[{"file_date_updated":"2020-07-14T12:47:13Z","doi":"10.3390/life9010009","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":9,"day":"15","publication":"Life","date_published":"2019-01-15T00:00:00Z","has_accepted_license":"1","intvolume":"         9","title":"Thermodynamics of duplication thresholds in synthetic protocell systems","article_number":"9","oa":1,"quality_controlled":"1","date_created":"2019-02-10T22:59:15Z","citation":{"chicago":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” <i>Life</i>. MDPI, 2019. <a href=\"https://doi.org/10.3390/life9010009\">https://doi.org/10.3390/life9010009</a>.","apa":"Corominas-Murtra, B. (2019). Thermodynamics of duplication thresholds in synthetic protocell systems. <i>Life</i>. MDPI. <a href=\"https://doi.org/10.3390/life9010009\">https://doi.org/10.3390/life9010009</a>","mla":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” <i>Life</i>, vol. 9, no. 1, 9, MDPI, 2019, doi:<a href=\"https://doi.org/10.3390/life9010009\">10.3390/life9010009</a>.","ista":"Corominas-Murtra B. 2019. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 9(1), 9.","short":"B. Corominas-Murtra, Life 9 (2019).","ieee":"B. Corominas-Murtra, “Thermodynamics of duplication thresholds in synthetic protocell systems,” <i>Life</i>, vol. 9, no. 1. MDPI, 2019.","ama":"Corominas-Murtra B. Thermodynamics of duplication thresholds in synthetic protocell systems. <i>Life</i>. 2019;9(1). doi:<a href=\"https://doi.org/10.3390/life9010009\">10.3390/life9010009</a>"},"license":"https://creativecommons.org/licenses/by/4.0/","author":[{"orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-24T14:43:41Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract—yet realistic—synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural—and eventually, functional—elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational, and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around ~ 10−13J , which results, in the case of duplication of all the vesicles contained in a liter of emulsion, in an amount of energy around ~ 1kJ . Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it."}],"month":"01","year":"2019","isi":1,"publication_identifier":{"eissn":["20751729"]},"department":[{"_id":"EdHa"}],"publisher":"MDPI","_id":"5944","issue":"1","external_id":{"isi":["000464125500001"]},"publication_status":"published","type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:13Z","access_level":"open_access","content_type":"application/pdf","date_created":"2019-02-11T10:45:27Z","checksum":"7d2322cd96ace41959909b66702d5cf4","file_size":963454,"file_name":"2019_Life_Corominas.pdf","relation":"main_file","file_id":"5951","creator":"dernst"}],"ddc":["570"]},{"status":"public","author":[{"last_name":"Petkova","full_name":"Petkova, Mariela D.","first_name":"Mariela D."},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"},{"last_name":"Wieschaus","full_name":"Wieschaus, Eric F.","first_name":"Eric F."},{"last_name":"Gregor","full_name":"Gregor, Thomas","first_name":"Thomas"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-24T14:42:47Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.01.007"}],"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/cells-find-their-identity-using-a-mathematically-optimal-strategy/","relation":"press_release"}]},"abstract":[{"text":"In developing organisms, spatially prescribed cell identities are thought to be determined by the expression levels of multiple genes. Quantitative tests of this idea, however, require a theoretical framework capable of exposing the rules and precision of cell specification over developmental time. We use the gap gene network in the early fly embryo as an example to show how expression levels of the four gap genes can be jointly decoded into an optimal specification of position with 1% accuracy. The decoder correctly predicts, with no free parameters, the dynamics of pair-rule expression patterns at different developmental time points and in various mutant backgrounds. Precise cellular identities are thus available at the earliest stages of development, contrasting the prevailing view of positional information being slowly refined across successive layers of the patterning network. Our results suggest that developmental enhancers closely approximate a mathematically optimal decoding strategy.","lang":"eng"}],"project":[{"grant_number":"P28844-B27","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"month":"02","year":"2019","isi":1,"article_type":"original","department":[{"_id":"GaTk"}],"publisher":"Cell Press","external_id":{"isi":["000457969200015"],"pmid":["30712870"]},"publication_status":"published","issue":"4","_id":"5945","type":"journal_article","oa_version":"Published Version","doi":"10.1016/j.cell.2019.01.007","article_processing_charge":"No","pmid":1,"publication":"Cell","day":"07","volume":176,"date_published":"2019-02-07T00:00:00Z","intvolume":"       176","page":"844-855.e15","title":"Optimal decoding of cellular identities in a genetic network","oa":1,"quality_controlled":"1","date_created":"2019-02-10T22:59:16Z","citation":{"apa":"Petkova, M. D., Tkačik, G., Bialek, W., Wieschaus, E. F., &#38; Gregor, T. (2019). Optimal decoding of cellular identities in a genetic network. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2019.01.007\">https://doi.org/10.1016/j.cell.2019.01.007</a>","chicago":"Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus, and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.” <i>Cell</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.01.007\">https://doi.org/10.1016/j.cell.2019.01.007</a>.","mla":"Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic Network.” <i>Cell</i>, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.01.007\">10.1016/j.cell.2019.01.007</a>.","ama":"Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of cellular identities in a genetic network. <i>Cell</i>. 2019;176(4):844-855.e15. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.01.007\">10.1016/j.cell.2019.01.007</a>","short":"M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019) 844–855.e15.","ieee":"M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal decoding of cellular identities in a genetic network,” <i>Cell</i>, vol. 176, no. 4. Cell Press, p. 844–855.e15, 2019.","ista":"Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal decoding of cellular identities in a genetic network. Cell. 176(4), 844–855.e15."}},{"publication":"ACM International Conference Proceeding Series","day":"04","date_published":"2019-01-04T00:00:00Z","doi":"10.1145/3288599.3288617","article_processing_charge":"No","oa":1,"quality_controlled":"1","arxiv":1,"conference":{"location":"Bangalore, India","end_date":"2019-01-07","name":"ICDCN: Conference on Distributed Computing and Networking","start_date":"2019-01-04"},"date_created":"2019-02-10T22:59:17Z","citation":{"ieee":"B. Chatterjee, S. Peri, M. Sa, and N. Singhal, “A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries,” in <i>ACM International Conference Proceeding Series</i>, Bangalore, India, 2019, pp. 168–177.","short":"B. Chatterjee, S. Peri, M. Sa, N. Singhal, in:, ACM International Conference Proceeding Series, ACM, 2019, pp. 168–177.","ista":"Chatterjee B, Peri S, Sa M, Singhal N. 2019. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. ACM International Conference Proceeding Series. ICDCN: Conference on Distributed Computing and Networking, 168–177.","ama":"Chatterjee B, Peri S, Sa M, Singhal N. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In: <i>ACM International Conference Proceeding Series</i>. ACM; 2019:168-177. doi:<a href=\"https://doi.org/10.1145/3288599.3288617\">10.1145/3288599.3288617</a>","mla":"Chatterjee, Bapi, et al. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” <i>ACM International Conference Proceeding Series</i>, ACM, 2019, pp. 168–77, doi:<a href=\"https://doi.org/10.1145/3288599.3288617\">10.1145/3288599.3288617</a>.","chicago":"Chatterjee, Bapi, Sathya Peri, Muktikanta Sa, and Nandini Singhal. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” In <i>ACM International Conference Proceeding Series</i>, 168–77. ACM, 2019. <a href=\"https://doi.org/10.1145/3288599.3288617\">https://doi.org/10.1145/3288599.3288617</a>.","apa":"Chatterjee, B., Peri, S., Sa, M., &#38; Singhal, N. (2019). A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In <i>ACM International Conference Proceeding Series</i> (pp. 168–177). Bangalore, India: ACM. <a href=\"https://doi.org/10.1145/3288599.3288617\">https://doi.org/10.1145/3288599.3288617</a>"},"page":"168-177","title":"A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-24T14:41:53Z","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1809.00896","open_access":"1"}],"abstract":[{"text":"Graph algorithms applied in many applications, including social networks, communication networks, VLSI design, graphics, and several others, require dynamic modifications - addition and removal of vertices and/or edges - in the graph. This paper presents a novel concurrent non-blocking algorithm to implement a dynamic unbounded directed graph in a shared-memory machine. The addition and removal operations of vertices and edges are lock-free. For a finite sized graph, the lookup operations are wait-free. Most significant component of the presented algorithm is the reachability query in a concurrent graph. The reachability queries in our algorithm are obstruction-free and thus impose minimal additional synchronization cost over other operations. We prove that each of the data structure operations are linearizable. We extensively evaluate a sample C/C++ implementation of the algorithm through a number of micro-benchmarks. The experimental results show that the proposed algorithm scales well with the number of threads and on an average provides 5 to 7x performance improvement over a concurrent graph implementation using coarse-grained