[{"type":"conference","abstract":[{"text":"A memory-hard function (MHF) ƒn with parameter n can be computed in sequential time and space n. Simultaneously, a high amortized parallel area-time complexity (aAT) is incurred per evaluation. In practice, MHFs are used to limit the rate at which an adversary (using a custom computational device) can evaluate a security sensitive function that still occasionally needs to be evaluated by honest users (using an off-the-shelf general purpose device). The most prevalent examples of such sensitive functions are Key Derivation Functions (KDFs) and password hashing algorithms where rate limits help mitigate off-line dictionary attacks. As the honest users' inputs to these functions are often (low-entropy) passwords special attention is given to a class of side-channel resistant MHFs called iMHFs.\r\n\r\nEssentially all iMHFs can be viewed as some mode of operation (making n calls to some round function) given by a directed acyclic graph (DAG) with very low indegree. Recently, a combinatorial property of a DAG has been identified (called \"depth-robustness\") which results in good provable security for an iMHF based on that DAG. Depth-robust DAGs have also proven useful in other cryptographic applications. Unfortunately, up till now, all known very depth-robust DAGs are impractically complicated and little is known about their exact (i.e. non-asymptotic) depth-robustness both in theory and in practice.\r\n\r\nIn this work we build and analyze (both formally and empirically) several exceedingly simple and efficient to navigate practical DAGs for use in iMHFs and other applications. For each DAG we:\r\n*Prove that their depth-robustness is asymptotically maximal.\r\n*Prove bounds of at least 3 orders of magnitude better on their exact depth-robustness compared to known bounds for other practical iMHF.\r\n*Implement and empirically evaluate their depth-robustness and aAT against a variety of state-of-the art (and several new) depth-reduction and low aAT attacks. \r\nWe find that, against all attacks, the new DAGs perform significantly better in practice than Argon2i, the most widely deployed iMHF in practice.\r\n\r\nAlong the way we also improve the best known empirical attacks on the aAT of Argon2i by implementing and testing several heuristic versions of a (hitherto purely theoretical) depth-reduction attack. Finally, we demonstrate practicality of our constructions by modifying the Argon2i code base to use one of the new high aAT DAGs. Experimental benchmarks on a standard off-the-shelf CPU show that the new modifications do not adversely affect the impressive throughput of Argon2i (despite seemingly enjoying significantly higher aAT).\r\n","lang":"eng"}],"ec_funded":1,"title":"Practical graphs for optimal side-channel resistant memory-hard functions","publication_status":"published","status":"public","department":[{"_id":"KrPi"}],"publisher":"ACM Press","_id":"6527","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","date_created":"2019-06-06T13:21:29Z","date_updated":"2021-01-12T08:07:53Z","oa_version":"Submitted Version","author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen","full_name":"Alwen, Joel F"},{"last_name":"Blocki","first_name":"Jeremiah","full_name":"Blocki, Jeremiah"},{"full_name":"Harsha, Ben","first_name":"Ben","last_name":"Harsha"}],"scopus_import":1,"day":"30","month":"10","publication_identifier":{"isbn":["9781450349468"]},"quality_controlled":"1","page":"1001-1017","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"publication":"Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security","main_file_link":[{"url":"https://eprint.iacr.org/2017/443","open_access":"1"}],"citation":{"ama":"Alwen JF, Blocki J, Harsha B. Practical graphs for optimal side-channel resistant memory-hard functions. In: Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security. ACM Press; 2017:1001-1017. doi:10.1145/3133956.3134031","ista":"Alwen JF, Blocki J, Harsha B. 2017. Practical graphs for optimal side-channel resistant memory-hard functions. Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security. CCS: Conference on Computer and Communications Security, 1001–1017.","ieee":"J. F. Alwen, J. Blocki, and B. Harsha, “Practical graphs for optimal side-channel resistant memory-hard functions,” in Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, Dallas, TX, USA, 2017, pp. 1001–1017.","apa":"Alwen, J. F., Blocki, J., & Harsha, B. (2017). Practical graphs for optimal side-channel resistant memory-hard functions. In Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security (pp. 1001–1017). Dallas, TX, USA: ACM Press. https://doi.org/10.1145/3133956.3134031","mla":"Alwen, Joel F., et al. