[{"file_date_updated":"2020-07-14T12:47:33Z","publist_id":"7092","ec_funded":1,"date_updated":"2022-06-10T09:55:08Z","date_created":"2018-12-11T11:47:43Z","volume":49,"author":[{"last_name":"Makohon Moore","first_name":"Alvin","full_name":"Makohon Moore, Alvin"},{"full_name":"Zhang, Ming","last_name":"Zhang","first_name":"Ming"},{"full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","first_name":"Johannes","last_name":"Reiter"},{"first_name":"Ivana","last_name":"Božić","full_name":"Božić, Ivana"},{"full_name":"Allen, Benjamin","last_name":"Allen","first_name":"Benjamin"},{"full_name":"Kundu, Deepanjan","last_name":"Kundu","first_name":"Deepanjan","id":"1d4c0f4f-e8a3-11ec-a351-e36772758c45"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Wong, Fay","first_name":"Fay","last_name":"Wong"},{"first_name":"Yuchen","last_name":"Jiao","full_name":"Jiao, Yuchen"},{"first_name":"Zachary","last_name":"Kohutek","full_name":"Kohutek, Zachary"},{"first_name":"Jungeui","last_name":"Hong","full_name":"Hong, Jungeui"},{"full_name":"Attiyeh, Marc","last_name":"Attiyeh","first_name":"Marc"},{"full_name":"Javier, Breanna","first_name":"Breanna","last_name":"Javier"},{"last_name":"Wood","first_name":"Laura","full_name":"Wood, Laura"},{"last_name":"Hruban","first_name":"Ralph","full_name":"Hruban, Ralph"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"},{"last_name":"Papadopoulos","first_name":"Nickolas","full_name":"Papadopoulos, Nickolas"},{"full_name":"Kinzler, Kenneth","last_name":"Kinzler","first_name":"Kenneth"},{"full_name":"Vogelstein, Bert","first_name":"Bert","last_name":"Vogelstein"},{"last_name":"Iacobuzio Donahue","first_name":"Christine","full_name":"Iacobuzio Donahue, Christine"}],"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"KrCh"}],"acknowledgement":"We thank the Memorial Sloan Kettering Cancer Center Molecular Cytology core facility for immunohistochemistry staining. This work was supported by Office of Naval Research grant N00014-16-1-2914, the Bill and Melinda Gates Foundation (OPP1148627), and a gift from B. Wu and E. Larson (M.A.N.), National Institutes of Health grants CA179991 (C.A.I.-D. and I.B.), F31 CA180682 (A.P.M.-M.), CA43460 (B.V.), and P50 CA62924, the Monastra Foundation, the Virginia and D.K. Ludwig Fund for Cancer Research, the Lustgarten Foundation for Pancreatic Cancer Research, the Sol Goldman Center for Pancreatic Cancer Research, the Sol Goldman Sequencing Center, ERC Start grant 279307: Graph Games (J.G.R., D.K., and C.K.), Austrian Science Fund (FWF) grant P23499-N23 (J.G.R., D.K., and C.K.), and FWF NFN grant S11407-N23 RiSE/SHiNE (J.G.R., D.K., and C.K.).","year":"2017","pmid":1,"month":"03","publication_identifier":{"issn":["10614036"]},"language":[{"iso":"eng"}],"doi":"10.1038/ng.3764","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"}],"oa":1,"external_id":{"pmid":["28092682"]},"abstract":[{"lang":"eng","text":"The extent of heterogeneity among driver gene mutations present in naturally occurring metastases - that is, treatment-naive metastatic disease - is largely unknown. To address this issue, we carried out 60× whole-genome sequencing of 26 metastases from four patients with pancreatic cancer. We found that identical mutations in known driver genes were present in every metastatic lesion for each patient studied. Passenger gene mutations, which do not have known or predicted functional consequences, accounted for all intratumoral heterogeneity. Even with respect to these passenger mutations, our analysis suggests that the genetic similarity among the founding cells of metastases was higher than that expected for any two cells randomly taken from a normal tissue. The uniformity of known driver gene mutations among metastases in the same patient has critical and encouraging implications for the success of future targeted therapies in advanced-stage disease."}],"issue":"3","type":"journal_article","oa_version":"Submitted Version","file":[{"file_id":"7050","relation":"main_file","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-11-19T08:13:50Z","checksum":"e442dc3b7420a36ec805e9bb45cc1a2e","file_name":"2017_NatureGenetics_Makohon.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":908099}],"status":"public","ddc":["000"],"title":"Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer","intvolume":" 49","_id":"653","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2017-03-01T00:00:00Z","article_type":"original","page":"358 - 366","publication":"Nature Genetics","citation":{"ama":"Makohon Moore A, Zhang M, Reiter J, et al. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. 2017;49(3):358-366. doi:10.1038/ng.3764","ista":"Makohon Moore A, Zhang M, Reiter J, Božić I, Allen B, Kundu D, Chatterjee K, Wong F, Jiao Y, Kohutek Z, Hong J, Attiyeh M, Javier B, Wood L, Hruban R, Nowak M, Papadopoulos N, Kinzler K, Vogelstein B, Iacobuzio Donahue C. 2017. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. 49(3), 358–366.","apa":"Makohon Moore, A., Zhang, M., Reiter, J., Božić, I., Allen, B., Kundu, D., … Iacobuzio Donahue, C. (2017). Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. Nature Publishing Group. https://doi.org/10.1038/ng.3764","ieee":"A. Makohon Moore et al., “Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer,” Nature Genetics, vol. 49, no. 3. Nature Publishing Group, pp. 358–366, 2017.","mla":"Makohon Moore, Alvin, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” Nature Genetics, vol. 49, no. 3, Nature Publishing Group, 2017, pp. 358–66, doi:10.1038/ng.3764.","short":"A. Makohon Moore, M. Zhang, J. Reiter, I. Božić, B. Allen, D. Kundu, K. Chatterjee, F. Wong, Y. Jiao, Z. Kohutek, J. Hong, M. Attiyeh, B. Javier, L. Wood, R. Hruban, M. Nowak, N. Papadopoulos, K. Kinzler, B. Vogelstein, C. Iacobuzio Donahue, Nature Genetics 49 (2017) 358–366.","chicago":"Makohon Moore, Alvin, Ming Zhang, Johannes Reiter, Ivana Božić, Benjamin Allen, Deepanjan Kundu, Krishnendu Chatterjee, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” Nature Genetics. Nature Publishing Group, 2017. https://doi.org/10.1038/ng.3764."}},{"title":"Practical graphs for optimal side-channel resistant memory-hard functions","publication_status":"published","status":"public","publisher":"ACM Press","department":[{"_id":"KrPi"}],"_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":[{"full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen"},{"first_name":"Jeremiah","last_name":"Blocki","full_name":"Blocki, Jeremiah"},{"full_name":"Harsha, Ben","last_name":"Harsha","first_name":"Ben"}],"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,"quality_controlled":"1","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"page":"1001-1017","publication":"Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/443"}],"oa":1,"citation":{"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.","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.","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.","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","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","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.","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."},"language":[{"iso":"eng"}],"conference":{"end_date":"2017-11-03","location":"Dallas, TX, USA","start_date":"2017-10-30","name":"CCS: Conference on Computer and Communications Security"},"date_published":"2017-10-30T00:00:00Z","doi":"10.1145/3133956.3134031","scopus_import":1,"day":"30","month":"10","publication_identifier":{"isbn":["9781450349468"]}},{"_id":"654","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 144","status":"public","ddc":["571"],"title":"Creating to understand – developmental biology meets engineering in Paris","pubrep_id":"987","oa_version":"Submitted Version","file":[{"file_size":228206,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2018-987-v1+1_2017_KichevaRivron__Creating_to.pdf","checksum":"eef22a0f42a55b232cb2d1188a2322cb","date_created":"2018-12-12T10:15:20Z","date_updated":"2020-07-14T12:47:33Z","relation":"main_file","file_id":"5139"}],"type":"journal_article","issue":"5","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"}],"citation":{"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.","short":"A. Kicheva, N. Rivron, Development 144 (2017) 733–736.","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.","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","ista":"Kicheva A, Rivron N. 2017. Creating to understand – developmental biology meets engineering in Paris. Development. 144(5), 733–736.","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.","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"},"publication":"Development","page":"733 - 736","date_published":"2017-03-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","year":"2017","department":[{"_id":"AnKi"}],"publisher":"Company of Biologists","publication_status":"published","author":[{"orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna","full_name":"Kicheva, Anna"},{"last_name":"Rivron","first_name":"Nicolas","full_name":"Rivron, Nicolas"}],"volume":144,"date_updated":"2021-01-12T08:07:54Z","date_created":"2018-12-11T11:47:44Z","ec_funded":1,"publist_id":"7089","file_date_updated":"2020-07-14T12:47:33Z","oa":1,"project":[{"grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020"}],"quality_controlled":"1","doi":"10.1242/dev.144915","language":[{"iso":"eng"}],"publication_identifier":{"issn":["09501991"]},"month":"03"},{"date_published":"2017-08-09T00:00:00Z","citation":{"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","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.","ieee":"M. Skórski, “On the complexity of estimating Rènyi divergences,” in 2017 IEEE International Symposium on Information Theory (ISIT), Aachen, Germany, 2017.","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","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.","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."},"publication":"2017 IEEE International Symposium on Information Theory (ISIT)","day":"09","scopus_import":1,"oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6526","title":"On the complexity of estimating Rènyi divergences","status":"public","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"}],"type":"conference","doi":"10.1109/isit.2017.8006529","conference":{"location":"Aachen, Germany","start_date":"2017-06-25","end_date":"2017-06-30","name":"ISIT: International Symposium on Information Theory"},"language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1702.01666"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.01666"}],"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publication_identifier":{"isbn":["9781509040964"]},"month":"08","author":[{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski","full_name":"Skórski, Maciej"}],"date_updated":"2021-01-12T08:07:53Z","date_created":"2019-06-06T12:53:09Z","year":"2017","publisher":"IEEE","department":[{"_id":"KrPi"}],"publication_status":"published","ec_funded":1,"article_number":"8006529"},{"publication_identifier":{"issn":["2050084X"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.7554/eLife.23136","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"},"license":"https://creativecommons.org/licenses/by/4.0/","publist_id":"7082","file_date_updated":"2020-07-14T12:47:33Z","article_number":"e23136","volume":6,"date_updated":"2021-01-12T08:07:55Z","date_created":"2018-12-11T11:47:44Z","author":[{"first_name":"Thibaud","last_name":"Renault","full_name":"Renault, Thibaud"},{"last_name":"Abraham","first_name":"Anthony","full_name":"Abraham, Anthony"},{"orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias"},{"first_name":"Guillaume","last_name":"Paradis","full_name":"Paradis, Guillaume"},{"first_name":"Simon","last_name":"Rainville","full_name":"Rainville, Simon"},{"first_name":"Emmanuelle","last_name":"Charpentier","full_name":"Charpentier, Emmanuelle"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"first_name":"Yuhai","last_name":"Tu","full_name":"Tu, Yuhai"},{"last_name":"Namba","first_name":"Keiichi","full_name":"Namba, Keiichi"},{"full_name":"Keener, James","first_name":"James","last_name":"Keener"},{"full_name":"Minamino, Tohru","last_name":"Minamino","first_name":"Tohru"},{"last_name":"Erhardt","first_name":"Marc","full_name":"Erhardt, Marc"}],"department":[{"_id":"CaGu"}],"publisher":"eLife Sciences Publications","publication_status":"published","year":"2017","has_accepted_license":"1","day":"06","scopus_import":1,"date_published":"2017-03-06T00:00:00Z","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.","ieee":"T. Renault et al., “Bacterial flagella grow through an injection diffusion mechanism,” eLife, vol. 6. eLife Sciences Publications, 2017.","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"},"publication":"eLife","abstract":[{"lang":"eng","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."}],"type":"journal_article","file":[{"file_name":"IST-2017-904-v1+1_elife-23136-v2.pdf","access_level":"open_access","file_size":5520359,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4716","date_created":"2018-12-12T10:08:53Z","date_updated":"2020-07-14T12:47:33Z","checksum":"39e1c3e82ddac83a30422fa72fa1a383"},{"creator":"system","content_type":"application/pdf","file_size":11242920,"access_level":"open_access","file_name":"IST-2017-904-v1+2_elife-23136-figures-v2.pdf","checksum":"a6d542253028f52e00aa29739ddffe8f","date_created":"2018-12-12T10:08:54Z","date_updated":"2020-07-14T12:47:33Z","file_id":"4717","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"904","intvolume":" 6","title":"Bacterial flagella grow through an injection diffusion mechanism","status":"public","ddc":["579"],"_id":"655","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"external_id":{"pmid":["28265057"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373392/"}],"quality_controlled":"1","doi":"10.1073/pnas.1616493114","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00278424"]},"month":"03","pmid":1,"year":"2017","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"full_name":"Möller, Barbara","first_name":"Barbara","last_name":"Möller"},{"first_name":"Colette","last_name":"Ten Hove","full_name":"Ten Hove, Colette"},{"last_name":"Xiang","first_name":"Daoquan","full_name":"Xiang, Daoquan"},{"last_name":"Williams","first_name":"Nerys","full_name":"Williams, Nerys"},{"last_name":"López","first_name":"Lorena","full_name":"López, Lorena"},{"full_name":"Yoshida, Saiko","first_name":"Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Smit, Margot","first_name":"Margot","last_name":"Smit"},{"full_name":"Datla, Raju","last_name":"Datla","first_name":"Raju"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"}],"volume":114,"date_updated":"2021-01-12T08:08:02Z","date_created":"2018-12-11T11:47:45Z","publist_id":"7076","citation":{"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.","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.","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.","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","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.","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","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."},"publication":"PNAS","page":"E2533 - E2539","date_published":"2017-03-21T00:00:00Z","scopus_import":1,"day":"21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"657","intvolume":" 114","status":"public","title":"Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo","oa_version":"Submitted Version","type":"journal_article","issue":"12","abstract":[{"lang":"eng","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."}]},{"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","department":[{"_id":"GaNo"}],"publisher":"American Association for the Advancement of Science","intvolume":" 9","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","oa_version":"None","volume":9,"article_number":"eaam9867","type":"journal_article","abstract":[{"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.","lang":"eng"}],"publist_id":"7079","issue":"381","publication":"Science Translational Medicine","citation":{"ama":"Novarino G. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 2017;9(381). doi:10.1126/scitranslmed.aam9867","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.","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.","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."},"quality_controlled":"1","doi":"10.1126/scitranslmed.aam9867","date_published":"2017-03-15T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"15","month":"03","publication_identifier":{"issn":["19466234"]}},{"scopus_import":1,"article_processing_charge":"Yes","has_accepted_license":"1","day":"16","citation":{"ama":"Der R, Martius GS. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 2017;11(MAR). doi:10.3389/fnbot.2017.00008","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.","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).","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."},"publication":"Frontiers in Neurorobotics","date_published":"2017-03-16T00:00:00Z","type":"journal_article","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."