[{"day":"13","scopus_import":"1","author":[{"last_name":"Moturu","full_name":"Moturu, Taraka Ramji","first_name":"Taraka Ramji"},{"last_name":"Thula","full_name":"Thula, Sravankumar","first_name":"Sravankumar"},{"first_name":"Ravi Kumar","full_name":"Singh, Ravi Kumar","last_name":"Singh"},{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"first_name":"Radka Svobodová","last_name":"Vařeková","full_name":"Vařeková, Radka Svobodová"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"first_name":"Sibu","last_name":"Simon","full_name":"Simon, Sibu"}],"oa_version":"None","title":"Molecular evolution and diversification of the SMXL gene family","volume":69,"date_created":"2022-03-18T12:43:22Z","article_type":"original","intvolume":"        69","abstract":[{"text":"Strigolactones (SLs) are a relatively recent addition to the list of plant hormones that control different aspects of plant development. SL signalling is perceived by an α/β hydrolase, DWARF 14 (D14). A close homolog of D14, KARRIKIN INSENSTIVE2 (KAI2), is involved in perception of an uncharacterized molecule called karrikin (KAR). Recent studies in Arabidopsis identified the SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE 7 (SMXL7) to be potential SCF–MAX2 complex-mediated proteasome targets of KAI2 and D14, respectively. Genetic studies on SMXL7 and SMAX1 demonstrated distinct developmental roles for each, but very little is known about these repressors in terms of their sequence features. In this study, we performed an extensive comparative analysis of SMXLs and determined their phylogenetic and evolutionary history in the plant lineage. Our results show that SMXL family members can be sub-divided into four distinct phylogenetic clades/classes, with an ancient SMAX1. Further, we identified the clade-specific motifs that have evolved and that might act as determinants of SL-KAR signalling specificity. These specificities resulted from functional diversities among the clades. Our results suggest that a gradual co-evolution of SMXL members with their upstream receptors D14/KAI2 provided an increased specificity to both the SL perception and response in land plants.","lang":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"month":"04","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"citation":{"ieee":"T. R. Moturu <i>et al.</i>, “Molecular evolution and diversification of the SMXL gene family,” <i>Journal of Experimental Botany</i>, vol. 69, no. 9. Oxford University Press, pp. 2367–2378, 2018.","short":"T.R. Moturu, S. Thula, R.K. Singh, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Journal of Experimental Botany 69 (2018) 2367–2378.","ama":"Moturu TR, Thula S, Singh RK, et al. Molecular evolution and diversification of the SMXL gene family. <i>Journal of Experimental Botany</i>. 2018;69(9):2367-2378. doi:<a href=\"https://doi.org/10.1093/jxb/ery097\">10.1093/jxb/ery097</a>","apa":"Moturu, T. R., Thula, S., Singh, R. K., Nodzyński, T., Vařeková, R. S., Friml, J., &#38; Simon, S. (2018). Molecular evolution and diversification of the SMXL gene family. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/ery097\">https://doi.org/10.1093/jxb/ery097</a>","mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of the SMXL Gene Family.” <i>Journal of Experimental Botany</i>, vol. 69, no. 9, Oxford University Press, 2018, pp. 2367–78, doi:<a href=\"https://doi.org/10.1093/jxb/ery097\">10.1093/jxb/ery097</a>.","ista":"Moturu TR, Thula S, Singh RK, Nodzyński T, Vařeková RS, Friml J, Simon S. 2018. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. 69(9), 2367–2378.","chicago":"Moturu, Taraka Ramji, Sravankumar Thula, Ravi Kumar Singh, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of the SMXL Gene Family.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/jxb/ery097\">https://doi.org/10.1093/jxb/ery097</a>."},"issue":"9","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","doi":"10.1093/jxb/ery097","publisher":"Oxford University Press","_id":"10881","date_updated":"2025-05-07T11:12:33Z","type":"journal_article","page":"2367-2378","quality_controlled":"1","year":"2018","isi":1,"external_id":{"pmid":["29538714"],"isi":["000430727000016"]},"keyword":["Plant Science","Physiology"],"status":"public","publication":"Journal of Experimental Botany","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"pmid":1,"acknowledgement":"This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions and it is co-financed by the South Moravian Region under grant agreement No. 665860 (SS). Access to computing and storage facilities owned by parties and projects contributing to the national grid infrastructure, MetaCentrum, provided under the program ‘Projects of Large Infrastructure for Research, Development, and Innovations’ (LM2010005) was greatly appreciated (RSV). The project was funded by The Ministry of Education, Youth and Sports/MES of the Czech Republic under the project CEITEC 2020 (LQ1601) (TN, TRM). JF was supported by the European Research Council (project ERC-2011-StG 20101109-PSDP) and the Czech Science Foundation GAČR (GA13-40637S). We thank Dr Kamel Chibani for active discussions on the evolutionary analysis and Nandan Mysore Vardarajan for his critical comments on the manuscript. This article reflects\r\nonly the authors’ views, and the EU is not responsible for any use that may be made of the information it contains. ","date_published":"2018-04-13T00:00:00Z"},{"language":[{"iso":"eng"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Uijlings, Jasper, Ksenia Konyushkova, Christoph Lampert, and Vittorio Ferrari. “Learning Intelligent Dialogs for Bounding Box Annotation.” In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 9175–84. IEEE, 2018. <a href=\"https://doi.org/10.1109/cvpr.2018.00956\">https://doi.org/10.1109/cvpr.2018.00956</a>.","ista":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. 2018. Learning intelligent dialogs for bounding box annotation. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVF: Conference on Computer Vision and Pattern Recognition, 9175–9184.","mla":"Uijlings, Jasper, et al. “Learning Intelligent Dialogs for Bounding Box Annotation.” <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2018, pp. 9175–84, doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00956\">10.1109/cvpr.2018.00956</a>.","apa":"Uijlings, J., Konyushkova, K., Lampert, C., &#38; Ferrari, V. (2018). Learning intelligent dialogs for bounding box annotation. In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 9175–9184). Salt Lake City, UT, United States: IEEE. <a href=\"https://doi.org/10.1109/cvpr.2018.00956\">https://doi.org/10.1109/cvpr.2018.00956</a>","ama":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. Learning intelligent dialogs for bounding box annotation. In: <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2018:9175-9184. doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00956\">10.1109/cvpr.2018.00956</a>","short":"J. Uijlings, K. Konyushkova, C. Lampert, V. Ferrari, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–9184.","ieee":"J. Uijlings, K. Konyushkova, C. Lampert, and V. Ferrari, “Learning intelligent dialogs for bounding box annotation,” in <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Salt Lake City, UT, United States, 2018, pp. 9175–9184."