[{"file":[{"date_created":"2019-11-07T12:55:20Z","date_updated":"2020-07-14T12:45:00Z","checksum":"ef6d2b4e1fd63948539639242610bfa6","file_id":"6994","relation":"main_file","creator":"lsazanov","file_size":2185385,"content_type":"application/pdf","file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","_id":"152","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Mammalian mitochondrial complex I structure and disease causing mutations","status":"public","ddc":["572"],"intvolume":" 28","abstract":[{"text":"Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context.","lang":"eng"}],"issue":"10","type":"journal_article","date_published":"2018-07-26T00:00:00Z","publication":"Trends in Cell Biology","citation":{"ama":"Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 2018;28(10):835-867. doi:10.1016/j.tcb.2018.06.006","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.","apa":"Fiedorczuk, K., & Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. Elsevier. https://doi.org/10.1016/j.tcb.2018.06.006","ieee":"K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” Trends in Cell Biology, vol. 28, no. 10. Elsevier, pp. 835–867, 2018.","mla":"Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:10.1016/j.tcb.2018.06.006.","short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.","chicago":"Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology. Elsevier, 2018. https://doi.org/10.1016/j.tcb.2018.06.006."},"article_type":"original","page":"835 - 867","day":"26","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","author":[{"full_name":"Fiedorczuk, Karol","last_name":"Fiedorczuk","first_name":"Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"date_updated":"2023-09-13T08:51:56Z","date_created":"2018-12-11T11:44:54Z","volume":28,"year":"2018","publication_status":"published","publisher":"Elsevier","department":[{"_id":"LeSa"}],"file_date_updated":"2020-07-14T12:45:00Z","publist_id":"7769","doi":"10.1016/j.tcb.2018.06.006","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000445118200007"]},"quality_controlled":"1","isi":1,"month":"07"},{"abstract":[{"lang":"eng","text":"A model of computation that is widely used in the formal analysis of reactive systems is symbolic algorithms. In this model the access to the input graph is restricted to consist of symbolic operations, which are expensive in comparison to the standard RAM operations. We give lower bounds on the number of symbolic operations for basic graph problems such as the computation of the strongly connected components and of the approximate diameter as well as for fundamental problems in model checking such as safety, liveness, and coliveness. Our lower bounds are linear in the number of vertices of the graph, even for constant-diameter graphs. For none of these problems lower bounds on the number of symbolic operations were known before. The lower bounds show an interesting separation of these problems from the reachability problem, which can be solved with O(D) symbolic operations, where D is the diameter of the graph. Additionally we present an approximation algorithm for the graph diameter which requires Õ(n/D) symbolic steps to achieve a (1 +ϵ)-approximation for any constant > 0. This compares to O(n/D) symbolic steps for the (naive) exact algorithm and O(D) symbolic steps for a 2-approximation. Finally we also give a refined analysis of the strongly connected components algorithms of [15], showing that it uses an optimal number of symbolic steps that is proportional to the sum of the diameters of the strongly connected components."}],"type":"conference","oa_version":"Preprint","title":"Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"310","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-01-01T00:00:00Z","page":"2341 - 2356","citation":{"ama":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. In: ACM; 2018:2341-2356. doi:10.1137/1.9781611975031.151","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States, 2018, pp. 2341–2356.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2018). Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter (pp. 2341–2356). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States: ACM. https://doi.org/10.1137/1.9781611975031.151","ista":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2018. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. SODA: Symposium on Discrete Algorithms, 2341–2356.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, ACM, 2018, pp. 2341–2356.","mla":"Chatterjee, Krishnendu, et al. Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter. ACM, 2018, pp. 2341–56, doi:10.1137/1.9781611975031.151.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter,” 2341–56. ACM, 2018. https://doi.org/10.1137/1.9781611975031.151."},"publist_id":"7555","ec_funded":1,"date_created":"2018-12-11T11:45:45Z","date_updated":"2023-09-13T08:50:16Z","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Dvorák","first_name":"Wolfgang","full_name":"Dvorák, Wolfgang"},{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"full_name":"Loitzenbauer, Veronika","first_name":"Veronika","last_name":"Loitzenbauer"}],"publication_status":"published","publisher":"ACM","department":[{"_id":"KrCh"}],"year":"2018","month":"01","language":[{"iso":"eng"}],"conference":{"end_date":"2018-01-10","location":"New Orleans, Louisiana, United States","start_date":"2018-01-07","name":"SODA: Symposium on Discrete Algorithms"},"doi":"10.1137/1.9781611975031.151","isi":1,"quality_controlled":"1","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.09148"}],"external_id":{"isi":["000483921200152"],"arxiv":["1711.09148"]},"oa":1},{"abstract":[{"text":"There has been significant interest recently in using complex quantum systems to create effective nonreciprocal dynamics. Proposals have been put forward for the realization of artificial magnetic fields for photons and phonons; experimental progress is fast making these proposals a reality. Much work has concentrated on the use of such systems for controlling the flow of signals, e.g., to create isolators or directional amplifiers for optical signals. In this Letter, we build on this work but move in a different direction. We develop the theory of and discuss a potential realization for the controllable flow of thermal noise in quantum systems. We demonstrate theoretically that the unidirectional flow of thermal noise is possible within quantum cascaded systems. Viewing an optomechanical platform as a cascaded system we show here that one can ultimately control the direction of the flow of thermal noise. By appropriately engineering the mechanical resonator, which acts as an artificial reservoir, the flow of thermal noise can be constrained to a desired direction, yielding a thermal rectifier. The proposed quantum thermal noise rectifier could potentially be used to develop devices such as a thermal modulator, a thermal router, and a thermal amplifier for nanoelectronic devices and superconducting circuits.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Preprint","title":"Manipulating the flow of thermal noise in quantum devices","status":"public","intvolume":" 120","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"436","day":"07","article_processing_charge":"No","scopus_import":"1","date_published":"2018-02-07T00:00:00Z","publication":"Physical Review Letters","citation":{"ista":"Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 120(6), 060601.","apa":"Barzanjeh, S., Aquilina, M., & Xuereb, A. (2018). Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.120.060601","ieee":"S. Barzanjeh, M. Aquilina, and A. Xuereb, “Manipulating the flow of thermal noise in quantum devices,” Physical Review Letters, vol. 120, no. 6. American Physical Society, 2018.","ama":"Barzanjeh S, Aquilina M, Xuereb A. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 2018;120(6). doi:10.1103/PhysRevLett.120.060601","chicago":"Barzanjeh, Shabir, Matteo Aquilina, and André Xuereb. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.060601.","mla":"Barzanjeh, Shabir, et al. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters, vol. 120, no. 6, 060601, American Physical Society, 2018, doi:10.1103/PhysRevLett.120.060601.","short":"S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018)."},"publist_id":"7387","ec_funded":1,"article_number":"060601 ","date_updated":"2023-09-13T08:52:27Z","date_created":"2018-12-11T11:46:28Z","volume":120,"author":[{"last_name":"Barzanjeh","first_name":"Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir"},{"full_name":"Aquilina, Matteo","first_name":"Matteo","last_name":"Aquilina"},{"last_name":"Xuereb","first_name":"André","full_name":"Xuereb, André"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/","description":"News on IST Homepage","relation":"press_release"}]},"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"JoFi"}],"year":"2018","month":"02","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.120.060601","quality_controlled":"1","isi":1,"project":[{"_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894","call_identifier":"H2020","name":"Hybrid Optomechanical Technologies"},{"_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM"}],"external_id":{"arxiv":["1706.09051"],"isi":["000424382100004"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.09051"}],"oa":1},{"date_published":"2018-12-05T00:00:00Z","publication":"Journal of the Royal Society Interface","citation":{"ista":"Hross S, Theis FJ, Sixt MK, Hasenauer J. 2018. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 15(149), 20180600.","ieee":"S. Hross, F. J. Theis, M. K. Sixt, and J. Hasenauer, “Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018.","apa":"Hross, S., Theis, F. J., Sixt, M. K., & Hasenauer, J. (2018). Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0600","ama":"Hross S, Theis FJ, Sixt MK, Hasenauer J. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0600","chicago":"Hross, Sabrina, Fabian J. Theis, Michael K Sixt, and Jan Hasenauer. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0600.","mla":"Hross, Sabrina, et al. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180600, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0600.","short":"S. Hross, F.J. Theis, M.K. Sixt, J. Hasenauer, Journal of the Royal Society Interface 15 (2018)."},"day":"05","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5925","checksum":"56eb4308a15b7190bff938fab1f780e8","date_updated":"2020-07-14T12:47:13Z","date_created":"2019-02-05T14:46:44Z","access_level":"open_access","file_name":"2018_Interface_Hross.pdf","content_type":"application/pdf","file_size":1464288,"creator":"dernst"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5858","title":"Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data","ddc":["570"],"status":"public","intvolume":" 15","abstract":[{"lang":"eng","text":"Spatial patterns are ubiquitous on the subcellular, cellular and tissue level, and can be studied using imaging techniques such as light and fluorescence microscopy. Imaging data provide quantitative information about biological systems; however, mechanisms causing spatial patterning often remain elusive. In recent years, spatio-temporal mathematical modelling has helped to overcome this problem. Yet, outliers and structured noise limit modelling of whole imaging data, and models often consider spatial summary statistics. Here, we introduce an integrated data-driven modelling approach that can cope with measurement artefacts and whole imaging data. Our approach combines mechanistic models of the biological processes with robust statistical models of the measurement process. The parameters of the integrated model are calibrated using a maximum-likelihood approach. We used this integrated modelling approach to study in vivo gradients of the chemokine (C-C motif) ligand 21 (CCL21). CCL21 gradients guide dendritic cells and are important in the adaptive immune response. Using artificial data, we verified that the integrated modelling approach provides reliable parameter estimates in the presence of measurement noise and that bias and variance of these estimates are reduced compared to conventional approaches. The application to experimental data allowed the parametrization and subsequent refinement of the model using additional mechanisms. Among other results, model-based hypothesis testing predicted lymphatic vessel-dependent concentration of heparan sulfate, the binding partner of CCL21. The selected model provided an accurate description of the experimental data and was partially validated using published data. Our findings demonstrate that integrated statistical modelling of whole imaging data is computationally feasible and can provide novel biological insights."}],"issue":"149","type":"journal_article","doi":"10.1098/rsif.2018.0600","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000456783800011"]},"oa":1,"isi":1,"quality_controlled":"1","month":"12","publication_identifier":{"issn":["17425689"]},"author":[{"first_name":"Sabrina","last_name":"Hross","full_name":"Hross, Sabrina"},{"full_name":"Theis, Fabian J.","last_name":"Theis","first_name":"Fabian J."},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"full_name":"Hasenauer, Jan","last_name":"Hasenauer","first_name":"Jan"}],"date_updated":"2023-09-13T08:55:05Z","date_created":"2019-01-20T22:59:18Z","volume":15,"year":"2018","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Royal Society Publishing","file_date_updated":"2020-07-14T12:47:13Z","article_number":"20180600"},{"issue":"10","abstract":[{"text":"We report quantitative evidence of mixing-layer elastic instability in a viscoelastic fluid flow between two widely spaced obstacles hindering a channel flow at Re 1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed in the region between the obstacles. The mixing-layer instability arises in the vicinity of an inflection point on the shear velocity profile with a steep variation in the elastic stress. The instability results in an intermittent appearance of small vortices in the mixing layers and an amplification of spatiotemporal averaged vorticity in the elastic turbulence regime. The latter is characterized through scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore, the observations reported provide improved understanding of the stability of the mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1 and oppose the current view of suppression of vorticity solely by polymer additives.","lang":"eng"}],"type":"journal_article","pubrep_id":"1062","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:45:04Z","date_created":"2018-12-12T10:13:56Z","checksum":"7fc0a2322214d1c04debef36d5bf2e8a","relation":"main_file","file_id":"5043","content_type":"application/pdf","file_size":1838431,"creator":"system","file_name":"IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf","access_level":"open_access"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"16","intvolume":" 3","status":"public","ddc":["532"],"title":"Mixing layer instability and vorticity amplification in a creeping viscoelastic flow","has_accepted_license":"1","article_processing_charge":"No","day":"16","scopus_import":"1","date_published":"2018-10-16T00:00:00Z","citation":{"ista":"Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303.","apa":"Varshney, A., & Steinberg, V. (2018). Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103303","ieee":"A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification in a creeping viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society, 2018.","ama":"Varshney A, Steinberg V. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103303","chicago":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103303.","mla":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103303, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103303.","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018)."},"publication":"Physical Review Fluids","article_type":"original","ec_funded":1,"publist_id":"8039","file_date_updated":"2020-07-14T12:45:04Z","article_number":"103303","author":[{"full_name":"Varshney, Atul","last_name":"Varshney","first_name":"Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Steinberg","first_name":"Victor","full_name":"Steinberg, Victor"}],"volume":3,"date_updated":"2023-09-13T08:57:05Z","date_created":"2018-12-11T11:44:10Z","acknowledgement":"This work was partially supported by the Israel Science Foundation (ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No. 2016145).","year":"2018","department":[{"_id":"BjHo"}],"publisher":"American Physical Society","publication_status":"published","month":"10","doi":"10.1103/PhysRevFluids.3.103303","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000447469200001"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1"},{"doi":"10.1073/pnas.1721061115","language":[{"iso":"eng"}],"external_id":{"isi":["000447491300057"]},"oa":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"month":"10","author":[{"full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","first_name":"Joel"},{"full_name":"Kisdi, Eva","last_name":"Kisdi","first_name":"Eva"},{"full_name":"Anttila, Jani","first_name":"Jani","last_name":"Anttila"}],"volume":115,"date_updated":"2023-09-13T08:57:38Z","date_created":"2018-12-11T11:44:19Z","acknowledgement":"J.R. and J.V.A. were also supported by the Academy of Finland Grants 1273253 and 267541.","year":"2018","publisher":"National Academy of Sciences","department":[{"_id":"DaAl"}],"publication_status":"published","ec_funded":1,"publist_id":"8011","file_date_updated":"2020-07-14T12:46:26Z","date_published":"2018-10-02T00:00:00Z","citation":{"mla":"Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS, vol. 115, no. 42, National Academy of Sciences, 2018, pp. 10690–95, doi:10.1073/pnas.1721061115.","short":"J. Rybicki, E. Kisdi, J. Anttila, PNAS 115 (2018) 10690–10695.","chicago":"Rybicki, Joel, Eva Kisdi, and Jani Anttila. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721061115.","ama":"Rybicki J, Kisdi E, Anttila J. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 2018;115(42):10690-10695. doi:10.1073/pnas.1721061115","ista":"Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 115(42), 10690–10695.","ieee":"J. Rybicki, E. Kisdi, and J. Anttila, “Model of bacterial toxin-dependent pathogenesis explains infective dose,” PNAS, vol. 115, no. 42. National Academy of Sciences, pp. 10690–10695, 2018.","apa":"Rybicki, J., Kisdi, E., & Anttila, J. (2018). Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1721061115"},"publication":"PNAS","page":"10690 - 10695","has_accepted_license":"1","article_processing_charge":"No","day":"02","scopus_import":"1","pubrep_id":"1063","oa_version":"Submitted Version","file":[{"file_id":"6258","relation":"main_file","date_updated":"2020-07-14T12:46:26Z","date_created":"2019-04-09T08:02:50Z","checksum":"df7ac544a587c06b75692653b9fabd18","file_name":"2018_PNAS_Rybicki.pdf","access_level":"open_access","creator":"dernst","file_size":4070777,"content_type":"application/pdf"}],"_id":"43","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 115","ddc":["570","577"],"title":"Model of bacterial toxin-dependent pathogenesis explains infective dose","status":"public","issue":"42","abstract":[{"lang":"eng","text":"The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics."}],"type":"journal_article"},{"publication_status":"published","publisher":"ACM","department":[{"_id":"BeBi"}],"year":"2018","date_updated":"2023-09-13T08:56:07Z","date_created":"2018-12-11T11:44:09Z","volume":37,"author":[{"full_name":"Alderighi, Thomas","last_name":"Alderighi","first_name":"Thomas"},{"full_name":"Malomo, Luigi","last_name":"Malomo","first_name":"Luigi"},{"full_name":"Giorgi, Daniela","first_name":"Daniela","last_name":"Giorgi"},{"first_name":"Nico","last_name":"Pietroni","full_name":"Pietroni, Nico"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"},{"full_name":"Cignoni, Paolo","first_name":"Paolo","last_name":"Cignoni"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/metamolds-molding-a-mold/","relation":"press_release","description":"News on IST Homepage"}]},"article_number":"136","file_date_updated":"2020-07-14T12:44:43Z","ec_funded":1,"publist_id":"8043","isi":1,"quality_controlled":"1","project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"oa":1,"external_id":{"isi":["000448185000097"]},"language":[{"iso":"eng"}],"doi":"10.1145/3197517.3201381","month":"08","status":"public","title":"Metamolds: Computational design of silicone molds","ddc":["004"],"intvolume":" 37","_id":"13","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","file":[{"file_name":"IST-2018-1038-v1+1_metamolds_authorversion.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":91939066,"file_id":"5374","relation":"main_file","date_created":"2018-12-12T10:18:52Z","date_updated":"2020-07-14T12:44:43Z","checksum":"61d46273dca4de626accef1d17a0aaad"}],"pubrep_id":"1038","type":"journal_article","abstract":[{"text":"We propose a new method for fabricating digital objects through reusable silicone molds. Molds are generated by casting liquid silicone into custom 3D printed containers called metamolds. Metamolds automatically define the cuts that are needed to extract the cast object from the silicone mold. The shape of metamolds is designed through a novel segmentation technique, which takes into account both geometric and topological constraints involved in the process of mold casting. Our technique is simple, does not require changing the shape or topology of the input objects, and only requires off-the- shelf materials and technologies. We successfully tested our method on a set of challenging examples with complex shapes and rich geometric detail. © 2018 Association for Computing Machinery.","lang":"eng"}],"issue":"4","publication":"ACM Trans. Graph.","citation":{"short":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, P. Cignoni, ACM Trans. Graph. 37 (2018).","mla":"Alderighi, Thomas, et al. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph., vol. 37, no. 4, 136, ACM, 2018, doi:10.1145/3197517.3201381.","chicago":"Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201381.","ama":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. Metamolds: Computational design of silicone molds. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201381","ieee":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, and P. Cignoni, “Metamolds: Computational design of silicone molds,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","apa":"Alderighi, T., Malomo, L., Giorgi, D., Pietroni, N., Bickel, B., & Cignoni, P. (2018). Metamolds: Computational design of silicone molds. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201381","ista":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. 2018. Metamolds: Computational design of silicone molds. ACM Trans. Graph. 37(4), 136."},"date_published":"2018-08-04T00:00:00Z","scopus_import":"1","day":"04","has_accepted_license":"1","article_processing_charge":"No"},{"issue":"9","abstract":[{"lang":"eng","text":"Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli."}],"type":"journal_article","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"137","intvolume":" 14","title":"Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS","status":"public","article_processing_charge":"No","day":"30","scopus_import":"1","date_published":"2018-07-30T00:00:00Z","citation":{"ista":"Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger C. 2018. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 14(9), 861–869.","ieee":"W. Zhang et al., “Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS,” Nature Chemical Biology, vol. 14, no. 9. Nature Publishing Group, pp. 861–869, 2018.","apa":"Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V., … Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0108-2","ama":"Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 2018;14(9):861-869. doi:10.1038/s41589-018-0108-2","chicago":"Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0108-2.","mla":"Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology, vol. 14, no. 9, Nature Publishing Group, 2018, pp. 861–69, doi:10.1038/s41589-018-0108-2.","short":"W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I. Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak, C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869."},"publication":"Nature Chemical Biology","page":"861 - 869","article_type":"original","publist_id":"7786","author":[{"first_name":"William","last_name":"Zhang","full_name":"Zhang, William"},{"first_name":"Michel","last_name":"Herde","full_name":"Herde, Michel"},{"first_name":"Joshua","last_name":"Mitchell","full_name":"Mitchell, Joshua"},{"first_name":"Jason","last_name":"Whitfield","full_name":"Whitfield, Jason"},{"last_name":"Wulff","first_name":"Andreas","full_name":"Wulff, Andreas"},{"last_name":"Vongsouthi","first_name":"Vanessa","full_name":"Vongsouthi, Vanessa"},{"first_name":"Inmaculada","last_name":"Sanchez Romero","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","full_name":"Sanchez Romero, Inmaculada"},{"last_name":"Gulakova","first_name":"Polina","full_name":"Gulakova, Polina"},{"full_name":"Minge, Daniel","last_name":"Minge","first_name":"Daniel"},{"full_name":"Breithausen, Björn","first_name":"Björn","last_name":"Breithausen"},{"full_name":"Schoch, Susanne","last_name":"Schoch","first_name":"Susanne"},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"},{"last_name":"Jackson","first_name":"Colin","full_name":"Jackson, Colin"},{"last_name":"Henneberger","first_name":"Christian","full_name":"Henneberger, Christian"}],"volume":14,"date_updated":"2023-09-13T08:58:05Z","date_created":"2018-12-11T11:44:49Z","pmid":1,"year":"2018","department":[{"_id":"HaJa"}],"publisher":"Nature Publishing Group","publication_status":"published","month":"07","doi":"10.1038/s41589-018-0108-2","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30061718"}],"external_id":{"pmid":["30061718 "],"isi":["000442174500013"]},"oa":1,"project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1"},{"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_Plos_Frick.pdf","file_size":7682167,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5709","checksum":"95fc5dc3938b3ad3b7697d10c83cc143","date_created":"2018-12-17T14:10:32Z","date_updated":"2020-07-14T12:45:45Z"}],"intvolume":" 13","status":"public","title":"Nano-scale microfluidics to study 3D chemotaxis at the single cell level","ddc":["570"],"_id":"276","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"6","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"}],"type":"journal_article","date_published":"2018-06-07T00:00:00Z","article_type":"original","citation":{"mla":"Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” PLoS One, vol. 13, no. 6, e0198330, Public Library of Science, 2018, doi:10.1371/journal.pone.0198330.","short":"C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T. Schroeder, M. Mehling, PLoS One 13 (2018).","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.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0198330.","ama":"Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 2018;13(6). doi:10.1371/journal.pone.0198330","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.","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. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0198330","ieee":"C. Frick et al., “Nano-scale microfluidics to study 3D chemotaxis at the single cell level,” PLoS One, vol. 13, no. 6. Public Library of Science, 2018."},"publication":"PLoS One","article_processing_charge":"No","has_accepted_license":"1","day":"07","scopus_import":"1","volume":13,"date_updated":"2023-09-13T09:00:15Z","date_created":"2018-12-11T11:45:34Z","author":[{"full_name":"Frick, Corina","first_name":"Corina","last_name":"Frick"},{"full_name":"Dettinger, Philip","first_name":"Philip","last_name":"Dettinger"},{"orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","first_name":"Jörg","full_name":"Renkawitz, Jörg"},{"last_name":"Jauch","first_name":"Annaïse","full_name":"Jauch, Annaïse"},{"first_name":"Christoph","last_name":"Berger","full_name":"Berger, Christoph"},{"first_name":"Mike","last_name":"Recher","full_name":"Recher, Mike"},{"first_name":"Timm","last_name":"Schroeder","full_name":"Schroeder, Timm"},{"full_name":"Mehling, Matthias","first_name":"Matthias","last_name":"Mehling"}],"department":[{"_id":"MiSi"}],"publisher":"Public Library of Science","publication_status":"published","year":"2018","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.","publist_id":"7626","file_date_updated":"2020-07-14T12:45:45Z","article_number":"e0198330","language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0198330","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000434384900031"]},"oa":1,"month":"06"},{"_id":"283","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 8","status":"public","title":"Mutations in blind cavefish target the light regulated circadian clock gene period 2","ddc":["570"],"file":[{"file_name":"2018_ScientificReports_Ceinos.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1855324,"creator":"dernst","relation":"main_file","file_id":"5707","date_created":"2018-12-17T13:04:46Z","date_updated":"2020-07-14T12:45:49Z","checksum":"9c3942d772f84f3df032ffde0ed9a8ea"}],"oa_version":"Published Version","type":"journal_article","issue":"1","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"}],"citation":{"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. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-27080-2","ieee":"R. M. Ceinos et al., “Mutations in blind cavefish target the light regulated circadian clock gene period 2,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","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. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-27080-2","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.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-27080-2.","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).","mla":"Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” Scientific Reports, vol. 8, no. 1, 8754, Nature Publishing Group, 2018, doi:10.1038/s41598-018-27080-2."},"publication":"Scientific Reports","date_published":"2018-06-08T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"08","year":"2018","department":[{"_id":"EvBe"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"full_name":"Ceinos, Rosa Maria","last_name":"Ceinos","first_name":"Rosa Maria"},{"full_name":"Frigato, Elena","last_name":"Frigato","first_name":"Elena"},{"last_name":"Pagano","first_name":"Cristina","full_name":"Pagano, Cristina"},{"first_name":"Nadine","last_name":"Frohlich","full_name":"Frohlich, Nadine"},{"full_name":"Negrini, Pietro","last_name":"Negrini","first_name":"Pietro"},{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","last_name":"Cavallari","first_name":"Nicola","full_name":"Cavallari, Nicola"},{"full_name":"Vallone, Daniela","first_name":"Daniela","last_name":"Vallone"},{"first_name":"Silvia","last_name":"Fuselli","full_name":"Fuselli, Silvia"},{"first_name":"Cristiano","last_name":"Bertolucci","full_name":"Bertolucci, Cristiano"},{"full_name":"Foulkes, Nicholas S","last_name":"Foulkes","first_name":"Nicholas S"}],"volume":8,"date_updated":"2023-09-13T08:59:27Z","date_created":"2018-12-11T11:45:36Z","article_number":"8754","publist_id":"7616","file_date_updated":"2020-07-14T12:45:49Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000434640800008"]},"quality_controlled":"1","isi":1,"doi":"10.1038/s41598-018-27080-2","language":[{"iso":"eng"}],"month":"06"},{"month":"08","project":[{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000884993200004"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-00151-3_4","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","location":"Beijing, China","start_date":"2018-09-04","end_date":"2018-09-06"},"publist_id":"7973","file_date_updated":"2020-10-09T06:24:21Z","department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2018","volume":11022,"date_updated":"2023-09-13T08:58:34Z","date_created":"2018-12-11T11:44:31Z","author":[{"id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","first_name":"Adrian","last_name":"Elgyütt","full_name":"Elgyütt, Adrian"},{"last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"26","page":"53 - 70","citation":{"ama":"Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables. In: Vol 11022. Springer; 2018:53-70. doi:10.1007/978-3-030-00151-3_4","ista":"Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 53–70.","ieee":"A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.","apa":"Elgyütt, A., Ferrere, T., & Henzinger, T. A. (2018). Monitoring temporal logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_4","mla":"Elgyütt, Adrian, et al. Monitoring Temporal Logic with Clock Variables. Vol. 11022, Springer, 2018, pp. 53–70, doi:10.1007/978-3-030-00151-3_4.","short":"A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.","chicago":"Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal Logic with Clock Variables,” 11022:53–70. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_4."},"date_published":"2018-08-26T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"We solve the offline monitoring problem for timed propositional temporal logic (TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider extends linear temporal logic (LTL) with clock variables and reset quantifiers, providing a mechanism to specify real-time constraints. We first describe a general monitoring algorithm based on an exhaustive computation of the set of satisfying clock assignments as a finite union of zones. We then propose a specialized monitoring algorithm for the one-variable case using a partition of the time domain based on the notion of region equivalence, whose complexity is linear in the length of the signal, thereby generalizing a known result regarding the monitoring of metric temporal logic (MTL). The region and zone representations of time constraints are known from timed automata verification and can also be used in the discrete-time case. Our prototype implementation appears to outperform previous discrete-time implementations of TPTL monitoring,","lang":"eng"}],"intvolume":" 11022","title":"Monitoring temporal logic with clock variables","status":"public","ddc":["000"],"_id":"81","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"checksum":"e5d81c9b50a6bd9d8a2c16953aad7e23","success":1,"date_created":"2020-10-09T06:24:21Z","date_updated":"2020-10-09T06:24:21Z","relation":"main_file","file_id":"8638","file_size":537219,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_LNCS_Elgyuett.pdf"}],"oa_version":"Submitted Version"},{"month":"09","doi":"10.1007/s00446-018-0342-6","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000475627800005"]},"quality_controlled":"1","isi":1,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"file_date_updated":"2020-07-14T12:48:01Z","publist_id":"7978","author":[{"full_name":"Lenzen, Christoph","last_name":"Lenzen","first_name":"Christoph"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","first_name":"Joel","last_name":"Rybicki","full_name":"Rybicki, Joel"}],"date_updated":"2023-09-13T09:01:06Z","date_created":"2018-12-11T11:44:30Z","year":"2018","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Springer","day":"12","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2018-09-12T00:00:00Z","publication":"Distributed Computing","citation":{"ama":"Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads. Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6","apa":"Lenzen, C., & Rybicki, J. (2018). Near-optimal self-stabilising counting and firing squads. Distributed Computing. Springer. https://doi.org/10.1007/s00446-018-0342-6","ieee":"C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing squads,” Distributed Computing. Springer, 2018.","ista":"Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing squads. Distributed Computing.","short":"C. Lenzen, J. Rybicki, Distributed Computing (2018).","mla":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing, Springer, 2018, doi:10.1007/s00446-018-0342-6.","chicago":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-018-0342-6."},"abstract":[{"text":"Consider a fully-connected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous C-counting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C>1. In the self-stabilising firing squad problem, the task is to eventually guarantee that all non-faulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the not-too-distant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for self-stabilising Byzantine firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5711","date_created":"2018-12-17T14:21:22Z","date_updated":"2020-07-14T12:48:01Z","checksum":"872db70bba9b401500abe3c6ae2f1a61","file_name":"2018_DistributedComputing_Lenzen.pdf","access_level":"open_access","file_size":799337,"content_type":"application/pdf","creator":"dernst"}],"_id":"76","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Near-optimal self-stabilising counting and firing squads","ddc":["000"]},{"doi":"10.1016/j.comgeo.2017.06.014","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000415778300010"]},"project":[{"grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"month":"03","author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"full_name":"Iglesias Ham, Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","last_name":"Iglesias Ham","first_name":"Mabel"}],"volume":68,"date_updated":"2023-09-13T08:59:00Z","date_created":"2018-12-11T11:46:59Z","year":"2018","department":[{"_id":"HeEd"}],"publisher":"Elsevier","publication_status":"published","publist_id":"7289","ec_funded":1,"file_date_updated":"2020-07-14T12:46:38Z","date_published":"2018-03-01T00:00:00Z","citation":{"short":"H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications, vol. 68, Elsevier, 2018, pp. 119–33, doi:10.1016/j.comgeo.2017.06.014.","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications. Elsevier, 2018. https://doi.org/10.1016/j.comgeo.2017.06.014.","ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 2018;68:119-133. doi:10.1016/j.comgeo.2017.06.014","apa":"Edelsbrunner, H., & Iglesias Ham, M. (2018). Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.014","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,” Computational Geometry: Theory and Applications, vol. 68. Elsevier, pp. 119–133, 2018.","ista":"Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133."},"publication":"Computational Geometry: Theory and Applications","page":"119 - 133","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"date_created":"2019-02-12T06:47:52Z","date_updated":"2020-07-14T12:46:38Z","checksum":"1c8d58cd489a66cd3e2064c1141c8c5e","file_id":"5953","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":708357,"file_name":"2018_Edelsbrunner.pdf","access_level":"open_access"}],"oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"530","intvolume":" 68","ddc":["000"],"title":"Multiple covers with balls I: Inclusion–exclusion","status":"public","abstract":[{"text":"Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software.","lang":"eng"}],"type":"journal_article"},{"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000429454000015"],"arxiv":["1712.10127"]},"main_file_link":[{"url":"https://arxiv.org/abs/1712.10127","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.97.043812","month":"04","publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"American Physical Society","acknowledgement":"The work was partially supported by Russian Foundation for Basic Research (Grant No. 15-02-05657a) and by the Basic research program of Higher School of Economics (HSE).","year":"2018","date_created":"2018-12-11T11:45:44Z","date_updated":"2023-09-13T09:00:41Z","volume":97,"author":[{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","first_name":"Elena"},{"full_name":"Makarov, Alexander","first_name":"Alexander","last_name":"Makarov"},{"last_name":"Yudson","first_name":"Vladimir","full_name":"Yudson, Vladimir"}],"article_number":" 043812 ","publist_id":"7572","article_type":"original","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","citation":{"ieee":"E. Redchenko, A. Makarov, and V. Yudson, “Nanoscopy of pairs of atoms by fluorescence in a magnetic field,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018.","apa":"Redchenko, E., Makarov, A., & Yudson, V. (2018). Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043812","ista":"Redchenko E, Makarov A, Yudson V. 2018. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4), 043812.","ama":"Redchenko E, Makarov A, Yudson V. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043812","chicago":"Redchenko, Elena, Alexander Makarov, and Vladimir Yudson. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043812.","short":"E. Redchenko, A. Makarov, V. Yudson, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","mla":"Redchenko, Elena, et al. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, 043812, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043812."