}],"_id":"658","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","intvolume":" 11","ddc":["006"],"status":"public","title":"Self organized behavior generation for musculoskeletal robots","pubrep_id":"903","file":[{"date_updated":"2020-07-14T12:47:33Z","date_created":"2018-12-12T10:18:49Z","checksum":"b1bc43f96d1df3313c03032c2a46388d","file_id":"5371","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":8439566,"file_name":"IST-2017-903-v1+1_fnbot-11-00008.pdf","access_level":"open_access"}],"oa_version":"Published Version","publication_identifier":{"issn":["16625218"]},"month":"03","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"},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","doi":"10.3389/fnbot.2017.00008","language":[{"iso":"eng"}],"article_number":"00008","publist_id":"7078","ec_funded":1,"file_date_updated":"2020-07-14T12:47:33Z","year":"2017","publisher":"Frontiers Research Foundation","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publication_status":"published","author":[{"first_name":"Ralf","last_name":"Der","full_name":"Der, Ralf"},{"full_name":"Martius, Georg S","first_name":"Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"}],"volume":11,"date_updated":"2021-01-12T08:08:04Z","date_created":"2018-12-11T11:47:45Z"},{"type":"journal_article","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"}],"intvolume":" 8","title":"FMNL formins boost lamellipodial force generation","ddc":["570"],"status":"public","_id":"659","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:34Z","date_created":"2018-12-12T10:14:21Z","checksum":"dae30190291c3630e8102d8714a8d23e","relation":"main_file","file_id":"5072","file_size":9523746,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-902-v1+1_Kage_et_al-2017-Nature_Communications.pdf","access_level":"open_access"}],"pubrep_id":"902","scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"22","citation":{"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","ieee":"F. Kage et al., “FMNL formins boost lamellipodial force generation,” Nature Communications, vol. 8. Nature Publishing Group, 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.","ama":"Kage F, Winterhoff M, Dimchev V, et al. FMNL formins boost lamellipodial force generation. Nature Communications. 2017;8. doi:10.1038/ncomms14832","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.","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).","mla":"Kage, Frieda, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications, vol. 8, 14832, Nature Publishing Group, 2017, doi:10.1038/ncomms14832."},"publication":"Nature Communications","date_published":"2017-03-22T00:00:00Z","article_number":"14832","publist_id":"7075","file_date_updated":"2020-07-14T12:47:34Z","publisher":"Nature Publishing Group","department":[{"_id":"MiSi"}],"publication_status":"published","year":"2017","volume":8,"date_created":"2018-12-11T11:47:46Z","date_updated":"2021-01-12T08:08:06Z","author":[{"first_name":"Frieda","last_name":"Kage","full_name":"Kage, Frieda"},{"last_name":"Winterhoff","first_name":"Moritz","full_name":"Winterhoff, Moritz"},{"first_name":"Vanessa","last_name":"Dimchev","full_name":"Dimchev, Vanessa"},{"id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan","last_name":"Müller","full_name":"Müller, Jan"},{"first_name":"Tobias","last_name":"Thalheim","full_name":"Thalheim, Tobias"},{"first_name":"Anika","last_name":"Freise","full_name":"Freise, Anika"},{"last_name":"Brühmann","first_name":"Stefan","full_name":"Brühmann, Stefan"},{"full_name":"Kollasser, Jana","last_name":"Kollasser","first_name":"Jana"},{"full_name":"Block, Jennifer","last_name":"Block","first_name":"Jennifer"},{"first_name":"Georgi A","last_name":"Dimchev","full_name":"Dimchev, Georgi A"},{"full_name":"Geyer, Matthias","first_name":"Matthias","last_name":"Geyer"},{"full_name":"Schnittler, Hams","first_name":"Hams","last_name":"Schnittler"},{"first_name":"Cord","last_name":"Brakebusch","full_name":"Brakebusch, Cord"},{"first_name":"Theresia","last_name":"Stradal","full_name":"Stradal, Theresia"},{"full_name":"Carlier, Marie","last_name":"Carlier","first_name":"Marie"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Käs, Josef","first_name":"Josef","last_name":"Käs"},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"}],"publication_identifier":{"issn":["20411723"]},"month":"03","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"},"language":[{"iso":"eng"}],"doi":"10.1038/ncomms14832"},{"month":"03","publication_identifier":{"issn":["00278424"]},"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"}],"publist_id":"7073","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":[{"first_name":"Jamie","last_name":"Rickman","full_name":"Rickman, Jamie"},{"orcid":"0000-0001-6335-9748","id":"459064DC-F248-11E8-B48F-1D18A9856A87","last_name":"Düllberg","first_name":"Christian F","full_name":"Düllberg, Christian F"},{"full_name":"Cade, Nicholas","last_name":"Cade","first_name":"Nicholas"},{"full_name":"Griffin, Lewis","first_name":"Lewis","last_name":"Griffin"},{"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,"scopus_import":1,"day":"28","publication":"PNAS","citation":{"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","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.","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","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.","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.","short":"J. Rickman, C.F. Düllberg, N. Cade, L. Griffin, T. Surrey, PNAS 114 (2017) 3427–3432.","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."},"page":"3427 - 3432","date_published":"2017-03-28T00:00:00Z","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","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"},{"scopus_import":1,"day":"01","publication":"Physics of Fluids","citation":{"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.","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."},"date_published":"2017-04-01T00:00:00Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"4","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"662","title":"Hydrodynamic turbulence in quasi Keplerian rotating flows","status":"public","intvolume":" 29","oa_version":"Submitted Version","month":"04","publication_identifier":{"issn":["10706631"]},"main_file_link":[{"url":"https://arxiv.org/abs/1703.01714","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"_id":"2511D90C-B435-11E9-9278-68D0E5697425","grant_number":"SFB 963 TP A8","name":"Astrophysical instability of currents and turbulences"}],"doi":"10.1063/1.4981525","language":[{"iso":"eng"}],"article_number":"044107","publist_id":"7072","year":"2017","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"American Institute of Physics","author":[{"full_name":"Shi, Liang","last_name":"Shi","first_name":"Liang"},{"full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"},{"first_name":"Markus","last_name":"Rampp","full_name":"Rampp, Markus"},{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"}],"date_created":"2018-12-11T11:47:47Z","date_updated":"2021-01-12T08:08:15Z","volume":29},{"author":[{"full_name":"Kong, Hui","first_name":"Hui","last_name":"Kong","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941"},{"last_name":"Bogomolov","first_name":"Sergiy","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy"},{"first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian"},{"last_name":"Jiang","first_name":"Yu","full_name":"Jiang, Yu"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"}],"date_created":"2018-12-11T11:47:47Z","date_updated":"2021-01-12T08:08:17Z","year":"2017","department":[{"_id":"ToHe"}],"publisher":"ACM","publication_status":"published","publist_id":"7067","file_date_updated":"2020-07-14T12:47:34Z","doi":"10.1145/3049797.3049814","conference":{"start_date":"2017-04-18","location":"Pittsburgh, PA, United States","end_date":"2017-04-20","name":"HSCC: Hybrid Systems Computation and Control "},"language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","publication_identifier":{"isbn":["978-145034590-3"]},"month":"04","pubrep_id":"817","oa_version":"Submitted Version","file":[{"checksum":"b7667434cbf5b5f0ade3bea1dbe5bf63","date_updated":"2020-07-14T12:47:34Z","date_created":"2018-12-12T10:11:20Z","file_id":"4873","relation":"main_file","creator":"system","file_size":1650530,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-817-v1+1_p163-kong.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"663","ddc":["000"],"title":"Safety verification of nonlinear hybrid systems based on invariant clusters","status":"public","abstract":[{"lang":"eng","text":"In this paper, we propose an approach to automatically compute invariant clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for an ordinary differential equation (ODE) is a multivariate polynomial invariant g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete invariants by assigning different values to u→ so that every trajectory of the system can be overapproximated precisely by the intersection of a group of concrete invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant cluster can be obtained by first computing the remainder of the Lie derivative of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations obtained from the coefficients of the remainder. Based on invariant clusters and sum-of-squares (SOS) programming, we present a new method for the safety verification of hybrid systems. Experiments on nonlinear benchmark systems from biology and control theory show that our approach is efficient. "}],"type":"conference","date_published":"2017-04-01T00:00:00Z","citation":{"ama":"Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. Safety verification of nonlinear hybrid systems based on invariant clusters. In: Proceedings of the 20th International Conference on Hybrid Systems. ACM; 2017:163-172. doi:10.1145/3049797.3049814","ieee":"H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, and T. A. Henzinger, “Safety verification of nonlinear hybrid systems based on invariant clusters,” in Proceedings of the 20th International Conference on Hybrid Systems, Pittsburgh, PA, United States, 2017, pp. 163–172.","apa":"Kong, H., Bogomolov, S., Schilling, C., Jiang, Y., & Henzinger, T. A. (2017). Safety verification of nonlinear hybrid systems based on invariant clusters. In Proceedings of the 20th International Conference on Hybrid Systems (pp. 163–172). Pittsburgh, PA, United States: ACM. https://doi.org/10.1145/3049797.3049814","ista":"Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. 2017. Safety verification of nonlinear hybrid systems based on invariant clusters. Proceedings of the 20th International Conference on Hybrid Systems. HSCC: Hybrid Systems Computation and Control , 163–172.","short":"H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, T.A. Henzinger, in:, Proceedings of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–172.","mla":"Kong, Hui, et al. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” Proceedings of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–72, doi:10.1145/3049797.3049814.","chicago":"Kong, Hui, Sergiy Bogomolov, Christian Schilling, Yu Jiang, and Thomas A Henzinger. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” In Proceedings of the 20th International Conference on Hybrid Systems, 163–72. ACM, 2017. https://doi.org/10.1145/3049797.3049814."},"publication":"Proceedings of the 20th International Conference on Hybrid Systems","page":"163 - 172","has_accepted_license":"1","day":"01","scopus_import":1},{"abstract":[{"lang":"eng","text":"Perinatal exposure to penicillin may result in longlasting gut and behavioral changes."}],"publist_id":"7060","issue":"387","article_number":"2786","type":"journal_article","author":[{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"}],"date_updated":"2021-01-12T08:08:30Z","date_created":"2018-12-11T11:47:48Z","volume":9,"oa_version":"None","_id":"667","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2017","title":"The antisocial side of antibiotics","status":"public","publication_status":"published","department":[{"_id":"GaNo"}],"intvolume":" 9","publisher":"American Association for the Advancement of Science","day":"26","month":"04","publication_identifier":{"issn":["19466234"]},"scopus_import":1,"doi":"10.1126/scitranslmed.aan2786","date_published":"2017-04-26T00:00:00Z","language":[{"iso":"eng"}],"publication":"Science Translational Medicine","citation":{"ista":"Novarino G. 2017. The antisocial side of antibiotics. Science Translational Medicine. 9(387), 2786.","ieee":"G. Novarino, “The antisocial side of antibiotics,” Science Translational Medicine, vol. 9, no. 387. American Association for the Advancement of Science, 2017.","apa":"Novarino, G. (2017). The antisocial side of antibiotics. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan2786","ama":"Novarino G. The antisocial side of antibiotics. Science Translational Medicine. 2017;9(387). doi:10.1126/scitranslmed.aan2786","chicago":"Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan2786.","mla":"Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational Medicine, vol. 9, no. 387, 2786, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aan2786.","short":"G. Novarino, Science Translational Medicine 9 (2017)."},"quality_controlled":"1"},{"citation":{"ieee":"M. Horsthemke et al., “Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion,” Journal of Biological Chemistry, vol. 292, no. 17. American Society for Biochemistry and Molecular Biology, pp. 7258–7273, 2017.","apa":"Horsthemke, M., Bachg, A., Groll, K., Moyzio, S., Müther, B., Hemkemeyer, S., … Hanley, P. (2017). Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M116.766923","ista":"Horsthemke M, Bachg A, Groll K, Moyzio S, Müther B, Hemkemeyer S, Wedlich Söldner R, Sixt MK, Tacke S, Bähler M, Hanley P. 2017. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. 292(17), 7258–7273.","ama":"Horsthemke M, Bachg A, Groll K, et al. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. 2017;292(17):7258-7273. doi:10.1074/jbc.M116.766923","chicago":"Horsthemke, Markus, Anne Bachg, Katharina Groll, Sven Moyzio, Barbara Müther, Sandra Hemkemeyer, Roland Wedlich Söldner, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2017. https://doi.org/10.1074/jbc.M116.766923.","short":"M. Horsthemke, A. Bachg, K. Groll, S. Moyzio, B. Müther, S. Hemkemeyer, R. Wedlich Söldner, M.K. Sixt, S. Tacke, M. Bähler, P. Hanley, Journal of Biological Chemistry 292 (2017) 7258–7273.","mla":"Horsthemke, Markus, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” Journal of Biological Chemistry, vol. 292, no. 17, American Society for Biochemistry and Molecular Biology, 2017, pp. 7258–73, doi:10.1074/jbc.M116.766923."},"publication":"Journal of Biological Chemistry","page":"7258 - 7273","article_type":"original","date_published":"2017-04-28T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"28","_id":"668","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 292","status":"public","title":"Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion","ddc":["570"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6971","date_created":"2019-10-24T15:25:42Z","date_updated":"2020-07-14T12:47:37Z","checksum":"d488162874326a4bb056065fa549dc4a","file_name":"2017_JBC_Horsthemke.pdf","access_level":"open_access","content_type":"application/pdf","file_size":5647880,"creator":"dernst"}],"type":"journal_article","issue":"17","abstract":[{"lang":"eng","text":"Macrophage filopodia, finger-like membrane protrusions, were first implicated in phagocytosis more than 100 years ago, but little is still known about the involvement of these actin-dependent structures in particle clearance. Using spinning disk confocal microscopy to image filopodial dynamics in mouse resident Lifeact-EGFP macrophages, we show that filopodia, or filopodia-like structures, support pathogen clearance by multiple means. Filopodia supported the phagocytic uptake of bacterial (Escherichia coli) particles by (i) capturing along the filopodial shaft and surfing toward the cell body, the most common mode of capture; (ii) capturing via the tip followed by retraction; (iii) combinations of surfing and retraction; or (iv) sweeping actions. In addition, filopodia supported the uptake of zymosan (Saccharomyces cerevisiae) particles by (i) providing fixation, (ii) capturing at the tip and filopodia-guided actin anterograde flow with phagocytic cup formation, and (iii) the rapid growth of new protrusions. To explore the role of filopodia-inducing Cdc42, we generated myeloid-restricted Cdc42 knock-out mice. Cdc42-deficient macrophages exhibited rapid phagocytic cup kinetics, but reduced particle clearance, which could be explained by the marked rounded-up morphology of these cells. Macrophages lacking Myo10, thought to act downstream of Cdc42, had normal morphology, motility, and phagocytic cup formation, but displayed markedly reduced filopodia formation. In conclusion, live-cell imaging revealed multiple mechanisms involving macrophage filopodia in particle capture and engulfment. Cdc42 is not critical for filopodia or phagocytic cup formation, but plays a key role in driving macrophage lamellipodial spreading."