},"arxiv":1,"month":"12","department":[{"_id":"ChLa"}],"abstract":[{"lang":"eng","text":"We introduce Intelligent Annotation Dialogs for bounding box annotation. We train an agent to automatically choose a sequence of actions for a human annotator to produce a bounding box in a minimal amount of time. Specifically, we consider two actions: box verification [34], where the annotator verifies a box generated by an object detector, and manual box drawing. We explore two kinds of agents, one based on predicting the probability that a box will be positively verified, and the other based on reinforcement learning. We demonstrate that (1) our agents are able to learn efficient annotation strategies in several scenarios, automatically adapting to the image difficulty, the desired quality of the boxes, and the detector strength; (2) in all scenarios the resulting annotation dialogs speed up annotation compared to manual box drawing alone and box verification alone, while also outperforming any fixed combination of verification and drawing in most scenarios; (3) in a realistic scenario where the detector is iteratively re-trained, our agents evolve a series of strategies that reflect the shifting trade-off between verification and drawing as the detector grows stronger."}],"publication_identifier":{"isbn":["9781538664209"],"eissn":["2575-7075"]},"publication_status":"published","title":"Learning intelligent dialogs for bounding box annotation","oa_version":"Preprint","day":"17","scopus_import":"1","author":[{"last_name":"Uijlings","full_name":"Uijlings, Jasper","first_name":"Jasper"},{"first_name":"Ksenia","full_name":"Konyushkova, Ksenia","last_name":"Konyushkova"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph"},{"last_name":"Ferrari","full_name":"Ferrari, Vittorio","first_name":"Vittorio"}],"date_created":"2022-03-18T12:45:09Z","status":"public","publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","conference":{"location":"Salt Lake City, UT, United States","name":"CVF: Conference on Computer Vision and Pattern Recognition","end_date":"2018-06-23","start_date":"2018-06-18"},"date_published":"2018-12-17T00:00:00Z","external_id":{"arxiv":["1712.08087"],"isi":["000457843609036"]},"isi":1,"year":"2018","page":"9175-9184","quality_controlled":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1712.08087","open_access":"1"}],"publisher":"IEEE","article_processing_charge":"No","doi":"10.1109/cvpr.2018.00956","type":"conference","_id":"10882","date_updated":"2023-09-19T15:11:49Z"},{"volume":57,"date_created":"2022-03-18T12:46:32Z","day":"23","scopus_import":"1","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dvořák","full_name":"Dvořák, Wolfgang","first_name":"Wolfgang"},{"first_name":"Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Svozil","full_name":"Svozil, Alexander","first_name":"Alexander"}],"oa_version":"Published Version","title":"Quasipolynomial set-based symbolic algorithms for parity games","file_date_updated":"2022-05-17T07:51:08Z","publication_identifier":{"issn":["2398-7340"]},"publication_status":"published","has_accepted_license":"1","intvolume":"        57","abstract":[{"lang":"eng","text":"Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space."}],"department":[{"_id":"KrCh"}],"file":[{"file_size":720893,"date_created":"2022-05-17T07:51:08Z","creator":"dernst","date_updated":"2022-05-17T07:51:08Z","file_id":"11392","success":1,"file_name":"2018_EPiCs_Chatterjee.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"1229aa8640bd6db610c85decf2265480"}],"arxiv":1,"month":"10","citation":{"ama":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>. Vol 57. EasyChair; 2018:233-253. doi:<a href=\"https://doi.org/10.29007/5z5k\">10.29007/5z5k</a>","ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253.","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253.","ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>, 57:233–53. EasyChair, 2018. <a href=\"https://doi.org/10.29007/5z5k\">https://doi.org/10.29007/5z5k</a>.","apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., &#38; Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i> (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. <a href=\"https://doi.org/10.29007/5z5k\">https://doi.org/10.29007/5z5k</a>","mla":"Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>, vol. 57, EasyChair, 2018, pp. 233–53, doi:<a href=\"https://doi.org/10.29007/5z5k\">10.29007/5z5k</a>."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","oa":1,"language":[{"iso":"eng"}],"_id":"10883","date_updated":"2022-07-29T09:24:31Z","type":"conference","article_processing_charge":"No","alternative_title":["EPiC Series in Computing"],"doi":"10.29007/5z5k","publisher":"EasyChair","quality_controlled":"1","page":"233-253","ddc":["000"],"year":"2018","external_id":{"arxiv":["1909.04983"]},"ec_funded":1,"acknowledgement":"A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph Games). For M.H the research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) /ERC Grant Agreement no. 340506.","conference":{"name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning","start_date":"2018-11-17","end_date":"2018-11-21","location":"Awassa, Ethiopia"},"date_published":"2018-10-23T00:00:00Z","status":"public","publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}]},{"doi":"10.1007/978-3-030-01602-9_9","publisher":"Springer","date_updated":"2021-01-12T06:48:16Z","_id":"11","type":"conference","page":"185 - 214","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.10843"}],"quality_controlled":"1","year":"2018","external_id":{"arxiv":["1806.10843"]},"publist_id":"8045","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"status":"public","ec_funded":1,"conference":{"name":"MaLiQS: Macroscopic Limits of Quantum Systems","end_date":"2017-04-01","start_date":"2017-03-30","location":"Munich, Germany"},"date_published":"2018-10-27T00:00:00Z","author":[{"orcid":"0000-0002-0495-6822","first_name":"Nikolai K","last_name":"Leopold","full_name":"Leopold, Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pickl","full_name":"Pickl, Peter","first_name":"Peter"}],"scopus_import":1,"day":"27","title":"Mean-field limits of particles in interaction with quantised radiation fields","oa_version":"Preprint","volume":270,"date_created":"2018-12-11T11:44:08Z","abstract":[{"lang":"eng","text":"We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm."}],"intvolume":"       270","publication_status":"published","arxiv":1,"month":"10","department":[{"_id":"RoSe"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"mla":"Leopold, Nikolai K., and Peter Pickl. <i>Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields</i>. Vol. 270, Springer, 2018, pp. 185–214, doi:<a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">10.1007/978-3-030-01602-9_9</a>.","apa":"Leopold, N. K., &#38; Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">https://doi.org/10.1007/978-3-030-01602-9_9</a>","chicago":"Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">https://doi.org/10.1007/978-3-030-01602-9_9</a>.","ista":"Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214.","short":"N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.","ieee":"N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.","ama":"Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:<a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">10.1007/978-3-030-01602-9_9</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"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."