[{"language":[{"iso":"eng"}],"intvolume":"        66","publication_status":"published","pmid":1,"isi":1,"_id":"163","date_published":"2018-12-01T00:00:00Z","type":"journal_article","month":"12","abstract":[{"text":"For ultrafast fixation of biological samples to avoid artifacts, high-pressure freezing (HPF) followed by freeze substitution (FS) is preferred over chemical fixation at room temperature. After HPF, samples are maintained at low temperature during dehydration and fixation, while avoiding damaging recrystallization. This is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample agitation during FS dramatically reduces the necessary time. Then, in 2015, we (H.G. and S.R.) introduced an agitation module into the cryochamber of an automated FS unit and demonstrated that the preparation of algae could be shortened from days to a couple of hours. We argued that variability in the processing, reproducibility, and safety issues are better addressed using automated FS units. For dissemination, we started low-cost manufacturing of agitation modules for two of the most widely used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from Leica Microsystems, using three dimensional (3D)-printing of the major components. To test them, several labs independently used the modules on a wide variety of specimens that had previously been processed by manual agitation, or without agitation. We demonstrate that automated processing with sample agitation saves time, increases flexibility with respect to sample requirements and protocols, and produces data of at least as good quality as other approaches.","lang":"eng"}],"external_id":{"isi":["000452277700005"],"pmid":["29969056"]},"publication_identifier":{"issn":["0022-1554"]},"department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"title":"Agitation modules: Flexible means to accelerate automated freeze substitution","oa_version":"Published Version","doi":"10.1369/0022155418786698","date_created":"2018-12-11T11:44:57Z","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1369/0022155418786698","open_access":"1"}],"publisher":"SAGE Publications","scopus_import":"1","publication":"Journal of Histochemistry and Cytochemistry","status":"public","citation":{"mla":"Reipert, Siegfried, et al. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” <i>Journal of Histochemistry and Cytochemistry</i>, vol. 66, no. 12, SAGE Publications, 2018, pp. 903–21, doi:<a href=\"https://doi.org/10.1369/0022155418786698\">10.1369/0022155418786698</a>.","ieee":"S. Reipert <i>et al.</i>, “Agitation modules: Flexible means to accelerate automated freeze substitution,” <i>Journal of Histochemistry and Cytochemistry</i>, vol. 66, no. 12. SAGE Publications, pp. 903–921, 2018.","apa":"Reipert, S., Goldammer, H., Richardson, C., Goldberg, M., Hawkins, T., Saeckl, E., … Stierhof, Y. (2018). Agitation modules: Flexible means to accelerate automated freeze substitution. <i>Journal of Histochemistry and Cytochemistry</i>. SAGE Publications. <a href=\"https://doi.org/10.1369/0022155418786698\">https://doi.org/10.1369/0022155418786698</a>","ama":"Reipert S, Goldammer H, Richardson C, et al. Agitation modules: Flexible means to accelerate automated freeze substitution. <i>Journal of Histochemistry and Cytochemistry</i>. 2018;66(12):903-921. doi:<a href=\"https://doi.org/10.1369/0022155418786698\">10.1369/0022155418786698</a>","ista":"Reipert S, Goldammer H, Richardson C, Goldberg M, Hawkins T, Saeckl E, Kaufmann W, Antreich S, Stierhof Y. 2018. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 66(12), 903–921.","short":"S. Reipert, H. Goldammer, C. Richardson, M. Goldberg, T. Hawkins, E. Saeckl, W. Kaufmann, S. Antreich, Y. Stierhof, Journal of Histochemistry and Cytochemistry 66 (2018) 903–921.","chicago":"Reipert, Siegfried, Helmuth Goldammer, Christine Richardson, Martin Goldberg, Timothy Hawkins, Elena Saeckl, Walter Kaufmann, Sebastian Antreich, and York Stierhof. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” <i>Journal of Histochemistry and Cytochemistry</i>. SAGE Publications, 2018. <a href=\"https://doi.org/10.1369/0022155418786698\">https://doi.org/10.1369/0022155418786698</a>."},"page":"903-921","author":[{"last_name":"Reipert","first_name":"Siegfried","full_name":"Reipert, Siegfried"},{"first_name":"Helmuth","last_name":"Goldammer","full_name":"Goldammer, Helmuth"},{"first_name":"Christine","last_name":"Richardson","full_name":"Richardson, Christine"},{"full_name":"Goldberg, Martin","first_name":"Martin","last_name":"Goldberg"},{"full_name":"Hawkins, Timothy","first_name":"Timothy","last_name":"Hawkins"},{"full_name":"Hollergschwandtner, Elena","first_name":"Elena","last_name":"Hollergschwandtner","id":"3C054040-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","first_name":"Walter","last_name":"Kaufmann"},{"full_name":"Antreich, Sebastian","first_name":"Sebastian","last_name":"Antreich"},{"last_name":"Stierhof","first_name":"York","full_name":"Stierhof, York"}],"year":"2018","date_updated":"2023-10-17T08:42:24Z","article_type":"original","quality_controlled":"1","oa":1,"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":66,"issue":"12"},{"date_published":"2018-10-15T00:00:00Z","_id":"17","isi":1,"publist_id":"8038","publication_status":"published","intvolume":"         3","language":[{"iso":"eng"}],"article_processing_charge":"No","doi":"10.1103/PhysRevFluids.3.103302","date_created":"2018-12-11T11:44:11Z","oa_version":"Published Version","title":"Drag enhancement and drag reduction in viscoelastic flow","department":[{"_id":"BjHo"}],"pubrep_id":"1061","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"external_id":{"isi":["000447311500001"]},"abstract":[{"lang":"eng","text":"Creeping