[{"oa":1,"title":"Extremal eigenvalues and eigenvectors of deformed Wigner matrices","type":"journal_article","doi":"10.1007/s00440-014-0610-8","main_file_link":[{"url":"http://arxiv.org/abs/1310.7057","open_access":"1"}],"corr_author":"1","scopus_import":"1","publication":"Probability Theory and Related Fields","author":[{"first_name":"Jioon","full_name":"Lee, Jioon","last_name":"Lee"},{"orcid":"0000-0003-0954-3231","first_name":"Kevin","last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin"}],"article_processing_charge":"No","date_created":"2018-12-11T11:54:31Z","project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804"}],"quality_controlled":"1","page":"165 - 241","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"LaEr"}],"volume":164,"month":"02","date_published":"2016-02-01T00:00:00Z","fulldoi":"https://doi.org/10.1007/s00440-014-0610-8","date_updated":"2025-09-18T10:46:46Z","publist_id":"5215","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"abstract":[{"text":"We consider random matrices of the form H=W+λV, λ∈ℝ+, where W is a real symmetric or complex Hermitian Wigner matrix of size N and V is a real bounded diagonal random matrix of size N with i.i.d.\\ entries that are independent of W. We assume subexponential decay for the matrix entries of W and we choose λ∼1, so that the eigenvalues of W and λV are typically of the same order. Further, we assume that the density of the entries of V is supported on a single interval and is convex near the edges of its support. In this paper we prove that there is λ+∈ℝ+ such that the largest eigenvalues of H are in the limit of large N determined by the order statistics of V for λ&gt;λ+. In particular, the largest eigenvalue of H has a Weibull distribution in the limit N→∞ if λ&gt;λ+. Moreover, for N sufficiently large, we show that the eigenvectors associated to the largest eigenvalues are partially localized for λ&gt;λ+, while they are completely delocalized for λ&lt;λ+. Similar results hold for the lowest eigenvalues. ","lang":"eng"}],"issue":"1-2","external_id":{"arxiv":["1310.7057"],"isi":["000373163300006"]},"intvolume":"       164","status":"public","_id":"1881","oa_version":"Preprint","isi":1,"day":"01","arxiv":1,"publisher":"Springer","citation":{"short":"J. Lee, K. Schnelli, Probability Theory and Related Fields 164 (2016) 165–241.","mla":"Lee, Jioon, and Kevin Schnelli. “Extremal Eigenvalues and Eigenvectors of Deformed Wigner Matrices.” <i>Probability Theory and Related Fields</i>, vol. 164, no. 1–2, Springer, 2016, pp. 165–241, doi:<a href=\"https://doi.org/10.1007/s00440-014-0610-8\">10.1007/s00440-014-0610-8</a>.","chicago":"Lee, Jioon, and Kevin Schnelli. “Extremal Eigenvalues and Eigenvectors of Deformed Wigner Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00440-014-0610-8\">https://doi.org/10.1007/s00440-014-0610-8</a>.","ieee":"J. Lee and K. Schnelli, “Extremal eigenvalues and eigenvectors of deformed Wigner matrices,” <i>Probability Theory and Related Fields</i>, vol. 164, no. 1–2. Springer, pp. 165–241, 2016.","apa":"Lee, J., &#38; Schnelli, K. (2016). Extremal eigenvalues and eigenvectors of deformed Wigner matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-014-0610-8\">https://doi.org/10.1007/s00440-014-0610-8</a>","ama":"Lee J, Schnelli K. Extremal eigenvalues and eigenvectors of deformed Wigner matrices. <i>Probability Theory and Related Fields</i>. 2016;164(1-2):165-241. doi:<a href=\"https://doi.org/10.1007/s00440-014-0610-8\">10.1007/s00440-014-0610-8</a>","ista":"Lee J, Schnelli K. 2016. Extremal eigenvalues and eigenvectors of deformed Wigner matrices. Probability Theory and Related Fields. 164(1–2), 165–241."},"acknowledgement":"Most of the presented work was obtained while Kevin Schnelli was staying at the IAS with the support of\r\nThe Fund For Math.","year":"2016"},{"fulldoi":"https://doi.org/10.3233/978-1-61499-672-9-1432","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"ddc":["004"],"has_accepted_license":"1","date_published":"2016-01-01T00:00:00Z","file_date_updated":"2020-07-14T12:46:35Z","abstract":[{"text":"Magic: the Gathering is a game about magical combat for any number of players. Formally it is a zero-sum, imperfect information stochastic game that consists of a potentially unbounded number of steps. We consider the problem of deciding if a move is legal in a given single step of Magic. We show that the problem is (a) coNP-complete in general; and (b) in P if either of two small sets of cards are not used. Our lower bound holds even for single-player Magic games. The significant aspects of our results are as follows: First, in most real-life game problems, the task of deciding whether a given move is legal in a single step is trivial, and the computationally hard task is to find the best sequence of legal moves in the presence of multiple players. In contrast, quite uniquely our hardness result holds for single step and with only one-player. Second, we establish efficient algorithms for important special cases of Magic.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","alternative_title":["Frontiers in Artificial Intelligence and Applications"],"publist_id":"7342","date_updated":"2025-09-22T14:26:27Z","file":[{"date_updated":"2020-07-14T12:46:35Z","content_type":"application/pdf","creator":"system","relation":"main_file","checksum":"848043c812ace05e459579c923f3d3cf","access_level":"open_access","file_name":"IST-2018-950-v1+1_2016_Chatterjee_The_complexity.pdf","date_created":"2018-12-12T10:07:59Z","file_size":2116225,"file_id":"4658"}],"intvolume":"       285","external_id":{"isi":["000385793700166"]},"year":"2016","citation":{"ieee":"K. Chatterjee and R. Ibsen-Jensen, “The complexity of deciding legality of a single step of magic: The gathering,” presented at the ECAI: European Conference on Artificial Intelligence, The Hague, Netherlands, 2016, vol. 285, pp. 1432–1439.","apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2016). The complexity of deciding legality of a single step of magic: The gathering (Vol. 285, pp. 1432–1439). Presented at the ECAI: European Conference on Artificial Intelligence, The Hague, Netherlands: IOS Press. <a href=\"https://doi.org/10.3233/978-1-61499-672-9-1432\">https://doi.org/10.3233/978-1-61499-672-9-1432</a>","ama":"Chatterjee K, Ibsen-Jensen R. The complexity of deciding legality of a single step of magic: The gathering. In: Vol 285. IOS Press; 2016:1432-1439. doi:<a href=\"https://doi.org/10.3233/978-1-61499-672-9-1432\">10.3233/978-1-61499-672-9-1432</a>","ista":"Chatterjee K, Ibsen-Jensen R. 2016. The complexity of deciding legality of a single step of magic: The gathering. ECAI: European Conference on Artificial Intelligence, Frontiers in Artificial Intelligence and Applications, vol. 285, 1432–1439.","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. <i>The Complexity of Deciding Legality of a Single Step of Magic: The Gathering</i>. Vol. 285, IOS Press, 2016, pp. 1432–39, doi:<a href=\"https://doi.org/10.3233/978-1-61499-672-9-1432\">10.3233/978-1-61499-672-9-1432</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, IOS Press, 2016, pp. 1432–1439.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Complexity of Deciding Legality of a Single Step of Magic: The Gathering,” 285:1432–39. IOS Press, 2016. <a href=\"https://doi.org/10.3233/978-1-61499-672-9-1432\">https://doi.org/10.3233/978-1-61499-672-9-1432</a>."