}],"intvolume":"     11022","has_accepted_license":"1","publication_status":"published","publication_identifier":{"isbn":["978-3-030-00150-6"]},"file_date_updated":"2020-07-14T12:48:03Z","oa_version":"Submitted Version","title":"Online timed pattern matching using automata","author":[{"first_name":"Alexey","last_name":"Bakhirkin","full_name":"Bakhirkin, Alexey"},{"orcid":"0000-0001-5199-3143","first_name":"Thomas","last_name":"Ferrere","full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"},{"full_name":"Maler, Oded","last_name":"Maler","first_name":"Oded"},{"full_name":"Asarin, Eugene","last_name":"Asarin","first_name":"Eugene"}],"day":"26","scopus_import":"1","date_created":"2018-12-11T11:44:31Z","volume":11022,"language":[{"iso":"eng"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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>.","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.","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>.","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>","short":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer, 2018, pp. 215–232.","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."},"month":"08","file":[{"file_id":"7831","date_created":"2020-05-14T11:34:34Z","file_size":374851,"date_updated":"2020-07-14T12:48:03Z","creator":"dernst","relation":"main_file","checksum":"436b7574934324cfa7d1d3986fddc65b","file_name":"2018_LNCS_Bakhirkin.pdf","access_level":"open_access","content_type":"application/pdf"}],"department":[{"_id":"ToHe"}],"ddc":["000"],"page":"215 - 232","quality_controlled":"1","publisher":"Springer","doi":"10.1007/978-3-030-00151-3_13","article_processing_charge":"No","alternative_title":["LNCS"],"type":"conference","date_updated":"2023-09-13T09:35:46Z","_id":"78","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}],"status":"public","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","end_date":"2018-09-06","start_date":"2018-09-04","location":"Bejing, China"},"date_published":"2018-08-26T00:00:00Z","external_id":{"isi":["000884993200013"]},"year":"2018","isi":1,"publist_id":"7976"},{"file_date_updated":"2020-07-14T12:48:03Z","quality_controlled":"1","publication_status":"published","ddc":["000"],"abstract":[{"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.","lang":"eng"}],"has_accepted_license":"1","date_created":"2020-05-10T22:00:51Z","type":"conference","_id":"7812","date_updated":"2023-02-23T13:18:41Z","oa_version":"Published Version","title":"Model compression via distillation and quantization","article_processing_charge":"No","day":"01","scopus_import":1,"author":[{"first_name":"Antonio","last_name":"Polino","full_name":"Polino, Antonio"},{"full_name":"Pascanu, Razvan","last_name":"Pascanu","first_name":"Razvan"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-05-01T00:00:00Z","conference":{"location":"Vancouver, Canada","start_date":"2018-04-30","end_date":"2018-05-03","name":"ICLR: International Conference on Learning Representations"},"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.","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.","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.","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.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: <i>6th International Conference on Learning Representations</i>. ; 2018."},"status":"public","language":[{"iso":"eng"}],"publication":"6th International Conference on Learning Representations","oa":1,"file":[{"date_updated":"2020-07-14T12:48:03Z","creator":"dernst","file_size":308339,"date_created":"2020-05-26T13:02:00Z","file_id":"7894","content_type":"application/pdf","access_level":"open_access","file_name":"2018_ICLR_Polino.pdf","checksum":"a4336c167978e81891970e4e4517a8c3","relation":"main_file"}],"department":[{"_id":"DaAl"}],"month":"05","arxiv":1,"external_id":{"arxiv":["1802.05668"]},"year":"2018"},{"type":"conference","date_updated":"2023-09-13T09:38:28Z","_id":"79","publisher":"Springer","doi":"10.1007/978-3-319-99154-2_4","alternative_title":["LNCS"],"article_processing_charge":"No","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1806.05126","open_access":"1"}],"page":"53-70","publist_id":"7975","external_id":{"arxiv":["1806.05126"],"isi":["000548912200004"]},"year":"2018","isi":1,"date_published":"2018-08-15T00:00:00Z","conference":{"location":"Beijing, China","name":"QEST: Quantitative Evaluation of Systems","start_date":"2018-09-04","end_date":"2018-09-07"},"status":"public","date_created":"2018-12-11T11:44:31Z","volume":11024,"oa_version":"Preprint","title":"Parameter-independent strategies for pMDPs via POMDPs","author":[{"first_name":"Sebastian","last_name":"Arming","full_name":"Arming, Sebastian"},{"last_name":"Bartocci","full_name":"Bartocci, Ezio","first_name":"Ezio"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","full_name":"Katoen, Joost P","last_name":"Katoen"},{"last_name":"Sokolova","full_name":"Sokolova, Ana","first_name":"Ana"}],"day":"15","scopus_import":"1","publication_status":"published","intvolume":"     11024","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."}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"month":"08","arxiv":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","short":"S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer, 2018, pp. 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:<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>.","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>.","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."},"language":[{"iso":"eng"}],"oa":1},{"date_published":"2018-01-07T00:00:00Z","publication":"Annual Review of Entomology","status":"public","publist_id":"6844","external_id":{"isi":["000424633700008"]},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"819"}]},"year":"2018","isi":1,"quality_controlled":"1","page":"105 - 123","type":"journal_article","date_updated":"2023-09-19T09:29:45Z","_id":"806","publisher":"Annual Reviews","doi":"10.1146/annurev-ento-020117-043110","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Cremer S, Pull C, Fürst M. Social immunity: Emergence and evolution of colony-level disease protection. <i>Annual Review of Entomology</i>. 2018;63:105-123. doi:<a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">10.1146/annurev-ento-020117-043110</a>","ieee":"S. Cremer, C. Pull, and M. Fürst, “Social immunity: Emergence and evolution of colony-level disease protection,” <i>Annual Review of Entomology</i>, vol. 63. Annual Reviews, pp. 105–123, 2018.","short":"S. Cremer, C. Pull, M. Fürst, Annual Review of Entomology 63 (2018) 105–123.","ista":"Cremer S, Pull C, Fürst M. 2018. Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. 