[{"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady"},{"full_name":"Pourdamghani, Arash","last_name":"Pourdamghani","first_name":"Arash"}],"external_id":{"arxiv":["1902.07986"]},"title":"Probabilistic smart contracts: Secure randomness on the blockchain","citation":{"chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani. “Probabilistic Smart Contracts: Secure Randomness on the Blockchain.” In IEEE International Conference on Blockchain and Cryptocurrency. IEEE, 2019. https://doi.org/10.1109/BLOC.2019.8751326.","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.","mla":"Chatterjee, Krishnendu, et al. “Probabilistic Smart Contracts: Secure Randomness on the Blockchain.” IEEE International Conference on Blockchain and Cryptocurrency, 8751326, IEEE, 2019, doi:10.1109/BLOC.2019.8751326.","ama":"Chatterjee K, Goharshady AK, Pourdamghani A. Probabilistic smart contracts: Secure randomness on the blockchain. In: IEEE International Conference on Blockchain and Cryptocurrency. IEEE; 2019. doi:10.1109/BLOC.2019.8751326","apa":"Chatterjee, K., Goharshady, A. K., & Pourdamghani, A. (2019). Probabilistic smart contracts: Secure randomness on the blockchain. In IEEE International Conference on Blockchain and Cryptocurrency. Seoul, Korea: IEEE. https://doi.org/10.1109/BLOC.2019.8751326","short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, IEEE International Conference on Blockchain and Cryptocurrency, IEEE, 2019.","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Probabilistic smart contracts: Secure randomness on the blockchain,” in IEEE International Conference on Blockchain and Cryptocurrency, Seoul, Korea, 2019."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"article_number":"8751326","doi":"10.1109/BLOC.2019.8751326","date_published":"2019-05-01T00:00:00Z","date_created":"2019-02-26T09:03:15Z","year":"2019","day":"01","publication":"IEEE International Conference on Blockchain and Cryptocurrency","quality_controlled":"1","publisher":"IEEE","oa":1,"department":[{"_id":"KrCh"}],"date_updated":"2024-03-27T23:30:33Z","type":"conference","conference":{"name":"IEEE International Conference on Blockchain and Cryptocurrency","start_date":"2019-05-14","location":"Seoul, Korea","end_date":"2019-05-17"},"status":"public","_id":"6056","related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07986"}],"month":"05","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"}],"oa_version":"Preprint"},{"year":"2019","isi":1,"has_accepted_license":"1","publication":"Proceedings of the 34th ACM Symposium on Applied Computing","day":"01","page":"374-381","date_created":"2019-05-06T12:11:36Z","doi":"10.1145/3297280.3297319","date_published":"2019-04-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"ACM","citation":{"chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” In Proceedings of the 34th ACM Symposium on Applied Computing, Part F147772:374–81. ACM, 2019. https://doi.org/10.1145/3297280.3297319.","ista":"Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. Proceedings of the 34th ACM Symposium on Applied Computing. ACM Symposium on Applied Computing vol. Part F147772, 374–381.","mla":"Chatterjee, Krishnendu, et al. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” Proceedings of the 34th ACM Symposium on Applied Computing, vol. Part F147772, ACM, 2019, pp. 374–81, doi:10.1145/3297280.3297319.","ama":"Chatterjee K, Goharshady AK, Pourdamghani A. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In: Proceedings of the 34th ACM Symposium on Applied Computing. Vol Part F147772. ACM; 2019:374-381. doi:10.1145/3297280.3297319","apa":"Chatterjee, K., Goharshady, A. K., & Pourdamghani, A. (2019). Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In Proceedings of the 34th ACM Symposium on Applied Computing (Vol. Part F147772, pp. 374–381). Limassol, Cyprus: ACM. https://doi.org/10.1145/3297280.3297319","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving,” in Proceedings of the 34th ACM Symposium on Applied Computing, Limassol, Cyprus, 2019, vol. Part F147772, pp. 374–381.","short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, 2019, pp. 374–381."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000474685800049"]},"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady"},{"first_name":"Arash","last_name":"Pourdamghani","full_name":"Pourdamghani, Arash"}],"title":"Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_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","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"publication_status":"published","publication_identifier":{"isbn":["9781450359337"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2019_ACM_Chatterjee.pdf","date_created":"2019-05-06T12:09:27Z","file_size":1023934,"date_updated":"2020-07-14T12:47:29Z","creator":"dernst","file_id":"6379","checksum":"fbfbcd5a0c7a743862bfc3045539a614","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"volume":"Part F147772","abstract":[{"lang":"eng","text":"In today's cryptocurrencies, Hashcash proof of work is the most commonly-adopted approach to mining. In Hashcash, when a miner decides to add a block to the chain, she has to solve the difficult computational puzzle of inverting a hash function. While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it has attracted significant and harsh criticism due to its massive waste of electricity, its carbon footprint and environmental effects, and the inherent lack of usefulness in inverting a hash function. Various other mining protocols have been suggested, including proof of stake, in which a miner's chance of adding the next block is proportional to her current balance. However, such protocols lead to a higher entry cost for new miners who might not still have any stake in the cryptocurrency, and can in the worst case lead to an oligopoly, where the rich have complete control over mining. In this paper, we propose Hybrid Mining: a new mining protocol that combines solving real-world useful problems with Hashcash. Our protocol allows new miners to join the network by taking part in Hashcash mining without having to own an initial stake. It also allows nodes of the network to submit hard computational problems whose solutions are of interest in the real world, e.g.~protein folding problems. Then, miners can choose to compete in solving these problems, in lieu of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners to solve useful problems, such as hard computational problems arising in biology, in a distributed manner. It also gives researchers in other areas an easy-to-use tool to outsource their hard computations to the blockchain network, which has enormous computational power, by paying a reward to the miner who solves the problem for them. Moreover, our protocol provides strong security guarantees and is at least as resilient to double spending as Bitcoin."}],"oa_version":"Submitted Version","scopus_import":"1","month":"04","date_updated":"2024-03-27T23:30:33Z","ddc":["004"],"file_date_updated":"2020-07-14T12:47:29Z","department":[{"_id":"KrCh"}],"_id":"6378","conference":{"start_date":"2019-04-08","location":"Limassol, Cyprus","end_date":"2019-04-12","name":"ACM Symposium on Applied Computing"},"type":"conference","pubrep_id":"1069","status":"public"},{"ddc":["000"],"date_updated":"2024-03-27T23:30:33Z","file_date_updated":"2020-07-14T12:47:20Z","department":[{"_id":"KrCh"}],"_id":"6175","status":"public","keyword":["Program Cost Analysis","Program Termination","Probabilistic Programs","Martingales"],"type":"conference","conference":{"end_date":"2019-06-26","location":"Phoenix, AZ, United States","start_date":"2019-06-22","name":"PLDI: Conference on Programming Language Design and Implementation"},"file":[{"date_created":"2019-03-25T10:11:22Z","file_name":"paper.pdf","creator":"akafshda","date_updated":"2020-07-14T12:47:20Z","file_size":4051066,"checksum":"703a5e9b8c8587f2a44085ffd9a4db64","file_id":"6176","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"earlier_version","id":"5457","status":"public"},{"relation":"dissertation_contains","status":"public","id":"8934"}]},"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"text":"We consider the problem of expected cost analysis over nondeterministic probabilistic programs,\r\nwhich aims at automated methods for analyzing the resource-usage of such programs.\r\nPrevious approaches for this problem could only handle nonnegative bounded costs.\r\nHowever, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols,\r\nboth positive and negative costs are necessary and the costs are unbounded as well.\r\n\r\nIn this work, we present a sound and efficient approach to obtain polynomial bounds on the\r\nexpected accumulated cost of nondeterministic probabilistic programs.\r\nOur approach can handle (a) general positive and negative costs with bounded updates in\r\nvariables; and (b) nonnegative costs with general updates to variables.\r\nWe show that several natural examples which could not be\r\nhandled by previous approaches are captured in our framework.\r\n\r\nMoreover, our approach leads to an efficient polynomial-time algorithm, while no\r\nprevious approach for cost analysis of probabilistic programs could guarantee polynomial runtime.\r\nFinally, we show the effectiveness of our approach using experimental results on a variety of programs for which we efficiently synthesize tight resource-usage bounds.","lang":"eng"}],"month":"06","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Wang, Peixin, Hongfei Fu, Amir Kafshdar Goharshady, Krishnendu Chatterjee, Xudong Qin, and Wenjun Shi. “Cost Analysis of Nondeterministic Probabilistic Programs.” In PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, 204–20. Association for Computing Machinery, 2019. https://doi.org/10.1145/3314221.3314581.","ista":"Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. 