locking.","lang":"eng"}],"status":"public","author":[{"full_name":"Chatterjee, Bapi","last_name":"Chatterjee","orcid":"0000-0002-2742-4028","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","first_name":"Bapi"},{"last_name":"Peri","full_name":"Peri, Sathya","first_name":"Sathya"},{"full_name":"Sa, Muktikanta","last_name":"Sa","first_name":"Muktikanta"},{"first_name":"Nandini","last_name":"Singhal","full_name":"Singhal, Nandini"}],"publisher":"ACM","external_id":{"arxiv":["1809.00896"],"isi":["000484491600019"]},"publication_status":"published","_id":"5947","type":"conference","oa_version":"Preprint","month":"01","year":"2019","publication_identifier":{"isbn":["978-1-4503-6094-4 "]},"isi":1,"department":[{"_id":"DaAl"}]},{"publisher":"Springer Nature","publication_status":"published","alternative_title":["LNCS"],"external_id":{"isi":["000931943000022"],"arxiv":["1701.02944"]},"_id":"5948","type":"conference","oa_version":"Preprint","project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"year":"2019","month":"01","isi":1,"department":[{"_id":"KrCh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2025-06-02T08:53:41Z","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1701.02944"}],"abstract":[{"lang":"eng","text":"We study the termination problem for nondeterministic probabilistic programs. We consider the bounded termination problem that asks whether the supremum of the expected termination time over all schedulers is bounded. First, we show that ranking supermartingales (RSMs) are both sound and complete for proving bounded termination over nondeterministic probabilistic programs. For nondeterministic probabilistic programs a previous result claimed that RSMs are not complete for bounded termination, whereas our result corrects the previous flaw and establishes completeness with a rigorous proof. Second, we present the first sound approach to establish lower bounds on expected termination time through RSMs."}],"status":"public","author":[{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","arxiv":1,"conference":{"end_date":"2019-01-15","location":"Cascais, Portugal","name":"VMCAI: Verification, Model Checking, and Abstract Interpretation","start_date":"2019-01-13"},"date_created":"2019-02-10T22:59:17Z","citation":{"mla":"Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>, vol. 11388, Springer Nature, 2019, pp. 468–90, doi:<a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">10.1007/978-3-030-11245-5_22</a>.","apa":"Fu, H., &#38; Chatterjee, K. (2019). Termination of nondeterministic probabilistic programs. In <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i> (Vol. 11388, pp. 468–490). Cascais, Portugal: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">https://doi.org/10.1007/978-3-030-11245-5_22</a>","chicago":"Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” In <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>, 11388:468–90. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">https://doi.org/10.1007/978-3-030-11245-5_22</a>.","ama":"Fu H, Chatterjee K. Termination of nondeterministic probabilistic programs. In: <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>. Vol 11388. Springer Nature; 2019:468-490. doi:<a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">10.1007/978-3-030-11245-5_22</a>","ista":"Fu H, Chatterjee K. 2019. Termination of nondeterministic probabilistic programs. International Conference on Verification, Model Checking, and Abstract Interpretation. VMCAI: Verification, Model Checking, and Abstract Interpretation, LNCS, vol. 11388, 468–490.","short":"H. Fu, K. Chatterjee, in:, International Conference on Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2019, pp. 468–490.","ieee":"H. Fu and K. Chatterjee, “Termination of nondeterministic probabilistic programs,” in <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>, Cascais, Portugal, 2019, vol. 11388, pp. 468–490."},"page":"468-490","title":"Termination of nondeterministic probabilistic programs","day":"11","publication":"International Conference on Verification, Model Checking, and Abstract Interpretation","volume":11388,"date_published":"2019-01-11T00:00:00Z","intvolume":"     11388","doi":"10.1007/978-3-030-11245-5_22","article_processing_charge":"No"},{"publisher":"Wiley","external_id":{"isi":["000480635400003"]},"publication_status":"published","issue":"9","_id":"5949","file":[{"relation":"main_file","creator":"dernst","file_id":"5950","file_name":"2019_Hippocampus_Kaefer.pdf","date_created":"2019-02-11T10:42:51Z","checksum":"5e8de271ca04aef92a5de42d6aac4404","file_size":2132893,"date_updated":"2020-07-14T12:47:13Z","content_type":"application/pdf","access_level":"open_access"}],"ddc":["570"],"oa_version":"Published Version","type":"journal_article","project":[{"grant_number":"607616","name":"Inter-and intracellular signalling in schizophrenia","call_identifier":"FP7","_id":"257BBB4C-B435-11E9-9278-68D0E5697425"}],"year":"2019","month":"09","isi":1,"article_type":"original","department":[{"_id":"JoCs"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2024-03-25T23:30:11Z","scopus_import":"1","related_material":{"record":[{"id":"6825","relation":"dissertation_contains","status":"public"}]},"abstract":[{"text":"Aberrant proteostasis of protein aggregation may lead to behavior disorders including chronic mental illnesses (CMI). Furthermore, the neuronal activity alterations that underlie CMI are not well understood. We recorded the local field potential and single-unit activity of the hippocampal CA1 region in vivo in rats transgenically overexpressing the Disrupted-in-Schizophrenia 1 (DISC1) gene (tgDISC1), modeling sporadic CMI. These tgDISC1 rats have previously been shown to exhibit DISC1 protein aggregation, disturbances in the dopaminergic system and attention-related deficits. Recordings were performed during exploration of familiar and novel open field environments and during sleep, allowing investigation of neuronal abnormalities in unconstrained behavior. Compared to controls, tgDISC1 place cells exhibited smaller place fields and decreased speed-modulation of their firing rates, demonstrating altered spatial coding and deficits in encoding location-independent sensory inputs. Oscillation analyses showed that tgDISC1 pyramidal neurons had higher theta phase locking strength during novelty, limiting their phase coding ability. However, their mean theta phases were more variable at the population level, reducing oscillatory network synchronization. Finally, tgDISC1 pyramidal neurons showed a lack of novelty-induced shift in their preferred theta and gamma firing phases, indicating deficits in coding of novel environments with oscillatory firing. By combining single cell and neuronal population analyses, we link DISC1 protein pathology with abnormal hippocampal neural coding and network synchrony, and thereby gain a more comprehensive understanding of CMI mechanisms.","lang":"eng"}],"status":"public","author":[{"last_name":"Käfer","full_name":"Käfer, Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","first_name":"Karola"},{"full_name":"Malagon-Vina, Hugo","last_name":"Malagon-Vina","first_name":"Hugo"},{"id":"444EB89E-F248-11E8-B48F-1D18A9856A87","first_name":"Desiree","full_name":"Dickerson, Desiree","last_name":"Dickerson"},{"first_name":"Joseph","full_name":"O'Neill, Joseph","last_name":"O'Neill"},{"last_name":"Trossbach","full_name":"Trossbach, Svenja V.","first_name":"Svenja V."},{"full_name":"Korth, Carsten","last_name":"Korth","first_name":"Carsten"},{"last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"quality_controlled":"1","date_created":"2019-02-10T22:59:18Z","citation":{"mla":"Käfer, Karola, et al. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” <i>Hippocampus</i>, vol. 29, no. 9, Wiley, 2019, pp. 802–16, doi:<a href=\"https://doi.org/10.1002/hipo.23076\">10.1002/hipo.23076</a>.","chicago":"Käfer, Karola, Hugo Malagon-Vina, Desiree Dickerson, Joseph O’Neill, Svenja V. Trossbach, Carsten Korth, and Jozsef L Csicsvari. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” <i>Hippocampus</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/hipo.23076\">https://doi.org/10.1002/hipo.23076</a>.","apa":"Käfer, K., Malagon-Vina, H., Dickerson, D., O’Neill, J., Trossbach, S. V., Korth, C., &#38; Csicsvari, J. L. (2019). Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. <i>Hippocampus</i>. Wiley. <a href=\"https://doi.org/10.1002/hipo.23076\">https://doi.org/10.1002/hipo.23076</a>","ista":"Käfer K, Malagon-Vina H, Dickerson D, O’Neill J, Trossbach SV, Korth C, Csicsvari JL. 2019. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. 29(9), 802–816.","short":"K. Käfer, H. Malagon-Vina, D. Dickerson, J. O’Neill, S.V. Trossbach, C. Korth, J.L. Csicsvari, Hippocampus 29 (2019) 802–816.","ieee":"K. Käfer <i>et al.</i>, “Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization,” <i>Hippocampus</i>, vol. 29, no. 9. Wiley, pp. 802–816, 2019.","ama":"Käfer K, Malagon-Vina H, Dickerson D, et al. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. <i>Hippocampus</i>. 