[{"quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","abstract":[{"text":"It is common knowledge that there is no single best strategy for graph clustering, which justifies a plethora of existing approaches. In this paper, we present a general memetic algorithm, VieClus, to tackle the graph clustering problem. This algorithm can be adapted to optimize different objective functions. A key component of our contribution are natural recombine operators that employ ensemble clusterings as well as multi-level techniques. Lastly, we combine these techniques with a scalable communication protocol, producing a system that is able to compute high-quality solutions in a short amount of time. We instantiate our scheme with local search for modularity and show that our algorithm successfully improves or reproduces all entries of the 10th DIMACS implementation challenge under consideration using a small amount of time.","lang":"eng"}],"publication_status":"published","type":"conference","citation":{"short":"S. Biedermann, M.H. Henzinger, C. Schulz, B. Schuster, in:, 17th International Symposium on Experimental Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","apa":"Biedermann, S., Henzinger, M. H., Schulz, C., &#38; Schuster, B. (2018). Memetic graph clustering. In <i>17th International Symposium on Experimental Algorithms</i> (Vol. 103). L’Aquila, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.SEA.2018.3\">https://doi.org/10.4230/LIPICS.SEA.2018.3</a>","ieee":"S. Biedermann, M. H. Henzinger, C. Schulz, and B. Schuster, “Memetic graph clustering,” in <i>17th International Symposium on Experimental Algorithms</i>, L’Aquila, Italy, 2018, vol. 103.","chicago":"Biedermann, Sonja, Monika H Henzinger, Christian Schulz, and Bernhard Schuster. “Memetic Graph Clustering.” In <i>17th International Symposium on Experimental Algorithms</i>, Vol. 103. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPICS.SEA.2018.3\">https://doi.org/10.4230/LIPICS.SEA.2018.3</a>.","ama":"Biedermann S, Henzinger MH, Schulz C, Schuster B. Memetic graph clustering. In: <i>17th International Symposium on Experimental Algorithms</i>. Vol 103. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPICS.SEA.2018.3\">10.4230/LIPICS.SEA.2018.3</a>","mla":"Biedermann, Sonja, et al. “Memetic Graph Clustering.” <i>17th International Symposium on Experimental Algorithms</i>, vol. 103, 3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPICS.SEA.2018.3\">10.4230/LIPICS.SEA.2018.3</a>.","ista":"Biedermann S, Henzinger MH, Schulz C, Schuster B. 2018. Memetic graph clustering. 17th International Symposium on Experimental Algorithms. SEA: Symposium on Experimental Algorithms, LIPIcs, vol. 103, 3."},"author":[{"full_name":"Biedermann, Sonja","last_name":"Biedermann","first_name":"Sonja"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"last_name":"Schulz","full_name":"Schulz, Christian","first_name":"Christian"},{"first_name":"Bernhard","last_name":"Schuster","full_name":"Schuster, Bernhard"}],"conference":{"location":"L'Aquila, Italy","start_date":"2018-07-27","end_date":"2018-07-29","name":"SEA: Symposium on Experimental Algorithms"},"year":"2018","publication_identifier":{"isbn":["9783959770705"],"issn":["1868-8969"]},"day":"01","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","arxiv":1,"oa_version":"Published Version","doi":"10.4230/LIPICS.SEA.2018.3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"       103","article_number":"3","alternative_title":["LIPIcs"],"volume":103,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.4230/LIPICS.SEA.2018.3"}],"scopus_import":"1","extern":"1","date_published":"2018-07-01T00:00:00Z","article_processing_charge":"No","month":"07","title":"Memetic graph clustering","date_updated":"2023-02-16T11:45:14Z","date_created":"2022-08-18T06:49:40Z","external_id":{"arxiv":["1802.07034"]},"_id":"11911","publication":"17th International Symposium on Experimental Algorithms"},{"type":"journal_article","citation":{"ista":"Pieber B, Shalom M, Antonietti M, Seeberger PH, Gilmore K. 2018. Continuous heterogeneous photocatalysis in serial micro-batch reactors. Angewandte Chemie International Edition. 57(31), 9976–9979.","mla":"Pieber, Bartholomäus, et al. “Continuous Heterogeneous Photocatalysis in Serial Micro-Batch Reactors.” <i>Angewandte Chemie International Edition</i>, vol. 57, no. 31, Wiley, 2018, pp. 9976–79, doi:<a href=\"https://doi.org/10.1002/anie.201712568\">10.1002/anie.201712568</a>.","ama":"Pieber B, Shalom M, Antonietti M, Seeberger PH, Gilmore K. Continuous heterogeneous photocatalysis in serial micro-batch reactors. <i>Angewandte Chemie International Edition</i>. 2018;57(31):9976-9979. doi:<a href=\"https://doi.org/10.1002/anie.201712568\">10.1002/anie.201712568</a>","chicago":"Pieber, Bartholomäus, Menny Shalom, Markus Antonietti, Peter H. Seeberger, and Kerry Gilmore. “Continuous Heterogeneous Photocatalysis in Serial Micro-Batch Reactors.” <i>Angewandte Chemie International Edition</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/anie.201712568\">https://doi.org/10.1002/anie.201712568</a>.","ieee":"B. Pieber, M. Shalom, M. Antonietti, P. H. Seeberger, and K. Gilmore, “Continuous heterogeneous photocatalysis in serial micro-batch reactors,” <i>Angewandte Chemie International Edition</i>, vol. 57, no. 31. Wiley, pp. 9976–9979, 2018.","short":"B. Pieber, M. Shalom, M. Antonietti, P.H. Seeberger, K. Gilmore, Angewandte Chemie International Edition 57 (2018) 9976–9979.","apa":"Pieber, B., Shalom, M., Antonietti, M., Seeberger, P. H., &#38; Gilmore, K. (2018). Continuous heterogeneous photocatalysis in serial micro-batch reactors. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201712568\">https://doi.org/10.1002/anie.201712568</a>"},"article_type":"letter_note","abstract":[{"text":"Solid reagents, leaching catalysts, and heterogeneous photocatalysts are commonly employed in batch processes but are ill-suited for continuous-flow chemistry. Heterogeneous catalysts for thermal reactions are typically used in packed-bed reactors, which cannot be penetrated by light and thus are not suitable for photocatalytic reactions involving solids. We demonstrate that serial micro-batch reactors (SMBRs) allow for the continuous utilization of solid materials together with liquids and gases in flow. This technology was utilized to develop selective and efficient fluorination reactions using a modified graphitic carbon nitride heterogeneous catalyst instead of costly homogeneous metal polypyridyl complexes. The merger of this inexpensive, recyclable catalyst and the SMBR approach enables sustainable and scalable photocatalysis.","lang":"eng"}],"publication_status":"published","language":[{"iso":"eng"}],"pmid":1,"status":"public","quality_controlled":"1","doi":"10.1002/anie.201712568","oa_version":"None","publisher":"Wiley","day":"26","publication_identifier":{"issn":["1433-7851"],"eissn":[" 1521-3773"]},"author":[{"id":"93e5e5b2-0da6-11ed-8a41-af589a024726","first_name":"Bartholomäus","last_name":"Pieber","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus"},{"first_name":"Menny","full_name":"Shalom, Menny","last_name":"Shalom"},{"full_name":"Antonietti, Markus","last_name":"Antonietti","first_name":"Markus"},{"last_name":"Seeberger","full_name":"Seeberger, Peter H.","first_name":"Peter H."},{"first_name":"Kerry","last_name":"Gilmore","full_name":"Gilmore, Kerry"}],"year":"2018","scopus_import":"1","extern":"1","volume":57,"issue":"31","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        57","publication":"Angewandte Chemie International Edition","page":"9976-9979","_id":"11958","date_created":"2022-08-24T10:57:25Z","external_id":{"pmid":["29377383"]},"date_updated":"2023-02-21T10:09:18Z","title":"Continuous heterogeneous photocatalysis in serial micro-batch reactors","month":"07","date_published":"2018-07-26T00:00:00Z","article_processing_charge":"No"},{"citation":{"chicago":"Nakashima, Kazutaka, Thomas Auzinger, Emmanuel Iarussi, Ran Zhang, Takeo Igarashi, and Bernd Bickel. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” <i>ACM Transaction on Graphics</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3197517.3201341\">https://doi.org/10.1145/3197517.3201341</a>.","ama":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. <i>ACM Transaction on Graphics</i>. 2018;37(4). doi:<a href=\"https://doi.org/10.1145/3197517.3201341\">10.1145/3197517.3201341</a>","ista":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. 2018. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 37(4), 135.","mla":"Nakashima, Kazutaka, et al. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” <i>ACM Transaction on Graphics</i>, vol. 37, no. 4, 135, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3197517.3201341\">10.1145/3197517.3201341</a>.","apa":"Nakashima, K., Auzinger, T., Iarussi, E., Zhang, R., Igarashi, T., &#38; Bickel, B. (2018). CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. <i>ACM Transaction on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3197517.3201341\">https://doi.org/10.1145/3197517.3201341</a>","short":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, B. Bickel, ACM Transaction on Graphics 37 (2018).","ieee":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, and B. Bickel, “CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds,” <i>ACM Transaction on Graphics</i>, vol. 37, no. 4. ACM, 2018."