[{"publication_status":"published","language":[{"iso":"eng"}],"_id":"571","project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"747687"}],"department":[{"_id":"MiSi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"}],"ec_funded":1,"publication_identifier":{"issn":["00928674"]},"scopus_import":1,"type":"journal_article","year":"2017","publist_id":"7243","doi":"10.1016/j.cell.2017.11.001","oa_version":"None","issue":"6","publisher":"Cell Press","page":"1368 - 1382","quality_controlled":"1","intvolume":"       171","publication":"Cell Press","title":"Migrating platelets are mechano scavengers that collect and bundle bacteria","status":"public","author":[{"orcid":"0000-0001-6120-3723","last_name":"Gärtner","first_name":"Florian R","full_name":"Gärtner, Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ahmad","first_name":"Zerkah","full_name":"Ahmad, Zerkah"},{"first_name":"Gerhild","last_name":"Rosenberger","full_name":"Rosenberger, Gerhild"},{"first_name":"Shuxia","last_name":"Fan","full_name":"Fan, Shuxia"},{"last_name":"Nicolai","first_name":"Leo","full_name":"Nicolai, Leo"},{"full_name":"Busch, Benjamin","first_name":"Benjamin","last_name":"Busch"},{"first_name":"Gökce","last_name":"Yavuz","full_name":"Yavuz, Gökce"},{"full_name":"Luckner, Manja","first_name":"Manja","last_name":"Luckner"},{"last_name":"Ishikawa Ankerhold","first_name":"Hellen","full_name":"Ishikawa Ankerhold, Hellen"},{"first_name":"Roman","last_name":"Hennel","full_name":"Hennel, Roman"},{"first_name":"Alexandre","last_name":"Benechet","full_name":"Benechet, Alexandre"},{"full_name":"Lorenz, Michael","first_name":"Michael","last_name":"Lorenz"},{"last_name":"Chandraratne","first_name":"Sue","full_name":"Chandraratne, Sue"},{"full_name":"Schubert, Irene","first_name":"Irene","last_name":"Schubert"},{"last_name":"Helmer","first_name":"Sebastian","full_name":"Helmer, Sebastian"},{"full_name":"Striednig, Bianca","first_name":"Bianca","last_name":"Striednig"},{"first_name":"Konstantin","last_name":"Stark","full_name":"Stark, Konstantin"},{"last_name":"Janko","first_name":"Marek","full_name":"Janko, Marek"},{"full_name":"Böttcher, Ralph","last_name":"Böttcher","first_name":"Ralph"},{"first_name":"Admar","last_name":"Verschoor","full_name":"Verschoor, Admar"},{"full_name":"Leon, Catherine","first_name":"Catherine","last_name":"Leon"},{"last_name":"Gachet","first_name":"Christian","full_name":"Gachet, Christian"},{"full_name":"Gudermann, Thomas","last_name":"Gudermann","first_name":"Thomas"},{"last_name":"Mederos Y Schnitzler","first_name":"Michael","full_name":"Mederos Y Schnitzler, Michael"},{"full_name":"Pincus, Zachary","last_name":"Pincus","first_name":"Zachary"},{"first_name":"Matteo","last_name":"Iannacone","full_name":"Iannacone, Matteo"},{"last_name":"Haas","first_name":"Rainer","full_name":"Haas, Rainer"},{"first_name":"Gerhard","last_name":"Wanner","full_name":"Wanner, Gerhard"},{"full_name":"Lauber, Kirsten","first_name":"Kirsten","last_name":"Lauber"},{"orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"last_name":"Massberg","first_name":"Steffen","full_name":"Massberg, Steffen"}],"citation":{"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.","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>","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.","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>.","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>.","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.","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>"},"day":"30","date_updated":"2021-01-12T08:03:15Z","volume":171,"date_created":"2018-12-11T11:47:15Z","date_published":"2017-11-30T00:00:00Z","month":"11"},{"publication_status":"published","ddc":["580"],"_id":"572","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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"}],"file_date_updated":"2020-07-14T12:47:10Z","article_processing_charge":"No","scopus_import":"1","year":"2017","type":"journal_article","pubrep_id":"917","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publist_id":"7242","doi":"10.3390/ijms18122587","oa_version":"Published Version","issue":"12","publisher":"MDPI","quality_controlled":"1","intvolume":"        18","publication":"International Journal of Molecular Sciences","article_number":"2587","title":"Control of endogenous auxin levels in plant root development","status":"public","oa":1,"author":[{"last_name":"Olatunji","first_name":"Damilola","full_name":"Olatunji, Damilola"},{"full_name":"Geelen, Danny","last_name":"Geelen","first_name":"Danny"},{"orcid":"0000-0001-7241-2328","last_name":"Verstraeten","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge"}],"file":[{"creator":"system","relation":"main_file","file_id":"4718","file_size":920962,"date_created":"2018-12-12T10:08:55Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:10Z","file_name":"IST-2017-917-v1+1_ijms-18-02587.pdf","checksum":"82d51f11e493f7eec02976d9a9a9805e"}],"day":"01","citation":{"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.","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>.","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>.","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>","short":"D. Olatunji, D. Geelen, I. Verstraeten, International Journal of Molecular Sciences 18 (2017).","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."},"date_updated":"2021-01-12T08:03:16Z","has_accepted_license":"1","volume":18,"date_published":"2017-12-01T00:00:00Z","date_created":"2018-12-11T11:47:15Z","month":"12"},{"citation":{"mla":"Biswas, Ranita, et al. “On the Polyhedra of Graceful Spheres and Circular Geodesics.” <i>Discrete Applied Mathematics</i>, vol. 216, Elsevier, 2017, pp. 362–75, doi:<a href=\"https://doi.org/10.1016/j.dam.2015.11.017\">10.1016/j.dam.2015.11.017</a>.","ista":"Biswas R, Bhowmick P, Brimkov VE. 2017. On the polyhedra of graceful spheres and circular geodesics. Discrete Applied Mathematics. 216, 362–375.","ama":"Biswas R, Bhowmick P, Brimkov VE. On the polyhedra of graceful spheres and circular geodesics. <i>Discrete Applied Mathematics</i>. 2017;216:362-375. doi:<a href=\"https://doi.org/10.1016/j.dam.2015.11.017\">10.1016/j.dam.2015.11.017</a>","chicago":"Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Polyhedra of Graceful Spheres and Circular Geodesics.” <i>Discrete Applied Mathematics</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.dam.2015.11.017\">https://doi.org/10.1016/j.dam.2015.11.017</a>.","ieee":"R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the polyhedra of graceful spheres and circular geodesics,” <i>Discrete Applied Mathematics</i>, vol. 216. Elsevier, pp. 362–375, 2017.","short":"R. Biswas, P. Bhowmick, V.E. Brimkov, Discrete Applied Mathematics 216 (2017) 362–375.","apa":"Biswas, R., Bhowmick, P., &#38; Brimkov, V. E. (2017). On the polyhedra of graceful spheres and circular geodesics. <i>Discrete Applied Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.dam.2015.11.017\">https://doi.org/10.1016/j.dam.2015.11.017</a>"},"day":"10","date_updated":"2021-01-12T08:03:33Z","year":"2017","type":"journal_article","date_published":"2017-01-10T00:00:00Z","date_created":"2019-01-08T20:41:12Z","oa_version":"None","month":"01","doi":"10.1016/j.dam.2015.11.017","volume":216,"page":"362-375","quality_controlled":"1","publisher":"Elsevier","publication":"Discrete Applied Mathematics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       216","language":[{"iso":"eng"}],"_id":"5799","publication_status":"published","publication_identifier":{"issn":["0166-218X"]},"author":[{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890","first_name":"Ranita"},{"full_name":"Bhowmick, Partha","last_name":"Bhowmick","first_name":"Partha"},{"full_name":"Brimkov, Valentin E.","last_name":"Brimkov","first_name":"Valentin E."