[{"author":[{"full_name":"Makohon Moore, Alvin","first_name":"Alvin","last_name":"Makohon Moore"},{"last_name":"Zhang","first_name":"Ming","full_name":"Zhang, Ming"},{"first_name":"Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes"},{"full_name":"Božić, Ivana","first_name":"Ivana","last_name":"Božić"},{"full_name":"Allen, Benjamin","first_name":"Benjamin","last_name":"Allen"},{"full_name":"Kundu, Deepanjan","id":"1d4c0f4f-e8a3-11ec-a351-e36772758c45","last_name":"Kundu","first_name":"Deepanjan"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Fay","last_name":"Wong","full_name":"Wong, Fay"},{"full_name":"Jiao, Yuchen","last_name":"Jiao","first_name":"Yuchen"},{"full_name":"Kohutek, Zachary","last_name":"Kohutek","first_name":"Zachary"},{"first_name":"Jungeui","last_name":"Hong","full_name":"Hong, Jungeui"},{"first_name":"Marc","last_name":"Attiyeh","full_name":"Attiyeh, Marc"},{"full_name":"Javier, Breanna","last_name":"Javier","first_name":"Breanna"},{"full_name":"Wood, Laura","first_name":"Laura","last_name":"Wood"},{"first_name":"Ralph","last_name":"Hruban","full_name":"Hruban, Ralph"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"},{"full_name":"Papadopoulos, Nickolas","last_name":"Papadopoulos","first_name":"Nickolas"},{"full_name":"Kinzler, Kenneth","first_name":"Kenneth","last_name":"Kinzler"},{"full_name":"Vogelstein, Bert","last_name":"Vogelstein","first_name":"Bert"},{"last_name":"Iacobuzio Donahue","first_name":"Christine","full_name":"Iacobuzio Donahue, Christine"}],"volume":49,"date_created":"2018-12-11T11:47:43Z","date_updated":"2022-06-10T09:55:08Z","pmid":1,"year":"2017","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.).","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","publication_status":"published","publist_id":"7092","ec_funded":1,"file_date_updated":"2020-07-14T12:47:33Z","doi":"10.1038/ng.3764","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["28092682"]},"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"}],"quality_controlled":"1","publication_identifier":{"issn":["10614036"]},"month":"03","oa_version":"Submitted Version","file":[{"checksum":"e442dc3b7420a36ec805e9bb45cc1a2e","date_created":"2019-11-19T08:13:50Z","date_updated":"2020-07-14T12:47:33Z","relation":"main_file","file_id":"7050","file_size":908099,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2017_NatureGenetics_Makohon.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"653","intvolume":" 49","title":"Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer","ddc":["000"],"status":"public","issue":"3","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."}],"type":"journal_article","date_published":"2017-03-01T00:00:00Z","citation":{"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.","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.","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","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","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.","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."},"publication":"Nature Genetics","page":"358 - 366","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1"},{"author":[{"first_name":"Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alwen, Joel F"},{"last_name":"Blocki","first_name":"Jeremiah","full_name":"Blocki, Jeremiah"},{"full_name":"Harsha, Ben","first_name":"Ben","last_name":"Harsha"}],"oa_version":"Submitted Version","date_updated":"2021-01-12T08:07:53Z","date_created":"2019-06-06T13:21:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6527","year":"2017","publisher":"ACM Press","department":[{"_id":"KrPi"}],"title":"Practical graphs for optimal side-channel resistant memory-hard functions","status":"public","publication_status":"published","ec_funded":1,"abstract":[{"lang":"eng","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"}],"type":"conference","doi":"10.1145/3133956.3134031","date_published":"2017-10-30T00:00:00Z","conference":{"name":"CCS: Conference on Computer and Communications Security","end_date":"2017-11-03","location":"Dallas, TX, USA","start_date":"2017-10-30"},"language":[{"iso":"eng"}],"citation":{"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.","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","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.","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."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/443"}],"publication":"Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security","page":"1001-1017","project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"quality_controlled":"1","publication_identifier":{"isbn":["9781450349468"]},"month":"10","day":"30","scopus_import":1},{"date_updated":"2021-01-12T08:07:54Z","date_created":"2018-12-11T11:47:44Z","volume":144,"author":[{"last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"},{"last_name":"Rivron","first_name":"Nicolas","full_name":"Rivron, Nicolas"}],"publication_status":"published","department":[{"_id":"AnKi"}],"publisher":"Company of Biologists","year":"2017","file_date_updated":"2020-07-14T12:47:33Z","publist_id":"7089","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1242/dev.144915","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037"}],"oa":1,"month":"03","publication_identifier":{"issn":["09501991"]},"oa_version":"Submitted Version","file":[{"checksum":"eef22a0f42a55b232cb2d1188a2322cb","date_created":"2018-12-12T10:15:20Z","date_updated":"2020-07-14T12:47:33Z","relation":"main_file","file_id":"5139","content_type":"application/pdf","file_size":228206,"creator":"system","access_level":"open_access","file_name":"IST-2018-987-v1+1_2017_KichevaRivron__Creating_to.pdf"}],"pubrep_id":"987","title":"Creating to understand – developmental biology meets engineering in Paris","ddc":["571"],"status":"public","intvolume":" 144","_id":"654","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"In November 2016, developmental biologists, synthetic biologists and engineers gathered in Paris for a meeting called ‘Engineering the embryo’. The participants shared an interest in exploring how synthetic systems can reveal new principles of embryonic development, and how the in vitro manipulation and modeling of development using stem cells can be used to integrate ideas and expertise from physics, developmental biology and tissue engineering. As we review here, the conference pinpointed some of the challenges arising at the intersection of these fields, along with great enthusiasm for finding new approaches and collaborations.","lang":"eng"}],"issue":"5","type":"journal_article","date_published":"2017-03-01T00:00:00Z","page":"733 - 736","publication":"Development","citation":{"short":"A. Kicheva, N. Rivron, Development 144 (2017) 733–736.","mla":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” Development, vol. 144, no. 5, Company of Biologists, 2017, pp. 733–36, doi:10.1242/dev.144915.","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","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","ista":"Kicheva A, Rivron N. 2017. Creating to understand – developmental biology meets engineering in Paris. Development. 144(5), 733–736."},"day":"01","has_accepted_license":"1","scopus_import":1},{"type":"conference","abstract":[{"lang":"eng","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."}],"title":"On the complexity of estimating Rènyi divergences","status":"public","_id":"6526","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":1,"day":"09","publication":"2017 IEEE International Symposium on Information Theory (ISIT)","citation":{"apa":"Skórski, M. (2017). On the complexity of estimating Rènyi divergences. In 2017 IEEE International Symposium on Information Theory (ISIT). Aachen, Germany: IEEE. https://doi.org/10.1109/isit.2017.8006529","ieee":"M. Skórski, “On the complexity of estimating Rènyi divergences,” in 2017 IEEE International Symposium on Information Theory (ISIT), Aachen, Germany, 2017.","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.","ama":"Skórski M. On the complexity of estimating Rènyi divergences. In: 2017 IEEE International Symposium on Information Theory (ISIT). IEEE; 2017. doi:10.1109/isit.2017.8006529","chicago":"Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” In 2017 IEEE International Symposium on Information Theory (ISIT). IEEE, 2017. https://doi.org/10.1109/isit.2017.8006529.","short":"M. Skórski, in:, 2017 IEEE International Symposium on Information Theory (ISIT), IEEE, 2017.","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."},"date_published":"2017-08-09T00:00:00Z","article_number":"8006529","ec_funded":1,"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"IEEE","year":"2017","date_created":"2019-06-06T12:53:09Z","date_updated":"2021-01-12T08:07:53Z","author":[{"full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski"}],"month":"08","publication_identifier":{"isbn":["9781509040964"]},"quality_controlled":"1","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"external_id":{"arxiv":["1702.01666"]},"main_file_link":[{"url":"https://arxiv.org/abs/1702.01666","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"ISIT: International Symposium on Information Theory","end_date":"2017-06-30","start_date":"2017-06-25","location":"Aachen, Germany"},"doi":"10.1109/isit.2017.8006529"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"655","status":"public","title":"Bacterial flagella grow through an injection diffusion mechanism","ddc":["579"],"intvolume":" 6","pubrep_id":"904","oa_version":"Published Version","file":[{"file_id":"4716","relation":"main_file","date_updated":"2020-07-14T12:47:33Z","date_created":"2018-12-12T10:08:53Z","checksum":"39e1c3e82ddac83a30422fa72fa1a383","file_name":"IST-2017-904-v1+1_elife-23136-v2.pdf","access_level":"open_access","creator":"system","file_size":5520359,"content_type":"application/pdf"},{"checksum":"a6d542253028f52e00aa29739ddffe8f","date_created":"2018-12-12T10:08:54Z","date_updated":"2020-07-14T12:47:33Z","file_id":"4717","relation":"main_file","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"}],"type":"journal_article","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."}],"publication":"eLife","citation":{"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","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","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.","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).","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.","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."},"date_published":"2017-03-06T00:00:00Z","scopus_import":1,"day":"06","has_accepted_license":"1","year":"2017","publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"eLife Sciences Publications","author":[{"full_name":"Renault, Thibaud","last_name":"Renault","first_name":"Thibaud"},{"full_name":"Abraham, Anthony","first_name":"Anthony","last_name":"Abraham"},{"full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346"},{"first_name":"Guillaume","last_name":"Paradis","full_name":"Paradis, Guillaume"},{"last_name":"Rainville","first_name":"Simon","full_name":"Rainville, Simon"},{"last_name":"Charpentier","first_name":"Emmanuelle","full_name":"Charpentier, Emmanuelle"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"},{"full_name":"Tu, Yuhai","last_name":"Tu","first_name":"Yuhai"},{"last_name":"Namba","first_name":"Keiichi","full_name":"Namba, Keiichi"},{"last_name":"Keener","first_name":"James","full_name":"Keener, James"},{"first_name":"Tohru","last_name":"Minamino","full_name":"Minamino, Tohru"},{"full_name":"Erhardt, Marc","first_name":"Marc","last_name":"Erhardt"}],"date_created":"2018-12-11T11:47:44Z","date_updated":"2021-01-12T08:07:55Z","volume":6,"article_number":"e23136","file_date_updated":"2020-07-14T12:47:33Z","publist_id":"7082","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"},"quality_controlled":"1","doi":"10.7554/eLife.23136","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["2050084X"]}},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373392/"}],"external_id":{"pmid":["28265057"]},"quality_controlled":"1","doi":"10.1073/pnas.1616493114","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00278424"]},"month":"03","pmid":1,"year":"2017","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","publication_status":"published","author":[{"full_name":"Möller, Barbara","last_name":"Möller","first_name":"Barbara"},{"full_name":"Ten Hove, Colette","last_name":"Ten Hove","first_name":"Colette"},{"first_name":"Daoquan","last_name":"Xiang","full_name":"Xiang, Daoquan"},{"full_name":"Williams, Nerys","first_name":"Nerys","last_name":"Williams"},{"last_name":"López","first_name":"Lorena","full_name":"López, Lorena"},{"full_name":"Yoshida, Saiko","last_name":"Yoshida","first_name":"Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Smit","first_name":"Margot","full_name":"Smit, Margot"},{"full_name":"Datla, Raju","first_name":"Raju","last_name":"Datla"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"}],"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."}]},{"quality_controlled":"1","citation":{"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.","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.","short":"G. Novarino, Science Translational Medicine 9 (2017).","ista":"Novarino G. 2017. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 9(381), eaam9867.","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","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.","ama":"Novarino G. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 2017;9(381). doi:10.1126/scitranslmed.aam9867"},"publication":"Science Translational Medicine","language":[{"iso":"eng"}],"date_published":"2017-03-15T00:00:00Z","doi":"10.1126/scitranslmed.aam9867","scopus_import":1,"publication_identifier":{"issn":["19466234"]},"month":"03","day":"15","publisher":"American Association for the Advancement of Science","intvolume":" 9","department":[{"_id":"GaNo"}],"title":"Modeling Alzheimer's disease in mice with human neurons","status":"public","publication_status":"published","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"656","year":"2017","oa_version":"None","volume":9,"date_updated":"2021-01-12T08:07:59Z","date_created":"2018-12-11T11:47:45Z","author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia"}],"type":"journal_article","article_number":"eaam9867","issue":"381","publist_id":"7079","abstract":[{"lang":"eng","text":"Human neurons transplanted into a mouse model for Alzheimer’s disease show human-specific vulnerability to β-amyloid plaques and may help to identify new therapeutic targets."}]},{"ec_funded":1,"publist_id":"7078","file_date_updated":"2020-07-14T12:47:33Z","article_number":"00008","author":[{"last_name":"Der","first_name":"Ralf","full_name":"Der, Ralf"},{"full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","last_name":"Martius","first_name":"Georg S"}],"volume":11,"date_updated":"2021-01-12T08:08:04Z","date_created":"2018-12-11T11:47:45Z","year":"2017","publisher":"Frontiers Research Foundation","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publication_status":"published","publication_identifier":{"issn":["16625218"]},"month":"03","doi":"10.3389/fnbot.2017.00008","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,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","issue":"MAR","abstract":[{"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.","lang":"eng"}],"type":"journal_article","pubrep_id":"903","file":[{"creator":"system","content_type":"application/pdf","file_size":8439566,"access_level":"open_access","file_name":"IST-2017-903-v1+1_fnbot-11-00008.pdf","checksum":"b1bc43f96d1df3313c03032c2a46388d","date_updated":"2020-07-14T12:47:33Z","date_created":"2018-12-12T10:18:49Z","file_id":"5371","relation":"main_file"}],"oa_version":"Published Version","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","_id":"658","intvolume":" 11","ddc":["006"],"status":"public","title":"Self organized behavior generation for musculoskeletal robots","article_processing_charge":"Yes","has_accepted_license":"1","day":"16","scopus_import":1,"date_published":"2017-03-16T00:00:00Z","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"},{"publication":"Nature Communications","citation":{"mla":"Kage, Frieda, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications, vol. 8, 14832, Nature Publishing Group, 2017, doi:10.1038/ncomms14832.","short":"F. Kage, M. Winterhoff, V. Dimchev, J. Müller, T. Thalheim, A. Freise, S. Brühmann, J. Kollasser, J. Block, G.A. Dimchev, M. Geyer, H. Schnittler, C. Brakebusch, T. Stradal, M. Carlier, M.K. Sixt, J. Käs, J. Faix, K. Rottner, Nature Communications 8 (2017).","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.","ama":"Kage F, Winterhoff M, Dimchev V, et al. FMNL formins boost lamellipodial force generation. Nature Communications. 2017;8. doi:10.1038/ncomms14832","ista":"Kage F, Winterhoff M, Dimchev V, Müller J, Thalheim T, Freise A, Brühmann S, Kollasser J, Block J, Dimchev GA, Geyer M, Schnittler H, Brakebusch C, Stradal T, Carlier M, Sixt MK, Käs J, Faix J, Rottner K. 2017. FMNL formins boost lamellipodial force generation. Nature Communications. 8, 14832.","ieee":"F. Kage et al., “FMNL formins boost lamellipodial force generation,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","apa":"Kage, F., Winterhoff, M., Dimchev, V., Müller, J., Thalheim, T., Freise, A., … Rottner, K. (2017). FMNL formins boost lamellipodial force generation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14832"},"date_published":"2017-03-22T00:00:00Z","scopus_import":1,"day":"22","article_processing_charge":"No","has_accepted_license":"1","_id":"659","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"FMNL formins boost lamellipodial force generation","status":"public","ddc":["570"],"intvolume":" 8","pubrep_id":"902","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":9523746,"access_level":"open_access","file_name":"IST-2017-902-v1+1_Kage_et_al-2017-Nature_Communications.pdf","checksum":"dae30190291c3630e8102d8714a8d23e","date_created":"2018-12-12T10:14:21Z","date_updated":"2020-07-14T12:47:34Z","file_id":"5072","relation":"main_file"}],"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"}],"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"},"quality_controlled":"1","doi":"10.1038/ncomms14832","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["20411723"]},"year":"2017","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"MiSi"}],"author":[{"full_name":"Kage, Frieda","last_name":"Kage","first_name":"Frieda"},{"full_name":"Winterhoff, Moritz","last_name":"Winterhoff","first_name":"Moritz"},{"full_name":"Dimchev, Vanessa","first_name":"Vanessa","last_name":"Dimchev"},{"full_name":"Müller, Jan","last_name":"Müller","first_name":"Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D"},{"full_name":"Thalheim, Tobias","first_name":"Tobias","last_name":"Thalheim"},{"full_name":"Freise, Anika","last_name":"Freise","first_name":"Anika"},{"last_name":"Brühmann","first_name":"Stefan","full_name":"Brühmann, Stefan"},{"first_name":"Jana","last_name":"Kollasser","full_name":"Kollasser, Jana"},{"last_name":"Block","first_name":"Jennifer","full_name":"Block, Jennifer"},{"full_name":"Dimchev, Georgi A","first_name":"Georgi A","last_name":"Dimchev"},{"full_name":"Geyer, Matthias","last_name":"Geyer","first_name":"Matthias"},{"full_name":"Schnittler, Hams","first_name":"Hams","last_name":"Schnittler"},{"full_name":"Brakebusch, Cord","last_name":"Brakebusch","first_name":"Cord"},{"full_name":"Stradal, Theresia","first_name":"Theresia","last_name":"Stradal"},{"full_name":"Carlier, Marie","first_name":"Marie","last_name":"Carlier"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"},{"first_name":"Josef","last_name":"Käs","full_name":"Käs, Josef"},{"full_name":"Faix, Jan","first_name":"Jan","last_name":"Faix"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"}],"date_updated":"2021-01-12T08:08:06Z","date_created":"2018-12-11T11:47:46Z","volume":8,"article_number":"14832","file_date_updated":"2020-07-14T12:47:34Z","publist_id":"7075"},{"month":"03","publication_identifier":{"issn":["00278424"]},"quality_controlled":"1","external_id":{"pmid":["28280102"]},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5380103/","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1620274114","publist_id":"7073","publication_status":"published","department":[{"_id":"MaLo"}],"publisher":"National Academy of Sciences","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,"date_created":"2018-12-11T11:47:46Z","date_updated":"2021-01-12T08:08:09Z","volume":114,"author":[{"last_name":"Rickman","first_name":"Jamie","full_name":"Rickman, Jamie"},{"last_name":"Düllberg","first_name":"Christian F","orcid":"0000-0001-6335-9748","id":"459064DC-F248-11E8-B48F-1D18A9856A87","full_name":"Düllberg, Christian F"},{"full_name":"Cade, Nicholas","last_name":"Cade","first_name":"Nicholas"},{"last_name":"Griffin","first_name":"Lewis","full_name":"Griffin, Lewis"},{"first_name":"Thomas","last_name":"Surrey","full_name":"Surrey, Thomas"}],"scopus_import":1,"day":"28","page":"3427 - 3432","publication":"PNAS","citation":{"chicago":"Rickman, Jamie, Christian F Düllberg, Nicholas Cade, Lewis Griffin, and Thomas Surrey. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1620274114.","short":"J. Rickman, C.F. Düllberg, N. Cade, L. Griffin, T. Surrey, PNAS 114 (2017) 3427–3432.","mla":"Rickman, Jamie, et al. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS, vol. 114, no. 13, National Academy of Sciences, 2017, pp. 3427–32, doi:10.1073/pnas.1620274114.","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.","ista":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. 2017. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 114(13), 3427–3432.","ama":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 2017;114(13):3427-3432. doi:10.1073/pnas.1620274114"},"date_published":"2017-03-28T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"13","status":"public","title":"Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation","intvolume":" 114","_id":"660","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version"},{"article_number":"044107","publist_id":"7072","year":"2017","publisher":"American Institute of Physics","department":[{"_id":"BjHo"}],"publication_status":"published","author":[{"last_name":"Shi","first_name":"Liang","full_name":"Shi, Liang"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"},{"full_name":"Rampp, Markus","first_name":"Markus","last_name":"Rampp"},{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"}],"volume":29,"date_updated":"2021-01-12T08:08:15Z","date_created":"2018-12-11T11:47:47Z","publication_identifier":{"issn":["10706631"]},"month":"04","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1703.01714","open_access":"1"}],"project":[{"name":"Astrophysical instability of currents and turbulences","grant_number":"SFB 963 TP A8","_id":"2511D90C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1063/1.4981525","language":[{"iso":"eng"}],"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"We report a direct-numerical-simulation study of the Taylor-Couette flow in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian rotating flow has been investigated for decades as a simplified model system to study the origin of turbulence in accretion disks that is not fully understood. The flow in this study is axially periodic and thus the experimental end-wall effects on the stability of the flow are avoided. Using optimal linear perturbations as initial conditions, our simulations find no sustained turbulence: the strong initial perturbations distort the velocity profile and trigger turbulence that eventually decays."}],"_id":"662","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 29","title":"Hydrodynamic turbulence in quasi Keplerian rotating flows","status":"public","oa_version":"Submitted Version","scopus_import":1,"day":"01","citation":{"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.","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","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.","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)."},"publication":"Physics of Fluids","date_published":"2017-04-01T00:00:00Z"},{"publication_identifier":{"isbn":["978-145034590-3"]},"month":"04","oa":1,"quality_controlled":"1","doi":"10.1145/3049797.3049814","conference":{"location":"Pittsburgh, PA, United States","start_date":"2017-04-18","end_date":"2017-04-20","name":"HSCC: Hybrid Systems Computation and Control "},"language":[{"iso":"eng"}],"publist_id":"7067","file_date_updated":"2020-07-14T12:47:34Z","year":"2017","department":[{"_id":"ToHe"}],"publisher":"ACM","publication_status":"published","author":[{"full_name":"Kong, Hui","first_name":"Hui","last_name":"Kong","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941"},{"orcid":"0000-0002-0686-0365","last_name":"Bogomolov","first_name":"Sergiy","full_name":"Bogomolov, Sergiy"},{"full_name":"Schilling, Christian","first_name":"Christian","last_name":"Schilling"},{"last_name":"Jiang","first_name":"Yu","full_name":"Jiang, Yu"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"date_updated":"2021-01-12T08:08:17Z","date_created":"2018-12-11T11:47:47Z","scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"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.","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","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.","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."},"publication":"Proceedings of the 20th International Conference on Hybrid Systems","page":"163 - 172","date_published":"2017-04-01T00:00:00Z","type":"conference","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. "}],"_id":"663","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"title":"Safety verification of nonlinear hybrid systems based on invariant clusters","status":"public","pubrep_id":"817","oa_version":"Submitted Version","file":[{"creator":"system","content_type":"application/pdf","file_size":1650530,"access_level":"open_access","file_name":"IST-2017-817-v1+1_p163-kong.pdf","checksum":"b7667434cbf5b5f0ade3bea1dbe5bf63","date_created":"2018-12-12T10:11:20Z","date_updated":"2020-07-14T12:47:34Z","file_id":"4873","relation":"main_file"}]},{"publist_id":"7060","issue":"387","abstract":[{"lang":"eng","text":"Perinatal exposure to penicillin may result in longlasting gut and behavioral changes."}],"type":"journal_article","article_number":"2786","author":[{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"}],"volume":9,"oa_version":"None","date_created":"2018-12-11T11:47:48Z","date_updated":"2021-01-12T08:08:30Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"667","year":"2017","publisher":"American Association for the Advancement of Science","department":[{"_id":"GaNo"}],"intvolume":" 9","status":"public","title":"The antisocial side of antibiotics","publication_status":"published","publication_identifier":{"issn":["19466234"]},"day":"26","month":"04","scopus_import":1,"date_published":"2017-04-26T00:00:00Z","doi":"10.1126/scitranslmed.aan2786","language":[{"iso":"eng"}],"citation":{"short":"G. Novarino, Science Translational Medicine 9 (2017).","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.","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.","ama":"Novarino G. The antisocial side of antibiotics. Science Translational Medicine. 2017;9(387). doi:10.1126/scitranslmed.aan2786","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","ista":"Novarino G. 2017. The antisocial side of antibiotics. Science Translational Medicine. 9(387), 2786."