}],"oa":1,"quality_controlled":"1","doi":"10.1074/jbc.M116.766923","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00219258"]},"month":"04","year":"2017","department":[{"_id":"MiSi"}],"publisher":"American Society for Biochemistry and Molecular Biology","publication_status":"published","author":[{"full_name":"Horsthemke, Markus","first_name":"Markus","last_name":"Horsthemke"},{"full_name":"Bachg, Anne","last_name":"Bachg","first_name":"Anne"},{"last_name":"Groll","first_name":"Katharina","full_name":"Groll, Katharina"},{"first_name":"Sven","last_name":"Moyzio","full_name":"Moyzio, Sven"},{"first_name":"Barbara","last_name":"Müther","full_name":"Müther, Barbara"},{"full_name":"Hemkemeyer, Sandra","first_name":"Sandra","last_name":"Hemkemeyer"},{"full_name":"Wedlich Söldner, Roland","first_name":"Roland","last_name":"Wedlich Söldner"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"},{"full_name":"Tacke, Sebastian","last_name":"Tacke","first_name":"Sebastian"},{"last_name":"Bähler","first_name":"Martin","full_name":"Bähler, Martin"},{"first_name":"Peter","last_name":"Hanley","full_name":"Hanley, Peter"}],"volume":292,"date_updated":"2021-01-12T08:08:34Z","date_created":"2018-12-11T11:47:49Z","publist_id":"7059","file_date_updated":"2020-07-14T12:47:37Z"},{"type":"journal_article","issue":"1","abstract":[{"text":"The exocyst, a eukaryotic tethering complex, coregulates targeted exocytosis as an effector of small GTPases in polarized cell growth. In land plants, several exocyst subunits are encoded by double or triple paralogs, culminating in tens of EXO70 paralogs. Out of 23 Arabidopsis thaliana EXO70 isoforms, we analyzed seven isoforms expressed in pollen. Genetic and microscopic analyses of single mutants in EXO70A2, EXO70C1, EXO70C2, EXO70F1, EXO70H3, EXO70H5, and EXO70H6 genes revealed that only a loss-of-function EXO70C2 allele resulted in a significant male-specific transmission defect (segregation 40%:51%:9%) due to aberrant pollen tube growth. Mutant pollen tubes grown in vitro exhibited an enhanced growth rate and a decreased thickness of the tip cell wall, causing tip bursts. However, exo70C2 pollen tubes could frequently recover and restart their speedy elongation, resulting in a repetitive stop-and-go growth dynamics. A pollenspecific depletion of the closest paralog, EXO70C1, using artificial microRNA in the exo70C2 mutant background, resulted in a complete pollen-specific transmission defect, suggesting redundant functions of EXO70C1 and EXO70C2. Both EXO70C1 and EXO70C2, GFP tagged and expressed under the control of their native promoters, localized in the cytoplasm of pollen grains, pollen tubes, and also root trichoblast cells. The expression of EXO70C2-GFP complemented the aberrant growth of exo70C2 pollen tubes. The absent EXO70C2 interactions with core exocyst subunits in the yeast two-hybrid assay, cytoplasmic localization, and genetic effect suggest an unconventional EXO70 function possibly as a regulator of exocytosis outside the exocyst complex. In conclusion, EXO70C2 is a novel factor contributing to the regulation of optimal tip growth of Arabidopsis pollen tubes. ","lang":"eng"}],"intvolume":" 174","status":"public","ddc":["580"],"title":"EXO70C2 is a key regulatory factor for optimal tip growth of pollen","_id":"669","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"dernst","content_type":"application/pdf","file_size":2176903,"access_level":"open_access","file_name":"2017_PlantPhysio_Synek.pdf","checksum":"97155acc6aa5f0d0a78e0589a932fe02","date_created":"2019-11-18T16:16:18Z","date_updated":"2020-07-14T12:47:37Z","file_id":"7041","relation":"main_file"}],"oa_version":"Submitted Version","scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"223 - 240","article_type":"original","citation":{"short":"L. Synek, N. Vukašinović, I. Kulich, M. Hála, K. Aldorfová, M. Fendrych, V. Žárský, Plant Physiology 174 (2017) 223–240.","mla":"Synek, Lukáš, et al. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” Plant Physiology, vol. 174, no. 1, American Society of Plant Biologists, 2017, pp. 223–40, doi:10.1104/pp.16.01282.","chicago":"Synek, Lukáš, Nemanja Vukašinović, Ivan Kulich, Michal Hála, Klára Aldorfová, Matyas Fendrych, and Viktor Žárský. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” Plant Physiology. American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.01282.","ama":"Synek L, Vukašinović N, Kulich I, et al. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. 2017;174(1):223-240. doi:10.1104/pp.16.01282","ieee":"L. Synek et al., “EXO70C2 is a key regulatory factor for optimal tip growth of pollen,” Plant Physiology, vol. 174, no. 1. American Society of Plant Biologists, pp. 223–240, 2017.","apa":"Synek, L., Vukašinović, N., Kulich, I., Hála, M., Aldorfová, K., Fendrych, M., & Žárský, V. (2017). EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.01282","ista":"Synek L, Vukašinović N, Kulich I, Hála M, Aldorfová K, Fendrych M, Žárský V. 2017. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. 174(1), 223–240."},"publication":"Plant Physiology","date_published":"2017-05-01T00:00:00Z","publist_id":"7058","file_date_updated":"2020-07-14T12:47:37Z","department":[{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","publication_status":"published","pmid":1,"year":"2017","volume":174,"date_created":"2018-12-11T11:47:49Z","date_updated":"2021-01-12T08:08:35Z","author":[{"last_name":"Synek","first_name":"Lukáš","full_name":"Synek, Lukáš"},{"full_name":"Vukašinović, Nemanja","first_name":"Nemanja","last_name":"Vukašinović"},{"last_name":"Kulich","first_name":"Ivan","full_name":"Kulich, Ivan"},{"first_name":"Michal","last_name":"Hála","full_name":"Hála, Michal"},{"full_name":"Aldorfová, Klára","last_name":"Aldorfová","first_name":"Klára"},{"orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas","full_name":"Fendrych, Matyas"},{"first_name":"Viktor","last_name":"Žárský","full_name":"Žárský, Viktor"}],"publication_identifier":{"issn":["00320889"]},"month":"05","quality_controlled":"1","external_id":{"pmid":["28356503"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1104/pp.16.01282"},{"date_updated":"2021-01-12T08:08:37Z","date_created":"2018-12-11T11:47:50Z","volume":114,"author":[{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian"},{"first_name":"Vaquero","last_name":"Martinez","full_name":"Martinez, Vaquero"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"KrCh"}],"year":"2017","pmid":1,"ec_funded":1,"publist_id":"7053","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1621239114","quality_controlled":"1","project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"}],"external_id":{"pmid":["28420786"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422766/","open_access":"1"}],"oa":1,"month":"05","publication_identifier":{"issn":["00278424"]},"oa_version":"Published Version","status":"public","title":"Memory-n strategies of direct reciprocity","intvolume":" 114","_id":"671","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Humans routinely use conditionally cooperative strategies when interacting in repeated social dilemmas. They are more likely to cooperate if others cooperated before, and are ready to retaliate if others defected. To capture the emergence of reciprocity, most previous models consider subjects who can only choose from a restricted set of representative strategies, or who react to the outcome of the very last round only. As players memorize more rounds, the dimension of the strategy space increases exponentially. This increasing computational complexity renders simulations for individuals with higher cognitive abilities infeasible, especially if multiplayer interactions are taken into account. Here, we take an axiomatic approach instead. We propose several properties that a robust cooperative strategy for a repeated multiplayer dilemma should have. These properties naturally lead to a unique class of cooperative strategies, which contains the classical Win-Stay Lose-Shift rule as a special case. A comprehensive numerical analysis for the prisoner's dilemma and for the public goods game suggests that strategies of this class readily evolve across various memory-n spaces. Our results reveal that successful strategies depend not only on how cooperative others were in the past but also on the respective context of cooperation."}],"issue":"18","type":"journal_article","date_published":"2017-05-02T00:00:00Z","page":"4715 - 4720","publication":"PNAS","citation":{"ama":"Hilbe C, Martinez V, Chatterjee K, Nowak M. Memory-n strategies of direct reciprocity. PNAS. 2017;114(18):4715-4720. doi:10.1073/pnas.1621239114","ista":"Hilbe C, Martinez V, Chatterjee K, Nowak M. 2017. Memory-n strategies of direct reciprocity. PNAS. 114(18), 4715–4720.","apa":"Hilbe, C., Martinez, V., Chatterjee, K., & Nowak, M. (2017). Memory-n strategies of direct reciprocity. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1621239114","ieee":"C. Hilbe, V. Martinez, K. Chatterjee, and M. Nowak, “Memory-n strategies of direct reciprocity,” PNAS, vol. 114, no. 18. National Academy of Sciences, pp. 4715–4720, 2017.","mla":"Hilbe, Christian, et al. “Memory-n Strategies of Direct Reciprocity.” PNAS, vol. 114, no. 18, National Academy of Sciences, 2017, pp. 4715–20, doi:10.1073/pnas.1621239114.","short":"C. Hilbe, V. Martinez, K. Chatterjee, M. Nowak, PNAS 114 (2017) 4715–4720.","chicago":"Hilbe, Christian, Vaquero Martinez, Krishnendu Chatterjee, and Martin Nowak. “Memory-n Strategies of Direct Reciprocity.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621239114."},"day":"02","article_processing_charge":"Yes (in subscription journal)","scopus_import":1},{"language":[{"iso":"eng"}],"doi":"10.1111/cgf.13110","project":[{"call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images","grant_number":"P 24352-N23","_id":"25357BD2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01647113/file/eg_2017_schreck_paper_tearing.pdf"}],"publication_identifier":{"issn":["01677055"]},"month":"05","volume":36,"date_updated":"2021-01-12T08:08:37Z","date_created":"2018-12-11T11:47:49Z","author":[{"first_name":"Camille","last_name":"Schreck","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","full_name":"Schreck, Camille"},{"full_name":"Rohmer, Damien","first_name":"Damien","last_name":"Rohmer"},{"full_name":"Hahmann, Stefanie","first_name":"Stefanie","last_name":"Hahmann"}],"department":[{"_id":"ChWo"}],"publisher":"Wiley","publication_status":"published","year":"2017","publist_id":"7056","date_published":"2017-05-01T00:00:00Z","page":"95 - 106","article_type":"original","citation":{"ista":"Schreck C, Rohmer D, Hahmann S. 2017. Interactive paper tearing. Computer Graphics Forum. 36(2), 95–106.","apa":"Schreck, C., Rohmer, D., & Hahmann, S. (2017). Interactive paper tearing. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13110","ieee":"C. Schreck, D. Rohmer, and S. Hahmann, “Interactive paper tearing,” Computer Graphics Forum, vol. 36, no. 2. Wiley, pp. 95–106, 2017.","ama":"Schreck C, Rohmer D, Hahmann S. Interactive paper tearing. Computer Graphics Forum. 2017;36(2):95-106. doi:10.1111/cgf.13110","chicago":"Schreck, Camille, Damien Rohmer, and Stefanie Hahmann. “Interactive Paper Tearing.” Computer Graphics Forum. Wiley, 2017. https://doi.org/10.1111/cgf.13110.","mla":"Schreck, Camille, et al. “Interactive Paper Tearing.” Computer Graphics Forum, vol. 36, no. 2, Wiley, 2017, pp. 95–106, doi:10.1111/cgf.13110.","short":"C. Schreck, D. Rohmer, S. Hahmann, Computer Graphics Forum 36 (2017) 95–106."},"publication":"Computer Graphics Forum","article_processing_charge":"No","day":"01","scopus_import":1,"oa_version":"Published Version","intvolume":" 36","title":"Interactive paper tearing","ddc":["000"],"status":"public","_id":"670","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","abstract":[{"lang":"eng","text":"We propose an efficient method to model paper tearing in the context of interactive modeling. The method uses geometrical information to automatically detect potential starting points of tears. We further introduce a new hybrid geometrical and physical-based method to compute the trajectory of tears while procedurally synthesizing high resolution details of the tearing path using a texture based approach. The results obtained are compared with real paper and with previous studies on the expected geometric paths of paper that tears."}],"type":"journal_article"},{"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556"},{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF"}],"quality_controlled":"1","doi":"10.1016/j.celrep.2017.04.027","language":[{"iso":"eng"}],"publication_identifier":{"issn":["22111247"]},"month":"05","year":"2017","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publisher":"Cell Press","publication_status":"published","author":[{"full_name":"Vaahtomeri, Kari","first_name":"Kari","last_name":"Vaahtomeri","id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518"},{"first_name":"Markus","last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries","first_name":"Ingrid"},{"full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F"},{"first_name":"Matthias","last_name":"Mehling","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8599-1226","full_name":"Mehling, Matthias"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"volume":19,"date_updated":"2023-02-23T12:50:09Z","date_created":"2018-12-11T11:47:50Z","ec_funded":1,"publist_id":"7052","file_date_updated":"2020-07-14T12:47:38Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","citation":{"short":"K. Vaahtomeri, M. Brown, R. Hauschild, I. de Vries, A.F. Leithner, M. Mehling, W. Kaufmann, M.K. Sixt, Cell Reports 19 (2017) 902–909.","mla":"Vaahtomeri, Kari, et al. “Locally Triggered Release of the Chemokine CCL21 Promotes Dendritic Cell Transmigration across Lymphatic Endothelia.” Cell Reports, vol. 19, no. 5, Cell Press, 2017, pp. 902–09, doi:10.1016/j.celrep.2017.04.027.","chicago":"Vaahtomeri, Kari, Markus Brown, Robert Hauschild, Ingrid de Vries, Alexander F Leithner, Matthias Mehling, Walter Kaufmann, and Michael K Sixt. “Locally Triggered Release of the Chemokine CCL21 Promotes Dendritic Cell Transmigration across Lymphatic Endothelia.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.04.027.","ama":"Vaahtomeri K, Brown M, Hauschild R, et al. Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. 2017;19(5):902-909. doi:10.1016/j.celrep.2017.04.027","ieee":"K. Vaahtomeri et al., “Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia,” Cell Reports, vol. 19, no. 5. Cell Press, pp. 902–909, 2017.","apa":"Vaahtomeri, K., Brown, M., Hauschild, R., de Vries, I., Leithner, A. F., Mehling, M., … Sixt, M. K. (2017). Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.04.027","ista":"Vaahtomeri K, Brown M, Hauschild R, de Vries I, Leithner AF, Mehling M, Kaufmann W, Sixt MK. 2017. Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. 19(5), 902–909."},"publication":"Cell Reports","page":"902 - 909","date_published":"2017-05-02T00:00:00Z","scopus_import":1,"has_accepted_license":"1","article_processing_charge":"Yes","day":"02","_id":"672","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 19","status":"public","title":"Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia","ddc":["570"],"pubrep_id":"900","file":[{"file_id":"5109","relation":"main_file","date_updated":"2020-07-14T12:47:38Z","date_created":"2018-12-12T10:14:54Z","checksum":"8fdddaab1f1d76a6ec9ca94dcb6b07a2","file_name":"IST-2017-900-v1+1_1-s2.0-S2211124717305211-main.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":2248814}],"oa_version":"Published Version","type":"journal_article","issue":"5","abstract":[{"text":"Trafficking cells frequently transmigrate through epithelial and endothelial monolayers. How monolayers cooperate with the penetrating cells to support their transit is poorly understood. We studied dendritic cell (DC) entry into lymphatic capillaries as a model system for transendothelial migration. We find that the chemokine CCL21, which is the decisive guidance cue for intravasation, mainly localizes in the trans-Golgi network and intracellular vesicles of lymphatic endothelial cells. Upon DC transmigration, these Golgi deposits disperse and CCL21 becomes extracellularly enriched at the sites of endothelial cell-cell junctions. When we reconstitute the transmigration process in vitro, we find that secretion of CCL21-positive vesicles is triggered by a DC contact-induced calcium signal, and selective calcium chelation in lymphatic endothelium attenuates transmigration. Altogether, our data demonstrate a chemokine-mediated feedback between DCs and lymphatic endothelium, which facilitates transendothelial migration.","lang":"eng"}]},{"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF"}],"doi":"10.1016/j.cub.2017.04.004","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["09609822"]},"year":"2017","publication_status":"published","publisher":"Cell Press","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"author":[{"last_name":"Schwarz","first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan"},{"first_name":"Veronika","last_name":"Bierbaum","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","full_name":"Bierbaum, Veronika"},{"full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","first_name":"Kari"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","last_name":"Brown"},{"last_name":"De Vries","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"De Vries, Ingrid"},{"first_name":"Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F"},{"last_name":"Reversat","first_name":"Anne","orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87","full_name":"Reversat, Anne"},{"orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack"},{"full_name":"Tarrant, Teresa","first_name":"Teresa","last_name":"Tarrant"},{"full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Tobias"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"}],"date_created":"2018-12-11T11:47:51Z","date_updated":"2023-02-23T12:50:44Z","volume":27,"publist_id":"7050","ec_funded":1,"publication":"Current Biology","citation":{"chicago":"Schwarz, Jan, Veronika Bierbaum, Kari Vaahtomeri, Robert Hauschild, Markus Brown, Ingrid de Vries, Alexander F Leithner, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.04.004.","mla":"Schwarz, Jan, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” Current Biology, vol. 27, no. 9, Cell Press, 2017, pp. 1314–25, doi:10.1016/j.cub.2017.04.004.","short":"J. Schwarz, V. Bierbaum, K. Vaahtomeri, R. Hauschild, M. Brown, I. de Vries, A.F. Leithner, A. Reversat, J. Merrin, T. Tarrant, M.T. Bollenbach, M.K. Sixt, Current Biology 27 (2017) 1314–1325.","ista":"Schwarz J, Bierbaum V, Vaahtomeri K, Hauschild R, Brown M, de Vries I, Leithner AF, Reversat A, Merrin J, Tarrant T, Bollenbach MT, Sixt MK. 2017. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. 27(9), 1314–1325.","ieee":"J. Schwarz et al., “Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6,” Current Biology, vol. 27, no. 9. Cell Press, pp. 1314–1325, 2017.","apa":"Schwarz, J., Bierbaum, V., Vaahtomeri, K., Hauschild, R., Brown, M., de Vries, I., … Sixt, M. K. (2017). Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.04.004","ama":"Schwarz J, Bierbaum V, Vaahtomeri K, et al. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. 