2019. Cost analysis of nondeterministic probabilistic programs. PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Conference on Programming Language Design and Implementation, 204–220.","mla":"Wang, Peixin, et al. “Cost Analysis of Nondeterministic Probabilistic Programs.” PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2019, pp. 204–20, doi:10.1145/3314221.3314581.","short":"P. Wang, H. Fu, A.K. Goharshady, K. Chatterjee, X. Qin, W. Shi, in:, PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2019, pp. 204–220.","ieee":"P. Wang, H. Fu, A. K. Goharshady, K. Chatterjee, X. Qin, and W. Shi, “Cost analysis of nondeterministic probabilistic programs,” in PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, Phoenix, AZ, United States, 2019, pp. 204–220.","ama":"Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. Cost analysis of nondeterministic probabilistic programs. In: PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2019:204-220. doi:10.1145/3314221.3314581","apa":"Wang, P., Fu, H., Goharshady, A. K., Chatterjee, K., Qin, X., & Shi, W. (2019). Cost analysis of nondeterministic probabilistic programs. In PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 204–220). Phoenix, AZ, United States: Association for Computing Machinery. https://doi.org/10.1145/3314221.3314581"},"title":"Cost analysis of nondeterministic probabilistic programs","author":[{"last_name":"Wang","full_name":"Wang, Peixin","first_name":"Peixin"},{"id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","full_name":"Fu, Hongfei","last_name":"Fu"},{"orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Qin","full_name":"Qin, Xudong","first_name":"Xudong"},{"first_name":"Wenjun","full_name":"Shi, Wenjun","last_name":"Shi"}],"external_id":{"isi":["000523190300014"],"arxiv":["1902.04659"]},"article_processing_charge":"No","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"day":"08","publication":"PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation","isi":1,"has_accepted_license":"1","year":"2019","date_published":"2019-06-08T00:00:00Z","doi":"10.1145/3314221.3314581","date_created":"2019-03-25T10:13:25Z","page":"204-220","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1},{"abstract":[{"text":"Smart contracts are programs that are stored and executed on the Blockchain and can receive, manage and transfer money (cryptocurrency units). Two important problems regarding smart contracts are formal analysis and compiler optimization. Formal analysis is extremely important, because smart contracts hold funds worth billions of dollars and their code is immutable after deployment. Hence, an undetected bug can cause significant financial losses. Compiler optimization is also crucial, because every action of a smart contract has to be executed by every node in the Blockchain network. Therefore, optimizations in compiling smart contracts can lead to significant savings in computation, time and energy.\r\n\r\nTwo classical approaches in program analysis and compiler optimization are intraprocedural and interprocedural analysis. In intraprocedural analysis, each function is analyzed separately, while interprocedural analysis considers the entire program. In both cases, the analyses are usually reduced to graph problems over the control flow graph (CFG) of the program. These graph problems are often computationally expensive. Hence, there has been ample research on exploiting structural properties of CFGs for efficient algorithms. One such well-studied property is the treewidth, which is a measure of tree-likeness of graphs. It is known that intraprocedural CFGs of structured programs have treewidth at most 6, whereas the interprocedural treewidth cannot be bounded. This result has been used as a basis for many efficient intraprocedural analyses.\r\n\r\nIn this paper, we explore the idea of exploiting the treewidth of smart contracts for formal analysis and compiler optimization. First, similar to classical programs, we show that the intraprocedural treewidth of structured Solidity and Vyper smart contracts is at most 9. Second, for global analysis, we prove that the interprocedural treewidth of structured smart contracts is bounded by 10 and, in sharp contrast with classical programs, treewidth-based algorithms can be easily applied for interprocedural analysis. Finally, we supplement our theoretical results with experiments using a tool we implemented for computing treewidth of smart contracts and show that the treewidth is much lower in practice. We use 36,764 real-world Ethereum smart contracts as benchmarks and find that they have an average treewidth of at most 3.35 for the intraprocedural case and 3.65 for the interprocedural case.\r\n","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","month":"04","publication_status":"submitted","publication_identifier":{"isbn":["9781450359337"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-05-14T09:50:11Z","file_name":"2019_ACM_Chatterjee.pdf","date_updated":"2020-07-14T12:47:32Z","file_size":6937138,"creator":"dernst","file_id":"7827","checksum":"dddc20f6d9881f23b8755eb720ec9d6f","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"volume":"Part F147772","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"_id":"6490","conference":{"location":"Limassol, Cyprus","end_date":"2019-04-12","start_date":"2019-04-08","name":"SAC: Symposium on Applied Computing"},"type":"conference","pubrep_id":"1070","status":"public","date_updated":"2024-03-27T23:30:33Z","ddc":["000"],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:32Z","oa":1,"quality_controlled":"1","publisher":"ACM","year":"2019","has_accepted_license":"1","isi":1,"publication":"Proceedings of the 34th ACM Symposium on Applied Computing","day":"01","page":"400-408","date_created":"2019-05-26T21:59:15Z","date_published":"2019-04-01T00:00:00Z","doi":"10.1145/3297280.3297322","citation":{"ista":"Chatterjee K, Goharshady AK, Goharshady EK. The treewidth of smart contracts. Proceedings of the 34th ACM Symposium on Applied Computing. SAC: Symposium on Applied Computing vol. Part F147772, 400–408.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady. “The Treewidth of Smart Contracts.” In Proceedings of the 34th ACM Symposium on Applied Computing, Part F147772:400–408. ACM, n.d. https://doi.org/10.1145/3297280.3297322.","ama":"Chatterjee K, Goharshady AK, Goharshady EK. The treewidth of smart contracts. In: Proceedings of the 34th ACM Symposium on Applied Computing. Vol Part F147772. ACM; :400-408. doi:10.1145/3297280.3297322","apa":"Chatterjee, K., Goharshady, A. K., & Goharshady, E. K. (n.d.). The treewidth of smart contracts. In Proceedings of the 34th ACM Symposium on Applied Computing (Vol. Part F147772, pp. 400–408). Limassol, Cyprus: ACM. https://doi.org/10.1145/3297280.3297322","short":"K. Chatterjee, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, n.d., pp. 400–408.","ieee":"K. Chatterjee, A. K. Goharshady, and E. K. Goharshady, “The treewidth of smart contracts,” in Proceedings of the 34th ACM Symposium on Applied Computing, Limassol, Cyprus, vol. Part F147772, pp. 400–408.","mla":"Chatterjee, Krishnendu, et al. “The Treewidth of Smart Contracts.” Proceedings of the 34th ACM Symposium on Applied Computing, vol. Part F147772, ACM, pp. 400–08, doi:10.1145/3297280.3297322."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000474685800052"]},"article_processing_charge":"No","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584"},{"last_name":"Goharshady","full_name":"Goharshady, Ehsan Kafshdar","first_name":"Ehsan Kafshdar"}],"title":"The treewidth of smart contracts"},{"quality_controlled":"1","publisher":"ACM","oa":1,"date_published":"2019-11-01T00:00:00Z","doi":"10.1145/3363525","date_created":"2019-12-09T08:33:33Z","day":"01","publication":"ACM Transactions on Programming Languages and Systems","isi":1,"has_accepted_license":"1","year":"2019","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"article_number":"23","title":"Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar"},{"last_name":"Goyal","full_name":"Goyal, Prateesh","first_name":"Prateesh"},{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis"}],"external_id":{"isi":["000564108400004"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Dynamic Algebraic Queries in Basic RSMs with Constant Treewidth.” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4, 23, ACM, 2019, doi:10.1145/3363525.","ama":"Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. ACM Transactions on Programming Languages and Systems. 2019;41(4). doi:10.1145/3363525","apa":"Chatterjee, K., Goharshady, A. K., Goyal, P., Ibsen-Jensen, R., & Pavlogiannis, A. (2019). Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. ACM Transactions on Programming Languages and Systems. ACM. https://doi.org/10.1145/3363525","short":"K. Chatterjee, A.K. Goharshady, P. Goyal, R. Ibsen-Jensen, A. Pavlogiannis, ACM Transactions on Programming Languages and Systems 41 (2019).","ieee":"K. Chatterjee, A. K. Goharshady, P. Goyal, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth,” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4. ACM, 2019.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Prateesh Goyal, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Dynamic Algebraic Queries in Basic RSMs with Constant Treewidth.” ACM Transactions on Programming Languages and Systems. ACM, 2019. https://doi.org/10.1145/3363525.","ista":"Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. 