},"publisher":"IOS Press","day":"01","isi":1,"oa_version":"Published Version","_id":"478","status":"public","doi":"10.3233/978-1-61499-672-9-1432","type":"conference","oa":1,"title":"The complexity of deciding legality of a single step of magic: The gathering","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389"}],"scopus_import":"1","corr_author":"1","conference":{"start_date":"2016-08-29","end_date":"2016-09-02","name":"ECAI: European Conference on Artificial Intelligence","location":"The Hague, Netherlands"},"quality_controlled":"1","date_created":"2018-12-11T11:46:41Z","article_processing_charge":"No","month":"01","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"volume":285,"publication_status":"published","pubrep_id":"950","page":"1432 - 1439"},{"publisher":"IEEE","acknowledgement":"This work is supported by NSF CNS 13-30077, NSF CNS 13-29886, NSF CNS 15-45002, and NSFC 61303014.\r\nThe authors thank Dr.  Bobby and Dr.  Hill at Carle Hospital, Urbana, IL for their help with the discussion on medical  knowledge.\r\n\r\n","year":"2016","citation":{"chicago":"Jiang, Yu, Han Liu, Hui Kong, Rui Wang, Mohamad Hosseini, Jiaguang Sun, and Lui Sha. “Use Runtime Verification to Improve the Quality of Medical Care Practice.” In <i>Proceedings of the 38th International Conference on Software Engineering Companion </i>, 112–21. IEEE, 2016. <a href=\"https://doi.org/10.1145/2889160.2889233\">https://doi.org/10.1145/2889160.2889233</a>.","mla":"Jiang, Yu, et al. “Use Runtime Verification to Improve the Quality of Medical Care Practice.” <i>Proceedings of the 38th International Conference on Software Engineering Companion </i>, IEEE, 2016, pp. 112–21, doi:<a href=\"https://doi.org/10.1145/2889160.2889233\">10.1145/2889160.2889233</a>.","short":"Y. Jiang, H. Liu, H. Kong, R. Wang, M. Hosseini, J. Sun, L. Sha, in:, Proceedings of the 38th International Conference on Software Engineering Companion , IEEE, 2016, pp. 112–121.","ista":"Jiang Y, Liu H, Kong H, Wang R, Hosseini M, Sun J, Sha L. 2016. Use runtime verification to improve the quality of medical care practice. Proceedings of the 38th International Conference on Software Engineering Companion . ICSE: International Conference on Software Engineering, Proceedings International Conference on Software Engineering, , 112–121.","ama":"Jiang Y, Liu H, Kong H, et al. Use runtime verification to improve the quality of medical care practice. In: <i>Proceedings of the 38th International Conference on Software Engineering Companion </i>. IEEE; 2016:112-121. doi:<a href=\"https://doi.org/10.1145/2889160.2889233\">10.1145/2889160.2889233</a>","ieee":"Y. Jiang <i>et al.</i>, “Use runtime verification to improve the quality of medical care practice,” in <i>Proceedings of the 38th International Conference on Software Engineering Companion </i>, Austin, TX, USA, 2016, pp. 112–121.","apa":"Jiang, Y., Liu, H., Kong, H., Wang, R., Hosseini, M., Sun, J., &#38; Sha, L. (2016). Use runtime verification to improve the quality of medical care practice. In <i>Proceedings of the 38th International Conference on Software Engineering Companion </i> (pp. 112–121). Austin, TX, USA: IEEE. <a href=\"https://doi.org/10.1145/2889160.2889233\">https://doi.org/10.1145/2889160.2889233</a>"},"isi":1,"day":"14","oa_version":"None","status":"public","_id":"479","external_id":{"isi":["000402155300016"]},"abstract":[{"lang":"eng","text":"Clinical guidelines and decision support systems (DSS) play an important role in daily practices of medicine. Many text-based guidelines have been encoded for work-flow simulation of DSS to automate health care. During the collaboration with Carle hospital to develop a DSS, we identify that, for some complex and life-critical diseases, it is highly desirable to automatically rigorously verify some complex temporal properties in guidelines, which brings new challenges to current simulation based DSS with limited support of automatical formal verification and real-time data analysis. In this paper, we conduct the first study on applying runtime verification to cooperate with current DSS based on real-time data. Within the proposed technique, a user-friendly domain specific language, named DRTV, is designed to specify vital real-time data sampled by medical devices and temporal properties originated from clinical guidelines. Some interfaces are developed for data acquisition and communication. Then, for medical practice scenarios described in DRTV model, we will automatically generate event sequences and runtime property verifier automata. If a temporal property violates, real-time warnings will be produced by the formal verifier and passed to medical DSS. We have used DRTV to specify different kinds of medical care scenarios, and applied the proposed technique to assist existing DSS. As presented in experiment results, in terms of warning detection, it outperforms the only use of DSS or human inspection, and improves the quality of clinical health care of hospital"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:22:48Z","alternative_title":["Proceedings International Conference on Software Engineering"],"publist_id":"7341","fulldoi":"https://doi.org/10.1145/2889160.2889233","date_published":"2016-05-14T00:00:00Z","month":"05","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"page":"112 - 121","quality_controlled":"1","article_processing_charge":"No","date_created":"2018-12-11T11:46:42Z","author":[{"first_name":"Yu","last_name":"Jiang","full_name":"Jiang, Yu"},{"first_name":"Han","full_name":"Liu, Han","last_name":"Liu"},{"first_name":"Hui","orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","last_name":"Kong","full_name":"Kong, Hui"},{"first_name":"Rui","last_name":"Wang","full_name":"Wang, Rui"},{"last_name":"Hosseini","full_name":"Hosseini, Mohamad","first_name":"Mohamad"},{"first_name":"Jiaguang","full_name":"Sun, Jiaguang","last_name":"Sun"},{"full_name":"Sha, Lui","last_name":"Sha","first_name":"Lui"}],"publication":"Proceedings of the 38th International Conference on Software Engineering Companion ","scopus_import":"1","conference":{"location":"Austin, TX, USA","end_date":"2016-05-22","name":"ICSE: International Conference on Software Engineering","start_date":"2016-05-14"},"type":"conference","doi":"10.1145/2889160.2889233","title":"Use runtime verification to improve the quality of medical care practice"},{"abstract":[{"lang":"eng","text":"Graph games provide the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic reactive processes, the traditional model is perfect-information stochastic games, where some transitions of the game graph are controlled by two adversarial players, and the other transitions are executed probabilistically. We consider such games where the objective is the conjunction of several quantitative objectives (specified as mean-payoff conditions), which we refer to as generalized mean-payoff objectives. The basic decision problem asks for the existence of a finite-memory strategy for a player that ensures the generalized mean-payoff objective be satisfied with a desired probability against all strategies of the opponent. A special case of the decision problem is the almost-sure problem where the desired probability is 1. Previous results presented a semi-decision procedure for -approximations of the almost-sure problem. In this work, we show that both the almost-sure problem as well as the general basic decision problem are coNP-complete, significantly improving the previous results. Moreover, we show that in the case of 1-player stochastic games, randomized memoryless strategies are sufficient and the problem can be solved in polynomial time. In contrast, in two-player stochastic games, we show that even with randomized strategies exponential memory is required in general, and present a matching exponential upper bound. We also study the basic decision problem with infinite-memory strategies and present computational complexity results for the problem. Our results are relevant in the synthesis of stochastic reactive systems with multiple quantitative requirements."