2017;27(9):1314-1325. doi:10.1016/j.cub.2017.04.004"},"page":"1314 - 1325","date_published":"2017-05-09T00:00:00Z","scopus_import":1,"day":"09","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"674","title":"Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6","status":"public","intvolume":" 27","oa_version":"None","type":"journal_article","abstract":[{"text":"Navigation of cells along gradients of guidance cues is a determining step in many developmental and immunological processes. Gradients can either be soluble or immobilized to tissues as demonstrated for the haptotactic migration of dendritic cells (DCs) toward higher concentrations of immobilized chemokine CCL21. To elucidate how gradient characteristics govern cellular response patterns, we here introduce an in vitro system allowing to track migratory responses of DCs to precisely controlled immobilized gradients of CCL21. We find that haptotactic sensing depends on the absolute CCL21 concentration and local steepness of the gradient, consistent with a scenario where DC directionality is governed by the signal-to-noise ratio of CCL21 binding to the receptor CCR7. We find that the conditions for optimal DC guidance are perfectly provided by the CCL21 gradients we measure in vivo. Furthermore, we find that CCR7 signal termination by the G-protein-coupled receptor kinase 6 (GRK6) is crucial for haptotactic but dispensable for chemotactic CCL21 gradient sensing in vitro and confirm those observations in vivo. These findings suggest that stable, tissue-bound CCL21 gradients as sustainable “roads” ensure optimal guidance in vivo.","lang":"eng"}],"issue":"9"},{"day":"16","has_accepted_license":"1","scopus_import":1,"date_published":"2017-05-16T00:00:00Z","page":"1294 - 1303","publication":"Cell Reports","citation":{"ama":"Lademann C, Renkawitz J, Pfander B, Jentsch S. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 2017;19(7):1294-1303. doi:10.1016/j.celrep.2017.04.051","ista":"Lademann C, Renkawitz J, Pfander B, Jentsch S. 2017. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 19(7), 1294–1303.","ieee":"C. Lademann, J. Renkawitz, B. Pfander, and S. Jentsch, “The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination,” Cell Reports, vol. 19, no. 7. Cell Press, pp. 1294–1303, 2017.","apa":"Lademann, C., Renkawitz, J., Pfander, B., & Jentsch, S. (2017). The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.04.051","mla":"Lademann, Claudio, et al. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” Cell Reports, vol. 19, no. 7, Cell Press, 2017, pp. 1294–303, doi:10.1016/j.celrep.2017.04.051.","short":"C. Lademann, J. Renkawitz, B. Pfander, S. Jentsch, Cell Reports 19 (2017) 1294–1303.","chicago":"Lademann, Claudio, Jörg Renkawitz, Boris Pfander, and Stefan Jentsch. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.04.051."},"abstract":[{"text":"The INO80 complex (INO80-C) is an evolutionarily conserved nucleosome remodeler that acts in transcription, replication, and genome stability. It is required for resistance against genotoxic agents and is involved in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR). However, the causes of the HR defect in INO80-C mutant cells are controversial. Here, we unite previous findings using a system to study HR with high spatial resolution in budding yeast. We find that INO80-C has at least two distinct functions during HR—DNA end resection and presynaptic filament formation. Importantly, the second function is linked to the histone variant H2A.Z. In the absence of H2A.Z, presynaptic filament formation and HR are restored in INO80-C-deficient mutants, suggesting that presynaptic filament formation is the crucial INO80-C function during HR.","lang":"eng"}],"issue":"7","type":"journal_article","file":[{"checksum":"efc7287d9c6354983cb151880e9ad72a","date_updated":"2020-07-14T12:47:40Z","date_created":"2018-12-12T10:15:48Z","file_id":"5171","relation":"main_file","creator":"system","file_size":3005610,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-899-v1+1_1-s2.0-S2211124717305454-main.pdf"}],"oa_version":"Published Version","pubrep_id":"899","ddc":["570"],"status":"public","title":"The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination","intvolume":" 19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"677","month":"05","publication_identifier":{"issn":["22111247"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2017.04.051","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"file_date_updated":"2020-07-14T12:47:40Z","publist_id":"7046","date_updated":"2021-01-12T08:08:57Z","date_created":"2018-12-11T11:47:52Z","volume":19,"author":[{"full_name":"Lademann, Claudio","first_name":"Claudio","last_name":"Lademann"},{"full_name":"Renkawitz, Jörg","last_name":"Renkawitz","first_name":"Jörg","orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Boris","last_name":"Pfander","full_name":"Pfander, Boris"},{"full_name":"Jentsch, Stefan","last_name":"Jentsch","first_name":"Stefan"}],"publication_status":"published","publisher":"Cell Press","department":[{"_id":"MiSi"}],"year":"2017"},{"author":[{"full_name":"Petridou, Nicoletta","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8451-1195","first_name":"Nicoletta","last_name":"Petridou"},{"first_name":"Zoltan P","last_name":"Spiro","id":"426AD026-F248-11E8-B48F-1D18A9856A87","full_name":"Spiro, Zoltan P"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"volume":19,"oa_version":"None","date_created":"2018-12-11T11:47:53Z","date_updated":"2021-01-12T08:08:59Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"678","year":"2017","department":[{"_id":"CaHe"}],"intvolume":" 19","publisher":"Nature Publishing Group","publication_status":"published","status":"public","title":"Multiscale force sensing in development","publist_id":"7040","issue":"6","abstract":[{"text":"The seminal observation that mechanical signals can elicit changes in biochemical signalling within cells, a process commonly termed mechanosensation and mechanotransduction, has revolutionized our understanding of the role of cell mechanics in various fundamental biological processes, such as cell motility, adhesion, proliferation and differentiation. In this Review, we will discuss how the interplay and feedback between mechanical and biochemical signals control tissue morphogenesis and cell fate specification in embryonic development.","lang":"eng"}],"type":"journal_article","date_published":"2017-05-31T00:00:00Z","doi":"10.1038/ncb3524","language":[{"iso":"eng"}],"citation":{"short":"N. Petridou, Z.P. Spiro, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 581–588.","mla":"Petridou, Nicoletta, et al. “Multiscale Force Sensing in Development.” Nature Cell Biology, vol. 19, no. 6, Nature Publishing Group, 2017, pp. 581–88, doi:10.1038/ncb3524.","chicago":"Petridou, Nicoletta, Zoltan P Spiro, and Carl-Philipp J Heisenberg. “Multiscale Force Sensing in Development.” Nature Cell Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/ncb3524.","ama":"Petridou N, Spiro ZP, Heisenberg C-PJ. Multiscale force sensing in development. Nature Cell Biology. 2017;19(6):581-588. doi:10.1038/ncb3524","apa":"Petridou, N., Spiro, Z. P., & Heisenberg, C.-P. J. (2017). Multiscale force sensing in development. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3524","ieee":"N. Petridou, Z. P. Spiro, and C.-P. J. Heisenberg, “Multiscale force sensing in development,” Nature Cell Biology, vol. 19, no. 6. Nature Publishing Group, pp. 581–588, 2017.","ista":"Petridou N, Spiro ZP, Heisenberg C-PJ. 2017. Multiscale force sensing in development. Nature Cell Biology. 19(6), 581–588."},"publication":"Nature Cell Biology","project":[{"grant_number":"ALTF534-2016","_id":"25236028-B435-11E9-9278-68D0E5697425","name":"The generation and function of anisotropic tissue tension in zebrafish epiboly (EMBO Fellowship)"}],"page":"581 - 588","quality_controlled":"1","publication_identifier":{"issn":["14657392"]},"day":"31","month":"05","scopus_import":1},{"ec_funded":1,"publist_id":"7036","date_updated":"2023-02-21T16:06:02Z","date_created":"2018-12-11T11:47:53Z","volume":254,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"last_name":"Filiot","first_name":"Emmanuel","full_name":"Filiot, Emmanuel"},{"full_name":"Raskin, Jean","first_name":"Jean","last_name":"Raskin"}],"related_material":{"record":[{"id":"10885","relation":"earlier_version","status":"public"}]},"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Elsevier","year":"2017","month":"06","publication_identifier":{"issn":["08905401"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.ic.2016.10.012","quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"oa":1,"external_id":{"arxiv":["1311.3238"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.3238"}],"abstract":[{"lang":"eng","text":"Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information. In this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile where all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players' objective, then the objective of every player is violated. We present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games. We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games."}],"type":"journal_article","oa_version":"Submitted Version","title":"Doomsday equilibria for omega-regular games","status":"public","intvolume":" 254","_id":"681","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2017-06-01T00:00:00Z","article_type":"original","page":"296 - 315","publication":"Information and Computation","citation":{"ama":"Chatterjee K, Doyen L, Filiot E, Raskin J. Doomsday equilibria for omega-regular games. Information and Computation. 2017;254:296-315. doi:10.1016/j.ic.2016.10.012","ieee":"K. Chatterjee, L. Doyen, E. Filiot, and J. Raskin, “Doomsday equilibria for omega-regular games,” Information and Computation, vol. 254. Elsevier, pp. 296–315, 2017.","apa":"Chatterjee, K., Doyen, L., Filiot, E., & Raskin, J. (2017). Doomsday equilibria for omega-regular games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.012","ista":"Chatterjee K, Doyen L, Filiot E, Raskin J. 2017. Doomsday equilibria for omega-regular games. Information and Computation. 254, 296–315.","short":"K. Chatterjee, L. Doyen, E. Filiot, J. Raskin, Information and Computation 254 (2017) 296–315.","mla":"Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.” Information and Computation, vol. 254, Elsevier, 2017, pp. 296–315, doi:10.1016/j.ic.2016.10.012.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean Raskin. “Doomsday Equilibria for Omega-Regular Games.” Information and Computation. Elsevier, 2017. https://doi.org/10.1016/j.ic.2016.10.012."}},{"date_updated":"2021-01-12T08:09:17Z","date_created":"2019-09-01T22:01:00Z","oa_version":"Preprint","author":[{"full_name":"Martius, Georg S","first_name":"Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"title":"Extrapolation and learning equations","publication_status":"published","status":"public","publisher":"International Conference on Learning Representations","department":[{"_id":"ChLa"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6841","year":"2017","abstract":[{"lang":"eng","text":"In classical machine learning, regression is treated as a black box process of identifying a suitable function from a hypothesis set without attempting to gain insight into the mechanism connecting inputs and outputs. In the natural sciences, however, finding an interpretable function for a phenomenon is the prime goal as it allows to understand and generalize results. This paper proposes a novel type of function learning network, called equation learner (EQL), that can learn analytical expressions and is able to extrapolate to unseen domains. It is implemented as an end-to-end differentiable feed-forward network and allows for efficient gradient based training. Due to sparsity regularization concise interpretable expressions can be obtained. Often the true underlying source expression is identified."}],"ec_funded":1,"type":"conference","language":[{"iso":"eng"}],"conference":{"location":"Toulon, France","start_date":"2017-04-24","end_date":"2017-04-26","name":"ICLR: International Conference on Learning Representations"},"date_published":"2017-02-21T00:00:00Z","quality_controlled":"1","project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"publication":"5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings","external_id":{"arxiv":["1610.02995"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02995"}],"citation":{"short":"G.S. Martius, C. Lampert, in:, 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017.","mla":"Martius, Georg S., and Christoph Lampert. “Extrapolation and Learning Equations.” 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017.","chicago":"Martius, Georg S, and Christoph Lampert. “Extrapolation and Learning Equations.” In 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. International Conference on Learning Representations, 2017.","ama":"Martius GS, Lampert C. Extrapolation and learning equations. In: 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. International Conference on Learning Representations; 2017.","ieee":"G. S. Martius and C. Lampert, “Extrapolation and learning equations,” in 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, Toulon, France, 2017.","apa":"Martius, G. S., & Lampert, C. (2017). Extrapolation and learning equations. In 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. Toulon, France: International Conference on Learning Representations.","ista":"Martius GS, Lampert C. 2017. Extrapolation and learning equations. 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. ICLR: International Conference on Learning Representations."},"oa":1,"day":"21","month":"02","scopus_import":1},{"oa_version":"Submitted Version","_id":"684","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 82","title":"Obligation blackwell games and p-automata","status":"public","issue":"2","abstract":[{"lang":"eng","text":"We generalize winning conditions in two-player games by adding a structural acceptance condition called obligations. Obligations are orthogonal to the linear winning conditions that define whether a play is winning. Obligations are a declaration that player 0 can achieve a certain value from a configuration. If the obligation is met, the value of that configuration for player 0 is 1. We define the value in such games and show that obligation games are determined. For Markov chains with Borel objectives and obligations, and finite turn-based stochastic parity games with obligations we give an alternative and simpler characterization of the value function. Based on this simpler definition we show that the decision problem of winning finite turn-based stochastic parity games with obligations is in NP∩co-NP. We also show that obligation games provide a game framework for reasoning about p-automata. © 2017 The Association for Symbolic Logic."}],"type":"journal_article","date_published":"2017-06-01T00:00:00Z","citation":{"short":"K. Chatterjee, N. Piterman, Journal of Symbolic Logic 82 (2017) 420–452.","mla":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” Journal of Symbolic Logic, vol. 82, no. 2, Cambridge University Press, 2017, pp. 420–52, doi:10.1017/jsl.2016.71.","chicago":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” Journal of Symbolic Logic. Cambridge University Press, 2017. https://doi.org/10.1017/jsl.2016.71.","ama":"Chatterjee K, Piterman N. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 2017;82(2):420-452. doi:10.1017/jsl.2016.71","apa":"Chatterjee, K., & Piterman, N. (2017). Obligation blackwell games and p-automata. Journal of Symbolic Logic. Cambridge University Press. https://doi.org/10.1017/jsl.2016.71","ieee":"K. Chatterjee and N. Piterman, “Obligation blackwell games and p-automata,” Journal of Symbolic Logic, vol. 82, no. 2. Cambridge University Press, pp. 420–452, 2017.","ista":"Chatterjee K, Piterman N. 2017. Obligation blackwell games and p-automata. 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This has had a profound influence on subsequent generations of developmental biologists. We discuss how this influence can be traced through twentieth century morphologists, embryologists and theoreticians to current research that explores the molecular and cellular mechanisms of tissue growth and patterning, including our own studies of the vertebrate neural tube.","lang":"eng"}],"page":"26 - 31","citation":{"ista":"Briscoe J, Kicheva A. 2017. The physics of development 100 years after D’Arcy Thompson’s “on growth and form”. Mechanisms of Development. 145, 26–31.","apa":"Briscoe, J., & Kicheva, A. (2017). The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.005","ieee":"J. Briscoe and A. Kicheva, “The physics of development 100 years after D’Arcy Thompson’s ‘on growth and form,’” Mechanisms of Development, vol. 145. Elsevier, pp. 26–31, 2017.","ama":"Briscoe J, Kicheva A. The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” Mechanisms of Development. 2017;145:26-31. doi:10.1016/j.mod.2017.03.005","chicago":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.005.","mla":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 26–31, doi:10.1016/j.mod.2017.03.005.","short":"J. Briscoe, A. Kicheva, Mechanisms of Development 145 (2017) 26–31."},"publication":"Mechanisms of Development","date_published":"2017-06-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01"},{"abstract":[{"text":"We show that the framework of topological data analysis can be extended from metrics to general Bregman divergences, widening the scope of possible applications. Examples are the Kullback - Leibler divergence, which is commonly used for comparing text and images, and the Itakura - Saito divergence, popular for speech and sound. In particular, we prove that appropriately generalized čech and Delaunay (alpha) complexes capture the correct homotopy type, namely that of the corresponding union of Bregman balls. Consequently, their filtrations give the correct persistence diagram, namely the one generated by the uniformly growing Bregman balls. Moreover, we show that unlike the metric setting, the filtration of Vietoris-Rips complexes may fail to approximate the persistence diagram. We propose algorithms to compute the thus generalized čech, Vietoris-Rips and Delaunay complexes and experimentally test their efficiency. Lastly, we explain their surprisingly good performance by making a connection with discrete Morse theory. ","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"pubrep_id":"895","file":[{"date_created":"2018-12-12T10:11:03Z","date_updated":"2020-07-14T12:47:42Z","checksum":"067ab0cb3f962bae6c3af6bf0094e0f3","relation":"main_file","file_id":"4856","content_type":"application/pdf","file_size":990546,"creator":"system","file_name":"IST-2017-895-v1+1_LIPIcs-SoCG-2017-39.