},"date_published":"2018-04-09T00:00:00Z","scopus_import":"1","day":"09","article_processing_charge":"No","status":"public","title":"Nanoscopy of pairs of atoms by fluorescence in a magnetic field","intvolume":" 97","_id":"307","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Spontaneous emission spectra of two initially excited closely spaced identical atoms are very sensitive to the strength and the direction of the applied magnetic field. We consider the relevant schemes that ensure the determination of the mutual spatial orientation of the atoms and the distance between them by entirely optical means. A corresponding theoretical description is given accounting for the dipole-dipole interaction between the two atoms in the presence of a magnetic field and for polarizations of the quantum field interacting with magnetic sublevels of the two-atom system. "}],"issue":"4"},{"ddc":["570"],"status":"public","title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","intvolume":" 19","_id":"279","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_size":1414722,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_GenomeBiology_Zapata.pdf","checksum":"f3e4922486bd9bf1483271bdbed394a7","date_updated":"2020-07-14T12:45:47Z","date_created":"2018-12-17T14:05:01Z","relation":"main_file","file_id":"5708"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"publication":"Genome Biology","citation":{"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. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0","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.","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,” Genome Biology, vol. 19. BioMed Central, 2018.","apa":"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. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0","mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology, vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (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.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1434-0."},"date_published":"2018-05-31T00:00:00Z","scopus_import":"1","day":"31","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","publisher":"BioMed Central","department":[{"_id":"FyKo"}],"year":"2018","date_created":"2018-12-11T11:45:35Z","date_updated":"2023-09-13T09:01:32Z","volume":19,"author":[{"full_name":"Zapata, Luis","first_name":"Luis","last_name":"Zapata"},{"full_name":"Pich, Oriol","first_name":"Oriol","last_name":"Pich"},{"full_name":"Serrano, Luis","first_name":"Luis","last_name":"Serrano"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"},{"last_name":"Ossowski","first_name":"Stephan","full_name":"Ossowski, Stephan"},{"last_name":"Schaefer","first_name":"Martin","full_name":"Schaefer, Martin"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9811"},{"status":"public","relation":"research_data","id":"9812"}]},"article_number":"67","file_date_updated":"2020-07-14T12:45:47Z","publist_id":"7620","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Systematic investigation of epistasis in molecular evolution","grant_number":"335980","_id":"26120F5C-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000433986200001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1186/s13059-018-1434-0","month":"05"},{"abstract":[{"text":"Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization by secondary ion mass spectrometry enabled us to query the entire protein makeup of the actively recycling vesicles, which we found to be younger than that of non-recycling vesicles. The young vesicle proteins remained in use for up to ~ 24 h, during which they participated in recycling a few hundred times. They were afterward reluctant to release and were degraded after an additional ~ 24–48 h. We suggest that the recycling pool of synaptic vesicles relies on newly synthesized proteins, while the inactive reserve pool contains older proteins.","lang":"eng"}],"issue":"15","type":"journal_article","file":[{"checksum":"a540feb6c9af6aefc78de531461a8835","date_updated":"2020-07-14T12:44:56Z","date_created":"2018-12-17T14:17:29Z","relation":"main_file","file_id":"5710","file_size":2846470,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_EMBO_Truckenbrodt.pdf"}],"oa_version":"Published Version","title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission","status":"public","ddc":["570"],"intvolume":" 37","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"145","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-08-01T00:00:00Z","article_type":"original","publication":"The EMBO Journal","citation":{"ama":"Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 2018;37(15). doi:10.15252/embj.201798044","apa":"Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen, H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. Wiley. https://doi.org/10.15252/embj.201798044","ieee":"S. M. Truckenbrodt et al., “Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission,” The EMBO Journal, vol. 37, no. 15. Wiley, 2018.","ista":"Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 37(15), e98044.","short":"S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).","mla":"Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal, vol. 37, no. 15, e98044, Wiley, 2018, doi:10.15252/embj.201798044.","chicago":"Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal. Wiley, 2018. https://doi.org/10.15252/embj.201798044."},"file_date_updated":"2020-07-14T12:44:56Z","publist_id":"7778","article_number":"e98044","date_updated":"2023-09-13T09:02:48Z","date_created":"2018-12-11T11:44:52Z","volume":37,"author":[{"full_name":"Truckenbrodt, Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","first_name":"Sven M","last_name":"Truckenbrodt"},{"last_name":"Viplav","first_name":"Abhiyan","full_name":"Viplav, Abhiyan"},{"full_name":"Jähne, Sebsatian","first_name":"Sebsatian","last_name":"Jähne"},{"full_name":"Vogts, Angela","last_name":"Vogts","first_name":"Angela"},{"full_name":"Denker, Annette","first_name":"Annette","last_name":"Denker"},{"last_name":"Wildhagen","first_name":"Hanna","full_name":"Wildhagen, Hanna"},{"first_name":"Eugenio","last_name":"Fornasiero","full_name":"Fornasiero, Eugenio"},{"full_name":"Rizzoli, Silvio","first_name":"Silvio","last_name":"Rizzoli"}],"publication_status":"published","department":[{"_id":"JoDa"}],"publisher":"Wiley","year":"2018","acknowledgement":"We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We thank Erwin Neher for help with the development of the mathematical model of the synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner for providing the illustrations of synaptic vesicle and protein dynamics. We thank Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is a recipient of long-term fellowships from the European Molecular Biology Organization (ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013). The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05, and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the German Federal Ministry of Education and Research (03F0626A).","pmid":1,"month":"08","publication_identifier":{"issn":["0261-4189"]},"language":[{"iso":"eng"}],"doi":"10.15252/embj.201798044","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000440416900005"],"pmid":["29950309"]}},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"ama":"Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 2018;41:850-864. doi:10.1111/pce.13153","ista":"Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 41, 850–864.","apa":"Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018). NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. Wiley-Blackwell. https://doi.org/10.1111/pce.13153","ieee":"L. Fan et al., “NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development,” Plant, Cell and Environment, vol. 41. Wiley-Blackwell, pp. 850–864, 2018.","mla":"Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment, vol. 41, Wiley-Blackwell, 2018, pp. 850–64, doi:10.1111/pce.13153.","short":"L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J. Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864.","chicago":"Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad, Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment. Wiley-Blackwell, 2018. https://doi.org/10.1111/pce.13153."},"publication":"Plant, Cell and Environment","page":"850 - 864","article_type":"original","date_published":"2018-05-01T00:00:00Z","type":"journal_article","abstract":[{"text":"AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes. ","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"462","intvolume":" 41","title":"NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development","status":"public","ddc":["580"],"file":[{"file_name":"2018_PlantCellEnv_Fan.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1937976,"file_id":"7042","relation":"main_file","date_updated":"2020-07-14T12:46:32Z","date_created":"2019-11-18T16:22:22Z","checksum":"6a20f843565f962cb20281cdf5e40914"}],"oa_version":"Submitted Version","month":"05","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"pmid":["29360148"],"isi":["000426870500012"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1111/pce.13153","language":[{"iso":"eng"}],"publist_id":"7359","file_date_updated":"2020-07-14T12:46:32Z","pmid":1,"year":"2018","acknowledgement":"This work was supported by the National Natural Science Foundation of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope assay. ","publisher":"Wiley-Blackwell","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"full_name":"Fan, Ligang","last_name":"Fan","first_name":"Ligang"},{"first_name":"Lei","last_name":"Zhao","full_name":"Zhao, Lei"},{"full_name":"Hu, Wei","last_name":"Hu","first_name":"Wei"},{"last_name":"Li","first_name":"Weina","full_name":"Li, Weina"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"full_name":"Strnad, Miroslav","last_name":"Strnad","first_name":"Miroslav"},{"last_name":"Simon","first_name":"Sibu","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Simon, Sibu"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"full_name":"Shen, Jinbo","last_name":"Shen","first_name":"Jinbo"},{"first_name":"Liwen","last_name":"Jiang","full_name":"Jiang, Liwen"},{"first_name":"Quan","last_name":"Qiu","full_name":"Qiu, Quan"}],"volume":41,"date_created":"2018-12-11T11:46:36Z","date_updated":"2023-09-13T09:03:18Z"},{"has_accepted_license":"1","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2018-04-15T00:00:00Z","citation":{"chicago":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials. Elsevier, 2018. https://doi.org/10.1016/j.jmmm.2017.12.073.","mla":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials, vol. 452, Elsevier, 2018, pp. 427–41, doi:10.1016/j.jmmm.2017.12.073.","short":"S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441.","ista":"Altmeyer S. 2018. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 452, 427–441.","ieee":"S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow,” Journal of Magnetism and Magnetic Materials, vol. 452. Elsevier, pp. 427–441, 2018.","apa":"Altmeyer, S. (2018). Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. Elsevier. https://doi.org/10.1016/j.jmmm.2017.12.073","ama":"Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 2018;452:427-441. doi:10.1016/j.jmmm.2017.12.073"},"publication":"Journal of Magnetism and Magnetic Materials","page":"427 - 441","article_type":"original","abstract":[{"text":"This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined between two concentric independently rotating cylinders. We detected alternating ‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion. ","lang":"eng"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"7838","date_created":"2020-05-14T14:41:17Z","date_updated":"2020-07-14T12:46:37Z","checksum":"431f5cd4a628d7ca21161f82b14ccb4f","file_name":"2018_Magnetism_Altmeyer.pdf","access_level":"open_access","content_type":"application/pdf","file_size":17309535,"creator":"dernst"}],"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"519","intvolume":" 452","title":"Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow","ddc":["530"],"status":"public","month":"04","doi":"10.1016/j.jmmm.2017.12.073","language":[{"iso":"eng"}],"external_id":{"isi":["000425547700061"]},"oa":1,"quality_controlled":"1","isi":1,"publist_id":"7297","file_date_updated":"2020-07-14T12:46:37Z","author":[{"orcid":"0000-0001-5964-0203","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","last_name":"Altmeyer","first_name":"Sebastian","full_name":"Altmeyer, Sebastian"}],"volume":452,"date_updated":"2023-09-13T09:03:44Z","date_created":"2018-12-11T11:46:56Z","year":"2018","acknowledgement":"S.Altmeyer is a Serra Húnter Fellow","department":[{"_id":"BjHo"}],"publisher":"Elsevier","publication_status":"published"},{"month":"12","publication_identifier":{"isbn":["9783030027674"],"issn":["03029743"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1806.06683"}],"external_id":{"isi":["000916310900011"],"arxiv":["1806.06683"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"conference":{"name":"16th Asian Symposium on Programming Languages and Systems, APLAS","end_date":"2018-12-06","start_date":"2018-12-02","location":"Wellington, New Zealand"},"doi":"10.1007/978-3-030-02768-1_11","language":[{"iso":"eng"}],"year":"2018","editor":[{"last_name":"Ryu","first_name":"Sukyoung","full_name":"Ryu, Sukyoung"}],"department":[{"_id":"KrCh"}],"publisher":"Springer","author":[{"last_name":"Huang","first_name":"Mingzhang","full_name":"Huang, Mingzhang"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"date_created":"2018-12-16T22:59:20Z","date_updated":"2023-09-13T09:02:22Z","volume":11275,"scopus_import":"1","day":"01","article_processing_charge":"No","citation":{"ista":"Huang M, Fu H, Chatterjee K. 2018. New approaches for almost-sure termination of probabilistic programs. 16th Asian Symposium on Programming Languages and Systems, APLAS, LNCS, vol. 11275, 181–201.","apa":"Huang, M., Fu, H., & Chatterjee, K. (2018). New approaches for almost-sure termination of probabilistic programs. In S. Ryu (Ed.) (Vol. 11275, pp. 181–201). Presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand: Springer. https://doi.org/10.1007/978-3-030-02768-1_11","ieee":"M. Huang, H. Fu, and K. Chatterjee, “New approaches for almost-sure termination of probabilistic programs,” presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand, 2018, vol. 11275, pp. 181–201.","ama":"Huang M, Fu H, Chatterjee K. New approaches for almost-sure termination of probabilistic programs. In: Ryu S, ed. Vol 11275. Springer; 2018:181-201. doi:10.1007/978-3-030-02768-1_11","chicago":"Huang, Mingzhang, Hongfei Fu, and Krishnendu Chatterjee. “New Approaches for Almost-Sure Termination of Probabilistic Programs.” edited by Sukyoung Ryu, 11275:181–201. Springer, 2018. https://doi.org/10.1007/978-3-030-02768-1_11.","mla":"Huang, Mingzhang, et al. New Approaches for Almost-Sure Termination of Probabilistic Programs. Edited by Sukyoung Ryu, vol. 11275, Springer, 2018, pp. 181–201, doi:10.1007/978-3-030-02768-1_11.","short":"M. Huang, H. Fu, K. Chatterjee, in:, S. Ryu (Ed.), Springer, 2018, pp. 181–201."},"page":"181-201","date_published":"2018-12-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We study the almost-sure termination problem for probabilistic programs. First, we show that supermartingales with lower bounds on conditional absolute difference provide a sound approach for the almost-sure termination problem. Moreover, using this approach we can obtain explicit optimal bounds on tail probabilities of non-termination within a given number of steps. Second, we present a new approach based on Central Limit Theorem for the almost-sure termination problem, and show that this approach can establish almost-sure termination of programs which none of the existing approaches can handle. Finally, we discuss algorithmic approaches for the two above methods that lead to automated analysis techniques for almost-sure termination of probabilistic programs."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5679","title":"New approaches for almost-sure termination of probabilistic programs","status":"public","intvolume":" 11275","oa_version":"Preprint"},{"abstract":[{"text":"This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2021-08-06T12:58:25Z","date_updated":"2023-09-13T09:01:31Z","related_material":{"record":[{"id":"279","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Zapata, Luis","last_name":"Zapata","first_name":"Luis"},{"first_name":"Oriol","last_name":"Pich","full_name":"Pich, Oriol"},{"last_name":"Serrano","first_name":"Luis","full_name":"Serrano, Luis"},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"last_name":"Ossowski","first_name":"Stephan","full_name":"Ossowski, Stephan"},{"first_name":"Martin","last_name":"Schaefer","full_name":"Schaefer, Martin"}],"department":[{"_id":"FyKo"}],"publisher":"Springer Nature","status":"public","title":"Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","year":"2018","_id":"9812","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","day":"31","month":"05","doi":"10.6084/m9.figshare.6401414.v1","date_published":"2018-05-31T00:00:00Z","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.6401414.v1"}],"citation":{"ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401414.v1","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401414.v1","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401414.v1.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","mla":"Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401414.v1."}},{"oa_version":"Preprint","date_updated":"2023-09-13T09:01:31Z","date_created":"2021-08-06T12:53:49Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"279"}]},"author":[{"full_name":"Zapata, Luis","first_name":"Luis","last_name":"Zapata"},{"last_name":"Pich","first_name":"Oriol","full_name":"Pich, Oriol"},{"full_name":"Serrano, Luis","last_name":"Serrano","first_name":"Luis"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor"},{"full_name":"Ossowski, Stephan","first_name":"Stephan","last_name":"Ossowski"},{"full_name":"Schaefer, Martin","last_name":"Schaefer","first_name":"Martin"}],"department":[{"_id":"FyKo"}],"publisher":"Springer Nature","status":"public","title":"Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9811","year":"2018","abstract":[{"text":"This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb)","lang":"eng"}],"type":"research_data_reference","date_published":"2018-05-31T00:00:00Z","doi":"10.6084/m9.figshare.6401390.v1","citation":{"ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401390.v1","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","mla":"Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1."},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401390.v1","open_access":"1"}],"oa":1,"article_processing_charge":"No","month":"05","day":"31"},{"file_date_updated":"2020-07-14T12:45:23Z","publist_id":"8035","date_created":"2018-12-11T11:44:12Z","date_updated":"2023-09-13T09:10:47Z","volume":19,"author":[{"last_name":"Higareda Almaraz","first_name":"Juan","full_name":"Higareda Almaraz, Juan"},{"last_name":"Karbiener","first_name":"Michael","full_name":"Karbiener, Michael"},{"full_name":"Giroud, Maude","last_name":"Giroud","first_name":"Maude"},{"orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","first_name":"Florian","full_name":"Pauler, Florian"},{"full_name":"Gerhalter, Teresa","last_name":"Gerhalter","first_name":"Teresa"},{"full_name":"Herzig, Stephan","first_name":"Stephan","last_name":"Herzig"},{"full_name":"Scheideler, Marcel","first_name":"Marcel","last_name":"Scheideler"}],"related_material":{"record":[{"id":"9807","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9808"}]},"publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"BioMed Central","year":"2018","acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19).","month":"11","publication_identifier":{"issn":["1471-2164"]},"language":[{"iso":"eng"}],"doi":"10.1186/s12864-018-5173-0","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000450976700002"]},"abstract":[{"text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.","lang":"eng"}],"issue":"1","type":"journal_article","file":[{"file_name":"2018_BMCGenomics_Higareda.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":4629784,"file_id":"5712","relation":"main_file","date_created":"2018-12-17T14:52:57Z","date_updated":"2020-07-14T12:45:23Z","checksum":"a56516e734dab589dc7f3e1915973b4d"}],"oa_version":"Published Version","ddc":["570"],"status":"public","title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","intvolume":" 19","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"20","day":"03","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-11-03T00:00:00Z","article_type":"original","publication":"BMC Genomics","citation":{"chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0.","mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics, vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1).","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-018-5173-0","ieee":"J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” BMC Genomics, vol. 19, no. 1. BioMed Central, 2018.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0"}},{"author":[{"full_name":"Dziembowski, Stefan","last_name":"Dziembowski","first_name":"Stefan"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"},{"first_name":"Daniel","last_name":"Wichs","full_name":"Wichs, Daniel"}],"volume":65,"date_updated":"2023-09-13T09:05:17Z","date_created":"2018-12-11T11:44:40Z","year":"2018","publisher":"ACM","department":[{"_id":"KrPi"}],"publication_status":"published","publist_id":"7947","ec_funded":1,"article_number":"20","doi":"10.1145/3178432","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2009/608"}],"external_id":{"isi":["000442938200004"]},"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"},{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"month":"08","oa_version":"Preprint","_id":"107","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 65","status":"public","title":"Non-malleable codes","issue":"4","abstract":[{"lang":"eng","text":"We introduce the notion of “non-malleable codes” which relaxes the notion of error correction and error detection. Informally, a code is non-malleable if the message contained in a modified codeword is either the original message, or a completely unrelated value. In contrast to error correction and error detection, non-malleability can be achieved for very rich classes of modifications. We construct an efficient code that is non-malleable with respect to modifications that affect each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set it to either 0 or 1), but independently of the value of the other bits of the codeword. Using the probabilistic method, we also show a very strong and general statement: there exists a non-malleable code for every “small enough” family F of functions via which codewords can be modified. Although this probabilistic method argument does not directly yield efficient constructions, it gives us efficient non-malleable codes in the random-oracle model for very general classes of tampering functions—e.g., functions where every bit in the tampered codeword can depend arbitrarily on any 99% of the bits in the original codeword. As an application of non-malleable codes, we show that they provide an elegant algorithmic solution to the task of protecting functionalities implemented in hardware (e.g., signature cards) against “tampering attacks.” In such attacks, the secret state of a physical system is tampered, in the hopes that future interaction with the modified system will reveal some secret information. This problem was previously studied in the work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security” (ATP). We show that non-malleable codes can be used to achieve important improvements over the prior work. In particular, we show that any functionality can be made secure against a large class of tampering attacks, simply by encoding the secret state with a non-malleable code while it is stored in memory."}],"type":"journal_article","date_published":"2018-08-01T00:00:00Z","citation":{"chicago":"Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable Codes.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3178432.","short":"S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).","mla":"Dziembowski, Stefan, et al. “Non-Malleable Codes.” Journal of the ACM, vol. 65, no. 4, 20, ACM, 2018, doi:10.1145/3178432.","apa":"Dziembowski, S., Pietrzak, K. Z., & Wichs, D. (2018). Non-malleable codes. Journal of the ACM. ACM. https://doi.org/10.1145/3178432","ieee":"S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” Journal of the ACM, vol. 65, no. 4. ACM, 2018.","ista":"Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of the ACM. 65(4), 20.","ama":"Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. Journal of the ACM. 2018;65(4). doi:10.1145/3178432"},"publication":"Journal of the ACM","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1"},{"scopus_import":"1","article_processing_charge":"No","day":"01","page":"4267-4283","citation":{"ama":"Carvalho L, Patricio P, Ponte S, et al. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 2018;217(12):4267-4283. doi:10.1083/jcb.201804048","ieee":"L. Carvalho et al., “Occluding junctions as novel regulators of tissue mechanics during wound repair,” Journal of Cell Biology, vol. 217, no. 12. Rockefeller University Press, pp. 4267–4283, 2018.","apa":"Carvalho, L., Patricio, P., Ponte, S., Heisenberg, C.-P. J., Almeida, L., Nunes, A. S., … Jacinto, A. (2018). Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201804048","ista":"Carvalho L, Patricio P, Ponte S, Heisenberg C-PJ, Almeida L, Nunes AS, Araújo NAM, Jacinto A. 2018. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 217(12), 4267–4283.","short":"L. Carvalho, P. Patricio, S. Ponte, C.-P.J. Heisenberg, L. Almeida, A.S. Nunes, N.A.M. Araújo, A. Jacinto, Journal of Cell Biology 217 (2018) 4267–4283.","mla":"Carvalho, Lara, et al. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology, vol. 217, no. 12, Rockefeller University Press, 2018, pp. 4267–83, doi:10.1083/jcb.201804048.","chicago":"Carvalho, Lara, Pedro Patricio, Susana Ponte, Carl-Philipp J Heisenberg, Luis Almeida, André S. Nunes, Nuno A.M. Araújo, and Antonio Jacinto. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201804048."},"publication":"Journal of Cell Biology","date_published":"2018-12-01T00:00:00Z","type":"journal_article","issue":"12","abstract":[{"lang":"eng","text":"In epithelial tissues, cells tightly connect to each other through cell–cell junctions, but they also present the remarkable capacity of reorganizing themselves without compromising tissue integrity. Upon injury, simple epithelia efficiently resolve small lesions through the action of actin cytoskeleton contractile structures at the wound edge and cellular rearrangements. However, the underlying mechanisms and how they cooperate are still poorly understood. In this study, we combine live imaging and theoretical modeling to reveal a novel and indispensable role for occluding junctions (OJs) in this process. We demonstrate that OJ loss of function leads to defects in wound-closure dynamics: instead of contracting, wounds dramatically increase their area. OJ mutants exhibit phenotypes in cell shape, cellular rearrangements, and mechanical properties as well as in actin cytoskeleton dynamics at the wound edge. We propose that OJs are essential for wound closure by impacting on epithelial mechanics at the tissue level, which in turn is crucial for correct regulation of the cellular events occurring at the wound edge."}],"intvolume":" 217","title":"Occluding junctions as novel regulators of tissue mechanics during wound repair","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5676","oa_version":"Submitted Version","publication_identifier":{"issn":["00219525"]},"month":"12","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000451960800018"],"pmid":["30228162 "]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30228162","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1083/jcb.201804048","ec_funded":1,"publisher":"Rockefeller University Press","department":[{"_id":"CaHe"}],"publication_status":"published","pmid":1,"year":"2018","volume":217,"date_updated":"2023-09-13T09:11:17Z","date_created":"2018-12-16T22:59:19Z","author":[{"full_name":"Carvalho, Lara","last_name":"Carvalho","first_name":"Lara"},{"last_name":"Patricio","first_name":"Pedro","full_name":"Patricio, Pedro"},{"first_name":"Susana","last_name":"Ponte","full_name":"Ponte, Susana"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"first_name":"Luis","last_name":"Almeida","full_name":"Almeida, Luis"},{"full_name":"Nunes, André S.","last_name":"Nunes","first_name":"André S."},{"full_name":"Araújo, Nuno A.M.","last_name":"Araújo","first_name":"Nuno A.M."},{"full_name":"Jacinto, Antonio","last_name":"Jacinto","first_name":"Antonio"}]},{"date_published":"2018-11-03T00:00:00Z","doi":"10.6084/m9.figshare.7295339.v1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7295339.v1"}],"oa":1,"citation":{"ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295339.v1","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295339.v1.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295339.v1","ieee":"J. Higareda Almaraz et al., “Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","mla":"Higareda Almaraz, Juan, et al. Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295339.v1.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295339.v1."},"article_processing_charge":"No","day":"03","month":"11","oa_version":"Published Version","date_updated":"2023-09-13T09:10:47Z","date_created":"2021-08-06T12:26:53Z","related_material":{"record":[{"id":"20","relation":"used_in_publication","status":"public"}]},"author":[{"last_name":"Higareda Almaraz","first_name":"Juan","full_name":"Higareda Almaraz, Juan"},{"full_name":"Karbiener, Michael","first_name":"Michael","last_name":"Karbiener"},{"full_name":"Giroud, Maude","last_name":"Giroud","first_name":"Maude"},{"last_name":"Pauler","first_name":"Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian"},{"full_name":"Gerhalter, Teresa","last_name":"Gerhalter","first_name":"Teresa"},{"last_name":"Herzig","first_name":"Stephan","full_name":"Herzig, Stephan"},{"full_name":"Scheideler, Marcel","last_name":"Scheideler","first_name":"Marcel"}],"publisher":"Springer Nature","department":[{"_id":"SiHi"}],"title":"Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","status":"public","year":"2018","_id":"9807","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"Table S1. Genes with highest betweenness. Table S2. Local and Master regulators up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb).","lang":"eng"}],"type":"research_data_reference"},{"abstract":[{"text":"Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb).","lang":"eng"}],"type":"research_data_reference","author":[{"first_name":"Juan","last_name":"Higareda Almaraz","full_name":"Higareda Almaraz, Juan"},{"last_name":"Karbiener","first_name":"Michael","full_name":"Karbiener, Michael"},{"first_name":"Maude","last_name":"Giroud","full_name":"Giroud, Maude"},{"full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","first_name":"Florian"},{"first_name":"Teresa","last_name":"Gerhalter","full_name":"Gerhalter, Teresa"},{"first_name":"Stephan","last_name":"Herzig","full_name":"Herzig, Stephan"},{"full_name":"Scheideler, Marcel","last_name":"Scheideler","first_name":"Marcel"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"20"}]},"date_updated":"2023-09-13T09:10:47Z","date_created":"2021-08-06T12:31:57Z","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9808","year":"2018","status":"public","title":"Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","publisher":"Springer Nature","department":[{"_id":"SiHi"}],"month":"11","day":"03","article_processing_charge":"No","date_published":"2018-11-03T00:00:00Z","doi":"10.6084/m9.figshare.7295369.v1","citation":{"ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295369.v1.","ieee":"J. Higareda Almaraz et al., “Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295369.v1","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295369.v1","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295369.v1.","mla":"Higareda Almaraz, Juan, et al. Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295369.v1.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018)."},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7295369.v1","open_access":"1"}],"oa":1},{"date_published":"2018-06-01T00:00:00Z","citation":{"ama":"Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data independent password hashing functions. In: Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ACM; 2018:51-65. doi:10.1145/3196494.3196534","ista":"Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password hashing functions. Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ASIACCS: Asia Conference on Computer and Communications Security , 51–65.","ieee":"J. F. Alwen et al., “On the memory hardness of data independent password hashing functions,” in Proceedings of the 2018 on Asia Conference on Computer and Communication Security, Incheon, Republic of Korea, 2018, pp. 51–65.","apa":"Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak, K. Z., … Rybar, M. (2018). On the memory hardness of data independent password hashing functions. In Proceedings of the 2018 on Asia Conference on Computer and Communication Security (pp. 51–65). Incheon, Republic of Korea: ACM. https://doi.org/10.1145/3196494.3196534","mla":"Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password Hashing Functions.” Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65, doi:10.1145/3196494.3196534.","short":"J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak, L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65.","chicago":"Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar. “On the Memory Hardness of Data Independent Password Hashing Functions.” In Proceedings of the 2018 on Asia Conference on Computer and Communication Security, 51–65. ACM, 2018. https://doi.org/10.1145/3196494.3196534."},"publication":"Proceedings of the 2018 on Asia Conference on Computer and Communication Security","page":"51 - 65","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"193","status":"public","title":"On the memory hardness of data independent password hashing functions","abstract":[{"text":"We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki'16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block'16] for analyzing the hardware costs of an iMHF.","lang":"eng"}],"type":"conference","doi":"10.1145/3196494.3196534","conference":{"location":"Incheon, Republic of Korea","start_date":"2018-06-04","end_date":"2018-06-08","name":"ASIACCS: Asia Conference on Computer and Communications Security "},"language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000516620100005"]},"main_file_link":[{"url":"https://eprint.iacr.org/2016/783","open_access":"1"}],"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"},{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"isi":1,"quality_controlled":"1","month":"06","author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen","full_name":"Alwen, Joel F"},{"full_name":"Gazi, Peter","last_name":"Gazi","first_name":"Peter"},{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","first_name":"Chethan"},{"last_name":"Klein","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen"},{"full_name":"Osang, Georg F","first_name":"Georg F","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8882-5116"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"},{"first_name":"Lenoid","last_name":"Reyzin","full_name":"Reyzin, Lenoid"},{"full_name":"Rolinek, Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rolinek"},{"last_name":"Rybar","first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","full_name":"Rybar, Michal"}],"date_updated":"2023-09-13T09:13:12Z","date_created":"2018-12-11T11:45:07Z","year":"2018","acknowledgement":"Leonid Reyzin was supported in part by IST Austria and by US NSF grants 1012910, 1012798, and 1422965; this research was performed while he was visiting IST Austria.","department":[{"_id":"KrPi"},{"_id":"HeEd"},{"_id":"VlKo"}],"publisher":"ACM","publication_status":"published","publist_id":"7723","ec_funded":1},{"year":"2018","acknowledgement":"Research supported in part by the Defense Advanced Research Projects Agency (DARPA) and the U.S. Army Research Office under the SafeWare program. Opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views, position or policy of the Government. The second author was also supported by the European Research Council, ERC consolidator grant (682815 - TOCNeT).","publication_status":"published","publisher":"Springer","department":[{"_id":"KrPi"}],"author":[{"full_name":"Micciancio, Daniele","first_name":"Daniele","last_name":"Micciancio"},{"full_name":"Walter, Michael","orcid":"0000-0003-3186-2482","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","last_name":"Walter","first_name":"Michael"}],"date_updated":"2023-09-13T09:12:04Z","date_created":"2018-12-11T11:45:42Z","volume":10820,"publist_id":"7581","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/077"}],"oa":1,"external_id":{"isi":["000517097500001"]},"isi":1,"quality_controlled":"1","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"conference":{"name":"Eurocrypt: Advances in Cryptology","location":"Tel Aviv, Israel","start_date":"2018-04-29","end_date":"2018-05-03"},"doi":"10.1007/978-3-319-78381-9_1","language":[{"iso":"eng"}],"month":"03","_id":"300","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"On the bit security of cryptographic primitives","status":"public","intvolume":" 10820","oa_version":"Submitted Version","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We introduce a formal quantitative notion of “bit security” for a general type of cryptographic games (capturing both decision and search problems), aimed at capturing the intuition that a cryptographic primitive with k-bit security is as hard to break as an ideal cryptographic function requiring a brute force attack on a k-bit key space. Our new definition matches the notion of bit security commonly used by cryptographers and cryptanalysts when studying search (e.g., key recovery) problems, where the use of the traditional definition is well established. However, it produces a quantitatively different metric in the case of decision (indistinguishability) problems, where the use of (a straightforward generalization of) the traditional definition is more problematic and leads to a number of paradoxical situations or mismatches between theoretical/provable security and practical/common sense intuition. Key to our new definition is to consider adversaries that may explicitly declare failure of the attack. We support and justify the new definition by proving a number of technical results, including tight reductions between several standard cryptographic problems, a new hybrid theorem that preserves bit security, and an application to the security analysis of indistinguishability primitives making use of (approximate) floating point numbers. This is the first result showing that (standard precision) 53-bit floating point numbers can be used to achieve 100-bit security in the context of cryptographic primitives with general indistinguishability-based security definitions. Previous results of this type applied only to search problems, or special types of decision problems.","lang":"eng"}],"citation":{"mla":"Micciancio, Daniele, and Michael Walter. On the Bit Security of Cryptographic Primitives. Vol. 10820, Springer, 2018, pp. 3–28, doi:10.1007/978-3-319-78381-9_1.","short":"D. Micciancio, M. Walter, in:, Springer, 2018, pp. 3–28.","chicago":"Micciancio, Daniele, and Michael Walter. “On the Bit Security of Cryptographic Primitives,” 10820:3–28. Springer, 2018. https://doi.org/10.1007/978-3-319-78381-9_1.","ama":"Micciancio D, Walter M. On the bit security of cryptographic primitives. In: Vol 10820. Springer; 2018:3-28. doi:10.1007/978-3-319-78381-9_1","ista":"Micciancio D, Walter M. 2018. On the bit security of cryptographic primitives. Eurocrypt: Advances in Cryptology, LNCS, vol. 10820, 3–28.","ieee":"D. Micciancio and M. Walter, “On the bit security of cryptographic primitives,” presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10820, pp. 3–28.","apa":"Micciancio, D., & Walter, M. (2018). On the bit security of cryptographic primitives (Vol. 10820, pp. 3–28). Presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78381-9_1"},"page":"3 - 28","date_published":"2018-03-31T00:00:00Z","scopus_import":"1","day":"31","article_processing_charge":"No"},{"publist_id":"7553","date_updated":"2023-09-13T09:34:38Z","date_created":"2018-12-11T11:45:46Z","volume":32,"author":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"last_name":"Iglesias Ham","first_name":"Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","full_name":"Iglesias Ham, Mabel"}],"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Society for Industrial and Applied Mathematics ","year":"2018","acknowledgement":"This work was partially supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics,” through grant I02979-N35 of the Austrian Science Fund (FWF).","month":"03","publication_identifier":{"issn":["08954801"]},"language":[{"iso":"eng"}],"doi":"10.1137/16M1097201","quality_controlled":"1","isi":1,"project":[{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35"}],"oa":1,"main_file_link":[{"url":"http://pdfs.semanticscholar.org/d2d5/6da00fbc674e6a8b1bb9d857167e54200dc6.pdf","open_access":"1"}],"external_id":{"isi":["000428958900038"]},"abstract":[{"lang":"eng","text":"Motivated by biological questions, we study configurations of equal spheres that neither pack nor cover. Placing their centers on a lattice, we define the soft density of the configuration by penalizing multiple overlaps. Considering the 1-parameter family of diagonally distorted 3-dimensional integer lattices, we show that the soft density is maximized at the FCC lattice."