2019;29(9):802-816. doi:<a href=\"https://doi.org/10.1002/hipo.23076\">10.1002/hipo.23076</a>"},"page":"802-816","title":"Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization","day":"01","publication":"Hippocampus","volume":29,"date_published":"2019-09-01T00:00:00Z","intvolume":"        29","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:13Z","doi":"10.1002/hipo.23076","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","ec_funded":1},{"scopus_import":"1","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"683"},{"id":"7944","relation":"dissertation_contains","status":"public"}]},"abstract":[{"lang":"eng","text":"Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm (with 𝑂(𝑛8) being a crude bound on the run-time) to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of 𝑂(𝑛7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_updated":"2023-09-07T13:17:36Z","status":"public","author":[{"last_name":"Lubiw","full_name":"Lubiw, Anna","first_name":"Anna"},{"id":"45CFE238-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","last_name":"Masárová","full_name":"Masárová, Zuzana","orcid":"0000-0002-6660-1322"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","full_name":"Wagner, Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568"}],"publication_status":"published","external_id":{"arxiv":["1710.02741"],"isi":["000466130000009"]},"_id":"5986","issue":"4","type":"journal_article","ddc":["000"],"file":[{"file_name":"2018_DiscreteGeometry_Lubiw.pdf","relation":"main_file","creator":"dernst","file_id":"5988","date_updated":"2020-07-14T12:47:14Z","content_type":"application/pdf","access_level":"open_access","date_created":"2019-02-14T11:57:22Z","file_size":556276,"checksum":"e1bff88f1d77001b53b78c485ce048d7"}],"oa_version":"Published Version","publisher":"Springer Nature","article_type":"original","department":[{"_id":"UlWa"}],"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"month":"06","year":"2019","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"isi":1,"date_published":"2019-06-01T00:00:00Z","has_accepted_license":"1","intvolume":"        61","publication":"Discrete & Computational Geometry","day":"01","volume":61,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","file_date_updated":"2020-07-14T12:47:14Z","doi":"10.1007/s00454-018-0035-8","quality_controlled":"1","arxiv":1,"citation":{"chicago":"Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture for Flipping Edge-Labelled Triangulations.” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s00454-018-0035-8\">https://doi.org/10.1007/s00454-018-0035-8</a>.","apa":"Lubiw, A., Masárová, Z., &#38; Wagner, U. (2019). A proof of the orbit conjecture for flipping edge-labelled triangulations. <i>Discrete &#38; Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-018-0035-8\">https://doi.org/10.1007/s00454-018-0035-8</a>","mla":"Lubiw, Anna, et al. “A Proof of the Orbit Conjecture for Flipping Edge-Labelled Triangulations.” <i>Discrete &#38; Computational Geometry</i>, vol. 61, no. 4, Springer Nature, 2019, pp. 880–98, doi:<a href=\"https://doi.org/10.1007/s00454-018-0035-8\">10.1007/s00454-018-0035-8</a>.","ista":"Lubiw A, Masárová Z, Wagner U. 2019. A proof of the orbit conjecture for flipping edge-labelled triangulations. Discrete &#38; Computational Geometry. 61(4), 880–898.","ieee":"A. Lubiw, Z. Masárová, and U. Wagner, “A proof of the orbit conjecture for flipping edge-labelled triangulations,” <i>Discrete &#38; Computational Geometry</i>, vol. 61, no. 4. Springer Nature, pp. 880–898, 2019.","short":"A. Lubiw, Z. Masárová, U. Wagner, Discrete &#38; Computational Geometry 61 (2019) 880–898.","ama":"Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping edge-labelled triangulations. <i>Discrete &#38; Computational Geometry</i>. 2019;61(4):880-898. doi:<a href=\"https://doi.org/10.1007/s00454-018-0035-8\">10.1007/s00454-018-0035-8</a>"},"date_created":"2019-02-14T11:54:08Z","oa":1,"title":"A proof of the orbit conjecture for flipping edge-labelled triangulations","page":"880-898"},{"article_type":"original","department":[{"_id":"BjHo"}],"year":"2019","month":"02","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"publication_identifier":{"issn":["2041-1723"]},"_id":"6014","external_id":{"isi":["000458175300001"],"arxiv":["1902.03763"]},"publication_status":"published","type":"journal_article","ddc":["530"],"file":[{"file_name":"2019_NatureComm_Varshney.pdf","relation":"main_file","file_id":"6015","creator":"dernst","date_updated":"2020-07-14T12:47:17Z","access_level":"open_access","content_type":"application/pdf","date_created":"2019-02-15T07:15:00Z","file_size":1331490,"checksum":"d3acf07eaad95ec040d8e8565fc9ac37"}],"oa_version":"Published Version","publisher":"Springer Nature","author":[{"last_name":"Varshney","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul"},{"full_name":"Steinberg, Victor","last_name":"Steinberg","first_name":"Victor"}],"status":"public","scopus_import":"1","abstract":[{"lang":"eng","text":"Speed of sound waves in gases and liquids are governed by the compressibility of the medium. There exists another type of non-dispersive wave where the wave speed depends on stress instead of elasticity of the medium. A well-known example is the Alfven wave, which propagates through plasma permeated by a magnetic field with the speed determined by magnetic tension. An elastic analogue of Alfven waves has been predicted in a flow of dilute polymer solution where the elastic stress of the stretching polymers determines the elastic wave speed. Here we present quantitative evidence of elastic Alfven waves in elastic turbulence of a viscoelastic creeping flow between two obstacles in channel flow. The key finding in the experimental proof is a nonlinear dependence of the elastic wave speed cel on the Weissenberg number Wi, which deviates from predictions based on a model of linear polymer elasticity."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_updated":"2023-09-08T11:39:54Z","title":"Elastic alfven waves in elastic turbulence","quality_controlled":"1","arxiv":1,"citation":{"ista":"Varshney A, Steinberg V. 2019. Elastic alfven waves in elastic turbulence. Nature Communications. 10, 652.","short":"A. Varshney, V. Steinberg, Nature Communications 10 (2019).","ieee":"A. Varshney and V. Steinberg, “Elastic alfven waves in elastic turbulence,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019.","ama":"Varshney A, Steinberg V. Elastic alfven waves in elastic turbulence. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-08551-0\">10.1038/s41467-019-08551-0</a>","chicago":"Varshney, Atul, and Victor Steinberg. “Elastic Alfven Waves in Elastic Turbulence.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-08551-0\">https://doi.org/10.1038/s41467-019-08551-0</a>.","apa":"Varshney, A., &#38; Steinberg, V. (2019). Elastic alfven waves in elastic turbulence. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-08551-0\">https://doi.org/10.1038/s41467-019-08551-0</a>","mla":"Varshney, Atul, and Victor Steinberg. “Elastic Alfven Waves in Elastic Turbulence.” <i>Nature Communications</i>, vol. 10, 652, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-08551-0\">10.1038/s41467-019-08551-0</a>."},"date_created":"2019-02-15T07:10:46Z","article_number":"652","oa":1,"article_processing_charge":"No","ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:47:17Z","doi":"10.1038/s41467-019-08551-0","date_published":"2019-02-08T00:00:00Z","has_accepted_license":"1","intvolume":"        10","volume":10,"publication":"Nature Communications","day":"08"},{"year":"2019","month":"02","isi":1,"department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","publication_status":"published","external_id":{"isi":["000460317100001"]},"issue":"2","_id":"6022","file":[{"creator":"dernst","file_id":"6036","relation":"main_file","file_name":"2019_PLOS_Merrill.pdf","checksum":"5f34001617ee729314ca520c049b1112","file_size":2005949,"date_created":"2019-02-18T14:57:24Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:17Z"}],"type":"journal_article","oa_version":"Published Version","ddc":["570"],"license":"https://creativecommons.org/publicdomain/zero/1.0/","status":"public","author":[{"full_name":"Merrill, Richard M.","last_name":"Merrill","first_name":"Richard M."},{"first_name":"Pasi","last_name":"Rastas","full_name":"Rastas, Pasi"},{"last_name":"Martin","full_name":"Martin, Simon H.","first_name":"Simon H."},{"id":"386D7308-F248-11E8-B48F-1D18A9856A87","first_name":"Maria C","last_name":"Melo Hurtado","full_name":"Melo Hurtado, Maria C"},{"first_name":"Sarah","full_name":"Barker, Sarah","last_name":"Barker"},{"last_name":"Davey","full_name":"Davey, John","first_name":"John"},{"first_name":"W. Owen","last_name":"Mcmillan","full_name":"Mcmillan, W. Owen"},{"full_name":"Jiggins, Chris D.","last_name":"Jiggins","first_name":"Chris D."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-24T14:46:23Z","scopus_import":"1","related_material":{"record":[{"id":"9801","relation":"research_data","status":"public"}]},"abstract":[{"lang":"eng","text":"The evolution of new species is made easier when traits under divergent ecological selection are also mating cues. Such ecological mating cues are now considered more common than previously thought, but we still know little about the genetic changes underlying their evolution or more generally about the genetic basis for assortative mating behaviors. Both tight physical linkage and the existence of large-effect preference loci will strengthen genetic associations between behavioral and ecological barriers, promoting the evolution of assortative mating. The warning patterns of Heliconius melpomene and H. cydno are under disruptive selection due to increased predation of nonmimetic hybrids and are used during mate recognition. We carried out a genome-wide quantitative trait locus (QTL) analysis of preference behaviors between these species and showed that divergent male preference has a simple genetic basis. We identify three QTLs that together explain a large proportion (approximately 60%) of the difference in preference behavior observed between the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM) from the major color pattern gene optix, and, individually, all three have a large effect on the preference phenotype. Genomic divergence between H. cydno and H. melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix color pattern locus but not the other preference QTLs. The simple genetic architecture we reveal will facilitate the evolution and maintenance of new species despite ongoing gene flow by coupling behavioral and ecological aspects of reproductive isolation."