},"type":"journal_article","file":[{"date_created":"2018-12-12T10:18:38Z","creator":"system","file_id":"5360","file_name":"IST-2018-1037-v1+1_CoreCavity-AuthorVersion.pdf","access_level":"open_access","checksum":"6a5368bc86c4e1a9fcfe588fd1f14ee8","relation":"main_file","file_size":104225664,"content_type":"application/pdf","date_updated":"2020-07-14T12:44:38Z"},{"file_size":377743553,"content_type":"application/zip","date_updated":"2020-07-14T12:44:38Z","relation":"main_file","checksum":"3861e693ba47c51f3ec7b7867d573a61","access_level":"open_access","file_name":"IST-2018-1037-v1+2_CoreCavity-Supplemental.zip","file_id":"5361","creator":"system","date_created":"2018-12-12T10:18:39Z"},{"file_id":"5362","date_created":"2018-12-12T10:18:41Z","creator":"system","checksum":"490040c685ed869536e2a18f5a906b94","relation":"main_file","file_size":162634396,"date_updated":"2020-07-14T12:44:38Z","content_type":"video/vnd.objectvideo","file_name":"IST-2018-1037-v1+3_CoreCavity-Video.mp4","access_level":"open_access"},{"checksum":"be7fc8b229adda727419b6504b3b9352","relation":"main_file","file_size":527972,"content_type":"image/jpeg","date_updated":"2020-07-14T12:44:38Z","file_name":"IST-2018-1037-v1+4_CoreCavity-RepresentativeImage.jpg","access_level":"open_access","file_id":"5363","creator":"system","date_created":"2018-12-12T10:18:42Z"}],"ddc":["004","516","670"],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Molding is a popular mass production method, in which the initial expenses for the mold are offset by the low per-unit production cost. However, the physical fabrication constraints of the molding technique commonly restrict the shape of moldable objects. For a complex shape, a decomposition of the object into moldable parts is a common strategy to address these constraints, with plastic model kits being a popular and illustrative example. However, conducting such a decomposition requires considerable expertise, and it depends on the technical aspects of the fabrication technique, as well as aesthetic considerations. We present an interactive technique to create such decompositions for two-piece molding, in which each part of the object is cast between two rigid mold pieces. Given the surface description of an object, we decompose its thin-shell equivalent into moldable parts by first performing a coarse decomposition and then utilizing an active contour model for the boundaries between individual parts. Formulated as an optimization problem, the movement of the contours is guided by an energy reflecting fabrication constraints to ensure the moldability of each part. Simultaneously, the user is provided with editing capabilities to enforce aesthetic guidelines. Our interactive interface provides control of the contour positions by allowing, for example, the alignment of part boundaries with object features. Our technique enables a novel workflow, as it empowers novice users to explore the design space, and it generates fabrication-ready two-piece molds that can be used either for casting or industrial injection molding of free-form objects."}],"publication_status":"published","publist_id":"8044","quality_controlled":"1","oa_version":"Submitted Version","doi":"10.1145/3197517.3201341","day":"04","publisher":"ACM","department":[{"_id":"BeBi"}],"author":[{"last_name":"Nakashima","full_name":"Nakashima, Kazutaka","first_name":"Kazutaka"},{"first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87","last_name":"Auzinger","orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas"},{"full_name":"Iarussi, Emmanuel","last_name":"Iarussi","id":"33F19F16-F248-11E8-B48F-1D18A9856A87","first_name":"Emmanuel"},{"id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran","orcid":"0000-0002-3808-281X","full_name":"Zhang, Ran","last_name":"Zhang"},{"first_name":"Takeo","full_name":"Igarashi, Takeo","last_name":"Igarashi"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"}],"isi":1,"year":"2018","scopus_import":"1","volume":37,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/interactive-software-tool-makes-complex-mold-design-simple/","relation":"press_release"}]},"issue":"4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"        37","oa":1,"article_number":"135","pubrep_id":"1037","file_date_updated":"2020-07-14T12:44:38Z","publication":"ACM Transaction on Graphics","date_created":"2018-12-11T11:44:09Z","external_id":{"isi":["000448185000096"]},"project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"},{"name":"Distributed 3D Object Design","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","call_identifier":"H2020"}],"_id":"12","month":"08","date_updated":"2023-09-11T12:48:09Z","title":"CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds","ec_funded":1,"date_published":"2018-08-04T00:00:00Z","article_processing_charge":"No"},{"scopus_import":"1","volume":9,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6363"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/lateral-inhibition-keeps-similar-memories-apart/","relation":"press_release"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J..","issue":"1","intvolume":"         9","oa":1,"article_number":"4605","file_date_updated":"2020-07-14T12:45:28Z","publication":"Nature Communications","date_created":"2018-12-11T11:44:12Z","external_id":{"isi":["000449069700009"]},"_id":"21","project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"month":"11","date_updated":"2024-03-25T23:30:16Z","title":"Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus","ec_funded":1,"date_published":"2018-11-02T00:00:00Z","article_processing_charge":"No","type":"journal_article","citation":{"short":"C. Espinoza Martinez, J. Guzmán, X. Zhang, P.M. Jonas, Nature Communications 9 (2018).","apa":"Espinoza Martinez, C., Guzmán, J., Zhang, X., &#38; Jonas, P. M. (2018). Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-018-06899-3\">https://doi.org/10.1038/s41467-018-06899-3</a>","ieee":"C. Espinoza Martinez, J. Guzmán, X. Zhang, and P. M. Jonas, “Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus,” <i>Nature Communications</i>, vol. 9, no. 1. Nature Publishing Group, 2018.","ama":"Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-018-06899-3\">10.1038/s41467-018-06899-3</a>","chicago":"Espinoza Martinez, Claudia , José Guzmán, Xiaomin Zhang, and Peter M Jonas. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” <i>Nature Communications</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41467-018-06899-3\">https://doi.org/10.1038/s41467-018-06899-3</a>.","mla":"Espinoza Martinez, Claudia, et al. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” <i>Nature Communications</i>, vol. 9, no. 1, 4605, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-06899-3\">10.1038/s41467-018-06899-3</a>.","ista":"Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. 2018. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. 9(1), 4605."},"file":[{"file_id":"5715","creator":"dernst","date_created":"2018-12-17T15:41:57Z","checksum":"9fe2a63bd95a5067d896c087d07998f3","relation":"main_file","file_size":4651930,"date_updated":"2020-07-14T12:45:28Z","content_type":"application/pdf","file_name":"2018_NatureComm_Espinoza.pdf","access_level":"open_access"}],"article_type":"original","ddc":["570"],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Parvalbumin-positive (PV+) GABAergic interneurons in hippocampal microcircuits are thought to play a key role in several higher network functions, such as feedforward and feedback inhibition, network oscillations, and pattern separation. Fast lateral inhibition mediated by GABAergic interneurons may implement a winner-takes-all mechanism in the hippocampal input layer. However, it is not clear whether the functional connectivity rules of granule cells (GCs) and interneurons in the dentate gyrus are consistent with such a mechanism. Using simultaneous patch-clamp recordings from up to seven GCs and up to four PV+ interneurons in the dentate gyrus, we find that connectivity is structured in space, synapse-specific, and enriched in specific disynaptic motifs. In contrast to the neocortex, lateral inhibition in the dentate gyrus (in which a GC inhibits neighboring GCs via a PV+ interneuron) is ~ 10-times more abundant than recurrent inhibition (in which a GC inhibits itself). Thus, unique connectivity rules may enable the dentate gyrus to perform specific higher-order computations"}],"publication_status":"published","publist_id":"8034","quality_controlled":"1","oa_version":"Published Version","doi":"10.1038/s41467-018-06899-3","day":"02","publisher":"Nature Publishing Group","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"PeJo"}],"author":[{"first_name":"Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","full_name":"Espinoza Martinez, Claudia ","orcid":"0000-0003-4710-2082","last_name":"Espinoza Martinez"},{"last_name":"Guzmán","orcid":"0000-0003-2209-5242","full_name":"Guzmán, José","first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhang","full_name":"Zhang, Xiaomin","first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"isi":1,"year":"2018"},{"quality_controlled":"1","publication_status":"published","abstract":[{"text":"Conventional ultra-high sensitivity detectors in the millimeter-wave range are usually cooled as their own thermal noise at room temperature would mask the weak received radiation. The need for cryogenic systems increases the cost and complexity of the instruments, hindering the development of, among others, airborne and space applications. In this work, the nonlinear parametric upconversion of millimeter-wave radiation to the optical domain inside high-quality (Q) lithium niobate whispering-gallery mode (WGM) resonators is proposed for ultra-low noise detection. We experimentally demonstrate coherent upconversion of millimeter-wave signals to a 1550 nm telecom carrier, with a photon conversion efficiency surpassing the state-of-the-art by 2 orders of magnitude. Moreover, a theoretical model shows that the thermal equilibrium of counterpropagating WGMs is broken by overcoupling the millimeter-wave WGM, effectively cooling the upconverted mode and allowing ultra-low noise detection. By theoretically estimating the sensitivity of a correlation radiometer based on the presented scheme, it is found that room-temperature radiometers with better sensitivity than state-of-the-art high-electron-mobility transistor (HEMT)-based radiometers can be designed. This detection paradigm can be used to develop room-temperature instrumentation for radio astronomy, earth observation, planetary missions, and imaging systems.","lang":"eng"}],"publist_id":"8033","language":[{"iso":"eng"}],"status":"public","article_type":"original","citation":{"ama":"Botello G, Sedlmeir F, Rueda Sanchez AR, et al. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. <i>Optica</i>. 2018;5(10):1210-1219. doi:<a href=\"https://doi.org/10.1364/OPTICA.5.001210\">10.1364/OPTICA.5.001210</a>","chicago":"Botello, Gabriel, Florian Sedlmeir, Alfredo R Rueda Sanchez, Kerlos Abdalmalak, Elliott Brown, Gerd Leuchs, Sascha Preu, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” <i>Optica</i>, 2018. <a href=\"https://doi.org/10.1364/OPTICA.5.001210\">https://doi.org/10.1364/OPTICA.5.001210</a>.","mla":"Botello, Gabriel, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” <i>Optica</i>, vol. 5, no. 10, 2018, pp. 1210–19, doi:<a href=\"https://doi.org/10.1364/OPTICA.5.001210\">10.1364/OPTICA.5.001210</a>.","ista":"Botello G, Sedlmeir F, Rueda Sanchez AR, Abdalmalak K, Brown E, Leuchs G, Preu S, Segovia Vargas D, Strekalov D, Munoz L, Schwefel H. 2018. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. 5(10), 1210–1219.","apa":"Botello, G., Sedlmeir, F., Rueda Sanchez, A. R., Abdalmalak, K., Brown, E., Leuchs, G., … Schwefel, H. (2018). Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. <i>Optica</i>. <a href=\"https://doi.org/10.1364/OPTICA.5.001210\">https://doi.org/10.1364/OPTICA.5.001210</a>","short":"G. Botello, F. Sedlmeir, A.R. Rueda Sanchez, K. Abdalmalak, E. Brown, G. Leuchs, S. Preu, D. Segovia Vargas, D. Strekalov, L. Munoz, H. Schwefel, Optica 5 (2018) 1210–1219.","ieee":"G. Botello <i>et al.</i>, “Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters,” <i>Optica</i>, vol. 5, no. 10. pp. 1210–1219, 2018."},"type":"journal_article","author":[{"full_name":"Botello, Gabriel","last_name":"Botello","first_name":"Gabriel"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R"},{"first_name":"Kerlos","last_name":"Abdalmalak","full_name":"Abdalmalak, Kerlos"},{"first_name":"Elliott","last_name":"Brown","full_name":"Brown, Elliott"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"first_name":"Sascha","full_name":"Preu, Sascha","last_name":"Preu"},{"first_name":"Daniel","full_name":"Segovia Vargas, Daniel","last_name":"Segovia Vargas"},{"first_name":"Dmitry","last_name":"Strekalov","full_name":"Strekalov, Dmitry"},{"full_name":"Munoz, Luis","last_name":"Munoz","first_name":"Luis"},{"last_name":"Schwefel","full_name":"Schwefel, Harald","first_name":"Harald"}],"isi":1,"year":"2018","publication_identifier":{"issn":["23342536"]},"department":[{"_id":"JoFi"}],"day":"20","doi":"10.1364/OPTICA.5.001210","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"10","intvolume":"         5","oa":1,"volume":5,"main_file_link":[{"url":"www.doi.org/10.1364/OPTICA.5.001210 ","open_access":"1"}],"scopus_import":"1","date_published":"2018-10-20T00:00:00Z","article_processing_charge":"No","title":"Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters","date_updated":"2023-10-17T12:12:40Z","month":"10","_id":"22","date_created":"2018-12-11T11:44:12Z","external_id":{"isi":["000447853100007"]},"publication":"Optica","page":"1210 - 1219"},{"publisher":"American Chemical Society","day":"25","doi":"10.1021/acs.nanolett.8b03217","oa_version":"Published Version","isi":1,"author":[{"id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada","full_name":"Vukušić, Lada","orcid":"0000-0003-2424-8636","last_name":"Vukušić"},{"last_name":"Kukucka","full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip"},{"first_name":"Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","last_name":"Watzinger","full_name":"Watzinger, Hannes"},{"last_name":"Milem","full_name":"Milem, Joshua M","first_name":"Joshua M","id":"4CDE0A96-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schäffler","full_name":"Schäffler, Friedrich","first_name":"Friedrich"},{"last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"year":"2018","department":[{"_id":"GeKa"}],"publication_identifier":{"issn":["15306984"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"ddc":["530"],"file":[{"file_name":"IST-2018-1065-v1+1_ACS_nanoletters_8b03217.pdf","access_level":"open_access","relation":"main_file","checksum":"3e6034a94c6b5335e939145d88bdb371","date_updated":"2020-07-14T12:45:37Z","content_type":"application/pdf","file_size":1361441,"date_created":"2018-12-12T10:16:08Z","creator":"system","file_id":"5194"}],"citation":{"ieee":"L. Vukušić, J. Kukucka, H. Watzinger, J. M. Milem, F. Schäffler, and G. Katsaros, “Single-shot readout of hole spins in Ge,” <i>Nano Letters</i>, vol. 18, no. 11. American Chemical Society, pp. 7141–7145, 2018.","short":"L. Vukušić, J. Kukucka, H. Watzinger, J.M. Milem, F. Schäffler, G. Katsaros, Nano Letters 18 (2018) 7141–7145.","apa":"Vukušić, L., Kukucka, J., Watzinger, H., Milem, J. M., Schäffler, F., &#38; Katsaros, G. (2018). Single-shot readout of hole spins in Ge. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.8b03217\">https://doi.org/10.1021/acs.nanolett.8b03217</a>","ista":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. 2018. Single-shot readout of hole spins in Ge. Nano Letters. 18(11), 7141–7145.","mla":"Vukušić, Lada, et al. “Single-Shot Readout of Hole Spins in Ge.” <i>Nano Letters</i>, vol. 18, no. 11, American Chemical Society, 2018, pp. 7141–45, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.8b03217\">10.1021/acs.nanolett.8b03217</a>.","ama":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. Single-shot readout of hole spins in Ge. <i>Nano Letters</i>. 2018;18(11):7141-7145. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.8b03217\">10.1021/acs.nanolett.8b03217</a>","chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, Joshua M Milem, Friedrich Schäffler, and Georgios Katsaros. “Single-Shot Readout of Hole Spins in Ge.” <i>Nano Letters</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acs.nanolett.8b03217\">https://doi.org/10.1021/acs.nanolett.8b03217</a>."},"type":"journal_article","quality_controlled":"1","abstract":[{"lang":"eng","text":"The strong atomistic spin–orbit coupling of holes makes single-shot spin readout measurements difficult because it reduces the spin lifetimes. By integrating the charge sensor into a high bandwidth radio frequency reflectometry setup, we were able to demonstrate single-shot readout of a germanium quantum dot hole spin and measure the spin lifetime. Hole spin relaxation times of about 90 μs at 500 mT are reported, with a total readout visibility of about 70%. By analyzing separately the spin-to-charge conversion and charge readout fidelities, we have obtained insight into the processes limiting the visibilities of hole spins. The analyses suggest that high hole visibilities are feasible at realistic experimental conditions, underlying the potential of hole spins for the realization of viable qubit devices."}],"publication_status":"published","publist_id":"8032","language":[{"iso":"eng"}],"pmid":1,"status":"public","has_accepted_license":"1","project":[{"name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","_id":"25517E86-B435-11E9-9278-68D0E5697425","grant_number":"335497","call_identifier":"FP7"}],"_id":"23","date_created":"2018-12-11T11:44:13Z","external_id":{"isi":["000451102100064"],"pmid":["30359041"]},"file_date_updated":"2020-07-14T12:45:37Z","pubrep_id":"1065","publication":"Nano Letters","page":"7141 - 7145","date_published":"2018-10-25T00:00:00Z","article_processing_charge":"No","ec_funded":1,"date_updated":"2023-09-18T09:30:37Z","title":"Single-shot readout of hole spins in Ge","month":"10","scopus_import":"1","issue":"11","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"intvolume":"        18","volume":18,"related_material":{"record":[{"relation":"popular_science","id":"7977"},{"id":"69","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"7996"}]}},{"arxiv":1,"oa_version":"Preprint","doi":"10.24963/ijcai.2018/652","day":"01","publisher":"IJCAI","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"year":"2018","conference":{"location":"Stockholm, Sweden","start_date":"2018-07-13","end_date":"2018-07-19","name":"IJCAI: International Joint Conference on Artificial Intelligence"},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Elgyütt, Adrian","last_name":"Elgyütt","id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","first_name":"Adrian"},{"last_name":"Novotny","full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"first_name":"Owen","full_name":"Rouillé, Owen","last_name":"Rouillé"}],"isi":1,"citation":{"apa":"Chatterjee, K., Elgyütt, A., Novotný, P., &#38; Rouillé, O. (2018). Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives (Vol. 2018, pp. 4692–4699). Presented at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm, Sweden: IJCAI. <a href=\"https://doi.org/10.24963/ijcai.2018/652\">https://doi.org/10.24963/ijcai.2018/652</a>","short":"K. Chatterjee, A. Elgyütt, P. Novotný, O. Rouillé, in:, IJCAI, 2018, pp. 4692–4699.","ieee":"K. Chatterjee, A. Elgyütt, P. Novotný, and O. Rouillé, “Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives,” presented at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol. 2018, pp. 4692–4699.","ama":"Chatterjee K, Elgyütt A, Novotný P, Rouillé O. Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives. In: Vol 2018. IJCAI; 2018:4692-4699. doi:<a href=\"https://doi.org/10.24963/ijcai.2018/652\">10.24963/ijcai.2018/652</a>","chicago":"Chatterjee, Krishnendu, Adrian Elgyütt, Petr Novotný, and Owen Rouillé. “Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum Objectives,” 2018:4692–99. IJCAI, 2018. <a href=\"https://doi.org/10.24963/ijcai.2018/652\">https://doi.org/10.24963/ijcai.2018/652</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum Objectives</i>. Vol. 2018, IJCAI, 2018, pp. 4692–99, doi:<a href=\"https://doi.org/10.24963/ijcai.2018/652\">10.24963/ijcai.2018/652</a>.","ista":"Chatterjee K, Elgyütt A, Novotný P, Rouillé O. 2018. Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018, 4692–4699."},"type":"conference","status":"public","language":[{"iso":"eng"}],"publist_id":"8031","publication_status":"published","abstract":[{"lang":"eng","text":"Partially-observable Markov decision processes (POMDPs) with discounted-sum payoff are a standard framework to model a wide range of problems related to decision making under uncertainty. Traditionally, the goal has been to obtain policies that optimize the expectation of the discounted-sum payoff. A key drawback of the expectation measure is that even low probability events with extreme payoff can significantly affect the expectation, and thus the obtained policies are not necessarily risk-averse. An alternate approach is to optimize the probability that the payoff is above a certain threshold, which allows obtaining risk-averse policies, but ignores optimization of the expectation. We consider the expectation optimization with probabilistic guarantee (EOPG) problem, where the goal is to optimize the expectation ensuring that the payoff is above a given threshold with at least a specified probability. We present several results on the EOPG problem, including the first algorithm to solve it."}],"quality_controlled":"1","page":"4692 - 4699","external_id":{"arxiv":["1804.10601"],"isi":["000764175404117"]},"date_created":"2018-12-11T11:44:13Z","_id":"24","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"month":"07","date_updated":"2025-06-02T08:53:48Z","title":"Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives","ec_funded":1,"article_processing_charge":"No","date_published":"2018-07-01T00:00:00Z","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1804.10601","open_access":"1"}],"volume":2018,"intvolume":"      2018","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"This research was supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003; Austrian Science Fund (FWF): S11407-N23(RiSE/SHiNE);and an ERC Start Grant (279307:Graph Games).\r\n"},{"acknowledgement":"∗This work has been supported by Vienna Science and Technology Fund (WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Starting grant (279307: Graph Games). This research was sponsored by the Army Research Laboratory and was accomplished under Cooperative Agreement Number W911NF-13-2-0045 (ARL Cyber Security CRA). ","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"volume":"2018-July","main_file_link":[{"url":"https://doi.org/10.24963/ijcai.2018/662","open_access":"1"}],"scopus_import":"1","date_published":"2018-07-01T00:00:00Z","article_processing_charge":"No","ec_funded":1,"title":"Goal-HSVI: Heuristic search value iteration for goal-POMDPs","date_updated":"2025-06-02T08:53:40Z","month":"07","_id":"25","project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:44:13Z","external_id":{"isi":["000764175404127"]},"publication":"Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence","page":"4764 - 4770","quality_controlled":"1","publication_status":"published","abstract":[{"lang":"eng","text":"Partially observable Markov decision processes (POMDPs) are the standard models for planning under uncertainty with both finite and infinite horizon. Besides the well-known discounted-sum objective, indefinite-horizon objective (aka Goal-POMDPs) is another classical objective for POMDPs. In this case, given a set of target states and a positive cost for each transition, the optimization objective is to minimize the expected total cost until a target state is reached. In the literature, RTDP-Bel or heuristic search value iteration (HSVI) have been used for solving Goal-POMDPs. Neither of these algorithms has theoretical convergence guarantees, and HSVI may even fail to terminate its trials. We give the following contributions: (1) We discuss the challenges introduced in Goal-POMDPs and illustrate how they prevent the original HSVI from converging. (2) We present a novel algorithm inspired by HSVI, termed Goal-HSVI, and show that our algorithm has convergence guarantees. (3) We show that Goal-HSVI outperforms RTDP-Bel on a set of well-known examples."}],"publist_id":"8030","language":[{"iso":"eng"}],"status":"public","type":"conference","citation":{"ieee":"K. Horák, B. Bošanský, and K. Chatterjee, “Goal-HSVI: Heuristic search value iteration for goal-POMDPs,” in <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>, Stockholm, Sweden, 2018, vol. 2018–July, pp. 4764–4770.","apa":"Horák, K., Bošanský, B., &#38; Chatterjee, K. (2018). Goal-HSVI: Heuristic search value iteration for goal-POMDPs. In <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i> (Vol. 2018–July, pp. 4764–4770). Stockholm, Sweden: IJCAI. <a href=\"https://doi.org/10.24963/ijcai.2018/662\">https://doi.org/10.24963/ijcai.2018/662</a>","short":"K. Horák, B. Bošanský, K. Chatterjee, in:, Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4764–4770.","mla":"Horák, Karel, et al. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.” <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>, vol. 2018–July, IJCAI, 2018, pp. 4764–70, doi:<a href=\"https://doi.org/10.24963/ijcai.2018/662\">10.24963/ijcai.2018/662</a>.","ista":"Horák K, Bošanský B, Chatterjee K. 2018. Goal-HSVI: Heuristic search value iteration for goal-POMDPs. Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018–July, 4764–4770.","chicago":"Horák, Karel, Branislav Bošanský, and Krishnendu Chatterjee. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.” In <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>, 2018–July:4764–70. IJCAI, 2018. <a href=\"https://doi.org/10.24963/ijcai.2018/662\">https://doi.org/10.24963/ijcai.2018/662</a>.","ama":"Horák K, Bošanský B, Chatterjee K. Goal-HSVI: Heuristic search value iteration for goal-POMDPs. In: <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>. Vol 2018-July. IJCAI; 2018:4764-4770. doi:<a href=\"https://doi.org/10.24963/ijcai.2018/662\">10.24963/ijcai.2018/662</a>"},"isi":1,"author":[{"full_name":"Horák, Karel","last_name":"Horák","first_name":"Karel"},{"first_name":"Branislav","full_name":"Bošanský, Branislav","last_name":"Bošanský"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"conference":{"start_date":"2018-07-13","location":"Stockholm, Sweden","end_date":"2018-07-19","name":"IJCAI: International Joint Conference on Artificial Intelligence"},"year":"2018","department":[{"_id":"KrCh"}],"publisher":"IJCAI","day":"01","doi":"10.24963/ijcai.2018/662","oa_version":"Published Version"},{"alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"704","relation":"part_of_dissertation","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"month":"10","title":"The influence of sequence context on the evolution of bacterial gene expression","date_updated":"2023-09-07T12:48:43Z","date_published":"2018-10-30T00:00:00Z","article_processing_charge":"No","page":"109","pubrep_id":"1059","file_date_updated":"2021-02-11T11:17:14Z","supervisor":[{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:44:14Z","_id":"26","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer."}],"publist_id":"8029","type":"dissertation","citation":{"ieee":"M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018.","short":"M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018.","apa":"Steinrück, M. (2018). <i>The influence of sequence context on the evolution of bacterial gene expression</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>","mla":"Steinrück, Magdalena. <i>The Influence of Sequence Context on the Evolution of Bacterial Gene Expression</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>.","ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria.","chicago":"Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>.","ama":"Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>"},"file":[{"embargo_to":"open_access","file_name":"Thesis_Steinrueck_final.docx","access_level":"closed","checksum":"413cbce1cd1debeae3abe2a25dbc70d1","relation":"source_file","date_updated":"2020-07-14T12:45:43Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":9190845,"creator":"dernst","date_created":"2019-02-08T10:51:22Z","file_id":"5941"},{"relation":"main_file","checksum":"3def8b7854c8b42d643597ce0215efac","file_size":7521973,"date_updated":"2021-02-11T11:17:14Z","content_type":"application/pdf","file_name":"Thesis_Steinrueck_final.pdf","access_level":"open_access","file_id":"5942","creator":"dernst","embargo":"2019-11-02","date_created":"2019-02-08T10:51:22Z"}],"ddc":["576","579"],"degree_awarded":"PhD","department":[{"_id":"CaGu"}],"publication_identifier":{"issn":["2663-337X"]},"author":[{"orcid":"0000-0003-1229-9719","full_name":"Steinrück, Magdalena","last_name":"Steinrück","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","first_name":"Magdalena"}],"year":"2018","oa_version":"Published Version","doi":"10.15479/AT:ISTA:th1059","day":"30","publisher":"Institute of Science and Technology Austria"},{"quality_controlled":"1","publication_status":"published","abstract":[{"text":"The accuracy of information retrieval systems is often measured using complex loss functions such as the average precision (AP) or the