}],"ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"7340","alternative_title":["Proceedings Symposium on Logic in Computer Science"],"date_updated":"2025-09-22T14:22:08Z","fulldoi":"https://doi.org/10.1145/2933575.2934513","date_published":"2016-07-05T00:00:00Z","publisher":"IEEE","year":"2016","citation":{"chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Perfect-Information Stochastic Games with Generalized Mean-Payoff Objectives,” 05-08-July-2016:247–56. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2934513\">https://doi.org/10.1145/2933575.2934513</a>.","short":"K. Chatterjee, L. Doyen, in:, IEEE, 2016, pp. 247–256.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Perfect-Information Stochastic Games with Generalized Mean-Payoff Objectives</i>. Vol. 05-08-July-2016, IEEE, 2016, pp. 247–56, doi:<a href=\"https://doi.org/10.1145/2933575.2934513\">10.1145/2933575.2934513</a>.","ista":"Chatterjee K, Doyen L. 2016. Perfect-information stochastic games with generalized mean-payoff objectives. LICS: Logic in Computer Science, Proceedings Symposium on Logic in Computer Science, vol. 05-08-July-2016, 247–256.","ama":"Chatterjee K, Doyen L. Perfect-information stochastic games with generalized mean-payoff objectives. In: Vol 05-08-July-2016. IEEE; 2016:247-256. doi:<a href=\"https://doi.org/10.1145/2933575.2934513\">10.1145/2933575.2934513</a>","ieee":"K. Chatterjee and L. Doyen, “Perfect-information stochastic games with generalized mean-payoff objectives,” presented at the LICS: Logic in Computer Science, New York, NY, USA, 2016, vol. 05-08-July-2016, pp. 247–256.","apa":"Chatterjee, K., &#38; Doyen, L. (2016). Perfect-information stochastic games with generalized mean-payoff objectives (Vol. 05-08-July-2016, pp. 247–256). Presented at the LICS: Logic in Computer Science, New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2934513\">https://doi.org/10.1145/2933575.2934513</a>"},"isi":1,"day":"05","arxiv":1,"oa_version":"Preprint","status":"public","_id":"480","external_id":{"isi":["000387609200025"],"arxiv":["1604.06376"]},"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"}],"scopus_import":"1","conference":{"start_date":"2016-07-05","location":"New York, NY, USA","end_date":"2016-07-08","name":"LICS: Logic in Computer Science"},"type":"conference","doi":"10.1145/2933575.2934513","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.06376"}],"oa":1,"title":"Perfect-information stochastic games with generalized mean-payoff objectives","month":"07","publication_status":"published","language":[{"iso":"eng"}],"volume":"05-08-July-2016","department":[{"_id":"KrCh"}],"page":"247 - 256","quality_controlled":"1","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"article_processing_charge":"No","date_created":"2018-12-11T11:46:42Z"},{"conference":{"start_date":"2016-09-05","location":"Sydney, Australia","end_date":"2016-09-08","name":"NP: Nonlinear Photonics"},"publist_id":"7339","alternative_title":["Optics InfoBase Conference Papers"],"date_updated":"2023-10-17T12:16:43Z","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Nonlinear electro-optical conversion of microwave radiation into the optical telecommunication band is achieved within a crystalline whispering gallery mode resonator, reaching 0.1% photon number conversion efficiency with MHz bandwidth."}],"author":[{"first_name":"Alfredo","last_name":"Rueda","full_name":"Rueda, Alfredo"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"last_name":"Collodo","full_name":"Collodo, Michele","first_name":"Michele"},{"last_name":"Vogl","full_name":"Vogl, Ulrich","first_name":"Ulrich"},{"first_name":"Birgit","last_name":"Stiller","full_name":"Stiller, Birgit"},{"last_name":"Schunk","full_name":"Schunk, Gerhard","first_name":"Gerhard"},{"first_name":"Dmitry","full_name":"Strekalov, Dmitry","last_name":"Strekalov"},{"full_name":"Marquardt, Christoph","last_name":"Marquardt","first_name":"Christoph"},{"last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","first_name":"Johannes M","orcid":"0000-0001-8112-028X"},{"full_name":"Painter, Oskar","last_name":"Painter","first_name":"Oskar"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"full_name":"Schwefel, Harald","last_name":"Schwefel","first_name":"Harald"}],"date_published":"2016-08-29T00:00:00Z","title":"Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator","fulldoi":"https://doi.org/10.1364/NP.2016.NTh3A.6","doi":"10.1364/NP.2016.NTh3A.6","type":"conference","status":"public","_id":"482","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"oa_version":"None","publication_status":"published","day":"29","month":"08","citation":{"ama":"Rueda A, Sedlmeir F, Collodo M, et al. Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator. In: Optica Publishing Group; 2016. doi:<a href=\"https://doi.org/10.1364/NP.2016.NTh3A.6\">10.1364/NP.2016.NTh3A.6</a>","ista":"Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D, Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator. NP: Nonlinear Photonics, Optics InfoBase Conference Papers, .","ieee":"A. Rueda <i>et al.</i>, “Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator,” presented at the NP: Nonlinear Photonics, Sydney, Australia, 2016.","apa":"Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., … Schwefel, H. (2016). Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator. Presented at the NP: Nonlinear Photonics, Sydney, Australia: Optica Publishing Group. <a href=\"https://doi.org/10.1364/NP.2016.NTh3A.6\">https://doi.org/10.1364/NP.2016.NTh3A.6</a>","chicago":"Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit Stiller, Gerhard Schunk, Dmitry Strekalov, et al. “Nonlinear Single Sideband Microwave to Optical Conversion Using an Electro-Optic WGM-Resonator.” Optica Publishing Group, 2016. <a href=\"https://doi.org/10.1364/NP.2016.NTh3A.6\">https://doi.org/10.1364/NP.2016.NTh3A.6</a>.","mla":"Rueda, Alfredo, et al. <i>Nonlinear Single Sideband Microwave to Optical Conversion Using an Electro-Optic WGM-Resonator</i>. Optica Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1364/NP.2016.NTh3A.6\">10.1364/NP.2016.NTh3A.6</a>.","short":"A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov, C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, in:, Optica Publishing Group, 2016."},"year":"2016","publisher":"Optica Publishing Group","date_created":"2018-12-11T11:46:43Z","article_processing_charge":"No","quality_controlled":"1"},{"publisher":"Taylor & Francis","citation":{"short":"Z. Liu, N. Yang, Y. Lv, L. Pan, S. Lv, H. Han, G. Wang, Plant Signaling &#38; Behavior 11 (2016).","mla":"Liu, Zhijun, et al. “The CLE Gene Family in Populus Trichocarpa.” <i>Plant Signaling &#38; Behavior</i>, vol. 11, no. 6, e1191734, Taylor &#38; Francis, 2016, doi:<a href=\"https://doi.org/10.1080/15592324.2016.1191734\">10.1080/15592324.2016.1191734</a>.","chicago":"Liu, Zhijun, Nan Yang, Yanting Lv, Lixia Pan, Shuo Lv, Huibin Han, and Guodong Wang. “The CLE Gene Family in Populus Trichocarpa.” <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis, 2016. <a href=\"https://doi.org/10.1080/15592324.2016.1191734\">https://doi.org/10.1080/15592324.2016.1191734</a>.","ieee":"Z. Liu <i>et al.