}],"title":"Genetic dissection of assortative mating behavior","oa":1,"article_number":"e2005902","quality_controlled":"1","date_created":"2019-02-17T22:59:21Z","citation":{"apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Genetic dissection of assortative mating behavior. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005902\">https://doi.org/10.1371/journal.pbio.2005902</a>","chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Genetic Dissection of Assortative Mating Behavior.” <i>PLoS Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pbio.2005902\">https://doi.org/10.1371/journal.pbio.2005902</a>.","mla":"Merrill, Richard M., et al. “Genetic Dissection of Assortative Mating Behavior.” <i>PLoS Biology</i>, vol. 17, no. 2, e2005902, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005902\">10.1371/journal.pbio.2005902</a>.","ama":"Merrill RM, Rastas P, Martin SH, et al. Genetic dissection of assortative mating behavior. <i>PLoS Biology</i>. 2019;17(2). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005902\">10.1371/journal.pbio.2005902</a>","ieee":"R. M. Merrill <i>et al.</i>, “Genetic dissection of assortative mating behavior,” <i>PLoS Biology</i>, vol. 17, no. 2. Public Library of Science, 2019.","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, PLoS Biology 17 (2019).","ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Genetic dissection of assortative mating behavior. PLoS Biology. 17(2), e2005902."},"file_date_updated":"2020-07-14T12:47:17Z","doi":"10.1371/journal.pbio.2005902","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"article_processing_charge":"No","publication":"PLoS Biology","day":"07","volume":17,"date_published":"2019-02-07T00:00:00Z","has_accepted_license":"1","intvolume":"        17"},{"isi":1,"year":"2019","month":"02","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publisher":"Springer Nature","type":"journal_article","oa_version":"Submitted Version","_id":"6023","issue":"2","publication_status":"published","external_id":{"isi":["000460479600014"]},"author":[{"first_name":"Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","full_name":"Yoshida, Saiko","last_name":"Yoshida"},{"first_name":"Alja","last_name":"Van Der Schuren","full_name":"Van Der Schuren, Alja"},{"first_name":"Maritza","full_name":"Van Dop, Maritza","last_name":"Van Dop"},{"full_name":"Van Galen, Luc","last_name":"Van Galen","first_name":"Luc"},{"first_name":"Shunsuke","last_name":"Saiga","full_name":"Saiga, Shunsuke"},{"last_name":"Adibi","full_name":"Adibi, Milad","first_name":"Milad"},{"full_name":"Möller, Barbara","last_name":"Möller","first_name":"Barbara"},{"last_name":"Ten Hove","full_name":"Ten Hove, Colette A.","first_name":"Colette A."},{"orcid":"0000-0001-5227-5741","full_name":"Marhavy, Peter","last_name":"Marhavy","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"full_name":"Smith, Richard","last_name":"Smith","first_name":"Richard"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"first_name":"Dolf","full_name":"Weijers, Dolf","last_name":"Weijers"}],"status":"public","date_updated":"2023-08-24T14:46:47Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division 1–3 . In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical–basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation, together with a second domain that defines the polar membrane domain. Our work shows that SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation. Furthermore, this work reveals that, despite fundamental differences, cell polarity mechanisms in plants and animals converge on a similar protein domain.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/479113v1.abstract"}],"scopus_import":"1","page":"160-166","title":"A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis","oa":1,"citation":{"mla":"Yoshida, Saiko, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” <i>Nature Plants</i>, vol. 5, no. 2, Springer Nature, 2019, pp. 160–66, doi:<a href=\"https://doi.org/10.1038/s41477-019-0363-6\">10.1038/s41477-019-0363-6</a>.","chicago":"Yoshida, Saiko, Alja Van Der Schuren, Maritza Van Dop, Luc Van Galen, Shunsuke Saiga, Milad Adibi, Barbara Möller, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” <i>Nature Plants</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41477-019-0363-6\">https://doi.org/10.1038/s41477-019-0363-6</a>.","apa":"Yoshida, S., Van Der Schuren, A., Van Dop, M., Van Galen, L., Saiga, S., Adibi, M., … Weijers, D. (2019). A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-019-0363-6\">https://doi.org/10.1038/s41477-019-0363-6</a>","short":"S. Yoshida, A. Van Der Schuren, M. Van Dop, L. Van Galen, S. Saiga, M. Adibi, B. Möller, C.A. Ten Hove, P. Marhavý, R. Smith, J. Friml, D. Weijers, Nature Plants 5 (2019) 160–166.","ieee":"S. Yoshida <i>et al.</i>, “A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis,” <i>Nature Plants</i>, vol. 5, no. 2. Springer Nature, pp. 160–166, 2019.","ista":"Yoshida S, Van Der Schuren A, Van Dop M, Van Galen L, Saiga S, Adibi M, Möller B, Ten Hove CA, Marhavý P, Smith R, Friml J, Weijers D. 2019. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 5(2), 160–166.","ama":"Yoshida S, Van Der Schuren A, Van Dop M, et al. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. <i>Nature Plants</i>. 2019;5(2):160-166. doi:<a href=\"https://doi.org/10.1038/s41477-019-0363-6\">10.1038/s41477-019-0363-6</a>"},"date_created":"2019-02-17T22:59:21Z","quality_controlled":"1","doi":"10.1038/s41477-019-0363-6","ec_funded":1,"article_processing_charge":"No","volume":5,"day":"08","publication":"Nature Plants","intvolume":"         5","date_published":"2019-02-08T00:00:00Z"},{"title":"Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration","oa":1,"article_number":"e42093","quality_controlled":"1","citation":{"mla":"Capek, Daniel, et al. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” <i>ELife</i>, vol. 8, e42093, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.42093\">10.7554/eLife.42093</a>.","chicago":"Capek, Daniel, Michael Smutny, Alexandra Madelaine Tichy, Maurizio Morri, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.42093\">https://doi.org/10.7554/eLife.42093</a>.","apa":"Capek, D., Smutny, M., Tichy, A. M., Morri, M., Janovjak, H. L., &#38; Heisenberg, C.-P. J. (2019). Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.42093\">https://doi.org/10.7554/eLife.42093</a>","ieee":"D. Capek, M. Smutny, A. M. Tichy, M. Morri, H. L. Janovjak, and C.-P. J. Heisenberg, “Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","short":"D. Capek, M. Smutny, A.M. Tichy, M. Morri, H.L. Janovjak, C.-P.J. Heisenberg, ELife 8 (2019).","ista":"Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. 2019. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. eLife. 8, e42093.","ama":"Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.42093\">10.7554/eLife.42093</a>"},"date_created":"2019-02-17T22:59:22Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"file_date_updated":"2020-07-14T12:47:17Z","doi":"10.7554/eLife.42093","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"article_processing_charge":"No","publication":"eLife","day":"06","volume":8,"date_published":"2019-02-06T00:00:00Z","intvolume":"         8","has_accepted_license":"1","project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"}],"month":"02","year":"2019","isi":1,"department":[{"_id":"CaHe"},{"_id":"HaJa"}],"publisher":"eLife Sciences Publications","publication_status":"published","external_id":{"isi":["000458025300001"]},"_id":"6025","file":[{"file_id":"6041","creator":"dernst","relation":"main_file","file_name":"2019_elife_Capek.pdf","file_size":5500707,"checksum":"6cb4ca6d4aa96f6f187a5983aa3e660a","date_created":"2019-02-18T15:17:21Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:17Z"}],"oa_version":"Published Version","ddc":["570"],"type":"journal_article","status":"public","author":[{"id":"31C42484-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0001-5199-9940","full_name":"Capek, Daniel","last_name":"Capek"},{"orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael","last_name":"Smutny","first_name":"Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexandra Madelaine","full_name":"Tichy, Alexandra Madelaine","last_name":"Tichy"},{"first_name":"Maurizio","id":"4863116E-F248-11E8-B48F-1D18A9856A87","last_name":"Morri","full_name":"Morri, Maurizio"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","last_name":"Janovjak","full_name":"Janovjak, Harald L"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-24T14:46:01Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Non-canonical Wnt signaling plays a central role for coordinated cell polarization and directed migration in metazoan development. While spatiotemporally restricted activation of non-canonical Wnt-signaling drives cell polarization in epithelial tissues, it remains unclear whether such instructive activity is also critical for directed mesenchymal cell migration. Here, we developed a light-activated version of the non-canonical Wnt receptor Frizzled 7 (Fz7) to analyze how restricted activation of non-canonical Wnt signaling affects directed anterior axial mesendoderm (prechordal plate, ppl) cell migration within the zebrafish gastrula. We found that Fz7 signaling is required for ppl cell protrusion formation and migration and that spatiotemporally restricted ectopic activation is capable of redirecting their migration. Finally, we show that uniform activation of Fz7 signaling in ppl cells fully rescues defective directed cell migration in fz7 mutant embryos. Together, our findings reveal that in contrast to the situation in epithelial cells, non-canonical Wnt signaling functions permissively rather than instructively in directed mesenchymal cell migration during gastrulation."}]},{"publication":"Communications on Pure and Applied Mathematics","day":"08","volume":72,"intvolume":"        72","has_accepted_license":"1","date_published":"2019-02-08T00:00:00Z","doi":"10.1002/cpa.21816","file_date_updated":"2020-07-14T12:47:17Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","oa":1,"citation":{"apa":"Gerencser, M., &#38; Hairer, M. (2019). A solution theory for quasilinear singular SPDEs. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.21816\">https://doi.org/10.1002/cpa.21816</a>","chicago":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/cpa.21816\">https://doi.org/10.1002/cpa.21816</a>.","mla":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” <i>Communications on Pure and Applied Mathematics</i>, vol. 72, no. 9, Wiley, 2019, pp. 1983–2005, doi:<a href=\"https://doi.org/10.1002/cpa.21816\">10.1002/cpa.21816</a>.","ama":"Gerencser M, Hairer M. A solution theory for quasilinear singular SPDEs. <i>Communications on Pure and Applied Mathematics</i>. 2019;72(9):1983-2005. doi:<a href=\"https://doi.org/10.1002/cpa.21816\">10.1002/cpa.21816</a>","short":"M. Gerencser, M. Hairer, Communications on Pure and Applied Mathematics 72 (2019) 1983–2005.","ieee":"M. Gerencser and M. Hairer, “A solution theory for quasilinear singular SPDEs,” <i>Communications on Pure and Applied Mathematics</i>, vol. 72, no. 9. Wiley, pp. 1983–2005, 2019.","ista":"Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 72(9), 1983–2005."},"date_created":"2019-02-17T22:59:24Z","quality_controlled":"1","page":"1983-2005","title":"A solution theory for quasilinear singular SPDEs","date_updated":"2023-08-24T14:44:31Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We give a construction allowing us to build local renormalized solutions to general quasilinear stochastic PDEs within the theory of regularity structures, thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking, our construction covers quasilinear variants of all classes of equations for which the general construction of [3, 4, 7] applies, including in particular one‐dimensional systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less singular and more specific case, we furthermore show that the counterterms introduced by the renormalization procedure are given by local functionals of the solution. The main feature of our construction is that it allows exploitation of a number of existing results developed for the semilinear case, so that the number of additional arguments it requires is relatively small."}],"scopus_import":"1","status":"public","author":[{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","full_name":"Gerencser, Mate","last_name":"Gerencser"},{"full_name":"Hairer, Martin","last_name":"Hairer","first_name":"Martin"}],"publisher":"Wiley","file":[{"date_created":"2020-01-07T13:25:55Z","file_size":381350,"checksum":"09aec427eb48c0f96a1cce9ff53f013b","date_updated":"2020-07-14T12:47:17Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"kschuh","file_id":"7237","file_name":"2019_Wiley_Gerencser.pdf"}],"oa_version":"Published Version","ddc":["500"],"type":"journal_article","external_id":{"isi":["000475465000003"]},"publication_status":"published","issue":"9","_id":"6028","isi":1,"year":"2019","month":"02","department":[{"_id":"JaMa"}]},{"department":[{"_id":"JoDa"}],"year":"2019","month":"01","isi":1,"publication_identifier":{"eissn":["22962646"]},"_id":"6029","publication_status":"published","external_id":{"isi":["000456718000001"]},"oa_version":"Published Version","ddc":["540"],"type":"journal_article","file":[{"file_id":"6039","creator":"dernst","relation":"main_file","file_name":"2019_frontiers_Lindner.pdf","checksum":"7841301d7c53b56ef873791b4b6f7b24","file_size":1766820,"date_created":"2019-02-18T15:10:34Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:17Z"}],"publisher":"Frontiers Media S.A.","author":[{"first_name":"Marco","full_name":"Lindner, Marco","last_name":"Lindner"},{"first_name":"Aliz","full_name":"Tresztenyak, Aliz","last_name":"Tresztenyak"},{"first_name":"Gergö","full_name":"Fülöp, Gergö","last_name":"Fülöp"},{"last_name":"Jahr","full_name":"Jahr, Wiebke","first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Prinz, Adrian","last_name":"Prinz","first_name":"Adrian"},{"first_name":"Iris","full_name":"Prinz, Iris","last_name":"Prinz"},{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gerhard J.","last_name":"Schütz","full_name":"Schütz, Gerhard J."},{"last_name":"Sevcsik","full_name":"Sevcsik, Eva","first_name":"Eva"}],"status":"public","scopus_import":"1","abstract":[{"text":"Protein micropatterning has become an important tool for many biomedical applications as well as in academic research. Current techniques that allow to reduce the feature size of patterns below 1 μm are, however, often costly and require sophisticated equipment. We present here a straightforward and convenient method to generate highly condensed nanopatterns of proteins without the need for clean room facilities or expensive equipment. Our approach is based on nanocontact printing and allows for the fabrication of protein patterns with feature sizes of 80 nm and periodicities down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane) (X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle, different proteins at various scales were printed and the pattern quality was evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-24T14:45:38Z","title":"A fast and simple contact printing approach to generate 2D protein nanopatterns","quality_controlled":"1","date_created":"2019-02-17T22:59:24Z","citation":{"chicago":"Lindner, Marco, Aliz Tresztenyak, Gergö Fülöp, Wiebke Jahr, Adrian Prinz, Iris Prinz, Johann G Danzl, Gerhard J. Schütz, and Eva Sevcsik. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” <i>Frontiers in Chemistry</i>. Frontiers Media S.A., 2019. <a href=\"https://doi.org/10.3389/fchem.2018.00655\">https://doi.org/10.3389/fchem.2018.00655</a>.","apa":"Lindner, M., Tresztenyak, A., Fülöp, G., Jahr, W., Prinz, A., Prinz, I., … Sevcsik, E. (2019). A fast and simple contact printing approach to generate 2D protein nanopatterns. <i>Frontiers in Chemistry</i>. Frontiers Media S.A. <a href=\"https://doi.org/10.3389/fchem.2018.00655\">https://doi.org/10.3389/fchem.2018.00655</a>","mla":"Lindner, Marco, et al. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” <i>Frontiers in Chemistry</i>, vol. 6, 655, Frontiers Media S.A., 2019, doi:<a href=\"https://doi.org/10.3389/fchem.2018.00655\">10.3389/fchem.2018.00655</a>.","ieee":"M. Lindner <i>et al.</i>, “A fast and simple contact printing approach to generate 2D protein nanopatterns,” <i>Frontiers in Chemistry</i>, vol. 6. Frontiers Media S.A., 2019.","short":"M. Lindner, A. Tresztenyak, G. Fülöp, W. Jahr, A. Prinz, I. Prinz, J.G. Danzl, G.J. Schütz, E. Sevcsik, Frontiers in Chemistry 6 (2019).","ista":"Lindner M, Tresztenyak A, Fülöp G, Jahr W, Prinz A, Prinz I, Danzl JG, Schütz GJ, Sevcsik E. 2019. A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 6, 655.","ama":"Lindner M, Tresztenyak A, Fülöp G, et al. A fast and simple contact printing approach to generate 2D protein nanopatterns. <i>Frontiers in Chemistry</i>. 2019;6. doi:<a href=\"https://doi.org/10.3389/fchem.2018.00655\">10.3389/fchem.2018.00655</a>"},"article_number":"655","oa":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:47:17Z","doi":"10.3389/fchem.2018.00655","date_published":"2019-01-24T00:00:00Z","intvolume":"         6","has_accepted_license":"1","volume":6,"day":"24","publication":"Frontiers in Chemistry"},{"has_accepted_license":"1","intvolume":"        22","date_published":"2019-04-16T00:00:00Z","day":"16","publication":"Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control","volume":22,"ec_funded":1,"article_processing_charge":"No","doi":"10.1145/3302504.3311804","file_date_updated":"2020-07-14T12:47:17Z","citation":{"apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., &#38; Schilling, C. (2019). JuliaReach: A toolbox for set-based reachability. In <i>Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control</i> (Vol. 22, pp. 39–44). Montreal, QC, Canada: ACM. <a href=\"https://doi.org/10.1145/3302504.3311804\">https://doi.org/10.1145/3302504.3311804</a>","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “JuliaReach: A Toolbox for Set-Based Reachability.” In <i>Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control</i>, 22:39–44. ACM, 2019. <a href=\"https://doi.org/10.1145/3302504.3311804\">https://doi.org/10.1145/3302504.3311804</a>.","mla":"Bogomolov, Sergiy, et al. “JuliaReach: A Toolbox for Set-Based Reachability.” <i>Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control</i>, vol. 22, ACM, 2019, pp. 39–44, doi:<a href=\"https://doi.org/10.1145/3302504.3311804\">10.1145/3302504.3311804</a>.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. JuliaReach: A toolbox for set-based reachability. In: <i>Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control</i>. Vol 22. ACM; 2019:39-44. doi:<a href=\"https://doi.org/10.1145/3302504.3311804\">10.1145/3302504.3311804</a>","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2019. JuliaReach: A toolbox for set-based reachability. Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control vol. 22, 39–44.","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “JuliaReach: A toolbox for set-based reachability,” in <i>Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control</i>, Montreal, QC, Canada, 2019, vol. 22, pp. 39–44.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 39–44."