}],"issue":"1","type":"journal_article","oa_version":"Submitted Version","status":"public","title":"On the optimality of the FCC lattice for soft sphere packing","intvolume":" 32","_id":"312","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"29","article_processing_charge":"No","scopus_import":"1","date_published":"2018-03-29T00:00:00Z","article_type":"original","page":"750 - 782","publication":"SIAM J Discrete Math","citation":{"chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1097201.","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math, vol. 32, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 750–82, doi:10.1137/16M1097201.","short":"H. Edelsbrunner, M. Iglesias Ham, SIAM J Discrete Math 32 (2018) 750–782.","ista":"Edelsbrunner H, Iglesias Ham M. 2018. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 32(1), 750–782.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “On the optimality of the FCC lattice for soft sphere packing,” SIAM J Discrete Math, vol. 32, no. 1. Society for Industrial and Applied Mathematics , pp. 750–782, 2018.","apa":"Edelsbrunner, H., & Iglesias Ham, M. (2018). On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1097201","ama":"Edelsbrunner H, Iglesias Ham M. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 2018;32(1):750-782. doi:10.1137/16M1097201"}},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-04-01T00:00:00Z","publication":"Comptes Rendus Mathematique","citation":{"ama":"Akopyan A. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 2018;356(4):412-414. doi:10.1016/j.crma.2018.03.005","apa":"Akopyan, A. (2018). On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. Elsevier. https://doi.org/10.1016/j.crma.2018.03.005","ieee":"A. Akopyan, “On the number of non-hexagons in a planar tiling,” Comptes Rendus Mathematique, vol. 356, no. 4. Elsevier, pp. 412–414, 2018.","ista":"Akopyan A. 2018. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 356(4), 412–414.","short":"A. Akopyan, Comptes Rendus Mathematique 356 (2018) 412–414.","mla":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique, vol. 356, no. 4, Elsevier, 2018, pp. 412–14, doi:10.1016/j.crma.2018.03.005.","chicago":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique. Elsevier, 2018. https://doi.org/10.1016/j.crma.2018.03.005."},"article_type":"original","page":"412-414","abstract":[{"text":"We give a simple proof of T. Stehling's result [4], whereby in any normal tiling of the plane with convex polygons with number of sides not less than six, all tiles except a finite number are hexagons.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"Preprint","_id":"409","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"On the number of non-hexagons in a planar tiling","intvolume":" 356","month":"04","publication_identifier":{"issn":["1631073X"]},"doi":"10.1016/j.crma.2018.03.005","language":[{"iso":"eng"}],"external_id":{"arxiv":["1805.01652"],"isi":["000430402700009"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.01652"}],"isi":1,"quality_controlled":"1","publist_id":"7420","author":[{"first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"}],"date_updated":"2023-09-13T09:34:12Z","date_created":"2018-12-11T11:46:19Z","volume":356,"year":"2018","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Elsevier"},{"year":"2018","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","author":[{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","first_name":"Christian"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"related_material":{"link":[{"relation":"erratum","url":"http://doi.org/10.1038/s41562-018-0342-3"}]},"date_created":"2018-12-11T11:46:22Z","date_updated":"2023-09-13T09:38:54Z","volume":2,"file_date_updated":"2020-07-14T12:46:25Z","ec_funded":1,"publist_id":"7404","external_id":{"isi":["000446612000016"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41562-018-0320-9","language":[{"iso":"eng"}],"month":"03","_id":"419","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["000"],"title":"Partners and rivals in direct reciprocity","intvolume":" 2","oa_version":"Submitted Version","file":[{"file_id":"7052","relation":"main_file","date_created":"2019-11-19T08:19:51Z","date_updated":"2020-07-14T12:46:25Z","checksum":"571b8cc0ba14e8d5d8b18e439a9835eb","file_name":"2018_NatureHumanBeh_Hilbe.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":598033}],"type":"journal_article","abstract":[{"lang":"eng","text":"Reciprocity is a major factor in human social life and accounts for a large part of cooperation in our communities. Direct reciprocity arises when repeated interactions occur between the same individuals. The framework of iterated games formalizes this phenomenon. Despite being introduced more than five decades ago, the concept keeps offering beautiful surprises. Recent theoretical research driven by new mathematical tools has proposed a remarkable dichotomy among the crucial strategies: successful individuals either act as partners or as rivals. Rivals strive for unilateral advantages by applying selfish or extortionate strategies. Partners aim to share the payoff for mutual cooperation, but are ready to fight back when being exploited. Which of these behaviours evolves depends on the environment. Whereas small population sizes and a limited number of rounds favour rivalry, partner strategies are selected when populations are large and relationships stable. Only partners allow for evolution of cooperation, while the rivals’ attempt to put themselves first leads to defection. Hilbe et al. synthesize recent theoretical work on zero-determinant and ‘rival’ versus ‘partner’ strategies in social dilemmas. They describe the environments under which these contrasting selfish or cooperative strategies emerge in evolution."}],"publication":"Nature Human Behaviour","citation":{"chicago":"Hilbe, Christian, Krishnendu Chatterjee, and Martin Nowak. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0320-9.","mla":"Hilbe, Christian, et al. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 469–477, doi:10.1038/s41562-018-0320-9.","short":"C. Hilbe, K. Chatterjee, M. Nowak, Nature Human Behaviour 2 (2018) 469–477.","ista":"Hilbe C, Chatterjee K, Nowak M. 2018. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2, 469–477.","ieee":"C. Hilbe, K. Chatterjee, and M. Nowak, “Partners and rivals in direct reciprocity,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 469–477, 2018.","apa":"Hilbe, C., Chatterjee, K., & Nowak, M. (2018). Partners and rivals in direct reciprocity. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0320-9","ama":"Hilbe C, Chatterjee K, Nowak M. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2018;2:469–477. doi:10.1038/s41562-018-0320-9"},"article_type":"review","page":"469–477","date_published":"2018-03-19T00:00:00Z","scopus_import":"1","day":"19","article_processing_charge":"No","has_accepted_license":"1"},{"page":"215 - 232","citation":{"chicago":"Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_13.","mla":"Bakhirkin, Alexey, et al. Online Timed Pattern Matching Using Automata. Vol. 11022, Springer, 2018, pp. 215–32, doi:10.1007/978-3-030-00151-3_13.","short":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer, 2018, pp. 215–232.","ista":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. 2018. Online timed pattern matching using automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 215–232.","apa":"Bakhirkin, A., Ferrere, T., Nickovic, D., Maler, O., & Asarin, E. (2018). Online timed pattern matching using automata (Vol. 11022, pp. 215–232). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_13","ieee":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, and E. Asarin, “Online timed pattern matching using automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China, 2018, vol. 11022, pp. 215–232.","ama":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. Online timed pattern matching using automata. In: Vol 11022. Springer; 2018:215-232. doi:10.1007/978-3-030-00151-3_13"},"date_published":"2018-08-26T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"26","intvolume":" 11022","ddc":["000"],"title":"Online timed pattern matching using automata","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"78","file":[{"file_size":374851,"content_type":"application/pdf","creator":"dernst","file_name":"2018_LNCS_Bakhirkin.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-14T11:34:34Z","checksum":"436b7574934324cfa7d1d3986fddc65b","relation":"main_file","file_id":"7831"}],"oa_version":"Submitted Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by ϕ and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads ω, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated."}],"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000884993200013"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-00151-3_13","conference":{"end_date":"2018-09-06","location":"Bejing, China","start_date":"2018-09-04","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"publication_identifier":{"isbn":["978-3-030-00150-6"]},"month":"08","department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2018","volume":11022,"date_updated":"2023-09-13T09:35:46Z","date_created":"2018-12-11T11:44:31Z","author":[{"full_name":"Bakhirkin, Alexey","last_name":"Bakhirkin","first_name":"Alexey"},{"last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas"},{"last_name":"Nickovic","first_name":"Dejan","full_name":"Nickovic, Dejan"},{"full_name":"Maler, Oded","last_name":"Maler","first_name":"Oded"},{"full_name":"Asarin, Eugene","first_name":"Eugene","last_name":"Asarin"}],"publist_id":"7976","file_date_updated":"2020-07-14T12:48:03Z"},{"department":[{"_id":"GeKa"}],"publisher":"Nature Publishing Group","publication_status":"published","year":"2018","volume":8,"date_updated":"2023-09-13T09:38:00Z","date_created":"2018-12-11T11:45:47Z","author":[{"last_name":"Brauns","first_name":"Matthias","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","full_name":"Brauns, Matthias"},{"last_name":"Amitonov","first_name":"Sergey","full_name":"Amitonov, Sergey"},{"first_name":"Paul","last_name":"Spruijtenburg","full_name":"Spruijtenburg, Paul"},{"full_name":"Zwanenburg, Floris","first_name":"Floris","last_name":"Zwanenburg"}],"article_number":"5690","publist_id":"7548","file_date_updated":"2020-07-14T12:46:02Z","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000429404300013"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41598-018-24004-y","month":"04","intvolume":" 8","status":"public","title":"Palladium gates for reproducible quantum dots in silicon","ddc":["539"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"317","file":[{"checksum":"20af238ca4ba6491b77270be8d826bf5","date_updated":"2020-07-14T12:46:02Z","date_created":"2018-12-12T10:17:04Z","file_id":"5256","relation":"main_file","creator":"system","file_size":1850530,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-1016-v1+1_2018_Brauns_Palladium_gates.pdf"}],"oa_version":"Published Version","pubrep_id":"1016","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We replace the established aluminium gates for the formation of quantum dots in silicon with gates made from palladium. We study the morphology of both aluminium and palladium gates with transmission electron microscopy. The native aluminium oxide is found to be formed all around the aluminium gates, which could lead to the formation of unintentional dots. Therefore, we report on a novel fabrication route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined quantum dots, which are reproducibly fabricated. Furthermore, palladium enables us to further shrink the gate design, allowing us to perform electron transport measurements in the few-electron regime in devices comprising only two gate layers, a major technological advancement. It remains to be seen, whether the introduction of palladium gates can improve the excellent results on electron and nuclear spin qubits defined with an aluminium gate stack."}],"citation":{"chicago":"Brauns, Matthias, Sergey Amitonov, Paul Spruijtenburg, and Floris Zwanenburg. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-24004-y.","short":"M. Brauns, S. Amitonov, P. Spruijtenburg, F. Zwanenburg, Scientific Reports 8 (2018).","mla":"Brauns, Matthias, et al. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports, vol. 8, no. 1, 5690, Nature Publishing Group, 2018, doi:10.1038/s41598-018-24004-y.","apa":"Brauns, M., Amitonov, S., Spruijtenburg, P., & Zwanenburg, F. (2018). Palladium gates for reproducible quantum dots in silicon. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-24004-y","ieee":"M. Brauns, S. Amitonov, P. Spruijtenburg, and F. Zwanenburg, “Palladium gates for reproducible quantum dots in silicon,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","ista":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. 2018. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 8(1), 5690.","ama":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-24004-y"},"publication":"Scientific Reports","date_published":"2018-04-09T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"09"},{"external_id":{"pmid":["29939785"],"isi":["000449359700035"]},"oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.1096/fj.201800443"}],"isi":1,"quality_controlled":"1","project":[{"name":"Individual function and social role of oxytocin-like neuropeptides in ants","_id":"25E3D34E-B435-11E9-9278-68D0E5697425"}],"doi":"10.1096/fj.201800443","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["08926638"]},"year":"2018","pmid":1,"publication_status":"published","publisher":"FASEB","department":[{"_id":"SyCr"}],"author":[{"full_name":"Liutkeviciute, Zita","last_name":"Liutkeviciute","first_name":"Zita"},{"full_name":"Gil Mansilla, Esther","first_name":"Esther","last_name":"Gil Mansilla"},{"last_name":"Eder","first_name":"Thomas","full_name":"Eder, Thomas"},{"last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E"},{"first_name":"Maria","last_name":"Giulia Di Giglio","full_name":"Giulia Di Giglio, Maria"},{"full_name":"Muratspahić, Edin","first_name":"Edin","last_name":"Muratspahić"},{"first_name":"Florian","last_name":"Grebien","full_name":"Grebien, Florian"},{"full_name":"Rattei, Thomas","first_name":"Thomas","last_name":"Rattei"},{"full_name":"Muttenthaler, Markus","last_name":"Muttenthaler","first_name":"Markus"},{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia"},{"full_name":"Gruber, Christian","last_name":"Gruber","first_name":"Christian"}],"date_updated":"2023-09-13T09:37:32Z","date_created":"2018-12-11T11:45:08Z","volume":32,"publist_id":"7721","publication":"The FASEB Journal","citation":{"ama":"Liutkeviciute Z, Gil Mansilla E, Eder T, et al. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 2018;32(12):6808-6821. doi:10.1096/fj.201800443","apa":"Liutkeviciute, Z., Gil Mansilla, E., Eder, T., Casillas Perez, B. E., Giulia Di Giglio, M., Muratspahić, E., … Gruber, C. (2018). Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. FASEB. https://doi.org/10.1096/fj.201800443","ieee":"Z. Liutkeviciute et al., “Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity,” The FASEB Journal, vol. 32, no. 12. FASEB, pp. 6808–6821, 2018.","ista":"Liutkeviciute Z, Gil Mansilla E, Eder T, Casillas Perez BE, Giulia Di Giglio M, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber C. 2018. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 32(12), 6808–6821.","short":"Z. Liutkeviciute, E. Gil Mansilla, T. Eder, B.E. Casillas Perez, M. Giulia Di Giglio, E. Muratspahić, F. Grebien, T. Rattei, M. Muttenthaler, S. Cremer, C. Gruber, The FASEB Journal 32 (2018) 6808–6821.","mla":"Liutkeviciute, Zita, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal, vol. 32, no. 12, FASEB, 2018, pp. 6808–21, doi:10.1096/fj.201800443.","chicago":"Liutkeviciute, Zita, Esther Gil Mansilla, Thomas Eder, Barbara E Casillas Perez, Maria Giulia Di Giglio, Edin Muratspahić, Florian Grebien, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal. FASEB, 2018. https://doi.org/10.1096/fj.201800443."},"article_type":"original","page":"6808-6821","date_published":"2018-11-29T00:00:00Z","scopus_import":"1","day":"29","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"194","title":"Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity","status":"public","intvolume":" 32","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Ants are emerging model systems to study cellular signaling because distinct castes possess different physiologic phenotypes within the same colony. Here we studied the functionality of inotocin signaling, an insect ortholog of mammalian oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined that specialization within the colony, seasonal factors, and physiologic conditions down-regulated the expression of the OT-like signaling system. Given this natural variation, we interrogated its function using RNAi knockdowns. Next-generation RNA sequencing of OT-like precursor knock-down ants highlighted its role in the regulation of genes involved in metabolism. Knock-down ants exhibited higher walking activity and increased self-grooming in the brood chamber. We propose that OT-like signaling in ants is important for regulating metabolic processes and locomotion."}],"issue":"12"},{"scopus_import":"1","day":"16","has_accepted_license":"1","article_processing_charge":"No","publication":"Nature Chemical Biology","citation":{"ista":"Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 14(8), 764–767.","apa":"Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N., … Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0090-8","ieee":"T. Fehrentz et al., “Optical control of L-type Ca2+ channels using a diltiazem photoswitch,” Nature Chemical Biology, vol. 14, no. 8. Nature Publishing Group, pp. 764–767, 2018.","ama":"Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 2018;14(8):764-767. doi:10.1038/s41589-018-0090-8","chicago":"Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0090-8.","mla":"Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 764–67, doi:10.1038/s41589-018-0090-8.","short":"T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D. Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N. Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767."},"article_type":"original","page":"764 - 767","date_published":"2018-07-16T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction coupling and release of hormones from secretory cells. They are targets of antihypertensive and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell function and cardiac activity under optical control."}],"issue":"8","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"159","status":"public","ddc":["570"],"title":"Optical control of L-type Ca2+ channels using a diltiazem photoswitch","intvolume":" 14","file":[{"creator":"dernst","content_type":"application/pdf","file_size":6321000,"access_level":"open_access","file_name":"2018_NatureChemicalBiology_Fehrentz.pdf","checksum":"d42935094ec845f54a0688bf12986d62","date_created":"2020-05-14T12:14:09Z","date_updated":"2020-07-14T12:45:03Z","file_id":"7832","relation":"main_file"}],"oa_version":"Submitted Version","month":"07","external_id":{"isi":["000438970200010"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1038/s41589-018-0090-8","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:03Z","publist_id":"7762","year":"2018","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"JoDa"}],"author":[{"full_name":"Fehrentz, Timm","last_name":"Fehrentz","first_name":"Timm"},{"last_name":"Huber","first_name":"Florian","full_name":"Huber, Florian"},{"full_name":"Hartrampf, Nina","first_name":"Nina","last_name":"Hartrampf"},{"last_name":"Bruegmann","first_name":"Tobias","full_name":"Bruegmann, Tobias"},{"full_name":"Frank, James","first_name":"James","last_name":"Frank"},{"full_name":"Fine, Nicholas","first_name":"Nicholas","last_name":"Fine"},{"last_name":"Malan","first_name":"Daniela","full_name":"Malan, Daniela"},{"last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"},{"first_name":"Denis","last_name":"Tikhonov","full_name":"Tikhonov, Denis"},{"last_name":"Sumser","first_name":"Maritn","full_name":"Sumser, Maritn"},{"full_name":"Sasse, Philipp","first_name":"Philipp","last_name":"Sasse"},{"full_name":"Hodson, David","first_name":"David","last_name":"Hodson"},{"full_name":"Zhorov, Boris","first_name":"Boris","last_name":"Zhorov"},{"full_name":"Klocker, Nikolaj","first_name":"Nikolaj","last_name":"Klocker"},{"full_name":"Trauner, Dirk","first_name":"Dirk","last_name":"Trauner"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41589-021-00744-3","relation":"erratum"}]},"date_updated":"2023-09-13T09:36:35Z","date_created":"2018-12-11T11:44:56Z","volume":14},{"abstract":[{"text":"Markov Decision Processes (MDPs) are a popular class of models suitable for solving control decision problems in probabilistic reactive systems. We consider parametric MDPs (pMDPs) that include parameters in some of the transition probabilities to account for stochastic uncertainties of the environment such as noise or input disturbances. We study pMDPs with reachability objectives where the parameter values are unknown and impossible to measure directly during execution, but there is a probability distribution known over the parameter values. We study for the first time computing parameter-independent strategies that are expectation optimal, i.e., optimize the expected reachability probability under the probability distribution over the parameters. We present an encoding of our problem to partially observable MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating (repeated) learner model; a series of benchmarks of varying configurations of a robot moving on a grid; and a consensus protocol.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","intvolume":" 11024","title":"Parameter-independent strategies for pMDPs via POMDPs","status":"public","_id":"79","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2018-08-15T00:00:00Z","page":"53-70","citation":{"chicago":"Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen, and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70. Springer, 2018. https://doi.org/10.1007/978-3-319-99154-2_4.","short":"S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer, 2018, pp. 53–70.","mla":"Arming, Sebastian, et al. Parameter-Independent Strategies for PMDPs via POMDPs. Vol. 11024, Springer, 2018, pp. 53–70, doi:10.1007/978-3-319-99154-2_4.","ieee":"S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70.","apa":"Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., & Sokolova, A. (2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp. 53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-319-99154-2_4","ista":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11024, 53–70.","ama":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:10.1007/978-3-319-99154-2_4"},"publist_id":"7975","volume":11024,"date_updated":"2023-09-13T09:38:28Z","date_created":"2018-12-11T11:44:31Z","author":[{"full_name":"Arming, Sebastian","last_name":"Arming","first_name":"Sebastian"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Joost P","last_name":"Katoen","id":"4524F760-F248-11E8-B48F-1D18A9856A87","full_name":"Katoen, Joost P"},{"first_name":"Ana","last_name":"Sokolova","full_name":"Sokolova, Ana"}],"publisher":"Springer","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","year":"2018","month":"08","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-99154-2_4","conference":{"name":"QEST: Quantitative Evaluation of Systems","end_date":"2018-09-07","location":"Beijing, China","start_date":"2018-09-04"},"isi":1,"quality_controlled":"1","external_id":{"arxiv":["1806.05126"],"isi":["000548912200004"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.05126"}]},{"date_published":"2018-05-01T00:00:00Z","publication":"Annales Henri Poincare","citation":{"ista":"Deuchert A, Geisinge A, Hainzl C, Loss M. 2018. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 19(5), 1507–1527.","ieee":"A. Deuchert, A. Geisinge, C. Hainzl, and M. Loss, “Persistence of translational symmetry in the BCS model with radial pair interaction,” Annales Henri Poincare, vol. 19, no. 5. Springer, pp. 1507–1527, 2018.","apa":"Deuchert, A., Geisinge, A., Hainzl, C., & Loss, M. (2018). Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-0665-7","ama":"Deuchert A, Geisinge A, Hainzl C, Loss M. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 2018;19(5):1507-1527. doi:10.1007/s00023-018-0665-7","chicago":"Deuchert, Andreas, Alissa Geisinge, Christian Hainzl, and Michael Loss. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare. Springer, 2018. https://doi.org/10.1007/s00023-018-0665-7.","mla":"Deuchert, Andreas, et al. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare, vol. 19, no. 5, Springer, 2018, pp. 1507–27, doi:10.1007/s00023-018-0665-7.","short":"A. Deuchert, A. Geisinge, C. Hainzl, M. Loss, Annales Henri Poincare 19 (2018) 1507–1527."},"page":"1507 - 1527","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","pubrep_id":"1011","file":[{"date_updated":"2020-07-14T12:46:22Z","date_created":"2018-12-12T10:12:47Z","checksum":"04d2c9bd7cbf3ca1d7acaaf4e7dca3e5","file_id":"4966","relation":"main_file","creator":"system","file_size":582680,"content_type":"application/pdf","file_name":"IST-2018-1011-v1+1_2018_Deuchert_Persistence.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"400","ddc":["510"],"title":"Persistence of translational symmetry in the BCS model with radial pair interaction","status":"public","intvolume":" 19","abstract":[{"text":"We consider the two-dimensional BCS functional with a radial pair interaction. We show that the translational symmetry is not broken in a certain temperature interval below the critical temperature. In the case of vanishing angular momentum, our results carry over to the three-dimensional case.","lang":"eng"}],"issue":"5","type":"journal_article","doi":"10.1007/s00023-018-0665-7","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000429799900008"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"month":"05","author":[{"orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","last_name":"Deuchert","first_name":"Andreas","full_name":"Deuchert, Andreas"},{"full_name":"Geisinge, Alissa","last_name":"Geisinge","first_name":"Alissa"},{"full_name":"Hainzl, Christian","first_name":"Christian","last_name":"Hainzl"},{"full_name":"Loss, Michael","last_name":"Loss","first_name":"Michael"}],"date_created":"2018-12-11T11:46:15Z","date_updated":"2023-09-15T12:04:15Z","volume":19,"year":"2018","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer","file_date_updated":"2020-07-14T12:46:22Z","publist_id":"7429","ec_funded":1},{"month":"03","quality_controlled":"1","isi":1,"project":[{"_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000426896800032"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0193049","file_date_updated":"2020-07-14T12:46:22Z","publist_id":"7423","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","acknowledgement":"This work was supported by the Human Frontier Science Program RGP0065/2012 (GT, ES).","year":"2018","date_updated":"2023-09-15T12:06:19Z","date_created":"2018-12-11T11:46:18Z","volume":13,"author":[{"full_name":"Bod’Ová, Katarína","last_name":"Bod’Ová","first_name":"Katarína"},{"last_name":"Mitchell","first_name":"Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","full_name":"Mitchell, Gabriel"},{"full_name":"Harpaz, Roy","last_name":"Harpaz","first_name":"Roy"},{"full_name":"Schneidman, Elad","first_name":"Elad","last_name":"Schneidman"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9831"}]},"scopus_import":"1","day":"07","article_processing_charge":"Yes","has_accepted_license":"1","publication":"PLoS One","citation":{"ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic models of individual and collective animal behavior. PLoS One. 13(3).","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3. Public Library of Science, 2018.","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Probabilistic models of individual and collective animal behavior. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049","chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.","mla":"Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018)."},"date_published":"2018-03-07T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Recent developments in automated tracking allow uninterrupted, high-resolution recording of animal trajectories, sometimes coupled with the identification of stereotyped changes of body pose or other behaviors of interest. Analysis and interpretation of such data represents a challenge: the timing of animal behaviors may be stochastic and modulated by kinematic variables, by the interaction with the environment or with the conspecifics within the animal group, and dependent on internal cognitive or behavioral state of the individual. Existing models for collective motion typically fail to incorporate the discrete, stochastic, and internal-state-dependent aspects of behavior, while models focusing on individual animal behavior typically ignore the spatial aspects of the problem. Here we propose a probabilistic modeling framework to address this gap. Each animal can switch stochastically between different behavioral states, with each state resulting in a possibly different law of motion through space. Switching rates for behavioral transitions can depend in a very general way, which we seek to identify from data, on the effects of the environment as well as the interaction between the animals. We represent the switching dynamics as a Generalized Linear Model and show that: (i) forward simulation of multiple interacting animals is possible using a variant of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly, the maximum likelihood inference of switching rate functions is tractably solvable by gradient descent; (iii) model selection can be used to identify factors that modulate behavioral state switching and to appropriately adjust model complexity to data. To illustrate our framework, we apply it to two synthetic models of animal motion and to real zebrafish tracking data. "}],"issue":"3","ddc":["530","571"],"title":"Probabilistic models of individual and collective animal behavior","status":"public","intvolume":" 13","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"406","file":[{"creator":"system","content_type":"application/pdf","file_size":6887358,"access_level":"open_access","file_name":"IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf","checksum":"684229493db75b43e98a46cd922da497","date_created":"2018-12-12T10:15:43Z","date_updated":"2020-07-14T12:46:22Z","file_id":"5165","relation":"main_file"}],"oa_version":"Submitted Version","pubrep_id":"995"},{"publist_id":"7999","publication_status":"published","publisher":"Cell Press","department":[{"_id":"SyCr"}],"year":"2018","date_updated":"2023-09-15T12:06:46Z","date_created":"2018-12-11T11:44:23Z","volume":28,"author":[{"full_name":"Pull, Christopher","last_name":"Pull","first_name":"Christopher","orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sina","last_name":"Metzler","id":"48204546-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9547-2494","full_name":"Metzler, Sina"},{"first_name":"Elisabeth","last_name":"Naderlinger","id":"31757262-F248-11E8-B48F-1D18A9856A87","full_name":"Naderlinger, Elisabeth"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"}],"month":"10","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2018.08.063","open_access":"1"}],"external_id":{"isi":["000446693400008"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2018.08.063","type":"journal_article","abstract":[{"text":"Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to self-medicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation.","lang":"eng"}],"issue":"19","title":"Protection against the lethal side effects of social immunity in ants","status":"public","intvolume":" 28","_id":"55","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","scopus_import":"1","day":"08","article_processing_charge":"No","article_type":"original","page":"R1139 - R1140","publication":"Current Biology","citation":{"short":"C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140.","mla":"Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology, vol. 28, no. 19, Cell Press, 2018, pp. R1139–40, doi:10.1016/j.cub.2018.08.063.","chicago":"Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology. Cell Press, 2018. https://doi.org/10.1016/j.cub.2018.08.063.","ama":"Pull C, Metzler S, Naderlinger E, Cremer S. Protection against the lethal side effects of social immunity in ants. Current Biology. 2018;28(19):R1139-R1140. doi:10.1016/j.cub.2018.08.063","apa":"Pull, C., Metzler, S., Naderlinger, E., & Cremer, S. (2018). Protection against the lethal side effects of social immunity in ants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2018.08.063","ieee":"C. Pull, S. Metzler, E. Naderlinger, and S. Cremer, “Protection against the lethal side effects of social immunity in ants,” Current Biology, vol. 28, no. 19. Cell Press, pp. R1139–R1140, 2018.","ista":"Pull C, Metzler S, Naderlinger E, Cremer S. 2018. Protection against the lethal side effects of social immunity in ants. Current Biology. 28(19), R1139–R1140."},"date_published":"2018-10-08T00:00:00Z"},{"oa_version":"Published Version","_id":"181","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 50","status":"public","title":"Power law decay for systems of randomly coupled differential equations","issue":"3","abstract":[{"text":"We consider large random matrices X with centered, independent entries but possibly di erent variances. We compute the normalized trace of f(X)g(X∗) for f, g functions analytic on the spectrum of X. We use these results to compute the long time asymptotics for systems of coupled di erential equations with random coe cients. We show that when the coupling is critical, the norm squared of the solution decays like t−1/2.","lang":"eng"}],"type":"journal_article","date_published":"2018-01-01T00:00:00Z","citation":{"chicago":"Erdös, László, Torben H Krüger, and David T Renfrew. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/17M1143125.","short":"L. Erdös, T.H. Krüger, D.T. Renfrew, SIAM Journal on Mathematical Analysis 50 (2018) 3271–3290.","mla":"Erdös, László, et al. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 3271–90, doi:10.1137/17M1143125.","apa":"Erdös, L., Krüger, T. H., & Renfrew, D. T. (2018). Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/17M1143125","ieee":"L. Erdös, T. H. Krüger, and D. T. Renfrew, “Power law decay for systems of randomly coupled differential equations,” SIAM Journal on Mathematical Analysis, vol. 50, no. 3. Society for Industrial and Applied Mathematics , pp. 3271–3290, 2018.","ista":"Erdös L, Krüger TH, Renfrew DT. 2018. Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. 50(3), 3271–3290.","ama":"Erdös L, Krüger TH, Renfrew DT. Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. 2018;50(3):3271-3290. doi:10.1137/17M1143125"},"publication":"SIAM Journal on Mathematical Analysis","page":"3271 - 3290","article_processing_charge":"No","day":"01","scopus_import":"1","author":[{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"Erdös, László"},{"full_name":"Krüger, Torben H","last_name":"Krüger","first_name":"Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Renfrew, David T","first_name":"David T","last_name":"Renfrew","id":"4845BF6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3493-121X"}],"volume":50,"date_updated":"2023-09-15T12:05:52Z","date_created":"2018-12-11T11:45:03Z","year":"2018","acknowledgement":"The work of the second author was also partially supported by the Hausdorff Center of Mathematics.","publisher":"Society for Industrial and Applied Mathematics ","department":[{"_id":"LaEr"}],"publication_status":"published","publist_id":"7740","ec_funded":1,"doi":"10.1137/17M1143125","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01546"}],"external_id":{"isi":["000437018500032"],"arxiv":["1708.01546"]},"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"},{"call_identifier":"FWF","name":"Structured Non-Hermitian Random Matrices","grant_number":"M02080","_id":"258F40A4-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","month":"01"},{"scopus_import":"1","article_processing_charge":"No","day":"15","page":"92 - 128","citation":{"ista":"Ganev IV. 2018. Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. 506, 92–128.","apa":"Ganev, I. V. (2018). Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. World Scientific Publishing. https://doi.org/10.1016/j.jalgebra.2018.03.015","ieee":"I. V. Ganev, “Quantizations of multiplicative hypertoric varieties at a root of unity,” Journal of Algebra, vol. 506. World Scientific Publishing, pp. 92–128, 2018.","ama":"Ganev IV. Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. 2018;506:92-128. doi:10.1016/j.jalgebra.2018.03.015","chicago":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” Journal of Algebra. World Scientific Publishing, 2018. https://doi.org/10.1016/j.jalgebra.2018.03.015.","mla":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” Journal of Algebra, vol. 506, World Scientific Publishing, 2018, pp. 92–128, doi:10.1016/j.jalgebra.2018.03.015.","short":"I.V. Ganev, Journal of Algebra 506 (2018) 92–128."},"publication":"Journal of Algebra","date_published":"2018-07-15T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We construct quantizations of multiplicative hypertoric varieties using an algebra of q-difference operators on affine space, where q is a root of unity in C. The quantization defines a matrix bundle (i.e. Azumaya algebra) over the multiplicative hypertoric variety and admits an explicit finite étale splitting. The global sections of this Azumaya algebra is a hypertoric quantum group, and we prove a localization theorem. We introduce a general framework of Frobenius quantum moment maps and their Hamiltonian reductions; our results shed light on an instance of this framework."}],"intvolume":" 506","status":"public","title":"Quantizations of multiplicative hypertoric varieties at a root of unity","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"322","oa_version":"Preprint","month":"07","project":[{"call_identifier":"FP7","name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1412.7211","open_access":"1"}],"external_id":{"isi":["000433270600005"],"arxiv":["1412.7211"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.jalgebra.2018.03.015","publist_id":"7543","ec_funded":1,"department":[{"_id":"TaHa"}],"publisher":"World Scientific Publishing","publication_status":"published","year":"2018","acknowledgement":"National Science Foundation: Graduate Research Fellowship and grant No.0932078000; ERC Advanced Grant “Arithmetic and Physics of Higgs moduli spaces” No. 320593 \r\nThe author is grateful to David Jordan for suggesting this project and providing guidance throughout, particularly for the formulation of Frobenius quantum moment maps and key ideas in the proofs of Theorems 3.12 and 4.8. Special thanks to David Ben-Zvi (the author's PhD advisor) for numerous discussions and constant encouragement, and for suggesting the term ‘hypertoric quantum group.’ Many results appearing in the current paper were proven independently by Nicholas Cooney; the author is grateful to Nicholas for sharing his insight on various topics, including Proposition 3.8. The author also thanks Nicholas Proudfoot for relating the definition of multiplicative hypertoric varieties, as well as the content of Remark 2.14. The author also benefited immensely from the close reading and detailed comments of an anonymous referee, and from conversations with Justin Hilburn, Kobi Kremnitzer, Michael McBreen, Tom Nevins, Travis Schedler, and Ben Webster. \r\n\r\n\r\n\r\n","volume":506,"date_created":"2018-12-11T11:45:49Z","date_updated":"2023-09-15T12:08:38Z","author":[{"full_name":"Ganev, Iordan V","id":"447491B8-F248-11E8-B48F-1D18A9856A87","last_name":"Ganev","first_name":"Iordan V"}]},{"month":"07","language":[{"iso":"eng"}],"conference":{"location":"Oxford, United Kingdom","start_date":"2018-07-14","end_date":"2018-07-17","name":"CAV: Computer Aided Verification"},"doi":"10.1007/978-3-319-96145-3_24","isi":1,"quality_controlled":"1","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000491481600024"]},"file_date_updated":"2020-07-14T12:44:53Z","publist_id":"7781","date_created":"2018-12-11T11:44:51Z","date_updated":"2023-09-15T12:12:08Z","volume":10981,"author":[{"last_name":"Kong","first_name":"Hui","orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","full_name":"Kong, Hui"},{"full_name":"Bartocci, Ezio","first_name":"Ezio","last_name":"Bartocci"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","acknowledgement":"Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32","year":"2018","day":"18","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-07-18T00:00:00Z","page":"449 - 467","citation":{"short":"H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467.","mla":"Kong, Hui, et al. Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes. Vol. 10981, Springer, 2018, pp. 449–67, doi:10.1007/978-3-319-96145-3_24.","chicago":"Kong, Hui, Ezio Bartocci, and Thomas A Henzinger. “Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes,” 10981:449–67. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_24.","ama":"Kong H, Bartocci E, Henzinger TA. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. In: Vol 10981. Springer; 2018:449-467. doi:10.1007/978-3-319-96145-3_24","apa":"Kong, H., Bartocci, E., & Henzinger, T. A. (2018). Reachable set over-approximation for nonlinear systems using piecewise barrier tubes (Vol. 10981, pp. 449–467). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_24","ieee":"H. Kong, E. Bartocci, and T. A. Henzinger, “Reachable set over-approximation for nonlinear systems using piecewise barrier tubes,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 449–467.","ista":"Kong H, Bartocci E, Henzinger TA. 2018. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. CAV: Computer Aided Verification, LNCS, vol. 10981, 449–467."},"abstract":[{"lang":"eng","text":"We address the problem of analyzing the reachable set of a polynomial nonlinear continuous system by over-approximating the flowpipe of its dynamics. The common approach to tackle this problem is to perform a numerical integration over a given time horizon based on Taylor expansion and interval arithmetic. However, this method results to be very conservative when there is a large difference in speed between trajectories as time progresses. In this paper, we propose to use combinations of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse box which is big enough to contain the segment is constructed using sampled simulation and then in the box we compute by linear programming a set of barrier functions (called barrier tube or BT for short) which work together to form a tube surrounding the flowpipe. The benefit of using PBT is that (1) BT is independent of time and hence can avoid being stretched and deformed by time; and (2) a small number of BTs can form a tight over-approximation for the flowpipe, which means that the computation required to decide whether the BTs intersect the unsafe set can be reduced significantly. We implemented a prototype called PBTS in C++. Experiments on some benchmark systems show that our approach is effective."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Published Version","file":[{"checksum":"fd95e8026deacef3dc752a733bb9355f","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-17T15:57:06Z","file_id":"5718","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":5591566,"access_level":"open_access","file_name":"2018_LNCS_Kong.pdf"}],"status":"public","title":"Reachable set over-approximation for nonlinear systems using piecewise barrier tubes","ddc":["000"],"intvolume":" 10981","_id":"142","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"scopus_import":"1","day":"21","article_processing_charge":"No","article_type":"original","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","citation":{"ieee":"P. Amaro et al., “Quantum interference in laser spectroscopy of highly charged lithiumlike ions,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 2. American Physical Society, 2018.","apa":"Amaro, P., Loureiro, U., Safari, L., Fratini, F., Indelicato, P., Stöhlker, T., & Santos, J. (2018). Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.022510","ista":"Amaro P, Loureiro U, Safari L, Fratini F, Indelicato P, Stöhlker T, Santos J. 2018. Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. 97(2), 022510.","ama":"Amaro P, Loureiro U, Safari L, et al. Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(2). doi:10.1103/PhysRevA.97.022510","chicago":"Amaro, Pedro, Ulisses Loureiro, Laleh Safari, Filippo Fratini, Paul Indelicato, Thomas Stöhlker, and José Santos. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.022510.","short":"P. Amaro, U. Loureiro, L. Safari, F. Fratini, P. Indelicato, T. Stöhlker, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","mla":"Amaro, Pedro, et al. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 2, 022510, American Physical Society, 2018, doi:10.1103/PhysRevA.97.022510."},"date_published":"2018-02-21T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We investigate the quantum interference induced shifts between energetically close states in highly charged ions, with the energy structure being observed by laser spectroscopy. In this work, we focus on hyperfine states of lithiumlike heavy-Z isotopes and quantify how much quantum interference changes the observed transition frequencies. The process of photon excitation and subsequent photon decay for the transition 2s→2p→2s is implemented with fully relativistic and full-multipole frameworks, which are relevant for such relativistic atomic systems. We consider the isotopes Pb79+207 and Bi80+209 due to experimental interest, as well as other examples of isotopes with lower Z, namely Pr56+141 and Ho64+165. We conclude that quantum interference can induce shifts up to 11% of the linewidth in the measurable resonances of the considered isotopes, if interference between resonances is neglected. The inclusion of relativity decreases the cross section by 35%, mainly due to the complete retardation form of the electric dipole multipole. However, the contribution of the next higher multipoles (e.g., magnetic quadrupole) to the cross section is negligible. This makes the contribution of relativity and higher-order multipoles to the quantum interference induced shifts a minor effect, even for heavy-Z elements."}],"issue":"2","status":"public","title":"Quantum interference in laser spectroscopy of highly charged lithiumlike ions","intvolume":" 97","_id":"427","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","month":"02","isi":1,"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.07920"}],"external_id":{"isi":["000425601000004"],"arxiv":["1802.07920"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.97.022510","article_number":"022510","publist_id":"7396","ec_funded":1,"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","year":"2018","acknowledgement":"This work was funded by the Portuguese Fundação para a Ciência e a Tecnologia (FCT/MCTES/PIDDAC) under Grant No. UID/FIS/04559/2013 (LIBPhys). P.A. acknowledges the support of the FCT, under Contract No. SFRH/BPD/92329/2013. L.S. acknowledges financial support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. (291734). Laboratoire Kastler Brossel (LKB) is “Unité Mixte de Recherche de Sorbonne Université, de ENS-PSL Research University, du Collège de France et du CNRS No. 8552.” APPENDIX:\r\n","date_created":"2018-12-11T11:46:25Z","date_updated":"2023-09-15T12:09:35Z","volume":97,"author":[{"last_name":"Amaro","first_name":"Pedro","full_name":"Amaro, Pedro"},{"full_name":"Loureiro, Ulisses","last_name":"Loureiro","first_name":"Ulisses"},{"first_name":"Laleh","last_name":"Safari","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","full_name":"Safari, Laleh"},{"last_name":"Fratini","first_name":"Filippo","full_name":"Fratini, Filippo"},{"last_name":"Indelicato","first_name":"Paul","full_name":"Indelicato, Paul"},{"first_name":"Thomas","last_name":"Stöhlker","full_name":"Stöhlker, Thomas"},{"full_name":"Santos, José","last_name":"Santos","first_name":"José"}]},{"_id":"309","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Recognizing weak embeddings of graphs","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ' : G ! M of a graph G into a 2manifold M maps the vertices in V (G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to a common node or arc, due to data compression or low resolution. This raises the computational problem of deciding whether a given map ' : G ! M comes from an embedding. A map ' : G ! M is a weak embedding if it can be perturbed into an embedding ψ: G ! M with k' \"k < \" for every " > 0. A polynomial-time algorithm for recognizing weak embeddings was recently found by Fulek and Kyncl [14], which reduces to solving a system of linear equations over Z2. It runs in O(n2!) O(n4:75) time, where 2:373 is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler than [14]: We perform a sequence of local operations that gradually "untangles" the image '(G) into an embedding (G), or reports that ' is not a weak embedding. It generalizes a recent technique developed for the case that G is a cycle and the embedding is a simple polygon [1], and combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations."}],"citation":{"ama":"Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. In: ACM; 2018:274-292. doi:10.1137/1.9781611975031.20","ista":"Akitaya H, Fulek R, Tóth C. 2018. Recognizing weak embeddings of graphs. SODA: Symposium on Discrete Algorithms, 274–292.","ieee":"H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA, 2018, pp. 274–292.","apa":"Akitaya, H., Fulek, R., & Tóth, C. (2018). Recognizing weak embeddings of graphs (pp. 274–292). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA: ACM. https://doi.org/10.1137/1.9781611975031.20","mla":"Akitaya, Hugo, et al. Recognizing Weak Embeddings of Graphs. ACM, 2018, pp. 274–92, doi:10.1137/1.9781611975031.20.","short":"H. Akitaya, R. Fulek, C. Tóth, in:, ACM, 2018, pp. 274–292.","chicago":"Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings of Graphs,” 274–92. ACM, 2018. https://doi.org/10.1137/1.9781611975031.20."},"page":"274 - 292","date_published":"2018-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","year":"2018","acknowledgement":"∗Research supported in part by the NSF awards CCF-1422311 and CCF-1423615, and the Science Without Borders program. The second author gratefully acknowledges support from Austrian Science Fund (FWF): M2281-N35.","publication_status":"published","publisher":"ACM","department":[{"_id":"UlWa"}],"author":[{"full_name":"Akitaya, Hugo","last_name":"Akitaya","first_name":"Hugo"},{"full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774"},{"full_name":"Tóth, Csaba","last_name":"Tóth","first_name":"Csaba"}],"related_material":{"record":[{"id":"6982","relation":"later_version","status":"public"}]},"date_updated":"2023-09-15T12:19:32Z","date_created":"2018-12-11T11:45:45Z","publist_id":"7556","main_file_link":[{"url":"https://arxiv.org/abs/1709.09209","open_access":"1"}],"external_id":{"isi":["000483921200021"],"arxiv":["1709.09209"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs"}],"conference":{"end_date":"2018-01-10","location":"New Orleans, LA, USA","start_date":"2018-01-07","name":"SODA: Symposium on Discrete Algorithms"},"doi":"10.1137/1.9781611975031.20","language":[{"iso":"eng"}],"month":"01"},{"scopus_import":"1","day":"17","article_processing_charge":"No","article_type":"original","publication":"Physical Review Letters","citation":{"mla":"Yakaboylu, Enderalp, et al. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters, vol. 121, no. 25, 255302, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.255302.","short":"E. Yakaboylu, M. Shkolnikov, M. Lemeshko, Physical Review Letters 121 (2018).","chicago":"Yakaboylu, Enderalp, Mikhail Shkolnikov, and Mikhail Lemeshko. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.255302.","ama":"Yakaboylu E, Shkolnikov M, Lemeshko M. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 2018;121(25). doi:10.1103/PhysRevLett.121.255302","ista":"Yakaboylu E, Shkolnikov M, Lemeshko M. 2018. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 121(25), 255302.","apa":"Yakaboylu, E., Shkolnikov, M., & Lemeshko, M. (2018). Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.255302","ieee":"E. Yakaboylu, M. Shkolnikov, and M. Lemeshko, “Quantum groups as hidden symmetries of quantum impurities,” Physical Review Letters, vol. 121, no. 25. American Physical Society, 2018."},"date_published":"2018-12-17T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We present an approach to interacting quantum many-body systems based on the notion of quantum groups, also known as q-deformed Lie algebras. In particular, we show that, if the symmetry of a free quantum particle corresponds to a Lie group G, in the presence of a many-body environment this particle can be described by a deformed group, Gq. Crucially, the single deformation parameter, q, contains all the information about the many-particle interactions in the system. We exemplify our approach by considering a quantum rotor interacting with a bath of bosons, and demonstrate that extracting the value of q from closed-form solutions in the perturbative regime allows one to predict the behavior of the system for arbitrary values of the impurity-bath coupling strength, in good agreement with nonperturbative calculations. Furthermore, the value of the deformation parameter allows one to predict at which coupling strengths rotor-bath interactions result in a formation of a stable quasiparticle. The approach based on quantum groups does not only allow for a drastic simplification of impurity problems, but also provides valuable insights into hidden symmetries of interacting many-particle systems."}],"issue":"25","status":"public","title":"Quantum groups as hidden symmetries of quantum impurities","intvolume":" 121","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5794","oa_version":"Preprint","month":"12","publication_identifier":{"issn":["00319007"]},"quality_controlled":"1","isi":1,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment"}],"external_id":{"arxiv":["1809.00222"],"isi":["000454178600009"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.00222"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.121.255302","article_number":"255302","ec_funded":1,"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"year":"2018","date_created":"2019-01-06T22:59:12Z","date_updated":"2023-09-15T12:09:06Z","volume":121,"author":[{"full_name":"Yakaboylu, Enderalp","last_name":"Yakaboylu","first_name":"Enderalp","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shkolnikov, Mikhail","first_name":"Mikhail","last_name":"Shkolnikov","id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X"},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}]},{"publist_id":"7967","related_material":{"record":[{"id":"6287","relation":"dissertation_contains","status":"public"}]},"author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"first_name":"Anton","last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0659-3201","full_name":"Nikitenko, Anton"}],"volume":28,"date_updated":"2023-09-15T12:10:35Z","date_created":"2018-12-11T11:44:33Z","year":"2018","department":[{"_id":"HeEd"}],"publisher":"Institute of Mathematical Statistics","publication_status":"published","month":"10","doi":"10.1214/18-AAP1389","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1705.02870","open_access":"1"}],"external_id":{"arxiv":["1705.02870"],"isi":["000442893500018"]},"project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","issue":"5","abstract":[{"text":"Using the geodesic distance on the n-dimensional sphere, we study the expected radius function of the Delaunay mosaic of a random set of points. Specifically, we consider the partition of the mosaic into intervals of the radius function and determine the expected number of intervals whose radii are less than or equal to a given threshold. We find that the expectations are essentially the same as for the Poisson–Delaunay mosaic in n-dimensional Euclidean space. Assuming the points are not contained in a hemisphere, the Delaunay mosaic is isomorphic to the boundary complex of the convex hull in Rn+1, so we also get the expected number of faces of a random inscribed polytope. As proved in Antonelli et al. [Adv. in Appl. Probab. 9–12 (1977–1980)], an orthant section of the n-sphere is isometric to the standard n-simplex equipped with the Fisher information metric. It follows that the latter space has similar stochastic properties as the n-dimensional Euclidean space. Our results are therefore relevant in information geometry and in population genetics.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"87","intvolume":" 28","title":"Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-10-01T00:00:00Z","citation":{"chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability. Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/18-AAP1389.","mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability, vol. 28, no. 5, Institute of Mathematical Statistics, 2018, pp. 3215–38, doi:10.1214/18-AAP1389.","short":"H. Edelsbrunner, A. Nikitenko, Annals of Applied Probability 28 (2018) 3215–3238.","ista":"Edelsbrunner H, Nikitenko A. 2018. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 28(5), 3215–3238.","ieee":"H. Edelsbrunner and A. Nikitenko, “Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics,” Annals of Applied Probability, vol. 28, no. 5. Institute of Mathematical Statistics, pp. 3215–3238, 2018.","apa":"Edelsbrunner, H., & Nikitenko, A. (2018). Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AAP1389","ama":"Edelsbrunner H, Nikitenko A. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 2018;28(5):3215-3238. doi:10.1214/18-AAP1389"},"publication":"Annals of Applied Probability","page":"3215 - 3238","article_type":"original"},{"publist_id":"7728","date_created":"2018-12-11T11:45:07Z","date_updated":"2023-09-15T12:11:03Z","volume":4,"author":[{"last_name":"Fendrych","first_name":"Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","full_name":"Fendrych, Matyas"},{"full_name":"Akhmanova, Maria","last_name":"Akhmanova","first_name":"Maria","orcid":"0000-0003-1522-3162","id":"3425EC26-F248-11E8-B48F-1D18A9856A87"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack"},{"last_name":"Glanc","first_name":"Matous","full_name":"Glanc, Matous"},{"first_name":"Shinya","last_name":"Hagihara","full_name":"Hagihara, Shinya"},{"first_name":"Koji","last_name":"Takahashi","full_name":"Takahashi, Koji"},{"last_name":"Uchida","first_name":"Naoyuki","full_name":"Uchida, Naoyuki"},{"full_name":"Torii, Keiko U","last_name":"Torii","first_name":"Keiko U"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/"}]},"publication_status":"published","department":[{"_id":"JiFr"},{"_id":"DaSi"},{"_id":"NanoFab"}],"publisher":"Springer Nature","year":"2018","pmid":1,"month":"06","language":[{"iso":"eng"}],"doi":"10.1038/s41477-018-0190-1","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29942048","open_access":"1"}],"external_id":{"pmid":["29942048"],"isi":["000443221200017"]},"oa":1,"abstract":[{"lang":"eng","text":"The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway."}],"issue":"7","type":"journal_article","oa_version":"Submitted Version","status":"public","title":"Rapid and reversible root growth inhibition by TIR1 auxin signalling","intvolume":" 4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"192","day":"25","article_processing_charge":"No","scopus_import":"1","date_published":"2018-06-25T00:00:00Z","article_type":"original","page":"453 - 459","publication":"Nature Plants","citation":{"ama":"Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 2018;4(7):453-459. doi:10.1038/s41477-018-0190-1","ista":"Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 4(7), 453–459.","apa":"Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi, K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-018-0190-1","ieee":"M. Fendrych et al., “Rapid and reversible root growth inhibition by TIR1 auxin signalling,” Nature Plants, vol. 4, no. 7. Springer Nature, pp. 453–459, 2018.","mla":"Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants, vol. 4, no. 7, Springer Nature, 2018, pp. 453–59, doi:10.1038/s41477-018-0190-1.","short":"M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi, N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459.","chicago":"Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara, Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants. Springer Nature, 2018. https://doi.org/10.1038/s41477-018-0190-1."}},{"abstract":[{"lang":"eng","text":"The intercellular transport of auxin is driven by PIN-formed (PIN) auxin efflux carriers. PINs are localized at the plasma membrane (PM) and on constitutively recycling endomembrane vesicles. Therefore, PINs can mediate auxin transport either by direct translocation across the PM or by pumping auxin into secretory vesicles (SVs), leading to its secretory release upon fusion with the PM. Which of these two mechanisms dominates is a matter of debate. Here, we addressed the issue with a mathematical modeling approach. We demonstrate that the efficiency of secretory transport depends on SV size, half-life of PINs on the PM, pH, exocytosis frequency and PIN density. 3D structured illumination microscopy (SIM) was used to determine PIN density on the PM. Combining this data with published values of the other parameters, we show that the transport activity of PINs in SVs would have to be at least 1000× greater than on the PM in order to produce a comparable macroscopic auxin transport. If both transport mechanisms operated simultaneously and PINs were equally active on SVs and PM, the contribution of secretion to the total auxin flux would be negligible. In conclusion, while secretory vesicle-mediated transport of auxin is an intriguing and theoretically possible model, it is unlikely to be a major mechanism of auxin transport inplanta."}],"issue":"11","type":"journal_article","file":[{"checksum":"e4b59c2599b0ca26ebf5b8434bcde94a","date_updated":"2020-07-14T12:44:50Z","date_created":"2018-12-17T16:04:11Z","file_id":"5719","relation":"main_file","creator":"dernst","file_size":2200593,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_IJMS_Hille.pdf"}],"oa_version":"Published Version","title":"Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation","status":"public","ddc":["580"],"intvolume":" 19","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"14","day":"12","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-11-12T00:00:00Z","article_type":"original","publication":"International Journal of Molecular Sciences","citation":{"ieee":"S. Hille, M. Akhmanova, M. Glanc, A. J. Johnson, and J. Friml, “Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation,” International Journal of Molecular Sciences, vol. 19, no. 11. MDPI, 2018.","apa":"Hille, S., Akhmanova, M., Glanc, M., Johnson, A. J., & Friml, J. (2018). Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms19113566","ista":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. 2018. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 19(11).","ama":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 2018;19(11). doi:10.3390/ijms19113566","chicago":"Hille, Sander, Maria Akhmanova, Matous Glanc, Alexander J Johnson, and Jiří Friml. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences. MDPI, 2018. https://doi.org/10.3390/ijms19113566.","short":"S. Hille, M. Akhmanova, M. Glanc, A.J. Johnson, J. Friml, International Journal of Molecular Sciences 19 (2018).","mla":"Hille, Sander, et al. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences, vol. 19, no. 11, MDPI, 2018, doi:10.3390/ijms19113566."},"file_date_updated":"2020-07-14T12:44:50Z","publist_id":"8042","ec_funded":1,"date_created":"2018-12-11T11:44:09Z","date_updated":"2023-09-18T08:09:32Z","volume":19,"author":[{"last_name":"Hille","first_name":"Sander","full_name":"Hille, Sander"},{"orcid":"0000-0003-1522-3162","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","last_name":"Akhmanova","first_name":"Maria","full_name":"Akhmanova, Maria"},{"full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","first_name":"Matous"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson","full_name":"Johnson, Alexander J"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"publication_status":"published","publisher":"MDPI","department":[{"_id":"DaSi"},{"_id":"JiFr"}],"acknowledgement":"European Research Council (ERC): 742985 to Jiri Friml; M.A. was supported by the Austrian Science Fund (FWF) (M2379-B28); AJ was supported by the Austria Science Fund (FWF): I03630 to Jiri Friml.","year":"2018","month":"11","publication_identifier":{"eissn":["1422-0067"]},"language":[{"iso":"eng"}],"doi":"10.3390/ijms19113566","isi":1,"quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"external_id":{"isi":["000451528500282"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"date_published":"2018-12-04T00:00:00Z","article_type":"original","page":"1411-1427","publication":"Genetics","citation":{"ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","apa":"Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429","ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018.","ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301429.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427."},"day":"04","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Replicability of introgression under linked, polygenic selection","status":"public","intvolume":" 210","_id":"39","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation."}],"issue":"4","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.301429","quality_controlled":"1","isi":1,"external_id":{"isi":["000452315900021"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/379578v1"}],"month":"12","publication_identifier":{"issn":["00166731"]},"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-18T08:10:29Z","volume":210,"author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","year":"2018"},{"oa_version":"Preprint","intvolume":" 32","title":"Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"420","issue":"17","abstract":[{"text":"We analyze the theoretical derivation of the beyond-mean-field equation of state for two-dimensional gas of dilute, ultracold alkali-metal atoms in the Bardeen–Cooper–Schrieffer (BCS) to Bose–Einstein condensate (BEC) crossover. We show that at zero temperature our theory — considering Gaussian fluctuations on top of the mean-field equation of state — is in very good agreement with experimental data. Subsequently, we investigate the superfluid density at finite temperature and its renormalization due to the proliferation of vortex–antivortex pairs. By doing so, we determine the Berezinskii–Kosterlitz–Thouless (BKT) critical temperature — at which the renormalized superfluid density jumps to zero — as a function of the inter-atomic potential strength. We find that the Nelson–Kosterlitz criterion overestimates the BKT temperature with respect to the renormalization group equations, this effect being particularly relevant in the intermediate regime of the crossover.","lang":"eng"}],"type":"journal_article","date_published":"2018-07-10T00:00:00Z","page":"1840022","citation":{"ieee":"G. Bighin and L. Salasnich, “Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover,” International Journal of Modern Physics B, vol. 32, no. 17. World Scientific Publishing, p. 1840022, 2018.","apa":"Bighin, G., & Salasnich, L. (2018). Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. World Scientific Publishing. https://doi.org/10.1142/S0217979218400222","ista":"Bighin G, Salasnich L. 2018. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 32(17), 1840022.","ama":"Bighin G, Salasnich L. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 2018;32(17):1840022. doi:10.1142/S0217979218400222","chicago":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B. World Scientific Publishing, 2018. https://doi.org/10.1142/S0217979218400222.","short":"G. Bighin, L. Salasnich, International Journal of Modern Physics B 32 (2018) 1840022.","mla":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B, vol. 32, no. 17, World Scientific Publishing, 2018, p. 1840022, doi:10.1142/S0217979218400222."},"publication":"International Journal of Modern Physics B","article_processing_charge":"No","day":"10","scopus_import":"1","volume":32,"date_created":"2018-12-11T11:46:22Z","date_updated":"2023-09-18T08:09:59Z","author":[{"full_name":"Bighin, Giacomo","first_name":"Giacomo","last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777"},{"last_name":"Salasnich","first_name":"Luca","full_name":"Salasnich, Luca"}],"department":[{"_id":"MiLe"}],"publisher":"World Scientific Publishing","publication_status":"published","year":"2018","publist_id":"7402","language":[{"iso":"eng"}],"doi":"10.1142/S0217979218400222","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1710.11171","open_access":"1"}],"oa":1,"external_id":{"isi":["000438217300007"]},"month":"07"},{"publication_identifier":{"issn":["00278424"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1801832115","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["30297406"],"isi":["000448040500065"]},"publist_id":"8017","file_date_updated":"2020-07-14T12:46:16Z","volume":115,"date_updated":"2023-09-18T08:36:49Z","date_created":"2018-12-11T11:44:18Z","author":[{"last_name":"Tavares","first_name":"Hugo","full_name":"Tavares, Hugo"},{"last_name":"Whitley","first_name":"Annabel","full_name":"Whitley, Annabel"},{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field"},{"full_name":"Bradley, Desmond","last_name":"Bradley","first_name":"Desmond"},{"full_name":"Couchman, Matthew","first_name":"Matthew","last_name":"Couchman"},{"full_name":"Copsey, Lucy","last_name":"Copsey","first_name":"Lucy"},{"last_name":"Elleouet","first_name":"Joane","full_name":"Elleouet, Joane"},{"full_name":"Burrus, Monique","first_name":"Monique","last_name":"Burrus"},{"full_name":"Andalo, Christophe","last_name":"Andalo","first_name":"Christophe"},{"full_name":"Li, Miaomiao","first_name":"Miaomiao","last_name":"Li"},{"last_name":"Li","first_name":"Qun","full_name":"Li, Qun"},{"first_name":"Yongbiao","last_name":"Xue","full_name":"Xue, Yongbiao"},{"last_name":"Rebocho","first_name":"Alexandra B","full_name":"Rebocho, Alexandra B"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Coen, Enrico","last_name":"Coen","first_name":"Enrico"}],"publisher":"National Academy of Sciences","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"acknowledgement":" ERC Grant 201252 (to N.H.B.)","year":"2018","has_accepted_license":"1","article_processing_charge":"No","day":"23","scopus_import":"1","date_published":"2018-10-23T00:00:00Z","page":"11006 - 11011","citation":{"mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:10.1073/pnas.1801832115.","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1801832115.","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115","ieee":"H. Tavares et al., “Selection and gene flow shape genomic islands that control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018."},"publication":"PNAS","issue":"43","abstract":[{"text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","date_created":"2018-12-17T08:44:03Z","date_updated":"2020-07-14T12:46:16Z","file_id":"5683","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1911302,"access_level":"open_access","file_name":"11006.full.pdf"}],"intvolume":" 115","status":"public","ddc":["570"],"title":"Selection and gene flow shape genomic islands that control floral guides","_id":"38","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"month":"05","external_id":{"isi":["000453298500019"],"arxiv":["1806.01000"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.01000"}],"quality_controlled":"1","isi":1,"conference":{"name":"SPIE: The international society for optical engineering","start_date":"2018-04-22","location":"Strasbourg, France","end_date":"2018-04-26"},"doi":"10.1117/12.2309928","language":[{"iso":"eng"}],"article_number":"106721N","publist_id":"7766","year":"2018","publication_status":"published","publisher":"SPIE","department":[{"_id":"JoFi"}],"editor":[{"last_name":"Andrews","first_name":"D L","full_name":"Andrews, D L"},{"full_name":"Ostendorf, A","first_name":"A","last_name":"Ostendorf"},{"full_name":"Bain, A J","first_name":"A J","last_name":"Bain"},{"first_name":"J M","last_name":"Nunzi","full_name":"Nunzi, J M"}],"author":[{"last_name":"Xuereb","first_name":"André","full_name":"Xuereb, André"},{"full_name":"Aquilina, Matteo","last_name":"Aquilina","first_name":"Matteo"},{"first_name":"Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"}],"date_created":"2018-12-11T11:44:55Z","date_updated":"2023-09-18T08:12:24Z","volume":10672,"scopus_import":"1","day":"04","article_processing_charge":"No","citation":{"mla":"Xuereb, André, et al. Routing Thermal Noise through Quantum Networks. Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:10.1117/12.2309928.","short":"A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J. Bain, J.M. Nunzi (Eds.), SPIE, 2018.","chicago":"Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain, and J M Nunzi, Vol. 10672. SPIE, 2018. https://doi.org/10.1117/12.2309928.","ama":"Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks. In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:10.1117/12.2309928","ista":"Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum networks. SPIE: The international society for optical engineering, Proceedings of SPIE, vol. 10672, 106721N.","apa":"Xuereb, A., Aquilina, M., & Barzanjeh, S. (2018). Routing thermal noise through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, & J. M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society for optical engineering, Strasbourg, France: SPIE. https://doi.org/10.1117/12.2309928","ieee":"A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through quantum networks,” presented at the SPIE: The international society for optical engineering, Strasbourg, France, 2018, vol. 10672."},"date_published":"2018-05-04T00:00:00Z","type":"conference","alternative_title":["Proceedings of SPIE"],"abstract":[{"lang":"eng","text":"There is currently significant interest in operating devices in the quantum regime, where their behaviour cannot be explained through classical mechanics. Quantum states, including entangled states, are fragile and easily disturbed by excessive thermal noise. Here we address the question of whether it is possible to create non-reciprocal devices that encourage the flow of thermal noise towards or away from a particular quantum device in a network. Our work makes use of the cascaded systems formalism to answer this question in the affirmative, showing how a three-port device can be used as an effective thermal transistor, and illustrates how this formalism maps onto an experimentally-realisable optomechanical system. Our results pave the way to more resilient quantum devices and to the use of thermal noise as a resource."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"155","title":"Routing thermal noise through quantum networks","status":"public","intvolume":" 10672","oa_version":"Preprint"},{"issue":"6420","abstract":[{"text":"Cuprate superconductors have long been thought of as having strong electronic correlations but negligible spin-orbit coupling. Using spin- and angle-resolved photoemission spectroscopy, we discovered that one of the most studied cuprate superconductors, Bi2212, has a nontrivial spin texture with a spin-momentum locking that circles the Brillouin zone center and a spin-layer locking that allows states of opposite spin to be localized in different parts of the unit cell. Our findings pose challenges for the vast majority of models of cuprates, such as the Hubbard model and its variants, where spin-orbit interaction has been mostly neglected, and open the intriguing question of how the high-temperature superconducting state emerges in the presence of this nontrivial spin texture. ","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 362","status":"public","title":"Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor","_id":"5767","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"14","scopus_import":"1","date_published":"2018-12-14T00:00:00Z","page":"1271-1275","article_type":"original","citation":{"ista":"Gotlieb K, Lin C-Y, Serbyn M, Zhang W, Smallwood CL, Jozwiak C, Eisaki H, Hussain Z, Vishwanath A, Lanzara A. 2018. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 362(6420), 1271–1275.","apa":"Gotlieb, K., Lin, C.-Y., Serbyn, M., Zhang, W., Smallwood, C. L., Jozwiak, C., … Lanzara, A. (2018). Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aao0980","ieee":"K. Gotlieb et al., “Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor,” Science, vol. 362, no. 6420. American Association for the Advancement of Science, pp. 1271–1275, 2018.","ama":"Gotlieb K, Lin C-Y, Serbyn M, et al. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 2018;362(6420):1271-1275. doi:10.1126/science.aao0980","chicago":"Gotlieb, Kenneth, Chiu-Yun Lin, Maksym Serbyn, Wentao Zhang, Christopher L. Smallwood, Christopher Jozwiak, Hiroshi Eisaki, Zahid Hussain, Ashvin Vishwanath, and Alessandra Lanzara. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aao0980.","mla":"Gotlieb, Kenneth, et al. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science, vol. 362, no. 6420, American Association for the Advancement of Science, 2018, pp. 1271–75, doi:10.1126/science.aao0980.","short":"K. Gotlieb, C.-Y. Lin, M. Serbyn, W. Zhang, C.L. Smallwood, C. Jozwiak, H. Eisaki, Z. Hussain, A. Vishwanath, A. Lanzara, Science 362 (2018) 1271–1275."},"publication":"Science","volume":362,"date_created":"2018-12-19T14:53:50Z","date_updated":"2023-09-18T08:11:56Z","author":[{"last_name":"Gotlieb","first_name":"Kenneth","full_name":"Gotlieb, Kenneth"},{"full_name":"Lin, Chiu-Yun","first_name":"Chiu-Yun","last_name":"Lin"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"},{"first_name":"Wentao","last_name":"Zhang","full_name":"Zhang, Wentao"},{"last_name":"Smallwood","first_name":"Christopher L.","full_name":"Smallwood, Christopher L."},{"last_name":"Jozwiak","first_name":"Christopher","full_name":"Jozwiak, Christopher"},{"full_name":"Eisaki, Hiroshi","last_name":"Eisaki","first_name":"Hiroshi"},{"full_name":"Hussain, Zahid","first_name":"Zahid","last_name":"Hussain"},{"last_name":"Vishwanath","first_name":"Ashvin","full_name":"Vishwanath, Ashvin"},{"last_name":"Lanzara","first_name":"Alessandra","full_name":"Lanzara, Alessandra"}],"publisher":"American Association for the Advancement of Science","department":[{"_id":"MaSe"}],"publication_status":"published","acknowledgement":" M.S. was supported by the Gordon and Betty Moore Foundation s EPiQS Initiative through grant GBMF4307","year":"2018","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1126/science.aao0980","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000452994400048"]},"main_file_link":[{"url":"https://doi.org/10.1126/science.aao0980","open_access":"1"}]},{"publication":"eLife","citation":{"ama":"Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 2018;7. doi:10.7554/eLife.34465","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7, e34465.","ieee":"M. Kaucka et al., “Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage,” eLife, vol. 7. eLife Sciences Publications, 2018.","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M., … Adameyko, I. (2018). Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.34465","mla":"Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife, vol. 7, e34465, eLife Sciences Publications, 2018, doi:10.7554/eLife.34465.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018).","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.34465."},"date_published":"2018-06-13T00:00:00Z","scopus_import":"1","day":"13","has_accepted_license":"1","article_processing_charge":"No","ddc":["571"],"title":"Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","status":"public","intvolume":" 7","_id":"162","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_size":9816484,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_eLife_Kaucka.pdf","checksum":"da2378cdcf6b5461dcde194e4d608343","date_created":"2018-12-17T16:41:58Z","date_updated":"2020-07-14T12:45:07Z","relation":"main_file","file_id":"5727"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here, we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts."}],"isi":1,"quality_controlled":"1","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000436227500001"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.34465","month":"06","publication_status":"published","department":[{"_id":"AnKi"}],"publisher":"eLife Sciences Publications","year":"2018","date_updated":"2023-09-18T09:29:07Z","date_created":"2018-12-11T11:44:57Z","volume":7,"author":[{"last_name":"Kaucka","first_name":"Marketa","full_name":"Kaucka, Marketa"},{"full_name":"Petersen, Julian","last_name":"Petersen","first_name":"Julian"},{"full_name":"Tesarova, Marketa","first_name":"Marketa","last_name":"Tesarova"},{"full_name":"Szarowska, Bara","last_name":"Szarowska","first_name":"Bara"},{"first_name":"Maria","last_name":"Kastriti","full_name":"Kastriti, Maria"},{"full_name":"Xie, Meng","last_name":"Xie","first_name":"Meng"},{"full_name":"Kicheva, Anna","first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"},{"full_name":"Annusver, Karl","last_name":"Annusver","first_name":"Karl"},{"full_name":"Kasper, Maria","first_name":"Maria","last_name":"Kasper"},{"last_name":"Symmons","first_name":"Orsolya","full_name":"Symmons, Orsolya"},{"first_name":"Leslie","last_name":"Pan","full_name":"Pan, Leslie"},{"full_name":"Spitz, Francois","last_name":"Spitz","first_name":"Francois"},{"full_name":"Kaiser, Jozef","first_name":"Jozef","last_name":"Kaiser"},{"last_name":"Hovorakova","first_name":"Maria","full_name":"Hovorakova, Maria"},{"last_name":"Zikmund","first_name":"Tomas","full_name":"Zikmund, Tomas"},{"full_name":"Sunadome, Kazunori","last_name":"Sunadome","first_name":"Kazunori"},{"full_name":"Matise, Michael P","last_name":"Matise","first_name":"Michael P"},{"full_name":"Wang, Hui","last_name":"Wang","first_name":"Hui"},{"full_name":"Marklund, Ulrika","last_name":"Marklund","first_name":"Ulrika"},{"full_name":"Abdo, Hind","last_name":"Abdo","first_name":"Hind"},{"last_name":"Ernfors","first_name":"Patrik","full_name":"Ernfors, Patrik"},{"full_name":"Maire, Pascal","last_name":"Maire","first_name":"Pascal"},{"last_name":"Wurmser","first_name":"Maud","full_name":"Wurmser, Maud"},{"full_name":"Chagin, Andrei S","last_name":"Chagin","first_name":"Andrei S"},{"first_name":"Kaj","last_name":"Fried","full_name":"Fried, Kaj"},{"full_name":"Adameyko, Igor","last_name":"Adameyko","first_name":"Igor"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9838"}]},"article_number":"e34465","file_date_updated":"2020-07-14T12:45:07Z","ec_funded":1,"publist_id":"7759"},{"publist_id":"7579","ec_funded":1,"date_created":"2018-12-11T11:45:42Z","date_updated":"2023-09-18T09:29:33Z","volume":10821,"author":[{"full_name":"Cohen, Bram","last_name":"Cohen","first_name":"Bram"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"}],"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer","year":"2018","month":"05","language":[{"iso":"eng"}],"conference":{"location":"Tel Aviv, Israel","start_date":"2018-04-29","end_date":"2018-05-03","name":"Eurocrypt: Advances in Cryptology"},"doi":"10.1007/978-3-319-78375-8_15","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000517098700015"]},"main_file_link":[{"url":"https://eprint.iacr.org/2018/183.pdf","open_access":"1"}],"abstract":[{"lang":"eng","text":"At ITCS 2013, Mahmoody, Moran and Vadhan [MMV13] introduce and construct publicly verifiable proofs of sequential work, which is a protocol for proving that one spent sequential computational work related to some statement. The original motivation for such proofs included non-interactive time-stamping and universally verifiable CPU benchmarks. A more recent application, and our main motivation, are blockchain designs, where proofs of sequential work can be used – in combination with proofs of space – as a more ecological and economical substitute for proofs of work which are currently used to secure Bitcoin and other cryptocurrencies. The construction proposed by [MMV13] is based on a hash function and can be proven secure in the random oracle model, or assuming inherently sequential hash-functions, which is a new standard model assumption introduced in their work. In a proof of sequential work, a prover gets a “statement” χ, a time parameter N and access to a hash-function H, which for the security proof is modelled as a random oracle. Correctness requires that an honest prover can make a verifier accept making only N queries to H, while soundness requires that any prover who makes the verifier accept must have made (almost) N sequential queries to H. Thus a solution constitutes a proof that N time passed since χ was received. Solutions must be publicly verifiable in time at most polylogarithmic in N. The construction of [MMV13] is based on “depth-robust” graphs, and as a consequence has rather poor concrete parameters. But the major drawback is that the prover needs not just N time, but also N space to compute a proof. In this work we propose a proof of sequential work which is much simpler, more efficient and achieves much better concrete bounds. Most importantly, the space required can be as small as log (N) (but we get better soundness using slightly more memory than that). An open problem stated by [MMV13] that our construction does not solve either is achieving a “unique” proof, where even a cheating prover can only generate a single accepting proof. This property would be extremely useful for applications to blockchains."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","status":"public","title":"Simple proofs of sequential work","intvolume":" 10821","_id":"302","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"29","article_processing_charge":"No","scopus_import":"1","date_published":"2018-05-29T00:00:00Z","page":"451 - 467","citation":{"ama":"Cohen B, Pietrzak KZ. Simple proofs of sequential work. In: Vol 10821. Springer; 2018:451-467. doi:10.1007/978-3-319-78375-8_15","ista":"Cohen B, Pietrzak KZ. 2018. Simple proofs of sequential work. Eurocrypt: Advances in Cryptology, LNCS, vol. 10821, 451–467.","ieee":"B. Cohen and K. Z. Pietrzak, “Simple proofs of sequential work,” presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821, pp. 451–467.","apa":"Cohen, B., & Pietrzak, K. Z. (2018). Simple proofs of sequential work (Vol. 10821, pp. 451–467). Presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_15","mla":"Cohen, Bram, and Krzysztof Z. Pietrzak. Simple Proofs of Sequential Work. Vol. 10821, Springer, 2018, pp. 451–67, doi:10.1007/978-3-319-78375-8_15.","short":"B. Cohen, K.Z. Pietrzak, in:, Springer, 2018, pp. 451–467.","chicago":"Cohen, Bram, and Krzysztof Z Pietrzak. “Simple Proofs of Sequential Work,” 10821:451–67. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_15."}},{"date_updated":"2023-09-18T09:18:44Z","date_created":"2018-12-11T11:44:15Z","volume":98,"author":[{"first_name":"Ulisse","last_name":"Ferrari","full_name":"Ferrari, Ulisse"},{"full_name":"Deny, Stephane","first_name":"Stephane","last_name":"Deny"},{"last_name":"Chalk","first_name":"Matthew J","full_name":"Chalk, Matthew J"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"first_name":"Thierry","last_name":"Mora","full_name":"Mora, Thierry"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"GaTk"}],"acknowledgement":"This work was supported by ANR Trajectory, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche (LIFESENSES; ANR-10-LABX-65), EC Grant No. H2020-785907 from the Human Brain Project, NIH Grant No. U01NS090501, and an AVIESAN-UNADEV grant to O.M. M.C. was supported by the Agence Nationale de la Recherche Jeune Chercheur/Jeune Chercheuse grant (ANR-17-CE37-0013).","year":"2018","ec_funded":1,"publist_id":"8024","article_number":"042410","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.98.042410","isi":1,"quality_controlled":"1","project":[{"grant_number":"785907","_id":"26436750-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)"}],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/243816v2.full"}],"oa":1,"external_id":{"isi":["000447486100004"]},"month":"10","publication_identifier":{"issn":["24700045"]},"oa_version":"Preprint","title":"Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons","status":"public","intvolume":" 98","_id":"31","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Correlations in sensory neural networks have both extrinsic and intrinsic origins. Extrinsic or stimulus correlations arise from shared inputs to the network and, thus, depend strongly on the stimulus ensemble. Intrinsic or noise correlations reflect biophysical mechanisms of interactions between neurons, which are expected to be robust to changes in the stimulus ensemble. Despite the importance of this distinction for understanding how sensory networks encode information collectively, no method exists to reliably separate intrinsic interactions from extrinsic correlations in neural activity data, limiting our ability to build predictive models of the network response. In this paper we introduce a general strategy to infer population models of interacting neurons that collectively encode stimulus information. The key to disentangling intrinsic from extrinsic correlations is to infer the couplings between neurons separately from the encoding model and to combine the two using corrections calculated in a mean-field approximation. We demonstrate the effectiveness of this approach in retinal recordings. The same coupling network is inferred from responses to radically different stimulus ensembles, showing that these couplings indeed reflect stimulus-independent interactions between neurons. The inferred model predicts accurately the collective response of retinal ganglion cell populations as a function of the stimulus.","lang":"eng"}],"issue":"4","type":"journal_article","date_published":"2018-10-17T00:00:00Z","article_type":"original","publication":"Physical Review E","citation":{"ama":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 2018;98(4). doi:10.1103/PhysRevE.98.042410","ista":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. 2018. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 98(4), 042410.","ieee":"U. Ferrari, S. Deny, M. J. Chalk, G. Tkačik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” Physical Review E, vol. 98, no. 4. American Physical Society, 2018.","apa":"Ferrari, U., Deny, S., Chalk, M. J., Tkačik, G., Marre, O., & Mora, T. (2018). Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.042410","mla":"Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410.","short":"U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review E 98 (2018).","chicago":"Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gašper Tkačik, Olivier Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.042410."},"day":"17","article_processing_charge":"No","scopus_import":"1"},{"ec_funded":1,"publist_id":"7990","author":[{"first_name":"Nikita","last_name":"Kalinin","full_name":"Kalinin, Nikita"},{"first_name":"Aldo","last_name":"Guzmán Sáenz","full_name":"Guzmán Sáenz, Aldo"},{"full_name":"Prieto, Y","first_name":"Y","last_name":"Prieto"},{"full_name":"Shkolnikov, Mikhail","last_name":"Shkolnikov","first_name":"Mikhail","orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kalinina, V","last_name":"Kalinina","first_name":"V"},{"full_name":"Lupercio, Ernesto","first_name":"Ernesto","last_name":"Lupercio"}],"volume":115,"date_created":"2018-12-11T11:44:26Z","date_updated":"2023-09-18T08:41:16Z","year":"2018","publisher":"National Academy of Sciences","department":[{"_id":"TaHa"}],"publication_status":"published","publication_identifier":{"issn":["00278424"]},"month":"08","doi":"10.1073/pnas.1805847115","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.09153"}],"external_id":{"isi":["000442861600009"],"arxiv":["1806.09153"]},"oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","issue":"35","abstract":[{"lang":"eng","text":"Tropical geometry, an established field in pure mathematics, is a place where string theory, mirror symmetry, computational algebra, auction theory, and so forth meet and influence one another. In this paper, we report on our discovery of a tropical model with self-organized criticality (SOC) behavior. Our model is continuous, in contrast to all known models of SOC, and is a certain scaling limit of the sandpile model, the first and archetypical model of SOC. We describe how our model is related to pattern formation and proportional growth phenomena and discuss the dichotomy between continuous and discrete models in several contexts. Our aim in this context is to present an idealized tropical toy model (cf. Turing reaction-diffusion model), requiring further investigation."}],"type":"journal_article","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"64","intvolume":" 115","title":"Self-organized criticality and pattern emergence through the lens of tropical geometry","status":"public","article_processing_charge":"No","day":"28","scopus_import":"1","date_published":"2018-08-28T00:00:00Z","citation":{"ista":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. 2018. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 115(35), E8135–E8142.","apa":"Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., & Lupercio, E. (2018). Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1805847115","ieee":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E. Lupercio, “Self-organized criticality and pattern emergence through the lens of tropical geometry,” PNAS: Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35. National Academy of Sciences, pp. E8135–E8142, 2018.","ama":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 2018;115(35):E8135-E8142. doi:10.1073/pnas.1805847115","chicago":"Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina, and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1805847115.","mla":"Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35, National Academy of Sciences, 2018, pp. E8135–42, doi:10.1073/pnas.1805847115.","short":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio, PNAS: Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E8135–E8142."},"publication":"PNAS: Proceedings of the National Academy of Sciences of the United States of America","page":"E8135 - E8142","article_type":"original"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.f1s76f2"}],"citation":{"ama":"Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. 2018. doi:10.5061/dryad.f1s76f2","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage, Dryad, 10.5061/dryad.f1s76f2.","ieee":"M. Kaucka et al., “Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie, M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. Dryad. https://doi.org/10.5061/dryad.f1s76f2","mla":"Kaucka, Marketa, et al. Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage. Dryad, 2018, doi:10.5061/dryad.f1s76f2.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” Dryad, 2018. https://doi.org/10.5061/dryad.f1s76f2."},"oa":1,"doi":"10.5061/dryad.f1s76f2","date_published":"2018-06-14T00:00:00Z","day":"14","month":"06","article_processing_charge":"No","_id":"9838","year":"2018","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","status":"public","publisher":"Dryad","department":[{"_id":"AnKi"}],"author":[{"full_name":"Kaucka, Marketa","last_name":"Kaucka","first_name":"Marketa"},{"full_name":"Petersen, Julian","last_name":"Petersen","first_name":"Julian"},{"last_name":"Tesarova","first_name":"Marketa","full_name":"Tesarova, Marketa"},{"full_name":"Szarowska, Bara","last_name":"Szarowska","first_name":"Bara"},{"last_name":"Kastriti","first_name":"Maria Eleni","full_name":"Kastriti, Maria Eleni"},{"full_name":"Xie, Meng","last_name":"Xie","first_name":"Meng"},{"full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Annusver","first_name":"Karl","full_name":"Annusver, Karl"},{"full_name":"Kasper, Maria","first_name":"Maria","last_name":"Kasper"},{"full_name":"Symmons, Orsolya","last_name":"Symmons","first_name":"Orsolya"},{"full_name":"Pan, Leslie","first_name":"Leslie","last_name":"Pan"},{"last_name":"Spitz","first_name":"Francois","full_name":"Spitz, Francois"},{"first_name":"Jozef","last_name":"Kaiser","full_name":"Kaiser, Jozef"},{"full_name":"Hovorakova, Maria","last_name":"Hovorakova","first_name":"Maria"},{"full_name":"Zikmund, Tomas","first_name":"Tomas","last_name":"Zikmund"},{"last_name":"Sunadome","first_name":"Kazunori","full_name":"Sunadome, Kazunori"},{"last_name":"Matise","first_name":"Michael P","full_name":"Matise, Michael P"},{"last_name":"Wang","first_name":"Hui","full_name":"Wang, Hui"},{"full_name":"Marklund, Ulrika","last_name":"Marklund","first_name":"Ulrika"},{"full_name":"Abdo, Hind","last_name":"Abdo","first_name":"Hind"},{"first_name":"Patrik","last_name":"Ernfors","full_name":"Ernfors, Patrik"},{"last_name":"Maire","first_name":"Pascal","full_name":"Maire, Pascal"},{"first_name":"Maud","last_name":"Wurmser","full_name":"Wurmser, Maud"},{"last_name":"Chagin","first_name":"Andrei S","full_name":"Chagin, Andrei S"},{"first_name":"Kaj","last_name":"Fried","full_name":"Fried, Kaj"},{"last_name":"Adameyko","first_name":"Igor","full_name":"Adameyko, Igor"}],"related_material":{"record":[{"id":"162","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-09T12:54:35Z","date_updated":"2023-09-18T09:29:07Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"lang":"eng","text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts."}]},{"publication_identifier":{"issn":["16625102"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.3389/fncel.2018.00311","project":[{"call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","grant_number":"720270","_id":"25CBA828-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000445090100002"]},"publist_id":"8013","ec_funded":1,"file_date_updated":"2020-07-14T12:46:23Z","article_number":"311","volume":12,"date_created":"2018-12-11T11:44:19Z","date_updated":"2023-09-18T09:31:18Z","author":[{"full_name":"Luján, Rafæl","last_name":"Luján","first_name":"Rafæl"},{"last_name":"Aguado","first_name":"Carolina","full_name":"Aguado, Carolina"},{"full_name":"Ciruela, Francisco","first_name":"Francisco","last_name":"Ciruela"},{"full_name":"Arus, Xavier","last_name":"Arus","first_name":"Xavier"},{"full_name":"Martín Belmonte, Alejandro","last_name":"Martín Belmonte","first_name":"Alejandro"},{"last_name":"Alfaro Ruiz","first_name":"Rocío","full_name":"Alfaro Ruiz, Rocío"},{"first_name":"Jesus","last_name":"Martinez Gomez","full_name":"Martinez Gomez, Jesus"},{"full_name":"De La Ossa, Luis","first_name":"Luis","last_name":"De La Ossa"},{"last_name":"Watanabe","first_name":"Masahiko","full_name":"Watanabe, Masahiko"},{"full_name":"Adelman, John","first_name":"John","last_name":"Adelman"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"}],"department":[{"_id":"RySh"}],"publisher":"Frontiers Media","publication_status":"published","year":"2018","has_accepted_license":"1","article_processing_charge":"No","day":"19","scopus_import":"1","date_published":"2018-09-19T00:00:00Z","article_type":"original","citation":{"short":"R. Luján, C. Aguado, F. Ciruela, X. Arus, A. Martín Belmonte, R. Alfaro Ruiz, J. Martinez Gomez, L. De La Ossa, M. Watanabe, J. Adelman, R. Shigemoto, Y. Fukazawa, Frontiers in Cellular Neuroscience 12 (2018).","mla":"Luján, Rafæl, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience, vol. 12, 311, Frontiers Media, 2018, doi:10.3389/fncel.2018.00311.","chicago":"Luján, Rafæl, Carolina Aguado, Francisco Ciruela, Xavier Arus, Alejandro Martín Belmonte, Rocío Alfaro Ruiz, Jesus Martinez Gomez, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience. Frontiers Media, 2018. https://doi.org/10.3389/fncel.2018.00311.","ama":"Luján R, Aguado C, Ciruela F, et al. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 2018;12. doi:10.3389/fncel.2018.00311","apa":"Luján, R., Aguado, C., Ciruela, F., Arus, X., Martín Belmonte, A., Alfaro Ruiz, R., … Fukazawa, Y. (2018). Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. Frontiers Media. https://doi.org/10.3389/fncel.2018.00311","ieee":"R. Luján et al., “Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells,” Frontiers in Cellular Neuroscience, vol. 12. Frontiers Media, 2018.","ista":"Luján R, Aguado C, Ciruela F, Arus X, Martín Belmonte A, Alfaro Ruiz R, Martinez Gomez J, De La Ossa L, Watanabe M, Adelman J, Shigemoto R, Fukazawa Y. 2018. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 12, 311."},"publication":"Frontiers in Cellular Neuroscience","abstract":[{"lang":"eng","text":"The small-conductance, Ca2+-activated K+ (SK) channel subtype SK2 regulates the spike rate and firing frequency, as well as Ca2+ transients in Purkinje cells (PCs). To understand the molecular basis by which SK2 channels mediate these functions, we analyzed the exact location and densities of SK2 channels along the neuronal surface of the mouse cerebellar PCs using SDS-digested freeze-fracture replica labeling (SDS-FRL) of high sensitivity combined with quantitative analyses. Immunogold particles for SK2 were observed on post- and pre-synaptic compartments showing both scattered and clustered distribution patterns. We found an axo-somato-dendritic gradient of the SK2 particle density increasing 12-fold from soma to dendritic spines. Using two different immunogold approaches, we also found that SK2 immunoparticles were frequently adjacent to, but never overlap with, the postsynaptic density of excitatory synapses in PC spines. Co-immunoprecipitation analysis demonstrated that SK2 channels form macromolecular complexes with two types of proteins that mobilize Ca2+: CaV2.1 channels and mGlu1α receptors in the cerebellum. Freeze-fracture replica double-labeling showed significant co-clustering of particles for SK2 with those for CaV2.1 channels and mGlu1α receptors. SK2 channels were also detected at presynaptic sites, mostly at the presynaptic active zone (AZ), where they are close to CaV2.1 channels, though they are not significantly co-clustered. These data demonstrate that SK2 channels located in different neuronal compartments can associate with distinct proteins mobilizing Ca2+, and suggest that the ultrastructural association of SK2 with CaV2.1 and mGlu1α provides the mechanism that ensures voltage (excitability) regulation by distinct intracellular Ca2+ transients in PCs."}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:46:23Z","date_created":"2018-12-17T08:49:03Z","checksum":"0bcaec8d596162af0b7fe3f31325d480","relation":"main_file","file_id":"5684","file_size":6834251,"content_type":"application/pdf","creator":"dernst","file_name":"fncel-12-00311.pdf","access_level":"open_access"}],"intvolume":" 12","status":"public","title":"Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"41"},{"month":"10","publication_identifier":{"issn":["15306984"]},"doi":"10.1021/acs.nanolett.8b03217","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000451102100064"],"pmid":["30359041"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","call_identifier":"FP7"}],"file_date_updated":"2020-07-14T12:45:37Z","ec_funded":1,"publist_id":"8032","author":[{"last_name":"Vukušić","first_name":"Lada","orcid":"0000-0003-2424-8636","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","full_name":"Vukušić, Lada"},{"full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","last_name":"Kukucka"},{"first_name":"Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes"},{"id":"4CDE0A96-F248-11E8-B48F-1D18A9856A87","last_name":"Milem","first_name":"Joshua M","full_name":"Milem, Joshua M"},{"full_name":"Schäffler, Friedrich","first_name":"Friedrich","last_name":"Schäffler"},{"last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios"}],"related_material":{"record":[{"relation":"popular_science","id":"7977"},{"id":"69","status":"public","relation":"dissertation_contains"},{"id":"7996","status":"public","relation":"dissertation_contains"}]},"date_updated":"2023-09-18T09:30:37Z","date_created":"2018-12-11T11:44:13Z","volume":18,"year":"2018","pmid":1,"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"GeKa"}],"day":"25","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-10-25T00:00:00Z","publication":"Nano Letters","citation":{"short":"L. Vukušić, J. Kukucka, H. Watzinger, J.M. Milem, F. Schäffler, G. Katsaros, Nano Letters 18 (2018) 7141–7145.","mla":"Vukušić, Lada, et al. “Single-Shot Readout of Hole Spins in Ge.” Nano Letters, vol. 18, no. 11, American Chemical Society, 2018, pp. 7141–45, doi:10.1021/acs.nanolett.8b03217.","chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, Joshua M Milem, Friedrich Schäffler, and Georgios Katsaros. “Single-Shot Readout of Hole Spins in Ge.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b03217.","ama":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. Single-shot readout of hole spins in Ge. Nano Letters. 2018;18(11):7141-7145. doi:10.1021/acs.nanolett.8b03217","ieee":"L. Vukušić, J. Kukucka, H. Watzinger, J. M. Milem, F. Schäffler, and G. Katsaros, “Single-shot readout of hole spins in Ge,” Nano Letters, vol. 18, no. 11. American Chemical Society, pp. 7141–7145, 2018.","apa":"Vukušić, L., Kukucka, J., Watzinger, H., Milem, J. M., Schäffler, F., & Katsaros, G. (2018). Single-shot readout of hole spins in Ge. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b03217","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."},"page":"7141 - 7145","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."}],"issue":"11","type":"journal_article","pubrep_id":"1065","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5194","checksum":"3e6034a94c6b5335e939145d88bdb371","date_created":"2018-12-12T10:16:08Z","date_updated":"2020-07-14T12:45:37Z","access_level":"open_access","file_name":"IST-2018-1065-v1+1_ACS_nanoletters_8b03217.pdf","content_type":"application/pdf","file_size":1361441,"creator":"system"}],"_id":"23","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["530"],"status":"public","title":"Single-shot readout of hole spins in Ge","intvolume":" 18"},{"publist_id":"7969","file_date_updated":"2020-07-14T12:48:14Z","volume":11014,"date_updated":"2023-09-18T09:32:36Z","date_created":"2018-12-11T11:44:33Z","author":[{"first_name":"Eran","last_name":"Gilad","full_name":"Gilad, Eran"},{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","first_name":"Trevor A","full_name":"Brown, Trevor A"},{"first_name":"Mark","last_name":"Oskin","full_name":"Oskin, Mark"},{"last_name":"Etsion","first_name":"Yoav","full_name":"Etsion, Yoav"}],"publisher":"Springer","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2018","acknowledgement":"Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14) and by a NSERC post-doctoral fellowship.","publication_identifier":{"issn":["03029743"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-96983-1_33","conference":{"location":"Turin, Italy","start_date":"2018-08-27","end_date":"2018-08-31","name":"Euro-Par: European Conference on Parallel Processing"},"project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000851042300031"]},"oa":1,"abstract":[{"lang":"eng","text":"Concurrent accesses to shared data structures must be synchronized to avoid data races. Coarse-grained synchronization, which locks the entire data structure, is easy to implement but does not scale. Fine-grained synchronization can scale well, but can be hard to reason about. Hand-over-hand locking, in which operations are pipelined as they traverse the data structure, combines fine-grained synchronization with ease of use. However, the traditional implementation suffers from inherent overheads. This paper introduces snapshot-based synchronization (SBS), a novel hand-over-hand locking mechanism. SBS decouples the synchronization state from the data, significantly improving cache utilization. Further, it relies on guarantees provided by pipelining to minimize synchronization that requires cross-thread communication. Snapshot-based synchronization thus scales much better than traditional hand-over-hand locking, while maintaining the same ease of use."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","file":[{"file_id":"5954","relation":"main_file","date_updated":"2020-07-14T12:48:14Z","date_created":"2019-02-12T07:40:40Z","checksum":"13a3f250be8878405e791b53c19722ad","file_name":"2018_Brown.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":665372}],"intvolume":" 11014","status":"public","ddc":["000"],"title":"Snapshot based synchronization: A fast replacement for Hand-over-Hand locking","_id":"85","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2018-08-01T00:00:00Z","page":"465 - 479","citation":{"ama":"Gilad E, Brown TA, Oskin M, Etsion Y. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. In: Vol 11014. Springer; 2018:465-479. doi:10.1007/978-3-319-96983-1_33","apa":"Gilad, E., Brown, T. A., Oskin, M., & Etsion, Y. (2018). Snapshot based synchronization: A fast replacement for Hand-over-Hand locking (Vol. 11014, pp. 465–479). Presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy: Springer. https://doi.org/10.1007/978-3-319-96983-1_33","ieee":"E. Gilad, T. A. Brown, M. Oskin, and Y. Etsion, “Snapshot based synchronization: A fast replacement for Hand-over-Hand locking,” presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy, 2018, vol. 11014, pp. 465–479.","ista":"Gilad E, Brown TA, Oskin M, Etsion Y. 2018. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11014, 465–479.","short":"E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479.","mla":"Gilad, Eran, et al. Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking. Vol. 11014, Springer, 2018, pp. 465–79, doi:10.1007/978-3-319-96983-1_33.","chicago":"Gilad, Eran, Trevor A Brown, Mark Oskin, and Yoav Etsion. “Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking,” 11014:465–79. Springer, 2018. https://doi.org/10.1007/978-3-319-96983-1_33."}},{"date_published":"2018-03-19T00:00:00Z","publication":"Physical Review B","citation":{"short":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, Z. Papić, Physical Review B 97 (2018).","mla":"Michailidis, Alexios, et al. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B, vol. 97, no. 10, 104307, American Physical Society, 2018, doi:10.1103/PhysRevB.97.104307.","chicago":"Michailidis, Alexios, Marko Žnidarič, Mariya Medvedyeva, Dmitry Abanin, Tomaž Prosen, and Zlatko Papić. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.97.104307.","ama":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 2018;97(10). doi:10.1103/PhysRevB.97.104307","ieee":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, and Z. Papić, “Slow dynamics in translation-invariant quantum lattice models,” Physical Review B, vol. 97, no. 10. American Physical Society, 2018.","apa":"Michailidis, A., Žnidarič, M., Medvedyeva, M., Abanin, D., Prosen, T., & Papić, Z. (2018). Slow dynamics in translation-invariant quantum lattice models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.97.104307","ista":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. 2018. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 97(10), 104307."},"day":"19","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Slow dynamics in translation-invariant quantum lattice models","status":"public","intvolume":" 97","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"327","abstract":[{"lang":"eng","text":"Many-body quantum systems typically display fast dynamics and ballistic spreading of information. Here we address the open problem of how slow the dynamics can be after a generic breaking of integrability by local interactions. We develop a method based on degenerate perturbation theory that reveals slow dynamical regimes and delocalization processes in general translation invariant models, along with accurate estimates of their delocalization time scales. Our results shed light on the fundamental questions of the robustness of quantum integrable systems and the possibility of many-body localization without disorder. As an example, we construct a large class of one-dimensional lattice models where, despite the absence of asymptotic localization, the transient dynamics is exceptionally slow, i.e., the dynamics is indistinguishable from that of many-body localized systems for the system sizes and time scales accessible in experiments and numerical simulations."}],"issue":"10","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.97.104307","isi":1,"quality_controlled":"1","external_id":{"isi":["000427798800005"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.05026"}],"oa":1,"month":"03","date_created":"2018-12-11T11:45:50Z","date_updated":"2023-09-18T09:31:46Z","volume":97,"author":[{"last_name":"Michailidis","first_name":"Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios"},{"full_name":"Žnidarič, Marko","first_name":"Marko","last_name":"Žnidarič"},{"last_name":"Medvedyeva","first_name":"Mariya","full_name":"Medvedyeva, Mariya"},{"last_name":"Abanin","first_name":"Dmitry","full_name":"Abanin, Dmitry"},{"first_name":"Tomaž","last_name":"Prosen","full_name":"Prosen, Tomaž"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"}],"publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","acknowledgement":"We thank F. Huveneers for useful discussions. Z.P. and A.M. acknowledge support by EPSRC Grant No. EP/P009409/1 and and the Royal Society Research Grant No. RG160635. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. D.A. acknowledges support by the Swiss National Science Foundation. M.Z., M.M. and T.P. acknowledge Grants J1-7279 (M.Z.) and N1-0025 (M.M. and T.P.) of Slovenian Research Agency, and Advanced Grant of European Research Council, Grant No. 694544 - OMNES (T.P.).","year":"2018","publist_id":"7538","article_number":"104307"},{"type":"journal_article","abstract":[{"text":"Social insects have evolved enormous capacities to collectively build nests and defend their colonies against both predators and pathogens. The latter is achieved by a combination of individual immune responses and sophisticated collective behavioral and organizational disease defenses, that is, social immunity. We investigated how the presence or absence of these social defense lines affects individual-level immunity in ant queens after bacterial infection. To this end, we injected queens of the ant Linepithema humile with a mix of gram+ and gram− bacteria or a control solution, reared them either with workers or alone and analyzed their gene expression patterns at 2, 4, 8, and 12 hr post-injection, using RNA-seq. This allowed us to test for the effect of bacterial infection, social context, as well as the interaction between the two over the course of infection and raising of an immune response. We found that social isolation per se affected queen gene expression for metabolism genes, but not for immune genes. When infected, queens reared with and without workers up-regulated similar numbers of innate immune genes revealing activation of Toll and Imd signaling pathways and melanization. Interestingly, however, they mostly regulated different genes along the pathways and showed a different pattern of overall gene up-regulation or down-regulation. Hence, we can conclude that the absence of workers does not compromise the onset of an individual immune response by the queens, but that the social environment impacts the route of the individual innate immune responses.","lang":"eng"}],"issue":"22","_id":"29","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Social environment affects the transcriptomic response to bacteria in ant queens","ddc":["576","591"],"status":"public","intvolume":" 8","file":[{"checksum":"0d1355c78627ca7210aadd9a17a01915","date_updated":"2020-07-14T12:45:52Z","date_created":"2018-12-17T08:27:04Z","file_id":"5682","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1272096,"access_level":"open_access","file_name":"Viljakainen_et_al-2018-Ecology_and_Evolution.pdf"}],"oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"Ecology and Evolution","citation":{"chicago":"Viljakainen, Lumi, Jaana Jurvansuu, Ida Holmberg, Tobias Pamminger, Silvio Erler, and Sylvia Cremer. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” Ecology and Evolution. Wiley, 2018. https://doi.org/10.1002/ece3.4573.","mla":"Viljakainen, Lumi, et al. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” Ecology and Evolution, vol. 8, no. 22, Wiley, 2018, pp. 11031–70, doi:10.1002/ece3.4573.","short":"L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, S. Cremer, Ecology and Evolution 8 (2018) 11031–11070.","ista":"Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. 2018. Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. 8(22), 11031–11070.","apa":"Viljakainen, L., Jurvansuu, J., Holmberg, I., Pamminger, T., Erler, S., & Cremer, S. (2018). Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.4573","ieee":"L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, and S. Cremer, “Social environment affects the transcriptomic response to bacteria in ant queens,” Ecology and Evolution, vol. 8, no. 22. Wiley, pp. 11031–11070, 2018.","ama":"Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. 2018;8(22):11031-11070. doi:10.1002/ece3.4573"},"page":"11031-11070","date_published":"2018-11-01T00:00:00Z","file_date_updated":"2020-07-14T12:45:52Z","publist_id":"8026","year":"2018","publication_status":"published","publisher":"Wiley","department":[{"_id":"SyCr"}],"author":[{"full_name":"Viljakainen, Lumi","first_name":"Lumi","last_name":"Viljakainen"},{"full_name":"Jurvansuu, Jaana","last_name":"Jurvansuu","first_name":"Jaana"},{"full_name":"Holmberg, Ida","last_name":"Holmberg","first_name":"Ida"},{"first_name":"Tobias","last_name":"Pamminger","full_name":"Pamminger, Tobias"},{"full_name":"Erler, Silvio","first_name":"Silvio","last_name":"Erler"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"}],"date_created":"2018-12-11T11:44:15Z","date_updated":"2023-09-19T09:29:12Z","volume":8,"month":"11","publication_identifier":{"issn":["20457758"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000451611000032"]},"quality_controlled":"1","isi":1,"doi":"10.1002/ece3.4573","language":[{"iso":"eng"}]},{"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","year":"2018","date_created":"2018-12-11T11:44:50Z","date_updated":"2023-09-19T09:30:43Z","volume":10981,"author":[{"full_name":"Frehse, Goran","first_name":"Goran","last_name":"Frehse"},{"full_name":"Giacobbe, Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904","first_name":"Mirco","last_name":"Giacobbe"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6894"}]},"file_date_updated":"2020-07-14T12:44:50Z","publist_id":"7783","quality_controlled":"1","isi":1,"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000491481600025"]},"language":[{"iso":"eng"}],"conference":{"location":"Oxford, United Kingdom","start_date":"2018-07-14","end_date":"2018-07-17","name":"CAV: Computer Aided Verification"},"doi":"10.1007/978-3-319-96145-3_25","month":"07","publication_identifier":{"issn":["03029743"]},"title":"Space-time interpolants","status":"public","ddc":["005"],"intvolume":" 10981","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"140","file":[{"date_updated":"2020-07-14T12:44:50Z","date_created":"2018-12-12T10:17:53Z","checksum":"6dca832f575d6b3f0ea9dff56f579142","file_id":"5310","relation":"main_file","creator":"system","file_size":563710,"content_type":"application/pdf","file_name":"IST-2018-1010-v1+1_space-time_interpolants.pdf","access_level":"open_access"}],"oa_version":"Published Version","pubrep_id":"1010","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Reachability analysis is difficult for hybrid automata with affine differential equations, because the reach set needs to be approximated. Promising abstraction techniques usually employ interval methods or template polyhedra. Interval methods account for dense time and guarantee soundness, and there are interval-based tools that overapproximate affine flowpipes. But interval methods impose bounded and rigid shapes, which make refinement expensive and fixpoint detection difficult. Template polyhedra, on the other hand, can be adapted flexibly and can be unbounded, but sound template refinement for unbounded reachability analysis has been implemented only for systems with piecewise constant dynamics. We capitalize on the advantages of both techniques, combining interval arithmetic and template polyhedra, using the former to abstract time and the latter to abstract space. During a CEGAR loop, whenever a spurious error trajectory is found, we compute additional space constraints and split time intervals, and use these space-time interpolants to eliminate the counterexample. Space-time interpolation offers a lazy, flexible framework for increasing precision while guaranteeing soundness, both for error avoidance and fixpoint detection. To the best of out knowledge, this is the first abstraction refinement scheme for the reachability analysis over unbounded and dense time of affine hybrid systems, which is both sound and automatic. We demonstrate the effectiveness of our algorithm with several benchmark examples, which cannot be handled by other tools."}],"page":"468 - 486","citation":{"ista":"Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer Aided Verification, LNCS, vol. 10981, 468–486.","apa":"Frehse, G., Giacobbe, M., & Henzinger, T. A. (2018). Space-time interpolants (Vol. 10981, pp. 468–486). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_25","ieee":"G. Frehse, M. Giacobbe, and T. A. Henzinger, “Space-time interpolants,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 468–486.","ama":"Frehse G, Giacobbe M, Henzinger TA. Space-time interpolants. In: Vol 10981. Springer; 2018:468-486. doi:10.1007/978-3-319-96145-3_25","chicago":"Frehse, Goran, Mirco Giacobbe, and Thomas A Henzinger. “Space-Time Interpolants,” 10981:468–86. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_25.","mla":"Frehse, Goran, et al. Space-Time Interpolants. Vol. 10981, Springer, 2018, pp. 468–86, doi:10.1007/978-3-319-96145-3_25.","short":"G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486."},"date_published":"2018-07-18T00:00:00Z","scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No"},{"abstract":[{"lang":"eng","text":"We give a lower bound on the ground state energy of a system of two fermions of one species interacting with two fermions of another species via point interactions. We show that there is a critical mass ratio m2 ≈ 0.58 such that the system is stable, i.e., the energy is bounded from below, for m∈[m2,m2−1]. So far it was not known whether this 2 + 2 system exhibits a stable region at all or whether the formation of four-body bound states causes an unbounded spectrum for all mass ratios, similar to the Thomas effect. Our result gives further evidence for the stability of the more general N + M system."