</i>, “The CLE gene family in Populus trichocarpa,” <i>Plant Signaling &#38; Behavior</i>, vol. 11, no. 6. Taylor &#38; Francis, 2016.","apa":"Liu, Z., Yang, N., Lv, Y., Pan, L., Lv, S., Han, H., &#38; Wang, G. (2016). The CLE gene family in Populus trichocarpa. <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15592324.2016.1191734\">https://doi.org/10.1080/15592324.2016.1191734</a>","ama":"Liu Z, Yang N, Lv Y, et al. The CLE gene family in Populus trichocarpa. <i>Plant Signaling &#38; Behavior</i>. 2016;11(6). doi:<a href=\"https://doi.org/10.1080/15592324.2016.1191734\">10.1080/15592324.2016.1191734</a>","ista":"Liu Z, Yang N, Lv Y, Pan L, Lv S, Han H, Wang G. 2016. The CLE gene family in Populus trichocarpa. Plant Signaling &#38; Behavior. 11(6), e1191734."},"acknowledgement":"We are grateful to Dr. Long (Laboratoire de Reproduction et Developpement des Plantes,CNRS,INRA,ENSLyon,UCBL,Universite de Lyon,France)for critical reading of the article. Work in our group is supported by the National Natural Science Foundation of China (31271575; 31200902), the Fundamental Research Funds for the Central Univ ersities (GK201103005), the Specialized Research Fund for the Doctoral Program of Higher Education from the Ministry of Education of China (20120202120009), the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry, and the Natural Science Basic Research Plan in Shaanxi Province of China (2014JM3064). ","year":"2016","isi":1,"day":"02","oa_version":"Submitted Version","status":"public","_id":"510","intvolume":"        11","issue":"6","external_id":{"isi":["000378740600025"]},"abstract":[{"lang":"eng","text":"The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted signaling peptides that are primarily involved in the regulation of stem cell homeostasis in different plant meristems. Particularly, the characterization of the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on the potential roles of CLE peptides in vascular development and wood formation. Nevertheless, our knowledge on this gene family in a tree species is limited. In a recent study, we reported on a systematically investigation of the CLE gene family in Populus trichocarpa . The potential roles of PtCLE genes were studied by comparative analysis and transcriptional pro fi ling. Among fi fty PtCLE members, many PtCLE proteins share identical CLE motifs or contain the same CLE motif as that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression patterns comparing to their Arabidopsis counterparts. These fi ndings indicate the existence of both functional conservation and functional divergence between PtCLEs and their AtCLE orthologues. Our results provide valuable resources for future functional investigations of these critical signaling molecules in woody plants. "}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"7308","date_updated":"2025-09-22T14:21:19Z","fulldoi":"https://doi.org/10.1080/15592324.2016.1191734","date_published":"2016-06-02T00:00:00Z","month":"06","publication_status":"published","language":[{"iso":"eng"}],"volume":11,"department":[{"_id":"JiFr"}],"quality_controlled":"1","article_processing_charge":"No","date_created":"2018-12-11T11:46:53Z","author":[{"last_name":"Liu","full_name":"Liu, Zhijun","first_name":"Zhijun"},{"full_name":"Yang, Nan","last_name":"Yang","first_name":"Nan"},{"last_name":"Lv","full_name":"Lv, Yanting","first_name":"Yanting"},{"first_name":"Lixia","full_name":"Pan, Lixia","last_name":"Pan"},{"first_name":"Shuo","last_name":"Lv","full_name":"Lv, Shuo"},{"full_name":"Han, Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin"},{"first_name":"Guodong","last_name":"Wang","full_name":"Wang, Guodong"}],"publication":"Plant Signaling & Behavior","scopus_import":"1","article_number":"e1191734","type":"journal_article","doi":"10.1080/15592324.2016.1191734","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973754/"}],"oa":1,"title":"The CLE gene family in Populus trichocarpa"},{"month":"03","pubrep_id":"523","publication_status":"published","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"page":"33","related_material":{"record":[{"status":"public","id":"1604","relation":"later_version"}]},"date_created":"2018-12-12T11:39:22Z","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis"},{"first_name":"Yaron","full_name":"Velner, Yaron","last_name":"Velner"}],"type":"technical_report","doi":"10.15479/AT:IST-2016-523-v1-1","title":"Quantitative interprocedural analysis","oa":1,"publication_identifier":{"issn":["2664-1690"]},"publisher":"IST Austria","citation":{"ama":"Chatterjee K, Pavlogiannis A, Velner Y. <i>Quantitative Interprocedural Analysis</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">10.15479/AT:IST-2016-523-v1-1</a>","ista":"Chatterjee K, Pavlogiannis A, Velner Y. 2016. Quantitative interprocedural analysis, IST Austria, 33p.","ieee":"K. Chatterjee, A. Pavlogiannis, and Y. Velner, <i>Quantitative interprocedural analysis</i>. IST Austria, 2016.","apa":"Chatterjee, K., Pavlogiannis, A., &#38; Velner, Y. (2016). <i>Quantitative interprocedural analysis</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">https://doi.org/10.15479/AT:IST-2016-523-v1-1</a>","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. <i>Quantitative Interprocedural Analysis</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">https://doi.org/10.15479/AT:IST-2016-523-v1-1</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Interprocedural Analysis</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">10.15479/AT:IST-2016-523-v1-1</a>.","short":"K. Chatterjee, A. Pavlogiannis, Y. Velner, Quantitative Interprocedural Analysis, IST Austria, 2016."},"year":"2016","day":"31","oa_version":"Published Version","status":"public","_id":"5445","file":[{"file_id":"5513","file_size":1012204,"date_created":"2018-12-12T11:53:52Z","file_name":"IST-2016-523-v1+1_main.pdf","relation":"main_file","access_level":"open_access","checksum":"cef516fa091925b5868813e355268fb4","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:46:58Z"}],"abstract":[{"text":"We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs. ","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["IST Austria Technical Report"],"date_updated":"2025-04-15T08:11:41Z","fulldoi":"https://doi.org/10.15479/AT:IST-2016-523-v1-1","has_accepted_license":"1","date_published":"2016-03-31T00:00:00Z","ddc":["005"]},{"file":[{"access_level":"open_access","checksum":"8345a8c1e7d7f0cd92516d182b7fc59e","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:46:58Z","creator":"system","file_id":"5529","file_name":"IST-2016-648-v1+1_tr.pdf","file_size":1264221,"date_created":"2018-12-12T11:54:07Z"}],"publisher":"IST Austria","year":"2016","citation":{"chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Amplification on Undirected Population Structures: Comets Beat Stars, IST Austria, 2016.","mla":"Pavlogiannis, Andreas, et al. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">10.15479/AT:IST-2016-648-v1-1</a>.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">10.15479/AT:IST-2016-648-v1-1</a>","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Amplification on undirected population structures: Comets beat stars, IST Austria, 22p.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria, 2016.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>"},"day":"09","oa_version":"Updated Version","_id":"5449","status":"public","fulldoi":"https://doi.org/10.15479/AT:IST-2016-648-v1-1","date_published":"2016-11-09T00:00:00Z","has_accepted_license":"1","ddc":["519"],"file_date_updated":"2020-07-14T12:46:58Z","abstract":[{"text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population.