[{"volume":19,"date_created":"2018-12-11T11:47:14Z","status":"public","day":"01","doi":"10.4310/HHA.2017.v19.n2.a16","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.04310"}],"publication":"Homology, Homotopy and Applications","ec_funded":1,"oa_version":"Submitted Version","intvolume":"        19","month":"01","date_published":"2017-01-01T00:00:00Z","date_updated":"2021-01-12T08:03:12Z","issue":"2","oa":1,"page":"313 - 342","year":"2017","publication_identifier":{"issn":["15320073"]},"citation":{"chicago":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” <i>Homology, Homotopy and Applications</i>. International Press, 2017. <a href=\"https://doi.org/10.4310/HHA.2017.v19.n2.a16\">https://doi.org/10.4310/HHA.2017.v19.n2.a16</a>.","ama":"Franek P, Krcál M. Persistence of zero sets. <i>Homology, Homotopy and Applications</i>. 2017;19(2):313-342. doi:<a href=\"https://doi.org/10.4310/HHA.2017.v19.n2.a16\">10.4310/HHA.2017.v19.n2.a16</a>","short":"P. Franek, M. Krcál, Homology, Homotopy and Applications 19 (2017) 313–342.","ista":"Franek P, Krcál M. 2017. Persistence of zero sets. Homology, Homotopy and Applications. 19(2), 313–342.","ieee":"P. Franek and M. Krcál, “Persistence of zero sets,” <i>Homology, Homotopy and Applications</i>, vol. 19, no. 2. International Press, pp. 313–342, 2017.","mla":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” <i>Homology, Homotopy and Applications</i>, vol. 19, no. 2, International Press, 2017, pp. 313–42, doi:<a href=\"https://doi.org/10.4310/HHA.2017.v19.n2.a16\">10.4310/HHA.2017.v19.n2.a16</a>.","apa":"Franek, P., &#38; Krcál, M. (2017). Persistence of zero sets. <i>Homology, Homotopy and Applications</i>. International Press. <a href=\"https://doi.org/10.4310/HHA.2017.v19.n2.a16\">https://doi.org/10.4310/HHA.2017.v19.n2.a16</a>"},"type":"journal_article","abstract":[{"lang":"eng","text":"We study robust properties of zero sets of continuous maps f: X → ℝn. Formally, we analyze the family Z&lt; r(f) := (g-1(0): ||g - f|| &lt; r) of all zero sets of all continuous maps g closer to f than r in the max-norm. All of these sets are outside A := (x: |f(x)| ≥ r) and we claim that Z&lt; r(f) is fully determined by A and an element of a certain cohomotopy group which (by a recent result) is computable whenever the dimension of X is at most 2n - 3. By considering all r &gt; 0 simultaneously, the pointed cohomotopy groups form a persistence module-a structure leading to persistence diagrams as in the case of persistent homology or well groups. Eventually, we get a descriptor of persistent robust properties of zero sets that has better descriptive power (Theorem A) and better computability status (Theorem B) than the established well diagrams. Moreover, if we endow every point of each zero set with gradients of the perturbation, the robust description of the zero sets by elements of cohomotopy groups is in some sense the best possible (Theorem C)."}],"scopus_import":1,"_id":"568","quality_controlled":"1","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","_id":"2590DB08-B435-11E9-9278-68D0E5697425","grant_number":"701309","call_identifier":"H2020"}],"publication_status":"published","publisher":"International Press","author":[{"first_name":"Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87","last_name":"Franek","full_name":"Franek, Peter"},{"id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek","last_name":"Krcál","full_name":"Krcál, Marek"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Persistence of zero sets","publist_id":"7246","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"language":[{"iso":"eng"}]},{"publication_status":"published","file_date_updated":"2020-07-14T12:47:10Z","type":"journal_article","scopus_import":1,"abstract":[{"lang":"eng","text":"The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings."}],"publication_identifier":{"issn":["2050084X"]},"citation":{"apa":"Spira, F., Cuylen Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma, A., … Gerlich, D. (2017). Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.30867\">https://doi.org/10.7554/eLife.30867</a>","mla":"Spira, Felix, et al. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” <i>ELife</i>, vol. 6, e30867, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.30867\">10.7554/eLife.30867</a>.","ama":"Spira F, Cuylen Haering S, Mehta S, et al. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.30867\">10.7554/eLife.30867</a>","ista":"Spira F, Cuylen Haering S, Mehta S, Samwer M, Reversat A, Verma A, Oldenbourg R, Sixt MK, Gerlich D. 2017. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 6, e30867.","short":"F. Spira, S. Cuylen Haering, S. Mehta, M. Samwer, A. Reversat, A. Verma, R. Oldenbourg, M.K. Sixt, D. Gerlich, ELife 6 (2017).","ieee":"F. Spira <i>et al.</i>, “Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","chicago":"Spira, Felix, Sara Cuylen Haering, Shalin Mehta, Matthias Samwer, Anne Reversat, Amitabh Verma, Rudolf Oldenbourg, Michael K Sixt, and Daniel Gerlich. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.30867\">https://doi.org/10.7554/eLife.30867</a>."},"quality_controlled":"1","_id":"569","department":[{"_id":"MiSi"}],"publist_id":"7245","pubrep_id":"919","language":[{"iso":"eng"}],"publisher":"eLife Sciences Publications","has_accepted_license":"1","file":[{"creator":"system","file_size":9666973,"file_id":"4829","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"ba09c1451153d39e4f4b7cee013e314c","file_name":"IST-2017-919-v1+1_elife-30867-figures-v1.pdf","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:10:40Z"},{"access_level":"open_access","checksum":"01eb51f1d6ad679947415a51c988e137","relation":"main_file","content_type":"application/pdf","file_id":"4830","creator":"system","file_size":5951246,"date_created":"2018-12-12T10:10:41Z","date_updated":"2020-07-14T12:47:10Z","file_name":"IST-2017-919-v1+2_elife-30867-v1.pdf"}],"author":[{"last_name":"Spira","first_name":"Felix","full_name":"Spira, Felix"},{"full_name":"Cuylen Haering, Sara","first_name":"Sara","last_name":"Cuylen Haering"},{"full_name":"Mehta, Shalin","first_name":"Shalin","last_name":"Mehta"},{"full_name":"Samwer, Matthias","first_name":"Matthias","last_name":"Samwer"},{"full_name":"Reversat, Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","orcid":"0000-0003-0666-8928","last_name":"Reversat"},{"last_name":"Verma","first_name":"Amitabh","full_name":"Verma, Amitabh"},{"full_name":"Oldenbourg, Rudolf","first_name":"Rudolf","last_name":"Oldenbourg"},{"full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179"},{"first_name":"Daniel","last_name":"Gerlich","full_name":"Gerlich, Daniel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments","doi":"10.7554/eLife.30867","publication":"eLife","oa_version":"Published Version","volume":6,"status":"public","day":"06","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:47:14Z","year":"2017","article_number":"e30867","intvolume":"         6","month":"11","date_published":"2017-11-06T00:00:00Z","oa":1,"date_updated":"2023-02-23T12:30:29Z"},{"day":"13","status":"public","date_created":"2018-12-11T11:47:14Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["576"],"volume":6,"oa_version":"Published Version","ec_funded":1,"doi":"10.7554/eLife.28921","publication":"eLife","oa":1,"date_updated":"2021-01-12T08:03:15Z","article_number":"e28921","month":"11","intvolume":"         6","date_published":"2017-11-13T00:00:00Z","year":"2017","quality_controlled":"1","_id":"570","file_date_updated":"2020-07-14T12:47:10Z","type":"journal_article","abstract":[{"lang":"eng","text":"Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. "}],"scopus_import":1,"publication_identifier":{"issn":["2050084X"]},"citation":{"mla":"Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” <i>ELife</i>, vol. 6, e28921, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.28921\">10.7554/eLife.28921</a>.","apa":"Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., &#38; Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.28921\">https://doi.org/10.7554/eLife.28921</a>","chicago":"Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.28921\">https://doi.org/10.7554/eLife.28921</a>.","ama":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.28921\">10.7554/eLife.28921</a>","ieee":"M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory network structure determines patterns of intermolecular epistasis,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","short":"M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).","ista":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 6, e28921."},"publication_status":"published","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"648440","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer"}],"file":[{"file_name":"IST-2017-918-v1+1_elife-28921-figures-v3.pdf","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:14:42Z","content_type":"application/pdf","file_id":"5096","creator":"system","file_size":8453470,"access_level":"open_access","relation":"main_file","checksum":"273ab17f33305e4eaafd911ff88e7c5b"},{"access_level":"open_access","checksum":"b433f90576c7be597cd43367946f8e7f","relation":"main_file","content_type":"application/pdf","file_id":"5097","creator":"system","file_size":1953221,"date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:14:43Z","file_name":"IST-2017-918-v1+2_elife-28921-v3.