},"publication":"Science Translational Medicine","quality_controlled":"1"},{"month":"04","publication_identifier":{"issn":["00219258"]},"oa":1,"quality_controlled":"1","doi":"10.1074/jbc.M116.766923","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:37Z","publist_id":"7059","year":"2017","publication_status":"published","publisher":"American Society for Biochemistry and Molecular Biology","department":[{"_id":"MiSi"}],"author":[{"last_name":"Horsthemke","first_name":"Markus","full_name":"Horsthemke, Markus"},{"first_name":"Anne","last_name":"Bachg","full_name":"Bachg, Anne"},{"full_name":"Groll, Katharina","first_name":"Katharina","last_name":"Groll"},{"full_name":"Moyzio, Sven","last_name":"Moyzio","first_name":"Sven"},{"last_name":"Müther","first_name":"Barbara","full_name":"Müther, Barbara"},{"full_name":"Hemkemeyer, Sandra","last_name":"Hemkemeyer","first_name":"Sandra"},{"full_name":"Wedlich Söldner, Roland","first_name":"Roland","last_name":"Wedlich Söldner"},{"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":"Tacke, Sebastian","first_name":"Sebastian","last_name":"Tacke"},{"full_name":"Bähler, Martin","last_name":"Bähler","first_name":"Martin"},{"full_name":"Hanley, Peter","last_name":"Hanley","first_name":"Peter"}],"date_updated":"2021-01-12T08:08:34Z","date_created":"2018-12-11T11:47:49Z","volume":292,"scopus_import":1,"day":"28","has_accepted_license":"1","publication":"Journal of Biological Chemistry","citation":{"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","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.","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."},"article_type":"original","page":"7258 - 7273","date_published":"2017-04-28T00:00:00Z","type":"journal_article","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."}],"issue":"17","_id":"668","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion","status":"public","ddc":["570"],"intvolume":" 292","oa_version":"Published Version","file":[{"checksum":"d488162874326a4bb056065fa549dc4a","date_created":"2019-10-24T15:25:42Z","date_updated":"2020-07-14T12:47:37Z","file_id":"6971","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":5647880,"access_level":"open_access","file_name":"2017_JBC_Horsthemke.pdf"}]},{"_id":"669","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 174","ddc":["580"],"title":"EXO70C2 is a key regulatory factor for optimal tip growth of pollen","status":"public","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:47:37Z","date_created":"2019-11-18T16:16:18Z","checksum":"97155acc6aa5f0d0a78e0589a932fe02","file_id":"7041","relation":"main_file","creator":"dernst","file_size":2176903,"content_type":"application/pdf","file_name":"2017_PlantPhysio_Synek.pdf","access_level":"open_access"}],"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"}],"citation":{"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.","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.","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","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.","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.","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"},"publication":"Plant Physiology","page":"223 - 240","article_type":"original","date_published":"2017-05-01T00:00:00Z","scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"01","pmid":1,"year":"2017","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"full_name":"Synek, Lukáš","last_name":"Synek","first_name":"Lukáš"},{"first_name":"Nemanja","last_name":"Vukašinović","full_name":"Vukašinović, Nemanja"},{"full_name":"Kulich, Ivan","last_name":"Kulich","first_name":"Ivan"},{"full_name":"Hála, Michal","first_name":"Michal","last_name":"Hála"},{"full_name":"Aldorfová, Klára","last_name":"Aldorfová","first_name":"Klára"},{"full_name":"Fendrych, Matyas","last_name":"Fendrych","first_name":"Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Žárský","first_name":"Viktor","full_name":"Žárský, Viktor"}],"volume":174,"date_updated":"2021-01-12T08:08:35Z","date_created":"2018-12-11T11:47:49Z","publist_id":"7058","file_date_updated":"2020-07-14T12:47:37Z","external_id":{"pmid":["28356503"]},"oa":1,"quality_controlled":"1","doi":"10.1104/pp.16.01282","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00320889"]},"month":"05"},{"doi":"10.1073/pnas.1621239114","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422766/","open_access":"1"}],"external_id":{"pmid":["28420786"]},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_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","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"}],"month":"05","publication_identifier":{"issn":["00278424"]},"author":[{"orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","first_name":"Christian","full_name":"Hilbe, Christian"},{"full_name":"Martinez, Vaquero","first_name":"Vaquero","last_name":"Martinez"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"date_updated":"2021-01-12T08:08:37Z","date_created":"2018-12-11T11:47:50Z","volume":114,"year":"2017","pmid":1,"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","ec_funded":1,"publist_id":"7053","date_published":"2017-05-02T00:00:00Z","publication":"PNAS","citation":{"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.","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","ista":"Hilbe C, Martinez V, Chatterjee K, Nowak M. 2017. Memory-n strategies of direct reciprocity. PNAS. 114(18), 4715–4720.","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","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.","short":"C. Hilbe, V. Martinez, K. Chatterjee, M. Nowak, PNAS 114 (2017) 4715–4720.","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."},"page":"4715 - 4720","day":"02","article_processing_charge":"Yes (in subscription journal)","scopus_import":1,"oa_version":"Published Version","_id":"671","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Memory-n strategies of direct reciprocity","intvolume":" 114","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"},{"publication_identifier":{"issn":["01677055"]},"month":"05","oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01647113/file/eg_2017_schreck_paper_tearing.pdf"}],"project":[{"call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images","_id":"25357BD2-B435-11E9-9278-68D0E5697425","grant_number":"P 24352-N23"}],"quality_controlled":"1","doi":"10.1111/cgf.13110","language":[{"iso":"eng"}],"publist_id":"7056","year":"2017","publisher":"Wiley","department":[{"_id":"ChWo"}],"publication_status":"published","author":[{"full_name":"Schreck, Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","first_name":"Camille","last_name":"Schreck"},{"full_name":"Rohmer, Damien","last_name":"Rohmer","first_name":"Damien"},{"full_name":"Hahmann, Stefanie","last_name":"Hahmann","first_name":"Stefanie"}],"volume":36,"date_created":"2018-12-11T11:47:49Z","date_updated":"2021-01-12T08:08:37Z","scopus_import":1,"article_processing_charge":"No","day":"01","citation":{"chicago":"Schreck, Camille, Damien Rohmer, and Stefanie Hahmann. “Interactive Paper Tearing.” Computer Graphics Forum. Wiley, 2017. https://doi.org/10.1111/cgf.13110.","short":"C. Schreck, D. Rohmer, S. Hahmann, Computer Graphics Forum 36 (2017) 95–106.","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.","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.","ista":"Schreck C, Rohmer D, Hahmann S. 2017. Interactive paper tearing. Computer Graphics Forum. 36(2), 95–106.","ama":"Schreck C, Rohmer D, Hahmann S. Interactive paper tearing. Computer Graphics Forum. 2017;36(2):95-106. doi:10.1111/cgf.13110"},"publication":"Computer Graphics Forum","page":"95 - 106","article_type":"original","date_published":"2017-05-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"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.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"670","intvolume":" 36","ddc":["000"],"status":"public","title":"Interactive paper tearing","oa_version":"Published Version"},{"type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"5","status":"public","title":"Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia","ddc":["570"],"intvolume":" 19","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"672","file":[{"access_level":"open_access","file_name":"IST-2017-900-v1+1_1-s2.0-S2211124717305211-main.pdf","creator":"system","file_size":2248814,"content_type":"application/pdf","file_id":"5109","relation":"main_file","checksum":"8fdddaab1f1d76a6ec9ca94dcb6b07a2","date_updated":"2020-07-14T12:47:38Z","date_created":"2018-12-12T10:14:54Z"}],"oa_version":"Published Version","pubrep_id":"900","scopus_import":1,"day":"02","article_processing_charge":"Yes","has_accepted_license":"1","page":"902 - 909","publication":"Cell Reports","citation":{"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.","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","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.","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."},"date_published":"2017-05-02T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:47:38Z","publist_id":"7052","ec_funded":1,"publication_status":"published","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publisher":"Cell Press","year":"2017","date_created":"2018-12-11T11:47:50Z","date_updated":"2023-02-23T12:50:09Z","volume":19,"author":[{"full_name":"Vaahtomeri, Kari","first_name":"Kari","last_name":"Vaahtomeri","id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518"},{"full_name":"Brown, Markus","first_name":"Markus","last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild"},{"last_name":"De Vries","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"De Vries, Ingrid"},{"full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F"},{"last_name":"Mehling","first_name":"Matthias","orcid":"0000-0001-8599-1226","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","full_name":"Mehling, Matthias"},{"last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"month":"05","publication_identifier":{"issn":["22111247"]},"quality_controlled":"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"}],"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,"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2017.04.027"},{"type":"journal_article","issue":"9","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"}],"intvolume":" 27","title":"Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6","status":"public","_id":"674","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"None","scopus_import":1,"day":"09","page":"1314 - 1325","citation":{"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","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.","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","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.","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.","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."},"publication":"Current Biology","date_published":"2017-05-09T00:00:00Z","ec_funded":1,"publist_id":"7050","publisher":"Cell Press","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"publication_status":"published","year":"2017","volume":27,"date_created":"2018-12-11T11:47:51Z","date_updated":"2023-02-23T12:50:44Z","author":[{"full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Schwarz"},{"full_name":"Bierbaum, Veronika","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","first_name":"Veronika","last_name":"Bierbaum"},{"first_name":"Kari","last_name":"Vaahtomeri","id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari"},{"first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","first_name":"Markus"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries","first_name":"Ingrid","full_name":"De Vries, Ingrid"},{"first_name":"Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F"},{"full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat","first_name":"Anne"},{"last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"last_name":"Tarrant","first_name":"Teresa","full_name":"Tarrant, Teresa"},{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Tobias","full_name":"Bollenbach, Tobias"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"publication_identifier":{"issn":["09609822"]},"month":"05","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_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","language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2017.04.004"},{"publication_status":"published","publisher":"Cell Press","department":[{"_id":"MiSi"}],"year":"2017","date_updated":"2021-01-12T08:08:57Z","date_created":"2018-12-11T11:47:52Z","volume":19,"author":[{"first_name":"Claudio","last_name":"Lademann","full_name":"Lademann, Claudio"},{"full_name":"Renkawitz, Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","first_name":"Jörg","last_name":"Renkawitz"},{"full_name":"Pfander, Boris","last_name":"Pfander","first_name":"Boris"},{"full_name":"Jentsch, Stefan","last_name":"Jentsch","first_name":"Stefan"}],"file_date_updated":"2020-07-14T12:47:40Z","publist_id":"7046","quality_controlled":"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"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2017.04.051","month":"05","publication_identifier":{"issn":["22111247"]},"ddc":["570"],"title":"The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination","status":"public","intvolume":" 19","_id":"677","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"IST-2017-899-v1+1_1-s2.0-S2211124717305454-main.pdf","access_level":"open_access","file_size":3005610,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5171","date_updated":"2020-07-14T12:47:40Z","date_created":"2018-12-12T10:15:48Z","checksum":"efc7287d9c6354983cb151880e9ad72a"}],"oa_version":"Published Version","pubrep_id":"899","type":"journal_article","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","page":"1294 - 1303","publication":"Cell Reports","citation":{"short":"C. Lademann, J. Renkawitz, B. Pfander, S. Jentsch, Cell Reports 19 (2017) 1294–1303.","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.","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.","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","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","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.","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."},"date_published":"2017-05-16T00:00:00Z","scopus_import":1,"day":"16","has_accepted_license":"1"},{"doi":"10.1038/ncb3524","date_published":"2017-05-31T00:00:00Z","language":[{"iso":"eng"}],"publication":"Nature Cell Biology","citation":{"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.","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.","short":"N. Petridou, Z.P. Spiro, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 581–588.","ista":"Petridou N, Spiro ZP, Heisenberg C-PJ. 2017. Multiscale force sensing in development. Nature Cell Biology. 19(6), 581–588.","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.","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","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"},"quality_controlled":"1","page":"581 - 588","project":[{"_id":"25236028-B435-11E9-9278-68D0E5697425","grant_number":"ALTF534-2016","name":"The generation and function of anisotropic tissue tension in zebrafish epiboly (EMBO Fellowship)"}],"month":"05","day":"31","publication_identifier":{"issn":["14657392"]},"scopus_import":1,"author":[{"full_name":"Petridou, Nicoletta","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8451-1195","first_name":"Nicoletta","last_name":"Petridou"},{"id":"426AD026-F248-11E8-B48F-1D18A9856A87","first_name":"Zoltan P","last_name":"Spiro","full_name":"Spiro, Zoltan P"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"date_created":"2018-12-11T11:47:53Z","date_updated":"2021-01-12T08:08:59Z","volume":19,"oa_version":"None","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"678","year":"2017","status":"public","publication_status":"published","title":"Multiscale force sensing in development","publisher":"Nature Publishing Group","intvolume":" 19","department":[{"_id":"CaHe"}],"abstract":[{"lang":"eng","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."}],"issue":"6","publist_id":"7040","type":"journal_article"},{"date_published":"2017-06-01T00:00:00Z","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","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","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.","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."},"article_type":"original","page":"296 - 315","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"681","title":"Doomsday equilibria for omega-regular games","status":"public","intvolume":" 254","abstract":[{"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.","lang":"eng"}],"type":"journal_article","doi":"10.1016/j.ic.2016.10.012","language":[{"iso":"eng"}],"external_id":{"arxiv":["1311.3238"]},"main_file_link":[{"url":"https://arxiv.org/abs/1311.3238","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"month":"06","publication_identifier":{"issn":["08905401"]},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"full_name":"Filiot, Emmanuel","first_name":"Emmanuel","last_name":"Filiot"},{"full_name":"Raskin, Jean","first_name":"Jean","last_name":"Raskin"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"10885"}]},"date_updated":"2023-02-21T16:06:02Z","date_created":"2018-12-11T11:47:53Z","volume":254,"year":"2017","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Elsevier","ec_funded":1,"publist_id":"7036"},{"language":[{"iso":"eng"}],"conference":{"start_date":"2017-04-24","location":"Toulon, France","end_date":"2017-04-26","name":"ICLR: International Conference on Learning Representations"},"date_published":"2017-02-21T00:00:00Z","quality_controlled":"1","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"}],"publication":"5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings","citation":{"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.","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.","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.","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.","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.","short":"G.S. Martius, C. Lampert, in:, 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017."},"main_file_link":[{"url":"https://arxiv.org/abs/1610.02995","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1610.02995"]},"month":"02","day":"21","scopus_import":1,"date_created":"2019-09-01T22:01:00Z","date_updated":"2021-01-12T08:09:17Z","oa_version":"Preprint","author":[{"first_name":"Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"publication_status":"published","title":"Extrapolation and learning equations","status":"public","department":[{"_id":"ChLa"}],"publisher":"International Conference on Learning Representations","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6841","year":"2017","abstract":[{"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.","lang":"eng"}],"ec_funded":1,"type":"conference"},{"month":"06","publication_identifier":{"eissn":["1943-5886"],"issn":["0022-4812"]},"doi":"10.1017/jsl.2016.71","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1206.5174","open_access":"1"}],"quality_controlled":"1","publist_id":"7026","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Piterman, Nir","last_name":"Piterman","first_name":"Nir"}],"date_created":"2018-12-11T11:47:54Z","date_updated":"2021-04-16T12:10:53Z","volume":82,"year":"2017","publication_status":"published","publisher":"Cambridge University Press","department":[{"_id":"KrCh"}],"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2017-06-01T00:00:00Z","publication":"Journal of Symbolic Logic","citation":{"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","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.","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","ista":"Chatterjee K, Piterman N. 2017. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 82(2), 420–452.","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."},"page":"420 - 452","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."}],"issue":"2","type":"journal_article","oa_version":"Submitted Version","_id":"684","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Obligation blackwell games and p-automata","intvolume":" 82"},{"month":"06","publication_identifier":{"issn":["09254773"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.mod.2017.03.005","quality_controlled":"1","project":[{"grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord"}],"oa":1,"external_id":{"pmid":["28366718"]},"file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1,"publist_id":"7025","date_created":"2018-12-11T11:47:55Z","date_updated":"2021-01-12T08:09:20Z","volume":145,"author":[{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"},{"full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"AnKi"}],"year":"2017","pmid":1,"day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2017-06-01T00:00:00Z","page":"26 - 31","publication":"Mechanisms of Development","citation":{"short":"J. Briscoe, A. Kicheva, Mechanisms of Development 145 (2017) 26–31.","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.","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.","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","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.","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."},"abstract":[{"text":"By applying methods and principles from the physical sciences to biological problems, D'Arcy Thompson's On Growth and Form demonstrated how mathematical reasoning reveals elegant, simple explanations for seemingly complex processes. 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"}],"type":"journal_article","file":[{"checksum":"727043d2e4199fbef6b3704e6d1ac105","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-04-17T07:58:48Z","relation":"main_file","file_id":"6335","file_size":652313,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2017_Briscoe_Kicheva_and_DArcy_accepted_version.pdf"}],"oa_version":"Submitted Version","pubrep_id":"985","status":"public","title":"The physics of development 100 years after D'Arcy Thompson's “on growth and form”","ddc":["571"],"intvolume":" 145","_id":"685","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"pubrep_id":"895","file":[{"date_created":"2018-12-12T10:11:03Z","date_updated":"2020-07-14T12:47:42Z","checksum":"067ab0cb3f962bae6c3af6bf0094e0f3","file_id":"4856","relation":"main_file","creator":"system","file_size":990546,"content_type":"application/pdf","file_name":"IST-2017-895-v1+1_LIPIcs-SoCG-2017-39.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"688","intvolume":" 77","status":"public","ddc":["514","516"],"title":"Topological data analysis with Bregman divergences","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"],"date_published":"2017-06-01T00:00:00Z","citation":{"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","ista":"Edelsbrunner H, Wagner H. 2017. Topological data analysis with Bregman divergences. Symposium on Computational Geometry, SoCG, LIPIcs, vol. 77, 391–3916.","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.","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","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.","short":"H. Edelsbrunner, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916.","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."},"page":"391-3916","has_accepted_license":"1","day":"01","scopus_import":1,"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"full_name":"Wagner, Hubert","first_name":"Hubert","last_name":"Wagner","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"}],"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","publist_id":"7021","file_date_updated":"2020-07-14T12:47:42Z","doi":"10.4230/LIPIcs.SoCG.2017.39","conference":{"end_date":"2017-07-07","start_date":"2017-07-04","location":"Brisbane, Australia","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","publication_identifier":{"issn":["18688969"]},"month":"06"},{"ec_funded":1,"publist_id":"7022","author":[{"orcid":"0000-0002-8944-4390","id":"4634AB1E-F248-11E8-B48F-1D18A9856A87","last_name":"Davison","first_name":"Ben","full_name":"Davison, Ben"}],"date_updated":"2021-01-12T08:09:24Z","date_created":"2018-12-11T11:47:55Z","volume":68,"year":"2017","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"TaHa"}],"month":"06","publication_identifier":{"issn":["00335606"]},"doi":"10.1093/qmath/haw053","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1311.7172","open_access":"1"}],"quality_controlled":"1","project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593","call_identifier":"FP7","name":"Arithmetic and physics of Higgs moduli spaces"}],"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","type":"journal_article","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"687","title":"The critical CoHA of a quiver with potential","status":"public","intvolume":" 68","day":"01","scopus_import":1,"date_published":"2017-06-01T00:00:00Z","publication":"Quarterly Journal of Mathematics","citation":{"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.","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."},"page":"635 - 703"},{"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"}],"scopus_import":1,"day":"01","month":"06","publication_identifier":{"issn":["09254773"]},"_id":"686","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","title":"D'Arcy Thompson's ‘on growth and form’: From soap bubbles to tissue self organization","status":"public","publication_status":"published","intvolume":" 145","department":[{"_id":"CaHe"}],"publisher":"Elsevier","author":[{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"date_updated":"2021-01-12T08:09:23Z","date_created":"2018-12-11T11:47:55Z","volume":145,"oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","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."}],"publist_id":"7024"},{"date_updated":"2021-01-12T08:09:29Z","date_created":"2018-12-11T11:47:56Z","volume":9,"oa_version":"None","author":[{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"status":"public","publication_status":"published","title":"Rett syndrome modeling goes simian","department":[{"_id":"GaNo"}],"intvolume":" 9","publisher":"American Association for the Advancement of Science","year":"2017","_id":"689","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Rett syndrome modeling in monkey mirrors the human disorder.","lang":"eng"}],"publist_id":"7019","issue":"393","article_number":"eaan8196","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1126/scitranslmed.aan8196","date_published":"2017-06-07T00:00:00Z","quality_controlled":"1","publication":"Science Translational Medicine","citation":{"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.","short":"G. Novarino, Science Translational Medicine 9 (2017).","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.","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","ieee":"G. Novarino, “Rett syndrome modeling goes simian,” Science Translational Medicine, vol. 9, no. 393. American Association for the Advancement of Science, 2017.","ista":"Novarino G. 2017. Rett syndrome modeling goes simian. Science Translational Medicine. 9(393), eaan8196.","ama":"Novarino G. Rett syndrome modeling goes simian. Science Translational Medicine. 2017;9(393). doi:10.1126/scitranslmed.aan8196"},"month":"06","day":"07","publication_identifier":{"issn":["19466234"]},"scopus_import":1},{"date_published":"2017-06-27T00:00:00Z","page":"E5246 - E5255","citation":{"short":"T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255.","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.","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.","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","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.","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."