\r\nThe fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure.\r\nAmplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade.\r\nIn this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["IST Austria Technical Report"],"date_updated":"2025-09-18T09:50:09Z","related_material":{"record":[{"id":"512","relation":"later_version","status":"public"}]},"date_created":"2018-12-12T11:39:24Z","month":"11","publication_status":"published","pubrep_id":"648","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"page":"22","type":"technical_report","doi":"10.15479/AT:IST-2016-648-v1-1","oa":1,"title":"Amplification on undirected population structures: Comets beat stars","publication_identifier":{"issn":["2664-1690"]},"author":[{"first_name":"Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"},{"orcid":"0000-0002-1097-9684","first_name":"Josef","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}]},{"author":[{"first_name":"Andreas","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis"},{"full_name":"Tkadlec, Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"file_date_updated":"2020-07-14T12:46:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["IST Austria Technical Report"],"date_updated":"2023-02-23T12:27:05Z","type":"technical_report","fulldoi":"https://doi.org/10.15479/AT:IST-2016-728-v1-1","doi":"10.15479/AT:IST-2016-728-v1-1","oa":1,"title":"Strong amplifiers of natural selection","has_accepted_license":"1","date_published":"2016-12-30T00:00:00Z","publication_identifier":{"issn":["2664-1690"]},"ddc":["000"],"publisher":"IST Austria","year":"2016","citation":{"ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">10.15479/AT:IST-2016-728-v1-1</a>","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Strong amplifiers of natural selection, IST Austria, 34p.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Strong amplifiers of natural selection</i>. IST Austria, 2016.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">https://doi.org/10.15479/AT:IST-2016-728-v1-1</a>","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">https://doi.org/10.15479/AT:IST-2016-728-v1-1</a>.","mla":"Pavlogiannis, Andreas, et al. <i>Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">10.15479/AT:IST-2016-728-v1-1</a>.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Strong Amplifiers of Natural Selection, IST Austria, 2016."},"month":"12","day":"30","oa_version":"Published Version","pubrep_id":"728","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"_id":"5451","status":"public","page":"34","file":[{"date_created":"2018-12-12T11:53:04Z","file_size":1014732,"file_name":"IST-2016-728-v1+1_main.pdf","file_id":"5465","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:46:59Z","checksum":"7b8bb17c322c0556acba6ac169fa71c1","access_level":"open_access","relation":"main_file"}],"date_created":"2018-12-12T11:39:24Z"},{"fulldoi":"https://doi.org/10.15479/AT:IST-2017-728-v2-1","ddc":["000"],"has_accepted_license":"1","date_published":"2016-12-30T00:00:00Z","file_date_updated":"2020-07-14T12:46:59Z","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-15T07:55:39Z","alternative_title":["IST Austria Technical Report"],"file":[{"relation":"main_file","access_level":"open_access","checksum":"58e895f26c82f560c0f0989bf8b08599","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:46:59Z","file_id":"5460","file_size":811558,"date_created":"2018-12-12T11:52:59Z","file_name":"IST-2017-728-v2+1_main.pdf"}],"citation":{"ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">10.15479/AT:IST-2017-728-v2-1</a>","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 32p.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria, 2016.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">https://doi.org/10.15479/AT:IST-2017-728-v2-1</a>","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">https://doi.org/10.15479/AT:IST-2017-728-v2-1</a>.","mla":"Pavlogiannis, Andreas, et al. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">10.15479/AT:IST-2017-728-v2-1</a>.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016."},"year":"2016","publisher":"IST Austria","day":"30","oa_version":"Published Version","status":"public","_id":"5452","doi":"10.15479/AT:IST-2017-728-v2-1","type":"technical_report","publication_identifier":{"issn":["2664-1690"]},"title":"Arbitrarily strong amplifiers of natural selection","oa":1,"author":[{"orcid":"0000-0002-8943-0722","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis"},{"orcid":"0000-0002-1097-9684","first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"5453"},{"id":"5559","relation":"popular_science","status":"public"}]},"project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"date_created":"2018-12-12T11:39:25Z","article_processing_charge":"No","month":"12","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"publication_status":"published","pubrep_id":"750","page":"32"},{"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5452"}]},"file":[{"creator":"system","date_updated":"2020-07-14T12:46:59Z","content_type":"application/pdf","checksum":"83b0313dab3bff4bdb6ac38695026fda","access_level":"open_access","relation":"main_file","file_size":1015647,"date_created":"2018-12-12T11:53:13Z","file_name":"IST-2017-749-v3+1_main.pdf","file_id":"5474"}],"date_created":"2018-12-12T11:39:25Z","citation":{"chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">https://doi.org/10.15479/AT:IST-2017-749-v3-1</a>.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","mla":"Pavlogiannis, Andreas, et al. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">10.15479/AT:IST-2017-749-v3-1</a>.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">10.15479/AT:IST-2017-749-v3-1</a>","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 34p.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">https://doi.org/10.15479/AT:IST-2017-749-v3-1</a>","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria, 2016."},"year":"2016","publisher":"IST Austria","day":"30","month":"12","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"publication_status":"published","oa_version":"Published Version","pubrep_id":"755","_id":"5453","status":"public","page":"34","doi":"10.15479/AT:IST-2017-749-v3-1","fulldoi":"https://doi.org/10.15479/AT:IST-2017-749-v3-1","type":"technical_report","publication_identifier":{"issn":["2664-1690"]},"ddc":["000"],"has_accepted_license":"1","title":"Arbitrarily strong amplifiers of natural selection","date_published":"2016-12-30T00:00:00Z","oa":1,"file_date_updated":"2020-07-14T12:46:59Z","author":[{"orcid":"0000-0002-8943-0722","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis"},{"full_name":"Tkadlec, Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","orcid":"0000-0002-1097-9684"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-15T07:55:37Z","alternative_title":["IST Austria Technical Report"]},{"date_updated":"2025-09-22T07:32:43Z","publist_id":"5828","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas","first_name":"Thomas","orcid":"0000-0002-8511-0254"},{"full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478"}],"abstract":[{"lang":"eng","text":"We collected flower colour information on species in the tribe Antirrhineae from taxonomic literature. We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)"}],"file_date_updated":"2020-07-14T12:47:00Z","ddc":["576"],"oa":1,"has_accepted_license":"1","date_published":"2016-02-19T00:00:00Z","title":"Flower colour data and phylogeny (NEXUS) files","fulldoi":"https://doi.org/10.15479/AT:ISTA:34","doi":"10.15479/AT:ISTA:34","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"type":"research_data","_id":"5550","status":"public","department":[{"_id":"NiBa"}],"oa_version":"Published Version","day":"19","month":"02","license":"https://creativecommons.org/publicdomain/zero/1.0/","year":"2016","citation":{"ama":"Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>","ista":"Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","apa":"Ellis, T., &#38; Field, D. (2016). Flower colour data and phylogeny (NEXUS) files. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>","ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016.","chicago":"Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS) Files.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>.","mla":"Ellis, Thomas, and David Field. <i>Flower Colour Data and Phylogeny (NEXUS) Files</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","short":"T. Ellis, D. Field, (2016)."},"publisher":"Institute of Science and Technology Austria","datarep_id":"34","date_created":"2018-12-12T12:31:29Z","article_processing_charge":"No","related_material":{"record":[{"relation":"research_paper","id":"1382","status":"public"}]},"file":[{"access_level":"open_access","checksum":"950f85b80427d357bfeff09608ba02e9","relation":"main_file","date_updated":"2020-07-14T12:47:00Z","content_type":"application/zip","creator":"system","file_id":"5594","file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","date_created":"2018-12-12T13:02:27Z","file_size":4468543}]},{"license":"https://creativecommons.org/licenses/by-sa/4.0/","citation":{"ama":"Lukacisin M, Landon M, Jajoo R. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>","ista":"Lukacisin M, Landon M, Jajoo R. 2016. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>.","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016.","apa":"Lukacisin, M., Landon, M., &#38; Jajoo, R. (2016). MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:45\">https://doi.org/10.15479/AT:ISTA:45</a>","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:45\">https://doi.org/10.15479/AT:ISTA:45</a>.","mla":"Lukacisin, Martin, et al. <i>MATLAB Analysis Code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.”</i> Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>.","short":"M. Lukacisin, M. Landon, R. Jajoo, (2016)."},"year":"2016","publisher":"Institute of Science and Technology Austria","day":"25","month":"08","department":[{"_id":"ToBo"}],"oa_version":"Published Version","_id":"5556","status":"public","related_material":{"record":[{"relation":"used_in_publication","id":"8431","status":"deleted"},{"relation":"research_paper","id":"1029","status":"public"}]},"file":[{"file_name":"IST-2016-45-v1+1_PaperCode.zip","file_size":296722548,"date_created":"2018-12-12T13:02:58Z","file_id":"5616","date_updated":"2020-07-14T12:47:02Z","content_type":"application/zip","creator":"system","checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","access_level":"open_access","relation":"main_file"}],"datarep_id":"45","date_created":"2018-12-12T12:31:31Z","article_processing_charge":"No","abstract":[{"lang":"eng","text":"MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions"}],"file_date_updated":"2020-07-14T12:47:02Z","author":[{"orcid":"0000-0001-6549-4177","first_name":"Martin","last_name":"Lukacisin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisin, Martin"},{"last_name":"Landon","full_name":"Landon, Matthieu","first_name":"Matthieu"},{"full_name":"Jajoo, Rishi","last_name":"Jajoo","first_name":"Rishi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-07-10T11:49:51Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:45","doi":"10.15479/AT:ISTA:45","keyword":["transcription","pausing","backtracking","polymerase","RNA","NET-seq","nucleosome","basepairing"],"tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png"},"type":"research_data","ddc":["571"],"date_published":"2016-08-25T00:00:00Z","has_accepted_license":"1","oa":1,"title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'"},{"publisher":"Institute of Science and Technology Austria","year":"2016","citation":{"chicago":"Swoboda, Paul. “Synthetic Discrete Tomography Problems.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:46\">https://doi.org/10.15479/AT:ISTA:46</a>.","short":"P. Swoboda, (2016).","mla":"Swoboda, Paul. <i>Synthetic Discrete Tomography Problems</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>.","ista":"Swoboda P. 2016. Synthetic discrete tomography problems, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>.","ama":"Swoboda P. Synthetic discrete tomography problems. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>","ieee":"P. Swoboda, “Synthetic discrete tomography problems.” Institute of Science and Technology Austria, 2016.","apa":"Swoboda, P. (2016). Synthetic discrete tomography problems. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:46\">https://doi.org/10.15479/AT:ISTA:46</a>"},"month":"09","day":"20","oa_version":"Published Version","department":[{"_id":"VlKo"}],"_id":"5557","status":"public","file":[{"file_name":"IST-2016-46-v1+1_discrete_tomography_synthetic.zip","file_size":36058401,"date_created":"2018-12-12T13:05:19Z","file_id":"5645","date_updated":"2020-07-14T12:47:02Z","content_type":"application/zip","creator":"system","relation":"main_file","checksum":"aa5a16a0dc888da7186fb8fc45e88439","access_level":"open_access"}],"article_processing_charge":"No","datarep_id":"46","date_created":"2018-12-12T12:31:31Z","author":[{"first_name":"Paul","last_name":"Swoboda","id":"446560C6-F248-11E8-B48F-1D18A9856A87","full_name":"Swoboda, Paul"}],"abstract":[{"lang":"eng","text":"Small synthetic discrete tomography problems.\r\nSizes are 32x32, 64z64 and 256x256.\r\nProjection angles are 2, 4, and 6.\r\nNumber of labels are 3 and 5."}],"file_date_updated":"2020-07-14T12:47:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:50:21Z","contributor":[{"last_name":"Kuske","contributor_type":"data_collector","first_name":"Jan"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"type":"research_data","keyword":["discrete tomography"],"doi":"10.15479/AT:ISTA:46","fulldoi":"https://doi.org/10.15479/AT:ISTA:46","has_accepted_license":"1","oa":1,"title":"Synthetic discrete tomography problems","date_published":"2016-09-20T00:00:00Z","ddc":["006"]},{"issue":"3","external_id":{"isi":["000371219500015"],"pmid":["26609077"]},"intvolume":"        33","file":[{"checksum":"47d9010690b6c5c17f2ac830cc63ac5c","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:47:10Z","content_type":"application/pdf","creator":"dernst","file_id":"5750","file_name":"2016_MolBiolEvol_Wielgoss.pdf","file_size":634037,"date_created":"2018-12-18T13:21:45Z"}],"isi":1,"day":"01","publisher":"Oxford University Press","citation":{"short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology and Evolution 33 (2016) 770–782.","mla":"Wielgoss, Sébastien, et al. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3, Oxford University Press, 2016, pp. 770–82, doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>.","chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>.","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria,” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3. Oxford University Press, pp. 770–782, 2016.","apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &#38; Hall, A. R. (2016). Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>","ista":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2016. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. Molecular Biology and Evolution. 33(3), 770–782.","ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. 