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, ACM Press, 2017, pp. 1001–17, doi:10.1145/3133956.3134031.","short":"J.F. Alwen, J. Blocki, B. Harsha, in:, Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, ACM Press, 2017, pp. 1001–1017.","chicago":"Alwen, Joel F, Jeremiah Blocki, and Ben Harsha. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” In Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, 1001–17. ACM Press, 2017. https://doi.org/10.1145/3133956.3134031."},"oa":1,"language":[{"iso":"eng"}],"conference":{"location":"Dallas, TX, USA","start_date":"2017-10-30","end_date":"2017-11-03","name":"CCS: Conference on Computer and Communications Security"},"doi":"10.1145/3133956.3134031","date_published":"2017-10-30T00:00:00Z"},{"oa":1,"quality_controlled":"1","project":[{"grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord"}],"doi":"10.1242/dev.144915","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["09501991"]},"year":"2017","publication_status":"published","department":[{"_id":"AnKi"}],"publisher":"Company of Biologists","author":[{"first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"},{"full_name":"Rivron, Nicolas","last_name":"Rivron","first_name":"Nicolas"}],"date_updated":"2021-01-12T08:07:54Z","date_created":"2018-12-11T11:47:44Z","volume":144,"file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"publist_id":"7089","publication":"Development","citation":{"apa":"Kicheva, A., & Rivron, N. (2017). Creating to understand – developmental biology meets engineering in Paris. Development. Company of Biologists. https://doi.org/10.1242/dev.144915","ieee":"A. Kicheva and N. Rivron, “Creating to understand – developmental biology meets engineering in Paris,” Development, vol. 144, no. 5. Company of Biologists, pp. 733–736, 2017.","ista":"Kicheva A, Rivron N. 2017. Creating to understand – developmental biology meets engineering in Paris. Development. 144(5), 733–736.","ama":"Kicheva A, Rivron N. Creating to understand – developmental biology meets engineering in Paris. Development. 2017;144(5):733-736. doi:10.1242/dev.144915","chicago":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.144915.","short":"A. Kicheva, N. Rivron, Development 144 (2017) 733–736.","mla":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” Development, vol. 144, no. 5, Company of Biologists, 2017, pp. 733–36, doi:10.1242/dev.144915."},"page":"733 - 736","date_published":"2017-03-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","_id":"654","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Creating to understand – developmental biology meets engineering in Paris","ddc":["571"],"status":"public","intvolume":" 144","pubrep_id":"987","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2018-987-v1+1_2017_KichevaRivron__Creating_to.pdf","file_size":228206,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5139","checksum":"eef22a0f42a55b232cb2d1188a2322cb","date_created":"2018-12-12T10:15:20Z","date_updated":"2020-07-14T12:47:33Z"}],"type":"journal_article","abstract":[{"text":"In November 2016, developmental biologists, synthetic biologists and engineers gathered in Paris for a meeting called ‘Engineering the embryo’. The participants shared an interest in exploring how synthetic systems can reveal new principles of embryonic development, and how the in vitro manipulation and modeling of development using stem cells can be used to integrate ideas and expertise from physics, developmental biology and tissue engineering. As we review here, the conference pinpointed some of the challenges arising at the intersection of these fields, along with great enthusiasm for finding new approaches and collaborations.","lang":"eng"}],"issue":"5"},{"month":"08","publication_identifier":{"isbn":["9781509040964"]},"quality_controlled":"1","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.01666"}],"external_id":{"arxiv":["1702.01666"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"ISIT: International Symposium on Information Theory","end_date":"2017-06-30","location":"Aachen, Germany","start_date":"2017-06-25"},"doi":"10.1109/isit.2017.8006529","article_number":"8006529","ec_funded":1,"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"IEEE","year":"2017","date_updated":"2021-01-12T08:07:53Z","date_created":"2019-06-06T12:53:09Z","author":[{"full_name":"Skórski, Maciej","first_name":"Maciej","last_name":"Skórski","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"}],"scopus_import":1,"day":"09","publication":"2017 IEEE International Symposium on Information Theory (ISIT)","citation":{"ista":"Skórski M. 2017. On the complexity of estimating Rènyi divergences. 