flow of polymeric fluid without inertia exhibits elastic instabilities and elastic turbulence accompanied by drag enhancement due to elastic stress produced by flow-stretched polymers. However, in inertia-dominated flow at high Re and low fluid elasticity El, a reduction in turbulent frictional drag is caused by an intricate competition between inertial and elastic stresses. Here we explore the effect of inertia on the stability of viscoelastic flow in a broad range of control parameters El and (Re,Wi). We present the stability diagram of observed flow regimes in Wi-Re coordinates and find that the instabilities' onsets show an unexpectedly nonmonotonic dependence on El. Further, three distinct regions in the diagram are identified based on El. Strikingly, for high-elasticity fluids we discover a complete relaminarization of flow at Reynolds number in the range of 1 to 10, different from a well-known turbulent drag reduction. These counterintuitive effects may be explained by a finite polymer extensibility and a suppression of vorticity at high Wi. Our results call for further theoretical and numerical development to uncover the role of inertial effect on elastic turbulence in a viscoelastic flow."}],"file_date_updated":"2020-07-14T12:45:12Z","type":"journal_article","month":"10","date_updated":"2025-04-14T07:43:59Z","year":"2018","author":[{"id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul","last_name":"Varshney","first_name":"Atul"},{"first_name":"Victor","last_name":"Steinberg","full_name":"Steinberg, Victor"}],"citation":{"apa":"Varshney, A., &#38; Steinberg, V. (2018). Drag enhancement and drag reduction in viscoelastic flow. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">https://doi.org/10.1103/PhysRevFluids.3.103302</a>","mla":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” <i>Physical Review Fluids</i>, vol. 3, no. 10, 103302, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">10.1103/PhysRevFluids.3.103302</a>.","ama":"Varshney A, Steinberg V. Drag enhancement and drag reduction in viscoelastic flow. <i>Physical Review Fluids</i>. 2018;3(10). doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">10.1103/PhysRevFluids.3.103302</a>","ieee":"A. Varshney and V. Steinberg, “Drag enhancement and drag reduction in viscoelastic flow,” <i>Physical Review Fluids</i>, vol. 3, no. 10. American Physical Society, 2018.","chicago":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” <i>Physical Review Fluids</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">https://doi.org/10.1103/PhysRevFluids.3.103302</a>.","ista":"Varshney A, Steinberg V. 2018. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 3(10), 103302.","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018)."},"ddc":["532"],"article_number":"103302 ","status":"public","publication":"Physical Review Fluids","scopus_import":"1","has_accepted_license":"1","ec_funded":1,"file":[{"file_name":"IST-2018-1061-v1+1_PhysRevFluids.3.103302.pdf","creator":"system","file_id":"4800","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:45:12Z","date_created":"2018-12-12T10:10:14Z","checksum":"e1445be33e8165114e96246275600750","content_type":"application/pdf","file_size":1409040}],"publisher":"American Physical Society","issue":"10","volume":3,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"15","oa":1,"quality_controlled":"1"},{"oa":1,"quality_controlled":"1","volume":11022,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["LNCS"],"day":"26","ddc":["000"],"citation":{"chicago":"Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-00151-3_13\">https://doi.org/10.1007/978-3-030-00151-3_13</a>.","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., &#38; 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. <a href=\"https://doi.org/10.1007/978-3-030-00151-3_13\">https://doi.org/10.1007/978-3-030-00151-3_13</a>","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:<a href=\"https://doi.org/10.1007/978-3-030-00151-3_13\">10.1007/978-3-030-00151-3_13</a>","mla":"Bakhirkin, Alexey, et al. <i>Online Timed Pattern Matching Using Automata</i>. Vol. 11022, Springer, 2018, pp. 215–32, doi:<a href=\"https://doi.org/10.1007/978-3-030-00151-3_13\">10.1007/978-3-030-00151-3_13</a>.","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."},"page":"215 - 232","status":"public","has_accepted_license":"1","scopus_import":"1","file":[{"file_name":"2018_LNCS_Bakhirkin.pdf","creator":"dernst","file_id":"7831","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-14T11:34:34Z","file_size":374851,"checksum":"436b7574934324cfa7d1d3986fddc65b","content_type":"application/pdf"}],"publisher":"Springer","conference":{"location":"Bejing, China","name":"FORMATS: Formal Modeling and Analysis of Timed Systems","end_date":"2018-09-06","start_date":"2018-09-04"},"date_updated":"2025-04-15T06:26:03Z","year":"2018","author":[{"last_name":"Bakhirkin","first_name":"Alexey","full_name":"Bakhirkin, Alexey"},{"last_name":"Ferrere","first_name":"Thomas","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"},{"last_name":"Maler","first_name":"Oded","full_name":"Maler, Oded"},{"full_name":"Asarin, Eugene","last_name":"Asarin","first_name":"Eugene"}],"publication_identifier":{"isbn":["978-3-030-00150-6"]},"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"external_id":{"isi":["000884993200013"]},"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."