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","last_name":"Lagator"},{"first_name":"Srdjan","id":"35F0286E-F248-11E8-B48F-1D18A9856A87","last_name":"Sarikas","full_name":"Sarikas, Srdjan"},{"full_name":"Acar, Hande","last_name":"Acar","orcid":"0000-0003-1986-9753","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","first_name":"Hande"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"title":"Regulatory network structure determines patterns of intermolecular epistasis","publisher":"eLife Sciences Publications","has_accepted_license":"1","pubrep_id":"918","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"},{"_id":"JoBo"},{"_id":"NiBa"}],"publist_id":"7244"},{"publication_status":"published","project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"747687"}],"quality_controlled":"1","_id":"571","scopus_import":1,"abstract":[{"text":"Blood platelets are critical for hemostasis and thrombosis and play diverse roles during immune responses. Despite these versatile tasks in mammalian biology, their skills on a cellular level are deemed limited, mainly consisting in rolling, adhesion, and aggregate formation. Here, we identify an unappreciated asset of platelets and show that adherent platelets use adhesion receptors to mechanically probe the adhesive substrate in their local microenvironment. When actomyosin-dependent traction forces overcome substrate resistance, platelets migrate and pile up the adhesive substrate together with any bound particulate material. They use this ability to act as cellular scavengers, scanning the vascular surface for potential invaders and collecting deposited bacteria. Microbe collection by migrating platelets boosts the activity of professional phagocytes, exacerbating inflammatory tissue injury in sepsis. This assigns platelets a central role in innate immune responses and identifies them as potential targets to dampen inflammatory tissue damage in clinical scenarios of severe systemic infection. In addition to their role in thrombosis and hemostasis, platelets can also migrate to sites of infection to help trap bacteria and clear the vascular surface.","lang":"eng"}],"type":"journal_article","publication_identifier":{"issn":["00928674"]},"citation":{"mla":"Gärtner, Florian R., et al. “Migrating Platelets Are Mechano Scavengers That Collect and Bundle Bacteria.” <i>Cell Press</i>, vol. 171, no. 6, Cell Press, 2017, pp. 1368–82, doi:<a href=\"https://doi.org/10.1016/j.cell.2017.11.001\">10.1016/j.cell.2017.11.001</a>.","apa":"Gärtner, F. R., Ahmad, Z., Rosenberger, G., Fan, S., Nicolai, L., Busch, B., … Massberg, S. (2017). Migrating platelets are mechano scavengers that collect and bundle bacteria. <i>Cell Press</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2017.11.001\">https://doi.org/10.1016/j.cell.2017.11.001</a>","chicago":"Gärtner, Florian R, Zerkah Ahmad, Gerhild Rosenberger, Shuxia Fan, Leo Nicolai, Benjamin Busch, Gökce Yavuz, et al. “Migrating Platelets Are Mechano Scavengers That Collect and Bundle Bacteria.” <i>Cell Press</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cell.2017.11.001\">https://doi.org/10.1016/j.cell.2017.11.001</a>.","ista":"Gärtner FR, Ahmad Z, Rosenberger G, Fan S, Nicolai L, Busch B, Yavuz G, Luckner M, Ishikawa Ankerhold H, Hennel R, Benechet A, Lorenz M, Chandraratne S, Schubert I, Helmer S, Striednig B, Stark K, Janko M, Böttcher R, Verschoor A, Leon C, Gachet C, Gudermann T, Mederos Y Schnitzler M, Pincus Z, Iannacone M, Haas R, Wanner G, Lauber K, Sixt MK, Massberg S. 2017. Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. 171(6), 1368–1382.","short":"F.R. Gärtner, Z. Ahmad, G. Rosenberger, S. Fan, L. Nicolai, B. Busch, G. Yavuz, M. Luckner, H. Ishikawa Ankerhold, R. Hennel, A. Benechet, M. Lorenz, S. Chandraratne, I. Schubert, S. Helmer, B. Striednig, K. Stark, M. Janko, R. Böttcher, A. Verschoor, C. Leon, C. Gachet, T. Gudermann, M. Mederos Y Schnitzler, Z. Pincus, M. Iannacone, R. Haas, G. Wanner, K. Lauber, M.K. Sixt, S. Massberg, Cell Press 171 (2017) 1368–1382.","ieee":"F. R. Gärtner <i>et al.</i>, “Migrating platelets are mechano scavengers that collect and bundle bacteria,” <i>Cell Press</i>, vol. 171, no. 6. Cell Press, pp. 1368–1382, 2017.","ama":"Gärtner FR, Ahmad Z, Rosenberger G, et al. Migrating platelets are mechano scavengers that collect and bundle bacteria. <i>Cell Press</i>. 2017;171(6):1368-1382. doi:<a href=\"https://doi.org/10.1016/j.cell.2017.11.001\">10.1016/j.cell.2017.11.001</a>"},"language":[{"iso":"eng"}],"publist_id":"7243","department":[{"_id":"MiSi"}],"title":"Migrating platelets are mechano scavengers that collect and bundle bacteria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Gärtner","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian R","full_name":"Gärtner, Florian R"},{"full_name":"Ahmad, Zerkah","first_name":"Zerkah","last_name":"Ahmad"},{"first_name":"Gerhild","last_name":"Rosenberger","full_name":"Rosenberger, Gerhild"},{"full_name":"Fan, Shuxia","first_name":"Shuxia","last_name":"Fan"},{"first_name":"Leo","last_name":"Nicolai","full_name":"Nicolai, Leo"},{"full_name":"Busch, Benjamin","first_name":"Benjamin","last_name":"Busch"},{"full_name":"Yavuz, Gökce","first_name":"Gökce","last_name":"Yavuz"},{"full_name":"Luckner, Manja","first_name":"Manja","last_name":"Luckner"},{"full_name":"Ishikawa Ankerhold, Hellen","first_name":"Hellen","last_name":"Ishikawa Ankerhold"},{"last_name":"Hennel","first_name":"Roman","full_name":"Hennel, Roman"},{"full_name":"Benechet, Alexandre","last_name":"Benechet","first_name":"Alexandre"},{"full_name":"Lorenz, Michael","first_name":"Michael","last_name":"Lorenz"},{"first_name":"Sue","last_name":"Chandraratne","full_name":"Chandraratne, Sue"},{"full_name":"Schubert, Irene","last_name":"Schubert","first_name":"Irene"},{"full_name":"Helmer, Sebastian","first_name":"Sebastian","last_name":"Helmer"},{"first_name":"Bianca","last_name":"Striednig","full_name":"Striednig, Bianca"},{"full_name":"Stark, Konstantin","last_name":"Stark","first_name":"Konstantin"},{"full_name":"Janko, Marek","first_name":"Marek","last_name":"Janko"},{"last_name":"Böttcher","first_name":"Ralph","full_name":"Böttcher, Ralph"},{"full_name":"Verschoor, Admar","last_name":"Verschoor","first_name":"Admar"},{"full_name":"Leon, Catherine","first_name":"Catherine","last_name":"Leon"},{"first_name":"Christian","last_name":"Gachet","full_name":"Gachet, Christian"},{"first_name":"Thomas","last_name":"Gudermann","full_name":"Gudermann, Thomas"},{"full_name":"Mederos Y Schnitzler, Michael","last_name":"Mederos Y Schnitzler","first_name":"Michael"},{"last_name":"Pincus","first_name":"Zachary","full_name":"Pincus, Zachary"},{"full_name":"Iannacone, Matteo","first_name":"Matteo","last_name":"Iannacone"},{"full_name":"Haas, Rainer","first_name":"Rainer","last_name":"Haas"},{"full_name":"Wanner, Gerhard","last_name":"Wanner","first_name":"Gerhard"},{"full_name":"Lauber, Kirsten","first_name":"Kirsten","last_name":"Lauber"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"first_name":"Steffen","last_name":"Massberg","full_name":"Massberg, Steffen"}],"publisher":"Cell Press","oa_version":"None","ec_funded":1,"publication":"Cell Press","doi":"10.1016/j.cell.2017.11.001","status":"public","day":"30","date_created":"2018-12-11T11:47:15Z","volume":171,"year":"2017","page":"1368 - 1382","issue":"6","date_updated":"2021-01-12T08:03:15Z","date_published":"2017-11-30T00:00:00Z","month":"11","intvolume":"       171"},{"file_date_updated":"2020-07-14T12:47:10Z","type":"journal_article","abstract":[{"text":"In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture.","lang":"eng"}],"scopus_import":"1","citation":{"chicago":"Olatunji, Damilola, Danny Geelen, and Inge Verstraeten. “Control of Endogenous Auxin Levels in Plant Root Development.” <i>International Journal of Molecular Sciences</i>. MDPI, 2017. <a href=\"https://doi.org/10.3390/ijms18122587\">https://doi.org/10.3390/ijms18122587</a>.","ieee":"D. Olatunji, D. Geelen, and I. Verstraeten, “Control of endogenous auxin levels in plant root development,” <i>International Journal of Molecular Sciences</i>, vol. 18, no. 12. MDPI, 2017.","ista":"Olatunji D, Geelen D, Verstraeten I. 2017. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 18(12), 2587.","short":"D. Olatunji, D. Geelen, I. Verstraeten, International Journal of Molecular Sciences 18 (2017).","ama":"Olatunji D, Geelen D, Verstraeten I. Control of endogenous auxin levels in plant root development. <i>International Journal of Molecular Sciences</i>. 2017;18(12). doi:<a href=\"https://doi.org/10.3390/ijms18122587\">10.3390/ijms18122587</a>","mla":"Olatunji, Damilola, et al. “Control of Endogenous Auxin Levels in Plant Root Development.” <i>International Journal of Molecular Sciences</i>, vol. 18, no. 12, 2587, MDPI, 2017, doi:<a href=\"https://doi.org/10.3390/ijms18122587\">10.3390/ijms18122587</a>.","apa":"Olatunji, D., Geelen, D., &#38; Verstraeten, I. (2017). Control of endogenous auxin levels in plant root development. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms18122587\">https://doi.org/10.3390/ijms18122587</a>"},"quality_controlled":"1","_id":"572","publication_status":"published","publisher":"MDPI","has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:08:55Z","file_name":"IST-2017-917-v1+1_ijms-18-02587.pdf","relation":"main_file","access_level":"open_access","checksum":"82d51f11e493f7eec02976d9a9a9805e","file_id":"4718","content_type":"application/pdf","file_size":920962,"creator":"system"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Control of endogenous auxin levels in plant root development","author":[{"full_name":"Olatunji, Damilola","last_name":"Olatunji","first_name":"Damilola"},{"last_name":"Geelen","first_name":"Danny","full_name":"Geelen, Danny"},{"last_name":"Verstraeten","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","full_name":"Verstraeten, Inge"}],"publist_id":"7242","department":[{"_id":"JiFr"}],"article_processing_charge":"No","pubrep_id":"917","language":[{"iso":"eng"}],"volume":18,"status":"public","day":"01","date_created":"2018-12-11T11:47:15Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"],"doi":"10.3390/ijms18122587","publication":"International Journal of Molecular Sciences","oa_version":"Published Version","article_number":"2587","month":"12","intvolume":"        18","date_published":"2017-12-01T00:00:00Z","issue":"12","oa":1,"date_updated":"2021-01-12T08:03:16Z","year":"2017"},{"article_processing_charge":"No","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"publisher":"Springer Nature","author":[{"last_name":"Biswas","orcid":"0000-0002-5372-7890","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita"},{"full_name":"Bhowmick, Partha","first_name":"Partha","last_name":"Bhowmick"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Construction of persistent Voronoi diagram on 3D digital plane","place":"Cham","publication_status":"published","publication_identifier":{"issn":["0302-9743","1611-3349"],"isbn":["978-3-319-59107-0","978-3-319-59108-7"]},"citation":{"apa":"Biswas, R., &#38; Bhowmick, P. (2017). Construction of persistent Voronoi diagram on 3D digital plane. In <i>Combinatorial image analysis</i> (Vol. 10256, pp. 93–104). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-59108-7_8\">https://doi.org/10.1007/978-3-319-59108-7_8</a>","mla":"Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” <i>Combinatorial Image Analysis</i>, vol. 10256, Springer Nature, 2017, pp. 93–104, doi:<a href=\"https://doi.org/10.1007/978-3-319-59108-7_8\">10.1007/978-3-319-59108-7_8</a>.","ieee":"R. Biswas and P. Bhowmick, “Construction of persistent Voronoi diagram on 3D digital plane,” in <i>Combinatorial image analysis</i>, vol. 10256, Cham: Springer Nature, 2017, pp. 93–104.","ista":"Biswas R, Bhowmick P. 2017.Construction of persistent Voronoi diagram on 3D digital plane. In: Combinatorial image analysis. LNCS, vol. 10256, 93–104.","short":"R. Biswas, P. Bhowmick, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2017, pp. 93–104.","ama":"Biswas R, Bhowmick P. Construction of persistent Voronoi diagram on 3D digital plane. In: <i>Combinatorial Image Analysis</i>. Vol 10256. Cham: Springer Nature; 2017:93-104. doi:<a href=\"https://doi.org/10.1007/978-3-319-59108-7_8\">10.1007/978-3-319-59108-7_8</a>","chicago":"Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” In <i>Combinatorial Image Analysis</i>, 10256:93–104. Cham: Springer Nature, 2017. <a href=\"https://doi.org/10.1007/978-3-319-59108-7_8\">https://doi.org/10.1007/978-3-319-59108-7_8</a>."},"extern":"1","type":"book_chapter","abstract":[{"lang":"eng","text":"Different distance metrics produce Voronoi diagrams with different properties. It is a well-known that on the (real) 2D plane or even on any 3D plane, a Voronoi diagram (VD) based on the Euclidean distance metric produces convex Voronoi regions. In this paper, we first show that this metric produces a persistent VD on the 2D digital plane, as it comprises digitally convex Voronoi regions and hence correctly approximates the corresponding VD on the 2D real plane. Next, we show that on a 3D digital plane D, the Euclidean metric spanning over its voxel set does not guarantee a digital VD which is persistent with the real-space VD. As a solution, we introduce a novel concept of functional-plane-convexity, which is ensured by the Euclidean metric spanning over the pedal set of D. Necessary proofs and some visual result have been provided to adjudge the merit and usefulness of the proposed concept."}],"_id":"5803","quality_controlled":"1","page":"93-104","conference":{"location":"Plovdiv, Bulgaria","name":"IWCIA: International Workshop on Combinatorial Image Analysis","start_date":"2017-06-19","end_date":"2017-06-21"},"year":"2017","month":"05","intvolume":"     10256","alternative_title":["LNCS"],"date_published":"2017-05-17T00:00:00Z","date_updated":"2022-01-28T07:48:24Z","doi":"10.1007/978-3-319-59108-7_8","publication":"Combinatorial image analysis","oa_version":"None","volume":10256,"date_created":"2019-01-08T20:42:56Z","day":"17","status":"public"},{"publication_status":"published","_id":"6013","quality_controlled":"1","citation":{"chicago":"Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin Laux, Yonghao Mi, Karen Z. Hatsagortsyan, Thomas Pfeifer, Christoph H. Keitel, and Robert Moshammer. “Experimental Evidence for Quantum Tunneling Time.” <i>Physical Review Letters</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevLett.119.023201\">https://doi.org/10.1103/PhysRevLett.119.023201</a>.","ama":"Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for quantum tunneling time. <i>Physical Review Letters</i>. 2017;119(2). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.119.023201\">10.1103/PhysRevLett.119.023201</a>","ista":"Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan KZ, Pfeifer T, Keitel CH, Moshammer R. 2017. Experimental evidence for quantum tunneling time. Physical Review Letters. 119(2), 023201.","ieee":"N. Camus <i>et al.</i>, “Experimental evidence for quantum tunneling time,” <i>Physical Review Letters</i>, vol. 119, no. 2. American Physical Society, 2017.","short":"N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K.Z. Hatsagortsyan, T. Pfeifer, C.H. Keitel, R. Moshammer, Physical Review Letters 119 (2017).","mla":"Camus, Nicolas, et al. “Experimental Evidence for Quantum Tunneling Time.” <i>Physical Review Letters</i>, vol. 119, no. 2, 023201, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.119.023201\">10.1103/PhysRevLett.119.023201</a>.","apa":"Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer, R. (2017). Experimental evidence for quantum tunneling time. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.119.023201\">https://doi.org/10.1103/PhysRevLett.119.023201</a>"},"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"type":"journal_article","abstract":[{"lang":"eng","text":"The first hundred attoseconds of the electron dynamics during strong field tunneling ionization are investigated. We quantify theoretically how the electron’s classical trajectories in the continuum emerge from the tunneling process and test the results with those achieved in parallel from attoclock measurements. An especially high sensitivity on the tunneling barrier is accomplished here by comparing the momentum distributions of two atomic species of slightly deviating atomic potentials (argon and krypton) being ionized under absolutely identical conditions with near-infrared laser pulses (1300 nm). The agreement between experiment and theory provides clear evidence for a nonzero tunneling time delay and a nonvanishing longitudinal momentum of the electron at the “tunnel exit.”"}],"scopus_import":1,"arxiv":1,"language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"title":"Experimental evidence for quantum tunneling time","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Camus","first_name":"Nicolas","full_name":"Camus, Nicolas"},{"id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","first_name":"Enderalp","orcid":"0000-0001-5973-0874","last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp"},{"last_name":"Fechner","first_name":"Lutz","full_name":"Fechner, Lutz"},{"full_name":"Klaiber, Michael","first_name":"Michael","last_name":"Klaiber"},{"first_name":"Martin","last_name":"Laux","full_name":"Laux, Martin"},{"full_name":"Mi, Yonghao","last_name":"Mi","first_name":"Yonghao"},{"last_name":"Hatsagortsyan","first_name":"Karen Z.","full_name":"Hatsagortsyan, Karen Z."},{"first_name":"Thomas","last_name":"Pfeifer","full_name":"Pfeifer, Thomas"},{"last_name":"Keitel","first_name":"Christoph H.","full_name":"Keitel, Christoph H."},{"first_name":"Robert","last_name":"Moshammer","full_name":"Moshammer, Robert"}],"publisher":"American Physical Society","related_material":{"record":[{"id":"313","status":"public","relation":"earlier_version"}]},"oa_version":"Preprint","doi":"10.1103/PhysRevLett.119.023201","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.03701"}],"publication":"Physical Review Letters","date_created":"2019-02-14T15:24:13Z","status":"public","day":"14","volume":119,"year":"2017","external_id":{"arxiv":["1611.03701"]},"date_updated":"2023-02-23T11:13:36Z","issue":"2","oa":1,"intvolume":"       119","month":"07","date_published":"2017-07-14T00:00:00Z","article_number":"023201"},{"publication_status":"published","scopus_import":1,"abstract":[{"text":"In several settings of physics and chemistry one has to deal with molecules interacting with some kind of an external environment, be it a gas, a solution, or a crystal surface. Understanding molecular processes in the presence of such a many-particle bath is inherently challenging, and usually requires large-scale numerical computations. Here, we present an alternative approach to the problem, based on the notion of the angulon quasiparticle. We show that molecules rotating inside superfluid helium nanodroplets and Bose–Einstein condensates form angulons, and therefore can be described by straightforward solutions of a simple microscopic Hamiltonian. Casting the problem in the language of angulons allows us not only to greatly simplify it, but also to gain insights into the origins of the observed phenomena and to make predictions for future experimental studies.","lang":"eng"}],"type":"book_chapter","citation":{"chicago":"Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.” In <i>Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero </i>, edited by Oliver Dulieu and Andreas Osterwalder, 11:444–95. Theoretical and Computational Chemistry Series. The Royal Society of Chemistry, 2017. <a href=\"https://doi.org/10.1039/9781782626800-00444\">https://doi.org/10.1039/9781782626800-00444</a>.","short":"M. Lemeshko, R. Schmidt, in:, O. Dulieu, A. Osterwalder (Eds.), Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , The Royal Society of Chemistry, 2017, pp. 444–495.","ista":"Lemeshko M, Schmidt R. 2017.Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In: Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero . Theoretical and Computational Chemistry Series, vol. 11, 444–495.","ieee":"M. Lemeshko and R. Schmidt, “Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets,” in <i>Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero </i>, vol. 11, O. Dulieu and A. Osterwalder, Eds. The Royal Society of Chemistry, 2017, pp. 444–495.","ama":"Lemeshko M, Schmidt R. Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In: Dulieu O, Osterwalder A, eds. <i>Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero </i>. Vol 11. Theoretical and Computational Chemistry Series. The Royal Society of Chemistry; 2017:444-495. doi:<a href=\"https://doi.org/10.1039/9781782626800-00444\">10.1039/9781782626800-00444</a>","mla":"Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.” <i>Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero </i>, edited by Oliver Dulieu and Andreas Osterwalder, vol. 11, The Royal Society of Chemistry, 2017, pp. 444–95, doi:<a href=\"https://doi.org/10.1039/9781782626800-00444\">10.1039/9781782626800-00444</a>.","apa":"Lemeshko, M., &#38; Schmidt, R. (2017). Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In O. Dulieu &#38; A. Osterwalder (Eds.), <i>Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero </i> (Vol. 11, pp. 444–495). The Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/9781782626800-00444\">https://doi.org/10.1039/9781782626800-00444</a>"},"publication_identifier":{"issn":["20413181"]},"quality_controlled":"1","_id":"604","editor":[{"first_name":"Oliver","last_name":"Dulieu","full_name":"Dulieu, Oliver"},{"full_name":"Osterwalder, Andreas","last_name":"Osterwalder","first_name":"Andreas"}],"department":[{"_id":"MiLe"}],"publist_id":"7201","language":[{"iso":"eng"}],"publisher":"The Royal Society of Chemistry","author":[{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"last_name":"Schmidt","first_name":"Richard","full_name":"Schmidt, Richard"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets","publication":"Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero ","doi":"10.1039/9781782626800-00444","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.06753"}],"oa_version":"Submitted Version","volume":11,"status":"public","day":"14","date_created":"2018-12-11T11:47:27Z","page":"444 - 495","series_title":"Theoretical and Computational Chemistry Series","year":"2017","date_published":"2017-12-14T00:00:00Z","alternative_title":["Theoretical and Computational Chemistry Series"],"intvolume":"        11","month":"12","oa":1,"date_updated":"2021-01-12T08:05:50Z"},{"citation":{"ama":"Brody J, Dziembowski S, Faust S, Pietrzak KZ. Position based cryptography and multiparty communication complexity. In: Kalai Y, Reyzin L, eds. Vol 10677. Springer; 2017:56-81. doi:<a href=\"https://doi.org/10.1007/978-3-319-70500-2_3\">10.1007/978-3-319-70500-2_3</a>","ista":"Brody J, Dziembowski S, Faust S, Pietrzak KZ. 2017. Position based cryptography and multiparty communication complexity. TCC: Theory of Cryptography Conference, LNCS, vol. 10677, 56–81.","ieee":"J. Brody, S. Dziembowski, S. Faust, and K. Z. Pietrzak, “Position based cryptography and multiparty communication complexity,” presented at the TCC: Theory of Cryptography Conference, Baltimore, MD, United States, 2017, vol. 10677, pp. 56–81.","short":"J. Brody, S. Dziembowski, S. Faust, K.Z. Pietrzak, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017, pp. 56–81.","chicago":"Brody, Joshua, Stefan Dziembowski, Sebastian Faust, and Krzysztof Z Pietrzak. “Position Based Cryptography and Multiparty Communication Complexity.” edited by Yael Kalai and Leonid Reyzin, 10677:56–81. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-70500-2_3\">https://doi.org/10.1007/978-3-319-70500-2_3</a>.","apa":"Brody, J., Dziembowski, S., Faust, S., &#38; Pietrzak, K. Z. (2017). Position based cryptography and multiparty communication complexity. In Y. Kalai &#38; L. Reyzin (Eds.) (Vol. 10677, pp. 56–81). Presented at the TCC: Theory of Cryptography Conference, Baltimore, MD, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-319-70500-2_3\">https://doi.org/10.1007/978-3-319-70500-2_3</a>","mla":"Brody, Joshua, et al. <i>Position Based Cryptography and Multiparty Communication Complexity</i>. Edited by Yael Kalai and Leonid Reyzin, vol. 10677, Springer, 2017, pp. 56–81, doi:<a href=\"https://doi.org/10.1007/978-3-319-70500-2_3\">10.1007/978-3-319-70500-2_3</a>."},"publication_identifier":{"isbn":["978-331970499-9"]},"scopus_import":1,"abstract":[{"lang":"eng","text":"Position based cryptography (PBC), proposed in the seminal work of Chandran, Goyal, Moriarty, and Ostrovsky (SIAM J. Computing, 2014), aims at constructing cryptographic schemes in which the identity of the user is his geographic position. Chandran et al. construct PBC schemes for secure positioning and position-based key agreement in the bounded-storage model (Maurer, J. Cryptology, 1992). Apart from bounded memory, their security proofs need a strong additional restriction on the power of the adversary: he cannot compute joint functions of his inputs. Removing this assumption is left as an open problem. We show that an answer to this question would resolve a long standing open problem in multiparty communication complexity: finding a function that is hard to compute with low communication complexity in the simultaneous message model, but easy to compute in the fully adaptive model. On a more positive side: we also show some implications in the other direction, i.e.: we prove that lower bounds on the communication complexity of certain multiparty problems imply existence of PBC primitives. Using this result we then show two attractive ways to “bypass” our hardness result: the first uses the random oracle model, the second weakens the locality requirement in the bounded-storage model to online computability. The random oracle construction is arguably one of the simplest proposed so far in this area. Our results indicate that constructing improved provably secure protocols for PBC requires a better understanding of multiparty communication complexity. This is yet another example where negative results in one area (in our case: lower bounds in multiparty communication complexity) can be used to construct secure cryptographic schemes."}],"type":"conference","_id":"605","editor":[{"last_name":"Kalai","first_name":"Yael","full_name":"Kalai, Yael"},{"last_name":"Reyzin","first_name":"Leonid","full_name":"Reyzin, Leonid"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks"}],"publication_status":"published","publisher":"Springer","title":"Position based cryptography and multiparty communication complexity","author":[{"full_name":"Brody, Joshua","last_name":"Brody","first_name":"Joshua"},{"last_name":"Dziembowski","first_name":"Stefan","full_name":"Dziembowski, Stefan"},{"last_name":"Faust","first_name":"Sebastian","full_name":"Faust, Sebastian"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7200","department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"volume":10677,"date_created":"2018-12-11T11:47:27Z","status":"public","day":"05","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/536"}],"doi":"10.1007/978-3-319-70500-2_3","oa_version":"Submitted Version","ec_funded":1,"date_published":"2017-11-05T00:00:00Z","alternative_title":["LNCS"],"intvolume":"     10677","month":"11","date_updated":"2021-01-12T08:05:53Z","oa":1,"page":"56 - 81","conference":{"location":"Baltimore, MD, United States","name":"TCC: Theory of Cryptography Conference","end_date":"2017-11-15","start_date":"2017-11-12"},"year":"2017"},{"volume":10677,"status":"public","day":"05","date_created":"2018-12-11T11:47:28Z","main_file_link":[{"url":"https://eprint.iacr.org/2017/945","open_access":"1"}],"doi":"10.1007/978-3-319-70500-2_17","oa_version":"Submitted Version","intvolume":"     10677","month":"11","date_published":"2017-11-05T00:00:00Z","alternative_title":["LNCS"],"oa":1,"date_updated":"2021-01-12T08:06:04Z","conference":{"name":"TCC: Theory of Cryptography","start_date":"2017-11-12","end_date":"2017-11-15","location":"Baltimore, MD, United States"},"page":"493 - 526","year":"2017","type":"conference","scopus_import":1,"abstract":[{"text":"Several cryptographic schemes and applications are based on functions that are both reasonably efficient to compute and moderately hard to invert, including client puzzles for Denial-of-Service protection, password protection via salted hashes, or recent proof-of-work blockchain systems. Despite their wide use, a definition of this concept has not yet been distilled and formalized explicitly. Instead, either the applications are proven directly based on the assumptions underlying the function, or some property of the function is proven, but the security of the application is argued only informally. The goal of this work is to provide a (universal) definition that decouples the efforts of designing new moderately hard functions and of building protocols based on them, serving as an interface between the two. On a technical level, beyond the mentioned definitions, we instantiate the model for four different notions of hardness. We extend the work of Alwen and Serbinenko (STOC 2015) by providing a general tool for proving security for the first notion of memory-hard functions that allows for provably secure applications. The tool allows us to recover all of the graph-theoretic techniques developed for proving security under the older, non-composable, notion of security used by Alwen and Serbinenko. As an application of our definition of moderately hard functions, we prove the security of two different schemes for proofs of effort (PoE). We also formalize and instantiate the concept of a non-interactive proof of effort (niPoE), in which the proof is not bound to a particular communication context but rather any bit-string chosen by the prover.","lang":"eng"}],"publication_identifier":{"isbn":["978-331970499-9"]},"citation":{"mla":"Alwen, Joel F., and Björn Tackmann. <i>Moderately Hard Functions: Definition, Instantiations, and Applications</i>. Edited by Yael Kalai and Leonid Reyzin, vol. 10677, Springer, 2017, pp. 493–526, doi:<a href=\"https://doi.org/10.1007/978-3-319-70500-2_17\">10.1007/978-3-319-70500-2_17</a>.","apa":"Alwen, J. F., &#38; Tackmann, B. (2017). Moderately hard functions: Definition, instantiations, and applications. In Y. Kalai &#38; L. Reyzin (Eds.) (Vol. 10677, pp. 493–526). Presented at the TCC: Theory of Cryptography, Baltimore, MD, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-319-70500-2_17\">https://doi.org/10.1007/978-3-319-70500-2_17</a>","chicago":"Alwen, Joel F, and Björn Tackmann. “Moderately Hard Functions: Definition, Instantiations, and Applications.” edited by Yael Kalai and Leonid Reyzin, 10677:493–526. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-70500-2_17\">https://doi.org/10.1007/978-3-319-70500-2_17</a>.","ama":"Alwen JF, Tackmann B. Moderately hard functions: Definition, instantiations, and applications. In: Kalai Y, Reyzin L, eds. Vol 10677. Springer; 2017:493-526. doi:<a href=\"https://doi.org/10.1007/978-3-319-70500-2_17\">10.1007/978-3-319-70500-2_17</a>","ista":"Alwen JF, Tackmann B. 2017. Moderately hard functions: Definition, instantiations, and applications. TCC: Theory of Cryptography, LNCS, vol. 10677, 493–526.","short":"J.F. Alwen, B. Tackmann, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017, pp. 493–526.","ieee":"J. F. Alwen and B. Tackmann, “Moderately hard functions: Definition, instantiations, and applications,” presented at the TCC: Theory of Cryptography, Baltimore, MD, United States, 2017, vol. 10677, pp. 493–526."},"quality_controlled":"1","editor":[{"full_name":"Kalai, Yael","first_name":"Yael","last_name":"Kalai"},{"full_name":"Reyzin, Leonid","last_name":"Reyzin","first_name":"Leonid"}],"_id":"609","publication_status":"published","publisher":"Springer","author":[{"full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen"},{"full_name":"Tackmann, Björn","first_name":"Björn","last_name":"Tackmann"}],"title":"Moderately hard functions: Definition, instantiations, and applications","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrPi"}],"publist_id":"7196","language":[{"iso":"eng"}]},{"main_file_link":[{"url":"https://arxiv.org/abs/1610.09063","open_access":"1"}],"doi":"10.1007/s11856-017-1607-7","publication":"Israel Journal of Mathematics","oa_version":"Preprint","ec_funded":1,"related_material":{"record":[{"id":"1511","relation":"earlier_version","status":"public"}]},"volume":222,"day":"01","status":"public","date_created":"2018-12-11T11:47:29Z","page":"841 - 866","year":"2017","acknowledgement":"The work by Z. P. was partially supported by the Israel Science Foundation grant ISF-768/12. The work by Z. P. and M. T. was partially supported by the project CE-ITI (GACR P202/12/G061) of the Czech Science Foundation and by the ERC Advanced Grant No. 267165. Part of the research work of M.T. was conducted at IST Austria, supported by an IST Fellowship. The research of P. P. was supported by the ERC Advanced grant no. 320924. The work by I. M. and U. W. was supported by the Swiss National Science Foundation (grants SNSF-200020-138230 and SNSF-PP00P2-138948). The collaboration between U. W. and X. G. was partially supported by the LabEx Bézout (ANR-10-LABX-58).","month":"10","intvolume":"       222","date_published":"2017-10-01T00:00:00Z","issue":"2","oa":1,"date_updated":"2023-02-23T10:02:13Z","publication_status":"published","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"type":"journal_article","scopus_import":1,"abstract":[{"lang":"eng","text":"The fact that the complete graph K5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph Kn embeds in a closed surface M (other than the Klein bottle) if and only if (n−3)(n−4) ≤ 6b1(M), where b1(M) is the first Z2-Betti number of M. On the other hand, van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of Kn+1) embeds in R2k if and only if n ≤ 2k + 1. Two decades ago, Kühnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k − 1)-connected 2k-manifold with kth Z2-Betti number bk only if the following generalized Heawood inequality holds: (k+1 n−k−1) ≤ (k+1 2k+1)bk. This is a common generalization of the case of graphs on surfaces as well as the van Kampen–Flores theorem. In the spirit of Kühnel’s conjecture, we prove that if the k-skeleton of the n-simplex embeds in a compact 2k-manifold with kth Z2-Betti number bk, then n ≤ 2bk(k 2k+2)+2k+4. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k−1)-connected. Our results generalize to maps without q-covered points, in the spirit of Tverberg’s theorem, for q a prime power. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition."}],"citation":{"chicago":"Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A van Kampen–Flores Type Nonembeddability Result.” <i>Israel Journal of Mathematics</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s11856-017-1607-7\">https://doi.org/10.1007/s11856-017-1607-7</a>.","ama":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. <i>Israel Journal of Mathematics</i>. 2017;222(2):841-866. doi:<a href=\"https://doi.org/10.1007/s11856-017-1607-7\">10.1007/s11856-017-1607-7</a>","ieee":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result,” <i>Israel Journal of Mathematics</i>, vol. 222, no. 2. Springer, pp. 841–866, 2017.","short":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, Israel Journal of Mathematics 222 (2017) 841–866.","ista":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2017. On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. 222(2), 841–866.","mla":"Goaoc, Xavier, et al. “On Generalized Heawood Inequalities for Manifolds: A van Kampen–Flores Type Nonembeddability Result.” <i>Israel Journal of Mathematics</i>, vol. 222, no. 2, Springer, 2017, pp. 841–66, doi:<a href=\"https://doi.org/10.1007/s11856-017-1607-7\">10.1007/s11856-017-1607-7</a>.","apa":"Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., &#38; Wagner, U. (2017). On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. <i>Israel Journal of Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s11856-017-1607-7\">https://doi.org/10.1007/s11856-017-1607-7</a>"},"quality_controlled":"1","_id":"610","publist_id":"7194","department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"publisher":"Springer","title":"On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result","author":[{"last_name":"Goaoc","first_name":"Xavier","full_name":"Goaoc, Xavier"},{"full_name":"Mabillard, Isaac","last_name":"Mabillard","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac"},{"last_name":"Paták","first_name":"Pavel","full_name":"Paták, Pavel"},{"full_name":"Patakova, Zuzana","last_name":"Patakova","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana"},{"last_name":"Tancer","orcid":"0000-0002-1191-6714","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Tancer, Martin"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner","full_name":"Wagner, Uli"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication":"Science","doi":"10.1126/science.aao3526","publication_status":"published","oa_version":"None","volume":358,"citation":{"mla":"Bradley, Desmond, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” <i>Science</i>, vol. 358, no. 6365, American Association for the Advancement of Science, 2017, pp. 925–28, doi:<a href=\"https://doi.org/10.1126/science.aao3526\">10.1126/science.aao3526</a>.","apa":"Bradley, D., Xu, P., Mohorianu, I., Whibley, A., Field, D., Tavares, H., … Coen, E. (2017). Evolution of flower color pattern through selection on regulatory small RNAs. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aao3526\">https://doi.org/10.1126/science.aao3526</a>","chicago":"Bradley, Desmond, Ping Xu, Irina Mohorianu, Annabel Whibley, David Field, Hugo Tavares, Matthew Couchman, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aao3526\">https://doi.org/10.1126/science.aao3526</a>.","ama":"Bradley D, Xu P, Mohorianu I, et al. Evolution of flower color pattern through selection on regulatory small RNAs. <i>Science</i>. 2017;358(6365):925-928. doi:<a href=\"https://doi.org/10.1126/science.aao3526\">10.1126/science.aao3526</a>","ista":"Bradley D, Xu P, Mohorianu I, Whibley A, Field D, Tavares H, Couchman M, Copsey L, Carpenter R, Li M, Li Q, Xue Y, Dalmay T, Coen E. 2017. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 358(6365), 925–928.","short":"D. Bradley, P. Xu, I. Mohorianu, A. Whibley, D. Field, H. Tavares, M. Couchman, L. Copsey, R. Carpenter, M. Li, Q. Li, Y. Xue, T. Dalmay, E. Coen, Science 358 (2017) 925–928.","ieee":"D. Bradley <i>et al.</i>, “Evolution of flower color pattern through selection on regulatory small RNAs,” <i>Science</i>, vol. 358, no. 6365. American Association for the Advancement of Science, pp. 925–928, 2017."},"publication_identifier":{"issn":["00368075"]},"scopus_import":1,"abstract":[{"text":"Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity.","lang":"eng"}],"type":"journal_article","date_created":"2018-12-11T11:47:29Z","_id":"611","status":"public","day":"17","quality_controlled":"1","page":"925 - 928","publist_id":"7193","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"year":"2017","date_published":"2017-11-17T00:00:00Z","month":"11","intvolume":"       358","publisher":"American Association for the Advancement of Science","date_updated":"2021-01-12T08:06:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Evolution of flower color pattern through selection on regulatory small RNAs","author":[{"full_name":"Bradley, Desmond","last_name":"Bradley","first_name":"Desmond"},{"full_name":"Xu, Ping","last_name":"Xu","first_name":"Ping"},{"full_name":"Mohorianu, Irina","first_name":"Irina","last_name":"Mohorianu"},{"first_name":"Annabel","last_name":"Whibley","full_name":"Whibley, Annabel"},{"full_name":"Field, David","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","orcid":"0000-0002-4014-8478"},{"full_name":"Tavares, Hugo","last_name":"Tavares","first_name":"Hugo"},{"full_name":"Couchman, Matthew","first_name":"Matthew","last_name":"Couchman"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"first_name":"Rosemary","last_name":"Carpenter","full_name":"Carpenter, Rosemary"},{"first_name":"Miaomiao","last_name":"Li","full_name":"Li, Miaomiao"},{"full_name":"Li, Qun","first_name":"Qun","last_name":"Li"},{"last_name":"Xue","first_name":"Yongbiao","full_name":"Xue, Yongbiao"},{"last_name":"Dalmay","first_name":"Tamas","full_name":"Dalmay, Tamas"},{"last_name":"Coen","first_name":"Enrico","full_name":"Coen, Enrico"}],"issue":"6365"},{"publication":"Nature Communications","doi":"10.1038/s41467-017-01683-1","oa_version":"Published Version","ec_funded":1,"volume":8,"ddc":["576","579"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:47:30Z","status":"public","day":"01","year":"2017","date_published":"2017-12-01T00:00:00Z","month":"12","intvolume":"         8","article_number":"1535","acknowledgement":"We are grateful to M. Lang, H. Janovjak, M. Khammash, A. Milias-Argeitis, M. Rullan, G. Batt, A. Bosma-Moody, Aryan, S. Leibler, and members of the Guet and Tkačik groups for helpful discussion, comments, and suggestions. We thank A. Moglich, T. Mathes, J. Tabor, and S. Schmidl for kind gifts of strains, and R. Hauschild, B. Knep, M. Lang, T. Asenov, E. Papusheva, T. Menner, T. Adletzberger, and J. Merrin for technical assistance. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. (to R.C. and J.R.), Austrian Science Fund grant FWF P28844 (to G.T.), and internal IST Austria Interdisciplinary Project Support. J.R. acknowledges support from the Agence Nationale de la Recherche (ANR) under Grant Nos. ANR-16-CE33-0018 (MEMIP), ANR-16-CE12-0025 (COGEX) and ANR-10-BINF-06-01 (ICEBERG).","date_updated":"2021-01-12T08:06:15Z","oa":1,"issue":"1","project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"}],"publication_status":"published","citation":{"chicago":"Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01683-1\">https://doi.org/10.1038/s41467-017-01683-1</a>.","ista":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. 2017. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 8(1), 1535.","ieee":"R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","short":"R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications 8 (2017).","ama":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population behavior through computer interfaced control of individual cells. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01683-1\">10.1038/s41467-017-01683-1</a>","mla":"Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” <i>Nature Communications</i>, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01683-1\">10.1038/s41467-017-01683-1</a>.","apa":"Chait, R. P., Ruess, J., Bergmiller, T., Tkačik, G., &#38; Guet, C. C. (2017). Shaping bacterial population behavior through computer interfaced control of individual cells. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01683-1\">https://doi.org/10.1038/s41467-017-01683-1</a>"},"publication_identifier":{"issn":["20411723"]},"abstract":[{"text":"Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.","lang":"eng"}],"scopus_import":1,"type":"journal_article","file_date_updated":"2020-07-14T12:47:20Z","_id":"613","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publist_id":"7191","language":[{"iso":"eng"}],"pubrep_id":"911","has_accepted_license":"1","publisher":"Nature Publishing Group","author":[{"orcid":"0000-0003-0876-3187","last_name":"Chait","first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P"},{"full_name":"Ruess, Jakob","first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","orcid":"0000-0003-1615-3282"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Shaping bacterial population behavior through computer interfaced control of individual cells","file":[{"file_name":"IST-2017-911-v1+1_s41467-017-01683-1.pdf","date_created":"2018-12-12T10:16:05Z","date_updated":"2020-07-14T12:47:20Z","content_type":"application/pdf","file_id":"5190","file_size":1951699,"creator":"system","relation":"main_file","access_level":"open_access","checksum":"44bb5d0229926c23a9955d9fe0f9723f"}]},{"project":[{"call_identifier":"FWF","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","citation":{"chicago":"Fraisse, Christelle, Marion A L Picard, and Beatriz Vicoso. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01663-5\">https://doi.org/10.1038/s41467-017-01663-5</a>.","ama":"Fraisse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01663-5\">10.1038/s41467-017-01663-5</a>","ista":"Fraisse C, Picard MAL, Vicoso B. 2017. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. 8(1), 1486.","short":"C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017).","ieee":"C. Fraisse, M. A. L. Picard, and B. Vicoso, “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","mla":"Fraisse, Christelle, et al. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” <i>Nature Communications</i>, vol. 8, no. 1, 1486, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01663-5\">10.1038/s41467-017-01663-5</a>.","apa":"Fraisse, C., Picard, M. A. L., &#38; Vicoso, B. (2017). The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01663-5\">https://doi.org/10.1038/s41467-017-01663-5</a>"},"publication_identifier":{"issn":["20411723"]},"abstract":[{"text":"Moths and butterflies (Lepidoptera) usually have a pair of differentiated WZ sex chromosomes. However, in most lineages outside of the division Ditrysia, as well as in the sister order Trichoptera, females lack a W chromosome. The W is therefore thought to have been acquired secondarily. Here we compare the genomes of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment of a B chromosome). We show that the gene content of the Z is highly conserved across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome fusion). Our comparative genomics analysis therefore supports the secondary acquisition of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme stability of well-differentiated sex chromosomes.","lang":"eng"}],"scopus_import":1,"file_date_updated":"2020-07-14T12:47:20Z","type":"journal_article","_id":"614","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publist_id":"7190","language":[{"iso":"eng"}],"article_type":"original","pubrep_id":"910","has_accepted_license":"1","publisher":"Nature Publishing Group","author":[{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"full_name":"Picard, Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A","orcid":"0000-0002-8101-2518","last_name":"Picard"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"title":"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","checksum":"4da2651303c8afc2f7fc419be42a2433","access_level":"open_access","creator":"dernst","file_size":1201520,"file_id":"7562","content_type":"application/pdf","date_created":"2020-03-03T15:55:50Z","date_updated":"2020-07-14T12:47:20Z","file_name":"2017_NatureComm_Fraisse.pdf"}],"publication":"Nature Communications","doi":"10.1038/s41467-017-01663-5","related_material":{"record":[{"id":"7163","status":"public","relation":"popular_science"}]},"oa_version":"Published Version","volume":8,"pmid":1,"date_created":"2018-12-11T11:47:30Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570","576"],"day":"01","status":"public","external_id":{"pmid":["29133797"]},"year":"2017","date_published":"2017-12-01T00:00:00Z","month":"12","intvolume":"         8","article_number":"1486","date_updated":"2024-02-21T13:47:47Z","oa":1,"issue":"1"},{"project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804"}],"publication_status":"published","_id":"615","quality_controlled":"1","citation":{"chicago":"Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows with Time Dependent Density.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics, 2017. <a href=\"https://doi.org/10.1214/16-AIHP765\">https://doi.org/10.1214/16-AIHP765</a>.","ama":"Erdös L, Schnelli K. Universality for random matrix flows with time dependent density. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. 2017;53(4):1606-1656. doi:<a href=\"https://doi.org/10.1214/16-AIHP765\">10.1214/16-AIHP765</a>","ieee":"L. Erdös and K. Schnelli, “Universality for random matrix flows with time dependent density,” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 53, no. 4. Institute of Mathematical Statistics, pp. 1606–1656, 2017.","short":"L. Erdös, K. Schnelli, Annales de l’institut Henri Poincare (B) Probability and Statistics 53 (2017) 1606–1656.","ista":"Erdös L, Schnelli K. 2017. Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. 53(4), 1606–1656.","mla":"Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows with Time Dependent Density.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 53, no. 4, Institute of Mathematical Statistics, 2017, pp. 1606–56, doi:<a href=\"https://doi.org/10.1214/16-AIHP765\">10.1214/16-AIHP765</a>.","apa":"Erdös, L., &#38; Schnelli, K. (2017). Universality for random matrix flows with time dependent density. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/16-AIHP765\">https://doi.org/10.1214/16-AIHP765</a>"},"publication_identifier":{"issn":["02460203"]},"scopus_import":1,"abstract":[{"lang":"eng","text":"We show that the Dyson Brownian Motion exhibits local universality after a very short time assuming that local rigidity and level repulsion of the eigenvalues hold. These conditions are verified, hence bulk spectral universality is proven, for a large class of Wigner-like matrices, including deformed Wigner ensembles and ensembles with non-stochastic variance matrices whose limiting densities differ from Wigner's semicircle law."}],"type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"LaEr"}],"publist_id":"7189","author":[{"full_name":"Erdös, László","last_name":"Erdös","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"orcid":"0000-0003-0954-3231","last_name":"Schnelli","first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Universality for random matrix flows with time dependent density","publisher":"Institute of Mathematical Statistics","oa_version":"Submitted Version","ec_funded":1,"publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","doi":"10.1214/16-AIHP765","main_file_link":[{"url":"https://arxiv.org/abs/1504.00650","open_access":"1"}],"date_created":"2018-12-11T11:47:30Z","day":"01","status":"public","volume":53,"year":"2017","page":"1606 - 1656","date_updated":"2021-01-12T08:06:22Z","oa":1,"issue":"4","date_published":"2017-11-01T00:00:00Z","intvolume":"        53","month":"11"},{"has_accepted_license":"1","publisher":"Ruhr University Bochum","file":[{"checksum":"f23161d685dd957ae8d7274132999684","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6197","creator":"dernst","file_size":597335,"date_created":"2019-04-04T13:53:58Z","date_updated":"2020-07-14T12:47:24Z","file_name":"2017_IACR_Gazi.pdf"}],"author":[{"last_name":"Gazi","first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","full_name":"Gazi, Peter"},{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","last_name":"Rybar","full_name":"Rybar, Michal"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"The exact security of PMAC","department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"citation":{"apa":"Gazi, P., Pietrzak, K. Z., &#38; Rybar, M. (2017). The exact security of PMAC. <i>IACR Transactions on Symmetric Cryptology</i>. Ruhr University Bochum. <a href=\"https://doi.org/10.13154/TOSC.V2016.I2.145-161\">https://doi.org/10.13154/TOSC.V2016.I2.145-161</a>","mla":"Gazi, Peter, et al. “The Exact Security of PMAC.” <i>IACR Transactions on Symmetric Cryptology</i>, vol. 2016, no. 2, Ruhr University Bochum, 2017, pp. 145–61, doi:<a href=\"https://doi.org/10.13154/TOSC.V2016.I2.145-161\">10.13154/TOSC.V2016.I2.145-161</a>.","ama":"Gazi P, Pietrzak KZ, Rybar M. The exact security of PMAC. <i>IACR Transactions on Symmetric Cryptology</i>. 