63, 105–123.","chicago":"Cremer, Sylvia, Christopher Pull, and Matthias Fürst. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” <i>Annual Review of Entomology</i>. Annual Reviews, 2018. <a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">https://doi.org/10.1146/annurev-ento-020117-043110</a>.","apa":"Cremer, S., Pull, C., &#38; Fürst, M. (2018). Social immunity: Emergence and evolution of colony-level disease protection. <i>Annual Review of Entomology</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">https://doi.org/10.1146/annurev-ento-020117-043110</a>","mla":"Cremer, Sylvia, et al. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” <i>Annual Review of Entomology</i>, vol. 63, Annual Reviews, 2018, pp. 105–23, doi:<a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">10.1146/annurev-ento-020117-043110</a>."},"language":[{"iso":"eng"}],"department":[{"_id":"SyCr"}],"month":"01","publication_status":"published","publication_identifier":{"issn":["1545-4487"]},"intvolume":"        63","abstract":[{"lang":"eng","text":"Social insect colonies have evolved many collectively performed adaptations that reduce the impact of infectious disease and that are expected to maximize their fitness. This colony-level protection is termed social immunity, and it enhances the health and survival of the colony. In this review, we address how social immunity emerges from its mechanistic components to produce colony-level disease avoidance, resistance, and tolerance. To understand the evolutionary causes and consequences of social immunity, we highlight the need for studies that evaluate the effects of social immunity on colony fitness. We discuss the role that host life history and ecology have on predicted eco-evolutionary dynamics, which differ among the social insect lineages. Throughout the review, we highlight current gaps in our knowledge and promising avenues for future research, which we hope will bring us closer to an integrated understanding of socio-eco-evo-immunology."}],"date_created":"2018-12-11T11:48:36Z","volume":63,"oa_version":"None","title":"Social immunity: Emergence and evolution of colony-level disease protection","author":[{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia"},{"full_name":"Pull, Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull","first_name":"Christopher","orcid":"0000-0003-1122-3982"},{"first_name":"Matthias","orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst"}],"day":"07","scopus_import":"1"},{"status":"public","project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"conference":{"end_date":"2018-09-06","start_date":"2018-09-04","name":"FORMATS: Formal Modeling and Analysis of Timed Systems","location":"Beijing, China"},"date_published":"2018-08-26T00:00:00Z","external_id":{"isi":["000884993200004"]},"isi":1,"year":"2018","publist_id":"7973","ddc":["000"],"page":"53 - 70","quality_controlled":"1","publisher":"Springer","alternative_title":["LNCS"],"article_processing_charge":"No","doi":"10.1007/978-3-030-00151-3_4","type":"conference","_id":"81","date_updated":"2023-09-13T08:58:34Z","language":[{"iso":"eng"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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>","short":"A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 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.","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.","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>.","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>.","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>"},"month":"08","file":[{"relation":"main_file","checksum":"e5d81c9b50a6bd9d8a2c16953aad7e23","success":1,"file_name":"2018_LNCS_Elgyuett.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"8638","file_size":537219,"date_created":"2020-10-09T06:24:21Z","creator":"dernst","date_updated":"2020-10-09T06:24:21Z"}],"department":[{"_id":"ToHe"}],"intvolume":"     11022","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"}],"has_accepted_license":"1","file_date_updated":"2020-10-09T06:24:21Z","publication_status":"published","oa_version":"Submitted Version","title":"Monitoring temporal logic with clock variables","day":"26","scopus_import":"1","author":[{"first_name":"Adrian","last_name":"Elgyütt","id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","full_name":"Elgyütt, Adrian"},{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas","last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A"}],"date_created":"2018-12-11T11:44:31Z","volume":11022},{"file":[{"file_size":4007095,"date_created":"2018-12-17T12:55:31Z","date_updated":"2020-07-14T12:48:10Z","creator":"dernst","file_id":"5706","file_name":"2018_Plos_Chaudhry.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"527076f78265cd4ea192cd1569851587"}],"article_number":"2005971","department":[{"_id":"CaGu"}],"month":"08","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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>.","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>","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.","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>.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","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.","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>"},"issue":"8","language":[{"iso":"eng"}],"oa":1,"date_created":"2018-12-11T11:44:32Z","volume":16,"oa_version":"Published Version","title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","day":"16","scopus_import":"1","author":[{"first_name":"Waqas","full_name":"Chaudhry, Waqas","last_name":"Chaudhry"},{"first_name":"Maros","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska"},{"full_name":"Shah, Nilang","last_name":"Shah","first_name":"Nilang"},{"first_name":"Howard","last_name":"Weiss","full_name":"Weiss, Howard"},{"last_name":"Mccall","full_name":"Mccall, Ingrid","first_name":"Ingrid"},{"last_name":"Meyer","full_name":"Meyer, Justin","first_name":"Justin"},{"first_name":"Animesh","last_name":"Gupta","full_name":"Gupta, Animesh"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052"},{"full_name":"Levin, Bruce","last_name":"Levin","first_name":"Bruce"}],"file_date_updated":"2020-07-14T12:48:10Z","publication_status":"published","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"license":"https://creativecommons.org/licenses/by/4.0/","intvolume":"        16","abstract":[{"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.”