},"date_created":"2019-02-18T14:43:28Z","quality_controlled":"1","arxiv":1,"conference":{"location":"Montreal, QC, Canada","end_date":"2019-04-18","start_date":"2019-04-16","name":"HSCC: Hybrid Systems Computation and Control"},"oa":1,"title":"JuliaReach: A toolbox for set-based reachability","page":"39-44","keyword":["reachability analysis","hybrid systems","lazy computation"],"abstract":[{"text":"We present JuliaReach, a toolbox for set-based reachability analysis of dynamical systems. JuliaReach consists of two main packages: Reachability, containing implementations of reachability algorithms for continuous and hybrid systems, and LazySets, a standalone library that implements state-of-the-art algorithms for calculus with convex sets. The library offers both concrete and lazy set representations, where the latter stands for the ability to delay set computations until they are needed. The choice of the programming language Julia and the accompanying documentation of our toolbox allow researchers to easily translate set-based algorithms from mathematics to software in a platform-independent way, while achieving runtime performance that is comparable to statically compiled languages. Combining lazy operations in high dimensions and explicit computations in low dimensions, JuliaReach can be applied to solve complex, large-scale problems.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-08-24T14:47:21Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"status":"public","author":[{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","orcid":"0000-0002-0686-0365"},{"last_name":"Forets","full_name":"Forets, Marcelo","first_name":"Marcelo"},{"first_name":"Goran","last_name":"Frehse","full_name":"Frehse, Goran"},{"first_name":"Kostiantyn","full_name":"Potomkin, Kostiantyn","last_name":"Potomkin"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065"}],"ddc":["000"],"type":"conference","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:47:17Z","access_level":"open_access","content_type":"application/pdf","date_created":"2019-03-05T09:27:18Z","file_size":3784414,"checksum":"28ed56439aea5991c3122d4730fd828f","file_name":"hscc19.pdf","relation":"main_file","file_id":"6067","creator":"cschilli"}],"publication_status":"published","external_id":{"arxiv":["1901.10736"],"isi":["000516713900005"]},"_id":"6035","publisher":"ACM","department":[{"_id":"ToHe"}],"publication_identifier":{"isbn":["9781450362825"]},"isi":1,"project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"year":"2019","month":"04"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-24T14:47:45Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Static program analyzers are increasingly effective in checking correctness properties of programs and reporting any errors found, often in the form of error traces. However, developers still spend a significant amount of time on debugging. This involves processing long error traces in an effort to localize a bug to a relatively small part of the program and to identify its cause. In this paper, we present a technique for automated fault localization that, given a program and an error trace, efficiently narrows down the cause of the error to a few statements. These statements are then ranked in terms of their suspiciousness. Our technique relies only on the semantics of the given program and does not require any test cases or user guidance. In experiments on a set of C benchmarks, we show that our technique is effective in quickly isolating the cause of error while out-performing other state-of-the-art fault-localization techniques."}],"status":"public","author":[{"full_name":"Christakis, Maria","last_name":"Christakis","first_name":"Maria"},{"last_name":"Heizmann","full_name":"Heizmann, Matthias","first_name":"Matthias"},{"first_name":"Muhammad Numair","last_name":"Mansur","full_name":"Mansur, Muhammad Numair"},{"first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065"},{"first_name":"Valentin","full_name":"Wüstholz, Valentin","last_name":"Wüstholz"}],"publisher":"Springer Nature","publication_status":"published","alternative_title":["LNCS"],"external_id":{"isi":["000681166500013"]},"_id":"6042","type":"conference","ddc":["000"],"oa_version":"Published Version","file":[{"file_name":"2019_LNCS_Christakis.pdf","relation":"main_file","file_id":"6408","creator":"dernst","date_updated":"2020-07-14T12:47:17Z","access_level":"open_access","content_type":"application/pdf","date_created":"2019-05-10T14:16:05Z","checksum":"9998496f6fe202c0a19124b4209154c6","file_size":773083}],"project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"month":"04","year":"2019","isi":1,"department":[{"_id":"ToHe"}],"day":"04","publication":"25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems ","volume":11427,"date_published":"2019-04-04T00:00:00Z","intvolume":"     11427","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:17Z","doi":"10.1007/978-3-030-17462-0_13","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"article_processing_charge":"No","oa":1,"quality_controlled":"1","conference":{"start_date":"2019-04-06","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2019-04-11","location":"Prague, Czech Republic"},"citation":{"ieee":"M. Christakis, M. Heizmann, M. N. Mansur, C. Schilling, and V. Wüstholz, “Semantic fault localization and suspiciousness ranking,” in <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>, Prague, Czech Republic, 2019, vol. 11427, pp. 226–243.","ista":"Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. 2019. Semantic fault localization and suspiciousness ranking. 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 11427, 226–243.","short":"M. Christakis, M. Heizmann, M.N. Mansur, C. Schilling, V. Wüstholz, in:, 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2019, pp. 226–243.","ama":"Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. Semantic fault localization and suspiciousness ranking. In: <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>. Vol 11427. Springer Nature; 2019:226-243. doi:<a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">10.1007/978-3-030-17462-0_13</a>","mla":"Christakis, Maria, et al. “Semantic Fault Localization and Suspiciousness Ranking.” <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>, vol. 11427, Springer Nature, 2019, pp. 226–43, doi:<a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">10.1007/978-3-030-17462-0_13</a>.","chicago":"Christakis, Maria, Matthias Heizmann, Muhammad Numair Mansur, Christian Schilling, and Valentin Wüstholz. “Semantic Fault Localization and Suspiciousness Ranking.” In <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>, 11427:226–43. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">https://doi.org/10.1007/978-3-030-17462-0_13</a>.","apa":"Christakis, M., Heizmann, M., Mansur, M. N., Schilling, C., &#38; Wüstholz, V. (2019). Semantic fault localization and suspiciousness ranking. In <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i> (Vol. 11427, pp. 226–243). Prague, Czech Republic: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">https://doi.org/10.1007/978-3-030-17462-0_13</a>"},"date_created":"2019-02-18T16:44:06Z","page":"226-243","title":"Semantic fault localization and suspiciousness ranking"},{"quality_controlled":"1","citation":{"mla":"Mitosch, Karin, et al. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” <i>Molecular Systems Biology</i>, vol. 15, no. 2, e8470, Embo Press, 2019, doi:<a href=\"https://doi.org/10.15252/msb.20188470\">10.15252/msb.20188470</a>.","chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” <i>Molecular Systems Biology</i>. Embo Press, 2019. <a href=\"https://doi.org/10.15252/msb.20188470\">https://doi.org/10.15252/msb.20188470</a>.","apa":"Mitosch, K., Rieckh, G., &#38; Bollenbach, M. T. (2019). Temporal order and precision of complex stress responses in individual bacteria. <i>Molecular Systems Biology</i>. Embo Press. <a href=\"https://doi.org/10.15252/msb.20188470\">https://doi.org/10.15252/msb.20188470</a>","ista":"Mitosch K, Rieckh G, Bollenbach MT. 2019. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 15(2), e8470.","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).","ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Temporal order and precision of complex stress responses in individual bacteria,” <i>Molecular systems biology</i>, vol. 15, no. 2. Embo Press, 2019.","ama":"Mitosch K, Rieckh G, Bollenbach MT. Temporal order and precision of complex stress responses in individual bacteria. <i>Molecular systems biology</i>. 2019;15(2). doi:<a href=\"https://doi.org/10.15252/msb.20188470\">10.15252/msb.20188470</a>"},"date_created":"2019-02-24T22:59:18Z","acknowledged_ssus":[{"_id":"Bio"}],"article_number":"e8470","oa":1,"title":"Temporal order and precision of complex stress responses in individual bacteria","date_published":"2019-02-14T00:00:00Z","intvolume":"        15","pmid":1,"volume":15,"publication":"Molecular systems biology","day":"14","article_processing_charge":"No","doi":"10.15252/msb.20188470","_id":"6046","issue":"2","external_id":{"isi":["000459628300003"],"pmid":["30765425"]},"publication_status":"published","type":"journal_article","oa_version":"Submitted Version","publisher":"Embo Press","department":[{"_id":"GaTk"}],"year":"2019","month":"02","project":[{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions"},{"name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013"}],"isi":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"Sudden stress often triggers diverse, temporally structured gene expression responses in microbes, but it is largely unknown how variable in time such responses are and if genes respond in the same temporal order in every single cell. Here, we quantified timing variability of individual promoters responding to sublethal antibiotic stress using fluorescent reporters, microfluidics, and time‐lapse microscopy. We identified lower and upper bounds that put definite constraints on timing variability, which varies strongly among promoters and conditions. Timing variability can be interpreted using results from statistical kinetics, which enable us to estimate the number of rate‐limiting molecular steps underlying different responses. We found that just a few critical steps control some responses while others rely on dozens of steps. To probe connections between different stress responses, we then tracked the temporal order and response time correlations of promoter pairs in individual cells. Our results support that, when bacteria are exposed to the antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are part of the same causal chain of molecular events. In contrast, under trimethoprim, the acid stress response and the SOS response are part of different chains of events running in parallel. Our approach reveals fundamental constraints on gene expression timing and provides new insights into the molecular events that underlie the timing of stress responses."