2019. Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. ACM Transactions on Programming Languages and Systems. 41(4), 23."},"month":"11","intvolume":" 41","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, and so on. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, and so on. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in an important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect we consider is that the control flow graphs for most programs have constant treewidth.\r\n\r\nOur main contributions are simple and implementable algorithms that support multiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing but can answer subsequent queries significantly faster as compared to the current algorithmic solutions for interprocedural dataflow analysis. We have also implemented our algorithms and evaluated their performance for performing on-demand interprocedural dataflow analysis on various domains, such as for live variable analysis and reaching definitions, on a standard benchmark set. Our experimental results align with our theoretical statements and show that after a lightweight preprocessing, on-demand queries are answered much faster than the standard existing algorithmic approaches.\r\n","lang":"eng"}],"volume":41,"related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"issue":"4","ec_funded":1,"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"291cc86a07bd010d4815e177dac57b70","file_id":"8632","success":1,"date_updated":"2020-10-08T12:58:10Z","file_size":667357,"creator":"dernst","date_created":"2020-10-08T12:58:10Z","file_name":"2019_ACMTransactions_Chatterjee.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0164-0925"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"7158","file_date_updated":"2020-10-08T12:58:10Z","department":[{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2024-03-27T23:30:34Z"},{"citation":{"apa":"Chatterjee, K., Fu, H., & Goharshady, A. K. (2019). Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. ACM. https://doi.org/10.1145/3339984","ama":"Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. 2019;41(4). doi:10.1145/3339984","short":"K. Chatterjee, H. Fu, A.K. Goharshady, ACM Transactions on Programming Languages and Systems 41 (2019).","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst-case analysis of recursive programs,” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4. ACM, 2019.","mla":"Chatterjee, Krishnendu, et al. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4, 20, ACM, 2019, doi:10.1145/3339984.","ista":"Chatterjee K, Fu H, Goharshady AK. 2019. Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. 41(4), 20.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming Languages and Systems. ACM, 2019. https://doi.org/10.1145/3339984."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000564108400001"],"arxiv":["1705.00317"]},"article_processing_charge":"No","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar"}],"title":"Non-polynomial worst-case analysis of recursive programs","article_number":"20","project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"year":"2019","isi":1,"publication":"ACM Transactions on Programming Languages and Systems","day":"01","date_created":"2019-11-13T08:33:43Z","doi":"10.1145/3339984","date_published":"2019-10-01T00:00:00Z","oa":1,"publisher":"ACM","quality_controlled":"1","date_updated":"2024-03-27T23:30:33Z","department":[{"_id":"KrCh"}],"_id":"7014","article_type":"original","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","id":"639","status":"public"},{"id":"8934","status":"public","relation":"dissertation_contains"}]},"volume":41,"issue":"4","abstract":[{"lang":"eng","text":"We study the problem of developing efficient approaches for proving\r\nworst-case bounds of non-deterministic recursive programs. Ranking functions\r\nare sound and complete for proving termination and worst-case bounds of\r\nnonrecursive programs. First, we apply ranking functions to recursion,\r\nresulting in measure functions. We show that measure functions provide a sound\r\nand complete approach to prove worst-case bounds of non-deterministic recursive\r\nprograms. Our second contribution is the synthesis of measure functions in\r\nnonpolynomial forms. We show that non-polynomial measure functions with\r\nlogarithm and exponentiation can be synthesized through abstraction of\r\nlogarithmic or exponentiation terms, Farkas' Lemma, and Handelman's Theorem\r\nusing linear programming. While previous methods obtain worst-case polynomial\r\nbounds, our approach can synthesize bounds of the form $\\mathcal{O}(n\\log n)$\r\nas well as $\\mathcal{O}(n^r)$ where $r$ is not an integer. We present\r\nexperimental results to demonstrate that our approach can obtain efficiently\r\nworst-case bounds of classical recursive algorithms such as (i) Merge-Sort, the\r\ndivide-and-conquer algorithm for the Closest-Pair problem, where we obtain\r\n$\\mathcal{O}(n \\log n)$ worst-case bound, and (ii) Karatsuba's algorithm for\r\npolynomial multiplication and Strassen's algorithm for matrix multiplication,\r\nwhere we obtain $\\mathcal{O}(n^r)$ bound such that $r$ is not an integer and\r\nclose to the best-known bounds for the respective algorithms."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1705.00317","open_access":"1"}],"scopus_import":"1","intvolume":" 41","month":"10"},{"day":"01","publication":"Journal of Fluids Engineering","isi":1,"year":"2019","date_published":"2019-11-01T00:00:00Z","doi":"10.1115/1.4043494","date_created":"2019-05-26T21:59:13Z","quality_controlled":"1","publisher":"ASME","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Kühnen, Jakob, Davide Scarselli, and Björn Hof. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” Journal of Fluids Engineering. ASME, 2019. https://doi.org/10.1115/1.4043494.","ista":"Kühnen J, Scarselli D, Hof B. 2019. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 141(11), 111105.","mla":"Kühnen, Jakob, et al. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” Journal of Fluids Engineering, vol. 141, no. 11, 111105, ASME, 2019, doi:10.1115/1.4043494.","ieee":"J. Kühnen, D. Scarselli, and B. Hof, “Relaminarization of pipe flow by means of 3D-printed shaped honeycombs,” Journal of Fluids Engineering, vol. 141, no. 11. ASME, 2019.","short":"J. Kühnen, D. Scarselli, B. Hof, Journal of Fluids Engineering 141 (2019).","ama":"Kühnen J, Scarselli D, Hof B. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 2019;141(11). doi:10.1115/1.4043494","apa":"Kühnen, J., Scarselli, D., & Hof, B. (2019). Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. ASME. https://doi.org/10.1115/1.4043494"},"title":"Relaminarization of pipe flow by means of 3D-printed shaped honeycombs","author":[{"first_name":"Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","full_name":"Kühnen, Jakob","orcid":"0000-0003-4312-0179","last_name":"Kühnen"},{"first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271","full_name":"Scarselli, Davide","last_name":"Scarselli"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof"}],"external_id":{"isi":["000487748600005"],"arxiv":["1809.07625"]},"article_processing_charge":"No","article_number":"111105","project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"306589","name":"Decoding the complexity of turbulence at its origin"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00982202"],"eissn":["1528901X"]},"publication_status":"published","volume":141,"related_material":{"record":[{"id":"7258","status":"public","relation":"dissertation_contains"}]},"issue":"11","ec_funded":1,"oa_version":"Preprint","abstract":[{"text":"Based on a novel control scheme, where a steady modification of the streamwise velocity profile leads to complete relaminarization of initially fully turbulent pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs for such control. The custom-shaped honeycombs are used as stationary flow management devices which generate specific modifications of the streamwise velocity profile. Stereoscopic particle image velocimetry and pressure drop measurements are used to investigate and capture the development of the relaminarizing flow downstream these devices. We compare the performance of straight (constant length across the radius of the pipe) honeycombs with custom-shaped ones (variable length across the radius) and try to determine the optimal shape for maximal relaminarization at minimal pressure loss. The optimally modified streamwise velocity profile is found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization is found to be of the order of 10,000. Consequently, the respective reduction in skin friction downstream of the device is almost by a factor of 5. The break-even point, where the additional pressure drop caused by the device is balanced by the savings due to relaminarization and a net gain is obtained, corresponds to a downstream stretch of distances as low as approximately 100 pipe diameters of laminar flow.