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"688","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 77","ddc":["514","516"],"status":"public","title":"Topological data analysis with Bregman divergences","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2017-06-01T00:00:00Z","citation":{"chicago":"Edelsbrunner, Herbert, and Hubert Wagner. “Topological Data Analysis with Bregman Divergences,” 77:391–3916. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.SoCG.2017.39.","short":"H. Edelsbrunner, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916.","mla":"Edelsbrunner, Herbert, and Hubert Wagner. Topological Data Analysis with Bregman Divergences. Vol. 77, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916, doi:10.4230/LIPIcs.SoCG.2017.39.","apa":"Edelsbrunner, H., & Wagner, H. (2017). Topological data analysis with Bregman divergences (Vol. 77, pp. 391–3916). Presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2017.39","ieee":"H. Edelsbrunner and H. Wagner, “Topological data analysis with Bregman divergences,” presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia, 2017, vol. 77, pp. 391–3916.","ista":"Edelsbrunner H, Wagner H. 2017. Topological data analysis with Bregman divergences. Symposium on Computational Geometry, SoCG, LIPIcs, vol. 77, 391–3916.","ama":"Edelsbrunner H, Wagner H. Topological data analysis with Bregman divergences. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:391-3916. doi:10.4230/LIPIcs.SoCG.2017.39"},"page":"391-3916","publist_id":"7021","file_date_updated":"2020-07-14T12:47:42Z","author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"last_name":"Wagner","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert"}],"volume":77,"date_created":"2018-12-11T11:47:56Z","date_updated":"2021-01-12T08:09:26Z","year":"2017","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"publication_status":"published","publication_identifier":{"issn":["18688969"]},"month":"06","doi":"10.4230/LIPIcs.SoCG.2017.39","conference":{"start_date":"2017-07-04","location":"Brisbane, Australia","end_date":"2017-07-07","name":"Symposium on Computational Geometry, SoCG"},"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"},{"year":"2017","publication_status":"published","department":[{"_id":"TaHa"}],"publisher":"Oxford University Press","author":[{"full_name":"Davison, Ben","last_name":"Davison","first_name":"Ben","orcid":"0000-0002-8944-4390","id":"4634AB1E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T08:09:24Z","date_created":"2018-12-11T11:47:55Z","volume":68,"publist_id":"7022","ec_funded":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1311.7172","open_access":"1"}],"quality_controlled":"1","project":[{"name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7","grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425"}],"doi":"10.1093/qmath/haw053","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"issn":["00335606"]},"_id":"687","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The critical CoHA of a quiver with potential","intvolume":" 68","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Pursuing the similarity between the Kontsevich-Soibelman construction of the cohomological Hall algebra (CoHA) of BPS states and Lusztig's construction of canonical bases for quantum enveloping algebras, and the similarity between the integrality conjecture for motivic Donaldson-Thomas invariants and the PBW theorem for quantum enveloping algebras, we build a coproduct on the CoHA associated to a quiver with potential. We also prove a cohomological dimensional reduction theorem, further linking a special class of CoHAs with Yangians, and explaining how to connect the study of character varieties with the study of CoHAs.","lang":"eng"}],"issue":"2","publication":"Quarterly Journal of Mathematics","citation":{"ama":"Davison B. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 2017;68(2):635-703. doi:10.1093/qmath/haw053","ista":"Davison B. 2017. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 68(2), 635–703.","apa":"Davison, B. (2017). The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haw053","ieee":"B. Davison, “The critical CoHA of a quiver with potential,” Quarterly Journal of Mathematics, vol. 68, no. 2. Oxford University Press, pp. 635–703, 2017.","mla":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics, vol. 68, no. 2, Oxford University Press, 2017, pp. 635–703, doi:10.1093/qmath/haw053.","short":"B. Davison, Quarterly Journal of Mathematics 68 (2017) 635–703.","chicago":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics. Oxford University Press, 2017. https://doi.org/10.1093/qmath/haw053."},"page":"635 - 703","date_published":"2017-06-01T00:00:00Z","scopus_import":1,"day":"01"},{"scopus_import":1,"day":"01","month":"06","publication_identifier":{"issn":["09254773"]},"publication":"Mechanisms of Development","citation":{"ama":"Heisenberg C-PJ. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 2017;145:32-37. doi:10.1016/j.mod.2017.03.006","ista":"Heisenberg C-PJ. 2017. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 145, 32–37.","ieee":"C.-P. J. Heisenberg, “D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization,” Mechanisms of Development, vol. 145. Elsevier, pp. 32–37, 2017.","apa":"Heisenberg, C.-P. J. (2017). D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.006","mla":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 32–37, doi:10.1016/j.mod.2017.03.006.","short":"C.-P.J. Heisenberg, Mechanisms of Development 145 (2017) 32–37.","chicago":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.006."},"quality_controlled":"1","page":"32 - 37","date_published":"2017-06-01T00:00:00Z","doi":"10.1016/j.mod.2017.03.006","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Tissues are thought to behave like fluids with a given surface tension. Differences in tissue surface tension (TST) have been proposed to trigger cell sorting and tissue envelopment. D'Arcy Thompson in his seminal book ‘On Growth and Form’ has introduced this concept of differential TST as a key physical mechanism dictating tissue formation and organization within the developing organism. Over the past century, many studies have picked up the concept of differential TST and analyzed the role and cell biological basis of TST in development, underlining the importance and influence of this concept in developmental biology.","lang":"eng"}],"publist_id":"7024","year":"2017","_id":"686","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"D'Arcy Thompson's ‘on growth and form’: From soap bubbles to tissue self organization","status":"public","publication_status":"published","intvolume":" 145","publisher":"Elsevier","department":[{"_id":"CaHe"}],"author":[{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"date_created":"2018-12-11T11:47:55Z","date_updated":"2021-01-12T08:09:23Z","oa_version":"None","volume":145},{"language":[{"iso":"eng"}],"doi":"10.1126/scitranslmed.aan8196","date_published":"2017-06-07T00:00:00Z","quality_controlled":"1","citation":{"ama":"Novarino G. Rett syndrome modeling goes simian. Science Translational Medicine. 2017;9(393). doi:10.1126/scitranslmed.aan8196","ista":"Novarino G. 2017. Rett syndrome modeling goes simian. Science Translational Medicine. 9(393), eaan8196.","ieee":"G. Novarino, “Rett syndrome modeling goes simian,” Science Translational Medicine, vol. 9, no. 393. American Association for the Advancement of Science, 2017.","apa":"Novarino, G. (2017). Rett syndrome modeling goes simian. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan8196","mla":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine, vol. 9, no. 393, eaan8196, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aan8196.","short":"G. Novarino, Science Translational Medicine 9 (2017).","chicago":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan8196."},"publication":"Science Translational Medicine","publication_identifier":{"issn":["19466234"]},"month":"06","day":"07","scopus_import":1,"volume":9,"oa_version":"None","date_created":"2018-12-11T11:47:56Z","date_updated":"2021-01-12T08:09:29Z","author":[{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"}],"intvolume":" 9","publisher":"American Association for the Advancement of Science","department":[{"_id":"GaNo"}],"publication_status":"published","status":"public","title":"Rett syndrome modeling goes simian","_id":"689","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2017","issue":"393","publist_id":"7019","abstract":[{"text":"Rett syndrome modeling in monkey mirrors the human disorder.","lang":"eng"}],"type":"journal_article","article_number":"eaan8196"},{"oa_version":"Published Version","file":[{"creator":"kschuh","content_type":"application/pdf","file_size":2721544,"access_level":"open_access","file_name":"2017_PNAS_Miki.pdf","checksum":"2ab75d554f3df4a34d20fa8040589b7e","date_created":"2020-01-03T13:27:29Z","date_updated":"2020-07-14T12:47:44Z","file_id":"7223","relation":"main_file"}],"_id":"693","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 114","status":"public","title":"Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses","ddc":["570"],"issue":"26","abstract":[{"text":"Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. ","lang":"eng"}],"type":"journal_article","date_published":"2017-06-27T00:00:00Z","citation":{"chicago":"Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1704470114.","mla":"Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:10.1073/pnas.1704470114.","short":"T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255.","ista":"Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255.","apa":"Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1704470114","ieee":"T. Miki et al., “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” PNAS, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017.","ama":"Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 2017;114(26):E5246-E5255. doi:10.1073/pnas.1704470114"},"publication":"PNAS","page":"E5246 - E5255","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"27","scopus_import":1,"author":[{"full_name":"Miki, Takafumi","last_name":"Miki","first_name":"Takafumi"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Malagon, Gerardo","last_name":"Malagon","first_name":"Gerardo"},{"full_name":"Gomez, Laura","last_name":"Gomez","first_name":"Laura"},{"last_name":"Tabuchi","first_name":"Katsuhiko","full_name":"Tabuchi, Katsuhiko"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"full_name":"Marty, Alain","last_name":"Marty","first_name":"Alain"}],"volume":114,"date_created":"2018-12-11T11:47:57Z","date_updated":"2023-02-23T12:54:57Z","pmid":1,"year":"2017","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"publisher":"National Academy of Sciences","publication_status":"published","publist_id":"7013","file_date_updated":"2020-07-14T12:47:44Z","doi":"10.1073/pnas.1704470114","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["28607047"]},"quality_controlled":"1","publication_identifier":{"issn":["00278424"]},"month":"06"},{"language":[{"iso":"eng"}],"doi":"10.1242/jcs.200899","quality_controlled":"1","external_id":{"pmid":["28515231"]},"oa":1,"publication_identifier":{"issn":["00219533"]},"month":"07","volume":130,"date_updated":"2021-01-12T08:09:41Z","date_created":"2018-12-11T11:47:58Z","author":[{"last_name":"Veß","first_name":"Astrid","full_name":"Veß, Astrid"},{"first_name":"Ulrich","last_name":"Blache","full_name":"Blache, Ulrich"},{"full_name":"Leitner, Laura","first_name":"Laura","last_name":"Leitner"},{"first_name":"Angela","last_name":"Kurz","full_name":"Kurz, Angela"},{"first_name":"Anja","last_name":"Ehrenpfordt","full_name":"Ehrenpfordt, Anja"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"full_name":"Posern, Guido","last_name":"Posern","first_name":"Guido"}],"publisher":"Company of Biologists","department":[{"_id":"MiSi"}],"publication_status":"published","pmid":1,"year":"2017","publist_id":"7008","file_date_updated":"2020-07-14T12:47:45Z","date_published":"2017-07-01T00:00:00Z","page":"2172 - 2184","article_type":"original","citation":{"chicago":"Veß, Astrid, Ulrich Blache, Laura Leitner, Angela Kurz, Anja Ehrenpfordt, Michael K Sixt, and Guido Posern. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science. Company of Biologists, 2017. https://doi.org/10.1242/jcs.200899.","short":"A. Veß, U. Blache, L. Leitner, A. Kurz, A. Ehrenpfordt, M.K. Sixt, G. Posern, Journal of Cell Science 130 (2017) 2172–2184.","mla":"Veß, Astrid, et al. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science, vol. 130, no. 13, Company of Biologists, 2017, pp. 2172–84, doi:10.1242/jcs.200899.","ieee":"A. Veß et al., “A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity,” Journal of Cell Science, vol. 130, no. 13. Company of Biologists, pp. 2172–2184, 2017.","apa":"Veß, A., Blache, U., Leitner, L., Kurz, A., Ehrenpfordt, A., Sixt, M. K., & Posern, G. (2017). A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.200899","ista":"Veß A, Blache U, Leitner L, Kurz A, Ehrenpfordt A, Sixt MK, Posern G. 2017. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 130(13), 2172–2184.","ama":"Veß A, Blache U, Leitner L, et al. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 2017;130(13):2172-2184. doi:10.1242/jcs.200899"},"publication":"Journal of Cell Science","has_accepted_license":"1","day":"01","scopus_import":1,"file":[{"content_type":"application/pdf","file_size":10847596,"creator":"dernst","access_level":"open_access","file_name":"2017_CellScience_Vess.pdf","checksum":"42c81a0a4fc3128883b391c3af3f74bc","date_updated":"2020-07-14T12:47:45Z","date_created":"2019-10-24T09:43:56Z","relation":"main_file","file_id":"6966"}],"oa_version":"Published Version","intvolume":" 130","title":"A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"694","issue":"13","abstract":[{"text":"A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells.","lang":"eng"}],"type":"journal_article"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2017","volume":80,"date_created":"2018-12-11T11:47:59Z","date_updated":"2021-01-12T08:11:15Z","author":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"},{"first_name":"Maciej","last_name":"Skórski","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","full_name":"Skórski, Maciej"}],"article_number":"39","publist_id":"7003","ec_funded":1,"file_date_updated":"2020-07-14T12:47:46Z","project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"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,"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.ICALP.2017.39","conference":{"end_date":"2017-07-14","location":"Warsaw, Poland","start_date":"2017-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"publication_identifier":{"issn":["18688969"]},"month":"07","intvolume":" 80","ddc":["005"],"title":"Non uniform attacks against pseudoentropy","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"697","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-893-v1+1_LIPIcs-ICALP-2017-39.pdf","creator":"system","content_type":"application/pdf","file_size":601004,"file_id":"4701","relation":"main_file","checksum":"e95618a001692f1af2d68f5fde43bc1f","date_updated":"2020-07-14T12:47:46Z","date_created":"2018-12-12T10:08:40Z"}],"pubrep_id":"893","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions. "}],"citation":{"short":"K.Z. Pietrzak, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Pietrzak, Krzysztof Z., and Maciej Skórski. Non Uniform Attacks against Pseudoentropy. Vol. 80, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.ICALP.2017.39.","chicago":"Pietrzak, Krzysztof Z, and Maciej Skórski. “Non Uniform Attacks against Pseudoentropy,” Vol. 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.ICALP.2017.39.","ama":"Pietrzak KZ, Skórski M. Non uniform attacks against pseudoentropy. In: Vol 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.ICALP.2017.39","apa":"Pietrzak, K. Z., & Skórski, M. (2017). Non uniform attacks against pseudoentropy (Vol. 80). Presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2017.39","ieee":"K. Z. Pietrzak and M. Skórski, “Non uniform attacks against pseudoentropy,” presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland, 2017, vol. 80.","ista":"Pietrzak KZ, Skórski M. 2017. Non uniform attacks against pseudoentropy. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 80, 39."},"date_published":"2017-07-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01"},{"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","publist_id":"7001","file_date_updated":"2020-07-14T12:47:46Z","publisher":"American Society for Cell Biology","department":[{"_id":"CaUh"}],"publication_status":"published","year":"2017","volume":28,"date_updated":"2021-01-12T08:11:17Z","date_created":"2018-12-11T11:47:59Z","author":[{"first_name":"Yejun","last_name":"Wang","full_name":"Wang, Yejun"},{"full_name":"Nagarajan, Mallika","last_name":"Nagarajan","first_name":"Mallika"},{"full_name":"Uhler, Caroline","first_name":"Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216"},{"last_name":"Shivashankar","first_name":"Gv","full_name":"Shivashankar, Gv"}],"publication_identifier":{"issn":["10591524"]},"month":"07","project":[{"call_identifier":"FWF","name":"Gaussian Graphical Models: Theory and Applications","_id":"2530CA10-B435-11E9-9278-68D0E5697425","grant_number":"Y 903-N35"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"language":[{"iso":"eng"}],"doi":"10.1091/mbc.E16-12-0825","type":"journal_article","issue":"14","abstract":[{"text":"Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases. ","lang":"eng"}],"intvolume":" 28","title":"Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression","ddc":["519"],"status":"public","_id":"698","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"4844","date_created":"2018-12-12T10:10:53Z","date_updated":"2020-07-14T12:47:46Z","checksum":"de01dac9e30970cfa6ae902480a4e04d","file_name":"IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1086097,"creator":"system"}],"oa_version":"Published Version","pubrep_id":"892","scopus_import":1,"has_accepted_license":"1","day":"07","page":"1997 - 2009","citation":{"chicago":"Wang, Yejun, Mallika Nagarajan, Caroline Uhler, and Gv Shivashankar. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell. American Society for Cell Biology, 2017. https://doi.org/10.1091/mbc.E16-12-0825.","mla":"Wang, Yejun, et al. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell, vol. 28, no. 14, American Society for Cell Biology, 2017, pp. 1997–2009, doi:10.1091/mbc.E16-12-0825.","short":"Y. Wang, M. Nagarajan, C. Uhler, G. Shivashankar, Molecular Biology of the Cell 28 (2017) 1997–2009.","ista":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. 2017. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 28(14), 1997–2009.","apa":"Wang, Y., Nagarajan, M., Uhler, C., & Shivashankar, G. (2017). Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.E16-12-0825","ieee":"Y. Wang, M. Nagarajan, C. Uhler, and G. Shivashankar, “Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression,” Molecular Biology of the Cell, vol. 28, no. 14. American Society for Cell Biology, pp. 1997–2009, 2017.","ama":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 2017;28(14):1997-2009. doi:10.1091/mbc.E16-12-0825"},"publication":"Molecular Biology of the Cell","date_published":"2017-07-07T00:00:00Z"},{"pmid":1,"year":"2017","department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","publication_status":"published","author":[{"first_name":"Carl","last_name":"Veller","full_name":"Veller, Carl"},{"last_name":"Hayward","first_name":"Laura","full_name":"Hayward, Laura"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian"}],"volume":114,"date_created":"2018-12-11T11:48:00Z","date_updated":"2021-01-12T08:11:21Z","publist_id":"7002","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/"}],"external_id":{"pmid":["28630336"]},"quality_controlled":"1","doi":"10.1073/pnas.1702020114","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00278424"]},"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"699","intvolume":" 114","status":"public","title":"The red queen and king in finite populations","oa_version":"Submitted Version","type":"journal_article","issue":"27","abstract":[{"text":"In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. ","lang":"eng"}],"citation":{"ama":"Veller C, Hayward L, Nowak M, Hilbe C. The red queen and king in finite populations. PNAS. 2017;114(27):E5396-E5405. doi:10.1073/pnas.1702020114","ieee":"C. Veller, L. Hayward, M. Nowak, and C. Hilbe, “The red queen and king in finite populations,” PNAS, vol. 114, no. 27. National Academy of Sciences, pp. E5396–E5405, 2017.","apa":"Veller, C., Hayward, L., Nowak, M., & Hilbe, C. (2017). The red queen and king in finite populations. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1702020114","ista":"Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405.","short":"C. Veller, L. Hayward, M. Nowak, C. Hilbe, PNAS 114 (2017) E5396–E5405.","mla":"Veller, Carl, et al. “The Red Queen and King in Finite Populations.” PNAS, vol. 114, no. 27, National Academy of Sciences, 2017, pp. E5396–405, doi:10.1073/pnas.1702020114.","chicago":"Veller, Carl, Laura Hayward, Martin Nowak, and Christian Hilbe. “The Red Queen and King in Finite Populations.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1702020114."},"publication":"PNAS","page":"E5396 - E5405","date_published":"2017-07-03T00:00:00Z","scopus_import":1,"day":"03"},{"type":"journal_article","issue":"1","abstract":[{"text":"Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs.","lang":"eng"}],"_id":"700","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 96","status":"public","title":"Optomechanical proposal for monitoring microtubule mechanical vibrations","oa_version":"Submitted Version","scopus_import":1,"day":"12","citation":{"short":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, C. Simon, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017).","mla":"Barzanjeh, Shabir, et al. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1, 012404, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.012404.","chicago":"Barzanjeh, Shabir, Vahid Salari, Jack Tuszynski, Michal Cifra, and Christoph Simon. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.012404.","ama":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;96(1). doi:10.1103/PhysRevE.96.012404","ieee":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, and C. Simon, “Optomechanical proposal for monitoring microtubule mechanical vibrations,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017.","apa":"Barzanjeh, S., Salari, V., Tuszynski, J., Cifra, M., & Simon, C. (2017). Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.012404","ista":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. 2017. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 012404."},"publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","date_published":"2017-07-12T00:00:00Z","article_number":"012404","publist_id":"6997","ec_funded":1,"year":"2017","department":[{"_id":"JoFi"}],"publisher":"American Institute of Physics","publication_status":"published","author":[{"full_name":"Barzanjeh, Shabir","first_name":"Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423"},{"full_name":"Salari, Vahid","last_name":"Salari","first_name":"Vahid"},{"full_name":"Tuszynski, Jack","last_name":"Tuszynski","first_name":"Jack"},{"full_name":"Cifra, Michal","last_name":"Cifra","first_name":"Michal"},{"full_name":"Simon, Christoph","last_name":"Simon","first_name":"Christoph"}],"volume":96,"date_updated":"2023-02-23T12:56:35Z","date_created":"2018-12-11T11:48:00Z","publication_identifier":{"issn":["24700045"]},"month":"07","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/1612.07061.pdf"}],"project":[{"call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","grant_number":"707438","_id":"258047B6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1103/PhysRevE.96.012404","language":[{"iso":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"701","intvolume":" 24","ddc":["500"],"status":"public","title":"On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4","pubrep_id":"984","oa_version":"Submitted Version","file":[{"file_name":"IST-2018-984-v1+1_Patakova_on_the_nonexistence_of_k-reptile_simplices_in_R_3_and_R_4_2017.pdf","access_level":"open_access","creator":"system","file_size":544042,"content_type":"application/pdf","file_id":"5077","relation":"main_file","date_updated":"2020-07-14T12:47:47Z","date_created":"2018-12-12T10:14:25Z","checksum":"a431e573e31df13bc0f66de3061006ec"}],"type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"A d-dimensional simplex S is called a k-reptile (or a k-reptile simplex) if it can be tiled by k simplices with disjoint interiors that are all mutually congruent and similar to S. For d = 2, triangular k-reptiles exist for all k of the form a^2, 3a^2 or a^2+b^2 and they have been completely characterized by Snover, Waiveris, and Williams. On the other hand, the only k-reptile simplices that are known for d ≥ 3, have k = m^d, where m is a positive integer. We substantially simplify the proof by Matoušek and the second author that for d = 3, k-reptile tetrahedra can exist only for k = m^3. We then prove a weaker analogue of this result for d = 4 by showing that four-dimensional k-reptile simplices can exist only for k = m^2."}],"citation":{"ista":"Kynčl J, Patakova Z. 2017. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 24(3), 1–44.","ieee":"J. Kynčl and Z. Patakova, “On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4,” The Electronic Journal of Combinatorics, vol. 24, no. 3. International Press, pp. 1–44, 2017.","apa":"Kynčl, J., & Patakova, Z. (2017). On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. International Press.","ama":"Kynčl J, Patakova Z. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 2017;24(3):1-44.","chicago":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics. International Press, 2017.","mla":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics, vol. 24, no. 3, International Press, 2017, pp. 1–44.","short":"J. Kynčl, Z. Patakova, The Electronic Journal of Combinatorics 24 (2017) 1–44."},"publication":"The Electronic Journal of Combinatorics","page":"1-44","date_published":"2017-07-14T00:00:00Z","has_accepted_license":"1","day":"14","year":"2017","department":[{"_id":"UlWa"}],"publisher":"International Press","publication_status":"published","author":[{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"},{"full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova","first_name":"Zuzana"}],"volume":24,"date_updated":"2021-01-12T08:11:28Z","date_created":"2018-12-11T11:48:00Z","publist_id":"6996","file_date_updated":"2020-07-14T12:47:47Z","oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["10778926"]},"month":"07"},{"language":[{"iso":"eng"}],"doi":"10.1126/scitranslmed.aao0972","date_published":"2017-07-19T00:00:00Z","quality_controlled":"1","page":"eaao0972","publication":"Science Translational Medicine","citation":{"ieee":"G. Novarino, “The riddle of CHD8 haploinsufficiency in autism spectrum disorder,” Science Translational Medicine, vol. 9, no. 399. American Association for the Advancement of Science, p. eaao0972, 2017.","apa":"Novarino, G. (2017). The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao0972","ista":"Novarino G. 2017. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 9(399), eaao0972.","ama":"Novarino G. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 2017;9(399):eaao0972. doi:10.1126/scitranslmed.aao0972","chicago":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao0972.","short":"G. Novarino, Science Translational Medicine 9 (2017) eaao0972.","mla":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” Science Translational Medicine, vol. 9, no. 399, American Association for the Advancement of Science, 2017, p. eaao0972, doi:10.1126/scitranslmed.aao0972."},"day":"19","month":"07","publication_identifier":{"issn":["19466234"]},"scopus_import":1,"date_updated":"2021-01-12T08:11:31Z","date_created":"2018-12-11T11:48:01Z","oa_version":"None","volume":9,"author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia"}],"title":"The riddle of CHD8 haploinsufficiency in autism spectrum disorder","publication_status":"published","status":"public","intvolume":" 9","department":[{"_id":"GaNo"}],"publisher":"American Association for the Advancement of Science","_id":"702","year":"2017","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Leading autism-associated mutation in mouse partially mimics human disorder.\r\n\r\n","lang":"eng"}],"issue":"399","publist_id":"6993","type":"journal_article"},{"citation":{"ama":"Geng X, Maruo T, Mandai K, et al. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 2017;22(8):715-722. doi:10.1111/gtc.12508","ieee":"X. Geng et al., “Roles of afadin in functional differentiations of hippocampal mossy fiber synapse,” Genes to Cells, vol. 22, no. 8. Wiley-Blackwell, pp. 715–722, 2017.","apa":"Geng, X., Maruo, T., Mandai, K., Supriyanto, I., Miyata, M., Sakakibara, S., … Mori, M. (2017). Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. Wiley-Blackwell. https://doi.org/10.1111/gtc.12508","ista":"Geng X, Maruo T, Mandai K, Supriyanto I, Miyata M, Sakakibara S, Mizoguchi A, Takai Y, Mori M. 2017. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 22(8), 715–722.","short":"X. Geng, T. Maruo, K. Mandai, I. Supriyanto, M. Miyata, S. Sakakibara, A. Mizoguchi, Y. Takai, M. Mori, Genes to Cells 22 (2017) 715–722.","mla":"Geng, Xiaoqi, et al. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” Genes to Cells, vol. 22, no. 8, Wiley-Blackwell, 2017, pp. 715–22, doi:10.1111/gtc.12508.","chicago":"Geng, Xiaoqi, Tomohiko Maruo, Kenji Mandai, Irwan Supriyanto, Muneaki Miyata, Shotaro Sakakibara, Akira Mizoguchi, Yoshimi Takai, and Masahiro Mori. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” Genes to Cells. Wiley-Blackwell, 2017. https://doi.org/10.1111/gtc.12508."},"publication":"Genes to Cells","page":"715 - 722","quality_controlled":"1","doi":"10.1111/gtc.12508","date_published":"2017-08-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"publication_identifier":{"issn":["13569597"]},"month":"08","day":"01","year":"2017","_id":"706","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 22","publisher":"Wiley-Blackwell","department":[{"_id":"PeJo"}],"publication_status":"published","status":"public","title":"Roles of afadin in functional differentiations of hippocampal mossy fiber synapse","author":[{"id":"3395256A-F248-11E8-B48F-1D18A9856A87","last_name":"Geng","first_name":"Xiaoqi","full_name":"Geng, Xiaoqi"},{"full_name":"Maruo, Tomohiko","last_name":"Maruo","first_name":"Tomohiko"},{"full_name":"Mandai, Kenji","last_name":"Mandai","first_name":"Kenji"},{"full_name":"Supriyanto, Irwan","last_name":"Supriyanto","first_name":"Irwan"},{"full_name":"Miyata, Muneaki","first_name":"Muneaki","last_name":"Miyata"},{"first_name":"Shotaro","last_name":"Sakakibara","full_name":"Sakakibara, Shotaro"},{"last_name":"Mizoguchi","first_name":"Akira","full_name":"Mizoguchi, Akira"},{"full_name":"Takai, Yoshimi","first_name":"Yoshimi","last_name":"Takai"},{"first_name":"Masahiro","last_name":"Mori","full_name":"Mori, Masahiro"}],"volume":22,"oa_version":"None","date_updated":"2021-01-12T08:11:37Z","date_created":"2018-12-11T11:48:02Z","type":"journal_article","publist_id":"6987","issue":"8","abstract":[{"text":"A hippocampal mossy fiber synapse has a complex structure and is implicated in learning and memory. In this synapse, the mossy fiber boutons attach to the dendritic shaft by puncta adherentia junctions and wrap around a multiply-branched spine, forming synaptic junctions. We have recently shown using transmission electron microscopy, immunoelectron microscopy and serial block face-scanning electron microscopy that atypical puncta adherentia junctions are formed in the afadin-deficient mossy fiber synapse and that the complexity of postsynaptic spines and mossy fiber boutons, the number of spine heads, the area of postsynaptic densities and the density of synaptic vesicles docked to active zones are decreased in the afadin-deficient synapse. We investigated here the roles of afadin in the functional differentiations of the mossy fiber synapse using the afadin-deficient mice. The electrophysiological studies showed that both the release probability of glutamate and the postsynaptic responsiveness to glutamate were markedly reduced, but not completely lost, in the afadin-deficient mossy fiber synapse, whereas neither long-term potentiation nor long-term depression was affected. These results indicate that afadin plays roles in the functional differentiations of the presynapse and the postsynapse of the hippocampal mossy fiber synapse.","lang":"eng"}]},{"oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"707","intvolume":" 49","title":"A tight estimate for the waist of the ball ","status":"public","issue":"4","abstract":[{"lang":"eng","text":"We answer a question of M. Gromov on the waist of the unit ball."}],"type":"journal_article","date_published":"2017-08-01T00:00:00Z","citation":{"mla":"Akopyan, Arseniy, and Roman Karasev. “A Tight Estimate for the Waist of the Ball .” Bulletin of the London Mathematical Society, vol. 49, no. 4, Wiley-Blackwell, 2017, pp. 690–93, doi:10.1112/blms.12062.","short":"A. Akopyan, R. Karasev, Bulletin of the London Mathematical Society 49 (2017) 690–693.","chicago":"Akopyan, Arseniy, and Roman Karasev. “A Tight Estimate for the Waist of the Ball .” Bulletin of the London Mathematical Society. Wiley-Blackwell, 2017. https://doi.org/10.1112/blms.12062.","ama":"Akopyan A, Karasev R. A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. 2017;49(4):690-693. doi:10.1112/blms.12062","ista":"Akopyan A, Karasev R. 2017. A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. 49(4), 690–693.","apa":"Akopyan, A., & Karasev, R. (2017). A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. Wiley-Blackwell. https://doi.org/10.1112/blms.12062","ieee":"A. Akopyan and R. Karasev, “A tight estimate for the waist of the ball ,” Bulletin of the London Mathematical Society, vol. 49, no. 4. Wiley-Blackwell, pp. 690–693, 2017."},"publication":"Bulletin of the London Mathematical Society","page":"690 - 693","day":"01","scopus_import":1,"author":[{"first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"last_name":"Karasev","first_name":"Roman","full_name":"Karasev, Roman"}],"volume":49,"date_created":"2018-12-11T11:48:02Z","date_updated":"2021-01-12T08:11:41Z","year":"2017","publisher":"Wiley-Blackwell","department":[{"_id":"HeEd"}],"publication_status":"published","ec_funded":1,"publist_id":"6982","doi":"10.1112/blms.12062","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1608.06279","open_access":"1"}],"oa":1,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","publication_identifier":{"issn":["00246093"]},"month":"08"},{"publication_identifier":{"issn":["15449173"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.2001993","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,"publist_id":"6983","file_date_updated":"2020-07-14T12:47:49Z","article_number":"e2001993","volume":15,"date_created":"2018-12-11T11:48:03Z","date_updated":"2021-01-12T08:11:45Z","author":[{"full_name":"Nagy, Balint","last_name":"Nagy","first_name":"Balint","orcid":"0000-0002-4002-4686","id":"30F830CE-02D1-11E9-9BAA-DAF4881429F2"},{"full_name":"Hovhannisyan, Anahit","last_name":"Hovhannisyan","first_name":"Anahit"},{"full_name":"Barzan, Ruxandra","last_name":"Barzan","first_name":"Ruxandra"},{"first_name":"Ting","last_name":"Chen","full_name":"Chen, Ting"},{"first_name":"Maria","last_name":"Kukley","full_name":"Kukley, Maria"}],"department":[{"_id":"SaSi"}],"publisher":"Public Library of Science","publication_status":"published","year":"2017","has_accepted_license":"1","day":"22","scopus_import":1,"date_published":"2017-08-22T00:00:00Z","citation":{"ama":"Nagy B, Hovhannisyan A, Barzan R, Chen T, Kukley M. Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. 