}],"title":"On the polyhedra of graceful spheres and circular geodesics","abstract":[{"lang":"eng","text":"We construct a polyhedral surface called a graceful surface, which provides best possible approximation to a given sphere regarding certain criteria. In digital geometry terms, the graceful surface is uniquely characterized by its minimality while guaranteeing the connectivity of certain discrete (polyhedral) curves defined on it. The notion of “gracefulness” was first proposed in Brimkov and Barneva (1999) and shown to be useful for triangular mesh discretization through graceful planes and graceful lines. In this paper we extend the considerations to a nonlinear object such as a sphere. In particular, we investigate the properties of a discrete geodesic path between two voxels and show that discrete 3D circles, circular arcs, and Mobius triangles are all constructible on a graceful sphere, with guaranteed minimum thickness and the desired connectivity in the discrete topological space."}],"extern":"1","status":"public"},{"oa_version":"None","date_published":"2017-09-01T00:00:00Z","date_created":"2019-01-08T20:42:08Z","month":"09","volume":59,"doi":"10.1007/s10851-017-0718-4","day":"01","citation":{"apa":"Biswas, R., &#38; Bhowmick, P. (2017). On the functionality and usefulness of Quadraginta octants of naive sphere. <i>Journal of Mathematical Imaging and Vision</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10851-017-0718-4\">https://doi.org/10.1007/s10851-017-0718-4</a>","short":"R. Biswas, P. Bhowmick, Journal of Mathematical Imaging and Vision 59 (2017) 69–83.","ieee":"R. Biswas and P. Bhowmick, “On the functionality and usefulness of Quadraginta octants of naive sphere,” <i>Journal of Mathematical Imaging and Vision</i>, vol. 59, no. 1. Springer Nature, pp. 69–83, 2017.","ama":"Biswas R, Bhowmick P. On the functionality and usefulness of Quadraginta octants of naive sphere. <i>Journal of Mathematical Imaging and Vision</i>. 2017;59(1):69-83. doi:<a href=\"https://doi.org/10.1007/s10851-017-0718-4\">10.1007/s10851-017-0718-4</a>","ista":"Biswas R, Bhowmick P. 2017. On the functionality and usefulness of Quadraginta octants of naive sphere. Journal of Mathematical Imaging and Vision. 59(1), 69–83.","mla":"Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness of Quadraginta Octants of Naive Sphere.” <i>Journal of Mathematical Imaging and Vision</i>, vol. 59, no. 1, Springer Nature, 2017, pp. 69–83, doi:<a href=\"https://doi.org/10.1007/s10851-017-0718-4\">10.1007/s10851-017-0718-4</a>.","chicago":"Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness of Quadraginta Octants of Naive Sphere.” <i>Journal of Mathematical Imaging and Vision</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1007/s10851-017-0718-4\">https://doi.org/10.1007/s10851-017-0718-4</a>."},"date_updated":"2021-01-12T08:03:34Z","type":"journal_article","year":"2017","publication_identifier":{"issn":["09249907"]},"author":[{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890"},{"last_name":"Bhowmick","first_name":"Partha","full_name":"Bhowmick, Partha"}],"extern":"1","title":"On the functionality and usefulness of Quadraginta octants of naive sphere","abstract":[{"lang":"eng","text":"This paper presents a novel study on the functional gradation of coordinate planes in connection with the thinnest and tunnel-free (i.e., naive) discretization of sphere in the integer space. For each of the 48-symmetric quadraginta octants of naive sphere with integer radius and integer center, we show that the corresponding voxel set forms a bijection with its projected pixel set on a unique coordinate plane, which thereby serves as its functional plane. We use this fundamental property to prove several other theoretical results for naive sphere. First, the quadraginta octants form symmetry groups and subgroups with certain equivalent topological properties. Second, a naive sphere is always unique and consists of fewest voxels. Third, it is efficiently constructible from its functional-plane projection. And finally, a special class of 4-symmetric discrete 3D circles can be constructed on a naive sphere based on back projection from the functional plane."}],"status":"public","publisher":"Springer Nature","quality_controlled":"1","page":"69-83","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        59","publication":"Journal of Mathematical Imaging and Vision","issue":"1","publication_status":"published","language":[{"iso":"eng"}],"_id":"5800"},{"publisher":"Springer Nature","quality_controlled":"1","page":"347-359","intvolume":"     10502","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication":"20th IAPR International Conference","publication_status":"published","language":[{"iso":"eng"}],"_id":"5801","publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-319-66272-5"],"isbn":["978-3-319-66271-8"],"eissn":["1611-3349"]},"article_processing_charge":"No","alternative_title":["LNCS"],"author":[{"full_name":"Dwivedi, Shivam","last_name":"Dwivedi","first_name":"Shivam"},{"last_name":"Gupta","first_name":"Aniket","full_name":"Gupta, Aniket"},{"full_name":"Roy, Siddhant","first_name":"Siddhant","last_name":"Roy"},{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890"},{"full_name":"Bhowmick, Partha","last_name":"Bhowmick","first_name":"Partha"}],"extern":"1","abstract":[{"text":"Space filling circles and spheres have various applications in mathematical imaging and physical modeling. In this paper, we first show how the thinnest (i.e., 2-minimal) model of digital sphere can be augmented to a space filling model by fixing certain “simple voxels” and “filler voxels” associated with it. Based on elementary number-theoretic properties of such voxels, we design an efficient incremental algorithm for generation of these space filling spheres with successively increasing radius. The novelty of the proposed technique is established further through circular space filling on 3D digital plane. As evident from a preliminary set of experimental result, this can particularly be useful for parallel computing of 3D Voronoi diagrams in the digital space.","lang":"eng"}],"title":"Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space","status":"public","day":"22","citation":{"ieee":"S. Dwivedi, A. Gupta, S. Roy, R. Biswas, and P. Bhowmick, “Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space,” in <i>20th IAPR International Conference</i>, Vienna, Austria, 2017, vol. 10502, pp. 347–359.","short":"S. Dwivedi, A. Gupta, S. Roy, R. Biswas, P. Bhowmick, in:, 20th IAPR International Conference, Springer Nature, Cham, 2017, pp. 347–359.","apa":"Dwivedi, S., Gupta, A., Roy, S., Biswas, R., &#38; Bhowmick, P. (2017). Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space. In <i>20th IAPR International Conference</i> (Vol. 10502, pp. 347–359). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-66272-5_28\">https://doi.org/10.1007/978-3-319-66272-5_28</a>","chicago":"Dwivedi, Shivam, Aniket Gupta, Siddhant Roy, Ranita Biswas, and Partha Bhowmick. “Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space.” In <i>20th IAPR International Conference</i>, 10502:347–59. Cham: Springer Nature, 2017. <a href=\"https://doi.org/10.1007/978-3-319-66272-5_28\">https://doi.org/10.1007/978-3-319-66272-5_28</a>.","mla":"Dwivedi, Shivam, et al. “Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space.” <i>20th IAPR International Conference</i>, vol. 10502, Springer Nature, 2017, pp. 347–59, doi:<a href=\"https://doi.org/10.1007/978-3-319-66272-5_28\">10.1007/978-3-319-66272-5_28</a>.","ama":"Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space. In: <i>20th IAPR International Conference</i>. Vol 10502. Cham: Springer Nature; 2017:347-359. doi:<a href=\"https://doi.org/10.1007/978-3-319-66272-5_28\">10.1007/978-3-319-66272-5_28</a>","ista":"Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. 2017. Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space. 20th IAPR International Conference. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 10502, 347–359."},"date_updated":"2022-01-27T15:34:25Z","type":"conference","year":"2017","conference":{"end_date":"2017-09-21","location":"Vienna, Austria","start_date":"2017-09-19","name":"DGCI: International Conference on Discrete Geometry for Computer Imagery"},"oa_version":"None","date_published":"2017-08-22T00:00:00Z","date_created":"2019-01-08T20:42:22Z","month":"08","volume":10502,"doi":"10.1007/978-3-319-66272-5_28","place":"Cham"},{"year":"2017","type":"conference","conference":{"start_date":"2017-09-19","location":"Vienna, Austria","end_date":"2017-09-21","name":"DGCI: International Conference on Discrete Geometry for Computer Imagery"},"day":"22","citation":{"chicago":"Andres, Eric, Ranita Biswas, and Partha Bhowmick. “Digital Primitives Defined by Weighted Focal Set.” In <i>20th IAPR International Conference</i>, 10502:388–98. Cham: Springer Nature, 2017. <a href=\"https://doi.org/10.1007/978-3-319-66272-5_31\">https://doi.org/10.1007/978-3-319-66272-5_31</a>.","ama":"Andres E, Biswas R, Bhowmick P. Digital primitives defined by weighted focal set. In: <i>20th IAPR International Conference</i>. Vol 10502. Cham: Springer Nature; 2017:388-398. doi:<a href=\"https://doi.org/10.1007/978-3-319-66272-5_31\">10.1007/978-3-319-66272-5_31</a>","ista":"Andres E, Biswas R, Bhowmick P. 2017. Digital primitives defined by weighted focal set. 20th IAPR International Conference. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 10502, 388–398.","mla":"Andres, Eric, et al. “Digital Primitives Defined by Weighted Focal Set.” <i>20th IAPR International Conference</i>, vol. 10502, Springer Nature, 2017, pp. 388–98, doi:<a href=\"https://doi.org/10.1007/978-3-319-66272-5_31\">10.1007/978-3-319-66272-5_31</a>.","apa":"Andres, E., Biswas, R., &#38; Bhowmick, P. (2017). Digital primitives defined by weighted focal set. In <i>20th IAPR International Conference</i> (Vol. 10502, pp. 388–398). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-66272-5_31\">https://doi.org/10.1007/978-3-319-66272-5_31</a>","short":"E. Andres, R. Biswas, P. Bhowmick, in:, 20th IAPR International Conference, Springer Nature, Cham, 2017, pp. 388–398.","ieee":"E. Andres, R. Biswas, and P. Bhowmick, “Digital primitives defined by weighted focal set,” in <i>20th IAPR International Conference</i>, Vienna, Austria, 2017, vol. 10502, pp. 388–398."},"date_updated":"2022-01-27T15:38:35Z","volume":10502,"doi":"10.1007/978-3-319-66272-5_31","place":"Cham","oa_version":"None","date_created":"2019-01-08T20:42:39Z","date_published":"2017-08-22T00:00:00Z","month":"08","publication_status":"published","language":[{"iso":"eng"}],"_id":"5802","publisher":"Springer Nature","page":"388-398","quality_controlled":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"     10502","publication":"20th IAPR International Conference","extern":"1","title":"Digital primitives defined by weighted focal set","abstract":[{"lang":"eng","text":"This papers introduces a definition of digital primitives based on focal points and weighted distances (with positive weights). The proposed definition is applicable to general dimensions and covers in its gamut various regular curves and surfaces like circles, ellipses, digital spheres and hyperspheres, ellipsoids and k-ellipsoids, Cartesian k-ovals, etc. Several interesting properties are presented for this class of digital primitives such as space partitioning, topological separation, and connectivity properties. To demonstrate further the potential of this new way of defining digital primitives, we propose, as extension, another class of digital conics defined by focus-directrix combination."}],"status":"public","publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-319-66272-5"],"isbn":["978-3-319-66271-8"],"eissn":["1611-3349"]},"article_processing_charge":"No","author":[{"first_name":"Eric","last_name":"Andres","full_name":"Andres, Eric"},{"first_name":"Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita"},{"last_name":"Bhowmick","first_name":"Partha","full_name":"Bhowmick, Partha"}],"alternative_title":["LNCS"]},{"conference":{"name":"IWCIA: International Workshop on Combinatorial Image Analysis","end_date":"2017-06-21","location":"Plovdiv, Bulgaria","start_date":"2017-06-19"},"date_updated":"2022-01-28T07:48:24Z","citation":{"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.","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>","short":"R. Biswas, P. Bhowmick, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2017, pp. 93–104.","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>.","ista":"Biswas R, Bhowmick P. 2017.Construction of persistent Voronoi diagram on 3D digital plane. In: Combinatorial image analysis. LNCS, vol. 10256, 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>."},"day":"17","volume":10256,"place":"Cham","month":"05","date_published":"2017-05-17T00:00:00Z","date_created":"2019-01-08T20:42:56Z","intvolume":"     10256","publication":"Combinatorial image analysis","publisher":"Springer Nature","page":"93-104","quality_controlled":"1","status":"public","title":"Construction of persistent Voronoi diagram on 3D digital plane","author":[{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita","first_name":"Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890"},{"last_name":"Bhowmick","first_name":"Partha","full_name":"Bhowmick, Partha"}],"year":"2017","type":"book_chapter","doi":"10.1007/978-3-319-59108-7_8","oa_version":"None","publication_status":"published","language":[{"iso":"eng"}],"_id":"5803","department":[{"_id":"HeEd"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","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."