normalized discounted cumulative gain (NDCG). Given a set of positive and negative samples, the parameters of a retrieval system can be estimated by minimizing these loss functions. However, the non-differentiability and non-decomposability of these loss functions does not allow for simple gradient based optimization algorithms. This issue is generally circumvented by either optimizing a structured hinge-loss upper bound to the loss function or by using asymptotic methods like the direct-loss minimization framework. Yet, the high computational complexity of loss-augmented inference, which is necessary for both the frameworks, prohibits its use in large training data sets. To alleviate this deficiency, we present a novel quicksort flavored algorithm for a large class of non-decomposable loss functions. We provide a complete characterization of the loss functions that are amenable to our algorithm, and show that it includes both AP and NDCG based loss functions. Furthermore, we prove that no comparison based algorithm can improve upon the computational complexity of our approach asymptotically. We demonstrate the effectiveness of our approach in the context of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning models for a variety of vision tasks. We show that our approach provides significantly better results than simpler decomposable loss functions, while requiring a comparable training time.","lang":"eng"}],"language":[{"iso":"eng"}],"status":"public","type":"conference","citation":{"ieee":"P. Mohapatra, M. Rolinek, C. V. Jawahar, V. Kolmogorov, and M. P. Kumar, “Efficient optimization for rank-based loss functions,” in <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Salt Lake City, UT, USA, 2018, pp. 3693–3701.","short":"P. Mohapatra, M. Rolinek, C.V. Jawahar, V. Kolmogorov, M.P. Kumar, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–3701.","apa":"Mohapatra, P., Rolinek, M., Jawahar, C. V., Kolmogorov, V., &#38; Kumar, M. P. (2018). Efficient optimization for rank-based loss functions. In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 3693–3701). Salt Lake City, UT, USA: IEEE. <a href=\"https://doi.org/10.1109/cvpr.2018.00389\">https://doi.org/10.1109/cvpr.2018.00389</a>","ista":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. 2018. Efficient optimization for rank-based loss functions. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 3693–3701.","mla":"Mohapatra, Pritish, et al. “Efficient Optimization for Rank-Based Loss Functions.” <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2018, pp. 3693–701, doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00389\">10.1109/cvpr.2018.00389</a>.","chicago":"Mohapatra, Pritish, Michal Rolinek, C V Jawahar, Vladimir Kolmogorov, and M Pawan Kumar. “Efficient Optimization for Rank-Based Loss Functions.” In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 3693–3701. IEEE, 2018. <a href=\"https://doi.org/10.1109/cvpr.2018.00389\">https://doi.org/10.1109/cvpr.2018.00389</a>.","ama":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. Efficient optimization for rank-based loss functions. In: <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2018:3693-3701. doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00389\">10.1109/cvpr.2018.00389</a>"},"author":[{"first_name":"Pritish","last_name":"Mohapatra","full_name":"Mohapatra, Pritish"},{"last_name":"Rolinek","full_name":"Rolinek, Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"},{"full_name":"Jawahar, C V","last_name":"Jawahar","first_name":"C V"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"},{"first_name":"M Pawan","full_name":"Kumar, M Pawan","last_name":"Kumar"}],"isi":1,"year":"2018","conference":{"start_date":"2018-06-18","location":"Salt Lake City, UT, USA","end_date":"2018-06-22","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"publication_identifier":{"isbn":["9781538664209"]},"department":[{"_id":"VlKo"}],"publisher":"IEEE","day":"28","doi":"10.1109/cvpr.2018.00389","arxiv":1,"oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1604.08269","open_access":"1"}],"scopus_import":"1","date_published":"2018-06-28T00:00:00Z","article_processing_charge":"No","ec_funded":1,"title":"Efficient optimization for rank-based loss functions","date_updated":"2023-09-11T13:24:43Z","month":"06","_id":"273","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"date_created":"2018-12-11T11:45:33Z","external_id":{"isi":["000457843603087"],"arxiv":["1604.08269"]},"publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","page":"3693-3701"},{"year":"2018","isi":1,"author":[{"id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","full_name":"Brown, Markus","last_name":"Brown"},{"first_name":"Louise","last_name":"Johnson","full_name":"Johnson, Louise"},{"last_name":"Leone","full_name":"Leone, Dario","first_name":"Dario"},{"first_name":"Peter","last_name":"Májek","full_name":"Májek, Peter"},{"first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518"},{"last_name":"Senfter","full_name":"Senfter, Daniel","first_name":"Daniel"},{"last_name":"Bukosza","full_name":"Bukosza, Nora","first_name":"Nora"},{"first_name":"Helga","full_name":"Schachner, Helga","last_name":"Schachner"},{"first_name":"Gabriele","last_name":"Asfour","full_name":"Asfour, Gabriele"},{"last_name":"Langer","full_name":"Langer, Brigitte","first_name":"Brigitte"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"full_name":"Parapatics, Katja","last_name":"Parapatics","first_name":"Katja"},{"first_name":"Young","last_name":"Hong","full_name":"Hong, Young"},{"first_name":"Keiryn","last_name":"Bennett","full_name":"Bennett, Keiryn"},{"full_name":"Kain, Renate","last_name":"Kain","first_name":"Renate"},{"last_name":"Detmar","full_name":"Detmar, Michael","first_name":"Michael"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"last_name":"Jackson","full_name":"Jackson, David","first_name":"David"},{"last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho","first_name":"Dontscho"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"MiSi"},{"_id":"Bio"}],"day":"12","publisher":"Rockefeller University Press","oa_version":"Published Version","doi":"10.1083/jcb.201612051","quality_controlled":"1","status":"public","pmid":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"7627","publication_status":"published","abstract":[{"text":"Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified &gt; 1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments.","lang":"eng"}],"ddc":["570"],"citation":{"ieee":"M. Brown <i>et al.</i>, “Lymphatic exosomes promote dendritic cell migration along guidance cues,” <i>Journal of Cell Biology</i>, vol. 217, no. 6. Rockefeller University Press, pp. 2205–2221, 2018.","apa":"Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D., … Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along guidance cues. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201612051\">https://doi.org/10.1083/jcb.201612051</a>","short":"M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza, H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett, R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology 217 (2018) 2205–2221.","mla":"Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” <i>Journal of Cell Biology</i>, vol. 217, no. 6, Rockefeller University Press, 2018, pp. 2205–21, doi:<a href=\"https://doi.org/10.1083/jcb.201612051\">10.1083/jcb.201612051</a>.","ista":"Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N, Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K, Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6), 2205–2221.","chicago":"Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri, Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1083/jcb.201612051\">https://doi.org/10.1083/jcb.201612051</a>.","ama":"Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell migration along guidance cues. <i>Journal of Cell Biology</i>. 2018;217(6):2205-2221. doi:<a href=\"https://doi.org/10.1083/jcb.201612051\">10.1083/jcb.201612051</a>"},"type":"journal_article","file":[{"file_name":"2018_JournalCellBiology_Brown.pdf","access_level":"open_access","relation":"main_file","checksum":"9c7eba51a35c62da8c13f98120b64df4","file_size":2252043,"date_updated":"2020-07-14T12:45:45Z","content_type":"application/pdf","date_created":"2018-12-17T12:50:07Z","creator":"dernst","file_id":"5704"}],"ec_funded":1,"article_processing_charge":"No","date_published":"2018-04-12T00:00:00Z","month":"04","title":"Lymphatic exosomes promote dendritic cell migration along guidance cues","date_updated":"2023-09-13T08:51:29Z","external_id":{"pmid":["29650776"],"isi":["000438077800026"]},"date_created":"2018-12-11T11:45:33Z","_id":"275","project":[{"name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12"},{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556"}],"page":"2205 - 2221","publication":"Journal of Cell Biology","file_date_updated":"2020-07-14T12:45:45Z","oa":1,"intvolume":"       217","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"6","acknowledgement":"M. Brown was supported by the Cell Communication in Health and Disease Graduate Study Program of the Austrian Science Fund and Medizinische Universität Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland postdoctoral research grant (287853). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 668036 (RELENT).","volume":217,"scopus_import":"1"},{"volume":13,"article_number":"e0198330","oa":1,"intvolume":"        13","acknowledgement":"This work was supported by the Swiss National Science Foundation (MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863 to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.), a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409) to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"6","scopus_import":"1","title":"Nano-scale microfluidics to study 3D chemotaxis at the single cell level","date_updated":"2023-09-13T09:00:15Z","month":"06","article_processing_charge":"No","date_published":"2018-06-07T00:00:00Z","publication":"PLoS One","file_date_updated":"2020-07-14T12:45:45Z","_id":"276","external_id":{"isi":["000434384900031"]},"date_created":"2018-12-11T11:45:34Z","publist_id":"7626","abstract":[{"text":"Directed migration of cells relies on their ability to sense directional guidance cues and to interact with pericellular structures in order to transduce contractile cytoskeletal- into mechanical forces. These biomechanical processes depend highly on microenvironmental factors such as exposure to 2D surfaces or 3D matrices. In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell migration are mostly derived from intravital microscopy or collagen-based in vitro assays. Both approaches offer only limited controlla-bility of experimental conditions. Here, we developed an automated microfluidic system that allows positioning of cells in 3D microenvironments containing highly controlled diffusion-based chemokine gradients. Tracking migration in such gradients was feasible in real time at the single cell level. Moreover, the setup allowed on-chip immunocytochemistry and thus linking of functional with phenotypical properties in individual cells. Spatially defined retrieval of cells from the device allows down-stream off-chip analysis. Using dendritic cells as a model, our setup specifically allowed us for the first time to quantitate key migration characteristics of cells exposed to identical gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration properties between 2D and 3D migration were distinct. Morphological features of cells migrating in an in vitro 3D environment were similar to those of cells migrating in animal tissues, but different from cells migrating on a surface. Our system thus offers a highly controllable in vitro-mimic of a 3D environment that cells traffic in vivo.","lang":"eng"}],"publication_status":"published","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","file":[{"relation":"main_file","checksum":"95fc5dc3938b3ad3b7697d10c83cc143","date_updated":"2020-07-14T12:45:45Z","content_type":"application/pdf","file_size":7682167,"file_name":"2018_Plos_Frick.pdf","access_level":"open_access","file_id":"5709","creator":"dernst","date_created":"2018-12-17T14:10:32Z"}],"type":"journal_article","citation":{"ieee":"C. Frick <i>et al.</i>, “Nano-scale microfluidics to study 3D chemotaxis at the single cell level,” <i>PLoS One</i>, vol. 13, no. 6. Public Library of Science, 2018.","short":"C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T. Schroeder, M. Mehling, PLoS One 13 (2018).","apa":"Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M., … Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single cell level. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0198330\">https://doi.org/10.1371/journal.pone.0198330</a>","mla":"Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” <i>PLoS One</i>, vol. 13, no. 6, e0198330, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pone.0198330\">10.1371/journal.pone.0198330</a>.","ista":"Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 13(6), e0198330.","ama":"Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. <i>PLoS One</i>. 2018;13(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0198330\">10.1371/journal.pone.0198330</a>","chicago":"Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” <i>PLoS One</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pone.0198330\">https://doi.org/10.1371/journal.pone.0198330</a>."},"ddc":["570"],"article_type":"original","department":[{"_id":"MiSi"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2018","isi":1,"author":[{"first_name":"Corina","last_name":"Frick","full_name":"Frick, Corina"},{"last_name":"Dettinger","full_name":"Dettinger, Philip","first_name":"Philip"},{"last_name":"Renkawitz","full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Annaïse","last_name":"Jauch","full_name":"Jauch, Annaïse"},{"full_name":"Berger, Christoph","last_name":"Berger","first_name":"Christoph"},{"full_name":"Recher, Mike","last_name":"Recher","first_name":"Mike"},{"full_name":"Schroeder, Timm","last_name":"Schroeder","first_name":"Timm"},{"full_name":"Mehling, Matthias","last_name":"Mehling","first_name":"Matthias"}],"doi":"10.1371/journal.pone.0198330","oa_version":"Published Version","publisher":"Public Library of Science","day":"07"},{"intvolume":"        97","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"5","volume":97,"scopus_import":"1","article_processing_charge":"No","date_published":"2018-06-12T00:00:00Z","date_updated":"2023-09-08T13:21:05Z","title":"An armadillo-domain protein participates in a telomerase interaction network","month":"06","_id":"277","external_id":{"isi":["000438981700009"]},"date_created":"2018-12-11T11:45:34Z","publication":"Plant Molecular Biology","file_date_updated":"2020-07-14T12:45:45Z","page":"407 - 420","quality_controlled":"1","publist_id":"7625","abstract":[{"text":"Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2. Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions. We previously identified interaction of the C-terminal domain of Arabidopsis telomerase reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing protein. Here we explore protein–protein interactions of the ARM protein, AtTERT domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both the N- and C-terminal domains of AtTERT in different cellular compartments. ARM interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly or through interaction with POT1a. The putative human ARM homolog co-precipitates telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis arm mutants shows no obvious changes in telomere length or telomerase activity, suggesting that ARM is not essential for telomere maintenance. The observed interactions with telomerase and Myb-like domain proteins (TRF-like family I) may therefore reflect possible non-telomeric functions. Transcript levels of several DNA repair and ribosomal genes are affected in arm mutants, and ARM, likely in association with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric functions of telomerase, and can also perform its own telomerase-independent functions.","lang":"eng"}],"publication_status":"published","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"ddc":["580"],"article_type":"original","file":[{"file_size":1150679,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:45Z","relation":"main_file","checksum":"451ae47616e6af2533099f596b2a47fb","access_level":"open_access","file_name":"2018_PlantMolecBio_Dokladal.pdf","file_id":"7834","date_created":"2020-05-14T12:23:08Z","creator":"dernst"}],"type":"journal_article","citation":{"short":"L. Dokládal, E. Benková, D. Honys, N. Dupláková, L. Lee, S. Gelvin, E. Sýkorová, Plant Molecular Biology 97 (2018) 407–420.","apa":"Dokládal, L., Benková, E., Honys, D., Dupláková, N., Lee, L., Gelvin, S., &#38; Sýkorová, E. (2018). An armadillo-domain protein participates in a telomerase interaction network. <i>Plant Molecular Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s11103-018-0747-4\">https://doi.org/10.1007/s11103-018-0747-4</a>","ieee":"L. Dokládal <i>et al.</i>, “An armadillo-domain protein participates in a telomerase interaction network,” <i>Plant Molecular Biology</i>, vol. 97, no. 5. Springer, pp. 407–420, 2018.","ama":"Dokládal L, Benková E, Honys D, et al. An armadillo-domain protein participates in a telomerase interaction network. <i>Plant Molecular Biology</i>. 2018;97(5):407-420. doi:<a href=\"https://doi.org/10.1007/s11103-018-0747-4\">10.1007/s11103-018-0747-4</a>","chicago":"Dokládal, Ladislav, Eva Benková, David Honys, Nikoleta Dupláková, Lan Lee, Stanton Gelvin, and Eva Sýkorová. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” <i>Plant Molecular Biology</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s11103-018-0747-4\">https://doi.org/10.1007/s11103-018-0747-4</a>.","mla":"Dokládal, Ladislav, et al. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” <i>Plant Molecular Biology</i>, vol. 97, no. 5, Springer, 2018, pp. 407–20, doi:<a href=\"https://doi.org/10.1007/s11103-018-0747-4\">10.1007/s11103-018-0747-4</a>.","ista":"Dokládal L, Benková E, Honys D, Dupláková N, Lee L, Gelvin S, Sýkorová E. 2018. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 97(5), 407–420."},"year":"2018","author":[{"full_name":"Dokládal, Ladislav","last_name":"Dokládal","first_name":"Ladislav"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"first_name":"David","last_name":"Honys","full_name":"Honys, David"},{"first_name":"Nikoleta","last_name":"Dupláková","full_name":"Dupláková, Nikoleta"},{"full_name":"Lee, Lan","last_name":"Lee","first_name":"Lan"},{"first_name":"Stanton","last_name":"Gelvin","full_name":"Gelvin, Stanton"},{"first_name":"Eva","full_name":"Sýkorová, Eva","last_name":"Sýkorová"}],"isi":1,"department":[{"_id":"EvBe"}],"publisher":"Springer","day":"12","doi":"10.1007/s11103-018-0747-4","oa_version":"Submitted Version"},{"type":"dissertation","citation":{"mla":"Villányi, Márton. <i>Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken</i>. Universität Wien, 2018.","ista":"Villányi M. 2018. Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken. Universität Wien.","chicago":"Villányi, Márton. “Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken.” Universität Wien, 2018.","ama":"Villányi M. Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken. 2018.","ieee":"M. Villányi, “Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken,” Universität Wien, 2018.","short":"M. Villányi, Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken, Universität Wien, 2018.","apa":"Villányi, M. (2018). <i>Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken</i>. Universität Wien."},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","language":[{"iso":"ger"}],"publist_id":"7624","main_file_link":[{"url":"http://othes.univie.ac.at/51113/","open_access":"1"}],"related_material":{"record":[{"id":"5577","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"5574"},{"relation":"dissertation_contains","status":"public","id":"5578"},{"relation":"dissertation_contains","status":"public","id":"5579"},{"id":"5576","status":"public","relation":"dissertation_contains"},{"id":"5575","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"5582"},{"status":"public","relation":"dissertation_contains","id":"5581"},{"relation":"dissertation_contains","status":"public","id":"5580"}]},"publication_status":"published","abstract":[{"lang":"eng","text":"Consortial subscription contracts regulate the digital access to publications between publishers and scientific libraries. However, since a couple of years the tendency towards a freely accessible publishing (Open Access) intensifies. As a consequence of this trend the contractual relationship between licensor and licensee is gradually changing as well: More and more contracts exercise influence on open access publishing. The present study attempts to compare Austrian examples of consortial licence contracts, which include components of open access. It describes the difference between pure subscription contracts and differing innovative deals including open access components. Thereby it becomes obvious that for the evaluation of this licence contracts new methods are needed. An essential new element of such analyses is the evaluation of the open access publication numbers. So this study tries to carry out such publication analyses for Austrian open access deals focusing on quantitative questions: How does the number of publications evolve? How does the open access share change? Publications reports of the publishers and database queries from Scopus form the data basis. The analysis of the data points out that differing approaches of contracts result in highly divergent results: Particular deals can prioritize a saving in costs or else the increase of the open access rate. It is to be assumed that within the following years further numerous open access deals will be negotiated. The finding of this study shall provide guidance."}],"day":"06","date_created":"2018-12-11T11:45:34Z","_id":"278","publisher":"Universität Wien","oa_version":"Published Version","page":"94","supervisor":[{"first_name":"Brigitte","full_name":"Kromp, Brigitte","last_name":"Kromp"}],"year":"2018","author":[{"id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","first_name":"Márton","full_name":"Villányi, Márton","orcid":"0000-0001-8126-0426","last_name":"Villányi"}],"date_published":"2018-04-06T00:00:00Z","month":"04","department":[{"_id":"E-Lib"}],"title":"Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken","date_updated":"2024-02-21T13:44:07Z"},{"year":"2018","isi":1,"author":[{"full_name":"Zapata, Luis","last_name":"Zapata","first_name":"Luis"},{"first_name":"Oriol","full_name":"Pich, Oriol","last_name":"Pich"},{"last_name":"Serrano","full_name":"Serrano, Luis","first_name":"Luis"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"full_name":"Ossowski, Stephan","last_name":"Ossowski","first_name":"Stephan"},{"full_name":"Schaefer, Martin","last_name":"Schaefer","first_name":"Martin"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"FyKo"}],"day":"31","publisher":"BioMed Central","oa_version":"Published Version","doi":"10.1186/s13059-018-1434-0","quality_controlled":"1","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"7620","abstract":[{"lang":"eng","text":"Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments."}],"publication_status":"published","ddc":["570"],"type":"journal_article","citation":{"short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” <i>Genome Biology</i>, vol. 19. BioMed Central, 2018.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” <i>Genome Biology</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. <i>Genome Biology</i>. 2018;19. doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67.","mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” <i>Genome Biology</i>, vol. 19, 67, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>."},"file":[{"file_id":"5708","creator":"dernst","date_created":"2018-12-17T14:05:01Z","relation":"main_file","checksum":"f3e4922486bd9bf1483271bdbed394a7","file_size":1414722,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:47Z","file_name":"2018_GenomeBiology_Zapata.pdf","access_level":"open_access"}],"ec_funded":1,"article_processing_charge":"No","date_published":"2018-05-31T00:00:00Z","month":"05","date_updated":"2023-09-13T09:01:32Z","title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","external_id":{"isi":["000433986200001"]},"date_created":"2018-12-11T11:45:35Z","_id":"279","project":[{"call_identifier":"FP7","_id":"26120F5C-B435-11E9-9278-68D0E5697425","grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution"}],"publication":"Genome Biology","file_date_updated":"2020-07-14T12:45:47Z","intvolume":"        19","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"67","related_material":{"record":[{"relation":"research_data","status":"public","id":"9811"},{"id":"9812","status":"public","relation":"research_data"}]},"volume":19,"scopus_import":"1"},{"date_updated":"2024-03-25T23:30:23Z","title":"Incorrect trafficking route leads to autism","month":"09","date_published":"2018-09-01T00:00:00Z","article_processing_charge":"No","publication":"Brain a journal of neurology","page":"2542 - 2544","_id":"28","date_created":"2018-12-11T11:44:14Z","external_id":{"isi":["000446548100012"]},"volume":141,"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7902"}]},"issue":"9","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"       141","scopus_import":"1","department":[{"_id":"SiHi"}],"author":[{"full_name":"Contreras, Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"year":"2018","doi":"10.1093/brain/awy218","oa_version":"None","publisher":"Oxford University Press","day":"01","publication_status":"published","abstract":[{"lang":"eng","text":"This scientific commentary refers to ‘NEGR1 and FGFR2 cooperatively regulate cortical development and core behaviours related to autism disorders in mice’ by Szczurkowska et al. "}],"language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","type":"journal_article","citation":{"ama":"Contreras X, Hippenmeyer S. Incorrect trafficking route leads to autism. <i>Brain a journal of neurology</i>. 2018;141(9):2542-2544. doi:<a href=\"https://doi.org/10.1093/brain/awy218\">10.1093/brain/awy218</a>","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” <i>Brain a Journal of Neurology</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/brain/awy218\">https://doi.org/10.1093/brain/awy218</a>.","ista":"Contreras X, Hippenmeyer S. 2018. Incorrect trafficking route leads to autism. Brain a journal of neurology. 141(9), 2542–2544.","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” <i>Brain a Journal of Neurology</i>, vol. 141, no. 9, Oxford University Press, 2018, pp. 2542–44, doi:<a href=\"https://doi.org/10.1093/brain/awy218\">10.1093/brain/awy218</a>.","apa":"Contreras, X., &#38; Hippenmeyer, S. (2018). Incorrect trafficking route leads to autism. <i>Brain a Journal of Neurology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/brain/awy218\">https://doi.org/10.1093/brain/awy218</a>","short":"X. Contreras, S. Hippenmeyer, Brain a Journal of Neurology 141 (2018) 2542–2544.","ieee":"X. Contreras and S. Hippenmeyer, “Incorrect trafficking route leads to autism,” <i>Brain a journal of neurology</i>, vol. 141, no. 9. Oxford University Press, pp. 2542–2544, 2018."}},{"date_created":"2018-12-11T11:45:35Z","external_id":{"isi":["000435571000017"]},"_id":"280","page":"365 - 375","publication":"Nature Plants","date_published":"2018-05-28T00:00:00Z","article_processing_charge":"No","month":"05","date_updated":"2023-09-13T08:24:17Z","title":"KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis","scopus_import":"1","acknowledgement":"We gratefully acknowledge funding from the Chinese Scholarship Council (CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek (FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.), the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH (project number 639234 to M.K.N.).","issue":"6","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"         4","volume":4,"day":"28","publisher":"Nature Publishing Group","oa_version":"None","doi":"10.1038/s41477-018-0160-7","author":[{"full_name":"Gao, Zhen","last_name":"Gao","first_name":"Zhen"},{"full_name":"Daneva, Anna","last_name":"Daneva","first_name":"Anna"},{"full_name":"Salanenka, Yuliya","last_name":"Salanenka","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","first_name":"Yuliya"},{"first_name":"Matthias","last_name":"Van Durme","full_name":"Van Durme, Matthias"},{"first_name":"Marlies","full_name":"Huysmans, Marlies","last_name":"Huysmans"},{"first_name":"Zongcheng","full_name":"Lin, Zongcheng","last_name":"Lin"},{"first_name":"Freya","last_name":"De Winter","full_name":"De Winter, Freya"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"last_name":"Karimi","full_name":"Karimi, Mansour","first_name":"Mansour"},{"first_name":"Jan","last_name":"Van De Velde","full_name":"Van De Velde, Jan"},{"last_name":"Vandepoele","full_name":"Vandepoele, Klaas","first_name":"Klaas"},{"last_name":"Van De Walle","full_name":"Van De Walle, Davy","first_name":"Davy"},{"first_name":"Koen","full_name":"Dewettinck, Koen","last_name":"Dewettinck"},{"full_name":"Lambrecht, Bart","last_name":"Lambrecht","first_name":"Bart"},{"last_name":"Nowack","full_name":"Nowack, Moritz","first_name":"Moritz"}],"isi":1,"year":"2018","department":[{"_id":"JiFr"}],"citation":{"ieee":"Z. Gao <i>et al.