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"month":"11","intvolume":" 141","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1809.07625","open_access":"1"}],"date_updated":"2024-03-27T23:30:35Z","department":[{"_id":"BjHo"}],"_id":"6486","status":"public","article_type":"original","type":"journal_article"},{"_id":"6228","type":"journal_article","status":"public","date_updated":"2024-03-27T23:30:35Z","department":[{"_id":"BjHo"}],"abstract":[{"lang":"eng","text":"Following the recent observation that turbulent pipe flow can be relaminarised bya relatively simple modification of the mean velocity profile, we here carry out aquantitative experimental investigation of this phenomenon. Our study confirms thata flat velocity profile leads to a collapse of turbulence and in order to achieve theblunted profile shape, we employ a moving pipe segment that is briefly and rapidlyshifted in the streamwise direction. The relaminarisation threshold and the minimumshift length and speeds are determined as a function of Reynolds number. Althoughturbulence is still active after the acceleration phase, the modulated profile possessesa severely decreased lift-up potential as measured by transient growth. As shown,this results in an exponential decay of fluctuations and the flow relaminarises. Whilethis method can be easily applied at low to moderate flow speeds, the minimumstreamwise length over which the acceleration needs to act increases linearly with theReynolds number."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.05357"}],"scopus_import":"1","intvolume":" 867","month":"05","publication_status":"published","publication_identifier":{"issn":["00221120"],"eissn":["14697645"]},"language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"7258","status":"public"}],"link":[{"url":"https://doi.org/10.1017/jfm.2019.191","relation":"supplementary_material"}]},"volume":867,"project":[{"call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589","name":"Decoding the complexity of turbulence at its origin"},{"call_identifier":"H2020","_id":"25104D44-B435-11E9-9278-68D0E5697425","name":"Eliminating turbulence in oil pipelines","grant_number":"737549"}],"citation":{"ama":"Scarselli D, Kühnen J, Hof B. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 2019;867:934-948. doi:10.1017/jfm.2019.191","apa":"Scarselli, D., Kühnen, J., & Hof, B. (2019). Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2019.191","short":"D. Scarselli, J. Kühnen, B. Hof, Journal of Fluid Mechanics 867 (2019) 934–948.","ieee":"D. Scarselli, J. Kühnen, and B. Hof, “Relaminarising pipe flow by wall movement,” Journal of Fluid Mechanics, vol. 867. Cambridge University Press, pp. 934–948, 2019.","mla":"Scarselli, Davide, et al. “Relaminarising Pipe Flow by Wall Movement.” Journal of Fluid Mechanics, vol. 867, Cambridge University Press, 2019, pp. 934–48, doi:10.1017/jfm.2019.191.","ista":"Scarselli D, Kühnen J, Hof B. 2019. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 867, 934–948.","chicago":"Scarselli, Davide, Jakob Kühnen, and Björn Hof. “Relaminarising Pipe Flow by Wall Movement.” Journal of Fluid Mechanics. Cambridge University Press, 2019. https://doi.org/10.1017/jfm.2019.191."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000462606100001"],"arxiv":["1807.05357"]},"article_processing_charge":"No","author":[{"last_name":"Scarselli","orcid":"0000-0001-5227-4271","full_name":"Scarselli, Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","first_name":"Davide"},{"first_name":"Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","full_name":"Kühnen, Jakob","orcid":"0000-0003-4312-0179","last_name":"Kühnen"},{"last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"title":"Relaminarising pipe flow by wall movement","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","year":"2019","isi":1,"publication":"Journal of Fluid Mechanics","day":"25","page":"934-948","date_created":"2019-04-07T21:59:14Z","date_published":"2019-05-25T00:00:00Z","doi":"10.1017/jfm.2019.191"},{"quality_controlled":"1","publisher":"ASPB","oa":1,"acknowledgement":"We thank Dr. H. Fukaki (University of Kobe), Dr. R. Offringa (Leiden University), Dr. Jianwei Pan (Zhejiang Normal University), and Dr. M. Estelle (University of California at San Diego) for providing mutants and transgenic line seeds.\r\nThis work was supported by the Ministry of Education, Culture, Sports, Science, and Technology (Grant-in-Aid for Scientific Research no. JP25114518 to K.H.), the Biotechnology and Biological Sciences Research Council (award no. BB/L009366/1 to R.N. and S.K.), and the European Union’s Horizon2020 program (European Research Council grant agreement no. 742985 to J.F.).","date_published":"2019-06-01T00:00:00Z","doi":"10.1104/pp.19.00201","date_created":"2019-04-09T08:38:20Z","page":"1152-1165","day":"01","publication":"Plant Physiology","isi":1,"year":"2019","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}],"title":"Pinstatic acid promotes auxin transport by inhibiting PIN internalization","author":[{"full_name":"Oochi, A","last_name":"Oochi","first_name":"A"},{"full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","last_name":"Hajny","first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fukui","full_name":"Fukui, K","first_name":"K"},{"full_name":"Nakao, Y","last_name":"Nakao","first_name":"Y"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","last_name":"Gallei"},{"last_name":"Quareshy","full_name":"Quareshy, M","first_name":"M"},{"first_name":"K","last_name":"Takahashi","full_name":"Takahashi, K"},{"first_name":"T","last_name":"Kinoshita","full_name":"Kinoshita, T"},{"first_name":"SR","last_name":"Harborough","full_name":"Harborough, SR"},{"last_name":"Kepinski","full_name":"Kepinski, S","first_name":"S"},{"first_name":"H","full_name":"Kasahara, H","last_name":"Kasahara"},{"first_name":"RM","last_name":"Napier","full_name":"Napier, RM"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"KI","last_name":"Hayashi","full_name":"Hayashi, KI"}],"external_id":{"isi":["000470086100045"],"pmid":["30936248"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Oochi A, Hajny J, Fukui K, Nakao Y, Gallei MC, Quareshy M, Takahashi K, Kinoshita T, Harborough S, Kepinski S, Kasahara H, Napier R, Friml J, Hayashi K. 2019. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 180(2), 1152–1165.","chicago":"Oochi, A, Jakub Hajny, K Fukui, Y Nakao, Michelle C Gallei, M Quareshy, K Takahashi, et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.19.00201.","ieee":"A. Oochi et al., “Pinstatic acid promotes auxin transport by inhibiting PIN internalization,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 1152–1165, 2019.","short":"A. Oochi, J. Hajny, K. Fukui, Y. Nakao, M.C. Gallei, M. Quareshy, K. Takahashi, T. Kinoshita, S. Harborough, S. Kepinski, H. Kasahara, R. Napier, J. Friml, K. Hayashi, Plant Physiology 180 (2019) 1152–1165.","ama":"Oochi A, Hajny J, Fukui K, et al. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 2019;180(2):1152-1165. doi:10.1104/pp.19.00201","apa":"Oochi, A., Hajny, J., Fukui, K., Nakao, Y., Gallei, M. C., Quareshy, M., … Hayashi, K. (2019). Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. ASPB. https://doi.org/10.1104/pp.19.00201","mla":"Oochi, A., et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 1152–65, doi:10.1104/pp.19.00201."},"month":"06","intvolume":" 180","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1104/pp.19.00201","open_access":"1"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Polar auxin transport plays a pivotal role in plant growth and development. PIN auxin efflux carriers regulate directional auxin movement by establishing local auxin maxima, minima, and gradients that drive multiple developmental processes and responses to environmental signals. Auxin has been proposed to modulate its own transport by regulating subcellular PIN trafficking via processes such as clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further investigated the mechanisms by which auxin affects PIN trafficking by screening auxin analogs and identified pinstatic acid (PISA) as a positive modulator of polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on hypocotyl elongation and adventitious root formation via positive regulation of auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN accumulation at the cell surface by inhibiting PIN internalization from the plasma membrane. This work demonstrates PISA to be a promising chemical tool to dissect the regulatory mechanisms behind subcellular PIN trafficking and auxin transport."}],"volume":180,"issue":"2","related_material":{"record":[{"status":"public","id":"11626","relation":"dissertation_contains"},{"status":"public","id":"8822","relation":"dissertation_contains"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"6260","department":[{"_id":"JiFr"}],"date_updated":"2024-03-27T23:30:37Z"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. 2019. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 177(6), 1463–1479.e18.","chicago":"Shamipour, Shayan, Roland Kardos, Shi-lei Xue, Björn Hof, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.030.","apa":"Shamipour, S., Kardos, R., Xue, S., Hof, B., Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.030","ama":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 2019;177(6):1463-1479.e18. doi:10.1016/j.cell.2019.04.030","short":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg, Cell 177 (2019) 1463–1479.e18.","ieee":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E. B. Hannezo, and C.-P. J. Heisenberg, “Bulk actin dynamics drive phase segregation in zebrafish oocytes,” Cell, vol. 177, no. 6. Elsevier, p. 1463–1479.e18, 2019.","mla":"Shamipour, Shayan, et al. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” Cell, vol. 177, no. 6, Elsevier, 2019, p. 1463–1479.e18, doi:10.1016/j.cell.2019.04.030."