}],"issue":"3","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"5729","relation":"main_file","date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-17T16:49:02Z","checksum":"411c4db5700d7297c9cd8ebc5dd29091","file_name":"2018_MathPhysics_Moser.pdf","access_level":"open_access","creator":"dernst","file_size":496973,"content_type":"application/pdf"}],"_id":"154","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Stability of the 2+2 fermionic system with point interactions","ddc":["530"],"intvolume":" 21","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-09-01T00:00:00Z","publication":"Mathematical Physics Analysis and Geometry","citation":{"ista":"Moser T, Seiringer R. 2018. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 21(3), 19.","ieee":"T. Moser and R. Seiringer, “Stability of the 2+2 fermionic system with point interactions,” Mathematical Physics Analysis and Geometry, vol. 21, no. 3. Springer, 2018.","apa":"Moser, T., & Seiringer, R. (2018). Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-018-9275-3","ama":"Moser T, Seiringer R. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 2018;21(3). doi:10.1007/s11040-018-9275-3","chicago":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” Mathematical Physics Analysis and Geometry. Springer, 2018. https://doi.org/10.1007/s11040-018-9275-3.","mla":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” Mathematical Physics Analysis and Geometry, vol. 21, no. 3, 19, Springer, 2018, doi:10.1007/s11040-018-9275-3.","short":"T. Moser, R. Seiringer, Mathematical Physics Analysis and Geometry 21 (2018)."},"article_type":"original","file_date_updated":"2020-07-14T12:45:01Z","ec_funded":1,"publist_id":"7767","article_number":"19","author":[{"full_name":"Moser, Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Moser"},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"related_material":{"record":[{"id":"52","status":"public","relation":"dissertation_contains"}]},"date_updated":"2023-09-19T09:31:15Z","date_created":"2018-12-11T11:44:55Z","volume":21,"acknowledgement":"Open access funding provided by Austrian Science Fund (FWF).","year":"2018","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer","month":"09","publication_identifier":{"issn":["13850172"],"eissn":["15729656"]},"doi":"10.1007/s11040-018-9275-3","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000439639700001"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}]},{"day":"09","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-12-09T00:00:00Z","page":"512-521","publication":"Development Growth and Differentiation","citation":{"chicago":"Hannezo, Edouard B, and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation. Wiley, 2018. https://doi.org/10.1111/dgd.12570.","mla":"Hannezo, Edouard B., and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation, vol. 60, no. 9, Wiley, 2018, pp. 512–21, doi:10.1111/dgd.12570.","short":"E.B. Hannezo, B.D. Simons, Development Growth and Differentiation 60 (2018) 512–521.","ista":"Hannezo EB, Simons BD. 2018. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 60(9), 512–521.","apa":"Hannezo, E. B., & Simons, B. D. (2018). Statistical theory of branching morphogenesis. Development Growth and Differentiation. Wiley. https://doi.org/10.1111/dgd.12570","ieee":"E. B. Hannezo and B. D. Simons, “Statistical theory of branching morphogenesis,” Development Growth and Differentiation, vol. 60, no. 9. Wiley, pp. 512–521, 2018.","ama":"Hannezo EB, Simons BD. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 2018;60(9):512-521. doi:10.1111/dgd.12570"},"abstract":[{"lang":"eng","text":"Branching morphogenesis remains a subject of abiding interest. Although much is \r\nknown about the gene regulatory programs and signaling pathways that operate at \r\nthe cellular scale, it has remained unclear how the macroscopic features of branched \r\norgans, including their size, network topology and spatial patterning, are encoded. \r\nLately, it has been proposed that, these features can be explained quantitatively in \r\nseveral organs within a single unifying framework. Based on large-\r\nscale organ recon\r\n-\r\nstructions and cell lineage tracing, it has been argued that morphogenesis follows \r\nfrom the collective dynamics of sublineage- \r\nrestricted self- \r\nrenewing progenitor cells, \r\nlocalized at ductal tips, that act cooperatively to drive a serial process of ductal elon\r\n-\r\ngation and stochastic tip bifurcation. By correlating differentiation or cell cycle exit \r\nwith proximity to maturing ducts, this dynamic results in the specification of a com-\r\nplex network of defined density and statistical organization. These results suggest \r\nthat, for several mammalian tissues, branched epithelial structures develop as a self- \r\norganized process, reliant upon a strikingly simple, but generic, set of local rules, \r\nwithout recourse to a rigid and deterministic sequence of genetically programmed \r\nevents. Here, we review the basis of these findings and discuss their implications."}],"issue":"9","type":"journal_article","oa_version":"Published Version","file":[{"checksum":"a6d30b0785db902c734a84fecb2eadd9","date_updated":"2020-07-14T12:47:11Z","date_created":"2019-02-06T10:40:46Z","relation":"main_file","file_id":"5933","file_size":1313606,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_DevGrowh_Hannezo.pdf"}],"ddc":["570"],"title":"Statistical theory of branching morphogenesis","status":"public","intvolume":" 60","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5787","month":"12","publication_identifier":{"issn":["00121592"]},"language":[{"iso":"eng"}],"doi":"10.1111/dgd.12570","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000453555100002"]},"oa":1,"file_date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-30T22:59:14Z","date_updated":"2023-09-19T09:32:49Z","volume":60,"author":[{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"first_name":"Benjamin D.","last_name":"Simons","full_name":"Simons, Benjamin D."}],"publisher":"Wiley","department":[{"_id":"EdHa"}],"year":"2018"},{"doi":"10.1007/978-3-319-89960-2_21","conference":{"name":"TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems","location":"Thessaloniki, Greece","start_date":"2018-04-14","end_date":"2018-04-20"},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000546326300021"]},"project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"month":"04","author":[{"last_name":"Brázdil","first_name":"Tomáš","full_name":"Brázdil, Tomáš"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","first_name":"Jan","full_name":"Kretinsky, Jan"},{"orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","last_name":"Toman","first_name":"Viktor","full_name":"Toman, Viktor"}],"volume":10805,"date_updated":"2023-09-19T09:57:08Z","date_created":"2018-12-11T11:45:41Z","year":"2018","publisher":"Springer","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","ec_funded":1,"publist_id":"7584","file_date_updated":"2020-07-14T12:45:57Z","date_published":"2018-04-12T00:00:00Z","citation":{"apa":"Brázdil, T., Chatterjee, K., Kretinsky, J., & Toman, V. (2018). Strategy representation by decision trees in reactive synthesis (Vol. 10805, pp. 385–407). Presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89960-2_21","ieee":"T. Brázdil, K. Chatterjee, J. Kretinsky, and V. Toman, “Strategy representation by decision trees in reactive synthesis,” presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece, 2018, vol. 10805, pp. 385–407.","ista":"Brázdil T, Chatterjee K, Kretinsky J, Toman V. 2018. Strategy representation by decision trees in reactive synthesis. TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10805, 385–407.","ama":"Brázdil T, Chatterjee K, Kretinsky J, Toman V. Strategy representation by decision trees in reactive synthesis. In: Vol 10805. Springer; 2018:385-407. doi:10.1007/978-3-319-89960-2_21","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Jan Kretinsky, and Viktor Toman. “Strategy Representation by Decision Trees in Reactive Synthesis,” 10805:385–407. Springer, 2018. https://doi.org/10.1007/978-3-319-89960-2_21.","short":"T. Brázdil, K. Chatterjee, J. Kretinsky, V. Toman, in:, Springer, 2018, pp. 385–407.","mla":"Brázdil, Tomáš, et al. Strategy Representation by Decision Trees in Reactive Synthesis. Vol. 10805, Springer, 2018, pp. 385–407, doi:10.1007/978-3-319-89960-2_21."},"page":"385 - 407","has_accepted_license":"1","article_processing_charge":"No","day":"12","scopus_import":"1","file":[{"file_id":"5723","relation":"main_file","date_created":"2018-12-17T16:29:08Z","date_updated":"2020-07-14T12:45:57Z","checksum":"b13874ffb114932ad9cc2586b7469db4","file_name":"2018_LNCS_Brazdil.pdf","access_level":"open_access","creator":"dernst","file_size":1829940,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"297","intvolume":" 10805","title":"Strategy representation by decision trees in reactive synthesis","status":"public","ddc":["000"],"abstract":[{"lang":"eng","text":"Graph games played by two players over finite-state graphs are central in many problems in computer science. In particular, graph games with ω -regular winning conditions, specified as parity objectives, which can express properties such as safety, liveness, fairness, are the basic framework for verification and synthesis of reactive systems. The decisions for a player at various states of the graph game are represented as strategies. While the algorithmic problem for solving graph games with parity objectives has been widely studied, the most prominent data-structure for strategy representation in graph games has been binary decision diagrams (BDDs). However, due to the bit-level representation, BDDs do not retain the inherent flavor of the decisions of strategies, and are notoriously hard to minimize to obtain succinct representation. In this work we propose decision trees for strategy representation in graph games. Decision trees retain the flavor of decisions of strategies and allow entropy-based minimization to obtain succinct trees. However, decision trees work in settings (e.g., probabilistic models) where errors are allowed, and overfitting of data is typically avoided. In contrast, for strategies in graph games no error is allowed, and the decision tree must represent the entire strategy. We develop new techniques to extend decision trees to overcome the above obstacles, while retaining the entropy-based techniques to obtain succinct trees. We have implemented our techniques to extend the existing decision tree solvers. We present experimental results for problems in reactive synthesis to show that decision trees provide a much more efficient data-structure for strategy representation as compared to BDDs."}],"type":"conference","alternative_title":["LNCS"]},{"abstract":[{"text":"Given a model and a specification, the fundamental model-checking problem asks for algorithmic verification of whether the model satisfies the specification. We consider graphs and Markov decision processes (MDPs), which are fundamental models for reactive systems. One of the very basic specifications that arise in verification of reactive systems is the strong fairness (aka Streett) objective. Given different types of requests and corresponding grants, the objective requires that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All ω -regular objectives can be expressed as Streett objectives and hence they are canonical in verification. To handle the state-space explosion, symbolic algorithms are required that operate on a succinct implicit representation of the system rather than explicitly accessing the system. While explicit algorithms for graphs and MDPs with Streett objectives have been widely studied, there has been no improvement of the basic symbolic algorithms. The worst-case numbers of symbolic steps required for the basic symbolic algorithms are as follows: quadratic for graphs and cubic for MDPs. In this work we present the first sub-quadratic symbolic algorithm for graphs with Streett objectives, and our algorithm is sub-quadratic even for MDPs. Based on our algorithmic insights we present an implementation of the new symbolic approach and show that it improves the existing approach on several academic benchmark examples.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5737","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-18T08:52:38Z","checksum":"1a6ffa4febe8bb8ac28be3adb3eafebc","file_name":"2018_LNCS_Chatterjee.pdf","access_level":"open_access","file_size":675606,"content_type":"application/pdf","creator":"dernst"}],"intvolume":" 10982","status":"public","title":"Symbolic algorithms for graphs and Markov decision processes with fairness objectives","ddc":["000"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"141","has_accepted_license":"1","article_processing_charge":"No","day":"18","scopus_import":"1","date_published":"2018-07-18T00:00:00Z","page":"178-197","citation":{"ama":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. In: Vol 10982. Springer; 2018:178-197. doi:10.1007/978-3-319-96142-2_13","ieee":"K. Chatterjee, M. H. Henzinger, V. Loitzenbauer, S. Oraee, and V. Toman, “Symbolic algorithms for graphs and Markov decision processes with fairness objectives,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10982, pp. 178–197.","apa":"Chatterjee, K., Henzinger, M. H., Loitzenbauer, V., Oraee, S., & Toman, V. (2018). Symbolic algorithms for graphs and Markov decision processes with fairness objectives (Vol. 10982, pp. 178–197). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96142-2_13","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. 2018. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. CAV: Computer Aided Verification, LNCS, vol. 10982, 178–197.","short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:, Springer, 2018, pp. 178–197.","mla":"Chatterjee, Krishnendu, et al. Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives. Vol. 10982, Springer, 2018, pp. 178–97, doi:10.1007/978-3-319-96142-2_13.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Veronika Loitzenbauer, Simin Oraee, and Viktor Toman. “Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives,” 10982:178–97. Springer, 2018. https://doi.org/10.1007/978-3-319-96142-2_13."},"publist_id":"7782","ec_funded":1,"file_date_updated":"2020-07-14T12:44:53Z","volume":10982,"date_created":"2018-12-11T11:44:51Z","date_updated":"2023-09-19T09:59:55Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10199"}]},"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer","first_name":"Veronika"},{"first_name":"Simin","last_name":"Oraee","full_name":"Oraee, Simin"},{"full_name":"Toman, Viktor","orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","last_name":"Toman","first_name":"Viktor"}],"publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"Acknowledgements. K. C. and M. H. are partially supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF): S11407-N23 (RiSE/SHiNE), and an ERC Start Grant (279307: Graph Games). V. T. is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie Grant Agreement No. 665385.","year":"2018","month":"07","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-96142-2_13","conference":{"name":"CAV: Computer Aided Verification","end_date":"2018-07-17","start_date":"2018-07-14","location":"Oxford, United Kingdom"},"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000491469700013"]},"oa":1},{"oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"298","title":"Sustained space complexity","status":"public","intvolume":" 10821","abstract":[{"text":"Memory-hard functions (MHF) are functions whose evaluation cost is dominated by memory cost. MHFs are egalitarian, in the sense that evaluating them on dedicated hardware (like FPGAs or ASICs) is not much cheaper than on off-the-shelf hardware (like x86 CPUs). MHFs have interesting cryptographic applications, most notably to password hashing and securing blockchains.\r\n\r\nAlwen and Serbinenko [STOC’15] define the cumulative memory complexity (cmc) of a function as the sum (over all time-steps) of the amount of memory required to compute the function. They advocate that a good MHF must have high cmc. Unlike previous notions, cmc takes into account that dedicated hardware might exploit amortization and parallelism. Still, cmc has been critizised as insufficient, as it fails to capture possible time-memory trade-offs; as memory cost doesn’t scale linearly, functions with the same cmc could still have very different actual hardware cost.\r\n\r\nIn this work we address this problem, and introduce the notion of sustained-memory complexity, which requires that any algorithm evaluating the function must use a large amount of memory for many steps. We construct functions (in the parallel random oracle model) whose sustained-memory complexity is almost optimal: our function can be evaluated using n steps and O(n/log(n)) memory, in each step making one query to the (fixed-input length) random oracle, while any algorithm that can make arbitrary many parallel queries to the random oracle, still needs Ω(n/log(n)) memory for Ω(n) steps.\r\n\r\nAs has been done for various notions (including cmc) before, we reduce the task of constructing an MHFs with high sustained-memory complexity to proving pebbling lower bounds on DAGs. Our main technical contribution is the construction is a family of DAGs on n nodes with constant indegree with high “sustained-space complexity”, meaning that any parallel black-pebbling strategy requires Ω(n/log(n)) pebbles for at least Ω(n) steps.\r\n\r\nAlong the way we construct a family of maximally “depth-robust” DAGs with maximum indegree O(logn) , improving upon the construction of Mahmoody et al. [ITCS’13] which had maximum indegree O(log2n⋅","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2018-03-31T00:00:00Z","citation":{"short":"J.F. Alwen, J. Blocki, K.Z. Pietrzak, in:, Springer, 2018, pp. 99–130.","mla":"Alwen, Joel F., et al. Sustained Space Complexity. Vol. 10821, Springer, 2018, pp. 99–130, doi:10.1007/978-3-319-78375-8_4.","chicago":"Alwen, Joel F, Jeremiah Blocki, and Krzysztof Z Pietrzak. “Sustained Space Complexity,” 10821:99–130. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_4.","ama":"Alwen JF, Blocki J, Pietrzak KZ. Sustained space complexity. In: Vol 10821. Springer; 2018:99-130. doi:10.1007/978-3-319-78375-8_4","ieee":"J. F. Alwen, J. Blocki, and K. Z. Pietrzak, “Sustained space complexity,” presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821, pp. 99–130.","apa":"Alwen, J. F., Blocki, J., & Pietrzak, K. Z. (2018). Sustained space complexity (Vol. 10821, pp. 99–130). Presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_4","ista":"Alwen JF, Blocki J, Pietrzak KZ. 2018. Sustained space complexity. Eurocrypt 2018: Advances in Cryptology, LNCS, vol. 10821, 99–130."},"page":"99 - 130","day":"31","article_processing_charge":"No","scopus_import":"1","author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","first_name":"Joel F","full_name":"Alwen, Joel F"},{"full_name":"Blocki, Jeremiah","first_name":"Jeremiah","last_name":"Blocki"},{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"}],"date_created":"2018-12-11T11:45:41Z","date_updated":"2023-09-19T09:59:30Z","volume":10821,"year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"KrPi"}],"ec_funded":1,"publist_id":"7583","conference":{"name":"Eurocrypt 2018: Advances in Cryptology","end_date":"2018-05-03","location":"Tel Aviv, Israel","start_date":"2018-04-29"},"doi":"10.1007/978-3-319-78375-8_4","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000517098700004"],"arxiv":["1705.05313"]},"main_file_link":[{"url":"https://arxiv.org/abs/1705.05313","open_access":"1"}],"isi":1,"quality_controlled":"1","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"month":"03"},{"status":"public","title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms","ddc":["581"],"intvolume":" 69","_id":"36","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"relation":"main_file","file_id":"5741","checksum":"34cb0a1611588b75bd6f4913fb4e30f1","date_created":"2018-12-18T09:47:51Z","date_updated":"2020-07-14T12:46:13Z","access_level":"open_access","file_name":"2018_JournalExperimBotany_Vu.pdf","content_type":"application/pdf","file_size":3359316,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity.","lang":"eng"}],"issue":"19","page":"4609 - 4624","publication":"Journal of Experimental Botany","citation":{"short":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624.","mla":"Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:10.1093/jxb/ery204.","chicago":"Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert, and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery204.","ama":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 2018;69(19):4609-4624. doi:10.1093/jxb/ery204","ieee":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet, “Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms,” Journal of Experimental Botany, vol. 69, no. 19. Oxford University Press, pp. 4609–4624, 2018.","apa":"Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., & De Smet, I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery204","ista":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624."},"date_published":"2018-08-31T00:00:00Z","scopus_import":"1","day":"31","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","year":"2018","date_updated":"2023-09-19T10:00:46Z","date_created":"2018-12-11T11:44:17Z","volume":69,"author":[{"first_name":"Lam","last_name":"Vu","full_name":"Vu, Lam"},{"full_name":"Zhu, Tingting","last_name":"Zhu","first_name":"Tingting"},{"full_name":"Verstraeten, Inge","last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van De Cotte, Brigitte","last_name":"Van De Cotte","first_name":"Brigitte"},{"full_name":"Gevaert, Kris","last_name":"Gevaert","first_name":"Kris"},{"first_name":"Ive","last_name":"De Smet","full_name":"De Smet, Ive"}],"file_date_updated":"2020-07-14T12:46:13Z","publist_id":"8019","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000443568700010"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/jxb/ery204","month":"08"},{"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1111/ejn.13901","quality_controlled":"1","isi":1,"external_id":{"isi":["000431496400001"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"month":"03","volume":47,"date_created":"2018-12-11T11:45:50Z","date_updated":"2023-09-19T09:58:40Z","author":[{"full_name":"Sawada, Kazuaki","first_name":"Kazuaki","last_name":"Sawada"},{"first_name":"Ryosuke","last_name":"Kawakami","full_name":"Kawakami, Ryosuke"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"full_name":"Nemoto, Tomomi","first_name":"Tomomi","last_name":"Nemoto"}],"publisher":"Wiley","department":[{"_id":"RySh"}],"publication_status":"published","year":"2018","publist_id":"7539","file_date_updated":"2020-07-14T12:46:06Z","date_published":"2018-03-07T00:00:00Z","page":"1033 - 1042","citation":{"ama":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 2018;47(9):1033-1042. doi:10.1111/ejn.13901","ista":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. 2018. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 47(9), 1033–1042.","apa":"Sawada, K., Kawakami, R., Shigemoto, R., & Nemoto, T. (2018). Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. Wiley. https://doi.org/10.1111/ejn.13901","ieee":"K. Sawada, R. Kawakami, R. Shigemoto, and T. Nemoto, “Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices,” European Journal of Neuroscience, vol. 47, no. 9. Wiley, pp. 1033–1042, 2018.","mla":"Sawada, Kazuaki, et al. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience, vol. 47, no. 9, Wiley, 2018, pp. 1033–42, doi:10.1111/ejn.13901.","short":"K. Sawada, R. Kawakami, R. Shigemoto, T. Nemoto, European Journal of Neuroscience 47 (2018) 1033–1042.","chicago":"Sawada, Kazuaki, Ryosuke Kawakami, Ryuichi Shigemoto, and Tomomi Nemoto. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience. Wiley, 2018. https://doi.org/10.1111/ejn.13901."},"publication":"European Journal of Neuroscience","article_processing_charge":"No","has_accepted_license":"1","day":"07","scopus_import":"1","oa_version":"Published Version","file":[{"checksum":"98e901d8229e44aa8f3b51d248dedd09","date_created":"2018-12-17T16:16:50Z","date_updated":"2020-07-14T12:46:06Z","relation":"main_file","file_id":"5721","file_size":4850261,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_EJN_Sawada.pdf"}],"intvolume":" 47","ddc":["570"],"status":"public","title":"Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices","_id":"326","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"9","abstract":[{"lang":"eng","text":"Three-dimensional (3D) super-resolution microscopy technique structured illumination microscopy (SIM) imaging of dendritic spines along the dendrite has not been previously performed in fixed tissues, mainly due to deterioration of the stripe pattern of the excitation laser induced by light scattering and optical aberrations. To address this issue and solve these optical problems, we applied a novel clearing reagent, LUCID, to fixed brains. In SIM imaging, the penetration depth and the spatial resolution were improved in LUCID-treated slices, and 160-nm spatial resolution was obtained in a large portion of the imaging volume on a single apical dendrite. Furthermore, in a morphological analysis of spine heads of layer V pyramidal neurons (L5PNs) in the medial prefrontal cortex (mPFC) of chronic dexamethasone (Dex)-treated mice, SIM imaging revealed an altered distribution of spine forms that could not be detected by high-NA confocal imaging. Thus, super-resolution SIM imaging represents a promising high-throughput method for revealing spine morphologies in single dendrites."}],"type":"journal_article"},{"issue":"50","abstract":[{"text":"Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 115","title":"Structure and architecture of immature and mature murine leukemia virus capsids","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5770","article_processing_charge":"No","day":"11","scopus_import":"1","date_published":"2018-12-11T00:00:00Z","page":"E11751-E11760","citation":{"ieee":"K. Qu et al., “Structure and architecture of immature and mature murine leukemia virus capsids,” Proceedings of the National Academy of Sciences, vol. 115, no. 50. Proceedings of the National Academy of Sciences, pp. E11751–E11760, 2018.","apa":"Qu, K., Glass, B., Doležal, M., Schur, F. K., Murciano, B., Rein, A., … Briggs, J. A. G. (2018). Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1811580115","ista":"Qu K, Glass B, Doležal M, Schur FK, Murciano B, Rein A, Rumlová M, Ruml T, Kräusslich H-G, Briggs JAG. 2018. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 115(50), E11751–E11760.","ama":"Qu K, Glass B, Doležal M, et al. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 2018;115(50):E11751-E11760. doi:10.1073/pnas.1811580115","chicago":"Qu, Kun, Bärbel Glass, Michal Doležal, Florian KM Schur, Brice Murciano, Alan Rein, Michaela Rumlová, Tomáš Ruml, Hans-Georg Kräusslich, and John A. G. Briggs. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1811580115.","short":"K. Qu, B. Glass, M. Doležal, F.K. Schur, B. Murciano, A. Rein, M. Rumlová, T. Ruml, H.-G. Kräusslich, J.A.G. Briggs, Proceedings of the National Academy of Sciences 115 (2018) E11751–E11760.","mla":"Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences, vol. 115, no. 50, Proceedings of the National Academy of Sciences, 2018, pp. E11751–60, doi:10.1073/pnas.1811580115."},"publication":"Proceedings of the National Academy of Sciences","volume":115,"date_updated":"2023-09-19T09:57:45Z","date_created":"2018-12-20T21:09:37Z","author":[{"full_name":"Qu, Kun","first_name":"Kun","last_name":"Qu"},{"last_name":"Glass","first_name":"Bärbel","full_name":"Glass, Bärbel"},{"full_name":"Doležal, Michal","first_name":"Michal","last_name":"Doležal"},{"full_name":"Schur, Florian","last_name":"Schur","first_name":"Florian","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Murciano, Brice","first_name":"Brice","last_name":"Murciano"},{"full_name":"Rein, Alan","first_name":"Alan","last_name":"Rein"},{"full_name":"Rumlová, Michaela","last_name":"Rumlová","first_name":"Michaela"},{"last_name":"Ruml","first_name":"Tomáš","full_name":"Ruml, Tomáš"},{"full_name":"Kräusslich, Hans-Georg","first_name":"Hans-Georg","last_name":"Kräusslich"},{"full_name":"Briggs, John A. G.","last_name":"Briggs","first_name":"John A. G."}],"publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"FlSc"}],"publication_status":"published","pmid":1,"year":"2018","publication_identifier":{"issn":["00278424"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1811580115","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30478053","open_access":"1"}],"external_id":{"isi":["000452866000022"],"pmid":["30478053"]}},{"publist_id":"7197","ec_funded":1,"author":[{"full_name":"Avni, Guy","last_name":"Avni","first_name":"Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"volume":712,"date_updated":"2023-09-19T10:00:21Z","date_created":"2018-12-11T11:47:28Z","year":"2018","publisher":"Elsevier","department":[{"_id":"ToHe"}],"publication_status":"published","month":"02","doi":"10.1016/j.tcs.2017.11.001","language":[{"iso":"eng"}],"external_id":{"isi":["000424959200003"]},"main_file_link":[{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.4529","open_access":"1"}],"oa":1,"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"quality_controlled":"1","isi":1,"abstract":[{"text":"Synthesis is the automated construction of a system from its specification. In real life, hardware and software systems are rarely constructed from scratch. Rather, a system is typically constructed from a library of components. Lustig and Vardi formalized this intuition and studied LTL synthesis from component libraries. In real life, designers seek optimal systems. In this paper we add optimality considerations to the setting. We distinguish between quality considerations (for example, size - the smaller a system is, the better it is), and pricing (for example, the payment to the company who manufactured the component). We study the problem of designing systems with minimal quality-cost and price. A key point is that while the quality cost is individual - the choices of a designer are independent of choices made by other designers that use the same library, pricing gives rise to a resource-allocation game - designers that use the same component share its price, with the share being proportional to the number of uses (a component can be used several times in a design). We study both closed and open settings, and in both we solve the problem of finding an optimal design. In a setting with multiple designers, we also study the game-theoretic problems of the induced resource-allocation game.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","_id":"608","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 712","title":"Synthesis from component libraries with costs","status":"public","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2018-02-15T00:00:00Z","citation":{"ama":"Avni G, Kupferman O. Synthesis from component libraries with costs. Theoretical Computer Science. 2018;712:50-72. doi:10.1016/j.tcs.2017.11.001","apa":"Avni, G., & Kupferman, O. (2018). Synthesis from component libraries with costs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2017.11.001","ieee":"G. Avni and O. Kupferman, “Synthesis from component libraries with costs,” Theoretical Computer Science, vol. 712. Elsevier, pp. 50–72, 2018.","ista":"Avni G, Kupferman O. 2018. Synthesis from component libraries with costs. Theoretical Computer Science. 712, 50–72.","short":"G. Avni, O. Kupferman, Theoretical Computer Science 712 (2018) 50–72.","mla":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science, vol. 712, Elsevier, 2018, pp. 50–72, doi:10.1016/j.tcs.2017.11.001.","chicago":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science. Elsevier, 2018. https://doi.org/10.1016/j.tcs.2017.11.001."},"publication":"Theoretical Computer Science","page":"50 - 72","article_type":"original"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2018.06.033","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417","open_access":"1"}],"oa":1,"external_id":{"pmid":["30007417"],"isi":["000438482800019"]},"month":"07","date_created":"2018-12-11T11:44:53Z","date_updated":"2023-09-19T10:02:47Z","volume":174,"author":[{"first_name":"Tomoaki","last_name":"Nishiyama","full_name":"Nishiyama, Tomoaki"},{"last_name":"Sakayama","first_name":"Hidetoshi","full_name":"Sakayama, Hidetoshi"},{"first_name":"Jan","last_name":"De Vries","full_name":"De Vries, Jan"},{"full_name":"Buschmann, Henrik","first_name":"Henrik","last_name":"Buschmann"},{"full_name":"Saint Marcoux, Denis","last_name":"Saint Marcoux","first_name":"Denis"},{"last_name":"Ullrich","first_name":"Kristian","full_name":"Ullrich, Kristian"},{"full_name":"Haas, Fabian","last_name":"Haas","first_name":"Fabian"},{"first_name":"Lisa","last_name":"Vanderstraeten","full_name":"Vanderstraeten, Lisa"},{"first_name":"Dirk","last_name":"Becker","full_name":"Becker, Dirk"},{"first_name":"Daniel","last_name":"Lang","full_name":"Lang, Daniel"},{"full_name":"Vosolsobě, Stanislav","first_name":"Stanislav","last_name":"Vosolsobě"},{"first_name":"Stephane","last_name":"Rombauts","full_name":"Rombauts, Stephane"},{"first_name":"Per","last_name":"Wilhelmsson","full_name":"Wilhelmsson, Per"},{"full_name":"Janitza, Philipp","first_name":"Philipp","last_name":"Janitza"},{"first_name":"Ramona","last_name":"Kern","full_name":"Kern, Ramona"},{"first_name":"Alexander","last_name":"Heyl","full_name":"Heyl, Alexander"},{"full_name":"Rümpler, Florian","last_name":"Rümpler","first_name":"Florian"},{"full_name":"Calderón Villalobos, Luz","first_name":"Luz","last_name":"Calderón Villalobos"},{"full_name":"Clay, John","last_name":"Clay","first_name":"John"},{"last_name":"Skokan","first_name":"Roman","full_name":"Skokan, Roman"},{"full_name":"Toyoda, Atsushi","first_name":"Atsushi","last_name":"Toyoda"},{"full_name":"Suzuki, Yutaka","last_name":"Suzuki","first_name":"Yutaka"},{"full_name":"Kagoshima, Hiroshi","last_name":"Kagoshima","first_name":"Hiroshi"},{"first_name":"Elio","last_name":"Schijlen","full_name":"Schijlen, Elio"},{"full_name":"Tajeshwar, Navindra","first_name":"Navindra","last_name":"Tajeshwar"},{"full_name":"Catarino, Bruno","first_name":"Bruno","last_name":"Catarino"},{"full_name":"Hetherington, Alexander","last_name":"Hetherington","first_name":"Alexander"},{"full_name":"Saltykova, Assia","first_name":"Assia","last_name":"Saltykova"},{"first_name":"Clemence","last_name":"Bonnot","full_name":"Bonnot, Clemence"},{"last_name":"Breuninger","first_name":"Holger","full_name":"Breuninger, Holger"},{"full_name":"Symeonidi, Aikaterini","last_name":"Symeonidi","first_name":"Aikaterini"},{"full_name":"Radhakrishnan, Guru","last_name":"Radhakrishnan","first_name":"Guru"},{"last_name":"Van Nieuwerburgh","first_name":"Filip","full_name":"Van Nieuwerburgh, Filip"},{"first_name":"Dieter","last_name":"Deforce","full_name":"Deforce, Dieter"},{"last_name":"Chang","first_name":"Caren","full_name":"Chang, Caren"},{"full_name":"Karol, Kenneth","first_name":"Kenneth","last_name":"Karol"},{"last_name":"Hedrich","first_name":"Rainer","full_name":"Hedrich, Rainer"},{"first_name":"Peter","last_name":"Ulvskov","full_name":"Ulvskov, Peter"},{"full_name":"Glöckner, Gernot","last_name":"Glöckner","first_name":"Gernot"},{"last_name":"Delwiche","first_name":"Charles","full_name":"Delwiche, Charles"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"first_name":"Yves","last_name":"Van De Peer","full_name":"Van De Peer, Yves"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Beilby","first_name":"Mary","full_name":"Beilby, Mary"},{"full_name":"Dolan, Liam","first_name":"Liam","last_name":"Dolan"},{"full_name":"Kohara, Yuji","first_name":"Yuji","last_name":"Kohara"},{"last_name":"Sugano","first_name":"Sumio","full_name":"Sugano, Sumio"},{"full_name":"Fujiyama, Asao","first_name":"Asao","last_name":"Fujiyama"},{"first_name":"Pierre Marc","last_name":"Delaux","full_name":"Delaux, Pierre Marc"},{"full_name":"Quint, Marcel","first_name":"Marcel","last_name":"Quint"},{"full_name":"Theissen, Gunter","last_name":"Theissen","first_name":"Gunter"},{"first_name":"Martin","last_name":"Hagemann","full_name":"Hagemann, Martin"},{"first_name":"Jesper","last_name":"Harholt","full_name":"Harholt, Jesper"},{"full_name":"Dunand, Christophe","first_name":"Christophe","last_name":"Dunand"},{"full_name":"Zachgo, Sabine","first_name":"Sabine","last_name":"Zachgo"},{"full_name":"Langdale, Jane","last_name":"Langdale","first_name":"Jane"},{"full_name":"Maumus, Florian","last_name":"Maumus","first_name":"Florian"},{"first_name":"Dominique","last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique"},{"full_name":"Gould, Sven B","first_name":"Sven B","last_name":"Gould"},{"full_name":"Rensing, Stefan","last_name":"Rensing","first_name":"Stefan"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Cell Press","year":"2018","acknowledgement":"In-Data-Review","pmid":1,"publist_id":"7774","ec_funded":1,"date_published":"2018-07-12T00:00:00Z","page":"448 - 464.e24","publication":"Cell","citation":{"chicago":"Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann, Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell. Cell Press, 2018. https://doi.org/10.1016/j.cell.2018.06.033.","short":"T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K. Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts, P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos, J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar, B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi, G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich, P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M. Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G. Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus, D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24.","mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:10.1016/j.cell.2018.06.033.","apa":"Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D., Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. Cell Press. https://doi.org/10.1016/j.cell.2018.06.033","ieee":"T. Nishiyama et al., “The Chara genome: Secondary complexity and implications for plant terrestrialization,” Cell, vol. 174, no. 2. Cell Press, p. 448–464.e24, 2018.","ista":"Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C, Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 174(2), 448–464.e24.","ama":"Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 2018;174(2):448-464.e24. doi:10.1016/j.cell.2018.06.033"},"day":"12","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","status":"public","intvolume":" 174","_id":"148","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.","lang":"eng"}],"issue":"2","type":"journal_article"},{"_id":"403","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A","ddc":["580"],"status":"public","intvolume":" 94","oa_version":"Published Version","file":[{"date_created":"2019-02-06T11:40:54Z","date_updated":"2020-07-14T12:46:22Z","checksum":"d9d3ad3215ac0e581731443fca312266","file_id":"5934","relation":"main_file","creator":"dernst","file_size":1543354,"content_type":"application/pdf","file_name":"2018_PlantJourn_Cavallari.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The ability to adapt growth and development to temperature variations is crucial to generate plant varieties resilient to predicted temperature changes. However, the mechanisms underlying plant response to progressive increases in temperature have just started to be elucidated. Here, we report that the Cyclin-dependent Kinase G1 (CDKG1) is a central element in a thermo-sensitive mRNA splicing cascade that transduces changes in ambient temperature into differential expression of the fundamental spliceosome component, ATU2AF65A. CDKG1 is alternatively spliced in a temperature-dependent manner. We found that this process is partly dependent on both the Cyclin-dependent Kinase G2 (CDKG2) and the interacting co-factor CYCLIN L1 resulting in two distinct messenger RNAs. Relative abundance of both CDKG1 transcripts correlates with ambient temperature and possibly with different expression levels of the associated protein isoforms. Both CDKG1 alternative transcripts are necessary to fully complement the expression of ATU2AF65A across the temperature range. Our data support a previously unidentified temperature-dependent mechanism based on the alternative splicing of CDKG1 and regulated by CDKG2 and CYCLIN L1. We propose that changes in ambient temperature affect the relative abundance of CDKG1 transcripts and this in turn translates into differential CDKG1 protein expression coordinating the alternative splicing of ATU2AF65A. This article is protected by copyright. All rights reserved."