2017;15(8). doi:10.1371/journal.pbio.2001993","ista":"Nagy B, Hovhannisyan A, Barzan R, Chen T, Kukley M. 2017. Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. 15(8), e2001993.","apa":"Nagy, B., Hovhannisyan, A., Barzan, R., Chen, T., & Kukley, M. (2017). Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001993","ieee":"B. Nagy, A. Hovhannisyan, R. Barzan, T. Chen, and M. Kukley, “Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum,” PLoS Biology, vol. 15, no. 8. Public Library of Science, 2017.","mla":"Nagy, Balint, et al. “Different Patterns of Neuronal Activity Trigger Distinct Responses of Oligodendrocyte Precursor Cells in the Corpus Callosum.” PLoS Biology, vol. 15, no. 8, e2001993, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001993.","short":"B. Nagy, A. Hovhannisyan, R. Barzan, T. Chen, M. Kukley, PLoS Biology 15 (2017).","chicago":"Nagy, Balint, Anahit Hovhannisyan, Ruxandra Barzan, Ting Chen, and Maria Kukley. “Different Patterns of Neuronal Activity Trigger Distinct Responses of Oligodendrocyte Precursor Cells in the Corpus Callosum.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001993."},"publication":"PLoS Biology","issue":"8","abstract":[{"lang":"eng","text":"In the developing and adult brain, oligodendrocyte precursor cells (OPCs) are influenced by neuronal activity: they are involved in synaptic signaling with neurons, and their proliferation and differentiation into myelinating glia can be altered by transient changes in neuronal firing. An important question that has been unanswered is whether OPCs can discriminate different patterns of neuronal activity and respond to them in a distinct way. Here, we demonstrate in brain slices that the pattern of neuronal activity determines the functional changes triggered at synapses between axons and OPCs. Furthermore, we show that stimulation of the corpus callosum at different frequencies in vivo affects proliferation and differentiation of OPCs in a dissimilar way. Our findings suggest that neurons do not influence OPCs in “all-or-none” fashion but use their firing pattern to tune the response and behavior of these nonneuronal cells."}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":18155365,"creator":"system","file_name":"IST-2017-889-v1+1_journal.pbio.2001993.pdf","access_level":"open_access","date_created":"2018-12-12T10:15:35Z","date_updated":"2020-07-14T12:47:49Z","checksum":"0c974f430682dc832ea7b27ab5a93124","relation":"main_file","file_id":"5156"}],"pubrep_id":"889","intvolume":" 15","ddc":["576","610"],"status":"public","title":"Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum","_id":"708","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"month":"08","day":"01","publication_identifier":{"issn":["10656995"]},"scopus_import":1,"doi":"10.1002/cbin.10783","date_published":"2017-08-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Cell Biology International","citation":{"chicago":"Sun, Wuping, Chen Li, Yonghong Zhang, Changyu Jiang, Ming-Zhu Zhai, Qian Zhou, Lizu Xiao, and Qiwen Deng. “Gene Expression Changes of Thermo Sensitive Transient Receptor Potential Channels in Obese Mice.” Cell Biology International. Wiley-Blackwell, 2017. https://doi.org/10.1002/cbin.10783.","mla":"Sun, Wuping, et al. “Gene Expression Changes of Thermo Sensitive Transient Receptor Potential Channels in Obese Mice.” Cell Biology International, vol. 41, no. 8, Wiley-Blackwell, 2017, pp. 908–13, doi:10.1002/cbin.10783.","short":"W. Sun, C. Li, Y. Zhang, C. Jiang, M.-Z. Zhai, Q. Zhou, L. Xiao, Q. Deng, Cell Biology International 41 (2017) 908–913.","ista":"Sun W, Li C, Zhang Y, Jiang C, Zhai M-Z, Zhou Q, Xiao L, Deng Q. 2017. Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. 41(8), 908–913.","ieee":"W. Sun et al., “Gene expression changes of thermo sensitive transient receptor potential channels in obese mice,” Cell Biology International, vol. 41, no. 8. Wiley-Blackwell, pp. 908–913, 2017.","apa":"Sun, W., Li, C., Zhang, Y., Jiang, C., Zhai, M.-Z., Zhou, Q., … Deng, Q. (2017). Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. Wiley-Blackwell. https://doi.org/10.1002/cbin.10783","ama":"Sun W, Li C, Zhang Y, et al. Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. 2017;41(8):908-913. doi:10.1002/cbin.10783"},"quality_controlled":"1","page":"908 - 913","abstract":[{"text":"Adipose tissues play key roles in energy homeostasis. Brown adipocytes and beige adipocytes in white adipose tissue (WAT) share the similar characters of thermogenesis, both of them could be potential targets for obesity management. Several thermo-sensitive transient receptor potential channels (thermoTRPs) are shown to be involved in adipocyte biology. However, the expression pattern of thermoTRPs in adipose tissues from obese mice is still unknown. The mRNA expression of thermoTRPs in subcutaneous WAT (sWAT) and interscapular brown adipose tissue (iBAT) from lean and obese mice were measured using reverse transcriptase-quantitative PCRs (RT-qPCR). The results demonstrated that all 10 thermoTRPs are expressed in both iBAT and sWAT, and without significant difference in the mRNA expression level of thermoTRPs between these two tissues. Moreover, Trpv1 and Trpv3 mRNA expression levels in both iBAT and sWAT were significantly decreased in high fat diet (HFD)-induced obese mice and db/db (leptin receptor deficient) mice. Trpm2 mRNA expression level was significantly decreased only in sWAT from HFD-induced obese mice and db/db mice. On the other hand, Trpv2 and Trpv4 mRNA expression levels in iBAT and sWAT were significantly increased in HFD-induced obese mice and db/db mice. Taken together, we conclude that all 10 thermoTRPs are expressed in iBAT and sWAT. And several thermoTRPs differentially expressed in adipose tissues from HFD-induced obese mice and db/db mice, suggesting a potential involvement in anti-obesity regulations.","lang":"eng"}],"issue":"8","publist_id":"6981","type":"journal_article","author":[{"last_name":"Sun","first_name":"Wuping","full_name":"Sun, Wuping"},{"first_name":"Chen","last_name":"Li","full_name":"Li, Chen"},{"full_name":"Zhang, Yonghong","first_name":"Yonghong","last_name":"Zhang"},{"first_name":"Changyu","last_name":"Jiang","full_name":"Jiang, Changyu"},{"id":"34009CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Zhai","first_name":"Ming-Zhu","full_name":"Zhai, Ming-Zhu"},{"full_name":"Zhou, Qian","first_name":"Qian","last_name":"Zhou"},{"first_name":"Lizu","last_name":"Xiao","full_name":"Xiao, Lizu"},{"last_name":"Deng","first_name":"Qiwen","full_name":"Deng, Qiwen"}],"date_updated":"2021-01-12T08:11:47Z","date_created":"2018-12-11T11:48:04Z","volume":41,"oa_version":"None","_id":"709","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2017","title":"Gene expression changes of thermo sensitive transient receptor potential channels in obese mice","status":"public","publication_status":"published","intvolume":" 41","publisher":"Wiley-Blackwell","department":[{"_id":"RySh"}]},{"date_published":"2017-08-01T00:00:00Z","citation":{"ista":"Obremski M, Skórski M. 2017. Renyi entropy estimation revisited. 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, LIPIcs, vol. 81, 20.","ieee":"M. Obremski and M. Skórski, “Renyi entropy estimation revisited,” presented at the 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, Berkeley, USA, 2017, vol. 81.","apa":"Obremski, M., & Skórski, M. (2017). Renyi entropy estimation revisited (Vol. 81). Presented at the 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, Berkeley, USA: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20","ama":"Obremski M, Skórski M. Renyi entropy estimation revisited. In: Vol 81. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.APPROX-RANDOM.2017.20","chicago":"Obremski, Maciej, and Maciej Skórski. “Renyi Entropy Estimation Revisited,” Vol. 81. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20.","mla":"Obremski, Maciej, and Maciej Skórski. Renyi Entropy Estimation Revisited. Vol. 81, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.APPROX-RANDOM.2017.20.","short":"M. Obremski, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017."},"day":"01","has_accepted_license":"1","scopus_import":1,"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-888-v1+1_LIPIcs-APPROX-RANDOM-2017-20.pdf","content_type":"application/pdf","file_size":604813,"creator":"system","relation":"main_file","file_id":"4991","checksum":"89225c7dcec2c93838458c9102858985","date_updated":"2020-07-14T12:47:49Z","date_created":"2018-12-12T10:13:10Z"}],"pubrep_id":"888","title":"Renyi entropy estimation revisited","ddc":["005","600"],"status":"public","intvolume":" 81","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"710","abstract":[{"text":"We revisit the problem of estimating entropy of discrete distributions from independent samples, studied recently by Acharya, Orlitsky, Suresh and Tyagi (SODA 2015), improving their upper and lower bounds on the necessary sample size n. For estimating Renyi entropy of order alpha, up to constant accuracy and error probability, we show the following * Upper bounds n = O(1) 2^{(1-1/alpha)H_alpha} for integer alpha>1, as the worst case over distributions with Renyi entropy equal to H_alpha. * Lower bounds n = Omega(1) K^{1-1/alpha} for any real alpha>1, with the constant being an inverse polynomial of the accuracy, as the worst case over all distributions on K elements. Our upper bounds essentially replace the alphabet size by a factor exponential in the entropy, which offers improvements especially in low or medium entropy regimes (interesting for example in anomaly detection). As for the lower bounds, our proof explicitly shows how the complexity depends on both alphabet and accuracy, partially solving the open problem posted in previous works. The argument for upper bounds derives a clean identity for the variance of falling-power sum of a multinomial distribution. Our approach for lower bounds utilizes convex optimization to find a distribution with possibly worse estimation performance, and may be of independent interest as a tool to work with Le Cam’s two point method. ","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","language":[{"iso":"eng"}],"conference":{"name":"20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX","end_date":"2017-08-18","location":"Berkeley, USA","start_date":"2017-08-18"},"doi":"10.4230/LIPIcs.APPROX-RANDOM.2017.20","quality_controlled":"1","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"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"},"month":"08","publication_identifier":{"issn":["18688969"]},"date_updated":"2021-01-12T08:11:50Z","date_created":"2018-12-11T11:48:04Z","volume":81,"author":[{"full_name":"Obremski, Maciej","first_name":"Maciej","last_name":"Obremski"},{"last_name":"Skórski","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","full_name":"Skórski, Maciej"}],"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrPi"}],"year":"2017","file_date_updated":"2020-07-14T12:47:49Z","ec_funded":1,"publist_id":"6979","article_number":"20"},{"abstract":[{"lang":"eng","text":"To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the Igf2r cluster extending over 10 Mb in placenta."}],"type":"journal_article","file":[{"date_updated":"2020-07-14T12:47:50Z","date_created":"2018-12-12T10:13:36Z","checksum":"1ace3462e64a971b9ead896091829549","file_id":"5020","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":6399510,"file_name":"IST-2017-885-v1+1_elife-25125-figures-v2.pdf","access_level":"open_access"},{"date_updated":"2020-07-14T12:47:50Z","date_created":"2018-12-12T10:13:36Z","checksum":"6241dc31eeb87b03facadec3a53a6827","relation":"main_file","file_id":"5021","file_size":4264398,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-885-v1+2_elife-25125-v2.pdf","access_level":"open_access"}],"oa_version":"Published Version","pubrep_id":"885","title":"Mapping the mouse Allelome reveals tissue specific regulation of allelic expression","status":"public","ddc":["576"],"intvolume":" 6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"713","day":"14","has_accepted_license":"1","scopus_import":1,"date_published":"2017-08-14T00:00:00Z","publication":"eLife","citation":{"short":"D. Andergassen, C. Dotter, D. Wenzel, V. Sigl, P. Bammer, M. Muckenhuber, D. Mayer, T. Kulinski, H. Theussl, J. Penninger, C. Bock, D. Barlow, F. Pauler, Q. Hudson, ELife 6 (2017).","mla":"Andergassen, Daniel, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” ELife, vol. 6, e25125, eLife Sciences Publications, 2017, doi:10.7554/eLife.25125.","chicago":"Andergassen, Daniel, Christoph Dotter, Dyniel Wenzel, Verena Sigl, Philipp Bammer, Markus Muckenhuber, Daniela Mayer, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25125.","ama":"Andergassen D, Dotter C, Wenzel D, et al. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. eLife. 2017;6. doi:10.7554/eLife.25125","ieee":"D. Andergassen et al., “Mapping the mouse Allelome reveals tissue specific regulation of allelic expression,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"Andergassen, D., Dotter, C., Wenzel, D., Sigl, V., Bammer, P., Muckenhuber, M., … Hudson, Q. (2017). Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25125","ista":"Andergassen D, Dotter C, Wenzel D, Sigl V, Bammer P, Muckenhuber M, Mayer D, Kulinski T, Theussl H, Penninger J, Bock C, Barlow D, Pauler F, Hudson Q. 2017. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. eLife. 6, e25125."},"file_date_updated":"2020-07-14T12:47:50Z","publist_id":"6971","article_number":"e25125","date_created":"2018-12-11T11:48:05Z","date_updated":"2021-01-12T08:11:57Z","volume":6,"author":[{"full_name":"Andergassen, Daniel","first_name":"Daniel","last_name":"Andergassen"},{"full_name":"Dotter, Christoph","last_name":"Dotter","first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dyniel","last_name":"Wenzel","full_name":"Wenzel, Dyniel"},{"full_name":"Sigl, Verena","first_name":"Verena","last_name":"Sigl"},{"full_name":"Bammer, Philipp","first_name":"Philipp","last_name":"Bammer"},{"first_name":"Markus","last_name":"Muckenhuber","full_name":"Muckenhuber, Markus"},{"first_name":"Daniela","last_name":"Mayer","full_name":"Mayer, Daniela"},{"first_name":"Tomasz","last_name":"Kulinski","full_name":"Kulinski, Tomasz"},{"full_name":"Theussl, Hans","first_name":"Hans","last_name":"Theussl"},{"last_name":"Penninger","first_name":"Josef","full_name":"Penninger, Josef"},{"last_name":"Bock","first_name":"Christoph","full_name":"Bock, Christoph"},{"first_name":"Denise","last_name":"Barlow","full_name":"Barlow, Denise"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian"},{"full_name":"Hudson, Quanah","first_name":"Quanah","last_name":"Hudson"}],"publication_status":"published","department":[{"_id":"GaNo"},{"_id":"SiHi"}],"publisher":"eLife Sciences Publications","year":"2017","month":"08","publication_identifier":{"issn":["2050084X"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.25125","quality_controlled":"1","project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"}],"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"}},{"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.CONCUR.2017.5","conference":{"location":"Berlin, Germany","start_date":"2017-09-05","end_date":"2017-09-08","name":"28th International Conference on Concurrency Theory, CONCUR"},"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,"publication_identifier":{"issn":["18688969"]},"month":"08","volume":85,"date_created":"2018-12-11T11:48:04Z","date_updated":"2021-01-12T08:11:53Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","year":"2017","publist_id":"6976","file_date_updated":"2020-07-14T12:47:49Z","article_number":"5","date_published":"2017-08-01T00:00:00Z","citation":{"ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Bidirectional nested weighted automata. 28th International Conference on Concurrency Theory, CONCUR, LIPIcs, vol. 85, 5.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Bidirectional nested weighted automata (Vol. 85). Presented at the 28th International Conference on Concurrency Theory, CONCUR, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.5","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Bidirectional nested weighted automata,” presented at the 28th International Conference on Concurrency Theory, CONCUR, Berlin, Germany, 2017, vol. 85.","ama":"Chatterjee K, Henzinger TA, Otop J. Bidirectional nested weighted automata. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.5","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Bidirectional Nested Weighted Automata,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.CONCUR.2017.5.","mla":"Chatterjee, Krishnendu, et al. Bidirectional Nested Weighted Automata. Vol. 85, 5, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.5.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017."