}],"month":"08","type":"conference","file_date_updated":"2020-07-14T12:48:03Z","article_processing_charge":"No","doi":"10.1007/978-3-030-00151-3_13","oa_version":"Submitted Version","date_created":"2018-12-11T11:44:31Z","title":"Online timed pattern matching using automata","department":[{"_id":"ToHe"}],"publist_id":"7976","publication_status":"published","intvolume":"     11022","language":[{"iso":"eng"}],"date_published":"2018-08-26T00:00:00Z","isi":1,"_id":"78"},{"acknowledgement":"We would like to thank Ce Zhang (ETH Zurich), Hantian Zhang (ETH Zurich) and Martin Jaggi ´\r\n(EPFL) for their support with experiments and valuable feedback.\r\n","external_id":{"arxiv":["1802.05668"]},"abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method,  differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model.  We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices."}],"month":"05","file_date_updated":"2020-07-14T12:48:03Z","arxiv":1,"type":"conference","article_processing_charge":"No","oa_version":"Published Version","date_created":"2020-05-10T22:00:51Z","title":"Model compression via distillation and quantization","department":[{"_id":"DaAl"}],"publication_status":"published","language":[{"iso":"eng"}],"date_published":"2018-05-01T00:00:00Z","_id":"7812","oa":1,"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","ddc":["000"],"citation":{"apa":"Polino, A., Pascanu, R., &#38; Alistarh, D.-A. (2018). Model compression via distillation and quantization. In <i>6th International Conference on Learning Representations</i>. Vancouver, Canada.","mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” <i>6th International Conference on Learning Representations</i>, 2018.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: <i>6th International Conference on Learning Representations</i>. ; 2018.","ieee":"A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in <i>6th International Conference on Learning Representations</i>, Vancouver, Canada, 2018.","short":"A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018.","ista":"Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation and quantization. 6th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","chicago":"Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In <i>6th International Conference on Learning Representations</i>, 2018."},"status":"public","publication":"6th International Conference on Learning Representations","has_accepted_license":"1","scopus_import":"1","file":[{"date_updated":"2020-07-14T12:48:03Z","access_level":"open_access","date_created":"2020-05-26T13:02:00Z","content_type":"application/pdf","checksum":"a4336c167978e81891970e4e4517a8c3","file_size":308339,"creator":"dernst","file_name":"2018_ICLR_Polino.pdf","relation":"main_file","file_id":"7894"}],"conference":{"end_date":"2018-05-03","start_date":"2018-04-30","name":"ICLR: International Conference on Learning Representations","location":"Vancouver, Canada"},"date_updated":"2025-06-30T10:04:44Z","year":"2018","author":[{"last_name":"Polino","first_name":"Antonio","full_name":"Polino, Antonio"},{"first_name":"Razvan","last_name":"Pascanu","full_name":"Pascanu, Razvan"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"}]},{"title":"Parameter-independent strategies for pMDPs via POMDPs","main_file_link":[{"url":"https://arxiv.org/abs/1806.05126","open_access":"1"}],"article_processing_charge":"No","date_created":"2018-12-11T11:44:31Z","doi":"10.1007/978-3-319-99154-2_4","oa_version":"Preprint","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"abstract":[{"lang":"eng","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."}],"month":"08","arxiv":1,"type":"conference","external_id":{"arxiv":["1806.05126"],"isi":["000548912200004"]},"date_published":"2018-08-15T00:00:00Z","_id":"79","isi":1,"publication_status":"published","intvolume":"     11024","publist_id":"7975","language":[{"iso":"eng"}],"volume":11024,"alternative_title":["LNCS"],"day":"15","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","oa":1,"date_updated":"2023-09-13T09:38:28Z","year":"2018","author":[{"full_name":"Arming, Sebastian","first_name":"Sebastian","last_name":"Arming"},{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Katoen, Joost P","last_name":"Katoen","first_name":"Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sokolova","first_name":"Ana","full_name":"Sokolova, Ana"}],"status":"public","page":"53-70","citation":{"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:<a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">10.1007/978-3-319-99154-2_4</a>","apa":"Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., &#38; 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. <a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">https://doi.org/10.1007/978-3-319-99154-2_4</a>","mla":"Arming, Sebastian, et al. <i>Parameter-Independent Strategies for PMDPs via POMDPs</i>. Vol. 11024, Springer, 2018, pp. 53–70, doi:<a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">10.1007/978-3-319-99154-2_4</a>.","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.","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.","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. <a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">https://doi.org/10.1007/978-3-319-99154-2_4</a>.","short":"S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer, 2018, pp. 53–70."