}],"issue":"6","publication":"The Plant Journal","citation":{"ama":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 2018;94(6):1010-1022. doi:10.1111/tpj.13914","ieee":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, and J. Doonan, “The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A,” The Plant Journal, vol. 94, no. 6. Wiley, pp. 1010–1022, 2018.","apa":"Cavallari, N., Nibau, C., Fuchs, A., Dadarou, D., Barta, A., & Doonan, J. (2018). The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.13914","ista":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. 2018. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 94(6), 1010–1022.","short":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, J. Doonan, The Plant Journal 94 (2018) 1010–1022.","mla":"Cavallari, Nicola, et al. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal, vol. 94, no. 6, Wiley, 2018, pp. 1010–22, doi:10.1111/tpj.13914.","chicago":"Cavallari, Nicola, Candida Nibau, Armin Fuchs, Despoina Dadarou, Andrea Barta, and John Doonan. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal. Wiley, 2018. https://doi.org/10.1111/tpj.13914."},"page":"1010 - 1022","date_published":"2018-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","acknowledgement":"CN, DD and JHD were funded by the BBSRC (grant number BB/M009459/1). NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna. AB and AF were supported by the Austrian Science Fund (FWF) [DK W1207; SFB RNAreg F43-P10]","year":"2018","publication_status":"published","publisher":"Wiley","department":[{"_id":"EvBe"}],"author":[{"last_name":"Cavallari","first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","full_name":"Cavallari, Nicola"},{"full_name":"Nibau, Candida","last_name":"Nibau","first_name":"Candida"},{"first_name":"Armin","last_name":"Fuchs","full_name":"Fuchs, Armin"},{"last_name":"Dadarou","first_name":"Despoina","full_name":"Dadarou, Despoina"},{"full_name":"Barta, Andrea","first_name":"Andrea","last_name":"Barta"},{"first_name":"John","last_name":"Doonan","full_name":"Doonan, John"}],"date_updated":"2023-09-19T10:07:08Z","date_created":"2018-12-11T11:46:17Z","volume":94,"file_date_updated":"2020-07-14T12:46:22Z","publist_id":"7426","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000434365500008"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1111/tpj.13914","language":[{"iso":"eng"}],"month":"06"},{"publist_id":"7765","file_date_updated":"2020-10-09T06:22:41Z","author":[{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","first_name":"Thomas","last_name":"Ferrere","full_name":"Ferrere, Thomas"}],"volume":10951,"date_updated":"2023-09-19T10:05:37Z","date_created":"2018-12-11T11:44:55Z","year":"2018","department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","month":"07","doi":"10.1007/978-3-319-95582-7_9","conference":{"location":"Oxford, UK","start_date":"2018-07-15","end_date":"2018-07-17","name":"FM: International Symposium on Formal Methods"},"language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000489765800009"]},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","isi":1,"abstract":[{"text":"Imprecision in timing can sometimes be beneficial: Metric interval temporal logic (MITL), disabling the expression of punctuality constraints, was shown to translate to timed automata, yielding an elementary decision procedure. We show how this principle extends to other forms of dense-time specification using regular expressions. By providing a clean, automaton-based formal framework for non-punctual languages, we are able to recover and extend several results in timed systems. Metric interval regular expressions (MIRE) are introduced, providing regular expressions with non-singular duration constraints. We obtain that MIRE are expressively complete relative to a class of one-clock timed automata, which can be determinized using additional clocks. Metric interval dynamic logic (MIDL) is then defined using MIRE as temporal modalities. We show that MIDL generalizes known extensions of MITL, while translating to timed automata at comparable cost.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Submitted Version","file":[{"creator":"dernst","file_size":485576,"content_type":"application/pdf","file_name":"2018_LNCS_Ferrere.pdf","access_level":"open_access","date_created":"2020-10-09T06:22:41Z","date_updated":"2020-10-09T06:22:41Z","success":1,"checksum":"a045c213c42c445f1889326f8db82a0a","file_id":"8637","relation":"main_file"}],"_id":"156","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 10951","ddc":["000"],"status":"public","title":"The compound interest in relaxing punctuality","has_accepted_license":"1","article_processing_charge":"No","day":"12","scopus_import":"1","date_published":"2018-07-12T00:00:00Z","citation":{"chicago":"Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64. Springer, 2018. https://doi.org/10.1007/978-3-319-95582-7_9.","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164.","mla":"Ferrere, Thomas. The Compound Interest in Relaxing Punctuality. Vol. 10951, Springer, 2018, pp. 147–64, doi:10.1007/978-3-319-95582-7_9.","ieee":"T. Ferrere, “The compound interest in relaxing punctuality,” presented at the FM: International Symposium on Formal Methods, Oxford, UK, 2018, vol. 10951, pp. 147–164.","apa":"Ferrere, T. (2018). The compound interest in relaxing punctuality (Vol. 10951, pp. 147–164). Presented at the FM: International Symposium on Formal Methods, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-95582-7_9","ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164.","ama":"Ferrere T. The compound interest in relaxing punctuality. In: Vol 10951. Springer; 2018:147-164. doi:10.1007/978-3-319-95582-7_9"},"page":"147 - 164"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"104","title":"The core effector Cce1 is required for early infection of maize by Ustilago maydis","ddc":["580"],"status":"public","intvolume":" 19","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5740","success":1,"date_created":"2018-12-18T09:46:00Z","date_updated":"2018-12-18T09:46:00Z","access_level":"open_access","file_name":"2018_MolecPlantPath_Seitner.pdf","content_type":"application/pdf","file_size":682335,"creator":"dernst"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The biotrophic pathogen Ustilago maydis, the causative agent of corn smut disease, infects one of the most important crops worldwide – Zea mays. To successfully colonize its host, U. maydis secretes proteins, known as effectors, that suppress plant defense responses and facilitate the establishment of biotrophy. In this work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence and is upregulated during infection. Through microscopic analysis and in vitro assays, we show that Cce1 is secreted from hyphae during filamentous growth of the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection and induce callose deposition as a plant defense response. Cce1 is highly conserved among smut fungi and the Ustilago bromivora ortholog complemented the virulence defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core effector with apoplastic localization that is essential for U. maydis to infect its host."}],"issue":"10","publication":"Molecular Plant Pathology","citation":{"chicago":"Seitner, Denise, Simon Uhse, Michelle C Gallei, and Armin Djamei. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” Molecular Plant Pathology. Wiley, 2018. https://doi.org/10.1111/mpp.12698.","mla":"Seitner, Denise, et al. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” Molecular Plant Pathology, vol. 19, no. 10, Wiley, 2018, pp. 2277–87, doi:10.1111/mpp.12698.","short":"D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19 (2018) 2277–2287.","ista":"Seitner D, Uhse S, Gallei MC, Djamei A. 2018. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 19(10), 2277–2287.","ieee":"D. Seitner, S. Uhse, M. C. Gallei, and A. Djamei, “The core effector Cce1 is required for early infection of maize by Ustilago maydis,” Molecular Plant Pathology, vol. 19, no. 10. Wiley, pp. 2277–2287, 2018.","apa":"Seitner, D., Uhse, S., Gallei, M. C., & Djamei, A. (2018). The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. Wiley. https://doi.org/10.1111/mpp.12698","ama":"Seitner D, Uhse S, Gallei MC, Djamei A. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 2018;19(10):2277-2287. doi:10.1111/mpp.12698"},"page":"2277 - 2287","date_published":"2018-10-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","year":"2018","acknowledgement":"the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22], and the Austrian Academy of Science (OEAW).","publication_status":"published","publisher":"Wiley","department":[{"_id":"GradSch"}],"author":[{"full_name":"Seitner, Denise","first_name":"Denise","last_name":"Seitner"},{"first_name":"Simon","last_name":"Uhse","full_name":"Uhse, Simon"},{"first_name":"Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C"},{"first_name":"Armin","last_name":"Djamei","full_name":"Djamei, Armin"}],"date_created":"2018-12-11T11:44:39Z","date_updated":"2023-09-19T10:06:42Z","volume":19,"file_date_updated":"2018-12-18T09:46:00Z","publist_id":"7950","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000445624100006"]},"isi":1,"quality_controlled":"1","doi":"10.1111/mpp.12698","language":[{"iso":"eng"}],"month":"10"},{"_id":"40","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["576"],"title":"The consequences of an introgression event","status":"public","intvolume":" 27","file":[{"creator":"apreinsp","content_type":"application/pdf","file_size":295452,"file_name":"2018_MolecularEcology_BartonNick.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:22Z","date_created":"2019-07-19T06:54:46Z","file_id":"6652","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance.","lang":"eng"}],"issue":"24","publication":"Molecular Ecology","citation":{"chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950.","mla":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:10.1111/mec.14950.","short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975.","ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975.","ieee":"N. H. Barton, “The consequences of an introgression event,” Molecular Ecology, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.","apa":"Barton, N. H. (2018). The consequences of an introgression event. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14950","ama":"Barton NH. The consequences of an introgression event. Molecular Ecology. 2018;27(24):4973-4975. doi:10.1111/mec.14950"},"article_type":"letter_note","page":"4973-4975","date_published":"2018-12-31T00:00:00Z","scopus_import":"1","day":"31","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","year":"2018","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9805"}]},"date_updated":"2023-09-19T10:06:08Z","date_created":"2018-12-11T11:44:18Z","volume":27,"file_date_updated":"2020-07-14T12:46:22Z","publist_id":"8014","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000454600500001"],"pmid":["30599087"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1111/mec.14950","language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["1365294X"]}},{"month":"06","publication_identifier":{"issn":["2050084X"]},"external_id":{"isi":["000434375000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.7554/eLife.37888","language":[{"iso":"eng"}],"article_number":"e37888","file_date_updated":"2020-07-14T12:47:13Z","year":"2018","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"eLife Sciences Publications","author":[{"full_name":"Alanko, Jonna H","orcid":"0000-0002-7698-3061","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alanko","first_name":"Jonna H"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-19T10:01:39Z","date_created":"2019-01-20T22:59:19Z","volume":7,"scopus_import":"1","day":"06","has_accepted_license":"1","article_processing_charge":"No","publication":"eLife","citation":{"ama":"Alanko JH, Sixt MK. The cell sets the tone. eLife. 2018;7. doi:10.7554/eLife.37888","ieee":"J. H. Alanko and M. K. Sixt, “The cell sets the tone,” eLife, vol. 7. eLife Sciences Publications, 2018.","apa":"Alanko, J. H., & Sixt, M. K. (2018). The cell sets the tone. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.37888","ista":"Alanko JH, Sixt MK. 2018. The cell sets the tone. eLife. 7, e37888.","short":"J.H. Alanko, M.K. Sixt, ELife 7 (2018).","mla":"Alanko, Jonna H., and Michael K. Sixt. “The Cell Sets the Tone.” ELife, vol. 7, e37888, eLife Sciences Publications, 2018, doi:10.7554/eLife.37888.","chicago":"Alanko, Jonna H, and Michael K Sixt. “The Cell Sets the Tone.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.37888."},"article_type":"original","date_published":"2018-06-06T00:00:00Z","type":"journal_article","abstract":[{"text":"In zebrafish larvae, it is the cell type that determines how the cell responds to a chemokine signal.","lang":"eng"}],"_id":"5861","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["570"],"title":"The cell sets the tone","intvolume":" 7","file":[{"content_type":"application/pdf","file_size":358141,"creator":"dernst","access_level":"open_access","file_name":"2018_eLife_Alanko.pdf","checksum":"f1c7ec2a809408d763c4b529a98f9a3b","date_updated":"2020-07-14T12:47:13Z","date_created":"2019-02-13T10:52:11Z","relation":"main_file","file_id":"5973"}],"oa_version":"Published Version"},{"issue":"10","abstract":[{"text":"The trafficking of subcellular cargos in eukaryotic cells crucially depends on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis, vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they are important for plant development, mainly through controlling the polar subcellular localization of PIN-FORMED (PIN) transporters of the plant hormone auxin. Here, using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin 4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally, Arabidopsis and yeast (Sacharomyces cerevisiae) mutants defective in ARF-GEF show altered sensitivity to ES4. ES4 interferes with the activation-based membrane association of the ARF1 GTPases, but not of their mutant variants that are activated independently of ARF-GEF activity. Biochemical approaches and docking simulations confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These observations collectively identify ES4 as a chemical tool enabling the study of ARF-GEF-mediated processes, including ARF-GEF-mediated plant development.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 30","title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"147","article_processing_charge":"No","day":"12","scopus_import":"1","date_published":"2018-11-12T00:00:00Z","page":"2553 - 2572","article_type":"original","citation":{"chicago":"Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx, Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” The Plant Cell. Oxford University Press, 2018. https://doi.org/10.1105/tpc.18.00127.","mla":"Kania, Urszula, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” The Plant Cell, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72, doi:10.1105/tpc.18.00127.","short":"U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois, J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant Cell 30 (2018) 2553–2572.","ista":"Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils J, De RRM, Grones P, Robert S, Russinova E, Friml J. 2018. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 30(10), 2553–2572.","apa":"Kania, U., Nodzyński, T., Lu, Q., Hicks, G. R., Nerinckx, W., Mishev, K., … Friml, J. (2018). The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. Oxford University Press. https://doi.org/10.1105/tpc.18.00127","ieee":"U. Kania et al., “The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,” The Plant Cell, vol. 30, no. 10. Oxford University Press, pp. 2553–2572, 2018.","ama":"Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 2018;30(10):2553-2572. doi:10.1105/tpc.18.00127"},"publication":"The Plant Cell","ec_funded":1,"publist_id":"7776","volume":30,"date_updated":"2023-09-19T10:09:12Z","date_created":"2018-12-11T11:44:52Z","author":[{"last_name":"Kania","first_name":"Urszula","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","full_name":"Kania, Urszula"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"first_name":"Qing","last_name":"Lu","full_name":"Lu, Qing"},{"first_name":"Glenn R","last_name":"Hicks","full_name":"Hicks, Glenn R"},{"full_name":"Nerinckx, Wim","first_name":"Wim","last_name":"Nerinckx"},{"full_name":"Mishev, Kiril","first_name":"Kiril","last_name":"Mishev"},{"full_name":"Peurois, Francois","last_name":"Peurois","first_name":"Francois"},{"full_name":"Cherfils, Jacqueline","first_name":"Jacqueline","last_name":"Cherfils"},{"full_name":"De, Rycke Riet Maria","first_name":"Rycke Riet Maria","last_name":"De"},{"first_name":"Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"full_name":"Robert, Stéphanie","first_name":"Stéphanie","last_name":"Robert"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank Gerd Jürgens, Sandra Richter, and Sheng Yang He for providing antibodies; Maciek Adamowski, Fernando Aniento, Sebastian Bednarek, Nico Callewaert, Matyás Fendrych, Elena Feraru, and Mugurel I. Feraru for helpful suggestions; Siamsa Doyle for critical reading of the manuscript and helpful comments and suggestions; and Stephanie Smith and Martine De Cock for help in editing and language corrections. We acknowledge the core facility Cellular Imaging of CEITEC supported by the Czech-BioImaging large RI project (LM2015062 funded by MEYS CR) for their support with obtaining scientific data presented in this article. Plant Sciences Core Facility of CEITEC Masaryk University is gratefully acknowledged for obtaining part of the scientific data presented in this article. We acknowledge support from the Fondation pour la Recherche Médicale and from the Institut National du Cancer (J.C.). The research leading to these results was funded by the European Research Council under the European Union's 7th Framework Program (FP7/2007-2013)/ERC grant agreement numbers 282300 and 742985 and the Czech Science Foundation GAČR (GA18-26981S; J.F.); Ministry of Education, Youth, and Sports/MEYS of the Czech Republic under the Project CEITEC 2020 (LQ1601; T.N.); the China Science Council for a predoctoral fellowship (Q.L.); a joint research project within the framework of cooperation between the Research Foundation-Flanders and the Bulgarian Academy of Sciences (VS.025.13N; K.M. and E.R.); Vetenskapsrådet and Vinnova (Verket för Innovationssystem; S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” Grant 2012.0050 (S.R.), Kempe stiftelserna (P.G.), Tryggers CTS410 (P.G.).","year":"2018","publication_identifier":{"issn":["1040-4651"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1105/tpc.18.00127","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1105/tpc.18.00127"}],"external_id":{"pmid":["30018156"],"isi":["000450000500023"]}},{"page":"596 - 604","article_type":"original","citation":{"ama":"Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 2018;4(8):596-604. doi:10.1038/s41477-018-0212-z","ista":"Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 4(8), 596–604.","ieee":"C. L. Shi et al., “The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 596–604, 2018.","apa":"Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf, A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0212-z","mla":"Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 596–604, doi:10.1038/s41477-018-0212-z.","short":"C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf, T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa, M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604.","chicago":"Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen, Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0212-z."},"publication":"Nature Plants","date_published":"2018-07-30T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"30","intvolume":" 4","ddc":["580"],"title":"The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"146","oa_version":"Submitted Version","file":[{"file_name":"2018_NaturePlants_Shi.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":226829,"file_id":"7043","relation":"main_file","date_created":"2019-11-18T16:24:07Z","date_updated":"2020-07-14T12:44:56Z","checksum":"da33101c76ee1b2dc5ab28fd2ccba9d0"}],"type":"journal_article","issue":"8","abstract":[{"text":"The root cap protects the stem cell niche of angiosperm roots from damage. In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are regularly lost through programmed cell death, while the outermost layer of the root cap covering the tip is repeatedly sloughed. Efficient coordination with stem cells producing new layers is needed to maintain a constant size of the cap. We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2 (HSL2), mediating such communication. Live imaging over several days characterized this process from initial fractures in LRC cell files to full separation of a layer. Enhanced expression of IDL1 in the separating root cap layers resulted in increased frequency of sloughing, balanced with generation of new layers in a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to the transcription factors BEARSKIN1/2 and genes associated with programmed cell death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the homeostatic balance between stem cell division and sloughing activity.","lang":"eng"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000443861300016"],"pmid":["30061750"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41477-018-0212-z","month":"07","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","publication_status":"published","pmid":1,"year":"2018","volume":4,"date_created":"2018-12-11T11:44:52Z","date_updated":"2023-09-19T10:08:45Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-process-in-root-development-discovered/"}]},"author":[{"full_name":"Shi, Chun Lin","first_name":"Chun Lin","last_name":"Shi"},{"full_name":"Von Wangenheim, Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","first_name":"Daniel","last_name":"Von Wangenheim"},{"last_name":"Herrmann","first_name":"Ullrich","full_name":"Herrmann, Ullrich"},{"first_name":"Mari","last_name":"Wildhagen","full_name":"Wildhagen, Mari"},{"last_name":"Kulik","first_name":"Ivan","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","full_name":"Kulik, Ivan"},{"first_name":"Andreas","last_name":"Kopf","full_name":"Kopf, Andreas"},{"first_name":"Takashi","last_name":"Ishida","full_name":"Ishida, Takashi"},{"last_name":"Olsson","first_name":"Vilde","full_name":"Olsson, Vilde"},{"first_name":"Mari Kristine","last_name":"Anker","full_name":"Anker, Mari Kristine"},{"last_name":"Albert","first_name":"Markus","full_name":"Albert, Markus"},{"first_name":"Melinka A","last_name":"Butenko","full_name":"Butenko, Melinka A"},{"last_name":"Felix","first_name":"Georg","full_name":"Felix, Georg"},{"last_name":"Sawa","first_name":"Shinichiro","full_name":"Sawa, Shinichiro"},{"full_name":"Claassen, Manfred","first_name":"Manfred","last_name":"Claassen"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"first_name":"Reidunn B","last_name":"Aalen","full_name":"Aalen, Reidunn B"}],"publist_id":"7777","file_date_updated":"2020-07-14T12:44:56Z"},{"month":"05","external_id":{"isi":["000435551300009"]},"oa":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41562-018-0354-z","language":[{"iso":"eng"}],"publist_id":"7588","ec_funded":1,"file_date_updated":"2020-07-14T12:45:54Z","acknowledgement":"This work was supported by a grant from the John Templeton Foundation and by the Office of Naval Research Grant N00014-16-1-2914 (M.A.N.). C.H. acknowledges generous support from the ISTFELLOW programme and by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475.","year":"2018","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","publication_status":"published","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/the-logic-of-modesty-why-it-pays-to-be-humble/"}]},"author":[{"full_name":"Hoffman, Moshe","last_name":"Hoffman","first_name":"Moshe"},{"first_name":"Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"volume":2,"date_created":"2018-12-11T11:45:39Z","date_updated":"2023-09-19T10:12:03Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"28","citation":{"chicago":"Hoffman, Moshe, Christian Hilbe, and Martin Nowak. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0354-z.","mla":"Hoffman, Moshe, et al. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 397–404, doi:10.1038/s41562-018-0354-z.","short":"M. Hoffman, C. Hilbe, M. Nowak, Nature Human Behaviour 2 (2018) 397–404.","ista":"Hoffman M, Hilbe C, Nowak M. 2018. The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. 2, 397–404.","apa":"Hoffman, M., Hilbe, C., & Nowak, M. (2018). The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0354-z","ieee":"M. Hoffman, C. Hilbe, and M. Nowak, “The signal-burying game can explain why we obscure positive traits and good deeds,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 397–404, 2018.","ama":"Hoffman M, Hilbe C, Nowak M. The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. 2018;2:397-404. doi:10.1038/s41562-018-0354-z"},"publication":"Nature Human Behaviour","page":"397 - 404","article_type":"original","date_published":"2018-05-28T00:00:00Z","type":"journal_article","abstract":[{"text":"People sometimes make their admirable deeds and accomplishments hard to spot, such as by giving anonymously or avoiding bragging. Such ‘buried’ signals are hard to reconcile with standard models of signalling or indirect reciprocity, which motivate costly pro-social behaviour by reputational gains. To explain these phenomena, we design a simple game theory model, which we call the signal-burying game. This game has the feature that senders can bury their signal by deliberately reducing the probability of the signal being observed. If the signal is observed, however, it is identified as having been buried. We show under which conditions buried signals can be maintained, using static equilibrium concepts and calculations of the evolutionary dynamics. We apply our analysis to shed light on a number of otherwise puzzling social phenomena, including modesty, anonymous donations, subtlety in art and fashion, and overeagerness.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"293","intvolume":" 2","ddc":["000"],"status":"public","title":"The signal-burying game can explain why we obscure positive traits and good deeds","oa_version":"Submitted Version","file":[{"date_created":"2019-11-19T08:17:23Z","date_updated":"2020-07-14T12:45:54Z","checksum":"32efaf06a597495c184df91b3fbb19c0","relation":"main_file","file_id":"7051","content_type":"application/pdf","file_size":194734,"creator":"dernst","file_name":"2018_NatureHumanBeh_Hoffman.pdf","access_level":"open_access"}]},{"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-04-01T00:00:00Z","publication":"Annales Henri Poincare","citation":{"ama":"Benedikter NP, Sok J, Solovej J. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 2018;19(4):1167-1214. doi:10.1007/s00023-018-0644-z","ista":"Benedikter NP, Sok J, Solovej J. 2018. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 19(4), 1167–1214.","apa":"Benedikter, N. P., Sok, J., & Solovej, J. (2018). The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-018-0644-z","ieee":"N. P. Benedikter, J. Sok, and J. Solovej, “The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations,” Annales Henri Poincare, vol. 19, no. 4. Birkhäuser, pp. 1167–1214, 2018.","mla":"Benedikter, Niels P., et al. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare, vol. 19, no. 4, Birkhäuser, 2018, pp. 1167–214, doi:10.1007/s00023-018-0644-z.","short":"N.P. Benedikter, J. Sok, J. Solovej, Annales Henri Poincare 19 (2018) 1167–1214.","chicago":"Benedikter, Niels P, Jérémy Sok, and Jan Solovej. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare. Birkhäuser, 2018. https://doi.org/10.1007/s00023-018-0644-z."},"page":"1167 - 1214","abstract":[{"text":"The derivation of effective evolution equations is central to the study of non-stationary quantum many-body systems, and widely used in contexts such as superconductivity, nuclear physics, Bose–Einstein condensation and quantum chemistry. We reformulate the Dirac–Frenkel approximation principle in terms of reduced density matrices and apply it to fermionic and bosonic many-body systems. We obtain the Bogoliubov–de Gennes and Hartree–Fock–Bogoliubov equations, respectively. While we do not prove quantitative error estimates, our formulation does show that the approximation is optimal within the class of quasifree states. Furthermore, we prove well-posedness of the Bogoliubov–de Gennes equations in energy space and discuss conserved quantities","lang":"eng"}],"issue":"4","type":"journal_article","alternative_title":["Annales Henri Poincare"],"pubrep_id":"993","oa_version":"Published Version","file":[{"file_name":"IST-2018-993-v1+1_2018_Benedikter_Dirac.pdf","access_level":"open_access","creator":"system","file_size":923252,"content_type":"application/pdf","file_id":"4914","relation":"main_file","date_updated":"2020-07-14T12:46:31Z","date_created":"2018-12-12T10:11:57Z","checksum":"883eeccba8384ad7fcaa28761d99a0fa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"455","ddc":["510","539"],"title":"The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations","status":"public","intvolume":" 19","month":"04","doi":"10.1007/s00023-018-0644-z","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000427578900006"]},"quality_controlled":"1","isi":1,"file_date_updated":"2020-07-14T12:46:31Z","publist_id":"7367","author":[{"first_name":"Niels P","last_name":"Benedikter","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1071-6091","full_name":"Benedikter, Niels P"},{"last_name":"Sok","first_name":"Jérémy","full_name":"Sok, Jérémy"},{"full_name":"Solovej, Jan","first_name":"Jan","last_name":"Solovej"}],"date_created":"2018-12-11T11:46:34Z","date_updated":"2023-09-19T10:07:41Z","volume":19,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors acknowledge support by ERC Advanced Grant 321029 and by VILLUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059). The authors would like to thank Sébastien Breteaux, Enno Lenzmann, Mathieu Lewin and Jochen Schmid for comments and discussions about well-posedness of the Bogoliubov–de Gennes equations.","year":"2018","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Birkhäuser"},{"publisher":"Cell Press","department":[{"_id":"AnKi"}],"publication_status":"published","pmid":1,"year":"2018","volume":6,"date_created":"2018-12-11T11:45:46Z","date_updated":"2023-09-19T10:11:25Z","author":[{"last_name":"Bauer","first_name":"Guntram","full_name":"Bauer, Guntram"},{"full_name":"Fakhri, Nikta","last_name":"Fakhri","first_name":"Nikta"},{"full_name":"Kicheva, Anna","first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"},{"first_name":"Jané","last_name":"Kondev","full_name":"Kondev, Jané"},{"last_name":"Kruse","first_name":"Karsten","full_name":"Kruse, Karsten"},{"full_name":"Noji, Hiroyuki","last_name":"Noji","first_name":"Hiroyuki"},{"full_name":"Riveline, Daniel","last_name":"Riveline","first_name":"Daniel"},{"last_name":"Saunders","first_name":"Timothy","full_name":"Saunders, Timothy"},{"full_name":"Thatta, Mukund","last_name":"Thatta","first_name":"Mukund"},{"first_name":"Eric","last_name":"Wieschaus","full_name":"Wieschaus, Eric"}],"publist_id":"7551","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cels.2018.04.003","open_access":"1"}],"oa":1,"external_id":{"isi":["000432192100003"],"pmid":["29698645"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cels.2018.04.003","publication_identifier":{"eissn":["2405-4712"]},"month":"04","intvolume":" 6","status":"public","title":"The science of living matter for tomorrow","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"314","oa_version":"Published Version","type":"journal_article","issue":"4","abstract":[{"text":"The interface of physics and biology pro-vides a fruitful environment for generatingnew concepts and exciting ways forwardto understanding living matter. Examplesof successful studies include the estab-lishment and readout of morphogen gra-dients during development, signal pro-cessing in protein and genetic networks,the role of fluctuations in determining thefates of cells and tissues, and collectiveeffects in proteins and in tissues. It is nothard to envision that significant further ad-vances will translate to societal benefitsby initiating the development of new de-vices and strategies for curing disease.However, research at the interface posesvarious challenges, in particular for youngscientists, and current institutions arerarely designed to facilitate such scientificprograms. In this Letter, we propose aninternational initiative that addressesthese challenges through the establish-ment of a worldwide network of platformsfor cross-disciplinary training and incuba-tors for starting new collaborations.","lang":"eng"}],"page":"400 - 402","article_type":"letter_note","citation":{"chicago":"Bauer, Guntram, Nikta Fakhri, Anna Kicheva, Jané Kondev, Karsten Kruse, Hiroyuki Noji, Daniel Riveline, Timothy Saunders, Mukund Thatta, and Eric Wieschaus. “The Science of Living Matter for Tomorrow.” Cell Systems. Cell Press, 2018. https://doi.org/10.1016/j.cels.2018.04.003.","mla":"Bauer, Guntram, et al. “The Science of Living Matter for Tomorrow.” Cell Systems, vol. 6, no. 4, Cell Press, 2018, pp. 400–02, doi:10.1016/j.cels.2018.04.003.","short":"G. Bauer, N. Fakhri, A. Kicheva, J. Kondev, K. Kruse, H. Noji, D. Riveline, T. Saunders, M. Thatta, E. Wieschaus, Cell Systems 6 (2018) 400–402.","ista":"Bauer G, Fakhri N, Kicheva A, Kondev J, Kruse K, Noji H, Riveline D, Saunders T, Thatta M, Wieschaus E. 2018. The science of living matter for tomorrow. Cell Systems. 6(4), 400–402.","apa":"Bauer, G., Fakhri, N., Kicheva, A., Kondev, J., Kruse, K., Noji, H., … Wieschaus, E. (2018). The science of living matter for tomorrow. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2018.04.003","ieee":"G. Bauer et al., “The science of living matter for tomorrow,” Cell Systems, vol. 6, no. 4. Cell Press, pp. 400–402, 2018.","ama":"Bauer G, Fakhri N, Kicheva A, et al. The science of living matter for tomorrow. Cell Systems. 2018;6(4):400-402. doi:10.1016/j.cels.2018.04.003"},"publication":"Cell Systems","date_published":"2018-04-25T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"25"},{"page":"377 - 382","article_type":"original","citation":{"chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” Genetics. Genetics , 2018. https://doi.org/10.1534/genetics.117.300426.","short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.","mla":"Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” Genetics, vol. 208, no. 1, Genetics , 2018, pp. 377–82, doi:10.1534/genetics.117.300426.","apa":"Charlesworth, B., & Barton, N. H. (2018). The spread of an inversion with migration and selection. Genetics. Genetics . https://doi.org/10.1534/genetics.117.300426","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” Genetics, vol. 208, no. 1. Genetics , pp. 377–382, 2018.","ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","ama":"Charlesworth B, Barton NH. The spread of an inversion with migration and selection. Genetics. 2018;208(1):377-382. doi:10.1534/genetics.117.300426"},"publication":"Genetics","date_published":"2018-01-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 208","title":"The spread of an inversion with migration and selection","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"565","oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We re-examine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. "}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/"}],"external_id":{"isi":["000419356300025"],"pmid":["29158424"]},"language":[{"iso":"eng"}],"doi":"10.1534/genetics.117.300426","month":"01","department":[{"_id":"NiBa"}],"publisher":"Genetics ","publication_status":"published","pmid":1,"year":"2018","volume":208,"date_created":"2018-12-11T11:47:12Z","date_updated":"2023-09-19T10:12:31Z","author":[{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"publist_id":"7249"},{"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1606.07355","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1606.07355"],"isi":["000422675800004"]},"language":[{"iso":"eng"}],"doi":"10.1002/cpa.21717","month":"03","publisher":"Wiley-Blackwell","department":[{"_id":"RoSe"}],"publication_status":"published","acknowledgement":"We thank the referee for helpful suggestions that improved the presentation of the paper. We also acknowledge partial support by National Science Foundation Grant DMS-1363432 (R.L.F.), Austrian Science Fund (FWF) Project Nr. P 27533-N27 (P.T.N.), CONICYT (Chile) through CONICYT–PCHA/ Doctorado Nacional/2014, and Iniciativa Científica Milenio (Chile) through Millenium Nucleus RC–120002 “Física Matemática” (H.V.D.B.).\r\n","year":"2018","volume":71,"date_created":"2018-12-11T11:46:31Z","date_updated":"2023-09-19T10:09:40Z","author":[{"first_name":"Rupert","last_name":"Frank","full_name":"Frank, Rupert"},{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Phan Thanh","first_name":"Nam","full_name":"Phan Thanh, Nam"},{"last_name":"Van Den Bosch","first_name":"Hanne","full_name":"Van Den Bosch, Hanne"}],"publist_id":"7377","page":"577 - 614","article_type":"original","citation":{"chicago":"Frank, Rupert, Phan Nam, and Hanne Van Den Bosch. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2018. https://doi.org/10.1002/cpa.21717.","mla":"Frank, Rupert, et al. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics, vol. 71, no. 3, Wiley-Blackwell, 2018, pp. 577–614, doi:10.1002/cpa.21717.","short":"R. Frank, P. Nam, H. Van Den Bosch, Communications on Pure and Applied Mathematics 71 (2018) 577–614.","ista":"Frank R, Nam P, Van Den Bosch H. 2018. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 71(3), 577–614.","apa":"Frank, R., Nam, P., & Van Den Bosch, H. (2018). The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21717","ieee":"R. Frank, P. Nam, and H. Van Den Bosch, “The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory,” Communications on Pure and Applied Mathematics, vol. 71, no. 3. Wiley-Blackwell, pp. 577–614, 2018.","ama":"Frank R, Nam P, Van Den Bosch H. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 2018;71(3):577-614. doi:10.1002/cpa.21717"},"publication":"Communications on Pure and Applied Mathematics","date_published":"2018-03-01T00:00:00Z","article_processing_charge":"No","day":"01","intvolume":" 71","status":"public","title":"The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"446","oa_version":"Preprint","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"We prove that in Thomas–Fermi–Dirac–von Weizsäcker theory, a nucleus of charge Z > 0 can bind at most Z + C electrons, where C is a universal constant. This result is obtained through a comparison with Thomas-Fermi theory which, as a by-product, gives bounds on the screened nuclear potential and the radius of the minimizer. A key ingredient of the proof is a novel technique to control the particles in the exterior region, which also applies to the liquid drop model with a nuclear background potential."}]},{"issue":"4","abstract":[{"lang":"eng","text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly."}],"type":"journal_article","pubrep_id":"1012","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4958","checksum":"3d838dc285df394376555b794b6a5ad1","date_updated":"2020-07-14T12:46:26Z","date_created":"2018-12-12T10:12:40Z","access_level":"open_access","file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","content_type":"application/pdf","file_size":500129,"creator":"system"}],"_id":"430","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 208","title":"Tread lightly interpreting polygenic tests of selection","ddc":["576"],"status":"public","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-04-01T00:00:00Z","citation":{"ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786","apa":"Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786","ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018.","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355.","short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:10.1534/genetics.118.300786.","chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786."