},"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes","external_id":{"pmid":["31080065"],"isi":["000469415100013"]},"article_processing_charge":"No","author":[{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour","full_name":"Shamipour, Shayan"},{"id":"4039350E-F248-11E8-B48F-1D18A9856A87","first_name":"Roland","full_name":"Kardos, Roland","last_name":"Kardos"},{"id":"31D2C804-F248-11E8-B48F-1D18A9856A87","first_name":"Shi-lei","full_name":"Xue, Shi-lei","last_name":"Xue"},{"last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton"}],"publication":"Cell","day":"30","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-06-02T21:59:12Z","date_published":"2019-05-30T00:00:00Z","doi":"10.1016/j.cell.2019.04.030","page":"1463-1479.e18","acknowledgement":"We would like to thank Pierre Recho, Guillaume Salbreux, and Silvia Grigolon for advice on the theory, Lila Solnica-Krezel for kindly providing us with zebrafish dachsous mutants, members of the Heisenberg and Hannezo groups for fruitful discussions, and the Bioimaging and zebrafish facilities at IST Austria for their continuous support. This project has received funding from the European Union (European Research Council Advanced Grant 742573 to C.P.H.) and from the Austrian Science Fund (FWF) (P 31639 to E.H.).","oa":1,"publisher":"Elsevier","quality_controlled":"1","ddc":["570"],"date_updated":"2024-03-27T23:30:38Z","file_date_updated":"2020-10-21T07:22:34Z","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"BjHo"}],"_id":"6508","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"date_created":"2020-10-21T07:22:34Z","file_name":"2019_Cell_Shamipour_accepted.pdf","creator":"dernst","date_updated":"2020-10-21T07:22:34Z","file_size":3356292,"checksum":"aea43726d80e35ce3885073a5f05c3e3","file_id":"8686","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"8350","status":"public"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/how-the-cytoplasm-separates-from-the-yolk/","description":"News on IST Homepage"}]},"issue":"6","volume":177,"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Segregation of maternal determinants within the oocyte constitutes the first step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming leads to the segregation of ooplasm from yolk granules along the animal-vegetal axis of the oocyte. Here, we show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the oocyte. This wave functions in segregation by both pulling ooplasm animally and pushing yolk granules vegetally. Using biophysical experimentation and theory, we show that ooplasm pulling is mediated by bulk actin network flows exerting friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. Our study defines a novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte polarization via ooplasmic segregation.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"intvolume":" 177","month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.04.030"}],"scopus_import":"1"},{"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"}],"citation":{"ista":"Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18.","chicago":"Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.10.006.","apa":"Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.10.006","ama":"Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 2019;179(4):937-952.e18. doi:10.1016/j.cell.2019.10.006","ieee":"C. Schwayer et al., “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Cell, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019.","short":"C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18.","mla":"Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:10.1016/j.cell.2019.10.006."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["31675500"],"isi":["000493898000012"]},"author":[{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia","orcid":"0000-0001-5130-2226","full_name":"Schwayer, Cornelia","last_name":"Schwayer"},{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour","full_name":"Shamipour, Shayan"},{"first_name":"Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","last_name":"Pranjic-Ferscha","full_name":"Pranjic-Ferscha, Kornelija"},{"first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra","last_name":"Schauer"},{"first_name":"M","last_name":"Balda","full_name":"Balda, M"},{"last_name":"Tada","full_name":"Tada, M","first_name":"M"},{"first_name":"K","last_name":"Matter","full_name":"Matter, K"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","oa":1,"publisher":"Cell Press","quality_controlled":"1","year":"2019","has_accepted_license":"1","isi":1,"publication":"Cell","day":"31","page":"937-952.e18","date_created":"2019-11-12T12:51:06Z","date_published":"2019-10-31T00:00:00Z","doi":"10.1016/j.cell.2019.10.006","_id":"7001","article_type":"original","type":"journal_article","status":"public","date_updated":"2024-03-27T23:30:38Z","ddc":["570"],"file_date_updated":"2020-10-21T07:09:45Z","department":[{"_id":"CaHe"},{"_id":"BjHo"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","intvolume":" 179","month":"10","publication_status":"published","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-10-21T07:09:45Z","file_size":8805878,"date_created":"2020-10-21T07:09:45Z","file_name":"2019_Cell_Schwayer_accepted.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"33dac4bb77ee630e2666e936b4d57980","file_id":"8684","success":1}],"ec_funded":1,"issue":"4","related_material":{"record":[{"id":"7186","status":"public","relation":"dissertation_contains"},{"id":"8350","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/","relation":"press_release","description":"News auf IST Website"}]},"volume":179},{"ddc":["570"],"supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"date_updated":"2023-10-18T08:49:17Z","file_date_updated":"2020-10-17T22:30:03Z","department":[{"_id":"MiSi"}],"_id":"6891","status":"public","keyword":["cell biology","immunology","leukocyte","migration","microfluidics"],"type":"dissertation","file":[{"file_id":"6950","checksum":"00d100d6468e31e583051e0a006b640c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","date_created":"2019-10-15T05:28:42Z","file_name":"Kopf_PhD_Thesis.docx","date_updated":"2020-10-17T22:30:03Z","file_size":74735267,"creator":"akopf"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6951","checksum":"5d1baa899993ae6ca81aebebe1797000","embargo":"2020-10-16","date_updated":"2020-10-17T22:30:03Z","file_size":52787224,"creator":"akopf","date_created":"2019-10-15T05:28:47Z","file_name":"Kopf_PhD_Thesis1.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-002-2"],"eissn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/feeling-like-a-cell/"}],"record":[{"relation":"part_of_dissertation","id":"6328","status":"public"},{"id":"15","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6877","status":"public"}]},"oa_version":"Published Version","abstract":[{"text":"While cells of mesenchymal or epithelial origin perform their effector functions in a purely anchorage dependent manner, cells derived from the hematopoietic lineage are not committed to operate only within a specific niche. Instead, these cells are able to function autonomously of the molecular composition in a broad range of tissue compartments. By this means, cells of the hematopoietic lineage retain the capacity to disseminate into connective tissue and recirculate between organs, building the foundation for essential processes such as tissue regeneration or immune surveillance. \r\nCells of the immune system, specifically leukocytes, are extraordinarily good at performing this task. These cells are able to flexibly shift their mode of migration between an adhesion-mediated and an adhesion-independent manner, instantaneously accommodating for any changes in molecular composition of the external scaffold. The key component driving directed leukocyte migration is the chemokine receptor 7, which guides the cell along gradients of chemokine ligand. Therefore, the physical destination of migrating leukocytes is purely deterministic, i.e. given by global directional cues such as chemokine gradients. \r\nNevertheless, these cells typically reside in three-dimensional scaffolds of inhomogeneous complexity, raising the question whether cells are able to locally discriminate between multiple optional migration routes. Current literature provides evidence that leukocytes, specifically dendritic cells, do indeed probe their surrounding by virtue of multiple explorative protrusions. However, it remains enigmatic how these cells decide which one is the more favorable route to follow and what are the key players involved in performing this task. Due to the heterogeneous environment of most tissues, and the vast adaptability of migrating leukocytes, at this time it is not clear to what extent leukocytes are able to optimize their migratory strategy by adapting their level of adhesiveness. And, given the fact that leukocyte migration is characterized by branched cell shapes in combination with high migration velocities, it is reasonable to assume that these cells require fine tuned shape maintenance mechanisms that tightly coordinate protrusion and adhesion dynamics in a spatiotemporal manner. \r\nTherefore, this study aimed to elucidate how rapidly migrating leukocytes opt for an ideal migratory path while maintaining a continuous cell shape and balancing adhesive forces to efficiently navigate through complex microenvironments. \r\nThe results of this study unraveled a role for the microtubule cytoskeleton in promoting the decision making process during path finding and for the first time point towards a microtubule-mediated function in cell shape maintenance of highly ramified cells such as dendritic cells. Furthermore, we found that migrating low-adhesive leukocytes are able to instantaneously adapt to increased tensile load by engaging adhesion receptors. This response was only occurring tangential to the substrate while adhesive properties in the vertical direction were not increased. As leukocytes are primed for rapid migration velocities, these results demonstrate that leukocyte integrins are able to confer a high level of traction forces parallel to the cell membrane along the direction of migration without wasting energy in gluing the cell to the substrate. \r\nThus, the data in the here presented thesis provide new insights into the pivotal role of cytoskeletal dynamics and the mechanisms of force transduction during leukocyte migration. \r\nThereby the here presented results help to further define fundamental principles underlying leukocyte migration and open up potential therapeutic avenues of clinical relevance.