[{"volume":18,"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"],"date_created":"2018-12-20T21:13:59Z","day":"22","status":"public","publication":"Current Opinion in Virology","doi":"10.1016/j.coviro.2016.02.008","oa_version":"Published Version","date_published":"2016-03-22T00:00:00Z","intvolume":"        18","month":"03","date_updated":"2021-01-12T08:03:22Z","oa":1,"issue":"6","page":"27-35","year":"2016","publication_identifier":{"issn":["1879-6257"]},"extern":"1","citation":{"apa":"Mattei, S., Schur, F. K., &#38; Briggs, J. A. (2016). Retrovirus maturation—an extraordinary structural transformation. <i>Current Opinion in Virology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coviro.2016.02.008\">https://doi.org/10.1016/j.coviro.2016.02.008</a>","mla":"Mattei, Simone, et al. “Retrovirus Maturation—an Extraordinary Structural Transformation.” <i>Current Opinion in Virology</i>, vol. 18, no. 6, Elsevier, 2016, pp. 27–35, doi:<a href=\"https://doi.org/10.1016/j.coviro.2016.02.008\">10.1016/j.coviro.2016.02.008</a>.","short":"S. Mattei, F.K. Schur, J.A. Briggs, Current Opinion in Virology 18 (2016) 27–35.","ista":"Mattei S, Schur FK, Briggs JA. 2016. Retrovirus maturation—an extraordinary structural transformation. Current Opinion in Virology. 18(6), 27–35.","ieee":"S. Mattei, F. K. Schur, and J. A. Briggs, “Retrovirus maturation—an extraordinary structural transformation,” <i>Current Opinion in Virology</i>, vol. 18, no. 6. Elsevier, pp. 27–35, 2016.","ama":"Mattei S, Schur FK, Briggs JA. Retrovirus maturation—an extraordinary structural transformation. <i>Current Opinion in Virology</i>. 2016;18(6):27-35. doi:<a href=\"https://doi.org/10.1016/j.coviro.2016.02.008\">10.1016/j.coviro.2016.02.008</a>","chicago":"Mattei, Simone, Florian KM Schur, and John AG Briggs. “Retrovirus Maturation—an Extraordinary Structural Transformation.” <i>Current Opinion in Virology</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.coviro.2016.02.008\">https://doi.org/10.1016/j.coviro.2016.02.008</a>."},"abstract":[{"text":"Retroviruses such as HIV-1 assemble and bud from infected cells in an immature, non-infectious form. Subsequently, a series of proteolytic cleavages catalysed by the viral protease leads to a spectacular structural rearrangement of the viral particle into a mature form that is competent to fuse with and infect a new cell. Maturation involves changes in the structures of protein domains, in the interactions between protein domains, and in the architecture of the viral components that are assembled by the proteins. Tight control of proteolytic cleavages at different sites is required for successful maturation, and the process is a major target of antiretroviral drugs. Here we will describe what is known about the structures of immature and mature retrovirus particles, and about the maturation process by which one transitions into the other. Despite a wealth of available data, fundamental questions about retroviral maturation remain unanswered.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:11Z","type":"journal_article","_id":"5771","quality_controlled":"1","publication_status":"published","has_accepted_license":"1","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Retrovirus maturation—an extraordinary structural transformation","author":[{"last_name":"Mattei","first_name":"Simone","full_name":"Mattei, Simone"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian"},{"full_name":"Briggs, John AG","first_name":"John AG","last_name":"Briggs"}],"file":[{"file_name":"2016_CurrentOpinion_Mattei.pdf","date_created":"2019-01-09T13:05:44Z","date_updated":"2020-07-14T12:47:11Z","file_id":"5812","content_type":"application/pdf","creator":"dernst","file_size":1773842,"checksum":"320939d28ebd1adfb122338019892508","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}]},{"date_created":"2019-01-08T20:44:24Z","day":"02","status":"public","volume":9667,"oa_version":"None","publication":"Computational Topology in Image Context","doi":"10.1007/978-3-319-39441-1_23","date_updated":"2022-01-28T08:01:22Z","alternative_title":["LNCS"],"date_published":"2016-06-02T00:00:00Z","intvolume":"      9667","month":"06","year":"2016","page":"253-264","conference":{"location":"Marseille, France","end_date":"2016-06-17","start_date":"2016-06-15","name":"CTIC: Computational Topology in Image Context"},"_id":"5805","quality_controlled":"1","extern":"1","citation":{"chicago":"Sen, Nabhasmita, Ranita Biswas, and Partha Bhowmick. “On Some Local Topological Properties of Naive Discrete Sphere.” In <i>Computational Topology in Image Context</i>, 9667:253–64. Cham: Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">https://doi.org/10.1007/978-3-319-39441-1_23</a>.","ama":"Sen N, Biswas R, Bhowmick P. On some local topological properties of naive discrete sphere. In: <i>Computational Topology in Image Context</i>. Vol 9667. Cham: Springer Nature; 2016:253-264. doi:<a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">10.1007/978-3-319-39441-1_23</a>","ieee":"N. Sen, R. Biswas, and P. Bhowmick, “On some local topological properties of naive discrete sphere,” in <i>Computational Topology in Image Context</i>, vol. 9667, Cham: Springer Nature, 2016, pp. 253–264.","ista":"Sen N, Biswas R, Bhowmick P. 2016.On some local topological properties of naive discrete sphere. In: Computational Topology in Image Context. LNCS, vol. 9667, 253–264.","short":"N. Sen, R. Biswas, P. Bhowmick, in:, Computational Topology in Image Context, Springer Nature, Cham, 2016, pp. 253–264.","mla":"Sen, Nabhasmita, et al. “On Some Local Topological Properties of Naive Discrete Sphere.” <i>Computational Topology in Image Context</i>, vol. 9667, Springer Nature, 2016, pp. 253–64, doi:<a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">10.1007/978-3-319-39441-1_23</a>.","apa":"Sen, N., Biswas, R., &#38; Bhowmick, P. (2016). On some local topological properties of naive discrete sphere. In <i>Computational Topology in Image Context</i> (Vol. 9667, pp. 253–264). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">https://doi.org/10.1007/978-3-319-39441-1_23</a>"},"publication_identifier":{"isbn":["978-3-319-39440-4"],"eisbn":["978-3-319-39441-1"],"eissn":["1611-3349"],"issn":["0302-9743"]},"abstract":[{"text":"Discretization of sphere in the integer space follows a particular discretization scheme, which, in principle, conforms to some topological model. This eventually gives rise to interesting topological properties of a discrete spherical surface, which need to be investigated for its analytical characterization. This paper presents some novel results on the local topological properties of the naive model of discrete sphere. They follow from the bijection of each quadraginta octant of naive sphere with its projection map called f -map on the corresponding functional plane and from the characterization of certain jumps in the f-map. As an application, we have shown how these properties can be used in designing an efficient reconstruction algorithm for a naive spherical surface from an input voxel set when it is sparse or noisy.","lang":"eng"}],"type":"book_chapter","publication_status":"published","place":"Cham","title":"On some local topological properties of naive discrete sphere","author":[{"full_name":"Sen, Nabhasmita","first_name":"Nabhasmita","last_name":"Sen"},{"full_name":"Biswas, Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita"},{"last_name":"Bhowmick","first_name":"Partha","full_name":"Bhowmick, Partha"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Springer Nature","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"HeEd"}]},{"publication_status":"published","place":"Cham","type":"conference","abstract":[{"lang":"eng","text":"Although the concept of functional plane for naive plane is studied and reported in the literature in great detail, no similar study is yet found for naive sphere. This article exposes the first study in this line, opening up further prospects of analyzing the topological properties of sphere in the discrete space. We show that each quadraginta octant Q of a naive sphere forms a bijection with its projected pixel set on a unique coordinate plane, which thereby serves as the functional plane of Q, and hence gives rise to merely mono-jumps during back projection. The other two coordinate planes serve as para-functional and dia-functional planes for Q, as the former is ‘mono-jumping’ but not bijective, whereas the latter holds neither of the two. Owing to this, the quadraginta octants form symmetry groups and subgroups with equivalent jump conditions. We also show a potential application in generating a special class of discrete 3D circles based on back projection and jump bridging by Steiner voxels. A circle in this class possesses 4-symmetry, uniqueness, and bounded distance from the underlying real sphere and real plane."}],"extern":"1","publication_identifier":{"issn":["0302-9743","1611-3349"],"isbn":["978-3-319-32359-6"],"eisbn":["978-3-319-32360-2"]},"citation":{"apa":"Biswas, R., &#38; Bhowmick, P. (2016). On functionality of quadraginta octants of naive sphere with application to circle drawing. In <i>Discrete Geometry for Computer Imagery</i> (Vol. 9647, pp. 256–267). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">https://doi.org/10.1007/978-3-319-32360-2_20</a>","mla":"Biswas, Ranita, and Partha Bhowmick. “On Functionality of Quadraginta Octants of Naive Sphere with Application to Circle Drawing.” <i>Discrete Geometry for Computer Imagery</i>, vol. 9647, Springer Nature, 2016, pp. 256–67, doi:<a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">10.1007/978-3-319-32360-2_20</a>.","ama":"Biswas R, Bhowmick P. On functionality of quadraginta octants of naive sphere with application to circle drawing. In: <i>Discrete Geometry for Computer Imagery</i>. Vol 9647. Cham: Springer Nature; 2016:256-267. doi:<a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">10.1007/978-3-319-32360-2_20</a>","ieee":"R. Biswas and P. Bhowmick, “On functionality of quadraginta octants of naive sphere with application to circle drawing,” in <i>Discrete Geometry for Computer Imagery</i>, Nantes, France, 2016, vol. 9647, pp. 256–267.","short":"R. Biswas, P. Bhowmick, in:, Discrete Geometry for Computer Imagery, Springer Nature, Cham, 2016, pp. 256–267.","ista":"Biswas R, Bhowmick P. 2016. On functionality of quadraginta octants of naive sphere with application to circle drawing. Discrete Geometry for Computer Imagery. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 9647, 256–267.","chicago":"Biswas, Ranita, and Partha Bhowmick. “On Functionality of Quadraginta Octants of Naive Sphere with Application to Circle Drawing.” In <i>Discrete Geometry for Computer Imagery</i>, 9647:256–67. Cham: Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">https://doi.org/10.1007/978-3-319-32360-2_20</a>."},"quality_controlled":"1","_id":"5806","department":[{"_id":"HeEd"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Springer Nature","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"orcid":"0000-0002-5372-7890","last_name":"Biswas","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita"},{"full_name":"Bhowmick, Partha","first_name":"Partha","last_name":"Bhowmick"}],"title":"On functionality of quadraginta octants of naive sphere with application to circle drawing","doi":"10.1007/978-3-319-32360-2_20","publication":"Discrete Geometry for Computer Imagery","oa_version":"None","volume":9647,"day":"09","status":"public","date_created":"2019-01-08T20:44:37Z","conference":{"location":"Nantes, France","name":"DGCI: International Conference on Discrete Geometry for Computer Imagery","end_date":"2016-04-20","start_date":"2016-04-18"},"page":"256-267","year":"2016","month":"04","intvolume":"      9647","date_published":"2016-04-09T00:00:00Z","alternative_title":["LNCS"],"date_updated":"2022-01-28T08:10:11Z"},{"department":[{"_id":"HeEd"}],"conference":{"name":"IWCIA: International Workshop on Combinatorial Image Analysis","start_date":"2015-11-24","end_date":"2015-11-27","location":"Kolkata, India"},"page":"86-100","article_processing_charge":"No","year":"2016","language":[{"iso":"eng"}],"publisher":"Springer Nature","month":"01","intvolume":"      9448","date_published":"2016-01-06T00:00:00Z","author":[{"orcid":"0000-0002-5372-7890","last_name":"Biswas","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","full_name":"Biswas, Ranita"},{"full_name":"Bhowmick, Partha","first_name":"Partha","last_name":"Bhowmick"},{"full_name":"Brimkov, Valentin E.","last_name":"Brimkov","first_name":"Valentin E."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"On the connectivity and smoothness of discrete spherical circles","date_updated":"2022-01-28T08:13:03Z","doi":"10.1007/978-3-319-26145-4_7","publication_status":"published","place":"Cham","publication":"Combinatorial image analysis","oa_version":"None","type":"book_chapter","abstract":[{"lang":"eng","text":"A discrete spherical circle is a topologically well-connected 3D circle in the integer space, which belongs to a discrete sphere as well as a discrete plane. It is one of the most important 3D geometric primitives, but has not possibly yet been studied up to its merit. This paper is a maiden exposition of some of its elementary properties, which indicates a sense of its profound theoretical prospects in the framework of digital geometry. We have shown how different types of discretization can lead to forbidden and admissible classes, when one attempts to define the discretization of a spherical circle in terms of intersection between a discrete sphere and a discrete plane. Several fundamental theoretical results have been presented, the algorithm for construction of discrete spherical circles has been discussed, and some test results have been furnished to demonstrate its practicality and usefulness."}],"citation":{"chicago":"Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Connectivity and Smoothness of Discrete Spherical Circles.” In <i>Combinatorial Image Analysis</i>, 9448:86–100. Cham: Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">https://doi.org/10.1007/978-3-319-26145-4_7</a>.","ama":"Biswas R, Bhowmick P, Brimkov VE. On the connectivity and smoothness of discrete spherical circles. In: <i>Combinatorial Image Analysis</i>. Vol 9448. Cham: Springer Nature; 2016:86-100. doi:<a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">10.1007/978-3-319-26145-4_7</a>","short":"R. Biswas, P. Bhowmick, V.E. Brimkov, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2016, pp. 86–100.","ista":"Biswas R, Bhowmick P, Brimkov VE. 2016.On the connectivity and smoothness of discrete spherical circles. In: Combinatorial image analysis. vol. 9448, 86–100.","ieee":"R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the connectivity and smoothness of discrete spherical circles,” in <i>Combinatorial image analysis</i>, vol. 9448, Cham: Springer Nature, 2016, pp. 86–100.","mla":"Biswas, Ranita, et al. “On the Connectivity and Smoothness of Discrete Spherical Circles.” <i>Combinatorial Image Analysis</i>, vol. 9448, Springer Nature, 2016, pp. 86–100, doi:<a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">10.1007/978-3-319-26145-4_7</a>.","apa":"Biswas, R., Bhowmick, P., &#38; Brimkov, V. E. (2016). On the connectivity and smoothness of discrete spherical circles. In <i>Combinatorial image analysis</i> (Vol. 9448, pp. 86–100). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">https://doi.org/10.1007/978-3-319-26145-4_7</a>"},"publication_identifier":{"isbn":["978-3-319-26144-7"],"eisbn":["978-3-319-26145-4"],"eissn":["1611-3349"],"issn":["0302-9743"]},"extern":"1","volume":9448,"status":"public","day":"06","quality_controlled":"1","_id":"5809","date_created":"2019-01-08T20:45:19Z"},{"type":"journal_article","abstract":[{"text":"Quantum metrology exploits entangled states of particles to improve sensing precision beyond the limit achievable with uncorrelated particles. All previous methods required detection noise levels below this standard quantum limit to realize the benefits of the intrinsic sensitivity provided by these states.We experimentally demonstrate a widely applicable method for entanglement-enhanced measurements without low-noise detection. The method involves an intermediate quantum phase magnification step that eases implementation complexity. We used it to perform squeezed-state metrology 8 decibels below the standard quantum limit with a detection system that has a noise floor 10 decibels above the standard quantum limit.","lang":"eng"}],"citation":{"chicago":"Hosten, Onur, Rajiv Krishnakumar, Nils Engelsen, and Mark Kasevich. “Quantum Phase Magnification.” <i>Science</i>. American Association for the Advancement of Science, 2016. <a href=\"https://doi.org/10.1126/science.aaf3397\">https://doi.org/10.1126/science.aaf3397</a>.","ama":"Hosten O, Krishnakumar R, Engelsen N, Kasevich M. Quantum phase magnification. <i>Science</i>. 2016;352(6293):1552-1555. doi:<a href=\"https://doi.org/10.1126/science.aaf3397\">10.1126/science.aaf3397</a>","short":"O. Hosten, R. Krishnakumar, N. Engelsen, M. Kasevich, Science 352 (2016) 1552–1555.","ista":"Hosten O, Krishnakumar R, Engelsen N, Kasevich M. 2016. Quantum phase magnification. Science. 352(6293), 1552–1555.","ieee":"O. Hosten, R. Krishnakumar, N. Engelsen, and M. Kasevich, “Quantum phase magnification,” <i>Science</i>, vol. 352, no. 6293. American Association for the Advancement of Science, pp. 1552–1555, 2016.","mla":"Hosten, Onur, et al. “Quantum Phase Magnification.” <i>Science</i>, vol. 352, no. 6293, American Association for the Advancement of Science, 2016, pp. 1552–55, doi:<a href=\"https://doi.org/10.1126/science.aaf3397\">10.1126/science.aaf3397</a>.","apa":"Hosten, O., Krishnakumar, R., Engelsen, N., &#38; Kasevich, M. (2016). Quantum phase magnification. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aaf3397\">https://doi.org/10.1126/science.aaf3397</a>"},"extern":1,"volume":352,"quality_controlled":0,"day":"24","status":"public","date_created":"2018-12-11T11:47:21Z","_id":"587","doi":"10.1126/science.aaf3397","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.07683"}],"publication":"Science","publisher":"American Association for the Advancement of Science","month":"06","intvolume":"       352","date_published":"2016-06-24T00:00:00Z","issue":"6293","author":[{"full_name":"Onur Hosten","first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","last_name":"Hosten"},{"first_name":"Rajiv","last_name":"Krishnakumar","full_name":"Krishnakumar, Rajiv"},{"full_name":"Engelsen, Nils J","last_name":"Engelsen","first_name":"Nils"},{"last_name":"Kasevich","first_name":"Mark","full_name":"Kasevich, Mark A"}],"oa":1,"title":"Quantum phase magnification","date_updated":"2021-01-12T08:05:06Z","publist_id":"7214","page":"1552 - 1555","year":"2016"},{"publist_id":"7215","page":"505 - 508","year":"2016","publisher":"Nature Publishing Group","intvolume":"       529","month":"01","date_published":"2016-01-28T00:00:00Z","issue":"7587","title":"Measurement noise 100 times lower than the quantum-projection limit using entangled atoms","author":[{"full_name":"Onur Hosten","last_name":"Hosten","orcid":"0000-0002-2031-204X","first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nils","last_name":"Engelsen","full_name":"Engelsen, Nils J"},{"full_name":"Krishnakumar, Rajiv","last_name":"Krishnakumar","first_name":"Rajiv"},{"full_name":"Kasevich, Mark A","last_name":"Kasevich","first_name":"Mark"}],"date_updated":"2021-01-12T08:05:07Z","doi":"10.1038/nature16176","publication_status":"published","publication":"Nature","type":"journal_article","abstract":[{"text":"Quantum metrology uses quantum entanglement - correlations in the properties of microscopic systems - to improve the statistical precision of physical measurements. When measuring a signal, such as the phase shift of a light beam or an atomic state, a prominent limitation to achievable precision arises from the noise associated with the counting of uncorrelated probe particles. This noise, commonly referred to as shot noise or projection noise, gives rise to the standard quantum limit (SQL) to phase resolution. However, it can be mitigated down to the fundamental Heisenberg limit by entangling the probe particles. Despite considerable experimental progress in a variety of physical systems, a question that persists is whether these methods can achieve performance levels that compare favourably with optimized conventional (non-entangled) systems. Here we demonstrate an approach that achieves unprecedented levels of metrological improvement using half a million 87Rb atoms in their 'clock' states. The ensemble is 20.1 ± 0.3 decibels (100-fold) spin-squeezed via an optical-cavity-based measurement. We directly resolve small microwave-induced rotations 18.5 ± 0.3 decibels (70-fold) beyond the SQL. The single-shot phase resolution of 147 microradians achieved by the apparatus is better than that achieved by the best engineered cold atom sensors despite lower atom numbers. We infer entanglement of more than 680 ± 35 particles in the atomic ensemble. Applications include atomic clocks, inertial sensors, and fundamental physics experiments such as tests of general relativity or searches for electron electric dipole moment. To this end, we demonstrate an atomic clock measurement with a quantum enhancement of 10.5 ± 0.3 decibels (11-fold), limited by the phase noise of our microwave source.","lang":"eng"}],"extern":1,"citation":{"chicago":"Hosten, Onur, Nils Engelsen, Rajiv Krishnakumar, and Mark Kasevich. “Measurement Noise 100 Times Lower than the Quantum-Projection Limit Using Entangled Atoms.” <i>Nature</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nature16176\">https://doi.org/10.1038/nature16176</a>.","short":"O. Hosten, N. Engelsen, R. Krishnakumar, M. Kasevich, Nature 529 (2016) 505–508.","ieee":"O. Hosten, N. Engelsen, R. Krishnakumar, and M. Kasevich, “Measurement noise 100 times lower than the quantum-projection limit using entangled atoms,” <i>Nature</i>, vol. 529, no. 7587. Nature Publishing Group, pp. 505–508, 2016.","ista":"Hosten O, Engelsen N, Krishnakumar R, Kasevich M. 2016. Measurement noise 100 times lower than the quantum-projection limit using entangled atoms. Nature. 529(7587), 505–508.","ama":"Hosten O, Engelsen N, Krishnakumar R, Kasevich M. Measurement noise 100 times lower than the quantum-projection limit using entangled atoms. <i>Nature</i>. 2016;529(7587):505-508. doi:<a href=\"https://doi.org/10.1038/nature16176\">10.1038/nature16176</a>","mla":"Hosten, Onur, et al. “Measurement Noise 100 Times Lower than the Quantum-Projection Limit Using Entangled Atoms.” <i>Nature</i>, vol. 529, no. 7587, Nature Publishing Group, 2016, pp. 505–08, doi:<a href=\"https://doi.org/10.1038/nature16176\">10.1038/nature16176</a>.","apa":"Hosten, O., Engelsen, N., Krishnakumar, R., &#38; Kasevich, M. (2016). Measurement noise 100 times lower than the quantum-projection limit using entangled atoms. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature16176\">https://doi.org/10.1038/nature16176</a>"},"volume":529,"day":"28","status":"public","quality_controlled":0,"_id":"588","date_created":"2018-12-11T11:47:21Z"},{"day":"16","quality_controlled":"1","status":"public","_id":"592","date_created":"2018-12-11T11:47:23Z","type":"conference","abstract":[{"text":"We create up to 20 dB spin-squeezed states of atomic ensembles using an optical cavity-based measurement. The prepared states are suitable for atomic sensors that require free space release of the atoms.","lang":"eng"}],"extern":"1","citation":{"chicago":"Engelsen, Nils, Onur Hosten, Rajiv Krishnakumar, and Mark Kasevich. “Engineering Spin Squeezed States for Quantum-Enhanced Atom Interferometry.” IEEE, 2016.","short":"N. Engelsen, O. Hosten, R. Krishnakumar, M. Kasevich, in:, IEEE, 2016.","ieee":"N. Engelsen, O. Hosten, R. Krishnakumar, and M. Kasevich, “Engineering spin squeezed states for quantum-enhanced atom interferometry,” presented at the CLEO: Conference on Lasers and Electro Optics, San Jose, CA, United States, 2016.","ista":"Engelsen N, Hosten O, Krishnakumar R, Kasevich M. 2016. Engineering spin squeezed states for quantum-enhanced atom interferometry. CLEO: Conference on Lasers and Electro Optics.","ama":"Engelsen N, Hosten O, Krishnakumar R, Kasevich M. Engineering spin squeezed states for quantum-enhanced atom interferometry. In: IEEE; 2016.","mla":"Engelsen, Nils, et al. <i>Engineering Spin Squeezed States for Quantum-Enhanced Atom Interferometry</i>. IEEE, 2016.","apa":"Engelsen, N., Hosten, O., Krishnakumar, R., &#38; Kasevich, M. (2016). Engineering spin squeezed states for quantum-enhanced atom interferometry. Presented at the CLEO: Conference on Lasers and Electro Optics, San Jose, CA, United States: IEEE."},"oa_version":"None","main_file_link":[{"url":"http://ieeexplore.ieee.org/document/7787611/"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Engelsen, Nils","first_name":"Nils","last_name":"Engelsen"},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur","orcid":"0000-0002-2031-204X","last_name":"Hosten","full_name":"Hosten, Onur"},{"full_name":"Krishnakumar, Rajiv","first_name":"Rajiv","last_name":"Krishnakumar"},{"last_name":"Kasevich","first_name":"Mark","full_name":"Kasevich, Mark"}],"title":"Engineering spin squeezed states for quantum-enhanced atom interferometry","date_updated":"2021-01-12T08:05:15Z","publisher":"IEEE","month":"12","date_published":"2016-12-16T00:00:00Z","year":"2016","language":[{"iso":"eng"}],"publist_id":"7213","conference":{"name":"CLEO: Conference on Lasers and Electro Optics","start_date":"2016-06-05","end_date":"2016-06-10","location":"San Jose, CA, United States"},"article_processing_charge":"No"},{"abstract":[{"lang":"eng","text":"RNA polymerase (Pol) II produces messenger RNA during transcription of protein-coding genes in all eukaryotic cells. The Pol II structure is known at high resolution from X-ray crystallography for two yeast species1-3. Structural studies of mammalian Pol II, however, remain limited to low-resolution electron microscopy analysis of human Pol II and its complexes with various proteins4-10. Here we report the 3.4 Å resolution cryo-electron microscopy structure of mammalian Pol II in the form of a transcribing complex comprising DNA template and RNA transcript. We use bovine Pol II, which is identical to the human enzyme except for seven amino-acid residues. The obtained atomic model closely resembles its yeast counterpart, but also reveals unknown features. Binding of nucleic acids to the polymerase involves 'induced fit' of the mobile Pol II clamp and active centre region. DNA downstream of the transcription bubble contacts a conserved 'TPSA motif' in the jaw domain of the Pol II subunit RPB5, an interaction that is apparently already established during transcription initiation7. Upstream DNA emanates from the active centre cleft at an angle of approximately 105° with respect to downstream DNA. This position of upstream DNA allows for binding of the general transcription elongation factor DSIF (SPT4-SPT5) that we localize over the active centre cleft in a conserved position on the clamp domain of Pol II. Our results define the structure of mammalian Pol II in its functional state, indicate that previous crystallographic analysis of yeast Pol II is relevant for understanding gene transcription in all eukaryotes, and provide a starting point for a mechanistic analysis of human transcription."