2017 IEEE International Symposium on Information Theory (ISIT). ISIT: International Symposium on Information Theory, 8006529.","apa":"Skórski, M. (2017). On the complexity of estimating Rènyi divergences. In 2017 IEEE International Symposium on Information Theory (ISIT). Aachen, Germany: IEEE. https://doi.org/10.1109/isit.2017.8006529","ieee":"M. Skórski, “On the complexity of estimating Rènyi divergences,” in 2017 IEEE International Symposium on Information Theory (ISIT), Aachen, Germany, 2017.","ama":"Skórski M. On the complexity of estimating Rènyi divergences. In: 2017 IEEE International Symposium on Information Theory (ISIT). IEEE; 2017. doi:10.1109/isit.2017.8006529","chicago":"Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” In 2017 IEEE International Symposium on Information Theory (ISIT). IEEE, 2017. https://doi.org/10.1109/isit.2017.8006529.","mla":"Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” 2017 IEEE International Symposium on Information Theory (ISIT), 8006529, IEEE, 2017, doi:10.1109/isit.2017.8006529.","short":"M. Skórski, in:, 2017 IEEE International Symposium on Information Theory (ISIT), IEEE, 2017."},"date_published":"2017-08-09T00:00:00Z","type":"conference","abstract":[{"text":"This paper studies the complexity of estimating Rényi divergences of discrete distributions: p observed from samples and the baseline distribution q known a priori. Extending the results of Acharya et al. (SODA'15) on estimating Rényi entropy, we present improved estimation techniques together with upper and lower bounds on the sample complexity. We show that, contrarily to estimating Rényi entropy where a sublinear (in the alphabet size) number of samples suffices, the sample complexity is heavily dependent on events occurring unlikely in q, and is unbounded in general (no matter what an estimation technique is used). For any divergence of integer order bigger than 1, we provide upper and lower bounds on the number of samples dependent on probabilities of p and q (the lower bounds hold for non-integer orders as well). We conclude that the worst-case sample complexity is polynomial in the alphabet size if and only if the probabilities of q are non-negligible. This gives theoretical insights into heuristics used in the applied literature to handle numerical instability, which occurs for small probabilities of q. Our result shows that they should be handled with care not only because of numerical issues, but also because of a blow up in the sample complexity.","lang":"eng"}],"status":"public","title":"On the complexity of estimating Rènyi divergences","_id":"6526","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"},{"doi":"10.7554/eLife.23136","language":[{"iso":"eng"}],"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,"quality_controlled":"1","month":"03","publication_identifier":{"issn":["2050084X"]},"author":[{"full_name":"Renault, Thibaud","last_name":"Renault","first_name":"Thibaud"},{"full_name":"Abraham, Anthony","first_name":"Anthony","last_name":"Abraham"},{"full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","first_name":"Tobias","last_name":"Bergmiller"},{"last_name":"Paradis","first_name":"Guillaume","full_name":"Paradis, Guillaume"},{"full_name":"Rainville, Simon","last_name":"Rainville","first_name":"Simon"},{"full_name":"Charpentier, Emmanuelle","last_name":"Charpentier","first_name":"Emmanuelle"},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"first_name":"Yuhai","last_name":"Tu","full_name":"Tu, Yuhai"},{"first_name":"Keiichi","last_name":"Namba","full_name":"Namba, Keiichi"},{"first_name":"James","last_name":"Keener","full_name":"Keener, James"},{"first_name":"Tohru","last_name":"Minamino","full_name":"Minamino, Tohru"},{"last_name":"Erhardt","first_name":"Marc","full_name":"Erhardt, Marc"}],"date_updated":"2021-01-12T08:07:55Z","date_created":"2018-12-11T11:47:44Z","volume":6,"year":"2017","publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:33Z","publist_id":"7082","license":"https://creativecommons.org/licenses/by/4.0/","article_number":"e23136","date_published":"2017-03-06T00:00:00Z","publication":"eLife","citation":{"mla":"Renault, Thibaud, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” ELife, vol. 6, e23136, eLife Sciences Publications, 2017, doi:10.7554/eLife.23136.","short":"T. Renault, A. Abraham, T. Bergmiller, G. Paradis, S. Rainville, E. Charpentier, C.C. Guet, Y. Tu, K. Namba, J. Keener, T. Minamino, M. Erhardt, ELife 6 (2017).","chicago":"Renault, Thibaud, Anthony Abraham, Tobias Bergmiller, Guillaume Paradis, Simon Rainville, Emmanuelle Charpentier, Calin C Guet, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.23136.","ama":"Renault T, Abraham A, Bergmiller T, et al. Bacterial flagella grow through an injection diffusion mechanism. eLife. 2017;6. doi:10.7554/eLife.23136","ista":"Renault T, Abraham A, Bergmiller T, Paradis G, Rainville S, Charpentier E, Guet CC, Tu Y, Namba K, Keener J, Minamino T, Erhardt M. 2017. Bacterial flagella grow through an injection diffusion mechanism. eLife. 6, e23136.","apa":"Renault, T., Abraham, A., Bergmiller, T., Paradis, G., Rainville, S., Charpentier, E., … Erhardt, M. (2017). Bacterial flagella grow through an injection diffusion mechanism. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.23136","ieee":"T. Renault et al., “Bacterial flagella grow through an injection diffusion mechanism,” eLife, vol. 6. eLife Sciences Publications, 2017."},"day":"06","has_accepted_license":"1","scopus_import":1,"pubrep_id":"904","file":[{"file_size":5520359,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2017-904-v1+1_elife-23136-v2.pdf","checksum":"39e1c3e82ddac83a30422fa72fa1a383","date_created":"2018-12-12T10:08:53Z","date_updated":"2020-07-14T12:47:33Z","relation":"main_file","file_id":"4716"},{"creator":"system","content_type":"application/pdf","file_size":11242920,"file_name":"IST-2017-904-v1+2_elife-23136-figures-v2.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:33Z","date_created":"2018-12-12T10:08:54Z","checksum":"a6d542253028f52e00aa29739ddffe8f","file_id":"4717","relation":"main_file"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"655","ddc":["579"],"status":"public","title":"Bacterial flagella grow through an injection diffusion mechanism","intvolume":" 6","abstract":[{"text":"The bacterial flagellum is a self-assembling nanomachine. The external flagellar filament, several times longer than a bacterial cell body, is made of a few tens of thousands subunits of a single protein: flagellin. A fundamental problem concerns the molecular mechanism of how the flagellum grows outside the cell, where no discernible energy source is available. Here, we monitored the dynamic assembly of individual flagella using in situ labelling and real-time immunostaining of elongating flagellar filaments. We report that the rate of flagellum growth, initially ~1,700 amino acids per second, decreases with length and that the previously proposed chain mechanism does not contribute to the filament elongation dynamics. Inhibition of the proton motive force-dependent export apparatus revealed a major contribution of substrate injection in driving filament elongation. The combination of experimental and mathematical evidence demonstrates that a simple, injection-diffusion mechanism controls bacterial flagella growth outside the cell.","lang":"eng"}],"type":"journal_article"},{"intvolume":" 114","status":"public","title":"Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo","_id":"657","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"12","abstract":[{"text":"Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo. The plant signaling molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors, is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts both cell-autonomously and noncell-autonomously to control embryonic vascular tissue formation and root initiation, respectively. Here we show that auxin response and ARF activity cell-autonomously control the asymmetric division of the first ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally initiates the ground tissue lineage and acts upstream of the regulatory network that controls ground tissue patterning and maintenance. Strikingly, whereas the SHR network depends on MP, this MP function is, at least in part, SHR independent. Our study therefore identifies auxin response as a regulator of ground tissue specification in the embryonic root, and reveals that ground tissue initiation and maintenance use different regulators and mechanisms. Moreover, our data provide a framework for the simultaneous formation of multiple cell types by the same transcriptional regulator.","lang":"eng"}],"page":"E2533 - E2539","citation":{"chicago":"Möller, Barbara, Colette Ten Hove, Daoquan Xiang, Nerys Williams, Lorena López, Saiko Yoshida, Margot Smit, Raju Datla, and Dolf Weijers. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1616493114.","mla":"Möller, Barbara, et al. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” PNAS, vol. 114, no. 12, National Academy of Sciences, 2017, pp. E2533–39, doi:10.1073/pnas.1616493114.","short":"B. Möller, C. Ten Hove, D. Xiang, N. Williams, L. López, S. Yoshida, M. Smit, R. Datla, D. Weijers, PNAS 114 (2017) E2533–E2539.","ista":"Möller B, Ten Hove C, Xiang D, Williams N, López L, Yoshida S, Smit M, Datla R, Weijers D. 2017. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 114(12), E2533–E2539.","apa":"Möller, B., Ten Hove, C., Xiang, D., Williams, N., López, L., Yoshida, S., … Weijers, D. (2017). Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1616493114","ieee":"B. Möller et al., “Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo,” PNAS, vol. 114, no. 12. National Academy of Sciences, pp. E2533–E2539, 2017.","ama":"Möller B, Ten Hove C, Xiang D, et al. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 2017;114(12):E2533-E2539. doi:10.1073/pnas.1616493114"},"publication":"PNAS","date_published":"2017-03-21T00:00:00Z","scopus_import":1,"day":"21","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2017","volume":114,"date_updated":"2021-01-12T08:08:02Z","date_created":"2018-12-11T11:47:45Z","author":[{"full_name":"Möller, Barbara","first_name":"Barbara","last_name":"Möller"},{"last_name":"Ten Hove","first_name":"Colette","full_name":"Ten Hove, Colette"},{"first_name":"Daoquan","last_name":"Xiang","full_name":"Xiang, Daoquan"},{"full_name":"Williams, Nerys","first_name":"Nerys","last_name":"Williams"},{"full_name":"López, Lorena","last_name":"López","first_name":"Lorena"},{"full_name":"Yoshida, Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","last_name":"Yoshida","first_name":"Saiko"},{"full_name":"Smit, Margot","last_name":"Smit","first_name":"Margot"},{"full_name":"Datla, Raju","last_name":"Datla","first_name":"Raju"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"}],"publist_id":"7076","quality_controlled":"1","oa":1,"external_id":{"pmid":["28265057"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373392/","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1616493114","publication_identifier":{"issn":["00278424"]},"month":"03"},{"scopus_import":1,"day":"15","month":"03","publication_identifier":{"issn":["19466234"]},"publication":"Science Translational Medicine","citation":{"ieee":"G. Novarino, “Modeling Alzheimer’s disease in mice with human neurons,” Science Translational Medicine, vol. 9, no. 381. American Association for the Advancement of Science, 2017.","apa":"Novarino, G. (2017). Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aam9867","ista":"Novarino G. 2017. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 9(381), eaam9867.","ama":"Novarino G. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 2017;9(381). doi:10.1126/scitranslmed.aam9867","chicago":"Novarino, Gaia. “Modeling Alzheimer’s Disease in Mice with Human Neurons.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aam9867.","short":"G. Novarino, Science Translational Medicine 9 (2017).","mla":"Novarino, Gaia. “Modeling Alzheimer’s Disease in Mice with Human Neurons.” Science Translational Medicine, vol. 9, no. 381, eaam9867, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aam9867."},"quality_controlled":"1","doi":"10.1126/scitranslmed.aam9867","date_published":"2017-03-15T00:00:00Z","language":[{"iso":"eng"}],"article_number":"eaam9867","type":"journal_article","abstract":[{"lang":"eng","text":"Human neurons transplanted into a mouse model for Alzheimer’s disease show human-specific vulnerability to β-amyloid plaques and may help to identify new therapeutic targets."}],"issue":"381","publist_id":"7079","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"656","year":"2017","status":"public","publication_status":"published","title":"Modeling Alzheimer's disease in mice with human neurons","intvolume":" 9","publisher":"American Association for the Advancement of Science","department":[{"_id":"GaNo"}],"author":[{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"}],"date_updated":"2021-01-12T08:07:59Z","date_created":"2018-12-11T11:47:45Z","volume":9,"oa_version":"None"},{"publication_identifier":{"issn":["16625218"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.3389/fnbot.2017.00008","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","oa":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"},"ec_funded":1,"publist_id":"7078","file_date_updated":"2020-07-14T12:47:33Z","article_number":"00008","volume":11,"date_updated":"2021-01-12T08:08:04Z","date_created":"2018-12-11T11:47:45Z","author":[{"first_name":"Ralf","last_name":"Der","full_name":"Der, Ralf"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","last_name":"Martius","full_name":"Martius, Georg S"}],"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publisher":"Frontiers Research Foundation","publication_status":"published","year":"2017","article_processing_charge":"Yes","has_accepted_license":"1","day":"16","scopus_import":1,"date_published":"2017-03-16T00:00:00Z","citation":{"ista":"Der R, Martius GS. 2017. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 11(MAR), 00008.","apa":"Der, R., & Martius, G. S. (2017). Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. Frontiers Research Foundation. https://doi.org/10.3389/fnbot.2017.00008","ieee":"R. Der and G. S. Martius, “Self organized behavior generation for musculoskeletal robots,” Frontiers in Neurorobotics, vol. 11, no. MAR. Frontiers Research Foundation, 2017.","ama":"Der R, Martius GS. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 2017;11(MAR). doi:10.3389/fnbot.2017.00008","chicago":"Der, Ralf, and Georg S Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” Frontiers in Neurorobotics. Frontiers Research Foundation, 2017. https://doi.org/10.3389/fnbot.2017.00008.","mla":"Der, Ralf, and Georg S. Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” Frontiers in Neurorobotics, vol. 11, no. MAR, 00008, Frontiers Research Foundation, 2017, doi:10.3389/fnbot.2017.00008.","short":"R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017)."