.","lang":"eng"}],"has_accepted_license":"1","publist_id":"7972","related_material":{"record":[{"status":"public","relation":"research_data","id":"9810"}]},"external_id":{"isi":["000443383300024"]},"year":"2018","isi":1,"date_published":"2018-08-16T00:00:00Z","publication":"PLoS Biology","status":"public","type":"journal_article","_id":"82","date_updated":"2023-09-13T08:45:41Z","publisher":"Public Library of Science","article_processing_charge":"Yes","doi":"10.1371/journal.pbio.2005971","quality_controlled":"1","ddc":["570"]},{"page":"59","ddc":["004"],"doi":"10.15479/AT:ISTA:TH_1046","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","date_updated":"2023-09-07T12:30:23Z","_id":"83","type":"dissertation","degree_awarded":"PhD","project":[{"name":"Provable Security for Physical Cryptography","grant_number":"259668","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425"},{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020"}],"status":"public","ec_funded":1,"date_published":"2018-09-05T00:00:00Z","year":"2018","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1229"},{"relation":"part_of_dissertation","status":"public","id":"1235"},{"status":"public","relation":"part_of_dissertation","id":"1236"},{"status":"public","relation":"part_of_dissertation","id":"559"}]},"publist_id":"7971","has_accepted_license":"1","abstract":[{"lang":"eng","text":"A proof system is a protocol between a prover and a verifier over a common input in which an honest prover convinces the verifier of the validity of true statements. Motivated by the success of decentralized cryptocurrencies, exemplified by Bitcoin, the focus of this thesis will be on proof systems which found applications in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies. In particular, we focus on proofs of space and proofs of sequential work.\r\nProofs of space (PoSpace) were suggested as more ecological, economical, and egalitarian alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling lower bounds, and are therefore complex. Moreover, when these PoSpace are used in cryptocurrencies like Spacemint, miners can only start mining after ensuring that a commitment to their space is already added in a special transaction to the blockchain. Proofs of sequential work (PoSW) are proof systems in which a prover, upon receiving a statement x and a time parameter T, computes a proof which convinces the verifier that T time units had passed since x was received. Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics, Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come up with more than one accepting proof for any true statement. In this thesis we construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and unlike current constructions of PoSW, which either achieve efficient verification of sequential work, or faster-than-recomputing verification of correctness of proofs, but not both at the same time, ours achieve the best of these two worlds."}],"publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2020-07-14T12:48:11Z","author":[{"last_name":"Abusalah","id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M","first_name":"Hamza M"}],"day":"05","title":"Proof systems for sustainable decentralized cryptocurrencies","oa_version":"Published Version","date_created":"2018-12-11T11:44:32Z","oa":1,"language":[{"iso":"eng"}],"pubrep_id":"1046","citation":{"ama":"Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">10.15479/AT:ISTA:TH_1046</a>","short":"H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies, Institute of Science and Technology Austria, 2018.","ieee":"H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,” Institute of Science and Technology Austria, 2018.","ista":"Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria.","chicago":"Abusalah, Hamza M. “Proof Systems for Sustainable Decentralized Cryptocurrencies.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">https://doi.org/10.15479/AT:ISTA:TH_1046</a>.","mla":"Abusalah, Hamza M. <i>Proof Systems for Sustainable Decentralized Cryptocurrencies</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">10.15479/AT:ISTA:TH_1046</a>.","apa":"Abusalah, H. M. (2018). <i>Proof systems for sustainable decentralized cryptocurrencies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">https://doi.org/10.15479/AT:ISTA:TH_1046</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","supervisor":[{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"}],"month":"09","department":[{"_id":"KrPi"}],"file":[{"file_id":"6245","file_size":876241,"date_created":"2019-04-09T06:43:41Z","date_updated":"2020-07-14T12:48:11Z","creator":"dernst","relation":"main_file","checksum":"c4b5f7d111755d1396787f41886fc674","file_name":"2018_Thesis_Abusalah.pdf","content_type":"application/pdf","access_level":"open_access"},{"date_updated":"2020-07-14T12:48:11Z","creator":"dernst","file_size":2029190,"date_created":"2019-04-09T06:43:41Z","file_id":"6246","access_level":"closed","content_type":"application/x-gzip","file_name":"2018_Thesis_Abusalah_source.tar.gz","checksum":"0f382ac56b471c48fd907d63eb87dafe","relation":"source_file"}]},{"publist_id":"7969","year":"2018","isi":1,"external_id":{"isi":["000851042300031"]},"acknowledgement":"Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14) and by a NSERC post-doctoral fellowship.","date_published":"2018-08-01T00:00:00Z","conference":{"name":"Euro-Par: European Conference on Parallel Processing","start_date":"2018-08-27","end_date":"2018-08-31","location":"Turin, Italy"},"project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"status":"public","date_updated":"2023-09-18T09:32:36Z","_id":"85","type":"conference","doi":"10.1007/978-3-319-96983-1_33","alternative_title":["LNCS"],"article_processing_charge":"No","publisher":"Springer","quality_controlled":"1","page":"465 - 479","ddc":["000"],"department":[{"_id":"DaAl"}],"file":[{"file_name":"2018_Brown.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"13a3f250be8878405e791b53c19722ad","file_size":665372,"date_created":"2019-02-12T07:40:40Z","date_updated":"2020-07-14T12:48:14Z","creator":"dernst","file_id":"5954"}],"month":"08","citation":{"apa":"Gilad, E., Brown, T. A., Oskin, M., &#38; 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. <a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">https://doi.org/10.1007/978-3-319-96983-1_33</a>","mla":"Gilad, Eran, et al. <i>Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking</i>. Vol. 11014, Springer, 2018, pp. 465–79, doi:<a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">10.1007/978-3-319-96983-1_33</a>.","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. <a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">https://doi.org/10.1007/978-3-319-96983-1_33</a>.","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.","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.","short":"E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479.","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:<a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">10.1007/978-3-319-96983-1_33</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"language":[{"iso":"eng"}],"volume":11014,"date_created":"2018-12-11T11:44:33Z","author":[{"first_name":"Eran","full_name":"Gilad, Eran","last_name":"Gilad"},{"first_name":"Trevor A","last_name":"Brown","full_name":"Brown, Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Oskin","full_name":"Oskin, Mark","first_name":"Mark"},{"full_name":"Etsion, Yoav","last_name":"Etsion","first_name":"Yoav"}],"day":"01","scopus_import":"1","oa_version":"Preprint","title":"Snapshot based synchronization: A fast replacement for Hand-over-Hand locking","publication_identifier":{"issn":["03029743"]},"publication_status":"published","file_date_updated":"2020-07-14T12:48:14Z","has_accepted_license":"1","intvolume":"     11014","abstract":[{"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.","lang":"eng"}]},{"abstract":[{"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.