}],"alternative_title":["LNCS"],"article_processing_charge":"No","publication_identifier":{"issn":["0302-9743","1611-3349"],"isbn":["978-3-319-59107-0","978-3-319-59108-7"]}},{"status":"public","title":"Bell correlations in spin-squeezed states of 500 000 atoms","abstract":[{"lang":"eng","text":"Bell correlations, indicating nonlocality in composite quantum systems, were until recently only seen in small systems. Here, we demonstrate Bell correlations in squeezed states of 5×105 Rb87 atoms. The correlations are inferred using collective measurements as witnesses and are statistically significant to 124 standard deviations. The states are both generated and characterized using optical-cavity aided measurements."}],"extern":"1","author":[{"full_name":"Engelsen, Nils","first_name":"Nils","last_name":"Engelsen"},{"full_name":"Krishnakumar, Rajiv","last_name":"Krishnakumar","first_name":"Rajiv"},{"orcid":"0000-0002-2031-204X","last_name":"Hosten","first_name":"Onur","full_name":"Hosten, Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kasevich","first_name":"Mark","full_name":"Kasevich, Mark"}],"language":[{"iso":"eng"}],"_id":"593","publication_status":"published","issue":"14","publication":"Physical Review Letters","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":"       118","publisher":"American Physical Society","publist_id":"7212","doi":"10.1103/PhysRevLett.118.140401","volume":118,"month":"04","date_published":"2017-04-03T00:00:00Z","date_created":"2018-12-11T11:47:23Z","oa_version":"None","year":"2017","type":"journal_article","date_updated":"2021-01-12T08:05:16Z","citation":{"chicago":"Engelsen, Nils, Rajiv Krishnakumar, Onur Hosten, and Mark Kasevich. “Bell Correlations in Spin-Squeezed States of 500 000 Atoms.” <i>Physical Review Letters</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevLett.118.140401\">https://doi.org/10.1103/PhysRevLett.118.140401</a>.","mla":"Engelsen, Nils, et al. “Bell Correlations in Spin-Squeezed States of 500 000 Atoms.” <i>Physical Review Letters</i>, vol. 118, no. 14, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.118.140401\">10.1103/PhysRevLett.118.140401</a>.","ista":"Engelsen N, Krishnakumar R, Hosten O, Kasevich M. 2017. Bell correlations in spin-squeezed states of 500 000 atoms. Physical Review Letters. 118(14).","ama":"Engelsen N, Krishnakumar R, Hosten O, Kasevich M. Bell correlations in spin-squeezed states of 500 000 atoms. <i>Physical Review Letters</i>. 2017;118(14). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.118.140401\">10.1103/PhysRevLett.118.140401</a>","ieee":"N. Engelsen, R. Krishnakumar, O. Hosten, and M. Kasevich, “Bell correlations in spin-squeezed states of 500 000 atoms,” <i>Physical Review Letters</i>, vol. 118, no. 14. American Physical Society, 2017.","short":"N. Engelsen, R. Krishnakumar, O. Hosten, M. Kasevich, Physical Review Letters 118 (2017).","apa":"Engelsen, N., Krishnakumar, R., Hosten, O., &#38; Kasevich, M. (2017). Bell correlations in spin-squeezed states of 500 000 atoms. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.118.140401\">https://doi.org/10.1103/PhysRevLett.118.140401</a>"},"day":"03"},{"date_published":"2017-03-23T00:00:00Z","date_created":"2018-12-11T11:47:25Z","oa_version":"None","month":"03","doi":"10.1016/j.cell.2017.03.003","publist_id":"7204","volume":169,"citation":{"ieee":"C. Engel <i>et al.</i>, “Structural basis of RNA polymerase I transcription initiation,” <i>Cell</i>, vol. 169, no. 1. Cell Press, p. 120–131.e22, 2017.","short":"C. Engel, T. Gubbey, S. Neyer, S. Sainsbury, C. Oberthuer, C. Baejen, C. Bernecky, P. Cramer, Cell 169 (2017) 120–131.e22.","apa":"Engel, C., Gubbey, T., Neyer, S., Sainsbury, S., Oberthuer, C., Baejen, C., … Cramer, P. (2017). Structural basis of RNA polymerase I transcription initiation. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2017.03.003\">https://doi.org/10.1016/j.cell.2017.03.003</a>","chicago":"Engel, Christoph, Tobias Gubbey, Simon Neyer, Sarah Sainsbury, Christiane Oberthuer, Carlo Baejen, Carrie Bernecky, and Patrick Cramer. “Structural Basis of RNA Polymerase I Transcription Initiation.” <i>Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cell.2017.03.003\">https://doi.org/10.1016/j.cell.2017.03.003</a>.","mla":"Engel, Christoph, et al. “Structural Basis of RNA Polymerase I Transcription Initiation.” <i>Cell</i>, vol. 169, no. 1, Cell Press, 2017, p. 120–131.e22, doi:<a href=\"https://doi.org/10.1016/j.cell.2017.03.003\">10.1016/j.cell.2017.03.003</a>.","ama":"Engel C, Gubbey T, Neyer S, et al. Structural basis of RNA polymerase I transcription initiation. <i>Cell</i>. 2017;169(1):120-131.e22. doi:<a href=\"https://doi.org/10.1016/j.cell.2017.03.003\">10.1016/j.cell.2017.03.003</a>","ista":"Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky C, Cramer P. 2017. Structural basis of RNA polymerase I transcription initiation. Cell. 169(1), 120–131.e22."},"day":"23","date_updated":"2021-01-12T08:05:36Z","type":"journal_article","year":"2017","publication_identifier":{"issn":["00928674"]},"author":[{"last_name":"Engel","first_name":"Christoph","full_name":"Engel, Christoph"},{"last_name":"Gubbey","first_name":"Tobias","full_name":"Gubbey, Tobias"},{"first_name":"Simon","last_name":"Neyer","full_name":"Neyer, Simon"},{"full_name":"Sainsbury, Sarah","first_name":"Sarah","last_name":"Sainsbury"},{"last_name":"Oberthuer","first_name":"Christiane","full_name":"Oberthuer, Christiane"},{"last_name":"Baejen","first_name":"Carlo","full_name":"Baejen, Carlo"},{"last_name":"Bernecky","orcid":"0000-0003-0893-7036","first_name":"Carrie A","full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cramer, Patrick","first_name":"Patrick","last_name":"Cramer"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for basal Pol I initiation. The three-subunit CF binds upstream promoter DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp domains enables cleft contraction, resulting in an active Pol I conformation and RNA synthesis. Comparison with the Pol II system suggests that promoter specificity relies on a distinct “bendability” and “meltability” of the promoter sequence that enables contacts between initiation factors, DNA, and polymerase."}],"title":"Structural basis of RNA polymerase I transcription initiation","extern":"1","status":"public","quality_controlled":"1","page":"120 - 131.e22","publisher":"Cell Press","publication":"Cell","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       169","issue":"1","_id":"600","language":[{"iso":"eng"}],"publication_status":"published"},{"oa_version":"Published Version","publist_id":"7203","doi":"10.1038/ncomms15741","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2017","type":"journal_article","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:16Z","publication_identifier":{"issn":["20411723"]},"abstract":[{"lang":"eng","text":"The conserved polymerase-Associated factor 1 complex (Paf1C) plays multiple roles in chromatin transcription and genomic regulation. Paf1C comprises the five subunits Paf1, Leo1, Ctr9, Cdc73 and Rtf1, and binds to the RNA polymerase II (Pol II) transcription elongation complex (EC). Here we report the reconstitution of Paf1C from Saccharomyces cerevisiae, and a structural analysis of Paf1C bound to a Pol II EC containing the elongation factor TFIIS. Cryo-electron microscopy and crosslinking data reveal that Paf1C is highly mobile and extends over the outer Pol II surface from the Rpb2 to the Rpb3 subunit. The Paf1-Leo1 heterodimer and Cdc73 form opposite ends of Paf1C, whereas Ctr9 bridges between them. Consistent with the structural observations, the initiation factor TFIIF impairs Paf1C binding to Pol II, whereas the elongation factor TFIIS enhances it. We further show that Paf1C is globally required for normal mRNA transcription in yeast. These results provide a three-dimensional framework for further analysis of Paf1C function in transcription through chromatin. "}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"_id":"601","publication_status":"published","ddc":["570"],"month":"06","date_published":"2017-06-06T00:00:00Z","date_created":"2018-12-11T11:47:25Z","volume":8,"has_accepted_license":"1","date_updated":"2021-01-12T08:05:40Z","citation":{"chicago":"Xu, Youwei, Carrie Bernecky, Chung Lee, Kerstin Maier, Björn Schwalb, Dimitri Tegunov, Jürgen Plitzko, Henning Urlaub, and Patrick Cramer. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms15741\">https://doi.org/10.1038/ncomms15741</a>.","mla":"Xu, Youwei, et al. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” <i>Nature Communications</i>, vol. 8, 15741, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms15741\">10.1038/ncomms15741</a>.","ista":"Xu Y, Bernecky C, Lee C, Maier K, Schwalb B, Tegunov D, Plitzko J, Urlaub H, Cramer P. 2017. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nature Communications. 8, 15741.","ama":"Xu Y, Bernecky C, Lee C, et al. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms15741\">10.1038/ncomms15741</a>","ieee":"Y. Xu <i>et al.</i>, “Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","apa":"Xu, Y., Bernecky, C., Lee, C., Maier, K., Schwalb, B., Tegunov, D., … Cramer, P. (2017). Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms15741\">https://doi.org/10.1038/ncomms15741</a>","short":"Y. Xu, C. Bernecky, C. Lee, K. Maier, B. Schwalb, D. Tegunov, J. Plitzko, H. Urlaub, P. Cramer, Nature Communications 8 (2017)."},"day":"06","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"5865","file_size":3018075,"date_created":"2019-01-21T14:48:10Z","checksum":"940742282a9a285dc4aeae0c2b5ebe96","date_updated":"2020-07-14T12:47:16Z","file_name":"2017_NatureComm_Xu.pdf"}],"author":[{"first_name":"Youwei","last_name":"Xu","full_name":"Xu, Youwei"},{"first_name":"Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A"},{"full_name":"Lee, Chung","last_name":"Lee","first_name":"Chung"},{"full_name":"Maier, Kerstin","last_name":"Maier","first_name":"Kerstin"},{"full_name":"Schwalb, Björn","last_name":"Schwalb","first_name":"Björn"},{"last_name":"Tegunov","first_name":"Dimitri","full_name":"Tegunov, Dimitri"},{"full_name":"Plitzko, Jürgen","first_name":"Jürgen","last_name":"Plitzko"},{"last_name":"Urlaub","first_name":"Henning","full_name":"Urlaub, Henning"},{"full_name":"Cramer, Patrick","first_name":"Patrick","last_name":"Cramer"}],"oa":1,"status":"public","title":"Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex","article_number":"15741","publication":"Nature Communications","intvolume":"         8","quality_controlled":"1","publisher":"Nature Publishing Group"},{"title":"Experimental evidence for quantum tunneling time","article_number":"023201","status":"public","oa":1,"author":[{"full_name":"Camus, Nicolas","last_name":"Camus","first_name":"Nicolas"},{"last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","first_name":"Enderalp","full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lutz","last_name":"Fechner","full_name":"Fechner, Lutz"},{"first_name":"Michael","last_name":"Klaiber","full_name":"Klaiber, Michael"},{"last_name":"Laux","first_name":"Martin","full_name":"Laux, Martin"},{"full_name":"Mi, Yonghao","first_name":"Yonghao","last_name":"Mi"},{"first_name":"Karen Z.","last_name":"Hatsagortsyan","full_name":"Hatsagortsyan, Karen Z."},{"full_name":"Pfeifer, Thomas","first_name":"Thomas","last_name":"Pfeifer"},{"full_name":"Keitel, Christoph H.","last_name":"Keitel","first_name":"Christoph H."},{"first_name":"Robert","last_name":"Moshammer","full_name":"Moshammer, Robert"}],"issue":"2","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.03701"}],"publisher":"American Physical Society","publication":"Physical Review Letters","intvolume":"       119","volume":119,"date_created":"2019-02-14T15:24:13Z","date_published":"2017-07-14T00:00:00Z","month":"07","related_material":{"record":[{"status":"public","id":"313","relation":"earlier_version"}]},"day":"14","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>.","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>.","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.","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>","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)."},"date_updated":"2023-02-23T11:13:36Z","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.”"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"_id":"6013","language":[{"iso":"eng"}],"publication_status":"published","external_id":{"arxiv":["1611.03701"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiLe"}],"doi":"10.1103/PhysRevLett.119.023201","oa_version":"Preprint","type":"journal_article","arxiv":1,"year":"2017","scopus_import":1},{"publication_status":"published","language":[{"iso":"eng"}],"_id":"603","issue":"10","intvolume":"        24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Nature Structural and Molecular Biology","publisher":"Nature Publishing Group","quality_controlled":"1","page":"809 - 815","status":"public","extern":"1","abstract":[{"lang":"eng","text":"During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA processing. We combined cryo-EM and X-ray crystallography to determine the structure of the mammalian Pol II-DSIF elongation complex at a nominal resolution of 3.4. Human DSIF has a modular structure with two domains forming a DNA clamp, two domains forming an RNA clamp, and one domain buttressing the RNA clamp. The clamps maintain the transcription bubble, position upstream DNA, and retain the RNA transcript in the exit tunnel. The mobile C-terminal region of DSIF is located near exiting RNA, where it can recruit factors for RNA processing. The structure provides insight into the roles of DSIF during mRNA synthesis."}],"title":"Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp","article_processing_charge":"No","author":[{"last_name":"Bernecky","orcid":"0000-0003-0893-7036","first_name":"Carrie A","full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Plitzko, Jürgen","first_name":"Jürgen","last_name":"Plitzko"},{"last_name":"Cramer","first_name":"Patrick","full_name":"Cramer, Patrick"}],"publication_identifier":{"issn":["15459993"]},"year":"2017","type":"journal_article","date_updated":"2021-01-12T08:05:47Z","day":"05","citation":{"ama":"Bernecky C, Plitzko J, Cramer P. Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. <i>Nature Structural and Molecular Biology</i>. 2017;24(10):809-815. doi:<a href=\"https://doi.org/10.1038/nsmb.3465\">10.1038/nsmb.3465</a>","ista":"Bernecky C, Plitzko J, Cramer P. 2017. Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. Nature Structural and Molecular Biology. 