},"publication":"Frontiers in Neurorobotics","issue":"MAR","abstract":[{"lang":"eng","text":"With the accelerated development of robot technologies, control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of specific objectives for the task at hand. While very successful in many applications, self-organized control schemes seem to be favored in large complex systems with unknown dynamics or which are difficult to model. Reasons are the expected scalability, robustness, and resilience of self-organizing systems. The paper presents a self-learning neurocontroller based on extrinsic differential plasticity introduced recently, applying it to an anthropomorphic musculoskeletal robot arm with attached objects of unknown physical dynamics. The central finding of the paper is the following effect: by the mere feedback through the internal dynamics of the object, the robot is learning to relate each of the objects with a very specific sensorimotor pattern. Specifically, an attached pendulum pilots the arm into a circular motion, a half-filled bottle produces axis oriented shaking behavior, a wheel is getting rotated, and wiping patterns emerge automatically in a table-plus-brush setting. By these object-specific dynamical patterns, the robot may be said to recognize the object's identity, or in other words, it discovers dynamical affordances of objects. Furthermore, when including hand coordinates obtained from a camera, a dedicated hand-eye coordination self-organizes spontaneously. These phenomena are discussed from a specific dynamical system perspective. Central is the dedicated working regime at the border to instability with its potentially infinite reservoir of (limit cycle) attractors "waiting" to be excited. Besides converging toward one of these attractors, variate behavior is also arising from a self-induced attractor morphing driven by the learning rule. We claim that experimental investigations with this anthropomorphic, self-learning robot not only generate interesting and potentially useful behaviors, but may also help to better understand what subjective human muscle feelings are, how they can be rooted in sensorimotor patterns, and how these concepts may feed back on robotics."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"IST-2017-903-v1+1_fnbot-11-00008.pdf","access_level":"open_access","file_size":8439566,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5371","date_updated":"2020-07-14T12:47:33Z","date_created":"2018-12-12T10:18:49Z","checksum":"b1bc43f96d1df3313c03032c2a46388d"}],"pubrep_id":"903","intvolume":" 11","status":"public","title":"Self organized behavior generation for musculoskeletal robots","ddc":["006"],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","_id":"658"},{"date_published":"2017-03-22T00:00:00Z","publication":"Nature Communications","citation":{"chicago":"Kage, Frieda, Moritz Winterhoff, Vanessa Dimchev, Jan Müller, Tobias Thalheim, Anika Freise, Stefan Brühmann, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14832.","mla":"Kage, Frieda, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications, vol. 8, 14832, Nature Publishing Group, 2017, doi:10.1038/ncomms14832.","short":"F. Kage, M. Winterhoff, V. Dimchev, J. Müller, T. Thalheim, A. Freise, S. Brühmann, J. Kollasser, J. Block, G.A. Dimchev, M. Geyer, H. Schnittler, C. Brakebusch, T. Stradal, M. Carlier, M.K. Sixt, J. Käs, J. Faix, K. Rottner, Nature Communications 8 (2017).","ista":"Kage F, Winterhoff M, Dimchev V, Müller J, Thalheim T, Freise A, Brühmann S, Kollasser J, Block J, Dimchev GA, Geyer M, Schnittler H, Brakebusch C, Stradal T, Carlier M, Sixt MK, Käs J, Faix J, Rottner K. 2017. FMNL formins boost lamellipodial force generation. Nature Communications. 8, 14832.","ieee":"F. Kage et al., “FMNL formins boost lamellipodial force generation,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","apa":"Kage, F., Winterhoff, M., Dimchev, V., Müller, J., Thalheim, T., Freise, A., … Rottner, K. (2017). FMNL formins boost lamellipodial force generation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14832","ama":"Kage F, Winterhoff M, Dimchev V, et al. FMNL formins boost lamellipodial force generation. Nature Communications. 