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/494088"}],"publication_status":"submitted","day":"13","article_processing_charge":"No","doi":"10.1101/494088","author":[{"first_name":"Alfredo","full_name":"Llorca, Alfredo","last_name":"Llorca"},{"first_name":"Gabriele","full_name":"Ciceri, Gabriele","last_name":"Ciceri"},{"full_name":"Beattie, Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","first_name":"Robert J","orcid":"0000-0002-8483-8753"},{"last_name":"Wong","full_name":"Wong, Fong K.","first_name":"Fong K."},{"last_name":"Diana","full_name":"Diana, Giovanni","first_name":"Giovanni"},{"last_name":"Serafeimidou","full_name":"Serafeimidou, Eleni","first_name":"Eleni"},{"last_name":"Fernández-Otero","full_name":"Fernández-Otero, Marian","first_name":"Marian"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen"},{"first_name":"Sebastian J.","full_name":"Arnold, Sebastian J.","last_name":"Arnold"},{"last_name":"Meyer","full_name":"Meyer, Martin","first_name":"Martin"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"},{"last_name":"Maravall","full_name":"Maravall, Miguel","first_name":"Miguel"},{"last_name":"Marín","full_name":"Marín, Oscar","first_name":"Oscar"}],"title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","oa_version":"Preprint","publisher":"Cold Spring Harbor Laboratory","_id":"8547","date_updated":"2021-01-12T08:20:00Z","date_created":"2020-09-21T12:01:50Z","type":"preprint","oa":1,"status":"public","publication":"bioRxiv","language":[{"iso":"eng"}],"project":[{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"grant_number":"M02416","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425"}],"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>","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.).","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>.","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>.","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>."},"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","date_published":"2018-12-13T00:00:00Z","year":"2018","month":"12","department":[{"_id":"SiHi"}]},{"publication_status":"published","file_date_updated":"2020-07-14T12:48:14Z","abstract":[{"lang":"eng","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."}],"intvolume":"     10760","has_accepted_license":"1","date_created":"2018-12-11T11:44:33Z","volume":10760,"title":"Computing average response time","oa_version":"Submitted Version","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Otop","full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"scopus_import":1,"day":"20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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>","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>.","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>.","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.","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.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.","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>"},"language":[{"iso":"eng"}],"oa":1,"file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"2018_PrinciplesModeling_Chatterjee.pdf","checksum":"9995c6ce6957333baf616fc4f20be597","relation":"main_file","date_updated":"2020-07-14T12:48:14Z","creator":"dernst","file_size":516307,"date_created":"2019-11-19T08:22:18Z","file_id":"7053"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"month":"07","quality_controlled":"1","ddc":["000"],"page":"143 - 161","type":"book_chapter","date_updated":"2021-01-12T08:20:14Z","_id":"86","editor":[{"full_name":"Lohstroh, Marten","last_name":"Lohstroh","first_name":"Marten"},{"full_name":"Derler, Patricia","last_name":"Derler","first_name":"Patricia"},{"first_name":"Marjan","last_name":"Sirjani","full_name":"Sirjani, Marjan"}],"publisher":"Springer","doi":"10.1007/978-3-319-95246-8_9","alternative_title":["LNCS"],"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.","date_published":"2018-07-20T00:00:00Z","ec_funded":1,"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"status":"public","publication":"Principles of Modeling","publist_id":"7968","year":"2018"},{"article_processing_charge":"No","doi":"10.1038/s41598-018-19947-1","publisher":"Springer Nature","_id":"8618","date_updated":"2023-09-19T15:04:49Z","type":"journal_article","ddc":["570"],"quality_controlled":"1","year":"2018","isi":1,"external_id":{"isi":["000424630400037"],"pmid":["29426833"]},"keyword":["Multidisciplinary"],"status":"public","publication":"Scientific Reports","pmid":1,"date_published":"2018-02-09T00:00:00Z","day":"09","author":[{"first_name":"Carola","last_name":"Gregor","full_name":"Gregor, Carola"},{"last_name":"Sidenstein","full_name":"Sidenstein, Sven C.","first_name":"Sven C."},{"full_name":"Andresen, Martin","last_name":"Andresen","first_name":"Martin"},{"last_name":"Sahl","full_name":"Sahl, Steffen J.","first_name":"Steffen J."},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973"},{"last_name":"Hell","full_name":"Hell, Stefan W.","first_name":"Stefan W."}],"oa_version":"Published Version","title":"Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA","volume":8,"date_created":"2020-10-06T16:33:37Z","article_type":"original","has_accepted_license":"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","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."}],"intvolume":"         8","file_date_updated":"2020-10-06T16:35:16Z","publication_status":"published","publication_identifier":{"issn":["2045-2322"]},"month":"02","department":[{"_id":"JoDa"}],"file":[{"checksum":"e642080fcbde9584c63544f587c74f03","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2018_ScientificReports_Gregor.pdf","success":1,"file_id":"8619","date_updated":"2020-10-06T16:35:16Z","creator":"dernst","file_size":2818077,"date_created":"2020-10-06T16:35:16Z"}],"article_number":"2724","oa":1,"language":[{"iso":"eng"}],"citation":{"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>","short":"C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell, Scientific Reports 8 (2018).","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.","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.","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>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"intvolume":"        28","abstract":[{"lang":"eng","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."}],"publication_status":"published","title":"Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics","oa_version":"Preprint","scopus_import":"1","day":"01","author":[{"first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","full_name":"Nikitenko, Anton","orcid":"0000-0002-0659-3201","first_name":"Anton"}],"date_created":"2018-12-11T11:44:33Z","article_type":"original","volume":28,"language":[{"iso":"eng"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Edelsbrunner H, Nikitenko A. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. <i>Annals of Applied Probability</i>. 