24(10), 809–815.","mla":"Bernecky, Carrie, et al. “Structure of a Transcribing RNA Polymerase II-DSIF Complex Reveals a Multidentate DNA-RNA Clamp.” <i>Nature Structural and Molecular Biology</i>, vol. 24, no. 10, Nature Publishing Group, 2017, pp. 809–15, doi:<a href=\"https://doi.org/10.1038/nsmb.3465\">10.1038/nsmb.3465</a>.","chicago":"Bernecky, Carrie, Jürgen Plitzko, and Patrick Cramer. “Structure of a Transcribing RNA Polymerase II-DSIF Complex Reveals a Multidentate DNA-RNA Clamp.” <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/nsmb.3465\">https://doi.org/10.1038/nsmb.3465</a>.","apa":"Bernecky, C., Plitzko, J., &#38; Cramer, P. (2017). Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nsmb.3465\">https://doi.org/10.1038/nsmb.3465</a>","short":"C. Bernecky, J. Plitzko, P. Cramer, Nature Structural and Molecular Biology 24 (2017) 809–815.","ieee":"C. Bernecky, J. Plitzko, and P. Cramer, “Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp,” <i>Nature Structural and Molecular Biology</i>, vol. 24, no. 10. Nature Publishing Group, pp. 809–815, 2017."},"volume":24,"publist_id":"7202","doi":"10.1038/nsmb.3465","month":"10","oa_version":"None","date_published":"2017-10-05T00:00:00Z","date_created":"2018-12-11T11:47:26Z"},{"oa":1,"author":[{"first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Richard","last_name":"Schmidt","full_name":"Schmidt, Richard"}],"title":"Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets","status":"public","publisher":"The Royal Society of Chemistry","quality_controlled":"1","page":"444 - 495","main_file_link":[{"url":"https://arxiv.org/abs/1703.06753","open_access":"1"}],"intvolume":"        11","publication":"Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero ","date_created":"2018-12-11T11:47:27Z","date_published":"2017-12-14T00:00:00Z","month":"12","volume":11,"citation":{"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>","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.","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>.","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.","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>","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."},"day":"14","editor":[{"last_name":"Dulieu","first_name":"Oliver","full_name":"Dulieu, Oliver"},{"first_name":"Andreas","last_name":"Osterwalder","full_name":"Osterwalder, Andreas"}],"date_updated":"2021-01-12T08:05:50Z","publication_identifier":{"issn":["20413181"]},"alternative_title":["Theoretical and Computational Chemistry Series"],"abstract":[{"lang":"eng","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."}],"department":[{"_id":"MiLe"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","series_title":"Theoretical and Computational Chemistry Series","publication_status":"published","_id":"604","language":[{"iso":"eng"}],"oa_version":"Submitted Version","publist_id":"7201","doi":"10.1039/9781782626800-00444","scopus_import":1,"type":"book_chapter","year":"2017"},{"publisher":"Springer","page":"56 - 81","quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2016/536","open_access":"1"}],"intvolume":"     10677","title":"Position based cryptography and multiparty communication complexity","status":"public","oa":1,"author":[{"full_name":"Brody, Joshua","last_name":"Brody","first_name":"Joshua"},{"full_name":"Dziembowski, Stefan","last_name":"Dziembowski","first_name":"Stefan"},{"last_name":"Faust","first_name":"Sebastian","full_name":"Faust, Sebastian"},{"orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"}],"conference":{"end_date":"2017-11-15","start_date":"2017-11-12","location":"Baltimore, MD, United States","name":"TCC: Theory of Cryptography Conference"},"citation":{"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>.","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.","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>.","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>","short":"J. Brody, S. Dziembowski, S. Faust, K.Z. Pietrzak, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017, pp. 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."},"day":"05","editor":[{"full_name":"Kalai, Yael","first_name":"Yael","last_name":"Kalai"},{"last_name":"Reyzin","first_name":"Leonid","full_name":"Reyzin, Leonid"}],"date_updated":"2021-01-12T08:05:53Z","volume":10677,"date_created":"2018-12-11T11:47:27Z","date_published":"2017-11-05T00:00:00Z","month":"11","publication_status":"published","language":[{"iso":"eng"}],"_id":"605","project":[{"grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks"}],"department":[{"_id":"KrPi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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."}],"ec_funded":1,"publication_identifier":{"isbn":["978-331970499-9"]},"alternative_title":["LNCS"],"scopus_import":1,"year":"2017","type":"conference","publist_id":"7200","doi":"10.1007/978-3-319-70500-2_3","oa_version":"Submitted Version"},{"day":"01","citation":{"chicago":"Balta, Emre, Julian A Stopp, Laura Castelletti, Henning Kirchgessner, Yvonne Samstag, and Guido H. Wabnitz. “Qualitative and Quantitative Analysis of PMN/T-Cell Interactions by InFlow and Super-Resolution Microscopy.” <i>Methods</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ymeth.2016.09.013\">https://doi.org/10.1016/j.ymeth.2016.09.013</a>.","mla":"Balta, Emre, et al. “Qualitative and Quantitative Analysis of PMN/T-Cell Interactions by InFlow and Super-Resolution Microscopy.” <i>Methods</i>, vol. 112, no. 1, Elsevier, 2017, pp. 25–38, doi:<a href=\"https://doi.org/10.1016/j.ymeth.2016.09.013\">10.1016/j.ymeth.2016.09.013</a>.","ama":"Balta E, Stopp JA, Castelletti L, Kirchgessner H, Samstag Y, Wabnitz GH. Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy. <i>Methods</i>. 2017;112(1):25-38. doi:<a href=\"https://doi.org/10.1016/j.ymeth.2016.09.013\">10.1016/j.ymeth.2016.09.013</a>","ista":"Balta E, Stopp JA, Castelletti L, Kirchgessner H, Samstag Y, Wabnitz GH. 2017. Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy. Methods. 112(1), 25–38.","ieee":"E. Balta, J. A. Stopp, L. Castelletti, H. Kirchgessner, Y. Samstag, and G. H. Wabnitz, “Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy,” <i>Methods</i>, vol. 112, no. 1. Elsevier, pp. 25–38, 2017.","apa":"Balta, E., Stopp, J. A., Castelletti, L., Kirchgessner, H., Samstag, Y., &#38; Wabnitz, G. H. (2017). Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy. <i>Methods</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ymeth.2016.09.013\">https://doi.org/10.1016/j.ymeth.2016.09.013</a>","short":"E. Balta, J.A. Stopp, L. Castelletti, H. Kirchgessner, Y. Samstag, G.H. Wabnitz, Methods 112 (2017) 25–38."