2017;8. doi:10.1038/ncomms14832"},"day":"22","article_processing_charge":"No","has_accepted_license":"1","scopus_import":1,"pubrep_id":"902","file":[{"file_id":"5072","relation":"main_file","checksum":"dae30190291c3630e8102d8714a8d23e","date_updated":"2020-07-14T12:47:34Z","date_created":"2018-12-12T10:14:21Z","access_level":"open_access","file_name":"IST-2017-902-v1+1_Kage_et_al-2017-Nature_Communications.pdf","creator":"system","content_type":"application/pdf","file_size":9523746}],"oa_version":"Published Version","_id":"659","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"FMNL formins boost lamellipodial force generation","status":"public","intvolume":" 8","abstract":[{"text":"Migration frequently involves Rac-mediated protrusion of lamellipodia, formed by Arp2/3 complex-dependent branching thought to be crucial for force generation and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors targeting to the lamellipodium tip and shown here to nucleate and elongate actin filaments with complementary activities in vitro. In migrating B16-F1 melanoma cells, both formins contribute to the velocity of lamellipodium protrusion. Loss of FMNL2/3 function in melanoma cells and fibroblasts reduces lamellipodial width, actin filament density and -bundling, without changing patterns of Arp2/3 complex incorporation. Strikingly, in melanoma cells, FMNL2/3 gene inactivation almost completely abolishes protrusion forces exerted by lamellipodia and modifies their ultrastructural organization. Consistently, CRISPR/Cas-mediated depletion of FMNL2/3 in fibroblasts reduces both migration and capability of cells to move against viscous media. Together, we conclude that force generation in lamellipodia strongly depends on FMNL formin activity, operating in addition to Arp2/3 complex-dependent filament branching.","lang":"eng"}],"type":"journal_article","doi":"10.1038/ncomms14832","language":[{"iso":"eng"}],"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,"quality_controlled":"1","month":"03","publication_identifier":{"issn":["20411723"]},"author":[{"first_name":"Frieda","last_name":"Kage","full_name":"Kage, Frieda"},{"last_name":"Winterhoff","first_name":"Moritz","full_name":"Winterhoff, Moritz"},{"full_name":"Dimchev, Vanessa","first_name":"Vanessa","last_name":"Dimchev"},{"last_name":"Müller","first_name":"Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","full_name":"Müller, Jan"},{"first_name":"Tobias","last_name":"Thalheim","full_name":"Thalheim, Tobias"},{"last_name":"Freise","first_name":"Anika","full_name":"Freise, Anika"},{"full_name":"Brühmann, Stefan","first_name":"Stefan","last_name":"Brühmann"},{"first_name":"Jana","last_name":"Kollasser","full_name":"Kollasser, Jana"},{"full_name":"Block, Jennifer","first_name":"Jennifer","last_name":"Block"},{"last_name":"Dimchev","first_name":"Georgi A","full_name":"Dimchev, Georgi A"},{"full_name":"Geyer, Matthias","first_name":"Matthias","last_name":"Geyer"},{"last_name":"Schnittler","first_name":"Hams","full_name":"Schnittler, Hams"},{"full_name":"Brakebusch, Cord","first_name":"Cord","last_name":"Brakebusch"},{"last_name":"Stradal","first_name":"Theresia","full_name":"Stradal, Theresia"},{"full_name":"Carlier, Marie","last_name":"Carlier","first_name":"Marie"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"last_name":"Käs","first_name":"Josef","full_name":"Käs, Josef"},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"}],"date_updated":"2021-01-12T08:08:06Z","date_created":"2018-12-11T11:47:46Z","volume":8,"year":"2017","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:47:34Z","publist_id":"7075","article_number":"14832"},{"publication":"PNAS","citation":{"chicago":"Rickman, Jamie, Christian F Düllberg, Nicholas Cade, Lewis Griffin, and Thomas Surrey. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1620274114.","short":"J. Rickman, C.F. Düllberg, N. Cade, L. Griffin, T. Surrey, PNAS 114 (2017) 3427–3432.","mla":"Rickman, Jamie, et al. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS, vol. 114, no. 13, National Academy of Sciences, 2017, pp. 3427–32, doi:10.1073/pnas.1620274114.","ieee":"J. Rickman, C. F. Düllberg, N. Cade, L. Griffin, and T. Surrey, “Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation,” PNAS, vol. 114, no. 13. National Academy of Sciences, pp. 3427–3432, 2017.","apa":"Rickman, J., Düllberg, C. F., Cade, N., Griffin, L., & Surrey, T. (2017). Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1620274114","ista":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. 2017. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 114(13), 3427–3432.","ama":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 2017;114(13):3427-3432. doi:10.1073/pnas.1620274114"},"page":"3427 - 3432","date_published":"2017-03-28T00:00:00Z","scopus_import":1,"day":"28","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"660","title":"Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation","status":"public","intvolume":" 114","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Growing microtubules are protected from depolymerization by the presence of a GTP or GDP/Pi cap. End-binding proteins of the EB1 family bind to the stabilizing cap, allowing monitoring of its size in real time. The cap size has been shown to correlate with instantaneous microtubule stability. Here we have quantitatively characterized the properties of cap size fluctuations during steadystate