2018;28(5):3215-3238. doi:<a href=\"https://doi.org/10.1214/18-AAP1389\">10.1214/18-AAP1389</a>","ieee":"H. Edelsbrunner and A. Nikitenko, “Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics,” <i>Annals of Applied Probability</i>, vol. 28, no. 5. Institute of Mathematical Statistics, pp. 3215–3238, 2018.","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.","chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2018. <a href=\"https://doi.org/10.1214/18-AAP1389\">https://doi.org/10.1214/18-AAP1389</a>.","apa":"Edelsbrunner, H., &#38; Nikitenko, A. (2018). Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/18-AAP1389\">https://doi.org/10.1214/18-AAP1389</a>","mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” <i>Annals of Applied Probability</i>, vol. 28, no. 5, Institute of Mathematical Statistics, 2018, pp. 3215–38, doi:<a href=\"https://doi.org/10.1214/18-AAP1389\">10.1214/18-AAP1389</a>."},"issue":"5","arxiv":1,"month":"10","department":[{"_id":"HeEd"}],"page":"3215 - 3238","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1705.02870","open_access":"1"}],"publisher":"Institute of Mathematical Statistics","article_processing_charge":"No","doi":"10.1214/18-AAP1389","type":"journal_article","_id":"87","date_updated":"2023-09-15T12:10:35Z","publication":"Annals of Applied Probability","status":"public","project":[{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"date_published":"2018-10-01T00:00:00Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6287"}]},"external_id":{"arxiv":["1705.02870"],"isi":["000442893500018"]},"year":"2018","isi":1,"publist_id":"7967"},{"has_accepted_license":"1","abstract":[{"text":"Immune cells migrating to the sites of infection navigate through diverse tissue architectures and switch their migratory mechanisms upon demand. However, little is known about systemic regulators that could allow the acquisition of these mechanisms. We performed a genetic screen in Drosophila melanogaster to identify regulators of germband invasion by embryonic macrophages into the confined space between the ectoderm and mesoderm. We have found that bZIP circadian transcription factors (TFs) Kayak (dFos) and Vrille (dNFIL3) have opposite effects on macrophage germband infiltration: Kayak facilitated and Vrille inhibited it. These TFs are enriched in the macrophages during migration and genetically interact to control it. Kayak sets a less coordinated mode of migration of the macrophage group and increases the probability and length of Levy walks. Intriguingly, the motility of kayak mutant macrophages was also strongly affected during initial germband invasion but not along another less confined route. Inhibiting Rho1 signaling within the tail ectoderm partially rescued the Kayak mutant phenotype, strongly suggesting that migrating macrophages have to overcome a barrier imposed by the stiffness of the ectoderm. Also, Kayak appeared to be important for the maintenance of the round cell shape and the rear edge translocation of the macrophages invading the germband. Complementary to this, the cortical actin cytoskeleton of Kayak- deficient macrophages was strongly affected. RNA sequencing revealed the filamin Cheerio and tetraspanin TM4SF to be downstream of Kayak. Chromatin immunoprecipitation and immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Indeed, Cheerio, TM4SF and Diaphanous are required within macrophages for germband invasion, and expression of constitutively active Diaphanous in macrophages was able to rescue the kayak mutant phenotype. Moreover, Cher and Diaphanous are also reduced in the macrophages overexpressing Vrille. We hypothesize that Kayak, through its targets, increases actin polymerization and cortical tension in macrophages and thus allows extra force generation necessary for macrophage dissemination and migration through confined stiff tissues, while Vrille counterbalances it.","lang":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","file_date_updated":"2021-02-11T11:17:16Z","author":[{"first_name":"Vera","last_name":"Belyaeva","full_name":"Belyaeva, Vera","id":"47F080FE-F248-11E8-B48F-1D18A9856A87"}],"day":"01","oa_version":"Published Version","title":"Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ","date_created":"2018-12-11T11:44:08Z","oa":1,"language":[{"iso":"eng"}],"pubrep_id":"1064","citation":{"chicago":"Belyaeva, Vera. “Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo .” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">https://doi.org/10.15479/AT:ISTA:th1064</a>.","ista":"Belyaeva V. 2018. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria.","apa":"Belyaeva, V. (2018). <i>Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">https://doi.org/10.15479/AT:ISTA:th1064</a>","mla":"Belyaeva, Vera. <i>Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo </i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">10.15479/AT:ISTA:th1064</a>.","ama":"Belyaeva V. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">10.15479/AT:ISTA:th1064</a>","ieee":"V. Belyaeva, “Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ,” Institute of Science and Technology Austria, 2018.","short":"V. Belyaeva, Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo , Institute of Science and Technology Austria, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","supervisor":[{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353"}],"month":"07","department":[{"_id":"DaSi"}],"file":[{"checksum":"d27b2465cb70d0c9678a0381b9b6ced1","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2018_Thesis_Belyaeva_source.docx","embargo_to":"open_access","file_id":"6243","creator":"dernst","date_updated":"2020-07-14T12:48:14Z","file_size":102737483,"date_created":"2019-04-08T14:13:12Z"},{"relation":"main_file","checksum":"a2939b61bde2de7b8ced77bbae0eaaed","file_name":"2018_Thesis_Belyaeva.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"6244","date_created":"2019-04-08T14:14:08Z","file_size":88077843,"embargo":"2019-11-19","date_updated":"2021-02-11T11:17:16Z","creator":"dernst"}],"page":"96","ddc":["570"],"doi":"10.15479/AT:ISTA:th1064","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","date_updated":"2023-09-07T12:43:10Z","_id":"9","type":"dissertation","degree_awarded":"PhD","status":"public","date_published":"2018-07-01T00:00:00Z","year":"2018","publist_id":"8047"},{"citation":{"mla":"Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” <i>ELife</i>, vol. 7, e34465, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.34465\">10.7554/eLife.34465</a>.","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. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.34465\">https://doi.org/10.7554/eLife.34465</a>","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.","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.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.34465\">https://doi.org/10.7554/eLife.34465</a>.","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).","ieee":"M. Kaucka <i>et al.