},"has_accepted_license":"1","day":"01","scopus_import":1,"oa_version":"Published Version","file":[{"file_size":570294,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2017-886-v1+1_LIPIcs-CONCUR-2017-5.pdf","checksum":"d2bda4783821a6358333fe27f11f4737","date_updated":"2020-07-14T12:47:49Z","date_created":"2018-12-12T10:08:02Z","relation":"main_file","file_id":"4661"}],"pubrep_id":"886","intvolume":" 85","status":"public","ddc":["004","005"],"title":"Bidirectional nested weighted automata","_id":"711","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Nested weighted automata (NWA) present a robust and convenient automata-theoretic formalism for quantitative specifications. Previous works have considered NWA that processed input words only in the forward direction. It is natural to allow the automata to process input words backwards as well, for example, to measure the maximal or average time between a response and the preceding request. We therefore introduce and study bidirectional NWA that can process input words in both directions. First, we show that bidirectional NWA can express interesting quantitative properties that are not expressible by forward-only NWA. Second, for the fundamental decision problems of emptiness and universality, we establish decidability and complexity results for the new framework which match the best-known results for the special case of forward-only NWA. Thus, for NWA, the increased expressiveness of bidirectionality is achieved at no additional computational complexity. This is in stark contrast to the unweighted case, where bidirectional finite automata are no more expressive but exponentially more succinct than their forward-only counterparts.","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference"},{"publisher":"Elsevier","intvolume":" 159","department":[{"_id":"JuFi"}],"title":"Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations","status":"public","publication_status":"published","_id":"712","year":"2017","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","volume":159,"oa_version":"Submitted Version","date_created":"2018-12-11T11:48:05Z","date_updated":"2021-01-12T08:11:55Z","author":[{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L","full_name":"Fischer, Julian L"}],"type":"journal_article","publist_id":"6975","abstract":[{"text":"We establish a weak–strong uniqueness principle for solutions to entropy-dissipating reaction–diffusion equations: As long as a strong solution to the reaction–diffusion equation exists, any weak solution and even any renormalized solution must coincide with this strong solution. Our assumptions on the reaction rates are just the entropy condition and local Lipschitz continuity; in particular, we do not impose any growth restrictions on the reaction rates. Therefore, our result applies to any single reversible reaction with mass-action kinetics as well as to systems of reversible reactions with mass-action kinetics satisfying the detailed balance condition. Renormalized solutions are known to exist globally in time for reaction–diffusion equations with entropy-dissipating reaction rates; in contrast, the global-in-time existence of weak solutions is in general still an open problem–even for smooth data–, thereby motivating the study of renormalized solutions. The key ingredient of our result is a careful adjustment of the usual relative entropy functional, whose evolution cannot be controlled properly for weak solutions or renormalized solutions.","lang":"eng"}],"page":"181 - 207","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1703.00730","open_access":"1"}],"oa":1,"citation":{"ama":"Fischer JL. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. 2017;159:181-207. doi:10.1016/j.na.2017.03.001","apa":"Fischer, J. L. (2017). Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. Elsevier. https://doi.org/10.1016/j.na.2017.03.001","ieee":"J. L. Fischer, “Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations,” Nonlinear Analysis: Theory, Methods and Applications, vol. 159. Elsevier, pp. 181–207, 2017.","ista":"Fischer JL. 2017. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. 159, 181–207.","short":"J.L. Fischer, Nonlinear Analysis: Theory, Methods and Applications 159 (2017) 181–207.","mla":"Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating Reaction–Diffusion Equations.” Nonlinear Analysis: Theory, Methods and Applications, vol. 159, Elsevier, 2017, pp. 181–207, doi:10.1016/j.na.2017.03.001.","chicago":"Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating Reaction–Diffusion Equations.” Nonlinear Analysis: Theory, Methods and Applications. Elsevier, 2017. https://doi.org/10.1016/j.na.2017.03.001."},"publication":"Nonlinear Analysis: Theory, Methods and Applications","language":[{"iso":"eng"}],"date_published":"2017-08-01T00:00:00Z","doi":"10.1016/j.na.2017.03.001","scopus_import":1,"publication_identifier":{"issn":["0362546X"]},"day":"01","month":"08"},{"abstract":[{"lang":"eng","text":"Background HIV-1 infection and drug abuse are frequently co-morbid and their association greatly increases the severity of HIV-1-induced neuropathology. While nucleus accumbens (NAcc) function is severely perturbed by drugs of abuse, little is known about how HIV-1 infection affects NAcc. Methods We used calcium and voltage imaging to investigate the effect of HIV-1 trans-activator of transcription (Tat) on rat NAcc. Based on previous neuronal studies, we hypothesized that Tat modulates intracellular Ca2+ homeostasis of NAcc neurons. Results We provide evidence that Tat triggers a Ca2+ signaling cascade in NAcc medium spiny neurons (MSN) expressing D1-like dopamine receptors leading to neuronal depolarization. Firstly, Tat induced inositol 1,4,5-trisphsophate (IP3) receptor-mediated Ca2+ release from endoplasmic reticulum, followed by Ca2+ and Na+ influx via transient receptor potential canonical channels. The influx of cations depolarizes the membrane promoting additional Ca2+ entry through voltage-gated P/Q-type Ca2+ channels and opening of tetrodotoxin-sensitive Na+ channels. By activating this mechanism, Tat elicits a feed-forward depolarization increasing the excitability of D1-phosphatidylinositol-linked NAcc MSN. We previously found that cocaine targets NAcc neurons directly (independent of the inhibition of dopamine transporter) only when IP3-generating mechanisms are concomitantly initiated. When tested here, cocaine produced a dose-dependent potentiation of the effect of Tat on cytosolic Ca2+. Conclusion We describe for the first time a HIV-1 Tat-triggered Ca2+ signaling in MSN of NAcc involving TRPC and depolarization and a potentiation of the effect of Tat by cocaine, which may be relevant for the reward axis in cocaine-abusing HIV-1-positive patients."}],"type":"journal_article","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"714","status":"public","title":"HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens","intvolume":" 178","day":"01","article_processing_charge":"No","scopus_import":1,"date_published":"2017-09-01T00:00:00Z","publication":"Drug and Alcohol Dependence","citation":{"ama":"Brailoiu G, Deliu E, Barr J, et al. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 2017;178:7-14. doi:10.1016/j.drugalcdep.2017.04.015","ista":"Brailoiu G, Deliu E, Barr J, Console Bram L, Ciuciu A, Abood M, Unterwald E, Brǎiloiu E. 2017. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 178, 7–14.","apa":"Brailoiu, G., Deliu, E., Barr, J., Console Bram, L., Ciuciu, A., Abood, M., … Brǎiloiu, E. (2017). HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. Elsevier. https://doi.org/10.1016/j.drugalcdep.2017.04.015","ieee":"G. Brailoiu et al., “HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens,” Drug and Alcohol Dependence, vol. 178. Elsevier, pp. 7–14, 2017.","mla":"Brailoiu, Gabriela, et al. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” Drug and Alcohol Dependence, vol. 178, Elsevier, 2017, pp. 7–14, doi:10.1016/j.drugalcdep.2017.04.015.","short":"G. Brailoiu, E. Deliu, J. Barr, L. Console Bram, A. Ciuciu, M. Abood, E. Unterwald, E. Brǎiloiu, Drug and Alcohol Dependence 178 (2017) 7–14.","chicago":"Brailoiu, Gabriela, Elena Deliu, Jeffrey Barr, Linda Console Bram, Alexandra Ciuciu, Mary Abood, Ellen Unterwald, and Eugen Brǎiloiu. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” Drug and Alcohol Dependence. Elsevier, 2017. https://doi.org/10.1016/j.drugalcdep.2017.04.015."},"article_type":"original","page":"7 - 14","publist_id":"6967","author":[{"first_name":"Gabriela","last_name":"Brailoiu","full_name":"Brailoiu, Gabriela"},{"full_name":"Deliu, Elena","first_name":"Elena","last_name":"Deliu","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5293"},{"full_name":"Barr, Jeffrey","last_name":"Barr","first_name":"Jeffrey"},{"full_name":"Console Bram, Linda","first_name":"Linda","last_name":"Console Bram"},{"last_name":"Ciuciu","first_name":"Alexandra","full_name":"Ciuciu, Alexandra"},{"last_name":"Abood","first_name":"Mary","full_name":"Abood, Mary"},{"last_name":"Unterwald","first_name":"Ellen","full_name":"Unterwald, Ellen"},{"last_name":"Brǎiloiu","first_name":"Eugen","full_name":"Brǎiloiu, Eugen"}],"date_created":"2018-12-11T11:48:05Z","date_updated":"2021-01-12T08:12:00Z","volume":178,"year":"2017","acknowledgement":"This work was supported by the National Institutes of Health grants DA035926 (to MEA), and P30DA013429 (to EMU).","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"GaNo"}],"month":"09","publication_identifier":{"issn":["03768716"]},"doi":"10.1016/j.drugalcdep.2017.04.015","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["28623807"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797705","open_access":"1"}],"quality_controlled":"1"},{"publist_id":"6968","issue":"405","abstract":[{"lang":"eng","text":"D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse model of Rett syndrome."}],"type":"journal_article","article_number":"aao4218","oa_version":"None","volume":9,"date_created":"2018-12-11T11:48:06Z","date_updated":"2021-01-12T08:12:04Z","author":[{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"}],"publisher":"American Association for the Advancement of Science","intvolume":" 9","department":[{"_id":"GaNo"}],"publication_status":"published","status":"public","title":"More excitation for Rett syndrome","_id":"715","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2017","publication_identifier":{"issn":["19466234"]},"month":"08","day":"30","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1126/scitranslmed.aao4218","date_published":"2017-08-30T00:00:00Z","quality_controlled":"1","citation":{"chicago":"Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao4218.","short":"G. Novarino, Science Translational Medicine 9 (2017).","mla":"Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational Medicine, vol. 9, no. 405, aao4218, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aao4218.","ieee":"G. Novarino, “More excitation for Rett syndrome,” Science Translational Medicine, vol. 9, no. 405. American Association for the Advancement of Science, 2017.","apa":"Novarino, G. (2017). More excitation for Rett syndrome. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao4218","ista":"Novarino G. 2017. More excitation for Rett syndrome. Science Translational Medicine. 9(405), aao4218.","ama":"Novarino G. More excitation for Rett syndrome. Science Translational Medicine. 2017;9(405). doi:10.1126/scitranslmed.aao4218"},"publication":"Science Translational Medicine"},{"publist_id":"6964","ec_funded":1,"volume":64,"date_created":"2018-12-11T11:48:06Z","date_updated":"2021-01-12T08:12:08Z","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Velner","first_name":"Yaron","full_name":"Velner, Yaron"}],"publisher":"ACM","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2017","publication_identifier":{"issn":["00045411"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1145/3121408","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1201.2829","open_access":"1"}],"external_id":{"arxiv":["1201.2829"]},"oa":1,"issue":"5","abstract":[{"lang":"eng","text":"Two-player games on graphs are central in many problems in formal verification and program analysis, such as synthesis and verification of open systems. In this work, we consider solving recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion.While pushdown games have been studied before with qualitative objectives-such as reachability and ?-regular objectives- in this work, we study for the first time such games with the most well-studied quantitative objective, the mean-payoff objective. In pushdown games, two types of strategies are relevant: (1) global strategies, which depend on the entire global history; and (2) modular strategies, which have only local memory and thus do not depend on the context of invocation but rather only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity by showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games and memoryless modular strategies are sufficient in two-player pushdown games. Finally, we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 64","title":"The complexity of mean-payoff pushdown games","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"716","day":"01","scopus_import":1,"date_published":"2017-09-01T00:00:00Z","page":"34","article_type":"original","citation":{"chicago":"Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” Journal of the ACM. ACM, 2017. https://doi.org/10.1145/3121408.","short":"K. Chatterjee, Y. Velner, Journal of the ACM 64 (2017) 34.","mla":"Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” Journal of the ACM, vol. 64, no. 5, ACM, 2017, p. 34, doi:10.1145/3121408.","ieee":"K. Chatterjee and Y. Velner, “The complexity of mean-payoff pushdown games,” Journal of the ACM, vol. 64, no. 5. ACM, p. 34, 2017.","apa":"Chatterjee, K., & Velner, Y. (2017). The complexity of mean-payoff pushdown games. Journal of the ACM. ACM. https://doi.org/10.1145/3121408","ista":"Chatterjee K, Velner Y. 2017. The complexity of mean-payoff pushdown games. Journal of the ACM. 64(5), 34.","ama":"Chatterjee K, Velner Y. The complexity of mean-payoff pushdown games. Journal of the ACM. 2017;64(5):34. doi:10.1145/3121408"},"publication":"Journal of the ACM"},{"publist_id":"6963","ec_funded":1,"volume":88,"date_updated":"2023-02-23T10:38:15Z","date_created":"2018-12-11T11:48:07Z","related_material":{"record":[{"id":"2329","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Velner","first_name":"Yaron","full_name":"Velner, Yaron"}],"publisher":"Academic Press","department":[{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the RICH Model Toolkit (ICT COST Action IC0901), and was carried out in partial fulfillment of the requirements for the Ph.D. degree of the second author.","year":"2017","month":"09","language":[{"iso":"eng"}],"doi":"10.1016/j.jcss.2017.04.005","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1210.3141","open_access":"1"}],"abstract":[{"lang":"eng","text":"We consider finite-state and recursive game graphs with multidimensional mean-payoff objectives. In recursive games two types of strategies are relevant: global strategies and modular strategies. Our contributions are: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of weights are fixed; whereas for arbitrary dimensions the problem is coNP-complete. (2) We show that one-player recursive games with multidimensional mean-payoff objectives can be solved in polynomial time. Both above algorithms are based on hyperplane separation technique. (3) For recursive games we show that under modular strategies the multidimensional problem is undecidable. We show that if the number of modules, exits, and the maximal absolute value of the weights are fixed, then one-dimensional recursive mean-payoff games under modular strategies can be solved in polynomial time, whereas for unbounded number of exits or modules the problem is NP-hard."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 88","status":"public","title":"Hyperplane separation technique for multidimensional mean-payoff games","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"717","day":"01","scopus_import":1,"date_published":"2017-09-01T00:00:00Z","page":"236 - 259","citation":{"chicago":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences. Academic Press, 2017. https://doi.org/10.1016/j.jcss.2017.04.005.","short":"K. Chatterjee, Y. Velner, Journal of Computer and System Sciences 88 (2017) 236–259.","mla":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences, vol. 88, Academic Press, 2017, pp. 236–59, doi:10.1016/j.jcss.2017.04.005.","ieee":"K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” Journal of Computer and System Sciences, vol. 88. Academic Press, pp. 236–259, 2017.","apa":"Chatterjee, K., & Velner, Y. (2017). Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. Academic Press. https://doi.org/10.1016/j.jcss.2017.04.005","ista":"Chatterjee K, Velner Y. 2017. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 88, 236–259.","ama":"Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 2017;88:236-259. doi:10.1016/j.jcss.2017.04.005"},"publication":"Journal of Computer and System Sciences"},{"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Ehlers","first_name":"Rüdiger","full_name":"Ehlers, Rüdiger"}],"date_updated":"2021-01-12T08:12:18Z","date_created":"2018-12-11T11:48:07Z","oa_version":"None","volume":54,"_id":"719","year":"2017","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Special issue: Synthesis and SYNT 2014","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}],"intvolume":" 54","abstract":[{"text":"The ubiquity of computation in modern machines and devices imposes a need to assert the correctness of their behavior. Especially in the case of safety-critical systems, their designers need to take measures that enforce their safe operation. Formal methods has emerged as a research field that addresses this challenge: by rigorously proving that all system executions adhere to their specifications, the correctness of an implementation under concern can be assured. To achieve this goal, a plethora of techniques are nowadays available, all of which are optimized for different system types and application domains.","lang":"eng"}],"publist_id":"6961","issue":"6","type":"journal_article","doi":"10.1007/s00236-017-0299-0","date_published":"2017-09-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Acta Informatica","citation":{"chicago":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-017-0299-0.","mla":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” Acta Informatica, vol. 54, no. 6, Springer, 2017, pp. 543–44, doi:10.1007/s00236-017-0299-0.","short":"K. Chatterjee, R. Ehlers, Acta Informatica 54 (2017) 543–544.","ista":"Chatterjee K, Ehlers R. 2017. Special issue: Synthesis and SYNT 2014. Acta Informatica. 54(6), 543–544.","ieee":"K. Chatterjee and R. Ehlers, “Special issue: Synthesis and SYNT 2014,” Acta Informatica, vol. 54, no. 6. Springer, pp. 543–544, 2017.","apa":"Chatterjee, K., & Ehlers, R. (2017). Special issue: Synthesis and SYNT 2014. Acta Informatica. Springer. https://doi.org/10.1007/s00236-017-0299-0","ama":"Chatterjee K, Ehlers R. Special issue: Synthesis and SYNT 2014. Acta Informatica. 2017;54(6):543-544. doi:10.1007/s00236-017-0299-0"},"quality_controlled":"1","page":"543 - 544","day":"01","month":"09","publication_identifier":{"issn":["00015903"]},"scopus_import":1}]