10.1137/17M1143125.","short":"L. Erdös, T.H. Krüger, D.T. Renfrew, SIAM Journal on Mathematical Analysis 50 (2018) 3271–3290."},"date_published":"2018-01-01T00:00:00Z","type":"journal_article","abstract":[{"text":"We consider large random matrices X with centered, independent entries but possibly di erent variances. We compute the normalized trace of f(X)g(X∗) for f, g functions analytic on the spectrum of X. We use these results to compute the long time asymptotics for systems of coupled di erential equations with random coe cients. We show that when the coupling is critical, the norm squared of the solution decays like t−1/2.","lang":"eng"}],"issue":"3","title":"Power law decay for systems of randomly coupled differential equations","status":"public","intvolume":" 50","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"181","oa_version":"Published Version"}]