},"scopus_import":"1","conference":{"location":"Beijing, China","name":"QEST: Quantitative Evaluation of Systems","start_date":"2018-09-04","end_date":"2018-09-07"},"publisher":"Springer"},{"publication_status":"published","intvolume":"     11022","publist_id":"7973","language":[{"iso":"eng"}],"date_published":"2018-08-26T00:00:00Z","isi":1,"_id":"81","abstract":[{"lang":"eng","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,"}],"file_date_updated":"2020-10-09T06:24:21Z","type":"conference","month":"08","project":[{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000884993200004"]},"title":"Monitoring temporal logic with clock variables","article_processing_charge":"No","oa_version":"Submitted Version","date_created":"2018-12-11T11:44:31Z","doi":"10.1007/978-3-030-00151-3_4","department":[{"_id":"ToHe"}],"status":"public","citation":{"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., &#38; 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. <a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">https://doi.org/10.1007/978-3-030-00151-3_4</a>","ama":"Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables. In: Vol 11022. Springer; 2018:53-70. doi:<a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">10.1007/978-3-030-00151-3_4</a>","mla":"Elgyütt, Adrian, et al. <i>Monitoring Temporal Logic with Clock Variables</i>. Vol. 11022, Springer, 2018, pp. 53–70, doi:<a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">10.1007/978-3-030-00151-3_4</a>.","chicago":"Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal Logic with Clock Variables,” 11022:53–70. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">https://doi.org/10.1007/978-3-030-00151-3_4</a>.","short":"A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.","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."},"page":"53 - 70","ddc":["000"],"has_accepted_license":"1","scopus_import":"1","publisher":"Springer","file":[{"file_id":"8638","relation":"main_file","file_name":"2018_LNCS_Elgyuett.pdf","creator":"dernst","success":1,"date_created":"2020-10-09T06:24:21Z","date_updated":"2020-10-09T06:24:21Z","access_level":"open_access","file_size":537219,"checksum":"e5d81c9b50a6bd9d8a2c16953aad7e23","content_type":"application/pdf"}],"conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","start_date":"2018-09-04","end_date":"2018-09-06","location":"Beijing, China"},"date_updated":"2025-04-15T06:26:03Z","year":"2018","author":[{"id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","full_name":"Elgyütt, Adrian","first_name":"Adrian","last_name":"Elgyütt"},{"orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ferrere","full_name":"Ferrere, Thomas"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"quality_controlled":"1","oa":1,"volume":11022,"alternative_title":["LNCS"],"day":"26","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_updated":"2023-09-13T08:45:41Z","year":"2018","author":[{"first_name":"Waqas","last_name":"Chaudhry","full_name":"Chaudhry, Waqas"},{"last_name":"Pleska","first_name":"Maros","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","id":"4569785E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shah, Nilang","first_name":"Nilang","last_name":"Shah"},{"first_name":"Howard","last_name":"Weiss","full_name":"Weiss, Howard"},{"full_name":"Mccall, Ingrid","first_name":"Ingrid","last_name":"Mccall"},{"last_name":"Meyer","first_name":"Justin","full_name":"Meyer, Justin"},{"first_name":"Animesh","last_name":"Gupta","full_name":"Gupta, Animesh"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet"},{"full_name":"Levin, Bruce","first_name":"Bruce","last_name":"Levin"}],"article_number":"2005971","citation":{"apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005971\">https://doi.org/10.1371/journal.pbio.2005971</a>","mla":"Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” <i>PLoS Biology</i>, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971\">10.1371/journal.pbio.2005971</a>.","ama":"Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. <i>PLoS Biology</i>. 2018;16(8). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971\">10.1371/journal.pbio.2005971</a>","ieee":"W. Chaudhry <i>et al.</i>, “Leaky resistance and the conditions for the existence of lytic bacteriophage,” <i>PLoS Biology</i>, vol. 16, no. 8. Public Library of Science, 2018.","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” <i>PLoS Biology</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pbio.2005971\">https://doi.org/10.1371/journal.pbio.2005971</a>.","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018)."},"ddc":["570"],"status":"public","publication":"PLoS Biology","has_accepted_license":"1","scopus_import":"1","publisher":"Public Library of Science","file":[{"relation":"main_file","file_id":"5706","creator":"dernst","file_name":"2018_Plos_Chaudhry.pdf","checksum":"527076f78265cd4ea192cd1569851587","file_size":4007095,"content_type":"application/pdf","date_created":"2018-12-17T12:55:31Z","access_level":"open_access","date_updated":"2020-07-14T12:48:10Z"}],"issue":"8","volume":16,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"16","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"quality_controlled":"1","date_published":"2018-08-16T00:00:00Z","isi":1,"_id":"82","related_material":{"record":[{"id":"9810","relation":"research_data","status":"public"}]},"publist_id":"7972","publication_status":"published","intvolume":"        16","language":[{"iso":"eng"}],"article_processing_charge":"Yes","license":"https://creativecommons.org/licenses/by/4.0/","date_created":"2018-12-11T11:44:32Z","oa_version":"Published Version","doi":"10.1371/journal.pbio.2005971","title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","department":[{"_id":"CaGu"}],"external_id":{"isi":["000443383300024"]},"abstract":[{"lang":"eng","text":"In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term &quot;leaky resistance.&quot; We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”."}],"month":"08","type":"journal_article","file_date_updated":"2020-07-14T12:48:10Z"},{"citation":{"ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/494088\">https://doi.org/10.1101/494088</a>","mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>.","ieee":"A. Llorca <i>et al.