2016;33(3):770-782. doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>"},"year":"2016","acknowledgement":"The authors thank three anonymous reviewers and the editor for helpful comments on the manuscript, as well as Dominique Schneider for feedback on an earlier draft, Jenna Gallie for lytic λ and Julien Capelle for T5 and T6. This work was supported by the Swiss National Science Foundation (PZ00P3_148255 to A.H.) and an EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development (FP7-PEOPLE-2012-IEF-331824 to S.W.).","_id":"5749","status":"public","oa_version":"Published Version","DOAJ_listed":"1","OA_place":"publisher","has_accepted_license":"1","OA_type":"gold","date_published":"2016-03-01T00:00:00Z","ddc":["576"],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"article_type":"original","fulldoi":"https://doi.org/10.1093/molbev/msv270","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance."}],"file_date_updated":"2020-07-14T12:47:10Z","date_updated":"2026-04-29T05:57:02Z","quality_controlled":"1","related_material":{"record":[{"id":"9719","relation":"research_data","status":"public"}]},"article_processing_charge":"No","date_created":"2018-12-18T13:18:10Z","month":"03","page":"770-782","publication_status":"published","pubrep_id":"587","department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"volume":33,"oa":1,"title":"Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria","pmid":1,"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"type":"journal_article","doi":"10.1093/molbev/msv270","publication":"Molecular Biology and Evolution","author":[{"full_name":"Wielgoss, Sébastien","last_name":"Wielgoss","first_name":"Sébastien"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","full_name":"Bergmiller, Tobias","first_name":"Tobias","orcid":"0000-0001-5396-4346"},{"last_name":"Bischofberger","full_name":"Bischofberger, Anna M.","first_name":"Anna M."},{"full_name":"Hall, Alex R.","last_name":"Hall","first_name":"Alex R."}],"scopus_import":"1"},{"conference":{"name":"CTIC: Computational Topology in Image Context","end_date":"2016-06-17","location":"Marseille, France","start_date":"2016-06-15"},"author":[{"last_name":"Sen","full_name":"Sen, Nabhasmita","first_name":"Nabhasmita"},{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas","first_name":"Ranita","orcid":"0000-0002-5372-7890"},{"last_name":"Bhowmick","full_name":"Bhowmick, Partha","first_name":"Partha"}],"publication":"Computational Topology in Image Context","doi":"10.1007/978-3-319-39441-1_23","type":"book_chapter","publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-319-39441-1"],"eissn":["1611-3349"],"isbn":["978-3-319-39440-4"]},"title":"On some local topological properties of naive discrete sphere","extern":"1","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"volume":9667,"publication_status":"published","page":"253-264","month":"06","date_created":"2019-01-08T20:44:24Z","article_processing_charge":"No","quality_controlled":"1","place":"Cham","alternative_title":["LNCS"],"date_updated":"2022-01-28T08:01:22Z","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"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","fulldoi":"https://doi.org/10.1007/978-3-319-39441-1_23","date_published":"2016-06-02T00:00:00Z","oa_version":"None","_id":"5805","status":"public","citation":{"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>","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.","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>","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.","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>.","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>."},"year":"2016","publisher":"Springer Nature","day":"02","intvolume":"      9667"},{"department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"volume":9647,"publication_status":"published","page":"256-267","month":"04","date_created":"2019-01-08T20:44:37Z","article_processing_charge":"No","quality_controlled":"1","place":"Cham","conference":{"start_date":"2016-04-18","location":"Nantes, France","name":"DGCI: International Conference on Discrete Geometry for Computer Imagery","end_date":"2016-04-20"},"author":[{"full_name":"Biswas, Ranita","last_name":"Biswas","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","first_name":"Ranita"},{"first_name":"Partha","full_name":"Bhowmick, Partha","last_name":"Bhowmick"}],"publication":"Discrete Geometry for Computer Imagery","doi":"10.1007/978-3-319-32360-2_20","type":"conference","publication_identifier":{"issn":["0302-9743","1611-3349"],"eisbn":["978-3-319-32360-2"],"isbn":["978-3-319-32359-6"]},"title":"On functionality of quadraginta octants of naive sphere with application to circle drawing","extern":"1","oa_version":"None","status":"public","_id":"5806","year":"2016","citation":{"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>","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.","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>","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.","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>.","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>.","short":"R. Biswas, P. Bhowmick, in:, Discrete Geometry for Computer Imagery, Springer Nature, Cham, 2016, pp. 256–267."},"publisher":"Springer Nature","day":"09","intvolume":"      9647","alternative_title":["LNCS"],"date_updated":"2022-01-28T08:10:11Z","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."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","fulldoi":"https://doi.org/10.1007/978-3-319-32360-2_20","date_published":"2016-04-09T00:00:00Z"},{"place":"Cham","quality_controlled":"1","article_processing_charge":"No","date_created":"2019-01-08T20:45:19Z","month":"01","page":"86-100","publication_status":"published","department":[{"_id":"HeEd"}],"volume":9448,"language":[{"iso":"eng"}],"extern":"1","title":"On the connectivity and smoothness of discrete spherical circles","publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-319-26144-7"],"eisbn":["978-3-319-26145-4"],"eissn":["1611-3349"]},"type":"book_chapter","doi":"10.1007/978-3-319-26145-4_7","publication":"Combinatorial image analysis","author":[{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas","first_name":"Ranita","orcid":"0000-0002-5372-7890"},{"full_name":"Bhowmick, Partha","last_name":"Bhowmick","first_name":"Partha"},{"first_name":"Valentin E.","full_name":"Brimkov, Valentin E.","last_name":"Brimkov"}],"conference":{"start_date":"2015-11-24","location":"Kolkata, India","name":"IWCIA: International Workshop on Combinatorial Image Analysis","end_date":"2015-11-27"},"intvolume":"      9448","day":"06","publisher":"Springer Nature","citation":{"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>","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.","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>","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>.","short":"R. Biswas, P. Bhowmick, V.E. Brimkov, in:, Combinatorial Image Analysis, Springer Nature, Cham, 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>."},"year":"2016","_id":"5809","status":"public","oa_version":"None","date_published":"2016-01-06T00:00:00Z","fulldoi":"https://doi.org/10.1007/978-3-319-26145-4_7","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","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."