}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30765425","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-24T14:49:53Z","author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin","full_name":"Mitosch, Karin","last_name":"Mitosch"},{"full_name":"Rieckh, Georg","last_name":"Rieckh","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias"}],"status":"public"},{"doi":"10.1088/1751-8121/aaf2dd","file_date_updated":"2020-07-14T12:47:17Z","ec_funded":1,"article_processing_charge":"Yes (in subscription journal)","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":52,"day":"07","publication":"Journal of Physics A: Mathematical and Theoretical","has_accepted_license":"1","intvolume":"        52","date_published":"2019-01-07T00:00:00Z","title":"Feedback-induced self-oscillations in large interacting systems subjected to phase transitions","article_number":"045002","oa":1,"date_created":"2019-02-24T22:59:19Z","citation":{"mla":"De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” <i>Journal of Physics A: Mathematical and Theoretical</i>, vol. 52, no. 4, 045002, IOP Publishing, 2019, doi:<a href=\"https://doi.org/10.1088/1751-8121/aaf2dd\">10.1088/1751-8121/aaf2dd</a>.","apa":"De Martino, D. (2019). Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. <i>Journal of Physics A: Mathematical and Theoretical</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1751-8121/aaf2dd\">https://doi.org/10.1088/1751-8121/aaf2dd</a>","chicago":"De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” <i>Journal of Physics A: Mathematical and Theoretical</i>. IOP Publishing, 2019. <a href=\"https://doi.org/10.1088/1751-8121/aaf2dd\">https://doi.org/10.1088/1751-8121/aaf2dd</a>.","ama":"De Martino D. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. <i>Journal of Physics A: Mathematical and Theoretical</i>. 2019;52(4). doi:<a href=\"https://doi.org/10.1088/1751-8121/aaf2dd\">10.1088/1751-8121/aaf2dd</a>","ista":"De Martino D. 2019. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. 52(4), 045002.","short":"D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).","ieee":"D. De Martino, “Feedback-induced self-oscillations in large interacting systems subjected to phase transitions,” <i>Journal of Physics A: Mathematical and Theoretical</i>, vol. 52, no. 4. IOP Publishing, 2019."},"quality_controlled":"1","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","full_name":"De Martino, Daniele","last_name":"De Martino","orcid":"0000-0002-5214-4706"}],"status":"public","date_updated":"2023-08-24T14:49:23Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"In this article it is shown that large systems with many interacting units endowing multiple phases display self-oscillations in the presence of linear feedback between the control and order parameters, where an Andronov–Hopf bifurcation takes over the phase transition. This is simply illustrated through the mean field Landau theory whose feedback dynamics turn out to be described by the Van der Pol equation and it is then validated for the fully connected Ising model following heat bath dynamics. Despite its simplicity, this theory accounts potentially for a rich range of phenomena: here it is applied to describe in a stylized way (i) excess demand-price cycles due to strong herding in a simple agent-based market model; (ii) congestion waves in queuing networks triggered by user feedback to delays in overloaded conditions; and (iii) metabolic network oscillations resulting from cell growth control in a bistable phenotypic landscape."}],"scopus_import":"1","isi":1,"month":"01","year":"2019","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"department":[{"_id":"GaTk"}],"publisher":"IOP Publishing","ddc":["570"],"oa_version":"Published Version","file":[{"date_created":"2019-04-19T12:18:57Z","file_size":1804557,"checksum":"1112304ad363a6d8afaeccece36473cf","date_updated":"2020-07-14T12:47:17Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"kschuh","file_id":"6344","file_name":"2019_IOP_DeMartino.pdf"}],"type":"journal_article","issue":"4","_id":"6049","publication_status":"published","external_id":{"isi":["000455379500001"]}},{"date_updated":"2023-08-24T14:48:59Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We answer a question of David Hilbert: given two circles it is not possible in general to construct their centers using only a straightedge. On the other hand, we give infinitely many families of pairs of circles for which such construction is possible. "}],"main_file_link":[{"url":"https://arxiv.org/abs/1709.02562","open_access":"1"}],"scopus_import":"1","author":[{"last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fedorov","full_name":"Fedorov, Roman","first_name":"Roman"}],"status":"public","publisher":"AMS","type":"journal_article","oa_version":"Preprint","_id":"6050","external_id":{"isi":["000450363900008"],"arxiv":["1709.02562"]},"publication_status":"published","isi":1,"year":"2019","month":"01","department":[{"_id":"HeEd"}],"volume":147,"day":"01","publication":"Proceedings of the American Mathematical Society","intvolume":"       147","date_published":"2019-01-01T00:00:00Z","doi":"10.1090/proc/14240","article_processing_charge":"No","oa":1,"citation":{"short":"A. Akopyan, R. Fedorov, Proceedings of the American Mathematical Society 147 (2019) 91–102.","ista":"Akopyan A, Fedorov R. 2019. Two circles and only a straightedge. Proceedings of the American Mathematical Society. 147, 91–102.","ieee":"A. Akopyan and R. Fedorov, “Two circles and only a straightedge,” <i>Proceedings of the American Mathematical Society</i>, vol. 147. AMS, pp. 91–102, 2019.","ama":"Akopyan A, Fedorov R. Two circles and only a straightedge. <i>Proceedings of the American Mathematical Society</i>. 2019;147:91-102. doi:<a href=\"https://doi.org/10.1090/proc/14240\">10.1090/proc/14240</a>","mla":"Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” <i>Proceedings of the American Mathematical Society</i>, vol. 147, AMS, 2019, pp. 91–102, doi:<a href=\"https://doi.org/10.1090/proc/14240\">10.1090/proc/14240</a>.","chicago":"Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” <i>Proceedings of the American Mathematical Society</i>. AMS, 2019. <a href=\"https://doi.org/10.1090/proc/14240\">https://doi.org/10.1090/proc/14240</a>.","apa":"Akopyan, A., &#38; Fedorov, R. (2019). Two circles and only a straightedge. <i>Proceedings of the American Mathematical Society</i>. AMS. <a href=\"https://doi.org/10.1090/proc/14240\">https://doi.org/10.1090/proc/14240</a>"},"date_created":"2019-02-24T22:59:19Z","arxiv":1,"quality_controlled":"1","page":"91-102","title":"Two circles and only a straightedge"},{"isi":1,"month":"03","year":"2019","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules"}],"department":[{"_id":"JoDa"},{"_id":"Bio"}],"article_type":"original","publisher":"Nature Publishing Group","ddc":["570"],"file":[{"date_created":"2021-06-29T14:41:46Z","checksum":"7efb9951e7ddf3e3dcc2fb92b859c623","success":1,"file_size":84478958,"date_updated":"2021-06-29T14:41:46Z","access_level":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"main_file","file_id":"9619","creator":"kschuh","file_name":"181031_Truckenbrodt_ExM_NatProtoc.docx"}],"oa_version":"Submitted Version","type":"journal_article","_id":"6052","issue":"3","publication_status":"published","external_id":{"pmid":["30778205"],"isi":["000459890700008"]},"author":[{"full_name":"Truckenbrodt, Sven M","last_name":"Truckenbrodt","first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105"},{"first_name":"Silvio O","full_name":"Rizzoli, Silvio O","last_name":"Rizzoli"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"}],"status":"public","date_updated":"2023-08-24T14:48:33Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Expansion microscopy is a relatively new approach to super-resolution imaging that uses expandable hydrogels to isotropically increase the physical distance between fluorophores in biological samples such as cell cultures or tissue slices. The classic gel recipe results in an expansion factor of ~4×, with a resolution of 60–80 nm. We have recently developed X10 microscopy, which uses a gel that achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide a step-by-step protocol for X10 expansion microscopy. A typical experiment consists of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization, (iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol presented here includes recommendations for optimization, pitfalls and their solutions, and detailed guidelines that should increase reproducibility. Although our protocol focuses on X10 expansion microscopy, we detail which of these suggestions are also applicable to classic fourfold expansion microscopy. We exemplify our protocol using primary hippocampal neurons from rats, but our approach can be used with other primary cells or cultured cell lines of interest. This protocol will enable any researcher with basic experience in immunostainings and access to an epifluorescence microscope to perform super-resolution microscopy with X10. The procedure takes 3 d and requires ~5 h of actively handling the sample for labeling and expansion, and another ~3 h for imaging and analysis."