},"date_updated":"2021-01-12T08:05:57Z","year":"2017","type":"journal_article","related_material":{"link":[{"relation":"supplementary_material","url":"http://dx.doi.org/10.1016/j.ymeth.2016.09.013"}]},"date_published":"2017-01-01T00:00:00Z","date_created":"2019-02-26T13:45:17Z","oa_version":"None","pmid":1,"month":"01","doi":"10.1016/j.ymeth.2016.09.013","volume":112,"page":"25-38","quality_controlled":"1","external_id":{"pmid":["27693880"]},"publisher":"Elsevier","publication":"Methods","intvolume":"       112","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","language":[{"iso":"eng"}],"_id":"6059","publication_status":"published","publication_identifier":{"issn":["1046-2023"]},"author":[{"first_name":"Emre","last_name":"Balta","full_name":"Balta, Emre"},{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A","last_name":"Stopp","first_name":"Julian A"},{"last_name":"Castelletti","first_name":"Laura","full_name":"Castelletti, Laura"},{"last_name":"Kirchgessner","first_name":"Henning","full_name":"Kirchgessner, Henning"},{"last_name":"Samstag","first_name":"Yvonne","full_name":"Samstag, Yvonne"},{"full_name":"Wabnitz, Guido H.","first_name":"Guido H.","last_name":"Wabnitz"}],"abstract":[{"text":"Neutrophils or polymorphonuclear cells (PMN) eliminate bacteria via phagocytosis and/or NETosis. Apartfrom these conventional roles, PMN also have immune-regulatory functions. They can transdifferentiateand upregulate MHCII as well as ligands for costimulatory receptors which enables them to behave asantigen presenting cells (APC). The initial step for activating T-cells is the formation of an immunesynapse between T-cells and antigen-presenting cells. However, the immune synapse that develops atthe PMN/T-cell contact zone is as yet hardly investigated due to the non-availability of methods foranalysis of large number of PMN interactions. In order to overcome these obstacles, we introduce herea workflow to analyse the immune synapse of primary human PMN and T-cells using multispectral imag-ing flow cytometry (InFlow microscopy) and super-resolution microscopy. For that purpose, we used CD3and CD66b as the lineage markers for T-cells and PMN, respectively. Thereafter, we applied and criticallydiscussed various ‘‘masks” for identification of T-cell PMN interactions. Using this approach, we foundthat a small fraction of transdifferentiated PMN (CD66b+CD86high) formed stable PMN/T-cell conjugates.Interestingly, while both CD3 and CD66b accumulation in the immune synapse was dependent on thematuration state of the PMN, only CD3 accumulation was greatly enhanced by the presence of superanti-gen. The actin cytoskeleton was weakly rearranged at the PMN side on the immune synapse upon contactwith a T-cell in the presence of superantigen. A more detailed analysis using super-resolution microscopy(structured-illumination microscopy, SIM) confirmed this finding. Together, we present an InFlow micro-scopy based approach for the large scale analysis of PMN/T-cell interactions and – combined with SIM – apossibility for an in-depth analysis of protein translocation at the site of interactions.","lang":"eng"}],"title":"Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy","extern":"1","status":"public"},{"department":[{"_id":"KrPi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","language":[{"iso":"eng"}],"_id":"609","publication_identifier":{"isbn":["978-331970499-9"]},"alternative_title":["LNCS"],"abstract":[{"lang":"eng","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."}],"scopus_import":1,"type":"conference","year":"2017","oa_version":"Submitted Version","publist_id":"7196","doi":"10.1007/978-3-319-70500-2_17","publisher":"Springer","main_file_link":[{"url":"https://eprint.iacr.org/2017/945","open_access":"1"}],"page":"493 - 526","quality_controlled":"1","intvolume":"     10677","oa":1,"author":[{"first_name":"Joel F","last_name":"Alwen","full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tackmann, Björn","first_name":"Björn","last_name":"Tackmann"}],"title":"Moderately hard functions: Definition, instantiations, and applications","status":"public","day":"05","citation":{"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.","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>.","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>.","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>","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."},"editor":[{"full_name":"Kalai, Yael","last_name":"Kalai","first_name":"Yael"},{"full_name":"Reyzin, Leonid","first_name":"Leonid","last_name":"Reyzin"}],"date_updated":"2021-01-12T08:06:04Z","conference":{"name":"TCC: Theory of Cryptography","location":"Baltimore, MD, United States","start_date":"2017-11-12","end_date":"2017-11-15"},"date_published":"2017-11-05T00:00:00Z","date_created":"2018-12-11T11:47:28Z","month":"11","volume":10677},{"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."}],"ec_funded":1,"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).","publication_status":"published","language":[{"iso":"eng"}],"_id":"610","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"UlWa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s11856-017-1607-7","publist_id":"7194","oa_version":"Preprint","scopus_import":1,"year":"2017","type":"journal_article","title":"On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result","status":"public","oa":1,"author":[{"first_name":"Xavier","last_name":"Goaoc","full_name":"Goaoc, Xavier"},{"id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac","last_name":"Mabillard","first_name":"Isaac"},{"first_name":"Pavel","last_name":"Paták","full_name":"Paták, Pavel"},{"id":"48B57058-F248-11E8-B48F-1D18A9856A87","full_name":"Patakova, Zuzana","first_name":"Zuzana","last_name":"Patakova","orcid":"0000-0002-3975-1683"},{"id":"38AC689C-F248-11E8-B48F-1D18A9856A87","full_name":"Tancer, Martin","last_name":"Tancer","orcid":"0000-0002-1191-6714","first_name":"Martin"},{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","last_name":"Wagner","first_name":"Uli"}],"issue":"2","publisher":"Springer","page":"841 - 866","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.09063"}],"intvolume":"       222","publication":"Israel Journal of Mathematics","volume":222,"date_created":"2018-12-11T11:47:29Z","date_published":"2017-10-01T00:00:00Z","month":"10","related_material":{"record":[{"status":"public","id":"1511","relation":"earlier_version"}]},"day":"01","citation":{"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.","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>","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>.","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>.","short":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, Israel Journal of Mathematics 222 (2017) 841–866.","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>","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."},"date_updated":"2023-02-23T10:02:13Z"},{"issue":"6365","language":[{"iso":"eng"}],"_id":"611","publication_status":"published","page":"925 - 928","quality_controlled":"1","publisher":"American Association for the Advancement of Science","publication":"Science","department":[{"_id":"NiBa"}],"intvolume":"       358","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Evolution of flower color pattern through selection on regulatory small RNAs","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"}],"status":"public","publication_identifier":{"issn":["00368075"]},"author":[{"full_name":"Bradley, Desmond","first_name":"Desmond","last_name":"Bradley"},{"full_name":"Xu, Ping","first_name":"Ping","last_name":"Xu"},{"full_name":"Mohorianu, Irina","first_name":"Irina","last_name":"Mohorianu"},{"full_name":"Whibley, Annabel","first_name":"Annabel","last_name":"Whibley"},{"first_name":"David","orcid":"0000-0002-4014-8478","last_name":"Field","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tavares","first_name":"Hugo","full_name":"Tavares, Hugo"},{"full_name":"Couchman, Matthew","first_name":"Matthew","last_name":"Couchman"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"full_name":"Carpenter, Rosemary","last_name":"Carpenter","first_name":"Rosemary"},{"first_name":"Miaomiao","last_name":"Li","full_name":"Li, Miaomiao"},{"full_name":"Li, Qun","last_name":"Li","first_name":"Qun"},{"last_name":"Xue","first_name":"Yongbiao","full_name":"Xue, Yongbiao"},{"full_name":"Dalmay, Tamas","first_name":"Tamas","last_name":"Dalmay"},{"first_name":"Enrico","last_name":"Coen","full_name":"Coen, Enrico"}],"type":"journal_article","year":"2017","scopus_import":1,"citation":{"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.","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.","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>.","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>.","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."