}],"date_updated":"2022-01-28T08:13:03Z"},{"day":"02","month":"02","year":"2016","acknowledgement":"We thank Mitsuru Ikeda for preparing replica images used in Fig. 2.","citation":{"mla":"Harada, Harumi, and Ryuichi Shigemoto. “High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” <i>Receptor and Ion Channel Detection in the Brain</i>, Springer Nature, 2016, pp. 233–45, doi:<a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">10.1007/978-1-4939-3064-7_17</a>.","short":"H. Harada, R. Shigemoto, in:, Receptor and Ion Channel Detection in the Brain, Springer Nature, 2016, pp. 233–245.","chicago":"Harada, Harumi, and Ryuichi Shigemoto. “High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” In <i>Receptor and Ion Channel Detection in the Brain</i>, 233–45. Neuromethods. Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">https://doi.org/10.1007/978-1-4939-3064-7_17</a>.","ieee":"H. Harada and R. Shigemoto, “High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL),” in <i>Receptor and Ion Channel Detection in the Brain</i>, Springer Nature, 2016, pp. 233–245.","apa":"Harada, H., &#38; Shigemoto, R. (2016). High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In <i>Receptor and Ion Channel Detection in the Brain</i> (pp. 233–245). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">https://doi.org/10.1007/978-1-4939-3064-7_17</a>","ista":"Harada H, Shigemoto R. 2016.High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. , 233–245.","ama":"Harada H, Shigemoto R. High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In: <i>Receptor and Ion Channel Detection in the Brain</i>. Neuromethods. Springer Nature; 2016:233-245. doi:<a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">10.1007/978-1-4939-3064-7_17</a>"},"publisher":"Springer Nature","series_title":"Neuromethods","_id":"19990","status":"public","page":"233-245","department":[{"_id":"RySh"}],"language":[{"iso":"eng"}],"publication_status":"published","oa_version":"None","quality_controlled":"1","date_created":"2025-07-10T13:56:06Z","article_processing_charge":"No","publication":"Receptor and Ion Channel Detection in the Brain","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","abstract":[{"text":"Visualizing molecular localization at high resolution contributes to understanding of their functions and roles in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study high-resolution two-dimensional distribution of transmembrane proteins and their tightly associated proteins on platinum-carbon replica. During treatment with SDS, unfixed proteins and intracellular organelle are dissolved and integral membrane proteins captured and stabilized by carbon and platinum deposition are denatured, retaining most of their antigenicity, and exposed on exoplasmic and protoplasmic surfaces of lipid monolayers. The exposure of these antigens on the surface of replica facilitates the accessibility of antibodies and therefore provides higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples and an additional procedure for fluorescence-guided electron microscopy for replica immunolabeling.","lang":"eng"}],"author":[{"full_name":"Harada, Harumi","last_name":"Harada","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Harumi","orcid":"0000-0001-7429-7896"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"}],"corr_author":"1","date_updated":"2026-04-07T08:32:03Z","publication_identifier":{"issn":["0893-2336"],"eissn":["1940-6045"],"eisbn":["9781493930647"],"isbn":["9781493930630"]},"title":"High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL)","date_published":"2016-02-02T00:00:00Z","OA_type":"closed access","fulldoi":"https://doi.org/10.1007/978-1-4939-3064-7_17","doi":"10.1007/978-1-4939-3064-7_17","type":"book_chapter"},{"publication_identifier":{"eisbn":["9781489975027"]},"OA_type":"closed access","date_published":"2016-07-06T00:00:00Z","title":"Learning Using Privileged Information","fulldoi":"https://doi.org/10.1007/978-1-4899-7502-7_892-1","doi":"10.1007/978-1-4899-7502-7_892-1","type":"book_chapter","publication":"Encyclopedia of Machine Learning and Data Mining","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"When applying machine learning techniques to real-world problems, prior knowledge plays a crucial role in enriching the learning system. This prior knowledge is typically defined by domain experts and can be integrated into machine learning algorithms in a variety of ways: as a preference of certain prediction functions over others, as a Bayesian prior over parameters, or as additional information about the samples in the training set used for learning a prediction function. The latter setup is called learning using privileged information (LUPI) and was adopted by Vapnik and Vashist in (Neural Netw, 2009). Formally, LUPI refers to the setting when, in addition to the main data modality, the learning system has access to an extra source of information about the training examples. The additional source of information is only available during training and therefore is called privileged. The main goal of LUPI is to utilize privileged information and to learn a better model in the main data modality than one would learn without the privileged source. As an illustration, for protein classification based on amino-acid sequences, the protein tertiary structure can be considered additional information. Another example is recognizing objects in images; the textual information in the form of image tags contains additional object descriptions and can be used as privileged.","lang":"eng"}],"author":[{"orcid":"0000-0003-0192-9308","first_name":"Viktoriia","last_name":"Sharmanska","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","full_name":"Sharmanska, Viktoriia"},{"first_name":"Novi","full_name":"Quadrianto, Novi","last_name":"Quadrianto"}],"corr_author":"1","date_updated":"2025-09-23T10:53:13Z","quality_controlled":"1","date_created":"2025-07-10T13:57:52Z","article_processing_charge":"No","day":"06","month":"07","year":"2016","citation":{"chicago":"Sharmanska, Viktoriia, and Novi Quadrianto. “Learning Using Privileged Information.” In <i>Encyclopedia of Machine Learning and Data Mining</i>, 1–4. Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-1-4899-7502-7_892-1\">https://doi.org/10.1007/978-1-4899-7502-7_892-1</a>.","short":"V. Sharmanska, N. Quadrianto, in:, Encyclopedia of Machine Learning and Data Mining, Springer Nature, 2016, pp. 1–4.","mla":"Sharmanska, Viktoriia, and Novi Quadrianto. “Learning Using Privileged Information.” <i>Encyclopedia of Machine Learning and Data Mining</i>, Springer Nature, 2016, pp. 1–4, doi:<a href=\"https://doi.org/10.1007/978-1-4899-7502-7_892-1\">10.1007/978-1-4899-7502-7_892-1</a>.","ista":"Sharmanska V, Quadrianto N. 2016.Learning Using Privileged Information. In: Encyclopedia of Machine Learning and Data Mining. , 1–4.","ama":"Sharmanska V, Quadrianto N. Learning Using Privileged Information. In: <i>Encyclopedia of Machine Learning and Data Mining</i>. Springer Nature; 2016:1-4. doi:<a href=\"https://doi.org/10.1007/978-1-4899-7502-7_892-1\">10.1007/978-1-4899-7502-7_892-1</a>","ieee":"V. Sharmanska and N. Quadrianto, “Learning Using Privileged Information,” in <i>Encyclopedia of Machine Learning and Data Mining</i>, Springer Nature, 2016, pp. 1–4.","apa":"Sharmanska, V., &#38; Quadrianto, N. (2016). Learning Using Privileged Information. In <i>Encyclopedia of Machine Learning and Data Mining</i> (pp. 1–4). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4899-7502-7_892-1\">https://doi.org/10.1007/978-1-4899-7502-7_892-1</a>"},"publisher":"Springer Nature","_id":"19991","status":"public","page":"1-4","department":[{"_id":"ChLa"}],"language":[{"iso":"eng"}],"publication_status":"published","oa_version":"None"}]