</i>, “Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","ama":"Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.34465\">10.7554/eLife.34465</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"AnKi"}],"article_number":"e34465","file":[{"checksum":"da2378cdcf6b5461dcde194e4d608343","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2018_eLife_Kaucka.pdf","file_id":"5727","date_updated":"2020-07-14T12:45:07Z","creator":"dernst","date_created":"2018-12-17T16:41:58Z","file_size":9816484}],"month":"06","file_date_updated":"2020-07-14T12:45:07Z","publication_status":"published","has_accepted_license":"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"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."}],"intvolume":"         7","volume":7,"date_created":"2018-12-11T11:44:57Z","day":"13","scopus_import":"1","author":[{"full_name":"Kaucka, Marketa","last_name":"Kaucka","first_name":"Marketa"},{"full_name":"Petersen, Julian","last_name":"Petersen","first_name":"Julian"},{"first_name":"Marketa","last_name":"Tesarova","full_name":"Tesarova, Marketa"},{"first_name":"Bara","last_name":"Szarowska","full_name":"Szarowska, Bara"},{"full_name":"Kastriti, Maria","last_name":"Kastriti","first_name":"Maria"},{"first_name":"Meng","full_name":"Xie, Meng","last_name":"Xie"},{"orcid":"0000-0003-4509-4998","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","last_name":"Kicheva"},{"first_name":"Karl","full_name":"Annusver, Karl","last_name":"Annusver"},{"last_name":"Kasper","full_name":"Kasper, Maria","first_name":"Maria"},{"last_name":"Symmons","full_name":"Symmons, Orsolya","first_name":"Orsolya"},{"first_name":"Leslie","last_name":"Pan","full_name":"Pan, Leslie"},{"first_name":"Francois","full_name":"Spitz, Francois","last_name":"Spitz"},{"first_name":"Jozef","last_name":"Kaiser","full_name":"Kaiser, Jozef"},{"full_name":"Hovorakova, Maria","last_name":"Hovorakova","first_name":"Maria"},{"first_name":"Tomas","full_name":"Zikmund, Tomas","last_name":"Zikmund"},{"full_name":"Sunadome, Kazunori","last_name":"Sunadome","first_name":"Kazunori"},{"first_name":"Michael P","last_name":"Matise","full_name":"Matise, Michael P"},{"first_name":"Hui","last_name":"Wang","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","full_name":"Ernfors, Patrik","last_name":"Ernfors"},{"last_name":"Maire","full_name":"Maire, Pascal","first_name":"Pascal"},{"last_name":"Wurmser","full_name":"Wurmser, Maud","first_name":"Maud"},{"first_name":"Andrei S","full_name":"Chagin, Andrei S","last_name":"Chagin"},{"full_name":"Fried, Kaj","last_name":"Fried","first_name":"Kaj"},{"first_name":"Igor","last_name":"Adameyko","full_name":"Adameyko, Igor"}],"title":"Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","oa_version":"Published Version","ec_funded":1,"date_published":"2018-06-13T00:00:00Z","publication":"eLife","status":"public","project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037"}],"publist_id":"7759","isi":1,"year":"2018","related_material":{"record":[{"id":"9838","relation":"research_data","status":"public"}]},"external_id":{"isi":["000436227500001"]},"quality_controlled":"1","ddc":["571"],"_id":"162","date_updated":"2023-09-18T09:29:07Z","type":"journal_article","article_processing_charge":"No","doi":"10.7554/eLife.34465","publisher":"eLife Sciences Publications"},{"month":"12","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"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.","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>.","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>","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>.","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>","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.","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."},"issue":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","day":"01","author":[{"last_name":"Reipert","full_name":"Reipert, Siegfried","first_name":"Siegfried"},{"last_name":"Goldammer","full_name":"Goldammer, Helmuth","first_name":"Helmuth"},{"first_name":"Christine","full_name":"Richardson, Christine","last_name":"Richardson"},{"first_name":"Martin","last_name":"Goldberg","full_name":"Goldberg, Martin"},{"first_name":"Timothy","last_name":"Hawkins","full_name":"Hawkins, Timothy"},{"first_name":"Elena","full_name":"Hollergschwandtner, Elena","id":"3C054040-F248-11E8-B48F-1D18A9856A87","last_name":"Hollergschwandtner"},{"orcid":"0000-0001-9735-5315","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","last_name":"Kaufmann"},{"first_name":"Sebastian","full_name":"Antreich, Sebastian","last_name":"Antreich"},{"first_name":"York","last_name":"Stierhof","full_name":"Stierhof, York"}],"oa_version":"Published Version","title":"Agitation modules: Flexible means to accelerate automated freeze substitution","volume":66,"date_created":"2018-12-11T11:44:57Z","article_type":"original","abstract":[{"lang":"eng","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."}],"intvolume":"        66","publication_identifier":{"issn":["0022-1554"]},"publication_status":"published","year":"2018","isi":1,"external_id":{"pmid":["29969056"],"isi":["000452277700005"]},"status":"public","publication":"Journal of Histochemistry and Cytochemistry","pmid":1,"date_published":"2018-12-01T00:00:00Z","article_processing_charge":"No","doi":"10.1369/0022155418786698","publisher":"SAGE Publications","_id":"163","date_updated":"2023-10-17T08:42:24Z","type":"journal_article","page":"903-921","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1369/0022155418786698"}],"quality_controlled":"1"},{"_id":"17","date_updated":"2023-09-11T12:59:28Z","type":"journal_article","article_processing_charge":"No","doi":"10.1103/PhysRevFluids.3.103302","publisher":"American Physical Society","quality_controlled":"1","ddc":["532"],"publist_id":"8038","isi":1,"year":"2018","external_id":{"isi":["000447311500001"]},"ec_funded":1,"date_published":"2018-10-15T00:00:00Z","publication":"Physical Review Fluids","status":"public","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"volume":3,"date_created":"2018-12-11T11:44:11Z","scopus_import":"1","day":"15","author":[{"first_name":"Atul","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","last_name":"Varshney"},{"first_name":"Victor","last_name":"Steinberg","full_name":"Steinberg, Victor"}],"title":"Drag enhancement and drag reduction in viscoelastic flow","oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:12Z","publication_status":"published","has_accepted_license":"1","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."}],"intvolume":"         3","department":[{"_id":"BjHo"}],"article_number":"103302 ","file":[{"file_name":"IST-2018-1061-v1+1_PhysRevFluids.3.103302.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"e1445be33e8165114e96246275600750","file_size":1409040,"date_created":"2018-12-12T10:10:14Z","date_updated":"2020-07-14T12:45:12Z","creator":"system","file_id":"4800"}],"month":"10","citation":{"short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","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.","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>","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>.","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>","ista":"Varshney A, Steinberg V. 2018. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 3(10), 103302.","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>."},"issue":"10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"pubrep_id":"1061","language":[{"iso":"eng"}]}]