</i>, “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.).","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/494088\">https://doi.org/10.1101/494088</a>.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, <a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>."},"publication_status":"submitted","publication":"bioRxiv","status":"public","language":[{"iso":"eng"}],"ec_funded":1,"publisher":"Cold Spring Harbor Laboratory","date_published":"2018-12-13T00:00:00Z","date_updated":"2024-10-22T10:46:39Z","year":"2018","author":[{"full_name":"Llorca, Alfredo","first_name":"Alfredo","last_name":"Llorca"},{"full_name":"Ciceri, Gabriele","first_name":"Gabriele","last_name":"Ciceri"},{"full_name":"Beattie, Robert J","first_name":"Robert J","last_name":"Beattie","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wong","first_name":"Fong K.","full_name":"Wong, Fong K."},{"full_name":"Diana, Giovanni","first_name":"Giovanni","last_name":"Diana"},{"first_name":"Eleni","last_name":"Serafeimidou","full_name":"Serafeimidou, Eleni"},{"last_name":"Fernández-Otero","first_name":"Marian","full_name":"Fernández-Otero, Marian"},{"full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Arnold, Sebastian J.","first_name":"Sebastian J.","last_name":"Arnold"},{"full_name":"Meyer, Martin","last_name":"Meyer","first_name":"Martin"},{"last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Maravall, Miguel","last_name":"Maravall","first_name":"Miguel"},{"full_name":"Marín, Oscar","first_name":"Oscar","last_name":"Marín"}],"_id":"8547","acknowledgement":"We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme.","project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Neocortex","grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425"}],"oa":1,"abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex."}],"type":"preprint","month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/494088"}],"article_processing_charge":"No","doi":"10.1101/494088","oa_version":"Preprint","date_created":"2020-09-21T12:01:50Z","title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SiHi"}],"day":"13"},{"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","abstract":[{"text":"Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms.","lang":"eng"}],"type":"book_chapter","month":"07","file_date_updated":"2020-07-14T12:48:14Z","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"title":"Computing average response time","oa_version":"Submitted Version","date_created":"2018-12-11T11:44:33Z","doi":"10.1007/978-3-319-95246-8_9","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","intvolume":"     10760","publist_id":"7968","language":[{"iso":"eng"}],"date_published":"2018-07-20T00:00:00Z","_id":"86","quality_controlled":"1","oa":1,"volume":10760,"alternative_title":["LNCS"],"day":"20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication":"Principles of Modeling","citation":{"apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, &#38; M. Sirjani (Eds.), <i>Principles of Modeling</i> (Vol. 10760, pp. 143–161). Springer. <a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">https://doi.org/10.1007/978-3-319-95246-8_9</a>","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in <i>Principles of Modeling</i>, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” <i>Principles of Modeling</i>, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:<a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">10.1007/978-3-319-95246-8_9</a>.","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. <i>Principles of Modeling</i>. Vol 10760. Springer; 2018:143-161. doi:<a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">10.1007/978-3-319-95246-8_9</a>","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In <i>Principles of Modeling</i>, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">https://doi.org/10.1007/978-3-319-95246-8_9</a>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161."},"ddc":["000"],"page":"143 - 161","has_accepted_license":"1","ec_funded":1,"scopus_import":1,"publisher":"Springer","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:48:14Z","date_created":"2019-11-19T08:22:18Z","checksum":"9995c6ce6957333baf616fc4f20be597","file_size":516307,"content_type":"application/pdf","creator":"dernst","file_name":"2018_PrinciplesModeling_Chatterjee.pdf","relation":"main_file","file_id":"7053"}],"date_updated":"2025-04-15T06:26:15Z","editor":[{"full_name":"Lohstroh, Marten","last_name":"Lohstroh","first_name":"Marten"},{"full_name":"Derler, Patricia","first_name":"Patricia","last_name":"Derler"},{"first_name":"Marjan","last_name":"Sirjani","full_name":"Sirjani, Marjan"}],"year":"2018","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"}]},{"oa":1,"quality_controlled":"1","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"09","volume":8,"has_accepted_license":"1","scopus_import":"1","publisher":"Springer Nature","file":[{"file_id":"8619","relation":"main_file","file_name":"2018_ScientificReports_Gregor.pdf","creator":"dernst","content_type":"application/pdf","checksum":"e642080fcbde9584c63544f587c74f03","file_size":2818077,"date_created":"2020-10-06T16:35:16Z","success":1,"date_updated":"2020-10-06T16:35:16Z","access_level":"open_access"}],"citation":{"chicago":"Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” <i>Scientific Reports</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41598-018-19947-1\">https://doi.org/10.1038/s41598-018-19947-1</a>.","ista":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.","short":"C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell, Scientific Reports 8 (2018).","mla":"Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” <i>Scientific Reports</i>, vol. 8, 2724, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-19947-1\">10.1038/s41598-018-19947-1</a>.","apa":"Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., &#38; Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-018-19947-1\">https://doi.org/10.1038/s41598-018-19947-1</a>","ama":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. <i>Scientific Reports</i>. 