}],"type":"journal_article","volume":529,"citation":{"ama":"Bernecky C, Herzog F, Baumeister W, Plitzko J, Cramer P. Structure of transcribing mammalian RNA polymerase II. <i>Nature</i>. 2016;529(7587):551-554. doi:<a href=\"https://doi.org/10.1038/nature16482\">10.1038/nature16482</a>","ieee":"C. Bernecky, F. Herzog, W. Baumeister, J. Plitzko, and P. Cramer, “Structure of transcribing mammalian RNA polymerase II,” <i>Nature</i>, vol. 529, no. 7587. Nature Publishing Group, pp. 551–554, 2016.","ista":"Bernecky C, Herzog F, Baumeister W, Plitzko J, Cramer P. 2016. Structure of transcribing mammalian RNA polymerase II. Nature. 529(7587), 551–554.","short":"C. Bernecky, F. Herzog, W. Baumeister, J. Plitzko, P. Cramer, Nature 529 (2016) 551–554.","chicago":"Bernecky, Carrie, Franz Herzog, Wolfgang Baumeister, Jürgen Plitzko, and Patrick Cramer. “Structure of Transcribing Mammalian RNA Polymerase II.” <i>Nature</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nature16482\">https://doi.org/10.1038/nature16482</a>.","apa":"Bernecky, C., Herzog, F., Baumeister, W., Plitzko, J., &#38; Cramer, P. (2016). Structure of transcribing mammalian RNA polymerase II. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature16482\">https://doi.org/10.1038/nature16482</a>","mla":"Bernecky, Carrie, et al. “Structure of Transcribing Mammalian RNA Polymerase II.” <i>Nature</i>, vol. 529, no. 7587, Nature Publishing Group, 2016, pp. 551–54, doi:<a href=\"https://doi.org/10.1038/nature16482\">10.1038/nature16482</a>."},"extern":"1","status":"public","day":"28","date_created":"2018-12-11T11:47:26Z","_id":"602","publication":"Nature","doi":"10.1038/nature16482","publication_status":"published","oa_version":"None","publisher":"Nature Publishing Group","date_published":"2016-01-28T00:00:00Z","month":"01","intvolume":"       529","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Structure of transcribing mammalian RNA polymerase II","author":[{"full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky"},{"first_name":"Franz","last_name":"Herzog","full_name":"Herzog, Franz"},{"last_name":"Baumeister","first_name":"Wolfgang","full_name":"Baumeister, Wolfgang"},{"full_name":"Plitzko, Jürgen","first_name":"Jürgen","last_name":"Plitzko"},{"last_name":"Cramer","first_name":"Patrick","full_name":"Cramer, Patrick"}],"issue":"7587","date_updated":"2021-01-12T08:05:43Z","publist_id":"7205","article_processing_charge":"No","page":"551 - 554","year":"2016","language":[{"iso":"eng"}]},{"year":"2016","article_number":"1865","intvolume":"      2016","month":"01","date_published":"2016-01-01T00:00:00Z","issue":"3","oa":1,"date_updated":"2021-01-12T06:50:41Z","doi":"10.7717/peerj.1865","publication":"PeerJ","oa_version":"Published Version","volume":2016,"day":"01","status":"public","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":"2018-12-11T11:51:59Z","ddc":["570"],"department":[{"_id":"SyCr"}],"publist_id":"5767","pubrep_id":"584","language":[{"iso":"eng"}],"publisher":"PeerJ","has_accepted_license":"1","file":[{"content_type":"application/pdf","file_id":"5272","file_size":1216360,"creator":"system","checksum":"c27d898598a1e3d7f629607a309254e1","relation":"main_file","access_level":"open_access","file_name":"IST-2016-584-v1+1_peerj-1865.pdf","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:17:19Z"}],"author":[{"first_name":"András","last_name":"Tartally","full_name":"Tartally, András"},{"full_name":"Kelager, Andreas","first_name":"Andreas","last_name":"Kelager"},{"orcid":"0000-0002-3712-925X","last_name":"Fürst","first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias"},{"first_name":"David","last_name":"Nash","full_name":"Nash, David"}],"title":"Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","type":"journal_article","file_date_updated":"2020-07-14T12:44:53Z","scopus_import":1,"abstract":[{"text":"The rare socially parasitic butterfly Maculinea alcon occurs in two forms, which are characteristic of hygric or xeric habitats and which exploit different host plants and host ants. The status of these two forms has been the subject of considerable controversy. Populations of the two forms are usually spatially distinct, but at Răscruci in Romania both forms occur on the same site (syntopically). We examined the genetic differentiation between the two forms using eight microsatellite markers, and compared with a nearby hygric site, Şardu. Our results showed that while the two forms are strongly differentiated at Răscruci, it is the xeric form there that is most similar to the hygric form at Şardu, and Bayesian clustering algorithms suggest that these two populations have exchanged genes relatively recently. We found strong evidence for population substructuring, caused by high within host ant nest relatedness, indicating very limited dispersal of most ovipositing females, but not association with particular host ant species. Our results are consistent with the results of larger scale phylogeographic studies that suggest that the two forms represent local ecotypes specialising on different host plants, each with a distinct flowering phenology, providing a temporal rather than spatial barrier to gene flow.","lang":"eng"}],"citation":{"apa":"Tartally, A., Kelager, A., Fürst, M., &#38; Nash, D. (2016). Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.1865\">https://doi.org/10.7717/peerj.1865</a>","mla":"Tartally, András, et al. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” <i>PeerJ</i>, vol. 2016, no. 3, 1865, PeerJ, 2016, doi:<a href=\"https://doi.org/10.7717/peerj.1865\">10.7717/peerj.1865</a>.","ama":"Tartally A, Kelager A, Fürst M, Nash D. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. <i>PeerJ</i>. 2016;2016(3). doi:<a href=\"https://doi.org/10.7717/peerj.1865\">10.7717/peerj.1865</a>","short":"A. Tartally, A. Kelager, M. Fürst, D. Nash, PeerJ 2016 (2016).","ieee":"A. Tartally, A. Kelager, M. Fürst, and D. Nash, “Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon,” <i>PeerJ</i>, vol. 2016, no. 3. PeerJ, 2016.","ista":"Tartally A, Kelager A, Fürst M, Nash D. 2016. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. 2016(3), 1865.","chicago":"Tartally, András, Andreas Kelager, Matthias Fürst, and David Nash. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” <i>PeerJ</i>. PeerJ, 2016. <a href=\"https://doi.org/10.7717/peerj.1865\">https://doi.org/10.7717/peerj.1865</a>."},"quality_controlled":"1","_id":"1431"},{"status":"public","day":"13","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"],"date_created":"2018-12-11T11:51:59Z","volume":7,"ec_funded":1,"oa_version":"Published Version","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1396"}]},"doi":"10.1038/ncomms11552","publication":"Nature Communications","oa":1,"date_updated":"2023-09-07T11:55:25Z","article_number":"11552","acknowledgement":"We thank Jozsef Csicsvari and Nelson Spruston for critically reading the manuscript. We also thank A. Schlögl for programming, F. Marr for technical assistance and E. Kramberger for manuscript editing. ","month":"05","intvolume":"         7","date_published":"2016-05-13T00:00:00Z","year":"2016","quality_controlled":"1","_id":"1432","file_date_updated":"2020-07-14T12:44:53Z","type":"journal_article","abstract":[{"lang":"eng","text":"CA3–CA3 recurrent excitatory synapses are thought to play a key role in memory storage and pattern completion. Whether the plasticity properties of these synapses are consistent with their proposed network functions remains unclear. Here, we examine the properties of spike timing-dependent plasticity (STDP) at CA3–CA3 synapses. Low-frequency pairing of excitatory postsynaptic potentials (EPSPs) and action potentials (APs) induces long-term potentiation (LTP), independent of temporal order. The STDP curve is symmetric and broad (half-width ~150 ms). Consistent with these STDP induction properties, AP–EPSP sequences lead to supralinear summation of spine [Ca2+] transients. Furthermore, afterdepolarizations (ADPs) following APs efficiently propagate into dendrites of CA3 pyramidal neurons, and EPSPs summate with dendritic ADPs. In autoassociative network models, storage and recall are more robust with symmetric than with asymmetric STDP rules. Thus, a specialized STDP induction rule allows reliable storage and recall of information in the hippocampal CA3 network."}],"scopus_import":1,"citation":{"chicago":"Mishra, Rajiv Kumar, Sooyun Kim, José Guzmán, and Peter M Jonas. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>.","short":"R.K. Mishra, S. Kim, J. Guzmán, P.M. Jonas, Nature Communications 7 (2016).","ieee":"R. K. Mishra, S. Kim, J. Guzmán, and P. M. Jonas, “Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","ista":"Mishra RK, Kim S, Guzmán J, Jonas PM. 2016. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. Nature Communications. 7, 11552.","ama":"Mishra RK, Kim S, Guzmán J, Jonas PM. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>","mla":"Mishra, Rajiv Kumar, et al. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>, vol. 7, 11552, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>.","apa":"Mishra, R. K., Kim, S., Guzmán, J., &#38; Jonas, P. M. (2016). Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>"},"publication_status":"published","project":[{"name":"Mechanisms of transmitter release at GABAergic synapses","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P24909-B24"},{"call_identifier":"FP7","grant_number":"268548","_id":"25C0F108-B435-11E9-9278-68D0E5697425","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"}],"file":[{"date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:18:33Z","file_name":"IST-2016-582-v1+1_ncomms11552.pdf","checksum":"7e84d0392348c874d473b62f1042de22","access_level":"open_access","relation":"main_file","file_id":"5355","content_type":"application/pdf","creator":"system","file_size":4510512}],"author":[{"first_name":"Rajiv Kumar","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87","last_name":"Mishra","full_name":"Mishra, Rajiv Kumar"},{"last_name":"Kim","first_name":"Sooyun","id":"394AB1C8-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Sooyun"},{"orcid":"0000-0003-2209-5242","last_name":"Guzmán","first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José"},{"full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"title":"Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Publishing Group","has_accepted_license":"1","pubrep_id":"582","language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"publist_id":"5766"},{"volume":271,"date_created":"2018-12-11T11:52:00Z","day":"01","status":"public","main_file_link":[{"url":"http://arxiv.org/abs/1508.05905","open_access":"1"}],"doi":"10.1016/j.jfa.2016.04.006","publication":"Journal of Functional Analysis","oa_version":"Preprint","ec_funded":1,"intvolume":"       271","month":"08","date_published":"2016-08-01T00:00:00Z","date_updated":"2021-01-12T06:50:42Z","issue":"3","oa":1,"page":"672 - 719","year":"2016","citation":{"mla":"Bao, Zhigang, et al. “Local Stability of the Free Additive Convolution.” <i>Journal of Functional Analysis</i>, vol. 271, no. 3, Academic Press, 2016, pp. 672–719, doi:<a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">10.1016/j.jfa.2016.04.006</a>.","apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2016). Local stability of the free additive convolution. <i>Journal of Functional Analysis</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">https://doi.org/10.1016/j.jfa.2016.04.006</a>","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Stability of the Free Additive Convolution.” <i>Journal of Functional Analysis</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">https://doi.org/10.1016/j.jfa.2016.04.006</a>.","ama":"Bao Z, Erdös L, Schnelli K. Local stability of the free additive convolution. <i>Journal of Functional Analysis</i>. 2016;271(3):672-719. doi:<a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">10.1016/j.jfa.2016.04.006</a>","ista":"Bao Z, Erdös L, Schnelli K. 2016. Local stability of the free additive convolution. Journal of Functional Analysis. 271(3), 672–719.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local stability of the free additive convolution,” <i>Journal of Functional Analysis</i>, vol. 271, no. 3. Academic Press, pp. 672–719, 2016.","short":"Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 271 (2016) 672–719."},"type":"journal_article","abstract":[{"text":"We prove that the system of subordination equations, defining the free additive convolution of two probability measures, is stable away from the edges of the support and blow-up singularities by showing that the recent smoothness condition of Kargin is always satisfied. As an application, we consider the local spectral statistics of the random matrix ensemble A+UBU⁎A+UBU⁎, where U is a Haar distributed random unitary or orthogonal matrix, and A and B   are deterministic matrices. In the bulk regime, we prove that the empirical spectral distribution of A+UBU⁎A+UBU⁎ concentrates around the free additive convolution of the spectral distributions of A and B   on scales down to N−2/3N−2/3.","lang":"eng"}],"scopus_import":1,"_id":"1434","quality_controlled":"1","project":[{"grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems"}],"publication_status":"published","publisher":"Academic Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Local stability of the free additive convolution","author":[{"last_name":"Bao","orcid":"0000-0003-3036-1475","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang","full_name":"Bao, Zhigang"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László"},{"first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","last_name":"Schnelli","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin"}],"publist_id":"5764","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}]},{"date_published":"2016-01-01T00:00:00Z","intvolume":"      2016","month":"01","article_number":"1207393","date_updated":"2021-01-12T06:50:43Z","oa":1,"year":"2016","volume":2016,"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":"2018-12-11T11:52:00Z","ddc":["570"],"day":"01","status":"public","publication":"Neural Plasticity","doi":"10.1155/2016/1207393","oa_version":"Published Version","has_accepted_license":"1","publisher":"Hindawi Publishing Corporation","title":"P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Guzmán, José","first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","last_name":"Guzmán"},{"full_name":"Gerevich, Zoltan","first_name":"Zoltan","last_name":"Gerevich"}],"file":[{"file_size":1395180,"creator":"system","file_id":"4740","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"8dc5c2f3d44d4775a6e7e3edb0d7a0da","file_name":"IST-2016-580-v1+1_1207393.pdf","date_updated":"2020-07-14T12:44:54Z","date_created":"2018-12-12T10:09:17Z"}],"publist_id":"5762","department":[{"_id":"PeJo"}],"language":[{"iso":"eng"}],"pubrep_id":"580","citation":{"mla":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” <i>Neural Plasticity</i>, vol. 2016, 1207393, Hindawi Publishing Corporation, 2016, doi:<a href=\"https://doi.org/10.1155/2016/1207393\">10.1155/2016/1207393</a>.","apa":"Guzmán, J., &#38; Gerevich, Z. (2016). P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. <i>Neural Plasticity</i>. Hindawi Publishing Corporation. <a href=\"https://doi.org/10.1155/2016/1207393\">https://doi.org/10.1155/2016/1207393</a>","chicago":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” <i>Neural Plasticity</i>. Hindawi Publishing Corporation, 2016. <a href=\"https://doi.org/10.1155/2016/1207393\">https://doi.org/10.1155/2016/1207393</a>.","ama":"Guzmán J, Gerevich Z. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. <i>Neural Plasticity</i>. 2016;2016. doi:<a href=\"https://doi.org/10.1155/2016/1207393\">10.1155/2016/1207393</a>","ieee":"J. Guzmán and Z. Gerevich, “P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction,” <i>Neural Plasticity</i>, vol. 2016. Hindawi Publishing Corporation, 2016.","ista":"Guzmán J, Gerevich Z. 2016. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016, 1207393.","short":"J. Guzmán, Z. Gerevich, Neural Plasticity 2016 (2016)."},"abstract":[{"lang":"eng","text":"ATP released from neurons and astrocytes during neuronal activity or under pathophysiological circumstances is able to influence information flow in neuronal circuits by activation of ionotropic P2X and metabotropic P2Y receptors and subsequent modulation of cellular excitability, synaptic strength, and plasticity. In the present paper we review cellular and network effects of P2Y receptors in the brain. We show that P2Y receptors inhibit the release of neurotransmitters, modulate voltage- and ligand-gated ion channels, and differentially influence the induction of synaptic plasticity in the prefrontal cortex, hippocampus, and cerebellum. The findings discussed here may explain how P2Y1 receptor activation during brain injury, hypoxia, inflammation, schizophrenia, or Alzheimer's disease leads to an impairment of cognitive processes. Hence, it is suggested that the blockade of P2Y1 receptors may have therapeutic potential against cognitive disturbances in these states."}],"scopus_import":1,"type":"journal_article","file_date_updated":"2020-07-14T12:44:54Z","_id":"1435","quality_controlled":"1","publication_status":"published"},{"volume":105,"day":"01","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2018-12-11T11:52:00Z","ddc":["510","530"],"publication":"Journal de Mathématiques Pures et Appliquées","doi":"10.1016/j.matpur.2015.09.003","ec_funded":1,"oa_version":"Published Version","date_published":"2016-01-01T00:00:00Z","month":"01","intvolume":"       105","oa":1,"issue":"1","date_updated":"2021-01-12T06:50:43Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","page":"1 - 30","year":"2016","scopus_import":1,"abstract":[{"lang":"eng","text":"We study the time evolution of a system of N spinless fermions in R3 which interact through a pair potential, e.g., the Coulomb potential. We compare the dynamics given by the solution to Schrödinger's equation with the time-dependent Hartree-Fock approximation, and we give an estimate for the accuracy of this approximation in terms of the kinetic energy of the system. This leads, in turn, to bounds in terms of the initial total energy of the system."}],"file_date_updated":"2020-07-14T12:44:54Z","type":"journal_article","citation":{"chicago":"Bach, Volker, Sébastien Breteaux, Sören P Petrat, Peter Pickl, and Tim Tzaneteas. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” <i>Journal de Mathématiques Pures et Appliquées</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">https://doi.org/10.1016/j.matpur.2015.09.003</a>.","ieee":"V. Bach, S. Breteaux, S. P. Petrat, P. Pickl, and T. Tzaneteas, “Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction,” <i>Journal de Mathématiques Pures et Appliquées</i>, vol. 105, no. 1. Elsevier, pp. 1–30, 2016.","short":"V. Bach, S. Breteaux, S.P. Petrat, P. Pickl, T. Tzaneteas, Journal de Mathématiques Pures et Appliquées 105 (2016) 1–30.","ista":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. 2016. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 105(1), 1–30.","ama":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. <i>Journal de Mathématiques Pures et Appliquées</i>. 2016;105(1):1-30. doi:<a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">10.1016/j.matpur.2015.09.003</a>","mla":"Bach, Volker, et al. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” <i>Journal de Mathématiques Pures et Appliquées</i>, vol. 105, no. 1, Elsevier, 2016, pp. 1–30, doi:<a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">10.1016/j.matpur.2015.09.003</a>.","apa":"Bach, V., Breteaux, S., Petrat, S. P., Pickl, P., &#38; Tzaneteas, T. (2016). Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. <i>Journal de Mathématiques Pures et Appliquées</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">https://doi.org/10.1016/j.matpur.2015.09.003</a>"},"quality_controlled":"1","_id":"1436","publication_status":"published","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"publisher":"Elsevier","has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction","author":[{"last_name":"Bach","first_name":"Volker","full_name":"Bach, Volker"},{"last_name":"Breteaux","first_name":"Sébastien","full_name":"Breteaux, Sébastien"},{"first_name":"Sören P","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrat","orcid":"0000-0002-9166-5889","full_name":"Petrat, Sören P"},{"first_name":"Peter","last_name":"Pickl","full_name":"Pickl, Peter"},{"full_name":"Tzaneteas, Tim","first_name":"Tim","last_name":"Tzaneteas"}],"file":[{"relation":"main_file","access_level":"open_access","checksum":"c5afe1f6935bc7f2b546adbde1d31a35","creator":"system","file_size":658491,"file_id":"4825","content_type":"application/pdf","date_updated":"2020-07-14T12:44:54Z","date_created":"2018-12-12T10:10:36Z","file_name":"IST-2016-581-v1+1_1-s2.0-S0021782415001191-main.pdf"}],"department":[{"_id":"RoSe"}],"publist_id":"5763","pubrep_id":"581","language":[{"iso":"eng"}]},{"date_created":"2018-12-11T11:52:01Z","day":"11","status":"public","volume":"20-22","related_material":{"record":[{"id":"5441","relation":"earlier_version","status":"public"},{"id":"5442","status":"public","relation":"earlier_version"},{"id":"821","status":"public","relation":"dissertation_contains"},{"relation":"later_version","status":"public","id":"6009"},{"id":"8934","relation":"dissertation_contains","status":"public"}]},"ec_funded":1,"oa_version":"Preprint","doi":"10.1145/2837614.2837624","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.07565"}],"date_updated":"2024-03-25T23:30:18Z","oa":1,"month":"01","date_published":"2016-01-11T00:00:00Z","alternative_title":["POPL"],"year":"2016","page":"733 - 747","external_id":{"arxiv":["1510.07565"]},"conference":{"name":"POPL: Principles of Programming Languages","end_date":"2016-01-22","start_date":"2016-01-20","location":"St. Petersburg, FL, USA"},"_id":"1437","quality_controlled":"1","citation":{"apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2016). Algorithms for algebraic path properties in concurrent systems of constant treewidth components (Vol. 20–22, pp. 733–747). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>","mla":"Chatterjee, Krishnendu, et al. <i>Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components</i>. Vol. 20–22, ACM, 2016, pp. 733–47, doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>.","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 733–747.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2016. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. POPL: Principles of Programming Languages, POPL, vol. 20–22, 733–747.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, ACM, 2016, pp. 733–747.","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. In: Vol 20-22. ACM; 2016:733-747. doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components,” 20–22:733–47. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>."},"type":"conference","arxiv":1,"abstract":[{"text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.","lang":"eng"}],"scopus_import":1,"project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"}],"publication_status":"published","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Goharshady, Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir","last_name":"Goharshady","orcid":"0000-0003-1702-6584"},{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722"}],"publisher":"ACM","language":[{"iso":"eng"}],"publist_id":"5761","department":[{"_id":"KrCh"}]},{"department":[{"_id":"KrCh"}],"publist_id":"5760","language":[{"iso":"eng"}],"publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Fu, Hongfei","first_name":"Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu"},{"full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotny"},{"last_name":"Hasheminezhad","first_name":"Rouzbeh","full_name":"Hasheminezhad, Rouzbeh"}],"publication_status":"published","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"type":"conference","scopus_import":1,"arxiv":1,"abstract":[{"text":"In this paper, we consider termination of probabilistic programs with real-valued variables. The questions concerned are: (a) qualitative ones that ask (i) whether the program terminates with probability 1 (almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); (b) quantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) to compute a bound B such that the probability to terminate after B steps decreases exponentially (concentration problem). To solve these questions, we utilize the notion of ranking supermartingales which is a powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmic synthesis of linear ranking-supermartingales over affine probabilistic programs (APP's) with both angelic and demonic non-determinism. An important subclass of APP's is LRAPP which is defined as the class of all APP's over which a linear ranking-supermartingale exists. Our main contributions are as follows. Firstly, we show that the membership problem of LRAPP (i) can be decided in polynomial time for APP's with at most demonic non-determinism, and (ii) is NP-hard and in PSPACE for APP's with angelic non-determinism; moreover, the NP-hardness result holds already for APP's without probability and demonic non-determinism. Secondly, we show that the concentration problem over LRAPP can be solved in the same complexity as for the membership problem of LRAPP. Finally, we show that the expectation problem over LRAPP can be solved in 2EXPTIME and is PSPACE-hard even for APP's without probability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate the effectiveness of our approach to answer the qualitative and quantitative questions over APP's with at most demonic non-determinism.","lang":"eng"}],"citation":{"apa":"Chatterjee, K., Fu, H., Novotný, P., &#38; Hasheminezhad, R. (2016). Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs (Vol. 20–22, pp. 327–342). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837639\">https://doi.org/10.1145/2837614.2837639</a>","mla":"Chatterjee, Krishnendu, et al. <i>Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs</i>. Vol. 20–22, ACM, 2016, pp. 327–42, doi:<a href=\"https://doi.org/10.1145/2837614.2837639\">10.1145/2837614.2837639</a>.","short":"K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, in:, ACM, 2016, pp. 327–342.","ista":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2016. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. POPL: Principles of Programming Languages, POPL, vol. 20–22, 327–342.","ieee":"K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 327–342.","ama":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. In: Vol 20-22. ACM; 2016:327-342. doi:<a href=\"https://doi.org/10.1145/2837614.2837639\">10.1145/2837614.2837639</a>","chicago":"Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs,” 20–22:327–42. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837639\">https://doi.org/10.1145/2837614.2837639</a>."