},"publication":"PNAS","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"27","scopus_import":1,"file":[{"relation":"main_file","file_id":"7223","date_updated":"2020-07-14T12:47:44Z","date_created":"2020-01-03T13:27:29Z","checksum":"2ab75d554f3df4a34d20fa8040589b7e","file_name":"2017_PNAS_Miki.pdf","access_level":"open_access","file_size":2721544,"content_type":"application/pdf","creator":"kschuh"}],"oa_version":"Published Version","intvolume":" 114","ddc":["570"],"title":"Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses","status":"public","_id":"693","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1704470114","quality_controlled":"1","oa":1,"external_id":{"pmid":["28607047"]},"publication_identifier":{"issn":["00278424"]},"month":"06","volume":114,"date_updated":"2023-02-23T12:54:57Z","date_created":"2018-12-11T11:47:57Z","author":[{"last_name":"Miki","first_name":"Takafumi","full_name":"Miki, Takafumi"},{"last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"full_name":"Malagon, Gerardo","first_name":"Gerardo","last_name":"Malagon"},{"full_name":"Gomez, Laura","first_name":"Laura","last_name":"Gomez"},{"last_name":"Tabuchi","first_name":"Katsuhiko","full_name":"Tabuchi, Katsuhiko"},{"full_name":"Watanabe, Masahiko","last_name":"Watanabe","first_name":"Masahiko"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"},{"first_name":"Alain","last_name":"Marty","full_name":"Marty, Alain"}],"publisher":"National Academy of Sciences","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"publication_status":"published","pmid":1,"year":"2017","publist_id":"7013","file_date_updated":"2020-07-14T12:47:44Z"},{"ddc":["570"],"title":"A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity","status":"public","intvolume":" 130","_id":"694","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2017_CellScience_Vess.pdf","file_size":10847596,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6966","checksum":"42c81a0a4fc3128883b391c3af3f74bc","date_updated":"2020-07-14T12:47:45Z","date_created":"2019-10-24T09:43:56Z"}],"type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"13","article_type":"original","page":"2172 - 2184","publication":"Journal of Cell Science","citation":{"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","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","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.","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.","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.","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."},"date_published":"2017-07-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","publication_status":"published","publisher":"Company of Biologists","department":[{"_id":"MiSi"}],"year":"2017","pmid":1,"date_created":"2018-12-11T11:47:58Z","date_updated":"2021-01-12T08:09:41Z","volume":130,"author":[{"full_name":"Veß, Astrid","first_name":"Astrid","last_name":"Veß"},{"full_name":"Blache, Ulrich","last_name":"Blache","first_name":"Ulrich"},{"full_name":"Leitner, Laura","last_name":"Leitner","first_name":"Laura"},{"full_name":"Kurz, Angela","last_name":"Kurz","first_name":"Angela"},{"last_name":"Ehrenpfordt","first_name":"Anja","full_name":"Ehrenpfordt, Anja"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Posern, Guido","first_name":"Guido","last_name":"Posern"}],"file_date_updated":"2020-07-14T12:47:45Z","publist_id":"7008","quality_controlled":"1","oa":1,"external_id":{"pmid":["28515231"]},"language":[{"iso":"eng"}],"doi":"10.1242/jcs.200899","month":"07","publication_identifier":{"issn":["00219533"]}},{"citation":{"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.","short":"K.Z. Pietrzak, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","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","ista":"Pietrzak KZ, Skórski M. 2017. Non uniform attacks against pseudoentropy. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 80, 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."},"date_published":"2017-07-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","_id":"697","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 80","status":"public","title":"Non uniform attacks against pseudoentropy","ddc":["005"],"pubrep_id":"893","oa_version":"Published Version","file":[{"creator":"system","file_size":601004,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-893-v1+1_LIPIcs-ICALP-2017-39.pdf","checksum":"e95618a001692f1af2d68f5fde43bc1f","date_updated":"2020-07-14T12:47:46Z","date_created":"2018-12-12T10:08:40Z","file_id":"4701","relation":"main_file"}],"type":"conference","alternative_title":["LIPIcs"],"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. "}],"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,"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"quality_controlled":"1","doi":"10.4230/LIPIcs.ICALP.2017.39","conference":{"start_date":"2017-07-10","location":"Warsaw, Poland","end_date":"2017-07-14","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["18688969"]},"month":"07","year":"2017","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrPi"}],"publication_status":"published","author":[{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Skórski","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","full_name":"Skórski, Maciej"}],"volume":80,"date_updated":"2021-01-12T08:11:15Z","date_created":"2018-12-11T11:47:59Z","article_number":"39","ec_funded":1,"publist_id":"7003","file_date_updated":"2020-07-14T12:47:46Z"},{"type":"journal_article","abstract":[{"lang":"eng","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. "}],"issue":"14","_id":"698","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression","ddc":["519"],"status":"public","intvolume":" 28","pubrep_id":"892","file":[{"access_level":"open_access","file_name":"IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf","creator":"system","file_size":1086097,"content_type":"application/pdf","file_id":"4844","relation":"main_file","checksum":"de01dac9e30970cfa6ae902480a4e04d","date_updated":"2020-07-14T12:47:46Z","date_created":"2018-12-12T10:10:53Z"}],"oa_version":"Published Version","scopus_import":1,"day":"07","has_accepted_license":"1","publication":"Molecular Biology of the Cell","citation":{"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.","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.","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","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","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."},"page":"1997 - 2009","date_published":"2017-07-07T00:00:00Z","file_date_updated":"2020-07-14T12:47:46Z","publist_id":"7001","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","year":"2017","publication_status":"published","publisher":"American Society for Cell Biology","department":[{"_id":"CaUh"}],"author":[{"first_name":"Yejun","last_name":"Wang","full_name":"Wang, Yejun"},{"first_name":"Mallika","last_name":"Nagarajan","full_name":"Nagarajan, Mallika"},{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","first_name":"Caroline"},{"last_name":"Shivashankar","first_name":"Gv","full_name":"Shivashankar, Gv"}],"date_created":"2018-12-11T11:47:59Z","date_updated":"2021-01-12T08:11:17Z","volume":28,"month":"07","publication_identifier":{"issn":["10591524"]},"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)"},"oa":1,"quality_controlled":"1","project":[{"name":"Gaussian Graphical Models: Theory and Applications","call_identifier":"FWF","grant_number":"Y 903-N35","_id":"2530CA10-B435-11E9-9278-68D0E5697425"}],"doi":"10.1091/mbc.E16-12-0825","language":[{"iso":"eng"}]},{"citation":{"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.","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","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","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.","ista":"Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405."},"publication":"PNAS","page":"E5396 - E5405","date_published":"2017-07-03T00:00:00Z","scopus_import":1,"day":"03","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":[{"lang":"eng","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. "}],"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/","open_access":"1"}],"external_id":{"pmid":["28630336"]},"quality_controlled":"1","doi":"10.1073/pnas.1702020114","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00278424"]},"month":"07","pmid":1,"year":"2017","department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","publication_status":"published","author":[{"full_name":"Veller, Carl","first_name":"Carl","last_name":"Veller"},{"first_name":"Laura","last_name":"Hayward","full_name":"Hayward, Laura"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"},{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe"}],"volume":114,"date_updated":"2021-01-12T08:11:21Z","date_created":"2018-12-11T11:48:00Z","publist_id":"7002"},{"month":"07","publication_identifier":{"issn":["24700045"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.96.012404","quality_controlled":"1","project":[{"grant_number":"707438","_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/1612.07061.pdf"}],"publist_id":"6997","ec_funded":1,"article_number":"012404","date_created":"2018-12-11T11:48:00Z","date_updated":"2023-02-23T12:56:35Z","volume":96,"author":[{"full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","first_name":"Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Salari, Vahid","first_name":"Vahid","last_name":"Salari"},{"full_name":"Tuszynski, Jack","first_name":"Jack","last_name":"Tuszynski"},{"full_name":"Cifra, Michal","last_name":"Cifra","first_name":"Michal"},{"first_name":"Christoph","last_name":"Simon","full_name":"Simon, Christoph"}],"publication_status":"published","publisher":"American Institute of Physics","department":[{"_id":"JoFi"}],"year":"2017","day":"12","scopus_import":1,"date_published":"2017-07-12T00:00:00Z","publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","citation":{"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","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.","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","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.","short":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, C. Simon, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017).","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."},"abstract":[{"lang":"eng","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."}],"issue":"1","type":"journal_article","oa_version":"Submitted Version","status":"public","title":"Optomechanical proposal for monitoring microtubule mechanical vibrations","intvolume":" 96","_id":"700","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"publication_identifier":{"issn":["10778926"]},"month":"07","language":[{"iso":"eng"}],"quality_controlled":"1","oa":1,"publist_id":"6996","file_date_updated":"2020-07-14T12:47:47Z","volume":24,"date_updated":"2021-01-12T08:11:28Z","date_created":"2018-12-11T11:48:00Z","author":[{"full_name":"Kynčl, Jan","last_name":"Kynčl","first_name":"Jan"},{"full_name":"Patakova, Zuzana","last_name":"Patakova","first_name":"Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"UlWa"}],"publisher":"International Press","publication_status":"published","year":"2017","has_accepted_license":"1","day":"14","date_published":"2017-07-14T00:00:00Z","page":"1-44","citation":{"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.","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.","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.","short":"J. Kynčl, Z. Patakova, The Electronic Journal of Combinatorics 24 (2017) 1–44.","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.","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."},"publication":"The Electronic Journal of Combinatorics","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."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"5077","checksum":"a431e573e31df13bc0f66de3061006ec","date_created":"2018-12-12T10:14:25Z","date_updated":"2020-07-14T12:47:47Z","access_level":"open_access","file_name":"IST-2018-984-v1+1_Patakova_on_the_nonexistence_of_k-reptile_simplices_in_R_3_and_R_4_2017.pdf","content_type":"application/pdf","file_size":544042,"creator":"system"}],"oa_version":"Submitted Version","pubrep_id":"984","intvolume":" 24","status":"public","title":"On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4","ddc":["500"],"_id":"701","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia"}],"date_created":"2018-12-11T11:48:01Z","date_updated":"2021-01-12T08:11:31Z","volume":9,"oa_version":"None","_id":"702","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2017","publication_status":"published","title":"The riddle of CHD8 haploinsufficiency in autism spectrum disorder","status":"public","department":[{"_id":"GaNo"}],"intvolume":" 9","publisher":"American Association for the Advancement of Science","abstract":[{"text":"Leading autism-associated mutation in mouse partially mimics human disorder.\r\n\r\n","lang":"eng"}],"publist_id":"6993","issue":"399","type":"journal_article","doi":"10.1126/scitranslmed.aao0972","date_published":"2017-07-19T00:00:00Z","language":[{"iso":"eng"}],"publication":"Science Translational Medicine","citation":{"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.","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.","ama":"Novarino G. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 2017;9(399):eaao0972. doi:10.1126/scitranslmed.aao0972","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","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.","ista":"Novarino G. 2017. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 9(399), eaao0972."},"quality_controlled":"1","page":"eaao0972","month":"07","day":"19","publication_identifier":{"issn":["19466234"]},"scopus_import":1},{"author":[{"full_name":"Geng, Xiaoqi","first_name":"Xiaoqi","last_name":"Geng","id":"3395256A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Maruo, Tomohiko","first_name":"Tomohiko","last_name":"Maruo"},{"full_name":"Mandai, Kenji","first_name":"Kenji","last_name":"Mandai"},{"full_name":"Supriyanto, Irwan","last_name":"Supriyanto","first_name":"Irwan"},{"first_name":"Muneaki","last_name":"Miyata","full_name":"Miyata, Muneaki"},{"full_name":"Sakakibara, Shotaro","first_name":"Shotaro","last_name":"Sakakibara"},{"first_name":"Akira","last_name":"Mizoguchi","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","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"706","year":"2017","intvolume":" 22","publisher":"Wiley-Blackwell","department":[{"_id":"PeJo"}],"status":"public","title":"Roles of afadin in functional differentiations of hippocampal mossy fiber synapse","publication_status":"published","issue":"8","publist_id":"6987","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"}],"type":"journal_article","date_published":"2017-08-01T00:00:00Z","doi":"10.1111/gtc.12508","language":[{"iso":"eng"}],"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","publication_identifier":{"issn":["13569597"]},"day":"01","month":"08","scopus_import":1},{"month":"08","publication_identifier":{"issn":["00246093"]},"doi":"10.1112/blms.12062","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.06279"}],"oa":1,"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"ec_funded":1,"publist_id":"6982","author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy"},{"last_name":"Karasev","first_name":"Roman","full_name":"Karasev, Roman"}],"date_created":"2018-12-11T11:48:02Z","date_updated":"2021-01-12T08:11:41Z","volume":49,"year":"2017","publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"HeEd"}],"day":"01","scopus_import":1,"date_published":"2017-08-01T00:00:00Z","publication":"Bulletin of the London Mathematical Society","citation":{"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.","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.","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.","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.","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","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"},"page":"690 - 693","abstract":[{"text":"We answer a question of M. Gromov on the waist of the unit ball.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"707","status":"public","title":"A tight estimate for the waist of the ball ","intvolume":" 49"},{"volume":15,"date_created":"2018-12-11T11:48:03Z","date_updated":"2021-01-12T08:11:45Z","author":[{"full_name":"Nagy, Balint","first_name":"Balint","last_name":"Nagy","id":"30F830CE-02D1-11E9-9BAA-DAF4881429F2","orcid":"0000-0002-4002-4686"},{"full_name":"Hovhannisyan, Anahit","first_name":"Anahit","last_name":"Hovhannisyan"},{"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","publist_id":"6983","file_date_updated":"2020-07-14T12:47:49Z","article_number":"e2001993","language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.2001993","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"},"publication_identifier":{"issn":["15449173"]},"month":"08","oa_version":"Published Version","file":[{"file_name":"IST-2017-889-v1+1_journal.pbio.2001993.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":18155365,"file_id":"5156","relation":"main_file","date_created":"2018-12-12T10:15:35Z","date_updated":"2020-07-14T12:47:49Z","checksum":"0c974f430682dc832ea7b27ab5a93124"}],"pubrep_id":"889","intvolume":" 15","ddc":["576","610"],"title":"Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum","status":"public","_id":"708","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"8","abstract":[{"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.","lang":"eng"}],"type":"journal_article","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","has_accepted_license":"1","day":"22","scopus_import":1},{"date_published":"2017-08-01T00:00:00Z","doi":"10.1002/cbin.10783","language":[{"iso":"eng"}],"citation":{"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.","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","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.","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","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."},"publication":"Cell Biology International","page":"908 - 913","quality_controlled":"1","publication_identifier":{"issn":["10656995"]},"day":"01","month":"08","scopus_import":1,"author":[{"full_name":"Sun, Wuping","last_name":"Sun","first_name":"Wuping"},{"full_name":"Li, Chen","last_name":"Li","first_name":"Chen"},{"full_name":"Zhang, Yonghong","first_name":"Yonghong","last_name":"Zhang"},{"first_name":"Changyu","last_name":"Jiang","full_name":"Jiang, Changyu"},{"first_name":"Ming-Zhu","last_name":"Zhai","id":"34009CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Zhai, Ming-Zhu"},{"first_name":"Qian","last_name":"Zhou","full_name":"Zhou, Qian"},{"full_name":"Xiao, Lizu","last_name":"Xiao","first_name":"Lizu"},{"full_name":"Deng, Qiwen","last_name":"Deng","first_name":"Qiwen"}],"oa_version":"None","volume":41,"date_created":"2018-12-11T11:48:04Z","date_updated":"2021-01-12T08:11:47Z","_id":"709","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2017","publisher":"Wiley-Blackwell","intvolume":" 41","department":[{"_id":"RySh"}],"title":"Gene expression changes of thermo sensitive transient receptor potential channels in obese mice","status":"public","publication_status":"published","publist_id":"6981","issue":"8","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"}],"type":"journal_article"},{"scopus_import":1,"has_accepted_license":"1","day":"01","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."},"date_published":"2017-08-01T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","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. "}],"intvolume":" 81","title":"Renyi entropy estimation revisited","status":"public","ddc":["005","600"],"_id":"710","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:49Z","date_created":"2018-12-12T10:13:10Z","checksum":"89225c7dcec2c93838458c9102858985","relation":"main_file","file_id":"4991","content_type":"application/pdf","file_size":604813,"creator":"system","file_name":"IST-2017-888-v1+1_LIPIcs-APPROX-RANDOM-2017-20.pdf","access_level":"open_access"}],"pubrep_id":"888","publication_identifier":{"issn":["18688969"]},"month":"08","project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"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.APPROX-RANDOM.2017.20","conference":{"start_date":"2017-08-18","location":"Berkeley, USA","end_date":"2017-08-18","name":"20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX"},"article_number":"20","publist_id":"6979","ec_funded":1,"file_date_updated":"2020-07-14T12:47:49Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2017","volume":81,"date_updated":"2021-01-12T08:11:50Z","date_created":"2018-12-11T11:48:04Z","author":[{"first_name":"Maciej","last_name":"Obremski","full_name":"Obremski, Maciej"},{"full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski"}]},{"pubrep_id":"885","oa_version":"Published Version","file":[{"file_id":"5020","relation":"main_file","date_created":"2018-12-12T10:13:36Z","date_updated":"2020-07-14T12:47:50Z","checksum":"1ace3462e64a971b9ead896091829549","file_name":"IST-2017-885-v1+1_elife-25125-figures-v2.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":6399510},{"relation":"main_file","file_id":"5021","checksum":"6241dc31eeb87b03facadec3a53a6827","date_created":"2018-12-12T10:13:36Z","date_updated":"2020-07-14T12:47:50Z","access_level":"open_access","file_name":"IST-2017-885-v1+2_elife-25125-v2.pdf","content_type":"application/pdf","file_size":4264398,"creator":"system"}],"_id":"713","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Mapping the mouse Allelome reveals tissue specific regulation of allelic expression","ddc":["576"],"intvolume":" 6","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","date_published":"2017-08-14T00:00:00Z","publication":"eLife","citation":{"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","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.","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","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.","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).","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."},"day":"14","has_accepted_license":"1","scopus_import":1,"author":[{"first_name":"Daniel","last_name":"Andergassen","full_name":"Andergassen, Daniel"},{"first_name":"Christoph","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph"},{"full_name":"Wenzel, Dyniel","last_name":"Wenzel","first_name":"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"},{"last_name":"Theussl","first_name":"Hans","full_name":"Theussl, Hans"},{"full_name":"Penninger, Josef","first_name":"Josef","last_name":"Penninger"},{"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"},{"last_name":"Hudson","first_name":"Quanah","full_name":"Hudson, Quanah"}],"date_updated":"2021-01-12T08:11:57Z","date_created":"2018-12-11T11:48:05Z","volume":6,"year":"2017","publication_status":"published","department":[{"_id":"GaNo"},{"_id":"SiHi"}],"publisher":"eLife Sciences Publications","file_date_updated":"2020-07-14T12:47:50Z","publist_id":"6971","article_number":"e25125","doi":"10.7554/eLife.25125","language":[{"iso":"eng"}],"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"},"quality_controlled":"1","project":[{"name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22"}],"month":"08","publication_identifier":{"issn":["2050084X"]}},{"citation":{"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.","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.","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","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Bidirectional nested weighted automata. 28th International Conference on Concurrency Theory, CONCUR, LIPIcs, vol. 85, 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.","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"},"date_published":"2017-08-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"711","title":"Bidirectional nested weighted automata","ddc":["004","005"],"status":"public","intvolume":" 85","pubrep_id":"886","oa_version":"Published Version","file":[{"checksum":"d2bda4783821a6358333fe27f11f4737","date_created":"2018-12-12T10:08:02Z","date_updated":"2020-07-14T12:47:49Z","relation":"main_file","file_id":"4661","content_type":"application/pdf","file_size":570294,"creator":"system","access_level":"open_access","file_name":"IST-2017-886-v1+1_LIPIcs-CONCUR-2017-5.pdf"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","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."}],"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","conference":{"name":"28th International Conference on Concurrency Theory, CONCUR","location":"Berlin, Germany","start_date":"2017-09-05","end_date":"2017-09-08"},"doi":"10.4230/LIPIcs.CONCUR.2017.5","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["18688969"]},"year":"2017","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"}],"date_updated":"2021-01-12T08:11:53Z","date_created":"2018-12-11T11:48:04Z","volume":85,"article_number":"5","file_date_updated":"2020-07-14T12:47:49Z","publist_id":"6976"},{"status":"public","title":"Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations","publication_status":"published","intvolume":" 159","publisher":"Elsevier","department":[{"_id":"JuFi"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"712","year":"2017","date_created":"2018-12-11T11:48:05Z","date_updated":"2021-01-12T08:11:55Z","volume":159,"oa_version":"Submitted Version","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L"}],"type":"journal_article","abstract":[{"lang":"eng","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."}],"publist_id":"6975","quality_controlled":"1","page":"181 - 207","publication":"Nonlinear Analysis: Theory, Methods and Applications","citation":{"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.","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.","short":"J.L. Fischer, Nonlinear Analysis: Theory, Methods and Applications 159 (2017) 181–207.","ista":"Fischer JL. 2017. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. 159, 181–207.","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.","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","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"},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1703.00730","open_access":"1"}],"language":[{"iso":"eng"}],"date_published":"2017-08-01T00:00:00Z","doi":"10.1016/j.na.2017.03.001","scopus_import":1,"month":"08","day":"01","publication_identifier":{"issn":["0362546X"]}},{"month":"09","publication_identifier":{"issn":["03768716"]},"doi":"10.1016/j.drugalcdep.2017.04.015","language":[{"iso":"eng"}],"external_id":{"pmid":["28623807"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797705"}],"quality_controlled":"1","publist_id":"6967","author":[{"full_name":"Brailoiu, Gabriela","first_name":"Gabriela","last_name":"Brailoiu"},{"orcid":"0000-0002-7370-5293","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","last_name":"Deliu","first_name":"Elena","full_name":"Deliu, Elena"},{"full_name":"Barr, Jeffrey","last_name":"Barr","first_name":"Jeffrey"},{"full_name":"Console Bram, Linda","last_name":"Console Bram","first_name":"Linda"},{"last_name":"Ciuciu","first_name":"Alexandra","full_name":"Ciuciu, Alexandra"},{"first_name":"Mary","last_name":"Abood","full_name":"Abood, Mary"},{"full_name":"Unterwald, Ellen","last_name":"Unterwald","first_name":"Ellen"},{"full_name":"Brǎiloiu, Eugen","first_name":"Eugen","last_name":"Brǎiloiu"}],"date_updated":"2021-01-12T08:12:00Z","date_created":"2018-12-11T11:48:05Z","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"}],"day":"01","article_processing_charge":"No","scopus_import":1,"date_published":"2017-09-01T00:00:00Z","publication":"Drug and Alcohol Dependence","citation":{"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.","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.","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","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","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.","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."