\r\n","lang":"eng"}],"month":"07","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Kopf A. 2019. The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria.","chicago":"Kopf, Aglaja. “The Implication of Cytoskeletal Dynamics on Leukocyte Migration.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6891.","ama":"Kopf A. The implication of cytoskeletal dynamics on leukocyte migration. 2019. doi:10.15479/AT:ISTA:6891","apa":"Kopf, A. (2019). The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6891","short":"A. Kopf, The Implication of Cytoskeletal Dynamics on Leukocyte Migration, Institute of Science and Technology Austria, 2019.","ieee":"A. Kopf, “The implication of cytoskeletal dynamics on leukocyte migration,” Institute of Science and Technology Austria, 2019.","mla":"Kopf, Aglaja. The Implication of Cytoskeletal Dynamics on Leukocyte Migration. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6891."},"title":"The implication of cytoskeletal dynamics on leukocyte migration","author":[{"orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja","last_name":"Kopf","first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","project":[{"call_identifier":"FWF","_id":"265E2996-B435-11E9-9278-68D0E5697425","name":"Nano-Analytics of Cellular Systems","grant_number":"W01250-B20"}],"day":"24","has_accepted_license":"1","year":"2019","doi":"10.15479/AT:ISTA:6891","date_published":"2019-07-24T00:00:00Z","date_created":"2019-09-19T08:19:44Z","page":"171","publisher":"Institute of Science and Technology Austria","oa":1},{"article_type":"letter_note","type":"journal_article","status":"public","_id":"6328","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"date_updated":"2024-03-27T23:30:39Z","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/","open_access":"1"}],"month":"04","intvolume":" 568","abstract":[{"lang":"eng","text":"During metazoan development, immune surveillance and cancer dissemination, cells migrate in complex three-dimensional microenvironments1,2,3. These spaces are crowded by cells and extracellular matrix, generating mazes with differently sized gaps that are typically smaller than the diameter of the migrating cell4,5. Most mesenchymal and epithelial cells and some—but not all—cancer cells actively generate their migratory path using pericellular tissue proteolysis6. By contrast, amoeboid cells such as leukocytes use non-destructive strategies of locomotion7, raising the question how these extremely fast cells navigate through dense tissues. Here we reveal that leukocytes sample their immediate vicinity for large pore sizes, and are thereby able to choose the path of least resistance. This allows them to circumnavigate local obstacles while effectively following global directional cues such as chemotactic gradients. Pore-size discrimination is facilitated by frontward positioning of the nucleus, which enables the cells to use their bulkiest compartment as a mechanical gauge. Once the nucleus and the closely associated microtubule organizing centre pass the largest pore, cytoplasmic protrusions still lingering in smaller pores are retracted. These retractions are coordinated by dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning in front of the microtubule organizing centre is a typical feature of amoeboid migration, our findings link the fundamental organization of cellular polarity to the strategy of locomotion."}],"acknowledged_ssus":[{"_id":"SSU"}],"pmid":1,"oa_version":"Submitted Version","related_material":{"record":[{"id":"14697","status":"public","relation":"dissertation_contains"},{"status":"public","id":"6891","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/"}]},"volume":568,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"724373","name":"Cellular navigation along spatial gradients"},{"_id":"265FAEBA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems","grant_number":"W01250-B20"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014","_id":"25A48D24-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369"},{"id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja","last_name":"Kopf","orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja"},{"first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","full_name":"Stopp, Julian A"},{"first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"de Vries, Ingrid","last_name":"de Vries"},{"last_name":"Driscoll","full_name":"Driscoll, Meghan K.","first_name":"Meghan K."},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"first_name":"Erik S.","full_name":"Welf, Erik S.","last_name":"Welf"},{"first_name":"Gaudenz","last_name":"Danuser","full_name":"Danuser, Gaudenz"},{"first_name":"Reto","last_name":"Fiolka","full_name":"Fiolka, Reto"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"pmid":["30944468"],"isi":["000465594200050"]},"title":"Nuclear positioning facilitates amoeboid migration along the path of least resistance","citation":{"short":"J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin, R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550.","ieee":"J. Renkawitz et al., “Nuclear positioning facilitates amoeboid migration along the path of least resistance,” Nature, vol. 568. Springer Nature, pp. 546–550, 2019.","ama":"Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 2019;568:546-550. doi:10.1038/s41586-019-1087-5","apa":"Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin, J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1087-5","mla":"Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature, vol. 568, Springer Nature, 2019, pp. 546–50, doi:10.1038/s41586-019-1087-5.","ista":"Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 568, 546–550.","chicago":"Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K. Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1087-5."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","quality_controlled":"1","oa":1,"page":"546-550","doi":"10.1038/s41586-019-1087-5","date_published":"2019-04-25T00:00:00Z","date_created":"2019-04-17T06:52:28Z","isi":1,"year":"2019","day":"25","publication":"Nature"},{"department":[{"_id":"MiSi"}],"date_updated":"2024-03-27T23:30:40Z","type":"journal_article","article_type":"original","status":"public","_id":"6877","issue":"1","volume":179,"related_material":{"record":[{"relation":"dissertation_contains","id":"6891","status":"public"}]},"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"09","intvolume":" 179","oa_version":"None","pmid":1,"author":[{"first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","last_name":"Kopf","full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"external_id":{"pmid":["31539498"],"isi":["000486618500011"]},"article_processing_charge":"No","title":"The neural crest pitches in to remove apoptotic debris","citation":{"ista":"Kopf A, Sixt MK. 2019. The neural crest pitches in to remove apoptotic debris. Cell. 179(1), 51–53.","chicago":"Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.08.047.","short":"A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53.","ieee":"A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,” Cell, vol. 179, no. 1. Elsevier, pp. 51–53, 2019.","ama":"Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. Cell. 2019;179(1):51-53. doi:10.1016/j.cell.2019.08.047","apa":"Kopf, A., & Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic debris. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.08.047","mla":"Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:10.1016/j.cell.2019.08.047."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"51-53","date_published":"2019-09-19T00:00:00Z","doi":"10.1016/j.cell.2019.08.047","date_created":"2019-09-15T22:00:46Z","isi":1,"year":"2019","day":"19","publication":"Cell","publisher":"Elsevier","quality_controlled":"1"},{"date_updated":"2024-03-27T23:30:41Z","department":[{"_id":"SiHi"}],"_id":"6830","type":"journal_article","article_type":"letter_note","status":"public","publication_identifier":{"issn":["08966273"],"eissn":["10974199"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"5","volume":103,"related_material":{"record":[{"relation":"part_of_dissertation","id":"7902","status":"public"}]},"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2019.08.021"}],"month":"09","intvolume":" 103","citation":{"mla":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron, vol. 103, no. 5, Elsevier, 2019, pp. 750–52, doi:10.1016/j.neuron.2019.08.021.","ieee":"X. Contreras and S. Hippenmeyer, “Memo1 tiles the radial glial cell grid,” Neuron, vol. 103, no. 5. Elsevier, pp. 750–752, 2019.","short":"X. Contreras, S. Hippenmeyer, Neuron 103 (2019) 750–752.","ama":"Contreras X, Hippenmeyer S. Memo1 tiles the radial glial cell grid. Neuron. 2019;103(5):750-752. doi:10.1016/j.neuron.2019.08.021","apa":"Contreras, X., & Hippenmeyer, S. (2019). Memo1 tiles the radial glial cell grid. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.021","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.021.","ista":"Contreras X, Hippenmeyer S. 2019. Memo1 tiles the radial glial cell grid. Neuron. 