},"quality_controlled":"1","_id":"1438","conference":{"location":"St. Petersburg, FL, USA","name":"POPL: Principles of Programming Languages","end_date":"2016-01-22","start_date":"2016-01-20"},"page":"327 - 342","external_id":{"arxiv":["1510.08517"]},"year":"2016","acknowledgement":"Supported by the Natural Science Foundation of China (NSFC) under Grant No. 61532019 ","month":"01","alternative_title":["POPL"],"date_published":"2016-01-11T00:00:00Z","oa":1,"date_updated":"2023-09-19T14:38:41Z","main_file_link":[{"url":"http://arxiv.org/abs/1510.08517","open_access":"1"}],"doi":"10.1145/2837614.2837639","oa_version":"Preprint","ec_funded":1,"related_material":{"record":[{"id":"5993","relation":"later_version","status":"public"}]},"volume":"20-22","status":"public","day":"11","date_created":"2018-12-11T11:52:01Z"},{"volume":"20-22","date_created":"2018-12-11T11:52:01Z","day":"11","status":"public","doi":"10.1145/2837614.2837650","main_file_link":[{"url":"https://hal.inria.fr/hal-01251199/","open_access":"1"}],"oa_version":"Preprint","ec_funded":1,"month":"01","alternative_title":["ACM SIGPLAN Notices"],"date_published":"2016-01-11T00:00:00Z","acknowledgement":"Damien Zufferey was supported by DARPA (Grants FA8650-11-C-7192 and FA8650-15-C-7564) and NSF (Grant CCF-1138967). ","date_updated":"2021-01-12T06:50:45Z","oa":1,"page":"400 - 415","conference":{"location":"St. Petersburg, FL, USA","name":"POPL: Principles of Programming Languages","end_date":"2016-01-22","start_date":"2016-01-20"},"year":"2016","citation":{"mla":"Dragoi, Cezara, et al. <i>PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms</i>. Vol. 20–22, ACM, 2016, pp. 400–15, doi:<a href=\"https://doi.org/10.1145/2837614.2837650\">10.1145/2837614.2837650</a>.","apa":"Dragoi, C., Henzinger, T. A., &#38; Zufferey, D. (2016). PSYNC: A partially synchronous language for fault-tolerant distributed algorithms (Vol. 20–22, pp. 400–415). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837650\">https://doi.org/10.1145/2837614.2837650</a>","chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms,” 20–22:400–415. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837650\">https://doi.org/10.1145/2837614.2837650</a>.","ista":"Dragoi C, Henzinger TA, Zufferey D. 2016. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. POPL: Principles of Programming Languages, ACM SIGPLAN Notices, vol. 20–22, 400–415.","ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “PSYNC: A partially synchronous language for fault-tolerant distributed algorithms,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 400–415.","short":"C. Dragoi, T.A. Henzinger, D. Zufferey, in:, ACM, 2016, pp. 400–415.","ama":"Dragoi C, Henzinger TA, Zufferey D. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. In: Vol 20-22. ACM; 2016:400-415. doi:<a href=\"https://doi.org/10.1145/2837614.2837650\">10.1145/2837614.2837650</a>"},"type":"conference","abstract":[{"lang":"eng","text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. We introduce PSYNC, a domain specific language based on the Heard-Of model, which views asynchronous faulty systems as synchronous ones with an adversarial environment that simulates asynchrony and faults by dropping messages. We define a runtime system for PSYNC that efficiently executes on asynchronous networks. We formalize the relation between the runtime system and PSYNC in terms of observational refinement. The high-level lockstep abstraction introduced by PSYNC simplifies the design and implementation of fault-tolerant distributed algorithms and enables automated formal verification. We have implemented an embedding of PSYNC in the SCALA programming language with a runtime system for asynchronous networks. We show the applicability of PSYNC by implementing several important fault-tolerant distributed algorithms and we compare the implementation of consensus algorithms in PSYNC against implementations in other languages in terms of code size, runtime efficiency, and verification."}],"scopus_import":1,"_id":"1439","quality_controlled":"1","project":[{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"}],"publication_status":"published","publisher":"ACM","title":"PSYNC: A partially synchronous language for fault-tolerant distributed algorithms","author":[{"full_name":"Dragoi, Cezara","last_name":"Dragoi","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","first_name":"Cezara"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736","last_name":"Zufferey","full_name":"Zufferey, Damien"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"publist_id":"5759","language":[{"iso":"eng"}]},{"publication":"Structure","publication_status":"published","doi":"10.1016/j.str.2016.01.002","project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012"},{"grant_number":"303564","call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"grant_number":"W1232-B24","call_identifier":"FWF","_id":"255A6082-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"ec_funded":1,"oa_version":"None","scopus_import":1,"type":"journal_article","volume":24,"citation":{"mla":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” <i>Structure</i>, vol. 24, no. 2, Cell Press, 2016, pp. 213–15, doi:<a href=\"https://doi.org/10.1016/j.str.2016.01.002\">10.1016/j.str.2016.01.002</a>.","apa":"Janovjak, H. L. (2016). Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. <i>Structure</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.str.2016.01.002\">https://doi.org/10.1016/j.str.2016.01.002</a>","chicago":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” <i>Structure</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.str.2016.01.002\">https://doi.org/10.1016/j.str.2016.01.002</a>.","short":"H.L. Janovjak, Structure 24 (2016) 213–215.","ieee":"H. L. Janovjak, “Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain,” <i>Structure</i>, vol. 24, no. 2. Cell Press, pp. 213–215, 2016.","ista":"Janovjak HL. 2016. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. 24(2), 213–215.","ama":"Janovjak HL. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. <i>Structure</i>. 2016;24(2):213-215. doi:<a href=\"https://doi.org/10.1016/j.str.2016.01.002\">10.1016/j.str.2016.01.002</a>"},"day":"02","status":"public","quality_controlled":"1","date_created":"2018-12-11T11:52:02Z","_id":"1440","publist_id":"5756","department":[{"_id":"HaJa"}],"page":"213 - 215","year":"2016","language":[{"iso":"eng"}],"acknowledgement":"The author thanks Banerjee et al. (2016) for providing coordinates prior to public release and apologizes to colleagues whose work was not cited or discussed due to the limited space available. The author is supported by grants from EU FP7 (CIG-303564), HFSP (RGY0084_2012), and FWF (W1232).","publisher":"Cell Press","date_published":"2016-02-02T00:00:00Z","month":"02","intvolume":"        24","title":"Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","full_name":"Janovjak, Harald L"}],"issue":"2","date_updated":"2021-01-12T06:50:46Z"},{"project":[{"_id":"25548C20-B435-11E9-9278-68D0E5697425","name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564","call_identifier":"FP7"},{"_id":"255A6082-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF"}],"publication_status":"published","_id":"1441","quality_controlled":"1","citation":{"chicago":"Gschaider-Reichhart, Eva, Álvaro Inglés Prieto, Alexandra-Madelaine Tichy, Catherine Mckenzie, and Harald L Janovjak. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2016. <a href=\"https://doi.org/10.1002/anie.201601736\">https://doi.org/10.1002/anie.201601736</a>.","ieee":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, and H. L. Janovjak, “A phytochrome sensory domain permits receptor activation by red light,” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 21. Wiley, pp. 6339–6342, 2016.","ista":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. 2016. A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie - International Edition. 55(21), 6339–6342.","short":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, H.L. Janovjak, Angewandte Chemie - International Edition 55 (2016) 6339–6342.","ama":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. A phytochrome sensory domain permits receptor activation by red light. <i>Angewandte Chemie - International Edition</i>. 2016;55(21):6339-6342. doi:<a href=\"https://doi.org/10.1002/anie.201601736\">10.1002/anie.201601736</a>","mla":"Gschaider-Reichhart, Eva, et al. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 21, Wiley, 2016, pp. 6339–42, doi:<a href=\"https://doi.org/10.1002/anie.201601736\">10.1002/anie.201601736</a>.","apa":"Gschaider-Reichhart, E., Inglés Prieto, Á., Tichy, A.-M., Mckenzie, C., &#38; Janovjak, H. L. (2016). A phytochrome sensory domain permits receptor activation by red light. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201601736\">https://doi.org/10.1002/anie.201601736</a>"},"file_date_updated":"2020-07-14T12:44:55Z","type":"journal_article","scopus_import":1,"abstract":[{"text":"Optogenetics and photopharmacology enable the spatio-temporal control of cell and animal behavior by light. Although red light offers deep-tissue penetration and minimal phototoxicity, very few red-light-sensitive optogenetic methods are currently available. We have now developed a red-light-induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non-invasively in mammalian tissue and in multicolor cell-signaling experiments. The light-controlled dimerizer and red-light-activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light. Go deep with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was repurposed to induce the homodimerization of proteins in living cells by red light. By using this domain, light-activated protein kinases were engineered that can be activated orthogonally from many fluorescent proteins and through mammalian tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1.","lang":"eng"}],"language":[{"iso":"eng"}],"pubrep_id":"840","department":[{"_id":"HaJa"}],"publist_id":"5755","file":[{"file_name":"IST-2017-840-v1+1_reichhart.pdf","date_created":"2018-12-12T10:17:03Z","date_updated":"2020-07-14T12:44:55Z","content_type":"application/pdf","file_id":"5255","file_size":1268662,"creator":"system","relation":"main_file","checksum":"26da07960e57ac4750b54179197ce57f","access_level":"open_access"}],"title":"A phytochrome sensory domain permits receptor activation by red light","author":[{"id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Gschaider-Reichhart","orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva"},{"full_name":"Inglés Prieto, Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro","orcid":"0000-0002-5409-8571","last_name":"Inglés Prieto"},{"first_name":"Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","last_name":"Tichy","full_name":"Tichy, Alexandra-Madelaine"},{"full_name":"Mckenzie, Catherine","last_name":"Mckenzie","first_name":"Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Janovjak","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","full_name":"Janovjak, Harald L"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","publisher":"Wiley","related_material":{"record":[{"id":"418","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"oa_version":"Submitted Version","doi":"10.1002/anie.201601736","publication":"Angewandte Chemie - International Edition","date_created":"2018-12-11T11:52:02Z","ddc":["571","576"],"day":"17","status":"public","volume":55,"year":"2016","page":"6339 - 6342","date_updated":"2023-09-07T12:49:08Z","issue":"21","oa":1,"intvolume":"        55","month":"05","date_published":"2016-05-17T00:00:00Z","acknowledgement":"A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W1232) and a FemTech fellowship (Austrian Research Promotion Agency: 3580812)."},{"citation":{"chicago":"Calatrava Moreno, Maria, Thomas Auzinger, and Hannes Werthner. “On the Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic Data.” <i>Scientometrics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11192-016-1842-4\">https://doi.org/10.1007/s11192-016-1842-4</a>.","ama":"Calatrava Moreno M, Auzinger T, Werthner H. On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. <i>Scientometrics</i>. 2016;107(1):213-232. doi:<a href=\"https://doi.org/10.1007/s11192-016-1842-4\">10.1007/s11192-016-1842-4</a>","short":"M. Calatrava Moreno, T. Auzinger, H. Werthner, Scientometrics 107 (2016) 213–232.","ieee":"M. Calatrava Moreno, T. Auzinger, and H. Werthner, “On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data,” <i>Scientometrics</i>, vol. 107, no. 1. Springer, pp. 213–232, 2016.","ista":"Calatrava Moreno M, Auzinger T, Werthner H. 2016. On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. Scientometrics. 107(1), 213–232.","mla":"Calatrava Moreno, Maria, et al. “On the Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic Data.” <i>Scientometrics</i>, vol. 107, no. 1, Springer, 2016, pp. 213–32, doi:<a href=\"https://doi.org/10.1007/s11192-016-1842-4\">10.1007/s11192-016-1842-4</a>.","apa":"Calatrava Moreno, M., Auzinger, T., &#38; Werthner, H. (2016). On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. <i>Scientometrics</i>. Springer. <a href=\"https://doi.org/10.1007/s11192-016-1842-4\">https://doi.org/10.1007/s11192-016-1842-4</a>"},"type":"journal_article","file_date_updated":"2020-07-14T12:44:55Z","scopus_import":"1","abstract":[{"lang":"eng","text":"The accuracy of interdisciplinarity measurements is directly related to the quality of the underlying bibliographic data. Existing indicators of interdisciplinarity are not capable of reflecting the inaccuracies introduced by incorrect and incomplete records because correct and complete bibliographic data can rarely be obtained. This is the case for the Rao–Stirling index, which cannot handle references that are not categorized into disciplinary fields. We introduce a method that addresses this problem. It extends the Rao–Stirling index to acknowledge missing data by calculating its interval of uncertainty using computational optimization. The evaluation of our method indicates that the uncertainty interval is not only useful for estimating the inaccuracy of interdisciplinarity measurements, but it also delivers slightly more accurate aggregated interdisciplinarity measurements than the Rao–Stirling index."}],"_id":"1446","quality_controlled":"1","publication_status":"published","has_accepted_license":"1","publisher":"Springer","file":[{"file_name":"IST-2016-530-v1+1_s11192-016-1842-4.pdf","date_updated":"2020-07-14T12:44:55Z","date_created":"2018-12-12T10:10:56Z","file_id":"4848","content_type":"application/pdf","file_size":806035,"creator":"system","access_level":"open_access","checksum":"32d46268588b87d9b686492018e6a2b2","relation":"main_file"}],"author":[{"first_name":"Maria","last_name":"Calatrava Moreno","full_name":"Calatrava Moreno, Maria"},{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Auzinger","orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas"},{"full_name":"Werthner, Hannes","first_name":"Hannes","last_name":"Werthner"}],"title":"On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","publist_id":"5750","department":[{"_id":"BeBi"}],"language":[{"iso":"eng"}],"pubrep_id":"530","volume":107,"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":"2018-12-11T11:52:04Z","status":"public","day":"01","doi":"10.1007/s11192-016-1842-4","publication":"Scientometrics","related_material":{"link":[{"url":"https://doi.org/10.1007/s11192-016-1902-9","relation":"erratum"}]},"oa_version":"Published Version","intvolume":"       107","month":"04","date_published":"2016-04-01T00:00:00Z","date_updated":"2021-11-16T08:29:11Z","issue":"1","oa":1,"page":"213 - 232","year":"2016"},{"publist_id":"5748","department":[{"_id":"JaMa"}],"language":[{"iso":"eng"}],"publisher":"Institute of Mathematical Statistics","author":[{"first_name":"Max","last_name":"Fathi","full_name":"Fathi, Max"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"title":"Entropic Ricci curvature bounds for discrete interacting systems","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","citation":{"ama":"Fathi M, Maas J. Entropic Ricci curvature bounds for discrete interacting systems. <i>The Annals of Applied Probability</i>. 2016;26(3):1774-1806. doi:<a href=\"https://doi.org/10.1214/15-AAP1133\">10.1214/15-AAP1133</a>","ieee":"M. Fathi and J. Maas, “Entropic Ricci curvature bounds for discrete interacting systems,” <i>The Annals of Applied Probability</i>, vol. 26, no. 3. Institute of Mathematical Statistics, pp. 1774–1806, 2016.","short":"M. Fathi, J. Maas, The Annals of Applied Probability 26 (2016) 1774–1806.","ista":"Fathi M, Maas J. 2016. Entropic Ricci curvature bounds for discrete interacting systems. The Annals of Applied Probability. 26(3), 1774–1806.","chicago":"Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting Systems.” <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2016. <a href=\"https://doi.org/10.1214/15-AAP1133\">https://doi.org/10.1214/15-AAP1133</a>.","apa":"Fathi, M., &#38; Maas, J. (2016). Entropic Ricci curvature bounds for discrete interacting systems. <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/15-AAP1133\">https://doi.org/10.1214/15-AAP1133</a>","mla":"Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting Systems.” <i>The Annals of Applied Probability</i>, vol. 26, no. 3, Institute of Mathematical Statistics, 2016, pp. 1774–806, doi:<a href=\"https://doi.org/10.1214/15-AAP1133\">10.1214/15-AAP1133</a>."},"abstract":[{"lang":"eng","text":"We develop a new and systematic method for proving entropic Ricci curvature lower bounds for Markov chains on discrete sets. Using different methods, such bounds have recently been obtained in several examples (e.g., 1-dimensional birth and death chains, product chains, Bernoulli–Laplace models, and random transposition models). However, a general method to obtain discrete Ricci bounds had been lacking. Our method covers all of the examples above. In addition we obtain new Ricci curvature bounds for zero-range processes on the complete graph. The method is inspired by recent work of Caputo, Dai Pra and Posta on discrete functional inequalities."}],"scopus_import":1,"type":"journal_article","_id":"1448","quality_controlled":"1","page":"1774 - 1806","year":"2016","date_published":"2016-06-01T00:00:00Z","intvolume":"        26","month":"06","acknowledgement":"Supported by the German Research Foundation through the Collaborative Research Center 1060\r\nThe Mathematics of Emergent Effects and the Hausdorff Center for Mathematics. Part of this work has been done while M. Fathi visited J. Maas at the University of Bonn in July 2014.We would like to thank the referees for their careful reading of the manuscript. ","date_updated":"2021-01-12T06:50:49Z","oa":1,"issue":"3","publication":"The Annals of Applied Probability","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.00562"}],"doi":"10.1214/15-AAP1133","oa_version":"Preprint","volume":26,"date_created":"2018-12-11T11:52:05Z","status":"public","day":"01"}]