2017;2016(2):145-161. doi:<a href=\"https://doi.org/10.13154/TOSC.V2016.I2.145-161\">10.13154/TOSC.V2016.I2.145-161</a>","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.","ieee":"P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact security of PMAC,” <i>IACR Transactions on Symmetric Cryptology</i>, vol. 2016, no. 2. Ruhr University Bochum, pp. 145–161, 2017.","chicago":"Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact Security of PMAC.” <i>IACR Transactions on Symmetric Cryptology</i>. Ruhr University Bochum, 2017. <a href=\"https://doi.org/10.13154/TOSC.V2016.I2.145-161\">https://doi.org/10.13154/TOSC.V2016.I2.145-161</a>."},"publication_identifier":{"eissn":["2519-173X"]},"type":"journal_article","file_date_updated":"2020-07-14T12:47:24Z","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"}],"_id":"6196","quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","month":"02","intvolume":"      2016","date_published":"2017-02-03T00:00:00Z","date_updated":"2023-09-07T12:02:27Z","issue":"2","oa":1,"page":"145-161","year":"2017","volume":2016,"ddc":["000"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2019-04-04T13:48:23Z","status":"public","day":"03","doi":"10.13154/TOSC.V2016.I2.145-161","publication":"IACR Transactions on Symmetric Cryptology","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"838"}]},"ec_funded":1,"oa_version":"Published Version"},{"quality_controlled":"1","_id":"621","type":"journal_article","file_date_updated":"2020-07-14T12:47:24Z","scopus_import":"1","abstract":[{"lang":"eng","text":"The mammalian cerebral cortex is responsible for higher cognitive functions such as perception, consciousness, and acquiring and processing information. The neocortex is organized into six distinct laminae, each composed of a rich diversity of cell types which assemble into highly complex cortical circuits. Radial glia progenitors (RGPs) are responsible for producing all neocortical neurons and certain glia lineages. Here, we discuss recent discoveries emerging from clonal lineage analysis at the single RGP cell level that provide us with an inaugural quantitative framework of RGP lineage progression. We further discuss the importance of the relative contribution of intrinsic gene functions and non-cell-autonomous or community effects in regulating RGP proliferation behavior and lineage progression."}],"publication_identifier":{"issn":["00145793"]},"citation":{"mla":"Beattie, Robert J., and Simon Hippenmeyer. “Mechanisms of Radial Glia Progenitor Cell Lineage Progression.” <i>FEBS Letters</i>, vol. 591, no. 24, Wiley-Blackwell, 2017, pp. 3993–4008, doi:<a href=\"https://doi.org/10.1002/1873-3468.12906\">10.1002/1873-3468.12906</a>.","apa":"Beattie, R. J., &#38; Hippenmeyer, S. (2017). Mechanisms of radial glia progenitor cell lineage progression. <i>FEBS Letters</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/1873-3468.12906\">https://doi.org/10.1002/1873-3468.12906</a>","chicago":"Beattie, Robert J, and Simon Hippenmeyer. “Mechanisms of Radial Glia Progenitor Cell Lineage Progression.” <i>FEBS Letters</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1002/1873-3468.12906\">https://doi.org/10.1002/1873-3468.12906</a>.","ieee":"R. J. Beattie and S. Hippenmeyer, “Mechanisms of radial glia progenitor cell lineage progression,” <i>FEBS letters</i>, vol. 591, no. 24. Wiley-Blackwell, pp. 3993–4008, 2017.","short":"R.J. Beattie, S. Hippenmeyer, FEBS Letters 591 (2017) 3993–4008.","ista":"Beattie RJ, Hippenmeyer S. 2017. Mechanisms of radial glia progenitor cell lineage progression. FEBS letters. 591(24), 3993–4008.","ama":"Beattie RJ, Hippenmeyer S. Mechanisms of radial glia progenitor cell lineage progression. <i>FEBS letters</i>. 2017;591(24):3993-4008. doi:<a href=\"https://doi.org/10.1002/1873-3468.12906\">10.1002/1873-3468.12906</a>"},"publication_status":"published","project":[{"_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618444"}],"file":[{"date_created":"2018-12-12T10:16:24Z","date_updated":"2020-07-14T12:47:24Z","file_name":"IST-2018-928-v1+1_Beattie_et_al-2017-FEBS_Letters.pdf","relation":"main_file","access_level":"open_access","checksum":"a46dadc84e0c28d389dd3e9e954464db","file_id":"5211","content_type":"application/pdf","creator":"system","file_size":644149}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753","last_name":"Beattie","first_name":"Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"title":"Mechanisms of radial glia progenitor cell lineage progression","publisher":"Wiley-Blackwell","has_accepted_license":"1","pubrep_id":"928","language":[{"iso":"eng"}],"department":[{"_id":"SiHi"}],"publist_id":"7183","article_processing_charge":"Yes (in subscription journal)","day":"01","status":"public","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"ddc":["571","610"],"date_created":"2018-12-11T11:47:32Z","pmid":1,"volume":591,"ec_funded":1,"oa_version":"Published Version","doi":"10.1002/1873-3468.12906","publication":"FEBS letters","issue":"24","oa":1,"date_updated":"2024-02-14T12:02:08Z","intvolume":"       591","month":"12","date_published":"2017-12-01T00:00:00Z","year":"2017","license":"https://creativecommons.org/licenses/by-nc/4.0/","external_id":{"pmid":["29121403"]},"page":"3993  - 4008"},{"doi":"10.1007/978-3-319-52498-6_9","publication":"Translational Anatomy and Cell Biology of Autism Spectrum Disorder","oa_version":"None","volume":224,"status":"public","day":"28","date_created":"2018-12-11T11:47:33Z","series_title":"Advances in Anatomy Embryology and Cell Biology","page":"159 - 187","year":"2017","month":"05","intvolume":"       224","date_published":"2017-05-28T00:00:00Z","alternative_title":["ADVSANAT"],"date_updated":"2021-01-12T08:06:46Z","publication_status":"published","type":"book_chapter","abstract":[{"text":"Genetic factors might be largely responsible for the development of autism spectrum disorder (ASD) that alone or in combination with specific environmental risk factors trigger the pathology. Multiple mutations identified in ASD patients that impair synaptic function in the central nervous system are well studied in animal models. How these mutations might interact with other risk factors is not fully understood though. Additionally, how systems outside of the brain are altered in the context of ASD is an emerging area of research. Extracerebral influences on the physiology could begin in utero and contribute to changes in the brain and in the development of other body systems and further lead to epigenetic changes. Therefore, multiple recent studies have aimed at elucidating the role of gene-environment interactions in ASD. Here we provide an overview on the extracerebral systems that might play an important associative role in ASD and review evidence regarding the potential roles of inflammation, trace metals, metabolism, genetic susceptibility, enteric nervous system function and the microbiota of the gastrointestinal (GI) tract on the development of endophenotypes in animal models of ASD. By influencing environmental conditions, it might be possible to reduce or limit the severity of ASD pathology.","lang":"eng"}],"scopus_import":1,"citation":{"chicago":"Hill Yardin, Elisa, Sonja Mckeown, Gaia Novarino, and Andreas Grabrucker. “Extracerebral Dysfunction in Animal Models of Autism Spectrum Disorder.” In <i>Translational Anatomy and Cell Biology of Autism Spectrum Disorder</i>, edited by Michael Schmeisser and Tobias Boekers, 224:159–87. Advances in Anatomy Embryology and Cell Biology. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-52498-6_9\">https://doi.org/10.1007/978-3-319-52498-6_9</a>.","short":"E. Hill Yardin, S. Mckeown, G. Novarino, A. Grabrucker, in:, M. Schmeisser, T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder, Springer, 2017, pp. 159–187.","ista":"Hill Yardin E, Mckeown S, Novarino G, Grabrucker A. 2017.Extracerebral dysfunction in animal models of autism spectrum disorder. In: Translational Anatomy and Cell Biology of Autism Spectrum Disorder. ADVSANAT, vol. 224, 159–187.","ieee":"E. Hill Yardin, S. Mckeown, G. Novarino, and A. Grabrucker, “Extracerebral dysfunction in animal models of autism spectrum disorder,” in <i>Translational Anatomy and Cell Biology of Autism Spectrum Disorder</i>, vol. 224, M. Schmeisser and T. Boekers, Eds. Springer, 2017, pp. 159–187.","ama":"Hill Yardin E, Mckeown S, Novarino G, Grabrucker A. Extracerebral dysfunction in animal models of autism spectrum disorder. In: Schmeisser M, Boekers T, eds. <i>Translational Anatomy and Cell Biology of Autism Spectrum Disorder</i>. Vol 224. Advances in Anatomy Embryology and Cell Biology. Springer; 2017:159-187. doi:<a href=\"https://doi.org/10.1007/978-3-319-52498-6_9\">10.1007/978-3-319-52498-6_9</a>","mla":"Hill Yardin, Elisa, et al. “Extracerebral Dysfunction in Animal Models of Autism Spectrum Disorder.” <i>Translational Anatomy and Cell Biology of Autism Spectrum Disorder</i>, edited by Michael Schmeisser and Tobias Boekers, vol. 224, Springer, 2017, pp. 159–87, doi:<a href=\"https://doi.org/10.1007/978-3-319-52498-6_9\">10.1007/978-3-319-52498-6_9</a>.","apa":"Hill Yardin, E., Mckeown, S., Novarino, G., &#38; Grabrucker, A. (2017). Extracerebral dysfunction in animal models of autism spectrum disorder. In M. Schmeisser &#38; T. Boekers (Eds.), <i>Translational Anatomy and Cell Biology of Autism Spectrum Disorder</i> (Vol. 224, pp. 159–187). Springer. <a href=\"https://doi.org/10.1007/978-3-319-52498-6_9\">https://doi.org/10.1007/978-3-319-52498-6_9</a>"},"publication_identifier":{"issn":["03015556"],"isbn":["978-3-319-52496-2"]},"quality_controlled":"1","editor":[{"last_name":"Schmeisser","first_name":"Michael","full_name":"Schmeisser, Michael"},{"last_name":"Boekers","first_name":"Tobias","full_name":"Boekers, Tobias"}],"_id":"623","department":[{"_id":"GaNo"}],"publist_id":"7177","language":[{"iso":"eng"}],"publisher":"Springer","author":[{"last_name":"Hill Yardin","first_name":"Elisa","full_name":"Hill Yardin, Elisa"},{"full_name":"Mckeown, Sonja","first_name":"Sonja","last_name":"Mckeown"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","full_name":"Novarino, Gaia"},{"first_name":"Andreas","last_name":"Grabrucker","full_name":"Grabrucker, Andreas"}],"title":"Extracerebral dysfunction in animal models of autism spectrum disorder","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","day":"21","ddc":["579"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:47:33Z","volume":2017,"oa_version":"Published Version","doi":"10.7717/peerj.3830","publication":"PeerJ","issue":"9","oa":1,"date_updated":"2021-01-12T08:06:48Z","article_number":"3830","acknowledgement":"Austrian Science Fund (FWF): M1697, P22249; Swiss National Science Foundation (SNF): 145706; European Commission;FWF Special Research Program: RNA-REG F43","month":"09","intvolume":"      2017","date_published":"2017-09-21T00:00:00Z","year":"2017","quality_controlled":"1","_id":"624","type":"journal_article","file_date_updated":"2020-07-14T12:47:24Z","scopus_import":1,"abstract":[{"text":"Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in this regulatory pathway is the endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF that is triggered by various stressful conditions. In general, MazF degrades the majority of transcripts by cleaving at ACA sites, which results in the retardation of bacterial growth. Furthermore, MazF can process a small subset of mRNAs and render them leaderless by removing their ribosome binding site. MazF concomitantly modifies ribosomes, making them selective for the translation of leaderless mRNAs. In this study, we employed fluorescent reporter-systems to investigate mazEF expression during stressful conditions, and to infer consequences of the mRNA processing mediated by MazF on gene expression at the single-cell level. Our results suggest that mazEF transcription is maintained at low levels in single cells encountering adverse conditions, such as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as a model for MazF-mediated mRNA processing, we found that MazF activation promotes heterogeneity in the grcA reporter expression, resulting in a subpopulation of cells with increased levels of GrcA reporter protein.","lang":"eng"}],"publication_identifier":{"issn":["21678359"]},"citation":{"apa":"Nikolic, N., Didara, Z., &#38; Moll, I. (2017). MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.3830\">https://doi.org/10.7717/peerj.3830</a>","mla":"Nikolic, Nela, et al. “MazF Activation Promotes Translational Heterogeneity of the GrcA MRNA in Escherichia Coli Populations.” <i>PeerJ</i>, vol. 2017, no. 9, 3830, PeerJ, 2017, doi:<a href=\"https://doi.org/10.7717/peerj.3830\">10.7717/peerj.3830</a>.","ieee":"N. Nikolic, Z. Didara, and I. Moll, “MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations,” <i>PeerJ</i>, vol. 2017, no. 9. PeerJ, 2017.","short":"N. Nikolic, Z. Didara, I. Moll, PeerJ 2017 (2017).","ista":"Nikolic N, Didara Z, Moll I. 2017. MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ. 2017(9), 3830.","ama":"Nikolic N, Didara Z, Moll I. MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. <i>PeerJ</i>. 2017;2017(9). doi:<a href=\"https://doi.org/10.7717/peerj.3830\">10.7717/peerj.3830</a>","chicago":"Nikolic, Nela, Zrinka Didara, and Isabella Moll. “MazF Activation Promotes Translational Heterogeneity of the GrcA MRNA in Escherichia Coli Populations.” <i>PeerJ</i>. PeerJ, 2017. <a href=\"https://doi.org/10.7717/peerj.3830\">https://doi.org/10.7717/peerj.3830</a>."},"publication_status":"published","file":[{"date_updated":"2020-07-14T12:47:24Z","date_created":"2018-12-12T10:11:51Z","file_name":"IST-2017-909-v1+1_peerj-3830.pdf","access_level":"open_access","relation":"main_file","checksum":"3d79ae6b6eabc90b0eaaed82ff3493b0","file_size":682064,"creator":"system","file_id":"4908","content_type":"application/pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","orcid":"0000-0001-9068-6090","last_name":"Nikolic","full_name":"Nikolic, Nela"},{"full_name":"Didara, Zrinka","first_name":"Zrinka","last_name":"Didara"},{"last_name":"Moll","first_name":"Isabella","full_name":"Moll, Isabella"}],"title":"MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations","publisher":"PeerJ","has_accepted_license":"1","pubrep_id":"909","language":[{"iso":"eng"}],"publist_id":"7172","department":[{"_id":"CaGu"}]},{"publication_status":"published","project":[{"name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"quality_controlled":"1","_id":"625","editor":[{"full_name":"Aceto, Luca","first_name":"Luca","last_name":"Aceto"},{"full_name":"Bacci, Giorgio","first_name":"Giorgio","last_name":"Bacci"},{"last_name":"Ingólfsdóttir","first_name":"Anna","full_name":"Ingólfsdóttir, Anna"},{"first_name":"Axel","last_name":"Legay","full_name":"Legay, Axel"},{"first_name":"Radu","last_name":"Mardare","full_name":"Mardare, Radu"}],"abstract":[{"text":"In the analysis of reactive systems a quantitative objective assigns a real value to every trace of the system. The value decision problem for a quantitative objective requires a trace whose value is at least a given threshold, and the exact value decision problem requires a trace whose value is exactly the threshold. We compare the computational complexity of the value and exact value decision problems for classical quantitative objectives, such as sum, discounted sum, energy, and mean-payoff for two standard models of reactive systems, namely, graphs and graph games.","lang":"eng"}],"scopus_import":"1","file_date_updated":"2020-07-14T12:47:25Z","type":"book_chapter","publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-319-63120-2"]},"citation":{"apa":"Chatterjee, K., Doyen, L., &#38; Henzinger, T. A. (2017). The cost of exactness in quantitative reachability. In L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, &#38; R. Mardare (Eds.), <i>Models, Algorithms, Logics and Tools</i> (Vol. 10460, pp. 367–381). Springer. <a href=\"https://doi.org/10.1007/978-3-319-63121-9_18\">https://doi.org/10.1007/978-3-319-63121-9_18</a>","mla":"Chatterjee, Krishnendu, et al. “The Cost of Exactness in Quantitative Reachability.” <i>Models, Algorithms, Logics and Tools</i>, edited by Luca Aceto et al., vol. 10460, Springer, 2017, pp. 367–81, doi:<a href=\"https://doi.org/10.1007/978-3-319-63121-9_18\">10.1007/978-3-319-63121-9_18</a>.","ama":"Chatterjee K, Doyen L, Henzinger TA. The cost of exactness in quantitative reachability. In: Aceto L, Bacci G, Ingólfsdóttir A, Legay A, Mardare R, eds. <i>Models, Algorithms, Logics and Tools</i>. Vol 10460. Theoretical Computer Science and General Issues. Springer; 2017:367-381. doi:<a href=\"https://doi.org/10.1007/978-3-319-63121-9_18\">10.1007/978-3-319-63121-9_18</a>","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “The cost of exactness in quantitative reachability,” in <i>Models, Algorithms, Logics and Tools</i>, vol. 10460, L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, and R. Mardare, Eds. Springer, 2017, pp. 367–381.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, in:, L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, R. Mardare (Eds.), Models, Algorithms, Logics and Tools, Springer, 2017, pp. 367–381.","ista":"Chatterjee K, Doyen L, Henzinger TA. 2017.The cost of exactness in quantitative reachability. In: Models, Algorithms, Logics and Tools. LNCS, vol. 10460, 367–381.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “The Cost of Exactness in Quantitative Reachability.” In <i>Models, Algorithms, Logics and Tools</i>, edited by Luca Aceto, Giorgio Bacci, Anna Ingólfsdóttir, Axel Legay, and Radu Mardare, 10460:367–81. Theoretical Computer Science and General Issues. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-63121-9_18\">https://doi.org/10.1007/978-3-319-63121-9_18</a>."},"language":[{"iso":"eng"}],"publist_id":"7170","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"article_processing_charge":"No","title":"The cost of exactness in quantitative reachability","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"file":[{"file_name":"2017_ModelsAlgorithms_Chatterjee.pdf","date_created":"2019-11-19T08:06:50Z","date_updated":"2020-07-14T12:47:25Z","file_id":"7048","content_type":"application/pdf","creator":"dernst","file_size":192826,"relation":"main_file","access_level":"open_access","checksum":"b2402766ec02c79801aac634bd8f9f6c"}],"publisher":"Springer","has_accepted_license":"1","oa_version":"Submitted Version","ec_funded":1,"publication":"Models, Algorithms, Logics and Tools","doi":"10.1007/978-3-319-63121-9_18","status":"public","day":"25","date_created":"2018-12-11T11:47:34Z","ddc":["000"],"volume":10460,"year":"2017","page":"367 - 381","series_title":"Theoretical Computer Science and General Issues","oa":1,"date_updated":"2025-06-02T08:53:45Z","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 and S11407-N23 (RiSE/SHiNE), and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003.","date_published":"2017-07-25T00:00:00Z","alternative_title":["LNCS"],"intvolume":"     10460","month":"07"}]