103(5), 750–752."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","full_name":"Contreras, Ximena"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["31487522"],"isi":["000484400200002"]},"article_processing_charge":"No","title":"Memo1 tiles the radial glial cell grid","isi":1,"year":"2019","day":"04","publication":"Neuron","page":"750-752","date_published":"2019-09-04T00:00:00Z","doi":"10.1016/j.neuron.2019.08.021","date_created":"2019-08-25T22:00:50Z","publisher":"Elsevier","quality_controlled":"1","oa":1},{"file_date_updated":"2020-07-14T12:47:34Z","department":[{"_id":"JiFr"}],"date_updated":"2024-03-27T23:30:43Z","ddc":["580"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"6627","ec_funded":1,"issue":"13","related_material":{"record":[{"relation":"dissertation_contains","id":"10083","status":"public"}]},"volume":20,"publication_status":"published","publication_identifier":{"eissn":["1422-0067"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2019_JournalMolecularScience_Adamowski.pdf","date_created":"2019-07-17T06:17:15Z","file_size":3330291,"date_updated":"2020-07-14T12:47:34Z","creator":"dernst","checksum":"dd9d1cbb933a72ceb666c9667890ac51","file_id":"6645","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"scopus_import":"1","intvolume":" 20","month":"07","abstract":[{"lang":"eng","text":"Cortical microtubule arrays in elongating epidermal cells in both the root and stem of plants have the propensity of dynamic reorientations that are correlated with the activation or inhibition of growth. Factors regulating plant growth, among them the hormone auxin, have been recognized as regulators of microtubule array orientations. Some previous work in the field has aimed at elucidating the causal relationship between cell growth, the signaling of auxin or other growth-regulating factors, and microtubule array reorientations, with various conclusions. Here, we revisit this problem of causality with a comprehensive set of experiments in Arabidopsis thaliana, using the now available pharmacological and genetic tools. We use isolated, auxin-depleted hypocotyls, an experimental system allowing for full control of both growth and auxin signaling. We demonstrate that reorientation of microtubules is not directly triggered by an auxin signal during growth activation. Instead, reorientation is triggered by the activation of the growth process itself and is auxin-independent in its nature. We discuss these findings in the context of previous relevant work, including that on the mechanical regulation of microtubule array orientation."}],"oa_version":"Published Version","pmid":1,"article_processing_charge":"Yes","external_id":{"pmid":["31284661"],"isi":["000477041100221"]},"author":[{"last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling","citation":{"mla":"Adamowski, Maciek, et al. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences, vol. 20, no. 13, 3337, MDPI, 2019, doi:10.3390/ijms20133337.","short":"M. Adamowski, L. Li, J. Friml, International Journal of Molecular Sciences 20 (2019).","ieee":"M. Adamowski, L. Li, and J. Friml, “Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling,” International Journal of Molecular Sciences, vol. 20, no. 13. MDPI, 2019.","apa":"Adamowski, M., Li, L., & Friml, J. (2019). Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms20133337","ama":"Adamowski M, Li L, Friml J. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 2019;20(13). doi:10.3390/ijms20133337","chicago":"Adamowski, Maciek, Lanxin Li, and Jiří Friml. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences. MDPI, 2019. https://doi.org/10.3390/ijms20133337.","ista":"Adamowski M, Li L, Friml J. 2019. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 20(13), 3337."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"article_number":"3337","date_created":"2019-07-11T12:00:32Z","date_published":"2019-07-07T00:00:00Z","doi":"10.3390/ijms20133337","year":"2019","isi":1,"has_accepted_license":"1","publication":"International Journal of Molecular Sciences","day":"07","oa":1,"quality_controlled":"1","publisher":"MDPI"},{"publication_identifier":{"issn":["0730-0301"]},"publication_status":"published","file":[{"checksum":"56a2fb019adcb556d2b022f5e5acb68c","file_id":"7119","content_type":"application/pdf","access_level":"open_access","relation":"supplementary_material","title":"X-CAD Supplemental Material","date_created":"2019-11-26T14:24:26Z","file_name":"xcad_sup_mat_siga19.pdf","date_updated":"2020-07-14T12:47:49Z","file_size":1673176,"creator":"bbickel"},{"date_created":"2019-11-26T14:24:27Z","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","file_name":"XCAD_authors_version.pdf","date_updated":"2020-07-14T12:47:49Z","file_size":14563618,"creator":"bbickel","checksum":"5f29d76aceb5102e766cbab9b17d776e","file_id":"7120","content_type":"application/pdf","description":"This is the author's version of the work.","access_level":"open_access","relation":"main_file"},{"content_type":"video/mp4","access_level":"open_access","relation":"main_file","checksum":"0d31e123286cbec9e28b2001c2bb0d55","file_id":"7121","date_updated":"2020-07-14T12:47:49Z","file_size":259979129,"creator":"bbickel","date_created":"2019-11-26T14:27:37Z","file_name":"XCAD_video.mp4"}],"language":[{"iso":"eng"}],"issue":"6","related_material":{"record":[{"relation":"dissertation_contains","id":"12897","status":"public"}]},"volume":38,"ec_funded":1,"abstract":[{"text":"We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","month":"11","intvolume":" 38","date_updated":"2024-03-27T23:30:46Z","ddc":["000"],"department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:47:49Z","_id":"7117","article_type":"original","type":"journal_article","status":"public","isi":1,"has_accepted_license":"1","year":"2019","day":"06","publication":"ACM Transactions on Graphics","date_published":"2019-11-06T00:00:00Z","doi":"10.1145/3355089.3356576","date_created":"2019-11-26T14:22:09Z","publisher":"ACM","quality_controlled":"1","oa":1,"citation":{"mla":"Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics, vol. 38, no. 6, 157, ACM, 2019, doi:10.1145/3355089.3356576.","ama":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 2019;38(6). doi:10.1145/3355089.3356576","apa":"Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., & Bächer, M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356576","short":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019).","ieee":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer, “X-CAD: Optimizing CAD Models with Extended Finite Elements,” ACM Transactions on Graphics, vol. 38, no. 6. ACM, 2019.","chicago":"Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger, Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356576.","ista":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 38(6), 157."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Hafner","full_name":"Hafner, Christian","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","full_name":"Schumacher, Christian","last_name":"Schumacher"},{"last_name":"Knoop","full_name":"Knoop, Espen","first_name":"Espen"},{"last_name":"Auzinger","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bächer","full_name":"Bächer, Moritz","first_name":"Moritz"}],"article_processing_charge":"No","external_id":{"isi":["000498397300007"]},"title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","article_number":"157","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}]},{"date_published":"2019-03-22T00:00:00Z","doi":"10.1103/PhysRevLett.122.114502","date_created":"2019-03-31T21:59:12Z","isi":1,"year":"2019","day":"22","publication":"Physical Review Letters","quality_controlled":"1","publisher":"American Physical Society","oa":1,"author":[{"full_name":"Agrawal, Nishchal","last_name":"Agrawal","id":"469E6004-F248-11E8-B48F-1D18A9856A87","first_name":"Nishchal"},{"id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","first_name":"George H","last_name":"Choueiri","full_name":"Choueiri, George H"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"external_id":{"arxiv":["1809.06358"],"isi":["000461922000006"]},"article_processing_charge":"No","title":"Transition to turbulence in particle laden flows","citation":{"chicago":"Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.114502.","ista":"Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502.","mla":"Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters, vol. 122, no. 11, 114502, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.114502.","apa":"Agrawal, N., Choueiri, G. H., & Hof, B. (2019). Transition to turbulence in particle laden flows. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.114502","ama":"Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows. Physical Review Letters. 2019;122(11). doi:10.1103/PhysRevLett.122.114502","ieee":"N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle laden flows,” Physical Review Letters, vol. 122, no. 11. American Physical Society, 2019.","short":"N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"114502","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9728"}]},"issue":"11","volume":122,"publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.06358"}],"month":"03","intvolume":" 122","abstract":[{"lang":"eng","text":"Suspended particles can alter the properties of fluids and in particular also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic) transition to turbulent puffs is affected by the addition of particles. Here weshow that in addition to this known transition, with increasing concentration a supercritical (i.e.,continuous) transition to a globally fluctuating state is found. At the same time the Newtonian-typetransition to puffs is delayed to larger Reynolds numbers. At even higher concentration only the globallyfluctuating state is found. The dynamics of particle laden flows are hence determined by two competinginstabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle inducedglobally fluctuating state at high, and a coexistence state at intermediate concentrations."