2018;8. doi:<a href=\"https://doi.org/10.1038/s41598-018-19947-1\">10.1038/s41598-018-19947-1</a>","ieee":"C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S. W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA,” <i>Scientific Reports</i>, vol. 8. Springer Nature, 2018."},"ddc":["570"],"article_number":"2724","status":"public","publication":"Scientific Reports","year":"2018","author":[{"last_name":"Gregor","first_name":"Carola","full_name":"Gregor, Carola"},{"first_name":"Sven C.","last_name":"Sidenstein","full_name":"Sidenstein, Sven C."},{"first_name":"Martin","last_name":"Andresen","full_name":"Andresen, Martin"},{"full_name":"Sahl, Steffen J.","first_name":"Steffen J.","last_name":"Sahl"},{"last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"},{"first_name":"Stefan W.","last_name":"Hell","full_name":"Hell, Stefan W."}],"date_updated":"2024-10-21T06:02:43Z","external_id":{"isi":["000424630400037"],"pmid":["29426833"]},"abstract":[{"text":"The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT nanoscopy have been developed from fluorescent proteins of the GFP superfamily. These proteins are bright, but exhibit several drawbacks such as relatively large size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore, RSFPs from other origins with improved properties need to be explored. Here, we report the development of two RSFPs based on the LOV domain of the photoreceptor protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by association with the abundant cellular cofactor flavin mononucleotide (FMN). Under illumination with blue and ultraviolet light, they undergo a photocycle, making these proteins inherently photoswitchable. Our first improved variant, rsLOV1, can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy of living cells with a resolution of down to 50 nm. In addition to their smaller size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date. Therefore, LOV-domain-based RSFPs have potential for applications where the switching speed of GFP-based proteins is limiting.","lang":"eng"}],"type":"journal_article","file_date_updated":"2020-10-06T16:35:16Z","month":"02","publication_identifier":{"issn":["2045-2322"]},"department":[{"_id":"JoDa"}],"article_processing_charge":"No","date_created":"2020-10-06T16:33:37Z","oa_version":"Published Version","doi":"10.1038/s41598-018-19947-1","title":"Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA","language":[{"iso":"eng"}],"pmid":1,"publication_status":"published","intvolume":"         8","keyword":["Multidisciplinary"],"_id":"8618","isi":1,"date_published":"2018-02-09T00:00:00Z"},{"department":[{"_id":"JiFr"}],"title":"PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana","article_processing_charge":"No","oa_version":"Published Version","doi":"10.1242/jcs.204198","date_created":"2018-12-11T11:49:10Z","abstract":[{"text":"Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We performed a microarray-based approach to find regulators of the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs (PATL). Here, we show that PATLs are expressed in partially overlapping cells types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia, and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests PATLs redundantly play a crucial role in polarity and patterning in Arabidopsis.","lang":"eng"}],"type":"journal_article","file_date_updated":"2020-07-14T12:48:15Z","month":"01","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"external_id":{"isi":["000424842400019"]},"publication_identifier":{"issn":["0021-9533"]},"pubrep_id":"988","corr_author":"1","_id":"913","isi":1,"date_published":"2018-01-29T00:00:00Z","language":[{"iso":"eng"}],"publication_status":"published","intvolume":"       131","publist_id":"6530","day":"29","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":131,"issue":"2","quality_controlled":"1","oa":1,"year":"2018","author":[{"first_name":"Ricardo","last_name":"Tejos","full_name":"Tejos, Ricardo"},{"first_name":"Cecilia","last_name":"Rodríguez Furlán","full_name":"Rodríguez Furlán, Cecilia"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","last_name":"Adamowski","first_name":"Maciek"},{"last_name":"Sauer","first_name":"Michael","full_name":"Sauer, Michael"},{"first_name":"Lorena","last_name":"Norambuena","full_name":"Norambuena, Lorena"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"date_updated":"2025-07-10T12:01:38Z","has_accepted_license":"1","ec_funded":1,"scopus_import":"1","publisher":"Company of Biologists","file":[{"relation":"main_file","file_id":"6299","creator":"dernst","file_name":"2017_adamowski_PATELLINS_are.pdf","content_type":"application/pdf","checksum":"bf156c20a4f117b4b932370d54cbac8c","file_size":14925985,"date_created":"2019-04-12T08:46:32Z","access_level":"open_access","date_updated":"2020-07-14T12:48:15Z"}],"status":"public","publication":"Journal of Cell Science","ddc":["581"],"citation":{"ama":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. <i>Journal of Cell Science</i>. 2018;131(2). doi:<a href=\"https://doi.org/10.1242/jcs.204198\">10.1242/jcs.204198</a>","mla":"Tejos, Ricardo, et al. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>, vol. 131, no. 2, jcs. 204198, Company of Biologists, 2018, doi:<a href=\"https://doi.org/10.1242/jcs.204198\">10.1242/jcs.204198</a>.","ieee":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, and J. Friml, “PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana,” <i>Journal of Cell Science</i>, vol. 131, no. 2. Company of Biologists, 2018.","apa":"Tejos, R., Rodríguez Furlán, C., Adamowski, M., Sauer, M., Norambuena, L., &#38; Friml, J. (2018). PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.204198\">https://doi.org/10.1242/jcs.204198</a>","ista":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. 2018. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. 131(2), jcs. 204198.","short":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, J. Friml, Journal of Cell Science 131 (2018).","chicago":"Tejos, Ricardo, Cecilia Rodríguez Furlán, Maciek Adamowski, Michael Sauer, Lorena Norambuena, and Jiří Friml. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>. Company of Biologists, 2018. <a href=\"https://doi.org/10.1242/jcs.204198\">https://doi.org/10.1242/jcs.204198</a>."},"article_number":"jcs.204198"},{"department":[{"_id":"JoDa"}],"title":"Diffraction-unlimited optical imaging for synaptic physiology","oa_version":"Published Version","doi":"10.20388/omp2018.00s1.001","date_created":"2021-03-07T23:01:25Z","article_processing_charge":"No","main_file_link":[{"url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience","open_access":"1"}],"month":"06","type":"journal_article","publication_identifier":{"issn":["2500-2287"],"eissn":["2500-2295"]},"_id":"9229","date_published":"2018-06-30T00:00:00Z","language":[{"iso":"eng"}],"intvolume":"         4","publication_status":"published","day":"30","alternative_title":["Molecular and cellular neuroscience"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":4,"issue":"S1","article_type":"letter_note","quality_controlled":"1","oa":1,"author":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl"}],"year":"2018","date_updated":"2021-12-03T07:31:05Z","publisher":"Lobachevsky State University of Nizhny Novgorod","scopus_import":"1","publication":"Opera Medica et Physiologica","status":"public","citation":{"chicago":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” <i>Opera Medica et Physiologica</i>. Lobachevsky State University of Nizhny Novgorod, 2018. <a href=\"https://doi.org/10.20388/omp2018.00s1.001\">https://doi.org/10.20388/omp2018.00s1.001</a>.","ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11.","short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. <i>Opera Medica et Physiologica</i>. 2018;4(S1):11. doi:<a href=\"https://doi.org/10.20388/omp2018.00s1.001\">10.20388/omp2018.00s1.001</a>","mla":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” <i>Opera Medica et Physiologica</i>, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:<a href=\"https://doi.org/10.20388/omp2018.00s1.001\">10.20388/omp2018.00s1.001</a>.","ieee":"J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” <i>Opera Medica et Physiologica</i>, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018.","apa":"Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. <i>Opera Medica et Physiologica</i>. Lobachevsky State University of Nizhny Novgorod. <a href=\"https://doi.org/10.20388/omp2018.00s1.001\">https://doi.org/10.20388/omp2018.00s1.001</a>"},"page":"11"},{"type":"journal_article","file_date_updated":"2021-06-07T06:16:38Z","month":"05","abstract":[{"text":"The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.","lang":"eng"}],"external_id":{"pmid":["29712855"]},"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"department":[{"_id":"DaZi"}],"title":"FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis","oa_version":"Published Version","date_created":"2021-06-07T06:11:28Z","doi":"10.1073/pnas.1713333115","article_processing_charge":"No","language":[{"iso":"eng"}],"intvolume":"       115","publication_status":"published","pmid":1,"_id":"9471","related_material":{"link":[{"url":"https://doi.org/10.1101/187674 ","relation":"earlier_version"}]},"keyword":["Multidisciplinary"],"date_published":"2018-05-15T00:00:00Z","article_type":"original","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"day":"15","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":115,"issue":"20","publisher":"National Academy of Sciences","file":[{"relation":"main_file","file_id":"9472","creator":"asandaue","file_name":"2018_PNAS_Frost.pdf","date_created":"2021-06-07T06:16:38Z","success":1,"date_updated":"2021-06-07T06:16:38Z","access_level":"open_access","content_type":"application/pdf","file_size":3045260,"checksum":"810260dc0e3cc3033e15c19ad0dc123e"}],"scopus_import":"1","has_accepted_license":"1","status":"public","publication":"Proceedings of the National Academy of Sciences","page":"E4720-E4729","citation":{"ista":"Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J, Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 115(20), E4720–E4729.","chicago":"Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1713333115\">https://doi.org/10.1073/pnas.1713333115</a>.","short":"J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H. Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 115 (2018) E4720–E4729.","apa":"Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S. J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1713333115\">https://doi.org/10.1073/pnas.1713333115</a>","ama":"Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(20):E4720-E4729. doi:<a href=\"https://doi.org/10.1073/pnas.1713333115\">10.1073/pnas.1713333115</a>","mla":"Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 20, National Academy of Sciences, 2018, pp. E4720–29, doi:<a href=\"https://doi.org/10.1073/pnas.1713333115\">10.1073/pnas.1713333115</a>.","ieee":"J. M. Frost <i>et al.