</i>, “KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis,” <i>Nature Plants</i>, vol. 4, no. 6. Nature Publishing Group, pp. 365–375, 2018.","short":"Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle, K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375.","apa":"Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., … Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0160-7\">https://doi.org/10.1038/s41477-018-0160-7</a>","ista":"Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375.","mla":"Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” <i>Nature Plants</i>, vol. 4, no. 6, Nature Publishing Group, 2018, pp. 365–75, doi:<a href=\"https://doi.org/10.1038/s41477-018-0160-7\">10.1038/s41477-018-0160-7</a>.","ama":"Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. <i>Nature Plants</i>. 2018;4(6):365-375. doi:<a href=\"https://doi.org/10.1038/s41477-018-0160-7\">10.1038/s41477-018-0160-7</a>","chicago":"Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans, Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0160-7\">https://doi.org/10.1038/s41477-018-0160-7</a>."},"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"text":"Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span.","lang":"eng"}],"publist_id":"7619"},{"type":"journal_article","citation":{"short":"A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093.","apa":"Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G., &#38; Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1716659115\">https://doi.org/10.1073/pnas.1716659115</a>","ieee":"A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” <i>PNAS</i>, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018.","ama":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. <i>PNAS</i>. 2018;115(23):6088-6093. doi:<a href=\"https://doi.org/10.1073/pnas.1716659115\">10.1073/pnas.1716659115</a>","chicago":"Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1716659115\">https://doi.org/10.1073/pnas.1716659115</a>.","ista":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093.","mla":"Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” <i>PNAS</i>, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:<a href=\"https://doi.org/10.1073/pnas.1716659115\">10.1073/pnas.1716659115</a>."},"article_type":"original","abstract":[{"text":"Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making.","lang":"eng"}],"publication_status":"published","publist_id":"7618","language":[{"iso":"eng"}],"status":"public","pmid":1,"quality_controlled":"1","doi":"10.1073/pnas.1716659115","oa_version":"Preprint","publisher":"National Academy of Sciences","day":"05","department":[{"_id":"GaTk"}],"isi":1,"author":[{"last_name":"Granados","full_name":"Granados, Alejandro","first_name":"Alejandro"},{"last_name":"Pietsch","full_name":"Pietsch, Julian","first_name":"Julian"},{"id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarah A","last_name":"Cepeda Humerez","full_name":"Cepeda Humerez, Sarah A"},{"first_name":"Isebail","full_name":"Farquhar, Isebail","last_name":"Farquhar"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"full_name":"Swain, Peter","last_name":"Swain","first_name":"Peter"}],"year":"2018","scopus_import":"1","volume":115,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/early/2017/09/21/192039"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6473"}]},"issue":"23","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to G.T.).","intvolume":"       115","oa":1,"publication":"PNAS","page":"6088 - 6093","_id":"281","project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:45:35Z","external_id":{"isi":["000434114900071"],"pmid":["29784812"]},"date_updated":"2023-09-11T12:58:24Z","title":"Distributed and dynamic intracellular organization of extracellular information","month":"06","date_published":"2018-06-05T00:00:00Z","article_processing_charge":"No"},{"quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci."}],"publist_id":"7617","citation":{"mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” <i>Genetics</i>, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:<a href=\"https://doi.org/10.1534/genetics.118.301018\">10.1534/genetics.118.301018</a>.","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. <i>Genetics</i>. 2018;209(4):1279-1303. doi:<a href=\"https://doi.org/10.1534/genetics.118.301018\">10.1534/genetics.118.301018</a>","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.301018\">https://doi.org/10.1534/genetics.118.301018</a>.","ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” <i>Genetics</i>, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","apa":"Sachdeva, H., &#38; Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.301018\">https://doi.org/10.1534/genetics.118.301018</a>"},"type":"journal_article","author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"isi":1,"year":"2018","department":[{"_id":"NiBa"}],"day":"01","publisher":"Genetics Society of America","oa_version":"Submitted Version","doi":"10.1534/genetics.118.301018","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"4","oa":1,"intvolume":"       209","volume":209,"main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/11/30/227082","open_access":"1"}],"scopus_import":"1","date_published":"2018-08-01T00:00:00Z","article_processing_charge":"No","month":"08","title":"Introgression of a block of genome under infinitesimal selection","date_updated":"2023-09-13T08:22:32Z","date_created":"2018-12-11T11:45:36Z","external_id":{"isi":["000440014100020"]},"_id":"282","page":"1279 - 1303","publication":"Genetics"},{"article_processing_charge":"No","date_published":"2018-06-08T00:00:00Z","date_updated":"2023-09-13T08:59:27Z","title":"Mutations in blind cavefish target the light regulated circadian clock gene period 2","month":"06","_id":"283","external_id":{"isi":["000434640800008"]},"date_created":"2018-12-11T11:45:36Z","publication":"Scientific Reports","file_date_updated":"2020-07-14T12:45:49Z","article_number":"8754","intvolume":"         8","oa":1,"issue":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":8,"scopus_import":"1","year":"2018","author":[{"first_name":"Rosa Maria","full_name":"Ceinos, Rosa Maria","last_name":"Ceinos"},{"full_name":"Frigato, Elena","last_name":"Frigato","first_name":"Elena"},{"first_name":"Cristina","full_name":"Pagano, Cristina","last_name":"Pagano"},{"full_name":"Frohlich, Nadine","last_name":"Frohlich","first_name":"Nadine"},{"full_name":"Negrini, Pietro","last_name":"Negrini","first_name":"Pietro"},{"first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","full_name":"Cavallari, Nicola","last_name":"Cavallari"},{"first_name":"Daniela","last_name":"Vallone","full_name":"Vallone, Daniela"},{"first_name":"Silvia","last_name":"Fuselli","full_name":"Fuselli, Silvia"},{"first_name":"Cristiano","full_name":"Bertolucci, Cristiano","last_name":"Bertolucci"},{"full_name":"Foulkes, Nicholas S","last_name":"Foulkes","first_name":"Nicholas S"}],"isi":1,"department":[{"_id":"EvBe"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Nature Publishing Group","day":"08","doi":"10.1038/s41598-018-27080-2","oa_version":"Published Version","quality_controlled":"1","publist_id":"7616","publication_status":"published","abstract":[{"text":"Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors.","lang":"eng"}],"status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"ddc":["570"],"file":[{"file_size":1855324,"date_updated":"2020-07-14T12:45:49Z","content_type":"application/pdf","checksum":"9c3942d772f84f3df032ffde0ed9a8ea","relation":"main_file","access_level":"open_access","file_name":"2018_ScientificReports_Ceinos.pdf","file_id":"5707","date_created":"2018-12-17T13:04:46Z","creator":"dernst"}],"citation":{"mla":"Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” <i>Scientific Reports</i>, vol. 8, no. 1, 8754, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-27080-2\">10.1038/s41598-018-27080-2</a>.","ista":"Ceinos RM, Frigato E, Pagano C, Frohlich N, Negrini P, Cavallari N, Vallone D, Fuselli S, Bertolucci C, Foulkes NS. 2018. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 8(1), 8754.","ama":"Ceinos RM, Frigato E, Pagano C, et al. Mutations in blind cavefish target the light regulated circadian clock gene period 2. <i>Scientific Reports</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-27080-2\">10.1038/s41598-018-27080-2</a>","chicago":"Ceinos, Rosa Maria, Elena Frigato, Cristina Pagano, Nadine Frohlich, Pietro Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci, and Nicholas S Foulkes. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” <i>Scientific Reports</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41598-018-27080-2\">https://doi.org/10.1038/s41598-018-27080-2</a>.","ieee":"R. M. Ceinos <i>et al.</i>, “Mutations in blind cavefish target the light regulated circadian clock gene period 2,” <i>Scientific Reports</i>, vol. 8, no. 1. Nature Publishing Group, 2018.","short":"R.M. Ceinos, E. Frigato, C. Pagano, N. Frohlich, P. Negrini, N. Cavallari, D. Vallone, S. Fuselli, C. Bertolucci, N.S. Foulkes, Scientific Reports 8 (2018).","apa":"Ceinos, R. M., Frigato, E., Pagano, C., Frohlich, N., Negrini, P., Cavallari, N., … Foulkes, N. S. (2018). Mutations in blind cavefish target the light regulated circadian clock gene period 2. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-018-27080-2\">https://doi.org/10.1038/s41598-018-27080-2</a>"},"type":"journal_article"}]