},"day":"17","date_updated":"2021-01-12T08:06:10Z","doi":"10.1126/science.aao3526","publist_id":"7193","volume":358,"date_published":"2017-11-17T00:00:00Z","date_created":"2018-12-11T11:47:29Z","oa_version":"None","month":"11"},{"date_updated":"2021-01-12T08:06:11Z","file":[{"date_updated":"2020-07-14T12:47:19Z","file_name":"2017_PNAS_Oda.pdf","checksum":"9e42ce47090ecdad7d76f2dbdebb924e","creator":"kschuh","relation":"main_file","file_id":"6114","file_size":1469622,"date_created":"2019-03-19T13:42:58Z","content_type":"application/pdf","access_level":"open_access"}],"day":"06","citation":{"apa":"Oda, S., Toyoshima, Y., &#38; de Bono, M. (2017). Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1614596114\">https://doi.org/10.1073/pnas.1614596114</a>","short":"S. Oda, Y. Toyoshima, M. de Bono, Proceedings of the National Academy of Sciences 114 (2017) E4658–E4665.","ieee":"S. Oda, Y. Toyoshima, and M. de Bono, “Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 23. National Academy of Sciences, pp. E4658–E4665, 2017.","chicago":"Oda, Shigekazu, Yu Toyoshima, and Mario de Bono. “Modulation of Sensory Information Processing by a Neuroglobin in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1614596114\">https://doi.org/10.1073/pnas.1614596114</a>.","ista":"Oda S, Toyoshima Y, de Bono M. 2017. Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 114(23), E4658–E4665.","ama":"Oda S, Toyoshima Y, de Bono M. Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(23):E4658-E4665. doi:<a href=\"https://doi.org/10.1073/pnas.1614596114\">10.1073/pnas.1614596114</a>","mla":"Oda, Shigekazu, et al. “Modulation of Sensory Information Processing by a Neuroglobin in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 23, National Academy of Sciences, 2017, pp. E4658–65, doi:<a href=\"https://doi.org/10.1073/pnas.1614596114\">10.1073/pnas.1614596114</a>."},"volume":114,"has_accepted_license":"1","month":"06","date_created":"2019-03-19T13:29:51Z","date_published":"2017-06-06T00:00:00Z","issue":"23","intvolume":"       114","publication":"Proceedings of the National Academy of Sciences","publisher":"National Academy of Sciences","page":"E4658-E4665","quality_controlled":"1","status":"public","title":"Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans","author":[{"last_name":"Oda","first_name":"Shigekazu","full_name":"Oda, Shigekazu"},{"full_name":"Toyoshima, Yu","first_name":"Yu","last_name":"Toyoshima"},{"first_name":"Mario","last_name":"de Bono","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario"}],"oa":1,"year":"2017","type":"journal_article","doi":"10.1073/pnas.1614596114","pmid":1,"oa_version":"Published Version","publication_status":"published","ddc":["570"],"language":[{"iso":"eng"}],"_id":"6113","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["28536200"]},"extern":"1","publication_identifier":{"issn":["0027-8424","1091-6490"]},"file_date_updated":"2020-07-14T12:47:19Z"},{"file_date_updated":"2020-07-14T12:47:20Z","publication_identifier":{"issn":["0027-8424","1091-6490"]},"abstract":[{"text":"Animals adjust their behavioral priorities according to momentary needs and prior experience. We show that Caenorhabditis elegans changes how it processes sensory information according to the oxygen environment it experienced recently. C. elegans acclimated to 7% O2 are aroused by CO2 and repelled by pheromones that attract animals acclimated to 21% O2. This behavioral plasticity arises from prolonged activity differences in a circuit that continuously signals O2 levels. A sustained change in the activity of O2-sensing neurons reprograms the properties of their postsynaptic partners, the RMG hub interneurons. RMG is gap-junctionally coupled to the ASK and ADL pheromone sensors that respectively drive pheromone attraction and repulsion. Prior O2 experience has opposite effects on the pheromone responsiveness of these neurons. These circuit changes provide a physiological correlate of altered pheromone valence. Our results suggest C. elegans stores a memory of recent O2 experience in the RMG circuit and illustrate how a circuit is flexibly sculpted to guide behavioral decisions in a context-dependent manner.","lang":"eng"}],"extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["28373553"]},"_id":"6115","language":[{"iso":"eng"}],"publication_status":"published","ddc":["570"],"pmid":1,"oa_version":"Published Version","doi":"10.1073/pnas.1618934114","type":"journal_article","year":"2017","author":[{"full_name":"Fenk, Lorenz A.","last_name":"Fenk","first_name":"Lorenz A."},{"full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","last_name":"de Bono","orcid":"0000-0001-8347-0443"}],"oa":1,"status":"public","title":"Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans","publication":"Proceedings of the National Academy of Sciences","intvolume":"       114","quality_controlled":"1","page":"4195-4200","publisher":"National Academy of Sciences","issue":"16","month":"04","date_published":"2017-04-18T00:00:00Z","date_created":"2019-03-19T13:46:36Z","volume":114,"has_accepted_license":"1","date_updated":"2021-01-12T08:06:11Z","day":"18","citation":{"ieee":"L. A. Fenk and M. de Bono, “Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 16. National Academy of Sciences, pp. 4195–4200, 2017.","apa":"Fenk, L. A., &#38; de Bono, M. (2017). Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1618934114\">https://doi.org/10.1073/pnas.1618934114</a>","short":"L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 114 (2017) 4195–4200.","mla":"Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience Switches Pheromone Valence InCaenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 16, National Academy of Sciences, 2017, pp. 4195–200, doi:<a href=\"https://doi.org/10.1073/pnas.1618934114\">10.1073/pnas.1618934114</a>.","ista":"Fenk LA, de Bono M. 2017. Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans. Proceedings of the National Academy of Sciences. 114(16), 4195–4200.","ama":"Fenk LA, de Bono M. Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(16):4195-4200. doi:<a href=\"https://doi.org/10.1073/pnas.1618934114\">10.1073/pnas.1618934114</a>","chicago":"Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience Switches Pheromone Valence InCaenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1618934114\">https://doi.org/10.1073/pnas.1618934114</a>."},"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6116","creator":"kschuh","file_size":1217696,"date_created":"2019-03-19T14:00:42Z","checksum":"1801bc8319b752fa17598004ec375279","date_updated":"2020-07-14T12:47:20Z","file_name":"2017_PNAS_Fenk.pdf"}]}]