</i>, “FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 20. National Academy of Sciences, pp. E4720–E4729, 2018."},"ddc":["580"],"author":[{"last_name":"Frost","first_name":"Jennifer M.","full_name":"Frost, Jennifer M."},{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"full_name":"Park, Guen Tae","last_name":"Park","first_name":"Guen Tae"},{"full_name":"Hsieh, Ping-Hung","last_name":"Hsieh","first_name":"Ping-Hung"},{"full_name":"Nakamura, Miyuki","first_name":"Miyuki","last_name":"Nakamura"},{"last_name":"Lin","first_name":"Samuel J. H.","full_name":"Lin, Samuel J. H."},{"full_name":"Yoo, Hyunjin","last_name":"Yoo","first_name":"Hyunjin"},{"first_name":"Jaemyung","last_name":"Choi","full_name":"Choi, Jaemyung"},{"last_name":"Ikeda","first_name":"Yoko","full_name":"Ikeda, Yoko"},{"full_name":"Kinoshita, Tetsu","last_name":"Kinoshita","first_name":"Tetsu"},{"full_name":"Choi, Yeonhee","last_name":"Choi","first_name":"Yeonhee"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."}],"year":"2018","date_updated":"2021-12-14T07:53:40Z","extern":"1"},{"day":"03","department":[{"_id":"SiHi"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","oa_version":"Published Version","date_created":"2021-08-06T12:26:53Z","doi":"10.6084/m9.figshare.7295339.v1","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7295339.v1","open_access":"1"}],"article_processing_charge":"No","type":"research_data_reference","month":"11","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"}],"oa":1,"_id":"9807","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"},{"first_name":"Maude","last_name":"Giroud","full_name":"Giroud, Maude"},{"first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Teresa","last_name":"Gerhalter","full_name":"Gerhalter, Teresa"},{"first_name":"Stephan","last_name":"Herzig","full_name":"Herzig, Stephan"},{"full_name":"Scheideler, Marcel","first_name":"Marcel","last_name":"Scheideler"}],"year":"2018","date_updated":"2023-09-13T09:10:47Z","date_published":"2018-11-03T00:00:00Z","publisher":"Springer Nature","status":"public","citation":{"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. <a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">https://doi.org/10.6084/m9.figshare.7295339.v1</a>.","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, <a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">10.6084/m9.figshare.7295339.v1</a>.","mla":"Higareda Almaraz, Juan, et al. <i>Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes</i>. Springer Nature, 2018, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">10.6084/m9.figshare.7295339.v1</a>.","ieee":"J. Higareda Almaraz <i>et al.</i>, “Additional file 1: 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., &#38; Scheideler, M. (2018). Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">https://doi.org/10.6084/m9.figshare.7295339.v1</a>","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:<a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">10.6084/m9.figshare.7295339.v1</a>"}},{"year":"2018","author":[{"last_name":"Higareda Almaraz","first_name":"Juan","full_name":"Higareda Almaraz, Juan"},{"full_name":"Karbiener, Michael","last_name":"Karbiener","first_name":"Michael"},{"last_name":"Giroud","first_name":"Maude","full_name":"Giroud, Maude"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","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"},{"first_name":"Marcel","last_name":"Scheideler","full_name":"Scheideler, Marcel"}],"_id":"9808","related_material":{"record":[{"id":"20","relation":"used_in_publication","status":"public"}]},"date_published":"2018-11-03T00:00:00Z","date_updated":"2023-09-13T09:10:47Z","publisher":"Springer Nature","citation":{"mla":"Higareda Almaraz, Juan, et al. <i>Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes</i>. Springer Nature, 2018, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7295369.v1\">10.6084/m9.figshare.7295369.v1</a>.","ieee":"J. Higareda Almaraz <i>et al.</i>, “Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","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:<a href=\"https://doi.org/10.6084/m9.figshare.7295369.v1\">10.6084/m9.figshare.7295369.v1</a>","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., &#38; Scheideler, M. (2018). Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.7295369.v1\">https://doi.org/10.6084/m9.figshare.7295369.v1</a>","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, <a href=\"https://doi.org/10.6084/m9.figshare.7295369.v1\">10.6084/m9.figshare.7295369.v1</a>.","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. <a href=\"https://doi.org/10.6084/m9.figshare.7295369.v1\">https://doi.org/10.6084/m9.figshare.7295369.v1</a>.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. 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If the Heisenberg chain is initially in the many-body localized (MBL) phase, we find that the coupling to the central spin suffices to delocalize the chain for a substantial range of coupling strengths. We calculate the phase diagram of the model and identify the phase boundary between the MBL and ergodic phase. Within the localized phase, the central spin significantly enhances the rate of the logarithmic entanglement growth and its saturation value. We attribute the increase in entanglement entropy to a nonextensive enhancement of magnetization fluctuations induced by the central spin. Finally, we demonstrate that correlation functions of the central spin can be utilized to distinguish between MBL and ergodic phases of the 1D chain. 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