growth and have developed a theory predicting their timescale and amplitude from the kinetics of microtubule growth and cap maturation. In contrast to growth speed fluctuations, cap size fluctuations show a characteristic timescale, which is defined by the lifetime of the cap sites. Growth fluctuations affect the amplitude of cap size fluctuations; however, cap size does not affect growth speed, indicating that microtubules are far from instability during most of their time of growth. Our theory provides the basis for a quantitative understanding of microtubule stability fluctuations during steady-state growth.","lang":"eng"}],"issue":"13","external_id":{"pmid":["28280102"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5380103/","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.1073/pnas.1620274114","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["00278424"]},"year":"2017","acknowledgement":"We thank Philippe Cluzel for helpful discussions and Gunnar Pruessner for data analysis advice. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK Grant FC001163, Medical Research Council Grant FC001163, and Wellcome Trust Grant FC001163. This work was also supported by European Research Council Advanced Grant Project 323042 (to C.D. and T.S.).","pmid":1,"publication_status":"published","department":[{"_id":"MaLo"}],"publisher":"National Academy of Sciences","author":[{"full_name":"Rickman, Jamie","first_name":"Jamie","last_name":"Rickman"},{"orcid":"0000-0001-6335-9748","id":"459064DC-F248-11E8-B48F-1D18A9856A87","last_name":"Düllberg","first_name":"Christian F","full_name":"Düllberg, Christian F"},{"last_name":"Cade","first_name":"Nicholas","full_name":"Cade, Nicholas"},{"last_name":"Griffin","first_name":"Lewis","full_name":"Griffin, Lewis"},{"full_name":"Surrey, Thomas","last_name":"Surrey","first_name":"Thomas"}],"date_created":"2018-12-11T11:47:46Z","date_updated":"2021-01-12T08:08:09Z","volume":114,"publist_id":"7073"},{"author":[{"full_name":"Shi, Liang","first_name":"Liang","last_name":"Shi"},{"last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"},{"last_name":"Rampp","first_name":"Markus","full_name":"Rampp, Markus"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"}],"date_updated":"2021-01-12T08:08:15Z","date_created":"2018-12-11T11:47:47Z","volume":29,"year":"2017","publication_status":"published","publisher":"American Institute of Physics","department":[{"_id":"BjHo"}],"publist_id":"7072","article_number":"044107","doi":"10.1063/1.4981525","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.01714"}],"quality_controlled":"1","project":[{"name":"Astrophysical instability of currents and turbulences","grant_number":"SFB 963 TP A8","_id":"2511D90C-B435-11E9-9278-68D0E5697425"}],"month":"04","publication_identifier":{"issn":["10706631"]},"oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"662","status":"public","title":"Hydrodynamic turbulence in quasi Keplerian rotating flows","intvolume":" 29","abstract":[{"lang":"eng","text":"We report a direct-numerical-simulation study of the Taylor-Couette flow in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian rotating flow has been investigated for decades as a simplified model system to study the origin of turbulence in accretion disks that is not fully understood. The flow in this study is axially periodic and thus the experimental end-wall effects on the stability of the flow are avoided. Using optimal linear perturbations as initial conditions, our simulations find no sustained turbulence: the strong initial perturbations distort the velocity profile and trigger turbulence that eventually decays."}],"issue":"4","type":"journal_article","date_published":"2017-04-01T00:00:00Z","publication":"Physics of Fluids","citation":{"ama":"Shi L, Hof B, Rampp M, Avila M. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 2017;29(4). doi:10.1063/1.4981525","ista":"Shi L, Hof B, Rampp M, Avila M. 2017. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 29(4), 044107.","apa":"Shi, L., Hof, B., Rampp, M., & Avila, M. (2017). Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. American Institute of Physics. https://doi.org/10.1063/1.4981525","ieee":"L. Shi, B. Hof, M. Rampp, and M. Avila, “Hydrodynamic turbulence in quasi Keplerian rotating flows,” Physics of Fluids, vol. 29, no. 4. American Institute of Physics, 2017.","mla":"Shi, Liang, et al. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” Physics of Fluids, vol. 29, no. 4, 044107, American Institute of Physics, 2017, doi:10.1063/1.4981525.","short":"L. Shi, B. Hof, M. Rampp, M. Avila, Physics of Fluids 29 (2017).","chicago":"Shi, Liang, Björn Hof, Markus Rampp, and Marc Avila. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” Physics of Fluids. American Institute of Physics, 2017. https://doi.org/10.1063/1.4981525."},"day":"01","scopus_import":1}]