}],"scopus_import":"1","page":"832–863","title":"A practical guide to optimization in X10 expansion microscopy","oa":1,"citation":{"mla":"Truckenbrodt, Sven M., et al. “A Practical Guide to Optimization in X10 Expansion Microscopy.” <i>Nature Protocols</i>, vol. 14, no. 3, Nature Publishing Group, 2019, pp. 832–863, doi:<a href=\"https://doi.org/10.1038/s41596-018-0117-3\">10.1038/s41596-018-0117-3</a>.","apa":"Truckenbrodt, S. M., Sommer, C. M., Rizzoli, S. O., &#38; Danzl, J. G. (2019). A practical guide to optimization in X10 expansion microscopy. <i>Nature Protocols</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41596-018-0117-3\">https://doi.org/10.1038/s41596-018-0117-3</a>","chicago":"Truckenbrodt, Sven M, Christoph M Sommer, Silvio O Rizzoli, and Johann G Danzl. “A Practical Guide to Optimization in X10 Expansion Microscopy.” <i>Nature Protocols</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41596-018-0117-3\">https://doi.org/10.1038/s41596-018-0117-3</a>.","ama":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. A practical guide to optimization in X10 expansion microscopy. <i>Nature Protocols</i>. 2019;14(3):832–863. doi:<a href=\"https://doi.org/10.1038/s41596-018-0117-3\">10.1038/s41596-018-0117-3</a>","ista":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. 2019. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 14(3), 832–863.","ieee":"S. M. Truckenbrodt, C. M. Sommer, S. O. Rizzoli, and J. G. Danzl, “A practical guide to optimization in X10 expansion microscopy,” <i>Nature Protocols</i>, vol. 14, no. 3. Nature Publishing Group, pp. 832–863, 2019.","short":"S.M. Truckenbrodt, C.M. Sommer, S.O. Rizzoli, J.G. Danzl, Nature Protocols 14 (2019) 832–863."},"date_created":"2019-02-24T22:59:20Z","quality_controlled":"1","doi":"10.1038/s41596-018-0117-3","file_date_updated":"2021-06-29T14:41:46Z","ec_funded":1,"article_processing_charge":"No","volume":14,"day":"01","publication":"Nature Protocols","pmid":1,"intvolume":"        14","has_accepted_license":"1","date_published":"2019-03-01T00:00:00Z"},{"scopus_import":"1","abstract":[{"lang":"eng","text":"Recent technical developments in the fields of quantum electromechanics and optomechanics have spawned nanoscale mechanical transducers with the sensitivity to measure mechanical displacements at the femtometre scale and the ability to convert electromagnetic signals at the single photon level. A key challenge in this field is obtaining strong coupling between motion and electromagnetic fields without adding additional decoherence. Here we present an electromechanical transducer that integrates a high-frequency (0.42 GHz) hypersonic phononic crystal with a superconducting microwave circuit. The use of a phononic bandgap crystal enables quantum-level transduction of hypersonic mechanical motion and concurrently eliminates decoherence caused by acoustic radiation. Devices with hypersonic mechanical frequencies provide a natural pathway for integration with Josephson junction quantum circuits, a leading quantum computing technology, and nanophotonic systems capable of optical networking and distributing quantum information."}],"main_file_link":[{"open_access":"1","url":"https://authors.library.caltech.edu/92123/"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-24T14:48:08Z","author":[{"last_name":"Kalaee","full_name":"Kalaee, Mahmoud","first_name":"Mahmoud"},{"full_name":"Mirhosseini, Mohammad","last_name":"Mirhosseini","first_name":"Mohammad"},{"first_name":"Paul B.","last_name":"Dieterle","full_name":"Dieterle, Paul B."},{"full_name":"Peruzzo, Matilda","last_name":"Peruzzo","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"},{"full_name":"Painter, Oskar","last_name":"Painter","first_name":"Oskar"}],"status":"public","issue":"4","_id":"6053","external_id":{"isi":["000463195700014"]},"publication_status":"published","oa_version":"Submitted Version","type":"journal_article","publisher":"Springer Nature","article_type":"original","department":[{"_id":"JoFi"}],"month":"04","year":"2019","isi":1,"publication_identifier":{"eissn":["1748-3395"],"issn":["1748-3387"]},"date_published":"2019-04-01T00:00:00Z","intvolume":"        14","volume":14,"publication":"Nature Nanotechnology","day":"01","article_processing_charge":"No","doi":"10.1038/s41565-019-0377-2","quality_controlled":"1","citation":{"chicago":"Kalaee, Mahmoud, Mohammad Mirhosseini, Paul B. Dieterle, Matilda Peruzzo, Johannes M Fink, and Oskar Painter. “Quantum Electromechanics of a Hypersonic Crystal.” <i>Nature Nanotechnology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41565-019-0377-2\">https://doi.org/10.1038/s41565-019-0377-2</a>.","apa":"Kalaee, M., Mirhosseini, M., Dieterle, P. B., Peruzzo, M., Fink, J. M., &#38; Painter, O. (2019). Quantum electromechanics of a hypersonic crystal. <i>Nature Nanotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41565-019-0377-2\">https://doi.org/10.1038/s41565-019-0377-2</a>","mla":"Kalaee, Mahmoud, et al. “Quantum Electromechanics of a Hypersonic Crystal.” <i>Nature Nanotechnology</i>, vol. 14, no. 4, Springer Nature, 2019, pp. 334–339, doi:<a href=\"https://doi.org/10.1038/s41565-019-0377-2\">10.1038/s41565-019-0377-2</a>.","ista":"Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. 2019. Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. 14(4), 334–339.","ieee":"M. Kalaee, M. Mirhosseini, P. B. Dieterle, M. Peruzzo, J. M. Fink, and O. Painter, “Quantum electromechanics of a hypersonic crystal,” <i>Nature Nanotechnology</i>, vol. 14, no. 4. Springer Nature, pp. 334–339, 2019.","short":"M. Kalaee, M. Mirhosseini, P.B. Dieterle, M. Peruzzo, J.M. Fink, O. Painter, Nature Nanotechnology 14 (2019) 334–339.","ama":"Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. Quantum electromechanics of a hypersonic crystal. <i>Nature Nanotechnology</i>. 2019;14(4):334–339. doi:<a href=\"https://doi.org/10.1038/s41565-019-0377-2\">10.1038/s41565-019-0377-2</a>"},"date_created":"2019-02-24T22:59:21Z","oa":1,"title":"Quantum electromechanics of a hypersonic crystal","page":"334–339"},{"scopus_import":1,"abstract":[{"text":"In today's programmable blockchains, smart contracts are limited to being deterministic and non-probabilistic. This lack of randomness is a consequential limitation, given that a wide variety of real-world financial contracts, such as casino games and lotteries, depend entirely on randomness. As a result, several ad-hoc random number generation approaches have been developed to be used in smart contracts. These include ideas such as using an oracle or relying on the block hash. However, these approaches are manipulatable, i.e. their output can be tampered with by parties who might not be neutral, such as the owner of the oracle or the miners.We propose a novel game-theoretic approach for generating provably unmanipulatable pseudorandom numbers on the blockchain. Our approach allows smart contracts to access a trustworthy source of randomness that does not rely on potentially compromised miners or oracles, hence enabling the creation of a new generation of smart contracts that are not limited to being non-probabilistic and can be drawn from the much more general class of probabilistic programs.","lang":"eng"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"main_file_link":[{"url":"https://arxiv.org/abs/1902.07986","open_access":"1"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2024-03-25T23:30:18Z","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584"},{"first_name":"Arash","last_name":"Pourdamghani","full_name":"Pourdamghani, Arash"}],"status":"public","_id":"6056","publication_status":"published","external_id":{"arxiv":["1902.07986"]},"oa_version":"Preprint","type":"conference","publisher":"IEEE","department":[{"_id":"KrCh"}],"year":"2019","month":"05","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"date_published":"2019-05-01T00:00:00Z","day":"01","publication":"IEEE International Conference on Blockchain and Cryptocurrency","ec_funded":1,"doi":"10.1109/BLOC.2019.8751326","conference":{"start_date":"2019-05-14","name":"IEEE International Conference on Blockchain and Cryptocurrency","end_date":"2019-05-17","location":"Seoul, Korea"},"arxiv":1,"quality_controlled":"1","citation":{"mla":"Chatterjee, Krishnendu, et al. “Probabilistic Smart Contracts: Secure Randomness on the Blockchain.” <i>IEEE International Conference on Blockchain and Cryptocurrency</i>, 8751326, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/BLOC.2019.8751326\">10.1109/BLOC.2019.8751326</a>.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani. “Probabilistic Smart Contracts: Secure Randomness on the Blockchain.” In <i>IEEE International Conference on Blockchain and Cryptocurrency</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/BLOC.2019.8751326\">https://doi.org/10.1109/BLOC.2019.8751326</a>.","apa":"Chatterjee, K., Goharshady, A. K., &#38; Pourdamghani, A. (2019). Probabilistic smart contracts: Secure randomness on the blockchain. In <i>IEEE International Conference on Blockchain and Cryptocurrency</i>. Seoul, Korea: IEEE. <a href=\"https://doi.org/10.1109/BLOC.2019.8751326\">https://doi.org/10.1109/BLOC.2019.8751326</a>","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Probabilistic smart contracts: Secure randomness on the blockchain,” in <i>IEEE International Conference on Blockchain and Cryptocurrency</i>, Seoul, Korea, 2019.","short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, IEEE International Conference on Blockchain and Cryptocurrency, IEEE, 2019.","ista":"Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Probabilistic smart contracts: Secure randomness on the blockchain. IEEE International Conference on Blockchain and Cryptocurrency. IEEE International Conference on Blockchain and Cryptocurrency, 8751326.","ama":"Chatterjee K, Goharshady AK, Pourdamghani A. Probabilistic smart contracts: Secure randomness on the blockchain. In: <i>IEEE International Conference on Blockchain and Cryptocurrency</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/BLOC.2019.8751326\">10.1109/BLOC.2019.8751326</a>"},"date_created":"2019-02-26T09:03:15Z","article_number":"8751326","oa":1,"title":"Probabilistic smart contracts: Secure randomness on the blockchain"}]