},"article_type":"original","page":"7 - 14","abstract":[{"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.","lang":"eng"}],"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"},{"scopus_import":1,"publication_identifier":{"issn":["19466234"]},"day":"30","month":"08","citation":{"ama":"Novarino G. More excitation for Rett syndrome. Science Translational Medicine. 2017;9(405). doi:10.1126/scitranslmed.aao4218","ista":"Novarino G. 2017. More excitation for Rett syndrome. Science Translational Medicine. 9(405), aao4218.","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","ieee":"G. Novarino, “More excitation for Rett syndrome,” Science Translational Medicine, vol. 9, no. 405. American Association for the Advancement of Science, 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.","short":"G. Novarino, Science Translational Medicine 9 (2017).","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."},"publication":"Science Translational Medicine","quality_controlled":"1","doi":"10.1126/scitranslmed.aao4218","date_published":"2017-08-30T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","article_number":"aao4218","publist_id":"6968","issue":"405","abstract":[{"lang":"eng","text":"D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse model of Rett syndrome."}],"year":"2017","_id":"715","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"American Association for the Advancement of Science","intvolume":" 9","department":[{"_id":"GaNo"}],"title":"More excitation for Rett syndrome","status":"public","publication_status":"published","author":[{"last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"}],"volume":9,"oa_version":"None","date_created":"2018-12-11T11:48:06Z","date_updated":"2021-01-12T08:12:04Z"},{"day":"01","scopus_import":1,"date_published":"2017-09-01T00:00:00Z","page":"34","article_type":"original","citation":{"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.","short":"K. Chatterjee, Y. Velner, Journal of the ACM 64 (2017) 34.","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.","ama":"Chatterjee K, Velner Y. The complexity of mean-payoff pushdown games. Journal of the ACM. 2017;64(5):34. doi:10.1145/3121408","ista":"Chatterjee K, Velner Y. 2017. The complexity of mean-payoff pushdown games. Journal of the ACM. 64(5), 34.","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"},"publication":"Journal of the ACM","issue":"5","abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 64","title":"The complexity of mean-payoff pushdown games","status":"public","_id":"716","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["00045411"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1145/3121408","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","name":"Game Theory","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","external_id":{"arxiv":["1201.2829"]},"main_file_link":[{"url":"https://arxiv.org/abs/1201.2829","open_access":"1"}],"oa":1,"publist_id":"6964","ec_funded":1,"volume":64,"date_created":"2018-12-11T11:48:06Z","date_updated":"2021-01-12T08:12:08Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Velner","first_name":"Yaron","full_name":"Velner, Yaron"}],"publisher":"ACM","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2017"},{"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.","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.","short":"K. Chatterjee, Y. Velner, Journal of Computer and System Sciences 88 (2017) 236–259.","ista":"Chatterjee K, Velner Y. 2017. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 88, 236–259.","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","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.","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","day":"01","scopus_import":1,"oa_version":"Preprint","intvolume":" 88","title":"Hyperplane separation technique for multidimensional mean-payoff games","status":"public","_id":"717","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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","language":[{"iso":"eng"}],"doi":"10.1016/j.jcss.2017.04.005","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1210.3141"}],"oa":1,"month":"09","volume":88,"date_created":"2018-12-11T11:48:07Z","date_updated":"2023-02-23T10:38:15Z","related_material":{"record":[{"id":"2329","status":"public","relation":"earlier_version"}]},"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"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","publist_id":"6963","ec_funded":1},{"type":"journal_article","issue":"6","publist_id":"6961","abstract":[{"lang":"eng","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."}],"year":"2017","_id":"719","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 54","department":[{"_id":"KrCh"}],"publisher":"Springer","status":"public","title":"Special issue: Synthesis and SYNT 2014","publication_status":"published","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Ehlers, Rüdiger","first_name":"Rüdiger","last_name":"Ehlers"}],"oa_version":"None","volume":54,"date_updated":"2021-01-12T08:12:18Z","date_created":"2018-12-11T11:48:07Z","scopus_import":1,"publication_identifier":{"issn":["00015903"]},"day":"01","month":"09","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"},"publication":"Acta Informatica","page":"543 - 544","quality_controlled":"1","date_published":"2017-09-01T00:00:00Z","doi":"10.1007/s00236-017-0299-0","language":[{"iso":"eng"}]},{"article_number":"e1005763","publist_id":"6960","file_date_updated":"2020-07-14T12:47:53Z","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","publication_status":"published","year":"2017","volume":13,"date_created":"2018-12-11T11:48:08Z","date_updated":"2021-01-12T08:12:21Z","author":[{"full_name":"Humplik, Jan","first_name":"Jan","last_name":"Humplik","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"publication_identifier":{"issn":["1553734X"]},"month":"09","project":[{"_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups"},{"grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF"}],"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":"10.1371/journal.pcbi.1005763","type":"journal_article","issue":"9","abstract":[{"text":"Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality.","lang":"eng"}],"intvolume":" 13","title":"Probabilistic models for neural populations that naturally capture global coupling and criticality","ddc":["530","571"],"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"720","file":[{"creator":"system","content_type":"application/pdf","file_size":14167050,"access_level":"open_access","file_name":"IST-2017-884-v1+1_journal.pcbi.1005763.pdf","checksum":"81107096c19771c36ddbe6f0282a3acb","date_created":"2018-12-12T10:18:30Z","date_updated":"2020-07-14T12:47:53Z","file_id":"5352","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"884","scopus_import":1,"article_processing_charge":"Yes","has_accepted_license":"1","day":"19","citation":{"mla":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763.","short":"J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).","chicago":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005763.","ama":"Humplik J, Tkačik G. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 2017;13(9). doi:10.1371/journal.pcbi.1005763","ista":"Humplik J, Tkačik G. 2017. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 13(9), e1005763.","ieee":"J. Humplik and G. Tkačik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” PLoS Computational Biology, vol. 13, no. 9. Public Library of Science, 2017.","apa":"Humplik, J., & Tkačik, G. (2017). Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005763"},"publication":"PLoS Computational Biology","date_published":"2017-09-19T00:00:00Z"},{"citation":{"apa":"Ajanki, O. H., Krüger, T. H., & Erdös, L. (2017). Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21639","ieee":"O. H. Ajanki, T. H. Krüger, and L. Erdös, “Singularities of solutions to quadratic vector equations on the complex upper half plane,” Communications on Pure and Applied Mathematics, vol. 70, no. 9. Wiley-Blackwell, pp. 1672–1705, 2017.","ista":"Ajanki OH, Krüger TH, Erdös L. 2017. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 70(9), 1672–1705.","ama":"Ajanki OH, Krüger TH, Erdös L. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 2017;70(9):1672-1705. doi:10.1002/cpa.21639","chicago":"Ajanki, Oskari H, Torben H Krüger, and László Erdös. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2017. https://doi.org/10.1002/cpa.21639.","short":"O.H. Ajanki, T.H. Krüger, L. Erdös, Communications on Pure and Applied Mathematics 70 (2017) 1672–1705.","mla":"Ajanki, Oskari H., et al. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics, vol. 70, no. 9, Wiley-Blackwell, 2017, pp. 1672–705, doi:10.1002/cpa.21639."},"publication":"Communications on Pure and Applied Mathematics","page":"1672 - 1705","date_published":"2017-09-01T00:00:00Z","scopus_import":1,"day":"01","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"721","intvolume":" 70","status":"public","title":"Singularities of solutions to quadratic vector equations on the complex upper half plane","oa_version":"Submitted Version","type":"journal_article","issue":"9","abstract":[{"text":"Let S be a positivity-preserving symmetric linear operator acting on bounded functions. The nonlinear equation -1/m=z+Sm with a parameter z in the complex upper half-plane ℍ has a unique solution m with values in ℍ. We show that the z-dependence of this solution can be represented as the Stieltjes transforms of a family of probability measures v on ℝ. Under suitable conditions on S, we show that v has a real analytic density apart from finitely many algebraic singularities of degree at most 3. Our motivation comes from large random matrices. The solution m determines the density of eigenvalues of two prominent matrix ensembles: (i) matrices with centered independent entries whose variances are given by S and (ii) matrices with correlated entries with a translation-invariant correlation structure. Our analysis shows that the limiting eigenvalue density has only square root singularities or cubic root cusps; no other singularities occur.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1512.03703","open_access":"1"}],"oa":1,"project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"quality_controlled":"1","doi":"10.1002/cpa.21639","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00103640"]},"month":"09","year":"2017","publisher":"Wiley-Blackwell","department":[{"_id":"LaEr"}],"publication_status":"published","author":[{"full_name":"Ajanki, Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","first_name":"Oskari H","last_name":"Ajanki"},{"first_name":"Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H"},{"full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"}],"volume":70,"date_created":"2018-12-11T11:48:08Z","date_updated":"2021-01-12T08:12:24Z","ec_funded":1,"publist_id":"6959"},{"ec_funded":1,"publist_id":"6956","file_date_updated":"2020-07-14T12:47:54Z","department":[{"_id":"JiFr"}],"publisher":"Cell Press","publication_status":"published","pmid":1,"year":"2017","volume":27,"date_updated":"2021-01-12T08:12:29Z","date_created":"2018-12-11T11:48:08Z","author":[{"full_name":"Morris, Emily","first_name":"Emily","last_name":"Morris"},{"last_name":"Griffiths","first_name":"Marcus","full_name":"Griffiths, Marcus"},{"full_name":"Golebiowska, Agata","last_name":"Golebiowska","first_name":"Agata"},{"full_name":"Mairhofer, Stefan","first_name":"Stefan","last_name":"Mairhofer"},{"last_name":"Burr Hersey","first_name":"Jasmine","full_name":"Burr Hersey, Jasmine"},{"first_name":"Tatsuaki","last_name":"Goh","full_name":"Goh, Tatsuaki"},{"full_name":"Von Wangenheim, Daniel","first_name":"Daniel","last_name":"Von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247"},{"first_name":"Brian","last_name":"Atkinson","full_name":"Atkinson, Brian"},{"full_name":"Sturrock, Craig","last_name":"Sturrock","first_name":"Craig"},{"full_name":"Lynch, Jonathan","first_name":"Jonathan","last_name":"Lynch"},{"full_name":"Vissenberg, Kris","last_name":"Vissenberg","first_name":"Kris"},{"last_name":"Ritz","first_name":"Karl","full_name":"Ritz, Karl"},{"full_name":"Wells, Darren","first_name":"Darren","last_name":"Wells"},{"first_name":"Sacha","last_name":"Mooney","full_name":"Mooney, Sacha"},{"full_name":"Bennett, Malcolm","last_name":"Bennett","first_name":"Malcolm"}],"publication_identifier":{"issn":["09609822"]},"month":"09","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","external_id":{"pmid":["28898665"]},"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,"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2017.06.043","type":"journal_article","issue":"17","abstract":[{"lang":"eng","text":"Plants are sessile organisms rooted in one place. The soil resources that plants require are often distributed in a highly heterogeneous pattern. To aid foraging, plants have evolved roots whose growth and development are highly responsive to soil signals. As a result, 3D root architecture is shaped by myriad environmental signals to ensure resource capture is optimised and unfavourable environments are avoided. The first signals sensed by newly germinating seeds — gravity and light — direct root growth into the soil to aid seedling establishment. Heterogeneous soil resources, such as water, nitrogen and phosphate, also act as signals that shape 3D root growth to optimise uptake. Root architecture is also modified through biotic interactions that include soil fungi and neighbouring plants. This developmental plasticity results in a ‘custom-made’ 3D root system that is best adapted to forage for resources in each soil environment that a plant colonises."}],"intvolume":" 27","ddc":["581"],"title":"Shaping 3D root system architecture","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"722","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1576593,"access_level":"open_access","file_name":"2017_CurrentBiology_Morris.pdf","checksum":"e45588b21097b408da6276a3e5eedb2e","date_created":"2019-04-17T07:46:40Z","date_updated":"2020-07-14T12:47:54Z","file_id":"6332","relation":"main_file"}],"oa_version":"Submitted Version","pubrep_id":"982","scopus_import":1,"has_accepted_license":"1","day":"11","page":"R919 - R930","citation":{"ama":"Morris E, Griffiths M, Golebiowska A, et al. Shaping 3D root system architecture. Current Biology. 2017;27(17):R919-R930. doi:10.1016/j.cub.2017.06.043","ieee":"E. Morris et al., “Shaping 3D root system architecture,” Current Biology, vol. 27, no. 17. Cell Press, pp. R919–R930, 2017.","apa":"Morris, E., Griffiths, M., Golebiowska, A., Mairhofer, S., Burr Hersey, J., Goh, T., … Bennett, M. (2017). Shaping 3D root system architecture. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.06.043","ista":"Morris E, Griffiths M, Golebiowska A, Mairhofer S, Burr Hersey J, Goh T, von Wangenheim D, Atkinson B, Sturrock C, Lynch J, Vissenberg K, Ritz K, Wells D, Mooney S, Bennett M. 2017. Shaping 3D root system architecture. Current Biology. 27(17), R919–R930.","short":"E. Morris, M. Griffiths, A. Golebiowska, S. Mairhofer, J. Burr Hersey, T. Goh, D. von Wangenheim, B. Atkinson, C. Sturrock, J. Lynch, K. Vissenberg, K. Ritz, D. Wells, S. Mooney, M. Bennett, Current Biology 27 (2017) R919–R930.","mla":"Morris, Emily, et al. “Shaping 3D Root System Architecture.” Current Biology, vol. 27, no. 17, Cell Press, 2017, pp. R919–30, doi:10.1016/j.cub.2017.06.043.","chicago":"Morris, Emily, Marcus Griffiths, Agata Golebiowska, Stefan Mairhofer, Jasmine Burr Hersey, Tatsuaki Goh, Daniel von Wangenheim, et al. “Shaping 3D Root System Architecture.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.06.043."},"publication":"Current Biology","date_published":"2017-09-11T00:00:00Z"},{"publication_identifier":{"issn":["00278424"]},"month":"09","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/"}],"oa":1,"external_id":{"pmid":["28874581"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1703817114","publist_id":"6953","publisher":"National Academy of Sciences","department":[{"_id":"GaTk"}],"publication_status":"published","pmid":1,"year":"2017","volume":114,"date_updated":"2021-01-12T08:12:36Z","date_created":"2018-12-11T11:48:10Z","author":[{"full_name":"Harpaz, Roy","first_name":"Roy","last_name":"Harpaz"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schneidman","first_name":"Elad","full_name":"Schneidman, Elad"}],"scopus_import":1,"day":"19","page":"10149 - 10154","citation":{"ista":"Harpaz R, Tkačik G, Schneidman E. 2017. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154.","apa":"Harpaz, R., Tkačik, G., & Schneidman, E. (2017). Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1703817114","ieee":"R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” PNAS, vol. 114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.","ama":"Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 2017;114(38):10149-10154. doi:10.1073/pnas.1703817114","chicago":"Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1703817114.","mla":"Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114.","short":"R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154."},"publication":"PNAS","date_published":"2017-09-19T00:00:00Z","type":"journal_article","issue":"38","abstract":[{"text":"Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here, we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an “active” mode, in which they are sensitive to the swimming patterns of conspecifics, and a “passive” mode, where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors’ behavior. At the group level, switching between active and passive modes is uncorrelated among fish, but correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multi-modal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates as well as to other species.","lang":"eng"}],"intvolume":" 114","status":"public","title":"Discrete modes of social information processing predict individual behavior of fish in a group","_id":"725","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version"},{"citation":{"ama":"Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. 2017;96(10). doi:10.1103/PhysRevB.96.104203","ista":"Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. 2017. Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. 96(10), 104203.","apa":"Hetterich, D., Serbyn, M., Domínguez, F., Pollmann, F., & Trauzettel, B. (2017). Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104203","ieee":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, and B. Trauzettel, “Noninteracting central site model localization and logarithmic entanglement growth,” Physical Review B, vol. 96, no. 10. American Physical Society, 2017.","mla":"Hetterich, Daniel, et al. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” Physical Review B, vol. 96, no. 10, 104203, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104203.","short":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, B. Trauzettel, Physical Review B 96 (2017).","chicago":"Hetterich, Daniel, Maksym Serbyn, Fernando Domínguez, Frank Pollmann, and Björn Trauzettel. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104203."},"publication":"Physical Review B","date_published":"2017-09-13T00:00:00Z","scopus_import":1,"day":"13","_id":"724","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 96","status":"public","title":"Noninteracting central site model localization and logarithmic entanglement growth","oa_version":"Submitted Version","type":"journal_article","issue":"10","abstract":[{"text":"We investigate the stationary and dynamical behavior of an Anderson localized chain coupled to a single central bound state. Although this coupling partially dilutes the Anderson localized peaks towards nearly resonant sites, the most weight of the original peaks remains unchanged. This leads to multifractal wave functions with a frozen spectrum of fractal dimensions, which is characteristic for localized phases in models with power-law hopping. Using a perturbative approach we identify two different dynamical regimes. At weak couplings to the central site, the transport of particles and information is logarithmic in time, a feature usually attributed to many-body localization. We connect such transport to the persistence of the Poisson statistics of level spacings in parts of the spectrum. In contrast, at stronger couplings the level repulsion is established in the entire spectrum, the problem can be mapped to the Fano resonance, and the transport is ballistic.","lang":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1701.02744","open_access":"1"}],"quality_controlled":"1","doi":"10.1103/PhysRevB.96.104203","language":[{"iso":"eng"}],"publication_identifier":{"issn":["24699950"]},"month":"09","year":"2017","acknowledgement":"We would like to thank Dmitry Abanin, Christophe De\r\nBeule, Joel Moore, Romain Vasseur, and Norman Yao for\r\nmany stimulating discussions. Financial support has been\r\nprovided by the Deutsche Forschungsgemeinschaft (DFG)\r\nvia Grant No. TR950/8-1, SFB 1170 “ToCoTronics” and the\r\nENB Graduate School on Topological Insulators. M.S. was\r\nsupported by Gordon and Betty Moore Foundation’s EPiQS\r\nInitiative through Grant No. GBMF4307. F.P. acknowledges\r\nsupport from the DFG Research Unit FOR 1807 through Grant\r\nNo. PO 1370/2-1.","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","author":[{"full_name":"Hetterich, Daniel","first_name":"Daniel","last_name":"Hetterich"},{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"},{"first_name":"Fernando","last_name":"Domínguez","full_name":"Domínguez, Fernando"},{"full_name":"Pollmann, Frank","last_name":"Pollmann","first_name":"Frank"},{"first_name":"Björn","last_name":"Trauzettel","full_name":"Trauzettel, Björn"}],"volume":96,"date_created":"2018-12-11T11:48:09Z","date_updated":"2021-01-12T08:12:35Z","article_number":"104203","publist_id":"6955"},{"oa_version":"None","volume":9,"date_created":"2018-12-11T11:48:12Z","date_updated":"2021-01-12T08:12:57Z","author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia"}],"intvolume":" 9","department":[{"_id":"GaNo"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","status":"public","title":"The science of love in ASD and ADHD","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"731","year":"2017","issue":"411","publist_id":"6938","abstract":[{"lang":"eng","text":"Genetic variations in the oxytocin receptor gene affect patients with ASD and ADHD differently."}],"type":"journal_article","article_number":"eaap8168","language":[{"iso":"eng"}],"doi":"10.1126/scitranslmed.aap8168","date_published":"2017-10-11T00:00:00Z","quality_controlled":"1","citation":{"chicago":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aap8168.","mla":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational Medicine, vol. 9, no. 411, eaap8168, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aap8168.","short":"G. Novarino, Science Translational Medicine 9 (2017).","ista":"Novarino G. 2017. The science of love in ASD and ADHD. Science Translational Medicine. 9(411), eaap8168.","apa":"Novarino, G. (2017). The science of love in ASD and ADHD. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aap8168","ieee":"G. Novarino, “The science of love in ASD and ADHD,” Science Translational Medicine, vol. 9, no. 411. American Association for the Advancement of Science, 2017.","ama":"Novarino G. The science of love in ASD and ADHD. Science Translational Medicine. 2017;9(411). doi:10.1126/scitranslmed.aap8168"},"publication":"Science Translational Medicine","publication_identifier":{"issn":["19466234"]},"month":"10","day":"11","scopus_import":1},{"file_date_updated":"2020-07-14T12:47:56Z","author":[{"last_name":"Smole","first_name":"Anže","full_name":"Smole, Anže"},{"full_name":"Lainšček, Duško","last_name":"Lainšček","first_name":"Duško"},{"full_name":"Bezeljak, Urban","last_name":"Bezeljak","first_name":"Urban","orcid":"0000-0003-1365-5631","id":"2A58201A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Horvat, Simon","last_name":"Horvat","first_name":"Simon"},{"first_name":"Roman","last_name":"Jerala","full_name":"Jerala, Roman"}],"volume":25,"date_updated":"2021-01-12T08:13:14Z","date_created":"2020-01-25T15:55:39Z","pmid":1,"year":"2017","publisher":"Elsevier","department":[{"_id":"MaLo"}],"publication_status":"published","publication_identifier":{"issn":["1525-0016"]},"month":"01","doi":"10.1016/j.ymthe.2016.10.005","language":[{"iso":"eng"}],"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,"external_id":{"pmid":["28129106"]},"quality_controlled":"1","issue":"1","abstract":[{"text":"Inflammation, which is a highly regulated host response against danger signals, may be harmful if it is excessive and deregulated. Ideally, anti-inflammatory therapy should autonomously commence as soon as possible after the onset of inflammation, should be controllable by a physician, and should not systemically block beneficial immune response in the long term. We describe a genetically encoded anti-inflammatory mammalian cell device based on a modular engineered genetic circuit comprising a sensor, an amplifier, a “thresholder” to restrict activation of a positive-feedback loop, a combination of advanced clinically used biopharmaceutical proteins, and orthogonal regulatory elements that linked modules into the functional device. This genetic circuit was autonomously activated by inflammatory signals, including endogenous cecal ligation and puncture (CLP)-induced inflammation in mice and serum from a systemic juvenile idiopathic arthritis (sIJA) patient, and could be reset externally by a chemical signal. The microencapsulated anti-inflammatory device significantly reduced the pathology in dextran sodium sulfate (DSS)-induced acute murine colitis, demonstrating a synthetic immunological approach for autonomous anti-inflammatory therapy.","lang":"eng"}],"type":"journal_article","file":[{"file_id":"7561","relation":"main_file","checksum":"ea8b1b28606dd1edab7379ba4fa3641f","date_created":"2020-03-03T10:55:13Z","date_updated":"2020-07-14T12:47:56Z","access_level":"open_access","file_name":"2017_MolecularTherapy_Smole.pdf","creator":"dernst","content_type":"application/pdf","file_size":3404806}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7360","intvolume":" 25","ddc":["570"],"status":"public","title":"A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation","has_accepted_license":"1","article_processing_charge":"No","day":"01","date_published":"2017-01-01T00:00:00Z","citation":{"apa":"Smole, A., Lainšček, D., Bezeljak, U., Horvat, S., & Jerala, R. (2017). A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. Elsevier. https://doi.org/10.1016/j.ymthe.2016.10.005","ieee":"A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, and R. Jerala, “A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation,” Molecular Therapy, vol. 25, no. 1. Elsevier, pp. 102–119, 2017.","ista":"Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. 2017. A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. 25(1), 102–119.","ama":"Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. 2017;25(1):102-119. doi:10.1016/j.ymthe.2016.10.005","chicago":"Smole, Anže, Duško Lainšček, Urban Bezeljak, Simon Horvat, and Roman Jerala. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” Molecular Therapy. Elsevier, 2017. https://doi.org/10.1016/j.ymthe.2016.10.005.","short":"A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, R. Jerala, Molecular Therapy 25 (2017) 102–119.","mla":"Smole, Anže, et al. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” Molecular Therapy, vol. 25, no. 1, Elsevier, 2017, pp. 102–19, doi:10.1016/j.ymthe.2016.10.005."