},"publication":"Genetics","page":"1351 - 1355","publist_id":"7393","file_date_updated":"2020-07-14T12:46:26Z","author":[{"last_name":"Novembre","first_name":"John","full_name":"Novembre, John"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"volume":208,"date_updated":"2023-09-19T10:17:30Z","date_created":"2018-12-11T11:46:26Z","year":"2018","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","publication_status":"published","month":"04","doi":"10.1534/genetics.118.300786","language":[{"iso":"eng"}],"external_id":{"isi":["000429094400005"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1"},{"article_number":"294","publist_id":"7714","file_date_updated":"2020-07-14T12:45:22Z","year":"2018","department":[{"_id":"BeVi"}],"publisher":"MDPI AG","publication_status":"published","author":[{"last_name":"Ma","first_name":"Wen","full_name":"Ma, Wen"},{"full_name":"Veltsos, Paris","last_name":"Veltsos","first_name":"Paris"},{"full_name":"Toups, Melissa A","last_name":"Toups","first_name":"Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rodrigues, Nicolas","first_name":"Nicolas","last_name":"Rodrigues"},{"first_name":"Roberto","last_name":"Sermier","full_name":"Sermier, Roberto"},{"full_name":"Jeffries, Daniel","first_name":"Daniel","last_name":"Jeffries"},{"full_name":"Perrin, Nicolas","last_name":"Perrin","first_name":"Nicolas"}],"volume":9,"date_created":"2018-12-11T11:45:09Z","date_updated":"2023-09-19T10:15:31Z","month":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000436494200026"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.3390/genes9060294","language":[{"iso":"eng"}],"type":"journal_article","issue":"6","abstract":[{"text":"Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"199","intvolume":" 9","status":"public","title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","ddc":["570"],"file":[{"creator":"dernst","file_size":3985796,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_Genes_Ma.pdf","checksum":"423069beb1cd3cdd25bf3f464b38f1d7","date_updated":"2020-07-14T12:45:22Z","date_created":"2019-02-01T07:52:28Z","file_id":"5905","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"12","citation":{"ama":"Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 2018;9(6). doi:10.3390/genes9060294","ista":"Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294.","apa":"Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., & Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. MDPI AG. https://doi.org/10.3390/genes9060294","ieee":"W. Ma et al., “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” Genes, vol. 9, no. 6. MDPI AG, 2018.","mla":"Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes, vol. 9, no. 6, 294, MDPI AG, 2018, doi:10.3390/genes9060294.","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","chicago":"Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9060294."},"publication":"Genes","date_published":"2018-06-12T00:00:00Z"},{"page":"186 - 191","publication":"PNAS","citation":{"ama":"Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115","apa":"Chalk, M. J., Marre, O., & Tkačik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1711114115","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” PNAS, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.","ista":"Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 115(1), 186–191.","short":"M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.","mla":"Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:10.1073/pnas.1711114115.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1711114115."},"date_published":"2018-01-02T00:00:00Z","scopus_import":"1","day":"02","article_processing_charge":"No","title":"Toward a unified theory of efficient, predictive, and sparse coding","status":"public","intvolume":" 115","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"543","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, “efficient coding” posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints. It is unclear how these types of efficient coding relate or what is expected when different coding objectives are combined. Here we present a unified framework that encompasses previously proposed efficient coding models and extends to unique regimes. We show that optimizing neural responses to encode predictive information can lead them to either correlate or decorrelate their inputs, depending on the stimulus statistics; in contrast, at low noise, efficiently encoding the past always predicts decorrelation. Later, we investigate coding of naturalistic movies and show that qualitatively different types of visual motion tuning and levels of response sparsity are predicted, depending on whether the objective is to recover the past or predict the future. Our approach promises a way to explain the observed diversity of sensory neural responses, as due to multiple functional goals and constraints fulfilled by different cell types and/or circuits."}],"issue":"1","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000419128700049"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/152660 "}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1711114115","month":"01","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"GaTk"}],"year":"2018","date_created":"2018-12-11T11:47:04Z","date_updated":"2023-09-19T10:16:35Z","volume":115,"author":[{"first_name":"Matthew J","last_name":"Chalk","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"publist_id":"7273"},{"article_processing_charge":"No","day":"27","scopus_import":"1","date_published":"2018-02-27T00:00:00Z","page":"968 - 977","citation":{"mla":"Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal, vol. 114, no. 4, Biophysical Society, 2018, pp. 968–77, doi:10.1016/j.bpj.2017.12.022.","short":"K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.","chicago":"Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal. Biophysical Society, 2018. https://doi.org/10.1016/j.bpj.2017.12.022.","ama":"Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 2018;114(4):968-977. doi:10.1016/j.bpj.2017.12.022","ista":"Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977.","ieee":"K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients,” Biophysical Journal, vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018.","apa":"Dasbiswas, K., Hannezo, E. B., & Gov, N. (2018). Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.12.022"},"publication":"Biophysical Journal","issue":"4","abstract":[{"lang":"eng","text":"Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underlie many morphogenetic events and involve spatial gradients in active cellular forces induced by complex chemical signaling. Here, we introduce a mechanochemical model based on the notion that cell shape changes may be induced by external diffusible biomolecules that influence cellular contractility (or equivalently, adhesions) in a concentration-dependent manner—and whose spatial profile in turn is affected by cell shape. We map out theoretically the possible interplay between chemical concentration and cellular structure. Besides providing a direct route to spatial gradients in cell shape profiles in tissues, we show that the dependence on cell shape helps create robust mechanochemical gradients."}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 114","status":"public","title":"Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"421","month":"02","language":[{"iso":"eng"}],"doi":"10.1016/j.bpj.2017.12.022","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000428016700021"],"arxiv":["1709.01486"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.01486"}],"publist_id":"7403","volume":114,"date_created":"2018-12-11T11:46:23Z","date_updated":"2023-09-19T10:13:55Z","author":[{"full_name":"Dasbiswas, Kinjal","last_name":"Dasbiswas","first_name":"Kinjal"},{"last_name":"Hannezo","first_name":"Claude-Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Claude-Edouard B"},{"full_name":"Gov, Nir","last_name":"Gov","first_name":"Nir"}],"publisher":"Biophysical Society","department":[{"_id":"EdHa"}],"publication_status":"published","year":"2018"},{"article_number":"480","publist_id":"7991","ec_funded":1,"file_date_updated":"2020-07-14T12:47:27Z","acknowledgement":"NSF DEB-1830753 and ISTPlus Fellowship","year":"2018","department":[{"_id":"BeVi"}],"publisher":"MDPI AG","publication_status":"published","author":[{"orcid":"0000-0001-9638-1220","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","last_name":"Gammerdinger","first_name":"William J","full_name":"Gammerdinger, William J"},{"full_name":"Kocher, Thomas","last_name":"Kocher","first_name":"Thomas"}],"volume":9,"date_updated":"2023-09-19T10:37:03Z","date_created":"2018-12-11T11:44:26Z","month":"10","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000448656700018"]},"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","isi":1,"doi":"10.3390/genes9100480","language":[{"iso":"eng"}],"type":"journal_article","issue":"10","abstract":[{"text":"African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"63","intvolume":" 9","title":"Unusual diversity of sex chromosomes in African cichlid fishes","ddc":["570"],"status":"public","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1415791,"file_name":"2018_Genes_Gammerdinger.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:27Z","date_created":"2018-12-18T09:54:46Z","checksum":"bec527692e2c9b56919c0429634ff337","file_id":"5743","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"04","citation":{"short":"W.J. Gammerdinger, T. Kocher, Genes 9 (2018).","mla":"Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes, vol. 9, no. 10, 480, MDPI AG, 2018, doi:10.3390/genes9100480.","chicago":"Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9100480.","ama":"Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 2018;9(10). doi:10.3390/genes9100480","apa":"Gammerdinger, W. J., & Kocher, T. (2018). Unusual diversity of sex chromosomes in African cichlid fishes. Genes. MDPI AG. https://doi.org/10.3390/genes9100480","ieee":"W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in African cichlid fishes,” Genes, vol. 9, no. 10. MDPI AG, 2018.","ista":"Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 9(10), 480."},"publication":"Genes","date_published":"2018-10-04T00:00:00Z"},{"publist_id":"7585","author":[{"full_name":"Turner, Christopher","first_name":"Christopher","last_name":"Turner"},{"full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","first_name":"Alexios"},{"full_name":"Abanin, Dmitry","first_name":"Dmitry","last_name":"Abanin"},{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"last_name":"Papić","first_name":"Zlatko","full_name":"Papić, Zlatko"}],"volume":14,"date_updated":"2023-09-19T10:37:55Z","date_created":"2018-12-11T11:45:40Z","acknowledgement":"C.J.T., A.M. and Z.P. acknowledge support from EPSRC grants EP/P009409/1 and EP/M50807X/1, and Royal Society Research Grant RG160635. D.A. acknowledges support from the Swiss National Science Foundation.","year":"2018","publisher":"Nature Publishing Group","department":[{"_id":"MaSe"}],"publication_status":"published","month":"05","doi":"10.1038/s41567-018-0137-5","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://eprints.whiterose.ac.uk/130860/","open_access":"1"}],"external_id":{"isi":["000438253600028"]},"oa":1,"isi":1,"quality_controlled":"1","abstract":[{"text":"The thermodynamic description of many-particle systems rests on the assumption of ergodicity, the ability of a system to explore all allowed configurations in the phase space. Recent studies on many-body localization have revealed the existence of systems that strongly violate ergodicity in the presence of quenched disorder. Here, we demonstrate that ergodicity can be weakly broken by a different mechanism, arising from the presence of special eigenstates in the many-body spectrum that are reminiscent of quantum scars in chaotic non-interacting systems. In the single-particle case, quantum scars correspond to wavefunctions that concentrate in the vicinity of unstable periodic classical trajectories. We show that many-body scars appear in the Fibonacci chain, a model with a constrained local Hilbert space that has recently been experimentally realized in a Rydberg-atom quantum simulator. The quantum scarred eigenstates are embedded throughout the otherwise thermalizing many-body spectrum but lead to direct experimental signatures, as we show for periodic recurrences that reproduce those observed in the experiment. Our results suggest that scarred many-body bands give rise to a new universality class of quantum dynamics, opening up opportunities for the creation of novel states with long-lived coherence in systems that are now experimentally realizable.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","_id":"296","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 14","status":"public","title":"Weak ergodicity breaking from quantum many-body scars","article_processing_charge":"No","day":"14","scopus_import":"1","date_published":"2018-05-14T00:00:00Z","citation":{"ama":"Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. Weak ergodicity breaking from quantum many-body scars. Nature Physics. 2018;14:745-749. doi:10.1038/s41567-018-0137-5","ieee":"C. Turner, A. Michailidis, D. Abanin, M. Serbyn, and Z. Papić, “Weak ergodicity breaking from quantum many-body scars,” Nature Physics, vol. 14. Nature Publishing Group, pp. 745–749, 2018.","apa":"Turner, C., Michailidis, A., Abanin, D., Serbyn, M., & Papić, Z. (2018). Weak ergodicity breaking from quantum many-body scars. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/s41567-018-0137-5","ista":"Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. 2018. Weak ergodicity breaking from quantum many-body scars. Nature Physics. 14, 745–749.","short":"C. Turner, A. Michailidis, D. Abanin, M. Serbyn, Z. Papić, Nature Physics 14 (2018) 745–749.","mla":"Turner, Christopher, et al. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature Physics, vol. 14, Nature Publishing Group, 2018, pp. 745–49, doi:10.1038/s41567-018-0137-5.","chicago":"Turner, Christopher, Alexios Michailidis, Dmitry Abanin, Maksym Serbyn, and Zlatko Papić. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-018-0137-5."},"publication":"Nature Physics","page":"745 - 749","article_type":"original"},{"publist_id":"7198","author":[{"first_name":"Katarina","last_name":"Bodova","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","full_name":"Bodova, Katarina"},{"full_name":"Haskovec, Jan","first_name":"Jan","last_name":"Haskovec"},{"full_name":"Markowich, Peter","first_name":"Peter","last_name":"Markowich"}],"volume":"376-377","date_updated":"2023-09-19T10:38:34Z","date_created":"2018-12-11T11:47:28Z","acknowledgement":"JH and PM are funded by KAUST baseline funds and grant no. 1000000193 .\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions. \r\n\r\n","year":"2018","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Elsevier","publication_status":"published","month":"08","doi":"10.1016/j.physd.2017.10.015","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.08757"}],"oa":1,"external_id":{"arxiv":["1704.08757"],"isi":["000437962900012"]},"quality_controlled":"1","isi":1,"abstract":[{"text":"We study the Fokker-Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker-Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain's boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker-Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","_id":"607","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Well posedness and maximum entropy approximation for the dynamics of quantitative traits","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-08-01T00:00:00Z","citation":{"short":"K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.","mla":"Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015.","chicago":"Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.","ama":"Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015","apa":"Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015","ieee":"K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” Physica D: Nonlinear Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.","ista":"Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 376–377, 108–120."},"publication":"Physica D: Nonlinear Phenomena","page":"108-120"},{"article_processing_charge":"No","day":"18","scopus_import":"1","date_published":"2018-04-18T00:00:00Z","citation":{"ama":"Fratini F, Safari L, Amaro P, Santos J. Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043842","ista":"Fratini F, Safari L, Amaro P, Santos J. 2018. Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4).","apa":"Fratini, F., Safari, L., Amaro, P., & Santos, J. (2018). Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043842","ieee":"F. Fratini, L. Safari, P. Amaro, and J. Santos, “Two-photon processes based on quantum commutators,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018.","mla":"Fratini, Filippo, et al. “Two-Photon Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043842.","short":"F. Fratini, L. Safari, P. Amaro, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","chicago":"Fratini, Filippo, Laleh Safari, Pedro Amaro, and José Santos. “Two-Photon Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043842."},"publication":"Physical Review A - Atomic, Molecular, and Optical Physics","issue":"4","abstract":[{"text":"We developed a method to calculate two-photon processes in quantum mechanics that replaces the infinite summation over the intermediate states by a perturbation expansion. This latter consists of a series of commutators that involve position, momentum, and Hamiltonian quantum operators. We analyzed several single- and many-particle cases for which a closed-form solution to the perturbation expansion exists, as well as more complicated cases for which a solution is found by convergence. Throughout the article, Rayleigh and Raman scattering are taken as examples of two-photon processes. The present method provides a clear distinction between the Thomson scattering, regarded as classical scattering, and quantum contributions. Such a distinction lets us derive general results concerning light scattering. Finally, possible extensions to the developed formalism are discussed.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 97","title":"Two-photon processes based on quantum commutators","status":"public","_id":"294","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"04","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.97.043842","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1801.06892","open_access":"1"}],"oa":1,"external_id":{"isi":["000430296800008"],"arxiv":["1801.06892"]},"ec_funded":1,"publist_id":"7587","volume":97,"date_created":"2018-12-11T11:45:40Z","date_updated":"2023-09-19T10:17:56Z","author":[{"last_name":"Fratini","first_name":"Filippo","full_name":"Fratini, Filippo"},{"full_name":"Safari, Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","last_name":"Safari","first_name":"Laleh"},{"first_name":"Pedro","last_name":"Amaro","full_name":"Amaro, Pedro"},{"first_name":"José","last_name":"Santos","full_name":"Santos, José"}],"department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","year":"2018"},{"publist_id":"7199","author":[{"first_name":"Mitia","last_name":"Duerinckx","full_name":"Duerinckx, Mitia"},{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L"}],"date_updated":"2023-09-19T10:39:09Z","date_created":"2018-12-11T11:47:27Z","volume":35,"acknowledgement":"The work of the author is supported by F.R.S.-FNRS ( Fonds de la Recherche Scientifique - FNRS ) through a Research Fellowship.\r\n\r\n","year":"2018","publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"Elsevier","month":"08","doi":"10.1016/j.anihpc.2017.11.004","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.00268"}],"external_id":{"arxiv":["1607.00268"],"isi":["000437975500005"]},"oa":1,"quality_controlled":"1","isi":1,"abstract":[{"lang":"eng","text":"We establish the existence of a global solution for a new family of fluid-like equations, which are obtained in certain regimes in as the mean-field evolution of the supercurrent density in a (2D section of a) type-II superconductor with pinning and with imposed electric current. We also consider general vortex-sheet initial data, and investigate the uniqueness and regularity properties of the solution. For some choice of parameters, the equation under investigation coincides with the so-called lake equation from 2D shallow water fluid dynamics, and our analysis then leads to a new existence result for rough initial data."}],"issue":"5","type":"journal_article","oa_version":"Submitted Version","_id":"606","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Well-posedness for mean-field evolutions arising in superconductivity","status":"public","intvolume":" 35","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-08-01T00:00:00Z","publication":"Annales de l'Institut Henri Poincare (C) Non Linear Analysis","citation":{"mla":"Duerinckx, Mitia, and Julian L. Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5, Elsevier, 2018, pp. 1267–319, doi:10.1016/j.anihpc.2017.11.004.","short":"M. Duerinckx, J.L. Fischer, Annales de l’Institut Henri Poincare (C) Non Linear Analysis 35 (2018) 1267–1319.","chicago":"Duerinckx, Mitia, and Julian L Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier, 2018. https://doi.org/10.1016/j.anihpc.2017.11.004.","ama":"Duerinckx M, Fischer JL. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 2018;35(5):1267-1319. doi:10.1016/j.anihpc.2017.11.004","ista":"Duerinckx M, Fischer JL. 2018. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 35(5), 1267–1319.","ieee":"M. Duerinckx and J. L. Fischer, “Well-posedness for mean-field evolutions arising in superconductivity,” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5. Elsevier, pp. 1267–1319, 2018.","apa":"Duerinckx, M., & Fischer, J. L. (2018). Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier. https://doi.org/10.1016/j.anihpc.2017.11.004"},"page":"1267-1319"},{"month":"09","publication_identifier":{"isbn":["9781538655603"]},"isi":1,"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"external_id":{"isi":["000492828500005"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2018-10-05","location":"Turin, Italy","start_date":"2018-09-30","name":"EMSOFT: International Conference on Embedded Software"},"doi":"10.1109/emsoft.2018.8537203","file_date_updated":"2020-07-14T12:47:13Z","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"IEEE","year":"2018","date_updated":"2023-09-19T10:41:29Z","date_created":"2019-02-13T09:19:28Z","author":[{"full_name":"Bakhirkin, Alexey","first_name":"Alexey","last_name":"Bakhirkin"},{"orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas","full_name":"Ferrere, Thomas"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"first_name":"Deian","last_name":"Nickovicl","full_name":"Nickovicl, Deian"}],"scopus_import":"1","day":"30","article_processing_charge":"No","has_accepted_license":"1","page":"1-10","publication":"2018 International Conference on Embedded Software","citation":{"chicago":"Bakhirkin, Alexey, Thomas Ferrere, Thomas A Henzinger, and Deian Nickovicl. “Keynote: The First-Order Logic of Signals.” In 2018 International Conference on Embedded Software, 1–10. IEEE, 2018. https://doi.org/10.1109/emsoft.2018.8537203.","mla":"Bakhirkin, Alexey, et al. “Keynote: The First-Order Logic of Signals.” 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10, doi:10.1109/emsoft.2018.8537203.","short":"A. Bakhirkin, T. Ferrere, T.A. Henzinger, D. Nickovicl, in:, 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10.","ista":"Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. 2018. Keynote: The first-order logic of signals. 2018 International Conference on Embedded Software. EMSOFT: International Conference on Embedded Software, 1–10.","ieee":"A. Bakhirkin, T. Ferrere, T. A. Henzinger, and D. Nickovicl, “Keynote: The first-order logic of signals,” in 2018 International Conference on Embedded Software, Turin, Italy, 2018, pp. 1–10.","apa":"Bakhirkin, A., Ferrere, T., Henzinger, T. A., & Nickovicl, D. (2018). Keynote: The first-order logic of signals. In 2018 International Conference on Embedded Software (pp. 1–10). Turin, Italy: IEEE. https://doi.org/10.1109/emsoft.2018.8537203","ama":"Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. Keynote: The first-order logic of signals. In: 2018 International Conference on Embedded Software. IEEE; 2018:1-10. doi:10.1109/emsoft.2018.8537203"},"date_published":"2018-09-30T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"Formalizing properties of systems with continuous dynamics is a challenging task. In this paper, we propose a formal framework for specifying and monitoring rich temporal properties of real-valued signals. We introduce signal first-order logic (SFO) as a specification language that combines first-order logic with linear-real arithmetic and unary function symbols interpreted as piecewise-linear signals. We first show that while the satisfiability problem for SFO is undecidable, its membership and monitoring problems are decidable. We develop an offline monitoring procedure for SFO that has polynomial complexity in the size of the input trace and the specification, for a fixed number of quantifiers and function symbols. We show that the algorithm has computation time linear in the size of the input trace for the important fragment of bounded-response specifications interpreted over input traces with finite variability. We can use our results to extend signal temporal logic with first-order quantifiers over time and value parameters, while preserving its efficient monitoring. We finally demonstrate the practical appeal of our logic through a case study in the micro-electronics domain."}],"ddc":["000"],"status":"public","title":"Keynote: The first-order logic of signals","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5959","oa_version":"Published Version","file":[{"file_id":"7839","relation":"main_file","checksum":"234a33ad9055b3458fcdda6af251b33a","date_created":"2020-05-14T16:01:29Z","date_updated":"2020-07-14T12:47:13Z","access_level":"open_access","file_name":"2018_EMSOFT_Bakhirkin.pdf","creator":"dernst","file_size":338006,"content_type":"application/pdf"}]},{"publication_identifier":{"isbn":["9781450357951"]},"month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1803.08841","open_access":"1"}],"oa":1,"external_id":{"isi":["000458186900022"],"arxiv":["1803.08841"]},"quality_controlled":"1","isi":1,"doi":"10.1145/3212734.3212763","conference":{"end_date":"2018-07-27","location":"Egham, United Kingdom","start_date":"2018-07-23","name":"PODC: Principles of Distributed Computing"},"language":[{"iso":"eng"}],"year":"2018","department":[{"_id":"DaAl"}],"publisher":"ACM Press","publication_status":"published","author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"first_name":"Christopher","last_name":"De Sa","full_name":"De Sa, Christopher"},{"first_name":"Nikola H","last_name":"Konstantinov","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","full_name":"Konstantinov, Nikola H"}],"date_created":"2019-02-13T09:58:58Z","date_updated":"2023-09-19T10:42:53Z","scopus_import":"1","article_processing_charge":"No","day":"23","citation":{"chicago":"Alistarh, Dan-Adrian, Christopher De Sa, and Nikola H Konstantinov. “The Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 169–78. ACM Press, 2018. https://doi.org/10.1145/3212734.3212763.","short":"D.-A. Alistarh, C. De Sa, N.H. Konstantinov, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 169–178.","mla":"Alistarh, Dan-Adrian, et al. “The Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 169–78, doi:10.1145/3212734.3212763.","ieee":"D.-A. Alistarh, C. De Sa, and N. H. Konstantinov, “The convergence of stochastic gradient descent in asynchronous shared memory,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 169–178.","apa":"Alistarh, D.-A., De Sa, C., & Konstantinov, N. H. (2018). The convergence of stochastic gradient descent in asynchronous shared memory. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 169–178). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212763","ista":"Alistarh D-A, De Sa C, Konstantinov NH. 2018. The convergence of stochastic gradient descent in asynchronous shared memory. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 169–178.","ama":"Alistarh D-A, De Sa C, Konstantinov NH. The convergence of stochastic gradient descent in asynchronous shared memory. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:169-178. doi:10.1145/3212734.3212763"},"publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","page":"169-178","date_published":"2018-07-23T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"Stochastic Gradient Descent (SGD) is a fundamental algorithm in machine learning, representing the optimization backbone for training several classic models, from regression to neural networks. Given the recent practical focus on distributed machine learning, significant work has been dedicated to the convergence properties of this algorithm under the inconsistent and noisy updates arising from execution in a distributed environment. However, surprisingly, the convergence properties of this classic algorithm in the standard shared-memory model are still not well-understood. In this work, we address this gap, and provide new convergence bounds for lock-free concurrent stochastic gradient descent, executing in the classic asynchronous shared memory model, against a strong adaptive adversary. Our results give improved upper and lower bounds on the \"price of asynchrony'' when executing the fundamental SGD algorithm in a concurrent setting. They show that this classic optimization tool can converge faster and with a wider range of parameters than previously known under asynchronous iterations. At the same time, we exhibit a fundamental trade-off between the maximum delay in the system and the rate at which SGD can converge, which governs the set of parameters under which this algorithm can still work efficiently."}],"_id":"5962","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"The convergence of stochastic gradient descent in asynchronous shared memory","oa_version":"Preprint"},{"external_id":{"arxiv":["1612.01605"],"isi":["000456783800002"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1612.01605","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1098/rsif.2018.0395","language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["17425689"]},"year":"2018","publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"Royal Society Publishing","author":[{"full_name":"Corominas-Murtra, Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643","first_name":"Bernat","last_name":"Corominas-Murtra"},{"last_name":"Seoane","first_name":"Luís F.","full_name":"Seoane, Luís F."},{"full_name":"Solé, Ricard","last_name":"Solé","first_name":"Ricard"}],"date_created":"2019-01-20T22:59:19Z","date_updated":"2023-09-19T10:40:38Z","volume":15,"article_number":"20180395","publication":"Journal of the Royal Society Interface","citation":{"chicago":"Corominas-Murtra, Bernat, Luís F. Seoane, and Ricard Solé. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0395.","mla":"Corominas-Murtra, Bernat, et al. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180395, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0395.","short":"B. Corominas-Murtra, L.F. Seoane, R. Solé, Journal of the Royal Society Interface 15 (2018).","ista":"Corominas-Murtra B, Seoane LF, Solé R. 2018. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 15(149), 20180395.","apa":"Corominas-Murtra, B., Seoane, L. F., & Solé, R. (2018). Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0395","ieee":"B. Corominas-Murtra, L. F. Seoane, and R. Solé, “Zipf’s Law, unbounded complexity and open-ended evolution,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018.","ama":"Corominas-Murtra B, Seoane LF, Solé R. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0395"},"date_published":"2018-12-12T00:00:00Z","scopus_import":"1","day":"12","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5860","status":"public","title":"Zipf's Law, unbounded complexity and open-ended evolution","intvolume":" 15","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"A major problem for evolutionary theory is understanding the so-called open-ended nature of evolutionary change, from its definition to its origins. Open-ended evolution (OEE) refers to the unbounded increase in complexity that seems to characterize evolution on multiple scales. This property seems to be a characteristic feature of biological and technological evolution and is strongly tied to the generative potential associated with combinatorics, which allows the system to grow and expand their available state spaces. Interestingly, many complex systems presumably displaying OEE, from language to proteins, share a common statistical property: the presence of Zipf's Law. Given an inventory of basic items (such as words or protein domains) required to build more complex structures (sentences or proteins) Zipf's Law tells us that most of these elements are rare whereas a few of them are extremely common. Using algorithmic information theory, in this paper we provide a fundamental definition for open-endedness, which can be understood as postulates. Its statistical counterpart, based on standard Shannon information theory, has the structure of a variational problem which is shown to lead to Zipf's Law as the expected consequence of an evolutionary process displaying OEE. We further explore the problem of information conservation through an OEE process and we conclude that statistical information (standard Shannon information) is not conserved, resulting in the paradoxical situation in which the increase of information content has the effect of erasing itself. We prove that this paradox is solved if we consider non-statistical forms of information. This last result implies that standard information theory may not be a suitable theoretical framework to explore the persistence and increase of the information content in OEE systems.","lang":"eng"}],"issue":"149"},{"month":"10","publication_identifier":{"issn":["0278-3649"],"eissn":["1741-3176"]},"quality_controlled":"1","isi":1,"external_id":{"arxiv":["1712.01341"],"isi":["000456881100004"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1712.01341","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1177/0278364918808367","publication_status":"published","publisher":"SAGE Publications","department":[{"_id":"UlWa"}],"year":"2018","date_created":"2019-02-13T09:36:20Z","date_updated":"2023-09-19T10:41:59Z","volume":37,"author":[{"full_name":"Rohou, Simon","last_name":"Rohou","first_name":"Simon"},{"full_name":"Franek, Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8878-8397","first_name":"Peter","last_name":"Franek"},{"full_name":"Aubry, Clément","last_name":"Aubry","first_name":"Clément"},{"first_name":"Luc","last_name":"Jaulin","full_name":"Jaulin, Luc"}],"scopus_import":"1","day":"24","article_processing_charge":"No","page":"1500-1516","publication":"The International Journal of Robotics Research","citation":{"short":"S. Rohou, P. Franek, C. Aubry, L. Jaulin, The International Journal of Robotics Research 37 (2018) 1500–1516.","mla":"Rohou, Simon, et al. “Proving the Existence of Loops in Robot Trajectories.” The International Journal of Robotics Research, vol. 37, no. 12, SAGE Publications, 2018, pp. 1500–16, doi:10.1177/0278364918808367.","chicago":"Rohou, Simon, Peter Franek, Clément Aubry, and Luc Jaulin. “Proving the Existence of Loops in Robot Trajectories.” The International Journal of Robotics Research. SAGE Publications, 2018. https://doi.org/10.1177/0278364918808367.","ama":"Rohou S, Franek P, Aubry C, Jaulin L. Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. 2018;37(12):1500-1516. doi:10.1177/0278364918808367","ieee":"S. Rohou, P. Franek, C. Aubry, and L. Jaulin, “Proving the existence of loops in robot trajectories,” The International Journal of Robotics Research, vol. 37, no. 12. SAGE Publications, pp. 1500–1516, 2018.","apa":"Rohou, S., Franek, P., Aubry, C., & Jaulin, L. (2018). Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. SAGE Publications. https://doi.org/10.1177/0278364918808367","ista":"Rohou S, Franek P, Aubry C, Jaulin L. 2018. Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. 37(12), 1500–1516."},"date_published":"2018-10-24T00:00:00Z","type":"journal_article","abstract":[{"text":"In this paper we present a reliable method to verify the existence of loops along the uncertain trajectory of a robot, based on proprioceptive measurements only, within a bounded-error context. The loop closure detection is one of the key points in simultaneous localization and mapping (SLAM) methods, especially in homogeneous environments with difficult scenes recognitions. The proposed approach is generic and could be coupled with conventional SLAM algorithms to reliably reduce their computing burden, thus improving the localization and mapping processes in the most challenging environments such as unexplored underwater extents. To prove that a robot performed a loop whatever the uncertainties in its evolution, we employ the notion of topological degree that originates in the field of differential topology. We show that a verification tool based on the topological degree is an optimal method for proving robot loops. This is demonstrated both on datasets from real missions involving autonomous underwater vehicles and by a mathematical discussion.","lang":"eng"}],"issue":"12","title":"Proving the existence of loops in robot trajectories","status":"public","intvolume":" 37","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5960","oa_version":"Preprint"},{"scopus_import":"1","article_processing_charge":"No","day":"23","citation":{"mla":"Alistarh, Dan-Adrian, et al. “Relaxed Schedulers Can Efficiently Parallelize Iterative Algorithms.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 377–86, doi:10.1145/3212734.3212756.","short":"D.-A. Alistarh, T.A. Brown, J. Kopinsky, G. Nadiradze, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 377–386.","chicago":"Alistarh, Dan-Adrian, Trevor A Brown, Justin Kopinsky, and Giorgi Nadiradze. “Relaxed Schedulers Can Efficiently Parallelize Iterative Algorithms.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 377–86. ACM Press, 2018. https://doi.org/10.1145/3212734.3212756.","ama":"Alistarh D-A, Brown TA, Kopinsky J, Nadiradze G. Relaxed schedulers can efficiently parallelize iterative algorithms. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:377-386. doi:10.1145/3212734.3212756","ista":"Alistarh D-A, Brown TA, Kopinsky J, Nadiradze G. 2018. Relaxed schedulers can efficiently parallelize iterative algorithms. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 377–386.","ieee":"D.-A. Alistarh, T. A. Brown, J. Kopinsky, and G. Nadiradze, “Relaxed schedulers can efficiently parallelize iterative algorithms,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 377–386.","apa":"Alistarh, D.-A., Brown, T. A., Kopinsky, J., & Nadiradze, G. (2018). Relaxed schedulers can efficiently parallelize iterative algorithms. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 377–386). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212756"},"publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","page":"377-386","date_published":"2018-07-23T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"There has been significant progress in understanding the parallelism inherent to iterative sequential algorithms: for many classic algorithms, the depth of the dependence structure is now well understood, and scheduling techniques have been developed to exploit this shallow dependence structure for efficient parallel implementations. A related, applied research strand has studied methods by which certain iterative task-based algorithms can be efficiently parallelized via relaxed concurrent priority schedulers. These allow for high concurrency when inserting and removing tasks, at the cost of executing superfluous work due to the relaxed semantics of the scheduler. In this work, we take a step towards unifying these two research directions, by showing that there exists a family of relaxed priority schedulers that can efficiently and deterministically execute classic iterative algorithms such as greedy maximal independent set (MIS) and matching. Our primary result shows that, given a randomized scheduler with an expected relaxation factor of k in terms of the maximum allowed priority inversions on a task, and any graph on n vertices, the scheduler is able to execute greedy MIS with only an additive factor of \\poly(k) expected additional iterations compared to an exact (but not scalable) scheduler. This counter-intuitive result demonstrates that the overhead of relaxation when computing MIS is not dependent on the input size or structure of the input graph. Experimental results show that this overhead can be clearly offset by the gain in performance due to the highly scalable scheduler. In sum, we present an efficient method to deterministically parallelize iterative sequential algorithms, with provable runtime guarantees in terms of the number of executed tasks to completion."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5963","title":"Relaxed schedulers can efficiently parallelize iterative algorithms","status":"public","oa_version":"Preprint","publication_identifier":{"isbn":["9781450357951"]},"month":"07","external_id":{"arxiv":["1808.04155"],"isi":["000458186900048"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04155"}],"isi":1,"quality_controlled":"1","doi":"10.1145/3212734.3212756","conference":{"name":"PODC: Principles of Distributed Computing","end_date":"2018-07-27","start_date":"2018-07-23","location":"Egham, United Kingdom"},"language":[{"iso":"eng"}],"year":"2018","publisher":"ACM Press","department":[{"_id":"DaAl"}],"publication_status":"published","author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"full_name":"Brown, Trevor A","last_name":"Brown","first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kopinsky, Justin","last_name":"Kopinsky","first_name":"Justin"},{"full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","first_name":"Giorgi"}],"date_updated":"2023-09-19T10:43:21Z","date_created":"2019-02-13T10:03:25Z"}]