},"publication":"Molecular Therapy","page":"102-119","article_type":"original"},{"abstract":[{"text":"Modern communication technologies allow first responders to contact thousands of potential volunteers simultaneously for support during a crisis or disaster event. However, such volunteer efforts must be well coordinated and monitored, in order to offer an effective relief to the professionals. In this paper we extend earlier work on optimally assigning volunteers to selected landmark locations. In particular, we emphasize the aspect that obtaining good assignments requires not only advanced computational tools, but also a realistic measure of distance between volunteers and landmarks. Specifically, we propose the use of the Open Street Map (OSM) driving distance instead of he previously used flight distance. We find the OSM driving distance to be better aligned with the interests of volunteers and first responders. Furthermore, we show that relying on the flying distance leads to a substantial underestimation of the number of required volunteers, causing negative side effects in case of an actual crisis situation.","lang":"eng"}],"publist_id":"6906","type":"conference","author":[{"full_name":"Pielorz, Jasmin","first_name":"Jasmin","last_name":"Pielorz","id":"49BC895A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Prandtstetter","first_name":"Matthias","full_name":"Prandtstetter, Matthias"},{"first_name":"Markus","last_name":"Straub","full_name":"Straub, Markus"},{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T08:13:55Z","date_created":"2018-12-11T11:48:18Z","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"750","year":"2017","publication_status":"published","title":"Optimal geospatial volunteer allocation needs realistic distances","status":"public","department":[{"_id":"ChLa"}],"publisher":"IEEE","day":"01","month":"12","publication_identifier":{"isbn":["978-153862714-3"]},"scopus_import":1,"conference":{"start_date":"2017-12-11","location":"Boston, MA, United States","end_date":"2017-12-14","name":"Big Data"},"doi":"10.1109/BigData.2017.8258375","date_published":"2017-12-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"2017 IEEE International Conference on Big Data","citation":{"ista":"Pielorz J, Prandtstetter M, Straub M, Lampert C. 2017. Optimal geospatial volunteer allocation needs realistic distances. 2017 IEEE International Conference on Big Data. Big Data, 3760–3763.","ieee":"J. Pielorz, M. Prandtstetter, M. Straub, and C. Lampert, “Optimal geospatial volunteer allocation needs realistic distances,” in 2017 IEEE International Conference on Big Data, Boston, MA, United States, 2017, pp. 3760–3763.","apa":"Pielorz, J., Prandtstetter, M., Straub, M., & Lampert, C. (2017). Optimal geospatial volunteer allocation needs realistic distances. In 2017 IEEE International Conference on Big Data (pp. 3760–3763). Boston, MA, United States: IEEE. https://doi.org/10.1109/BigData.2017.8258375","ama":"Pielorz J, Prandtstetter M, Straub M, Lampert C. Optimal geospatial volunteer allocation needs realistic distances. In: 2017 IEEE International Conference on Big Data. IEEE; 2017:3760-3763. doi:10.1109/BigData.2017.8258375","chicago":"Pielorz, Jasmin, Matthias Prandtstetter, Markus Straub, and Christoph Lampert. “Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” In 2017 IEEE International Conference on Big Data, 3760–63. IEEE, 2017. https://doi.org/10.1109/BigData.2017.8258375.","mla":"Pielorz, Jasmin, et al. “Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–63, doi:10.1109/BigData.2017.8258375.","short":"J. Pielorz, M. Prandtstetter, M. Straub, C. Lampert, in:, 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–3763."},"quality_controlled":"1","page":"3760 - 3763"},{"publication_identifier":{"issn":["10778926"]},"month":"07","doi":"10.37236/6663","language":[{"iso":"eng"}],"oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publist_id":"6859","ec_funded":1,"file_date_updated":"2020-07-14T12:48:06Z","article_number":"P3.18","author":[{"full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek"},{"full_name":"Kynčl, Jan","first_name":"Jan","last_name":"Kynčl"},{"first_name":"Dömötör","last_name":"Pálvölgyi","full_name":"Pálvölgyi, Dömötör"}],"volume":24,"date_created":"2018-12-11T11:48:32Z","date_updated":"2022-03-18T12:58:53Z","year":"2017","department":[{"_id":"UlWa"}],"publisher":"International Press","publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"28","scopus_import":"1","date_published":"2017-07-28T00:00:00Z","citation":{"ama":"Fulek R, Kynčl J, Pálvölgyi D. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 2017;24(3). doi:10.37236/6663","ieee":"R. Fulek, J. Kynčl, and D. Pálvölgyi, “Unified Hanani Tutte theorem,” Electronic Journal of Combinatorics, vol. 24, no. 3. International Press, 2017.","apa":"Fulek, R., Kynčl, J., & Pálvölgyi, D. (2017). Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. International Press. https://doi.org/10.37236/6663","ista":"Fulek R, Kynčl J, Pálvölgyi D. 2017. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 24(3), P3.18.","short":"R. Fulek, J. Kynčl, D. Pálvölgyi, Electronic Journal of Combinatorics 24 (2017).","mla":"Fulek, Radoslav, et al. “Unified Hanani Tutte Theorem.” Electronic Journal of Combinatorics, vol. 24, no. 3, P3.18, International Press, 2017, doi:10.37236/6663.","chicago":"Fulek, Radoslav, Jan Kynčl, and Dömötör Pálvölgyi. “Unified Hanani Tutte Theorem.” Electronic Journal of Combinatorics. International Press, 2017. https://doi.org/10.37236/6663."},"publication":"Electronic Journal of Combinatorics","article_type":"original","issue":"3","abstract":[{"text":"We introduce a common generalization of the strong Hanani–Tutte theorem and the weak Hanani–Tutte theorem: if a graph G has a drawing D in the plane where every pair of independent edges crosses an even number of times, then G has a planar drawing preserving the rotation of each vertex whose incident edges cross each other evenly in D. The theorem is implicit in the proof of the strong Hanani–Tutte theorem by Pelsmajer, Schaefer and Štefankovič. We give a new, somewhat simpler proof.","lang":"eng"}],"type":"journal_article","file":[{"file_id":"5853","relation":"main_file","date_updated":"2020-07-14T12:48:06Z","date_created":"2019-01-18T14:04:08Z","checksum":"ef320cff0f062051e858f929be6a3581","file_name":"2017_ElectrCombi_Fulek.pdf","access_level":"open_access","creator":"dernst","file_size":236944,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"795","intvolume":" 24","title":"Unified Hanani Tutte theorem","status":"public","ddc":["000"]},{"day":"01","month":"05","article_processing_charge":"No","quality_controlled":"1","article_type":"original","page":"111 - 113","publication":"Physik in unserer Zeit","citation":{"ama":"Fink JM. Photonenblockade aufgelöst. Physik in unserer Zeit. 2017;48(3):111-113. doi:10.1002/piuz.201770305","ista":"Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3), 111–113.","ieee":"J. M. Fink, “Photonenblockade aufgelöst,” Physik in unserer Zeit, vol. 48, no. 3. Wiley, pp. 111–113, 2017.","apa":"Fink, J. M. (2017). Photonenblockade aufgelöst. Physik in Unserer Zeit. Wiley. https://doi.org/10.1002/piuz.201770305","mla":"Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit, vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:10.1002/piuz.201770305.","short":"J.M. Fink, Physik in Unserer Zeit 48 (2017) 111–113.","chicago":"Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit. Wiley, 2017. https://doi.org/10.1002/piuz.201770305."},"language":[{"iso":"eng"}],"date_published":"2017-05-01T00:00:00Z","doi":"10.1002/piuz.201770305","type":"journal_article","abstract":[{"lang":"ger","text":"Phasenübergänge helfen beim Verständnis von Vielteilchensystemen in der Festkörperphysik und Fluiddynamik bis hin zur Teilchenphysik. Unserer internationalen Kollaboration ist es gelungen, einen neuartigen Phasenübergang in einem Quantensystem zu beobachten [1]. In einem Mikrowellenresonator konnte erstmals die spontane Zustandsänderung von undurchsichtig zu transparent nachgewiesen werden."}],"issue":"3","publist_id":"6856","status":"public","title":"Photonenblockade aufgelöst","publication_status":"published","intvolume":" 48","publisher":"Wiley","department":[{"_id":"JoFi"}],"_id":"797","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","date_created":"2018-12-11T11:48:33Z","date_updated":"2022-03-24T09:16:20Z","volume":48,"oa_version":"None","author":[{"full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}]},{"day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2017-08-01T00:00:00Z","page":"274 - 280","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","citation":{"chicago":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1898.","mla":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 274–80, doi:10.31263/voebm.v70i2.1898.","short":"M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 70 (2017) 274–280.","ista":"Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280.","ieee":"M. Andrae and M. Villányi, “Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 70, no. 2. VÖB, pp. 274–280, 2017.","apa":"Andrae, M., & Villányi, M. (2017). Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1898","ama":"Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2017;70(2):274-280. doi:10.31263/voebm.v70i2.1898"},"abstract":[{"text":"On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries and the publisher Springer took its effect: this deal covers accessing the licensed content on the one hand, and publishing open access on the other hand. More than 1000 papers by Austrian authors were published open access at Springer in the first year alone. The working group "Springer Compact Evaluierung" made the data for these articles available via the platform OpenAPC and would like to use this opportunity to give a short account of what this publishing agreement actually entails and the working group intends to do.","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5851","date_updated":"2020-07-14T12:48:09Z","date_created":"2019-01-18T13:39:26Z","checksum":"558c18bcf5580d87dd371ec626d52075","file_name":"2017_VOEB_Andrae.pdf","access_level":"open_access","file_size":125065,"content_type":"application/pdf","creator":"dernst"}],"popular_science":"1","ddc":["020"],"title":"Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung","status":"public","intvolume":" 70","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"807","month":"08","publication_identifier":{"issn":["10222588"]},"language":[{"iso":"eng"}],"doi":"10.31263/voebm.v70i2.1898","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"},"file_date_updated":"2020-07-14T12:48:09Z","publist_id":"6843","date_updated":"2021-01-12T08:16:45Z","date_created":"2018-12-11T11:48:36Z","volume":70,"author":[{"first_name":"Magdalena","last_name":"Andrae","full_name":"Andrae, Magdalena"},{"full_name":"Villányi, Márton","first_name":"Márton","last_name":"Villányi","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8126-0426"}],"publication_status":"published","department":[{"_id":"E-Lib"}],"publisher":"VÖB","year":"2017"},{"publist_id":"6823","file_date_updated":"2020-07-14T12:48:11Z","department":[{"_id":"E-Lib"}],"publisher":"VÖB","publication_status":"published","year":"2017","volume":70,"date_updated":"2021-01-12T08:17:44Z","date_created":"2018-12-11T11:48:42Z","author":[{"full_name":"Petritsch, Barbara","orcid":"0000-0003-2724-4614","id":"406048EC-F248-11E8-B48F-1D18A9856A87","last_name":"Petritsch","first_name":"Barbara"}],"publication_identifier":{"issn":["10222588"]},"month":"08","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":"10.31263/voebm.v70i2.1678","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep."}],"intvolume":" 70","title":"Metadata for research data in practice","status":"public","ddc":["020"],"_id":"825","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5850","date_created":"2019-01-18T13:32:17Z","date_updated":"2020-07-14T12:48:11Z","checksum":"7c4544d07efa2c2add8612b489abb4e2","file_name":"2017_VOEB_Petritsch.pdf","access_level":"open_access","content_type":"application/pdf","file_size":7843975,"creator":"dernst"}],"scopus_import":1,"has_accepted_license":"1","day":"01","page":"200 - 207","citation":{"ama":"Petritsch B. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 2017;70(2):200-207. doi:10.31263/voebm.v70i2.1678","ieee":"B. Petritsch, “Metadata for research data in practice,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2. VÖB, pp. 200–207, 2017.","apa":"Petritsch, B. (2017). Metadata for research data in practice. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1678","ista":"Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 70(2), 200–207.","short":"B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare 70 (2017) 200–207.","mla":"Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 200–07, doi:10.31263/voebm.v70i2.1678.","chicago":"Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1678."},"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare","date_published":"2017-08-01T00:00:00Z"},{"date_created":"2021-06-02T14:28:58Z","date_updated":"2021-12-14T07:54:36Z","volume":6,"author":[{"last_name":"Lyons","first_name":"David B","full_name":"Lyons, David B"},{"full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"publication_status":"published","department":[{"_id":"DaZi"}],"publisher":"eLife Sciences Publications","year":"2017","pmid":1,"extern":"1","file_date_updated":"2021-06-02T14:33:36Z","article_number":"e30674","language":[{"iso":"eng"}],"doi":"10.7554/elife.30674","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["29140247"]},"month":"11","publication_identifier":{"eissn":["2050-084X"]},"oa_version":"Published Version","file":[{"file_name":"2017_eLife_Lyons.pdf","access_level":"open_access","creator":"cziletti","content_type":"application/pdf","file_size":1603102,"file_id":"9446","relation":"main_file","date_created":"2021-06-02T14:33:36Z","date_updated":"2021-06-02T14:33:36Z","success":1,"checksum":"4cfcdd67511ae4aed3d993550e46e146"}],"ddc":["570"],"status":"public","title":"DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes","intvolume":" 6","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9445","abstract":[{"lang":"eng","text":"Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation."}],"type":"journal_article","date_published":"2017-11-15T00:00:00Z","article_type":"original","publication":"eLife","citation":{"ama":"Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674","ieee":"D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674","ista":"Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674.","short":"D.B. Lyons, D. Zilberman, ELife 6 (2017).","mla":"Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications, 2017, doi:10.7554/elife.30674.","chicago":"Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30674."},"day":"15","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"series_title":"Synthetic Protein Switches","scopus_import":1,"day":"15","page":"71 - 87","citation":{"short":"B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L. Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 71–87.","mla":"Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5.","chicago":"Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde, Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5.","ama":"Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5","apa":"Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer. https://doi.org/10.1007/978-1-4939-6940-1_5","ieee":"B. Clifton et al., “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.","ista":"Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 71–87."},"publication":"Synthetic Protein Switches","date_published":"2017-03-15T00:00:00Z","alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","abstract":[{"text":"Small molecule biosensors based on Forster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors.","lang":"eng"}],"intvolume":" 1596","title":"Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors","status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"957","oa_version":"None","publication_identifier":{"issn":["10643745"]},"month":"03","project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"}],"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-6940-1_5","publist_id":"6451","editor":[{"full_name":"Stein, Viktor","last_name":"Stein","first_name":"Viktor"}],"publisher":"Springer","department":[{"_id":"HaJa"}],"publication_status":"published","year":"2017","volume":1596,"date_created":"2018-12-11T11:49:24Z","date_updated":"2021-01-12T08:22:13Z","author":[{"full_name":"Clifton, Ben","last_name":"Clifton","first_name":"Ben"},{"first_name":"Jason","last_name":"Whitfield","full_name":"Whitfield, Jason"},{"last_name":"Sanchez Romero","first_name":"Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","full_name":"Sanchez Romero, Inmaculada"},{"full_name":"Herde, Michel","last_name":"Herde","first_name":"Michel"},{"full_name":"Henneberger, Christian","first_name":"Christian","last_name":"Henneberger"},{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"},{"last_name":"Jackson","first_name":"Colin","full_name":"Jackson, Colin"}]},{"article_number":"37","file_date_updated":"2020-07-14T12:48:18Z","publist_id":"6438","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"}],"year":"2017","date_created":"2018-12-11T11:49:26Z","date_updated":"2023-02-23T12:35:50Z","volume":83,"author":[{"first_name":"Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy"},{"last_name":"Guha","first_name":"Shibashis","full_name":"Guha, Shibashis"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"related_material":{"record":[{"id":"6005","status":"public","relation":"later_version"}]},"month":"06","publication_identifier":{"issn":["18688969"]},"quality_controlled":"1","project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"}],"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"}],"conference":{"location":"Aalborg, Denmark","start_date":"2017-08-21","end_date":"2017-08-25","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"doi":"10.4230/LIPIcs.MFCS.2017.37","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. ","lang":"eng"}],"ddc":["004"],"status":"public","title":"Timed network games with clocks","intvolume":" 83","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"963","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-829-v1+1_mfcs-cr.pdf","creator":"system","file_size":369730,"content_type":"application/pdf","file_id":"5059","relation":"main_file","checksum":"f55eaf7f3c36ea07801112acfedd17d5","date_created":"2018-12-12T10:14:10Z","date_updated":"2020-07-14T12:48:18Z"}],"pubrep_id":"829","scopus_import":1,"day":"01","has_accepted_license":"1","citation":{"ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37","apa":"Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks (Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark, 2017, vol. 83.","ista":"Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37.","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37."},"date_published":"2017-06-01T00:00:00Z"},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina."}],"publisher":"Dryad","department":[{"_id":"GaTk"}],"status":"public","title":"Data from: Error-robust modes of the retinal population code","_id":"9709","year":"2017","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_created":"2021-07-23T11:34:34Z","date_updated":"2023-02-21T16:34:41Z","related_material":{"record":[{"id":"1197","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Prentice, Jason","first_name":"Jason","last_name":"Prentice"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"first_name":"Mark","last_name":"Ioffe","full_name":"Ioffe, Mark"},{"full_name":"Loback, Adrianna","last_name":"Loback","first_name":"Adrianna"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"},{"full_name":"Berry, Michael","last_name":"Berry","first_name":"Michael"}],"article_processing_charge":"No","month":"10","day":"18","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.1f1rc"}],"oa":1,"citation":{"ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc.","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc","mla":"Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).","chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc."},"doi":"10.5061/dryad.1f1rc","date_published":"2017-10-18T00:00:00Z"},{"doi":"10.1371/journal.pgen.1007122","language":[{"iso":"eng"}],"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"},"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"month":"12","publication_identifier":{"issn":["15537390"]},"author":[{"orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","first_name":"Nela","full_name":"Nikolic, Nela"},{"last_name":"Schreiber","first_name":"Frank","full_name":"Schreiber, Frank"},{"full_name":"Dal Co, Alma","first_name":"Alma","last_name":"Dal Co"},{"full_name":"Kiviet, Daniel","first_name":"Daniel","last_name":"Kiviet"},{"last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"last_name":"Littmann","first_name":"Sten","full_name":"Littmann, Sten"},{"full_name":"Kuypers, Marcel","last_name":"Kuypers","first_name":"Marcel"},{"first_name":"Martin","last_name":"Ackermann","full_name":"Ackermann, Martin"}],"related_material":{"record":[{"id":"9844","status":"public","relation":"research_data"},{"id":"9845","status":"public","relation":"research_data"},{"id":"9846","status":"public","relation":"research_data"}]},"date_created":"2018-12-11T11:47:04Z","date_updated":"2023-02-23T14:10:34Z","volume":13,"year":"2017","publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:46:46Z","publist_id":"7275","ec_funded":1,"article_number":"e1007122","date_published":"2017-12-18T00:00:00Z","publication":"PLoS Genetics","citation":{"mla":"Nikolic, Nela, et al. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics, vol. 13, no. 12, e1007122, Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, PLoS Genetics 13 (2017).","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics. Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 2017;13(12). doi:10.1371/journal.pgen.1007122","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 13(12), e1007122.","ieee":"N. Nikolic et al., “Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations,” PLoS Genetics, vol. 13, no. 12. Public Library of Science, 2017.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122"},"day":"18","has_accepted_license":"1","scopus_import":1,"pubrep_id":"959","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5088","date_updated":"2020-07-14T12:46:46Z","date_created":"2018-12-12T10:14:35Z","checksum":"22426d9382f21554bad5fa5967afcfd0","file_name":"IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf","access_level":"open_access","file_size":1308475,"content_type":"application/pdf","creator":"system"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"541","ddc":["576","579"],"status":"public","title":"Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations","intvolume":" 13","abstract":[{"text":"While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed.","lang":"eng"}],"issue":"12","type":"journal_article"},{"date_published":"2017-11-27T00:00:00Z","doi":"10.6084/m9.figshare.5633917.v1","citation":{"apa":"Pleska, M., & Guet, C. C. (2017). Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification. The Royal Society. https://doi.org/10.6084/m9.figshare.5633917.v1","ieee":"M. Pleska and C. C. Guet, “Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification.” The Royal Society, 2017.","ista":"Pleska M, Guet CC. 2017. Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification, The Royal Society, 10.6084/m9.figshare.5633917.v1.","ama":"Pleska M, Guet CC. Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification. 2017. doi:10.6084/m9.figshare.5633917.v1","chicago":"Pleska, Maros, and Calin C Guet. “Supplementary Materials and Methods; Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” The Royal Society, 2017. https://doi.org/10.6084/m9.figshare.5633917.v1.","short":"M. Pleska, C.C. Guet, (2017).","mla":"Pleska, Maros, and Calin C. Guet. Supplementary Materials and Methods; Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification. The Royal Society, 2017, doi:10.6084/m9.figshare.5633917.v1."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.5633917.v1","open_access":"1"}],"month":"11","day":"27","article_processing_charge":"No","date_updated":"2023-02-23T12:29:44Z","date_created":"2021-08-09T13:54:38Z","oa_version":"Published Version","author":[{"full_name":"Pleska, Maros","first_name":"Maros","last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"561"}]},"status":"public","title":"Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification","publisher":"The Royal Society","department":[{"_id":"CaGu"}],"year":"2017","_id":"9847","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"information on culture conditions, phage mutagenesis, verification and lysate preparation; Raw data"}],"type":"research_data_reference"},{"year":"2017","_id":"9845","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"CaGu"}],"publisher":"Public Library of Science","title":"Mathematical model","status":"public","related_material":{"record":[{"id":"541","status":"public","relation":"used_in_publication"}]},"author":[{"orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","first_name":"Nela","full_name":"Nikolic, Nela"},{"full_name":"Schreiber, Frank","first_name":"Frank","last_name":"Schreiber"},{"last_name":"Dal Co","first_name":"Alma","full_name":"Dal Co, Alma"},{"full_name":"Kiviet, Daniel","first_name":"Daniel","last_name":"Kiviet"},{"last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"full_name":"Littmann, Sten","last_name":"Littmann","first_name":"Sten"},{"first_name":"Marcel","last_name":"Kuypers","full_name":"Kuypers, Marcel"},{"full_name":"Ackermann, Martin","last_name":"Ackermann","first_name":"Martin"}],"oa_version":"None","date_updated":"2023-02-23T12:25:04Z","date_created":"2021-08-09T13:31:51Z","type":"research_data_reference","abstract":[{"text":"Estimates of 13 C-arabinose and 2 H-glucose uptake from the fractions of heavy isotopes measured\tin single cells","lang":"eng"}],"citation":{"ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Mathematical model, Public Library of Science, 10.1371/journal.pgen.1007122.s017.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Mathematical model. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s017","ieee":"N. Nikolic et al., “Mathematical model.” Public Library of Science, 2017.","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Mathematical model. 2017. doi:10.1371/journal.pgen.1007122.s017","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Mathematical Model.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s017.","mla":"Nikolic, Nela, et al. Mathematical Model. Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s017.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. 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Crucially, they also need to compete for the interpretation of those signals with other neurons representing similar features. The form that this competition should take depends critically on the noise corrupting these signals. In this study we show that for the type of noise commonly observed in sensory systems, whose variance scales with the mean signal, sensory neurons should selectively divide their input signals by their predictions, suppressing ambiguous cues while amplifying others. Any change in the stimulus context alters which inputs are suppressed, leading to a deep dynamic reshaping of neural receptive fields going far beyond simple surround suppression. Paradoxically, these highly variable receptive fields go alongside and are in fact required for an invariant representation of external sensory features. In addition to offering a normative account of context-dependent changes in sensory responses, perceptual inference in the presence of signal-dependent noise accounts for ubiquitous features of sensory neurons such as divisive normalization, gain control and contrast dependent temporal dynamics.","lang":"eng"}],"issue":"6"},{"date_published":"2017-07-18T00:00:00Z","doi":"10.1371/journal.pcbi.1005609.s003","citation":{"ama":"Lukacisinova M, Novak S, Paixao T. Heuristic prediction for multiple stresses. 2017. doi:10.1371/journal.pcbi.1005609.s003","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Heuristic prediction for multiple stresses. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s003","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple stresses.” Public Library of Science, 2017.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. 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Paixao, (2017).","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Resistance Frequencies for Different Combination Strategies.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s004."}},{"_id":"9855","year":"2017","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Supplementary appendix","status":"public","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"author":[{"full_name":"Chalk, Matthew J","first_name":"Matthew J","last_name":"Chalk","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436"},{"full_name":"Masset, Paul","last_name":"Masset","first_name":"Paul"},{"first_name":"Boris","last_name":"Gutkin","full_name":"Gutkin, Boris"},{"first_name":"Sophie","last_name":"Denève","full_name":"Denève, Sophie"}],"related_material":{"record":[{"id":"680","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-10T07:05:10Z","date_updated":"2023-02-23T12:52:17Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"lang":"eng","text":"Includes derivation of optimal estimation algorithm, generalisation to non-poisson noise statistics, correlated input noise, and implementation of in a multi-layer neural network."}],"citation":{"short":"M.J. Chalk, P. Masset, B. Gutkin, S. Denève, (2017).","mla":"Chalk, Matthew J., et al. Supplementary Appendix. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005582.s001.","chicago":"Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Supplementary Appendix.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582.s001.","ama":"Chalk MJ, Masset P, Gutkin B, Denève S. Supplementary appendix. 2017. doi:10.1371/journal.pcbi.1005582.s001","ieee":"M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Supplementary appendix.” Public Library of Science, 2017.","apa":"Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Supplementary appendix. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005582.s001","ista":"Chalk MJ, Masset P, Gutkin B, Denève S. 2017. 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(2017). JFIX: Semantics-based repair of Java programs via symbolic PathFinder. In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis (pp. 376–379). Santa Barbara, CA, United States: ACM. https://doi.org/10.1145/3092703.3098225","ieee":"X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “JFIX: Semantics-based repair of Java programs via symbolic PathFinder,” in Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, Santa Barbara, CA, United States, 2017, pp. 376–379.","ista":"Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. JFIX: Semantics-based repair of Java programs via symbolic PathFinder. Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ISSTA: International Symposium on Software Testing and Analysis, 376–379.","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–379.","mla":"Le, Xuan, et al. “JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–79, doi:10.1145/3092703.3098225.","chicago":"Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, 376–79. ACM, 2017. https://doi.org/10.1145/3092703.3098225."},"language":[{"iso":"eng"}],"conference":{"name":"ISSTA: International Symposium on Software Testing and Analysis","location":"Santa Barbara, CA, United States","start_date":"2017-07-10","end_date":"2017-07-14"},"doi":"10.1145/3092703.3098225","date_published":"2017-07-10T00:00:00Z","scopus_import":1,"day":"10","month":"07","publication_status":"published","title":"JFIX: Semantics-based repair of Java programs via symbolic PathFinder","status":"public","publisher":"ACM","department":[{"_id":"ToHe"}],"year":"2017","_id":"941","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:49:19Z","date_updated":"2021-01-12T08:22:05Z","oa_version":"None","author":[{"last_name":"Le","first_name":"Xuan","full_name":"Le, Xuan"},{"full_name":"Chu, Duc Hiep","first_name":"Duc Hiep","last_name":"Chu","id":"3598E630-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lo, David","first_name":"David","last_name":"Lo"},{"full_name":"Le Goues, Claire","first_name":"Claire","last_name":"Le Goues"},{"full_name":"Visser, Willem","last_name":"Visser","first_name":"Willem"}],"type":"conference","abstract":[{"lang":"eng","text":"Recently there has been a proliferation of automated program repair (APR) techniques, targeting various programming languages. Such techniques can be generally classified into two families: syntactic- and semantics-based. Semantics-based APR, on which we focus, typically uses symbolic execution to infer semantic constraints and then program synthesis to construct repairs conforming to them. While syntactic-based APR techniques have been shown successful on bugs in real-world programs written in both C and Java, semantics-based APR techniques mostly target C programs. This leaves empirical comparisons of the APR families not fully explored, and developers without a Java-based semantics APR technique. We present JFix, a semantics-based APR framework that targets Java, and an associated Eclipse plugin. JFix is implemented atop Symbolic PathFinder, a well-known symbolic execution engine for Java programs. It extends one particular APR technique (Angelix), and is designed to be sufficiently generic to support a variety of such techniques. We demonstrate that semantics-based APR can indeed efficiently and effectively repair a variety of classes of bugs in large real-world Java programs. This supports our claim that the framework can both support developers seeking semantics-based repair of bugs in Java programs, as well as enable larger scale empirical studies comparing syntactic- and semantics-based APR targeting Java. The demonstration of our tool is available via the project website at: https://xuanbachle.github.io/semanticsrepair/ "}],"publist_id":"6478"},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"09","citation":{"ama":"Zilberman D. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 2017;18(1). doi:10.1186/s13059-017-1230-2","ista":"Zilberman D. 2017. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 18(1), 87.","ieee":"D. Zilberman, “An evolutionary case for functional gene body methylation in plants and animals,” Genome Biology, vol. 18, no. 1. Springer Nature, 2017.","apa":"Zilberman, D. (2017). An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-017-1230-2","mla":"Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology, vol. 18, no. 1, 87, Springer Nature, 2017, doi:10.1186/s13059-017-1230-2.","short":"D. Zilberman, Genome Biology 18 (2017).","chicago":"Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology. Springer Nature, 2017. https://doi.org/10.1186/s13059-017-1230-2."},"publication":"Genome Biology","date_published":"2017-05-09T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"text":"Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation.","lang":"eng"}],"_id":"9506","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 18","status":"public","title":"An evolutionary case for functional gene body methylation in plants and animals","ddc":["570"],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2017_GenomeBiology_Zilberman.pdf","file_size":278183,"content_type":"application/pdf","creator":"asandaue","relation":"main_file","file_id":"9507","checksum":"5a455ad914e7d225b1baa4ab07fd925e","success":1,"date_updated":"2021-06-07T12:31:36Z","date_created":"2021-06-07T12:31:36Z"}],"publication_identifier":{"eissn":["1465-6906"],"issn":["1474-760X"]},"month":"05","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"},"external_id":{"pmid":["28486944"]},"oa":1,"quality_controlled":"1","doi":"10.1186/s13059-017-1230-2","language":[{"iso":"eng"}],"article_number":"87","file_date_updated":"2021-06-07T12:31:36Z","extern":"1","pmid":1,"year":"2017","publisher":"Springer Nature","department":[{"_id":"DaZi"}],"publication_status":"published","author":[{"first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"volume":18,"date_updated":"2021-12-14T07:55:02Z","date_created":"2021-06-07T12:27:39Z"},{"oa_version":"None","intvolume":" 1596","status":"public","title":"Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"958","abstract":[{"lang":"eng","text":"Biosensors that exploit Forster resonance energy transfer (FRET) can be used to visualize biological and physiological processes and are capable of providing detailed information in both spatial and temporal dimensions. In a FRET-based biosensor, substrate binding is associated with a change in the relative positions of two fluorophores, leading to a change in FRET efficiency that may be observed in the fluorescence spectrum. As a result, their design requires a ligand-binding protein that exhibits a conformational change upon binding. However, not all ligand-binding proteins produce responsive sensors upon conjugation to fluorescent proteins or dyes, and identifying the optimum locations for the fluorophores often involves labor-intensive iterative design or high-throughput screening. Combining the genetic fusion of a fluorescent protein to the ligand-binding protein with site-specific covalent attachment of a fluorescent dye can allow fine control over the positions of the two fluorophores, allowing the construction of very sensitive sensors. This relies upon the accurate prediction of the locations of the two fluorophores in bound and unbound states. In this chapter, we describe a method for computational identification of dye-attachment sites that allows the use of cysteine modification to attach synthetic dyes that can be paired with a fluorescent protein for the purposes of creating FRET sensors."}],"alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","date_published":"2017-05-15T00:00:00Z","page":"89 - 99","citation":{"short":"J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 89–99.","mla":"Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 89–99, doi:10.1007/978-1-4939-6940-1_6.","chicago":"Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:89–99. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_6.","ama":"Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:89-99. doi:10.1007/978-1-4939-6940-1_6","ieee":"J. Mitchell et al., “Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 89–99.","apa":"Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara, M., & Jackson, C. (2017). Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 89–99). Springer. https://doi.org/10.1007/978-1-4939-6940-1_6","ista":"Mitchell J, Zhang W, Herde M, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2017.Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 89–99."},"publication":"Synthetic Protein Switches","day":"15","series_title":"Synthetic Protein Switches","scopus_import":1,"volume":1596,"date_created":"2018-12-11T11:49:24Z","date_updated":"2021-01-12T08:22:13Z","author":[{"first_name":"Joshua","last_name":"Mitchell","full_name":"Mitchell, Joshua"},{"full_name":"Zhang, William","last_name":"Zhang","first_name":"William"},{"full_name":"Herde, Michel","first_name":"Michel","last_name":"Herde"},{"last_name":"Henneberger","first_name":"Christian","full_name":"Henneberger, Christian"},{"full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"O'Mara, Megan","last_name":"O'Mara","first_name":"Megan"},{"last_name":"Jackson","first_name":"Colin","full_name":"Jackson, Colin"}],"publisher":"Springer","department":[{"_id":"HaJa"}],"editor":[{"last_name":"Stein","first_name":"Viktor","full_name":"Stein, Viktor"}],"publication_status":"published","year":"2017","publist_id":"6450","language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-6940-1_6","quality_controlled":"1","publication_identifier":{"issn":["10643745"]},"month":"05"},{"author":[{"full_name":"Riccio, Paul","last_name":"Riccio","first_name":"Paul"},{"full_name":"Cebrián, Christina","first_name":"Christina","last_name":"Cebrián"},{"full_name":"Zong, Hui","last_name":"Zong","first_name":"Hui"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"},{"full_name":"Costantini, Frank","last_name":"Costantini","first_name":"Frank"}],"related_material":{"record":[{"id":"9702","relation":"used_in_publication","status":"deleted"}]},"date_created":"2021-07-23T09:39:34Z","date_updated":"2022-08-25T13:34:55Z","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9707","year":"2017","status":"public","title":"Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","department":[{"_id":"SiHi"}],"publisher":"Dryad","abstract":[{"text":"Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis.","lang":"eng"}],"type":"research_data_reference","date_published":"2017-01-14T00:00:00Z","doi":"10.5061/dryad.pk16b","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.pk16b"}],"citation":{"ama":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. 2017. doi:10.5061/dryad.pk16b","ista":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2017. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis, Dryad, 10.5061/dryad.pk16b.","ieee":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis.” Dryad, 2017.","apa":"Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., & Costantini, F. (2017). Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. Dryad. https://doi.org/10.5061/dryad.pk16b","mla":"Riccio, Paul, et al. Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis. Dryad, 2017, doi:10.5061/dryad.pk16b.","short":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, (2017).","chicago":"Riccio, Paul, Christina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank Costantini. “Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” Dryad, 2017. https://doi.org/10.5061/dryad.pk16b."},"oa":1,"day":"14","month":"01","article_processing_charge":"No"},{"date_published":"2017-12-18T00:00:00Z","doi":"10.1371/journal.pgen.1007122.s018","citation":{"ama":"Nikolic N, Schreiber F, Dal Co A, et al. Source data for figures and tables. 2017. doi:10.1371/journal.pgen.1007122.s018","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Source data for figures and tables, Public Library of Science, 10.1371/journal.pgen.1007122.s018.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Source data for figures and tables. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s018","ieee":"N. Nikolic et al., “Source data for figures and tables.” Public Library of Science, 2017.","mla":"Nikolic, Nela, et al. Source Data for Figures and Tables. Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s018.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Source Data for Figures and Tables.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s018."},"day":"18","month":"12","article_processing_charge":"No","author":[{"full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","first_name":"Nela"},{"last_name":"Schreiber","first_name":"Frank","full_name":"Schreiber, Frank"},{"full_name":"Dal Co, Alma","first_name":"Alma","last_name":"Dal Co"},{"full_name":"Kiviet, Daniel","first_name":"Daniel","last_name":"Kiviet"},{"full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","first_name":"Tobias","last_name":"Bergmiller"},{"first_name":"Sten","last_name":"Littmann","full_name":"Littmann, Sten"},{"full_name":"Kuypers, Marcel","first_name":"Marcel","last_name":"Kuypers"},{"first_name":"Martin","last_name":"Ackermann","full_name":"Ackermann, Martin"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"541"}]},"date_updated":"2023-02-23T12:25:04Z","date_created":"2021-08-09T13:27:16Z","oa_version":"Published Version","_id":"9844","year":"2017","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Source data for figures and tables","publisher":"Public Library of Science","department":[{"_id":"CaGu"}],"type":"research_data_reference"},{"file_date_updated":"2023-05-16T07:20:50Z","type":"conference_abstract","oa_version":"Published Version","file":[{"date_created":"2023-05-16T07:20:50Z","date_updated":"2023-05-16T07:20:50Z","success":1,"checksum":"7bcc499479d4f4c5ce6c0071c24ca6c6","file_id":"12969","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1005486,"file_name":"2017_AHPC_Schloegl.pdf","access_level":"open_access"}],"date_updated":"2023-05-16T07:22:23Z","date_created":"2023-05-05T12:58:53Z","author":[{"first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois"},{"first_name":"Janos","last_name":"Kiss","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","full_name":"Kiss, Janos"}],"publisher":"FSP Scientific Computing","department":[{"_id":"ScienComp"}],"ddc":["000"],"title":"Scientific Computing at IST Austria","status":"public","publication_status":"published","year":"2017","_id":"12905","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","has_accepted_license":"1","day":"03","month":"03","language":[{"iso":"eng"}],"date_published":"2017-03-03T00:00:00Z","conference":{"name":"AHPC: Austrian HPC Meeting","end_date":"2017-03-03","start_date":"2017-03-01","location":"Grundlsee, Austria"},"page":"28","oa":1,"citation":{"mla":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28.","short":"A. Schlögl, J. Kiss, in:, AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28.","chicago":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” In AHPC17 – Austrian HPC Meeting 2017, 28. FSP Scientific Computing, 2017.","ama":"Schlögl A, Kiss J. Scientific Computing at IST Austria. In: AHPC17 – Austrian HPC Meeting 2017. FSP Scientific Computing; 2017:28.","ista":"Schlögl A, Kiss J. 2017. Scientific Computing at IST Austria. AHPC17 – Austrian HPC Meeting 2017. AHPC: Austrian HPC Meeting, 28.","ieee":"A. Schlögl and J. Kiss, “Scientific Computing at IST Austria,” in AHPC17 – Austrian HPC Meeting 2017, Grundlsee, Austria, 2017, p. 28.","apa":"Schlögl, A., & Kiss, J. (2017). Scientific Computing at IST Austria. In AHPC17 – Austrian HPC Meeting 2017 (p. 28). Grundlsee, Austria: FSP Scientific Computing."},"main_file_link":[{"url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc17/BOOKLET_AHPC17.pdf","open_access":"1"}],"publication":"AHPC17 – Austrian HPC Meeting 2017"},{"author":[{"full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky"},{"full_name":"Meggendorfer, Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","first_name":"Tobias","last_name":"Meggendorfer"},{"full_name":"Waldmann, Clara","last_name":"Waldmann","first_name":"Clara"},{"last_name":"Weininger","first_name":"Maximilian","full_name":"Weininger, Maximilian"}],"volume":10205,"date_created":"2023-06-21T13:21:14Z","date_updated":"2023-06-21T13:29:46Z","year":"2017","acknowledgement":"This work is partially funded by the DFG project “Verified Model Checkers” and by the Czech Science Foundation, grant No. P202/12/G061.","department":[{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783662545768"],"eisbn":["9783662545775"],"issn":["0302-9743"]},"month":"03","doi":"10.1007/978-3-662-54577-5_26","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2017-04-29","location":"Uppsala, Sweden","start_date":"2017-04-22"},"language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1701.05738"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1701.05738"}],"quality_controlled":"1","abstract":[{"text":"Transforming deterministic ω\r\n-automata into deterministic parity automata is traditionally done using variants of appearance records. We present a more efficient variant of this approach, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and find out that our method produces smaller automata than previous approaches. Moreover, the experiments demonstrate the potential of our method for LTL synthesis, using LTL-to-Rabin translators. It leads to significantly smaller parity automata when compared to state-of-the-art approaches on complex formulae.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13160","intvolume":" 10205","title":"Index appearance record for transforming Rabin automata into parity automata","status":"public","article_processing_charge":"No","day":"31","date_published":"2017-03-31T00:00:00Z","citation":{"chicago":"Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” In Tools and Algorithms for the Construction and Analysis of Systems, 10205:443–60. Springer, 2017. https://doi.org/10.1007/978-3-662-54577-5_26.","mla":"Kretinsky, Jan, et al. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” Tools and Algorithms for the Construction and Analysis of Systems, vol. 10205, Springer, 2017, pp. 443–60, doi:10.1007/978-3-662-54577-5_26.","short":"J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer, 2017, pp. 443–460.","ista":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2017. Index appearance record for transforming Rabin automata into parity automata. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 443–460.","ieee":"J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance record for transforming Rabin automata into parity automata,” in Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10205, pp. 443–460.","apa":"Kretinsky, J., Meggendorfer, T., Waldmann, C., & Weininger, M. (2017). Index appearance record for transforming Rabin automata into parity automata. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 10205, pp. 443–460). Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54577-5_26","ama":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record for transforming Rabin automata into parity automata. In: Tools and Algorithms for the Construction and Analysis of Systems. Vol 10205. Springer; 2017:443-460. doi:10.1007/978-3-662-54577-5_26"},"publication":"Tools and Algorithms for the Construction and Analysis of Systems","page":"443-460"},{"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2017-09-01T00:00:00Z","citation":{"ieee":"G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” presented at the CONCUR: Concurrency Theory, Berlin, Germany, 2017, vol. 85.","apa":"Avni, G., Henzinger, T. A., & Chonev, V. K. (2017). Infinite-duration bidding games (Vol. 85). Presented at the CONCUR: Concurrency Theory, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21","ista":"Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR: Concurrency Theory, LIPIcs, vol. 85, 17.","ama":"Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.21","chicago":"Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21.","short":"G. Avni, T.A. Henzinger, V.K. Chonev, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Avni, Guy, et al. Infinite-Duration Bidding Games. Vol. 85, 17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.21."},"abstract":[{"text":"Two-player games on graphs are widely studied in formal methods as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. Both players have separate budgets, which sum up to $1$. In each turn, a bidding takes place. Both players submit bids simultaneously, and a bid is legal if it does not exceed the available budget. The winner of the bidding pays his bid to the other player and moves the token. For reachability objectives, repeated bidding games have been studied and are called Richman games. There, a central question is the existence and computation of threshold budgets; namely, a value t\\in [0,1] such that if\\PO's budget exceeds $t$, he can win the game, and if\\PT's budget exceeds 1-t, he can win the game. We focus on parity games and mean-payoff games. We show the existence of threshold budgets in these games, and reduce the problem of finding them to Richman games. We also determine the strategy-complexity of an optimal strategy. Our most interesting result shows that memoryless strategies suffice for mean-payoff bidding games. \r\n","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"pubrep_id":"844","file":[{"file_id":"5318","relation":"main_file","checksum":"6d5cccf755207b91ccbef95d8275b013","date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:18:00Z","access_level":"open_access","file_name":"IST-2017-844-v1+1_concur-cr.pdf","creator":"system","file_size":335170,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"950","intvolume":" 85","title":"Infinite-duration bidding games","ddc":["000"],"status":"public","publication_identifier":{"issn":["1868-8969"]},"month":"09","doi":"10.4230/LIPIcs.CONCUR.2017.21","conference":{"name":"CONCUR: Concurrency Theory","start_date":"2017-09-05","location":"Berlin, Germany","end_date":"2017-09-07"},"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,"external_id":{"arxiv":["1705.01433"]},"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","publist_id":"6466","file_date_updated":"2020-07-14T12:48:16Z","article_number":"17","related_material":{"record":[{"status":"public","relation":"later_version","id":"6752"}]},"author":[{"full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","last_name":"Avni"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Chonev, Ventsislav K","last_name":"Chonev","first_name":"Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87"}],"volume":85,"date_created":"2018-12-11T11:49:22Z","date_updated":"2023-08-29T07:02:13Z","year":"2017","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_status":"published"},{"scopus_import":1,"day":"01","has_accepted_license":"1","citation":{"chicago":"Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations,” Vol. 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.SoCG.2017.49.","short":"A. Lubiw, Z. Masárová, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Lubiw, Anna, et al. A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations. Vol. 77, 49, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.SoCG.2017.49.","ieee":"A. Lubiw, Z. Masárová, and U. Wagner, “A proof of the orbit conjecture for flipping edge labelled triangulations,” presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia, 2017, vol. 77.","apa":"Lubiw, A., Masárová, Z., & Wagner, U. (2017). A proof of the orbit conjecture for flipping edge labelled triangulations (Vol. 77). Presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2017.49","ista":"Lubiw A, Masárová Z, Wagner U. 2017. A proof of the orbit conjecture for flipping edge labelled triangulations. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 77, 49.","ama":"Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping edge labelled triangulations. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.SoCG.2017.49"},"date_published":"2017-06-01T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of O(n7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture."}],"ddc":["514","516"],"title":"A proof of the orbit conjecture for flipping edge labelled triangulations","status":"public","intvolume":" 77","_id":"683","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_size":710007,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-896-v1+1_LIPIcs-SoCG-2017-49.pdf","access_level":"open_access","date_created":"2018-12-12T10:17:12Z","date_updated":"2020-07-14T12:47:41Z","checksum":"24fdde981cc513352a78dcf9b0660ae9","relation":"main_file","file_id":"5265"}],"pubrep_id":"896","month":"06","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"}],"conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Brisbane, Australia","start_date":"2017-07-04","end_date":"2017-07-07"},"doi":"10.4230/LIPIcs.SoCG.2017.49","article_number":"49","file_date_updated":"2020-07-14T12:47:41Z","publist_id":"7033","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"year":"2017","date_created":"2018-12-11T11:47:54Z","date_updated":"2023-09-05T15:01:43Z","volume":77,"author":[{"first_name":"Anna","last_name":"Lubiw","full_name":"Lubiw, Anna"},{"id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322","first_name":"Zuzana","last_name":"Masárová","full_name":"Masárová, Zuzana"},{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"5986"}]}},{"page":"163","citation":{"chicago":"Daca, Przemyslaw. “Statistical and Logical Methods for Property Checking.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:TH_730.","short":"P. Daca, Statistical and Logical Methods for Property Checking, Institute of Science and Technology Austria, 2017.","mla":"Daca, Przemyslaw. Statistical and Logical Methods for Property Checking. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:TH_730.","apa":"Daca, P. (2017). Statistical and logical methods for property checking. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_730","ieee":"P. Daca, “Statistical and logical methods for property checking,” Institute of Science and Technology Austria, 2017.","ista":"Daca P. 2017. Statistical and logical methods for property checking. Institute of Science and Technology Austria.","ama":"Daca P. Statistical and logical methods for property checking. 2017. doi:10.15479/AT:ISTA:TH_730"},"date_published":"2017-01-02T00:00:00Z","day":"02","has_accepted_license":"1","article_processing_charge":"No","status":"public","ddc":["004","005"],"title":"Statistical and logical methods for property checking","_id":"1155","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"checksum":"1406a681cb737508234fde34766be2c2","date_updated":"2020-07-14T12:44:34Z","date_created":"2018-12-12T10:11:26Z","relation":"main_file","file_id":"4880","file_size":1028586,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2017-730-v1+1_Statistical_and_Logical_Methods_for_Property_Checking.pdf"}],"pubrep_id":"730","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"This dissertation concerns the automatic verification of probabilistic systems and programs with arrays by statistical and logical methods. Although statistical and logical methods are different in nature, we show that they can be successfully combined for system analysis. In the first part of the dissertation we present a new statistical algorithm for the verification of probabilistic systems with respect to unbounded properties, including linear temporal logic. Our algorithm often performs faster than the previous approaches, and at the same time requires less information about the system. In addition, our method can be generalized to unbounded quantitative properties such as mean-payoff bounds. In the second part, we introduce two techniques for comparing probabilistic systems. Probabilistic systems are typically compared using the notion of equivalence, which requires the systems to have the equal probability of all behaviors. However, this notion is often too strict, since probabilities are typically only empirically estimated, and any imprecision may break the relation between processes. On the one hand, we propose to replace the Boolean notion of equivalence by a quantitative distance of similarity. For this purpose, we introduce a statistical framework for estimating distances between Markov chains based on their simulation runs, and we investigate which distances can be approximated in our framework. On the other hand, we propose to compare systems with respect to a new qualitative logic, which expresses that behaviors occur with probability one or a positive probability. This qualitative analysis is robust with respect to modeling errors and applicable to many domains. In the last part, we present a new quantifier-free logic for integer arrays, which allows us to express counting. Counting properties are prevalent in array-manipulating programs, however they cannot be expressed in the quantified fragments of the theory of arrays. We present a decision procedure for our logic, and provide several complexity results."}],"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"oa":1,"supervisor":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:TH_730","month":"01","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToHe"}],"acknowledgement":" First of all, I want to thank my advisor, prof. Thomas A. Henzinger, for his guidance during my PhD program. I am grateful for the freedom I was given to pursue my research interests, and his continuous support. Working with prof. Henzinger was a truly inspiring experience and taught me what it means to be a scientist. I want to express my gratitude to my collaborators: Nikola Beneš, Krishnendu Chatterjee, Martin Chmelík, Ashutosh Gupta, Willibald Krenn, Jan Kˇretínský, Dejan Nickovic, Andrey Kupriyanov, and Tatjana Petrov. I have learned a great deal from my collaborators, and without their help this thesis would not be possible. In addition, I want to thank the members of my thesis committee: Dirk Beyer, Dejan Nickovic, and Georg Weissenbacher for their advice and reviewing this dissertation. I would especially like to acknowledge the late Helmut Veith, who was a member of my committee. I will remember Helmut for his kindness, enthusiasm, and wit, as well as for being an inspiring scientist. Finally, I would like to thank my colleagues for making my stay at IST such a pleasant experience: Guy Avni, Sergiy Bogomolov, Ventsislav Chonev, Rasmus Ibsen-Jensen, Mirco Giacobbe, Bernhard Kragl, Hui Kong, Petr Novotný, Jan Otop, Andreas Pavlogiannis, Tantjana Petrov, Arjun Radhakrishna, Jakob Ruess, Thorsten Tarrach, as well as other members of groups Henzinger and Chatterjee. ","year":"2017","date_created":"2018-12-11T11:50:27Z","date_updated":"2023-09-07T11:58:34Z","author":[{"id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","first_name":"Przemyslaw","full_name":"Daca, Przemyslaw"}],"related_material":{"record":[{"id":"1093","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"1230"},{"id":"1234","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1391"},{"status":"public","relation":"part_of_dissertation","id":"1501"},{"status":"public","relation":"part_of_dissertation","id":"1502"},{"id":"2063","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"2167"}]},"file_date_updated":"2020-07-14T12:44:34Z","ec_funded":1,"publist_id":"6203"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"file_date_updated":"2021-02-22T13:45:59Z","abstract":[{"lang":"eng","text":"Bacteria and their pathogens – phages – are the most abundant living entities on Earth. Throughout their coevolution, bacteria have evolved multiple immune systems to overcome the ubiquitous threat from the phages. Although the molecu- lar details of these immune systems’ functions are relatively well understood, their epidemiological consequences for the phage-bacterial communities have been largely neglected. In this thesis we employed both experimental and theoretical methods to explore whether herd and social immunity may arise in bacterial popu- lations. Using our experimental system consisting of Escherichia coli strains with a CRISPR based immunity to the T7 phage we show that herd immunity arises in phage-bacterial communities and that it is accentuated when the populations are spatially structured. By fitting a mathematical model, we inferred expressions for the herd immunity threshold and the velocity of spread of a phage epidemic in partially resistant bacterial populations, which both depend on the bacterial growth rate, phage burst size and phage latent period. We also investigated the poten- tial for social immunity in Streptococcus thermophilus and its phage 2972 using a bioinformatic analysis of potentially coding short open reading frames with a signalling signature, encoded within the CRISPR associated genes. Subsequently, we tested one identified potentially signalling peptide and found that its addition to a phage-challenged culture increases probability of survival of bacteria two fold, although the results were only marginally significant. Together, these results demonstrate that the ubiquitous arms races between bacteria and phages have further consequences at the level of the population."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6291","year":"2017","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"publisher":"Institute of Science and Technology Austria","ddc":["570"],"publication_status":"published","title":"Bacterial herd and social immunity to phages","status":"public","author":[{"full_name":"Payne, Pavel","first_name":"Pavel","last_name":"Payne","id":"35F78294-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2711-9453"}],"file":[{"creator":"dernst","content_type":"application/pdf","file_size":3025175,"access_level":"closed","file_name":"thesis_pavel_payne_final_w_signature_page.pdf","checksum":"a0fc5c26a89c0ea759947ffba87d0d8f","date_created":"2019-04-09T15:15:32Z","date_updated":"2020-07-14T12:47:27Z","file_id":"6292","relation":"main_file"},{"file_id":"9187","relation":"main_file","success":1,"checksum":"af531e921a7f64a9e0af4cd8783b2226","date_updated":"2021-02-22T13:45:59Z","date_created":"2021-02-22T13:45:59Z","access_level":"open_access","file_name":"2017_Payne_Thesis.pdf","creator":"dernst","file_size":3111536,"content_type":"application/pdf"}],"oa_version":"Published Version","date_created":"2019-04-09T15:16:45Z","date_updated":"2023-09-07T12:00:00Z","article_processing_charge":"No","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"day":"01","month":"02","citation":{"chicago":"Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017.","short":"P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science and Technology Austria, 2017.","mla":"Payne, Pavel. Bacterial Herd and Social Immunity to Phages. Institute of Science and Technology Austria, 2017.","apa":"Payne, P. (2017). Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","ieee":"P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science and Technology Austria, 2017.","ista":"Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","ama":"Payne P. Bacterial herd and social immunity to phages. 2017."},"oa":1,"page":"83","date_published":"2017-02-01T00:00:00Z","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}]},{"citation":{"ama":"Pleska M, Guet CC. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 2017;13(12). doi:10.1098/rsbl.2017.0646","ista":"Pleska M, Guet CC. 2017. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 13(12), 20170646.","ieee":"M. Pleska and C. C. Guet, “Effects of mutations in phage restriction sites during escape from restriction–modification,” Biology Letters, vol. 13, no. 12. The Royal Society, 2017.","apa":"Pleska, M., & Guet, C. C. (2017). Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. The Royal Society. https://doi.org/10.1098/rsbl.2017.0646","mla":"Pleska, Maros, and Calin C. Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters, vol. 13, no. 12, 20170646, The Royal Society, 2017, doi:10.1098/rsbl.2017.0646.","short":"M. Pleska, C.C. Guet, Biology Letters 13 (2017).","chicago":"Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters. The Royal Society, 2017. https://doi.org/10.1098/rsbl.2017.0646."},"publication":"Biology Letters","article_type":"original","date_published":"2017-12-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"561","intvolume":" 13","status":"public","title":"Effects of mutations in phage restriction sites during escape from restriction–modification","oa_version":"Published Version","type":"journal_article","issue":"12","abstract":[{"text":"Restriction–modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction–modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage l and the restriction–modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction–modification systems and offer an insight into the events underlying the process of bacteriophage escape.","lang":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2017.0646","open_access":"1"}],"external_id":{"pmid":["29237814"]},"project":[{"name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant)","grant_number":"RGY0079/2011","_id":"251BCBEC-B435-11E9-9278-68D0E5697425"},{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","grant_number":"24210","_id":"251D65D8-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1098/rsbl.2017.0646","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1744-9561"]},"month":"12","pmid":1,"year":"2017","acknowledgement":"This work was funded by an HFSP Young Investigators' grant RGY0079/2011 (C.C.G.). M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria.","department":[{"_id":"CaGu"}],"publisher":"The Royal Society","publication_status":"published","related_material":{"record":[{"id":"9847","relation":"research_data","status":"public"},{"relation":"dissertation_contains","status":"public","id":"202"}]},"author":[{"first_name":"Maros","last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"}],"volume":13,"date_created":"2018-12-11T11:47:11Z","date_updated":"2023-09-07T11:59:32Z","article_number":"20170646","publist_id":"7253"},{"supervisor":[{"full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_862","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":"09","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-07T12:00:26Z","date_created":"2018-12-11T11:48:40Z","author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin","last_name":"Mitosch","full_name":"Mitosch, Karin"}],"related_material":{"record":[{"id":"2001","relation":"part_of_dissertation","status":"public"},{"id":"666","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToBo"}],"year":"2017","acknowledgement":"First of all, I would like to express great gratitude to my PhD supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom to explore different scientific directions during this project, and follow the research lines of my interest. I am thankful for constructive and often extensive discussions and his support and commitment during the different stages of my PhD. I want to thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest and their valuable input to this project. Special thanks to Nassos for career guidance, and for accepting me in his lab. A big thank you goes to the past, present and affiliated members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová, Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr, Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed working and discussing with you very much and I will miss our lengthy group meetings, our inspiring journal clubs, and our common lunches. Special thanks to Bor for great mental and professional support during the hard months of thesis writing, and to Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and collaborator Georg Rieckh for his enthusiasm and for getting so involved in these projects, for his endurance and for his company throughout the years. Thanks to the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange, and enjoyable time together. Thanks to everybody who contributed to the cover for Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh, Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by the graphic designer Martina Markus from the University of Cologne. Thanks to all my office mates in the first floor Bertalanffy building throughout the years: for ensuring a pleasant working atmosphere, and for your company! In general, I want to thank all the people that make IST such a great environment, with the many possibilities to shape our own social and research environment. I want to thank my family for all kind of practical support during the years, and my second family in Argentina for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being great siblings, and to Helena and Valentin for the joy you brought to my life. My deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and for believing in me. ","file_date_updated":"2020-07-14T12:48:09Z","publist_id":"6831","date_published":"2017-09-27T00:00:00Z","page":"113","citation":{"mla":"Mitosch, Karin. Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_862.","short":"K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and Technology Austria, 2017.","chicago":"Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_862.","ama":"Mitosch K. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. 2017. doi:10.15479/AT:ISTA:th_862","ista":"Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria.","apa":"Mitosch, K. (2017). Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_862","ieee":"K. Mitosch, “Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics,” Institute of Science and Technology Austria, 2017."},"day":"27","article_processing_charge":"No","has_accepted_license":"1","oa_version":"Published Version","file":[{"checksum":"da3993c5f90f59a8e8623cc31ad501dd","date_updated":"2020-07-14T12:48:09Z","date_created":"2019-04-05T08:48:51Z","file_id":"6210","relation":"source_file","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":6331071,"access_level":"closed","file_name":"Thesis_KarinMitosch.docx"},{"file_size":9289852,"content_type":"application/pdf","creator":"dernst","file_name":"Thesis_KarinMitosch.pdf","access_level":"open_access","date_created":"2019-04-05T08:48:51Z","date_updated":"2020-07-14T12:48:09Z","checksum":"24c3d9e51992f1b721f3df55aa13fcb8","relation":"main_file","file_id":"6211"}],"pubrep_id":"862","status":"public","ddc":["571","579"],"title":"Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics","_id":"818","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"666","ddc":["576","610"],"title":"Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment","status":"public","intvolume":" 4","pubrep_id":"901","oa_version":"Published Version","file":[{"checksum":"04ff20011c3d9a601c514aa999a5fe1a","date_created":"2018-12-12T10:13:54Z","date_updated":"2020-07-14T12:47:35Z","file_id":"5041","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":2438660,"access_level":"open_access","file_name":"IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors."}],"issue":"4","publication":"Cell Systems","citation":{"chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems. Cell Press, 2017. https://doi.org/10.1016/j.cels.2017.03.001.","mla":"Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems, vol. 4, no. 4, Cell Press, 2017, pp. 393–403, doi:10.1016/j.cels.2017.03.001.","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.","ista":"Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 4(4), 393–403.","apa":"Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2017). Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2017.03.001","ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment,” Cell Systems, vol. 4, no. 4. Cell Press, pp. 393–403, 2017.","ama":"Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 2017;4(4):393-403. doi:10.1016/j.cels.2017.03.001"},"page":"393 - 403","date_published":"2017-04-26T00:00:00Z","scopus_import":1,"day":"26","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","year":"2017","publication_status":"published","department":[{"_id":"ToBo"},{"_id":"GaTk"}],"publisher":"Cell Press","author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin","last_name":"Mitosch","full_name":"Mitosch, Karin"},{"full_name":"Rieckh, Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Rieckh"},{"full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Tobias"}],"related_material":{"record":[{"id":"818","status":"public","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:47:48Z","date_updated":"2023-09-07T12:00:25Z","volume":4,"file_date_updated":"2020-07-14T12:47:35Z","publist_id":"7061","ec_funded":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"},"quality_controlled":"1","project":[{"grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","name":"Optimality principles in responses to antibiotics","call_identifier":"FP7"},{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"},{"name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013"}],"doi":"10.1016/j.cels.2017.03.001","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["24054712"]}},{"pubrep_id":"854","oa_version":"Published Version","file":[{"creator":"system","file_size":4103115,"content_type":"application/pdf","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:10Z","date_created":"2018-12-12T10:11:44Z","checksum":"3a3ec003f6ee73f41f82a544d63dfc77","file_id":"4900","relation":"main_file"},{"checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83","date_updated":"2020-07-14T12:48:10Z","date_created":"2019-04-05T07:59:31Z","file_id":"6201","relation":"source_file","creator":"dernst","content_type":"application/zip","file_size":14744374,"access_level":"closed","file_name":"2017_thesis_Pavlogiannis.zip"}],"_id":"821","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"title":"Algorithmic advances in program analysis and their applications","status":"public","abstract":[{"text":"This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the\r\nstatic analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.\r\nOur contributions can be broadly grouped into five categories.\r\n\r\nOur first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.\r\nWe utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic treatment of the considered problem,\r\nwhere several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. \r\nWe exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, \r\nand provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.\r\nIn particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.\r\nIn this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.\r\nWe illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,\r\nand present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.\r\nWe present a new dynamic partial-order reduction method called the Data-centric Partial Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.\r\nDepending on the program, the new partitioning can be even exponentially coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.\r\nOn the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show\r\nhow the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2017-08-09T00:00:00Z","citation":{"chicago":"Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their Applications.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_854.","short":"A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017.","mla":"Pavlogiannis, Andreas. Algorithmic Advances in Program Analysis and Their Applications. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_854.","ieee":"A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017.","apa":"Pavlogiannis, A. (2017). Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_854","ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria.","ama":"Pavlogiannis A. Algorithmic advances in program analysis and their applications. 2017. doi:10.15479/AT:ISTA:th_854"},"page":"418","day":"09","has_accepted_license":"1","article_processing_charge":"No","author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"}],"related_material":{"record":[{"id":"1071","status":"public","relation":"part_of_dissertation"},{"id":"1437","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1602"},{"status":"public","relation":"part_of_dissertation","id":"1604"},{"status":"public","relation":"part_of_dissertation","id":"1607"},{"id":"1714","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2023-09-07T12:01:59Z","date_created":"2018-12-11T11:48:41Z","year":"2017","acknowledgement":"First, I am thankful to my advisor, Krishnendu Chatterjee, for offering me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide range of interesting topics, as well as for his constant availability and continuous support throughout my doctoral studies. I have had the privilege of collaborating with, discussing and getting inspired by all members of my committee: Thomas A. Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people has been very instrumental both to the research carried out for this dissertation, and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to results on low-treewidth graphs presented here. I thank Alex Kößler for our\r\ndiscussions on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our initial discussions on partial order reduction techniques in stateless model checking. I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful collaborations on\r\ntopics outside the scope of this dissertation, as well as the interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary and Marek Chalupa, with whom I have shared my excitement on various research topics. Together with my collaborators, I thank officemates and members of the Chatterjee and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta, Arjun Radhakrishna, Petr Novontý, Christian Hilbe, Jakob Ruess, Martin Chmelik,\r\nCezara Dragoi, Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong, Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey. Besides collaborations and office spaces, with many of the above people I have been fortunate to share numerous whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her continuous assistance in matters\r\nthat often exceeded her official duties, and who made my integration in Austria a smooth process.","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:48:10Z","publist_id":"6828","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","doi":"10.15479/AT:ISTA:th_854","supervisor":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"month":"08","publication_identifier":{"issn":["2663-337X"]}},{"abstract":[{"lang":"eng","text":"The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.\r\nIn Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.\r\nTo start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"857","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":3417773,"file_name":"IST-2017-857-v1+1_thesis_fabienne.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:10Z","date_created":"2018-12-12T10:17:00Z","checksum":"c62257a7bff0c5f39e1abffc6bfcca5c","file_id":"5252","relation":"main_file"},{"date_created":"2019-04-05T08:51:59Z","date_updated":"2020-07-14T12:48:10Z","checksum":"fc87d7d72fce52824a3ae7dcad0413a8","file_id":"6212","relation":"source_file","creator":"dernst","file_size":215899,"content_type":"application/x-tex","file_name":"2017_thesis_Jesse_source.tex","access_level":"closed"}],"_id":"820","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["576","577","579"],"status":"public","title":"The lac operon in the wild","has_accepted_license":"1","article_processing_charge":"No","day":"25","date_published":"2017-08-25T00:00:00Z","citation":{"ama":"Jesse F. The lac operon in the wild. 2017. doi:10.15479/AT:ISTA:th_857","ista":"Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria.","ieee":"F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017.","apa":"Jesse, F. (2017). The lac operon in the wild. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_857","mla":"Jesse, Fabienne. The Lac Operon in the Wild. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_857.","short":"F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017.","chicago":"Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_857."},"page":"87","ec_funded":1,"publist_id":"6829","file_date_updated":"2020-07-14T12:48:10Z","author":[{"full_name":"Jesse, Fabienne","first_name":"Fabienne","last_name":"Jesse","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:01:21Z","date_created":"2018-12-11T11:48:41Z","acknowledgement":"ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon Bollback for giving me the chance to do this work, for sharing the ideas that lay at the basis of this work, for his honesty and openness, showing himself to me as a person and not just as a boss. Thanks to Nick Barton for his guidance at the last stage, reading and commenting extensively on several versions of this manuscript, and for his encouragement; thanks to both Jon and Nick for their kindness and patience. Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter my thesis committee at the last moment, and for his very sharp, helpful and relevant comments during and after the defense. Thanks to my collaborators and discussion partners: Anne Kupczok, for her guidance, ideas and discussions during the construction of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh for making me aware of the issue of parameter identifiability, suggesting how to solve it, and for his unfortunate idea to start the plasmid enterprise in the first place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting, fast forwarding the analysis to turbo speed and making beautiful figures, and making the discussion fun on top of it all; Vanessa Barone for her last minute comments, especially on Chapter Three, providing a sharp and very helpful experimentalist perspective at the last moment; Maros Pleska and Marjon de Vos for their comments on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation between growth rate and lactose concentration; Bor Kavcic for his input on growth rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton, Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific environment to work in, as well as a lot of warmth and colour to everyday life. And thanks to the friends I found here, to the people who were there for me and to the people who changed my life, making it stranger and more beautiful than I could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof, Karin, Irene, Misha, Mato, Guillaume and Zanin. ","year":"2017","department":[{"_id":"JoBo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"08","doi":"10.15479/AT:ISTA:th_857","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback"}],"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,"project":[{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}]},{"language":[{"iso":"eng"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_828","oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"06","date_created":"2018-12-11T11:48:46Z","date_updated":"2023-09-07T12:02:28Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"2082"},{"id":"6196","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Rybar, Michal","last_name":"Rybar","first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"KrPi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2017","publist_id":"6810","file_date_updated":"2020-07-14T12:48:12Z","date_published":"2017-06-26T00:00:00Z","page":"86","citation":{"chicago":"Rybar, Michal. “(The Exact Security of) Message Authentication Codes.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_828.","short":"M. Rybar, (The Exact Security of) Message Authentication Codes, Institute of Science and Technology Austria, 2017.","mla":"Rybar, Michal. (The Exact Security of) Message Authentication Codes. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_828.","ieee":"M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017.","apa":"Rybar, M. (2017). (The exact security of) Message authentication codes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_828","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria.","ama":"Rybar M. (The exact security of) Message authentication codes. 2017. doi:10.15479/AT:ISTA:th_828"},"has_accepted_license":"1","article_processing_charge":"No","day":"26","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4799","checksum":"ff8639ec4bded6186f44c7bd3ee26804","date_created":"2018-12-12T10:10:13Z","date_updated":"2020-07-14T12:48:12Z","access_level":"open_access","file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf","file_size":847400,"content_type":"application/pdf","creator":"system"},{"relation":"source_file","file_id":"6202","date_updated":"2020-07-14T12:48:12Z","date_created":"2019-04-05T08:24:11Z","checksum":"3462101745ce8ad199c2d0f75dae4a7e","file_name":"2017_Thesis_Rybar_source.zip","access_level":"closed","content_type":"application/zip","file_size":26054879,"creator":"dernst"}],"pubrep_id":"828","title":"(The exact security of) Message authentication codes","ddc":["000"],"status":"public","_id":"838","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k > 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. "}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"date_published":"2017-02-03T00:00:00Z","citation":{"ama":"Gazi P, Pietrzak KZ, Rybar M. The exact security of PMAC. IACR Transactions on Symmetric Cryptology. 2017;2016(2):145-161. doi:10.13154/TOSC.V2016.I2.145-161","ieee":"P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact security of PMAC,” IACR Transactions on Symmetric Cryptology, vol. 2016, no. 2. Ruhr University Bochum, pp. 145–161, 2017.","apa":"Gazi, P., Pietrzak, K. Z., & Rybar, M. (2017). The exact security of PMAC. IACR Transactions on Symmetric Cryptology. Ruhr University Bochum. https://doi.org/10.13154/TOSC.V2016.I2.145-161","ista":"Gazi P, Pietrzak KZ, Rybar M. 2017. The exact security of PMAC. IACR Transactions on Symmetric Cryptology. 2016(2), 145–161.","short":"P. Gazi, K.Z. Pietrzak, M. Rybar, IACR Transactions on Symmetric Cryptology 2016 (2017) 145–161.","mla":"Gazi, Peter, et al. “The Exact Security of PMAC.” IACR Transactions on Symmetric Cryptology, vol. 2016, no. 2, Ruhr University Bochum, 2017, pp. 145–61, doi:10.13154/TOSC.V2016.I2.145-161.","chicago":"Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact Security of PMAC.” IACR Transactions on Symmetric Cryptology. Ruhr University Bochum, 2017. https://doi.org/10.13154/TOSC.V2016.I2.145-161."},"publication":"IACR Transactions on Symmetric Cryptology","page":"145-161","has_accepted_license":"1","day":"03","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6197","checksum":"f23161d685dd957ae8d7274132999684","date_created":"2019-04-04T13:53:58Z","date_updated":"2020-07-14T12:47:24Z","access_level":"open_access","file_name":"2017_IACR_Gazi.pdf","file_size":597335,"content_type":"application/pdf","creator":"dernst"}],"_id":"6196","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 2016","status":"public","ddc":["000"],"title":"The exact security of PMAC","issue":"2","abstract":[{"text":"PMAC is a simple and parallel block-cipher mode of operation, which was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a (pseudo)random permutation over n-bit strings, PMAC constitutes a provably secure variable input-length (pseudo)random function. For adversaries making q queries, each of length at most l (in n-bit blocks), and of total length σ ≤ ql, the original paper proves an upper bound on the distinguishing advantage of Ο(σ2/2n), while the currently best bound is Ο (qσ/2n).In this work we show that this bound is tight by giving an attack with advantage Ω (q2l/2n). In the PMAC construction one initially XORs a mask to every message block, where the mask for the ith block is computed as τi := γi·L, where L is a (secret) random value, and γi is the i-th codeword of the Gray code. Our attack applies more generally to any sequence of γi’s which contains a large coset of a subgroup of GF(2n). We then investigate if the security of PMAC can be further improved by using τi’s that are k-wise independent, for k > 1 (the original distribution is only 1-wise independent). We observe that the security of PMAC will not increase in general, even if the masks are chosen from a 2-wise independent distribution, and then prove that the security increases to O(q<2/2n), if the τi are 4-wise independent. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether 3-wise independence is already sufficient to get this level of security is left as an open problem.","lang":"eng"}],"type":"journal_article","doi":"10.13154/TOSC.V2016.I2.145-161","language":[{"iso":"eng"}],"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":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"quality_controlled":"1","publication_identifier":{"eissn":["2519-173X"]},"month":"02","related_material":{"record":[{"id":"838","relation":"dissertation_contains","status":"public"}]},"author":[{"id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Gazi","full_name":"Gazi, Peter"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"},{"id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rybar","full_name":"Rybar, Michal"}],"volume":2016,"date_updated":"2023-09-07T12:02:27Z","date_created":"2019-04-04T13:48:23Z","year":"2017","publisher":"Ruhr University Bochum","department":[{"_id":"KrPi"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:24Z"},{"doi":"10.15479/AT:ISTA:th_858","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari"}],"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"},"publication_identifier":{"issn":["2663-337X"]},"month":"08","related_material":{"record":[{"id":"5828","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Xu, Haibing","first_name":"Haibing","last_name":"Xu","id":"310349D0-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:06:38Z","date_created":"2018-12-11T11:48:46Z","acknowledgement":"I am very grateful for the opportunity I have had as a graduate student to explore and incredibly interesting branch of neuroscience, and for the people who made it possible. Firstly, I would like to offer my thanks to my supervisor Professor Jozsef Csicsvari for his great support, guidance and patience offered over the years. The door to his office was always open whenever I had questions. I have learned a lot from him about carefully designing experiments, asking interesting questions and how to integrate results into a broader picture. I also express my gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific role model who is always willing to teach , and advice and talk through problems with his full attention. Many thanks to my wonderful “office mates” over the years and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in the lab for the many useful discussions about science and for making the laboratory such a nice and friendly place to work in. A special thank goes to Michael LoBianco and Jago Wallenschus for wonderful technical support. I would also like to thank Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam and thesi s committee members despite their busy schedule. I am also very thankful to IST Austria for their support all throughout my PhD. ","year":"2017","department":[{"_id":"JoCs"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","publist_id":"6811","file_date_updated":"2020-07-14T12:48:12Z","date_published":"2017-08-23T00:00:00Z","citation":{"ista":"Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria.","apa":"Xu, H. (2017). Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_858","ieee":"H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017.","ama":"Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. 2017. doi:10.15479/AT:ISTA:th_858","chicago":"Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_858.","mla":"Xu, Haibing. Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_858.","short":"H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017."},"page":"93","article_processing_charge":"No","has_accepted_license":"1","day":"23","pubrep_id":"858","oa_version":"Published Version","file":[{"file_id":"6213","relation":"source_file","date_created":"2019-04-05T08:59:51Z","date_updated":"2020-07-14T12:48:12Z","checksum":"f11925fbbce31e495124b6bc4f10573c","file_name":"2017_Xu_Haibing_Thesis_Source.docx","access_level":"closed","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":3589490},{"file_name":"2017_Xu_Thesis_IST.pdf","access_level":"open_access","creator":"dernst","file_size":11668613,"content_type":"application/pdf","file_id":"6214","relation":"main_file","date_updated":"2020-07-14T12:48:12Z","date_created":"2019-04-05T08:59:51Z","checksum":"ffb10749a537d615fab1ef0937ccb157"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"837","ddc":["571"],"title":"Reactivation of the hippocampal cognitive map in goal-directed spatial tasks","status":"public","abstract":[{"lang":"eng","text":"The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. "}],"type":"dissertation","alternative_title":["ISTA Thesis"]},{"date_published":"2017-06-02T00:00:00Z","page":"117","citation":{"short":"M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017.","mla":"Adamowski, Maciek. Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_842.","chicago":"Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_842.","ama":"Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:10.15479/AT:ISTA:th_842","ieee":"M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017.","apa":"Adamowski, M. (2017). Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_842","ista":"Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria."},"has_accepted_license":"1","article_processing_charge":"No","day":"02","file":[{"checksum":"193425764d9aaaed3ac57062a867b315","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-04-05T09:03:20Z","file_id":"6215","relation":"source_file","creator":"dernst","file_size":46903863,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"2017_Adamowski-Thesis_Source.docx"},{"checksum":"df5ab01be81f821e1b958596a1ec8d21","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-04-05T09:03:19Z","relation":"main_file","file_id":"6216","file_size":8698888,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2017_Adamowski-Thesis.pdf"}],"oa_version":"Published Version","pubrep_id":"842","ddc":["581","583","580"],"title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","status":"public","_id":"938","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"doi":"10.15479/AT:ISTA:th_842","oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"06","date_created":"2018-12-11T11:49:18Z","date_updated":"2023-09-07T12:06:09Z","related_material":{"record":[{"id":"1591","relation":"part_of_dissertation","status":"public"}]},"author":[{"last_name":"Adamowski","first_name":"Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"publication_status":"published","year":"2017","publist_id":"6483","file_date_updated":"2020-07-14T12:48:15Z"},{"doi":"10.15479/AT:ISTA:th_815","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","oa":1,"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2663-337X"]},"month":"05","author":[{"full_name":"Rolinek, Michal","first_name":"Michal","last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:05:41Z","date_created":"2018-12-11T11:49:35Z","acknowledgement":"FP7/2007-2013/ERC grant agreement no 616160","year":"2017","publisher":"Institute of Science and Technology Austria","department":[{"_id":"VlKo"}],"publication_status":"published","ec_funded":1,"publist_id":"6407","file_date_updated":"2020-07-14T12:48:18Z","date_published":"2017-05-01T00:00:00Z","citation":{"apa":"Rolinek, M. (2017). Complexity of constraint satisfaction. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_815","ieee":"M. Rolinek, “Complexity of constraint satisfaction,” Institute of Science and Technology Austria, 2017.","ista":"Rolinek M. 2017. Complexity of constraint satisfaction. Institute of Science and Technology Austria.","ama":"Rolinek M. Complexity of constraint satisfaction. 2017. doi:10.15479/AT:ISTA:th_815","chicago":"Rolinek, Michal. “Complexity of Constraint Satisfaction.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_815.","short":"M. Rolinek, Complexity of Constraint Satisfaction, Institute of Science and Technology Austria, 2017.","mla":"Rolinek, Michal. Complexity of Constraint Satisfaction. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_815."},"page":"97","article_processing_charge":"No","has_accepted_license":"1","day":"01","pubrep_id":"815","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4654","date_created":"2018-12-12T10:07:55Z","date_updated":"2020-07-14T12:48:18Z","checksum":"81761fb939acb7585c36629f765b4373","file_name":"IST-2017-815-v1+3_final_blank_signature_maybe_pdfa.pdf","access_level":"open_access","file_size":786145,"content_type":"application/pdf","creator":"system"},{"access_level":"closed","file_name":"2017_Thesis_Rolinek_source.zip","file_size":5936337,"content_type":"application/zip","creator":"dernst","relation":"source_file","file_id":"6208","checksum":"2b2d7e1d6c1c79a9795a7aa0f860baf3","date_updated":"2020-07-14T12:48:18Z","date_created":"2019-04-05T08:43:24Z"}],"_id":"992","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["004"],"title":"Complexity of constraint satisfaction","status":"public","abstract":[{"text":"An instance of the Constraint Satisfaction Problem (CSP) is given by a finite set of\r\nvariables, a finite domain of labels, and a set of constraints, each constraint acting on\r\na subset of the variables. The goal is to find an assignment of labels to its variables\r\nthat satisfies all constraints (or decide whether one exists). If we allow more general\r\n“soft” constraints, which come with (possibly infinite) costs of particular assignments,\r\nwe obtain instances from a richer class called Valued Constraint Satisfaction Problem\r\n(VCSP). There the goal is to find an assignment with minimum total cost.\r\nIn this thesis, we focus (assuming that P\r\n6\r\n=\r\nNP) on classifying computational com-\r\nplexity of CSPs and VCSPs under certain restricting conditions. Two results are the core\r\ncontent of the work. In one of them, we consider VCSPs parametrized by a constraint\r\nlanguage, that is the set of “soft” constraints allowed to form the instances, and finish\r\nthe complexity classification modulo (missing pieces of) complexity classification for\r\nanalogously parametrized CSP. The other result is a generalization of Edmonds’ perfect\r\nmatching algorithm. This generalization contributes to complexity classfications in two\r\nways. First, it gives a new (largest known) polynomial-time solvable class of Boolean\r\nCSPs in which every variable may appear in at most two constraints and second, it\r\nsettles full classification of Boolean CSPs with planar drawing (again parametrized by a\r\nconstraint language).","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"]},{"type":"journal_article","issue":"3","abstract":[{"text":"Mapping every simplex in the Delaunay mosaic of a discrete point set to the radius of the smallest empty circumsphere gives a generalized discrete Morse function. Choosing the points from a Poisson point process in ℝ n , we study the expected number of simplices in the Delaunay mosaic as well as the expected number of critical simplices and nonsingular intervals in the corresponding generalized discrete gradient. Observing connections with other probabilistic models, we obtain precise expressions for the expected numbers in low dimensions. In particular, we obtain the expected numbers of simplices in the Poisson–Delaunay mosaic in dimensions n ≤ 4.","lang":"eng"}],"_id":"718","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 49","title":"Expected sizes of poisson Delaunay mosaics and their discrete Morse functions","status":"public","oa_version":"Preprint","scopus_import":1,"day":"01","citation":{"mla":"Edelsbrunner, Herbert, et al. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” Advances in Applied Probability, vol. 49, no. 3, Cambridge University Press, 2017, pp. 745–67, doi:10.1017/apr.2017.20.","short":"H. Edelsbrunner, A. Nikitenko, M. Reitzner, Advances in Applied Probability 49 (2017) 745–767.","chicago":"Edelsbrunner, Herbert, Anton Nikitenko, and Matthias Reitzner. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” Advances in Applied Probability. Cambridge University Press, 2017. https://doi.org/10.1017/apr.2017.20.","ama":"Edelsbrunner H, Nikitenko A, Reitzner M. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. 2017;49(3):745-767. doi:10.1017/apr.2017.20","ista":"Edelsbrunner H, Nikitenko A, Reitzner M. 2017. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. 49(3), 745–767.","apa":"Edelsbrunner, H., Nikitenko, A., & Reitzner, M. (2017). Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. Cambridge University Press. https://doi.org/10.1017/apr.2017.20","ieee":"H. Edelsbrunner, A. Nikitenko, and M. Reitzner, “Expected sizes of poisson Delaunay mosaics and their discrete Morse functions,” Advances in Applied Probability, vol. 49, no. 3. Cambridge University Press, pp. 745–767, 2017."},"publication":"Advances in Applied Probability","page":"745 - 767","date_published":"2017-09-01T00:00:00Z","publist_id":"6962","ec_funded":1,"year":"2017","publisher":"Cambridge University Press","department":[{"_id":"HeEd"}],"publication_status":"published","related_material":{"record":[{"id":"6287","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"full_name":"Nikitenko, Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0659-3201","first_name":"Anton","last_name":"Nikitenko"},{"full_name":"Reitzner, Matthias","first_name":"Matthias","last_name":"Reitzner"}],"volume":49,"date_created":"2018-12-11T11:48:07Z","date_updated":"2023-09-07T12:07:12Z","publication_identifier":{"issn":["00018678"]},"month":"09","main_file_link":[{"url":"https://arxiv.org/abs/1607.05915","open_access":"1"}],"external_id":{"arxiv":["1607.05915"]},"oa":1,"project":[{"grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","call_identifier":"FP7"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"quality_controlled":"1","doi":"10.1017/apr.2017.20","language":[{"iso":"eng"}]},{"department":[{"_id":"KrPi"}],"publisher":"Springer","publication_status":"published","year":"2017","volume":10625,"date_created":"2018-12-11T11:47:10Z","date_updated":"2023-09-07T12:30:22Z","related_material":{"record":[{"id":"83","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Abusalah","first_name":"Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M"},{"first_name":"Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alwen, Joel F"},{"last_name":"Cohen","first_name":"Bram","full_name":"Cohen, Bram"},{"last_name":"Khilko","first_name":"Danylo","full_name":"Khilko, Danylo"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"},{"full_name":"Reyzin, Leonid","last_name":"Reyzin","first_name":"Leonid"}],"publist_id":"7257","ec_funded":1,"project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2017/893.pdf","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-70697-9_13","conference":{"location":"Hong Kong, China","start_date":"2017-12-03","end_date":"2017-12-07","name":"ASIACRYPT: Theory and Applications of Cryptology and Information Security"},"publication_identifier":{"isbn":["978-331970696-2"]},"month":"11","intvolume":" 10625","title":"Beyond Hellman’s time-memory trade-offs with applications to proofs of space","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"559","oa_version":"Submitted Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Proofs of space (PoS) were suggested as more ecological and economical alternative to proofs of work, which are currently used in blockchain designs like Bitcoin. The existing PoS are based on rather sophisticated graph pebbling lower bounds. Much simpler and in several aspects more efficient schemes based on inverting random functions have been suggested, but they don’t give meaningful security guarantees due to existing time-memory trade-offs. In particular, Hellman showed that any permutation over a domain of size N can be inverted in time T by an algorithm that is given S bits of auxiliary information whenever (Formula presented). For functions Hellman gives a weaker attack with S2· T≈ N2 (e.g., S= T≈ N2/3). To prove lower bounds, one considers an adversary who has access to an oracle f: [ N] → [N] and can make T oracle queries. The best known lower bound is S· T∈ Ω(N) and holds for random functions and permutations. We construct functions that provably require more time and/or space to invert. Specifically, for any constant k we construct a function [N] → [N] that cannot be inverted unless Sk· T∈ Ω(Nk) (in particular, S= T≈ (Formula presented). Our construction does not contradict Hellman’s time-memory trade-off, because it cannot be efficiently evaluated in forward direction. However, its entire function table can be computed in time quasilinear in N, which is sufficient for the PoS application. Our simplest construction is built from a random function oracle g: [N] × [N] → [ N] and a random permutation oracle f: [N] → N] and is defined as h(x) = g(x, x′) where f(x) = π(f(x′)) with π being any involution without a fixed point, e.g. flipping all the bits. For this function we prove that any adversary who gets S bits of auxiliary information, makes at most T oracle queries, and inverts h on an ϵ fraction of outputs must satisfy S2· T∈ Ω(ϵ2N2)."}],"page":"357 - 379","citation":{"ieee":"H. M. Abusalah, J. F. Alwen, B. Cohen, D. Khilko, K. Z. Pietrzak, and L. Reyzin, “Beyond Hellman’s time-memory trade-offs with applications to proofs of space,” presented at the ASIACRYPT: Theory and Applications of Cryptology and Information Security, Hong Kong, China, 2017, vol. 10625, pp. 357–379.","apa":"Abusalah, H. M., Alwen, J. F., Cohen, B., Khilko, D., Pietrzak, K. Z., & Reyzin, L. (2017). Beyond Hellman’s time-memory trade-offs with applications to proofs of space (Vol. 10625, pp. 357–379). Presented at the ASIACRYPT: Theory and Applications of Cryptology and Information Security, Hong Kong, China: Springer. https://doi.org/10.1007/978-3-319-70697-9_13","ista":"Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. 2017. Beyond Hellman’s time-memory trade-offs with applications to proofs of space. ASIACRYPT: Theory and Applications of Cryptology and Information Security, LNCS, vol. 10625, 357–379.","ama":"Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. Beyond Hellman’s time-memory trade-offs with applications to proofs of space. In: Vol 10625. Springer; 2017:357-379. doi:10.1007/978-3-319-70697-9_13","chicago":"Abusalah, Hamza M, Joel F Alwen, Bram Cohen, Danylo Khilko, Krzysztof Z Pietrzak, and Leonid Reyzin. “Beyond Hellman’s Time-Memory Trade-Offs with Applications to Proofs of Space,” 10625:357–79. Springer, 2017. https://doi.org/10.1007/978-3-319-70697-9_13.","short":"H.M. Abusalah, J.F. Alwen, B. Cohen, D. Khilko, K.Z. Pietrzak, L. Reyzin, in:, Springer, 2017, pp. 357–379.","mla":"Abusalah, Hamza M., et al. Beyond Hellman’s Time-Memory Trade-Offs with Applications to Proofs of Space. Vol. 10625, Springer, 2017, pp. 357–79, doi:10.1007/978-3-319-70697-9_13."},"date_published":"2017-11-18T00:00:00Z","scopus_import":1,"day":"18"},{"article_number":"63","ec_funded":1,"publist_id":"7265","file_date_updated":"2020-07-14T12:47:00Z","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"publication_status":"published","year":"2017","volume":22,"date_updated":"2023-09-07T12:38:08Z","date_created":"2018-12-11T11:47:07Z","related_material":{"record":[{"id":"149","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","last_name":"Alt","first_name":"Johannes","full_name":"Alt, Johannes"}],"publication_identifier":{"issn":["1083589X"]},"month":"11","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"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":"10.1214/17-ECP97","type":"journal_article","abstract":[{"text":"For large random matrices X with independent, centered entries but not necessarily identical variances, the eigenvalue density of XX* is well-approximated by a deterministic measure on ℝ. We show that the density of this measure has only square and cubic-root singularities away from zero. We also extend the bulk local law in [5] to the vicinity of these singularities.","lang":"eng"}],"intvolume":" 22","title":"Singularities of the density of states of random Gram matrices","ddc":["539"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"550","oa_version":"Published Version","file":[{"file_id":"4663","relation":"main_file","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T10:08:04Z","checksum":"0ec05303a0de190de145654237984c79","file_name":"IST-2018-926-v1+1_euclid.ecp.1511233247.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":470876}],"pubrep_id":"926","scopus_import":1,"has_accepted_license":"1","day":"21","citation":{"mla":"Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.” Electronic Communications in Probability, vol. 22, 63, Institute of Mathematical Statistics, 2017, doi:10.1214/17-ECP97.","short":"J. Alt, Electronic Communications in Probability 22 (2017).","chicago":"Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/17-ECP97.","ama":"Alt J. Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. 2017;22. doi:10.1214/17-ECP97","ista":"Alt J. 2017. Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. 22, 63.","apa":"Alt, J. (2017). Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/17-ECP97","ieee":"J. Alt, “Singularities of the density of states of random Gram matrices,” Electronic Communications in Probability, vol. 22. Institute of Mathematical Statistics, 2017."},"publication":"Electronic Communications in Probability","date_published":"2017-11-21T00:00:00Z"}]