}],"oa_version":"Preprint","department":[{"_id":"BjHo"}],"date_updated":"2024-03-27T23:30:47Z","type":"journal_article","status":"public","_id":"6189"},{"page":"152","date_created":"2019-05-03T11:55:51Z","doi":"10.15479/AT:ISTA:6371","date_published":"2019-05-03T00:00:00Z","year":"2019","has_accepted_license":"1","day":"03","oa":1,"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","author":[{"last_name":"Igler","full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia"}],"title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","citation":{"mla":"Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371.","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371","apa":"Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019.","short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371.","ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"24573","name":"Design principles underlying genetic switch architecture (DOC Fellowship)","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"status":"public","id":"67","relation":"part_of_dissertation"},{"status":"public","id":"5585","relation":"popular_science"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-05-03T11:54:52Z","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","creator":"cigler","date_updated":"2021-02-11T11:17:13Z","file_size":12597663,"checksum":"c0085d47c58c9cbcab1b0a783480f6da","file_id":"6373","embargo":"2020-05-02","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","date_created":"2019-05-03T11:54:54Z","creator":"cigler","file_size":34644426,"date_updated":"2020-07-14T12:47:28Z","checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","file_id":"6374","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"alternative_title":["ISTA Thesis"],"month":"05","abstract":[{"lang":"eng","text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation. \r\n"}],"oa_version":"Published Version","file_date_updated":"2021-02-11T11:17:13Z","department":[{"_id":"CaGu"}],"date_updated":"2024-02-21T13:45:52Z","supervisor":[{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"ddc":["576","579"],"type":"dissertation","keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"status":"public","_id":"6371"},{"quality_controlled":"1","publisher":"International Association for Cryptologic Research","oa":1,"page":"214-242","date_published":"2018-01-01T00:00:00Z","doi":"10.13154/tches.v2018.i3.214-242","date_created":"2021-11-14T23:01:25Z","has_accepted_license":"1","year":"2018","day":"01","publication":"IACR Transactions on Cryptographic Hardware and Embedded Systems","author":[{"full_name":"Allini, Elie Noumon","last_name":"Allini","first_name":"Elie Noumon"},{"last_name":"Skórski","full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej"},{"first_name":"Oto","full_name":"Petura, Oto","last_name":"Petura"},{"last_name":"Bernard","full_name":"Bernard, Florent","first_name":"Florent"},{"full_name":"Laban, Marek","last_name":"Laban","first_name":"Marek"},{"first_name":"Viktor","full_name":"Fischer, Viktor","last_name":"Fischer"}],"article_processing_charge":"No","title":"Evaluation and monitoring of free running oscillators serving as source of randomness","citation":{"chicago":"Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research, 2018. https://doi.org/10.13154/tches.v2018.i3.214-242.","ista":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.","mla":"Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3, International Association for Cryptologic Research, 2018, pp. 214–42, doi:10.13154/tches.v2018.i3.214-242.","short":"E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.","ieee":"E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer, “Evaluation and monitoring of free running oscillators serving as source of randomness,” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3. International Association for Cryptologic Research, pp. 214–242, 2018.","apa":"Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., & Fischer, V. (2018). Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research. https://doi.org/10.13154/tches.v2018.i3.214-242","ama":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018;2018(3):214-242. doi:10.13154/tches.v2018.i3.214-242"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","scopus_import":"1","month":"01","intvolume":" 2018","abstract":[{"lang":"eng","text":"In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied."}],"oa_version":"Published Version","issue":"3","volume":2018,"publication_identifier":{"eissn":["2569-2925"]},"publication_status":"published","file":[{"file_size":955755,"date_updated":"2021-11-15T10:27:29Z","creator":"cchlebak","file_name":"2018_IACR_Allini.pdf","date_created":"2021-11-15T10:27:29Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10289","checksum":"b816b848f046c48a8357700d9305dce5"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"10286","department":[{"_id":"KrPi"}],"file_date_updated":"2021-11-15T10:27:29Z","date_updated":"2021-11-15T10:48:49Z","ddc":["000"]},{"day":"23","publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","has_accepted_license":"1","year":"2018","doi":"10.29007/5z5k","date_published":"2018-10-23T00:00:00Z","date_created":"2022-03-18T12:46:32Z","page":"233-253","acknowledgement":"A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph Games). For M.H the research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) /ERC Grant Agreement no. 340506.","publisher":"EasyChair","quality_controlled":"1","oa":1,"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k.","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253.","ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253.","ama":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair; 2018:233-253. doi:10.29007/5z5k","apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., & Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k","mla":"Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53, doi:10.29007/5z5k."},"title":"Quasipolynomial set-based symbolic algorithms for parity games","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Dvořák, Wolfgang","last_name":"Dvořák","first_name":"Wolfgang"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"first_name":"Alexander","full_name":"Svozil, Alexander","last_name":"Svozil"}],"article_processing_charge":"No","external_id":{"arxiv":["1909.04983"]},"project":[{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"file":[{"file_id":"11392","checksum":"1229aa8640bd6db610c85decf2265480","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2022-05-17T07:51:08Z","file_name":"2018_EPiCs_Chatterjee.pdf","date_updated":"2022-05-17T07:51:08Z","file_size":720893,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2398-7340"]},"publication_status":"published","volume":57,"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space.","lang":"eng"}],"month":"10","intvolume":" 57","scopus_import":"1","alternative_title":["EPiC Series in Computing"],"ddc":["000"],"date_updated":"2022-07-29T09:24:31Z","file_date_updated":"2022-05-17T07:51:08Z","department":[{"_id":"KrCh"}],"_id":"10883","status":"public","type":"conference","conference":{"start_date":"2018-11-17","end_date":"2018-11-21","location":"Awassa, Ethiopia","name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning"}},{"ec_funded":1,"volume":270,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.10843"}],"scopus_import":1,"intvolume":" 270","month":"10","abstract":[{"lang":"eng","text":"We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm."}],"oa_version":"Preprint","department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T06:48:16Z","conference":{"location":"Munich, Germany","end_date":"2017-04-01","start_date":"2017-03-30","name":"MaLiQS: Macroscopic Limits of Quantum Systems"},"type":"conference","status":"public","_id":"11","page":"185 - 214","date_created":"2018-12-11T11:44:08Z","date_published":"2018-10-27T00:00:00Z","doi":"10.1007/978-3-030-01602-9_9","year":"2018","day":"27","oa":1,"publisher":"Springer","quality_controlled":"1","external_id":{"arxiv":["1806.10843"]},"publist_id":"8045","author":[{"id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K","orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K","last_name":"Leopold"},{"first_name":"Peter","full_name":"Pickl, Peter","last_name":"Pickl"}],"title":"Mean-field limits of particles in interaction with quantised radiation fields","citation":{"mla":"Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp. 185–214, doi:10.1007/978-3-030-01602-9_9.","short":"N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.","ieee":"N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.","ama":"Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9","apa":"Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. https://doi.org/10.1007/978-3-030-01602-9_9","chicago":"Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9.","ista":"Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}]},{"pubrep_id":"712","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1215","department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:44:39Z","ddc":["519"],"date_updated":"2021-01-12T06:49:09Z","intvolume":" 31","month":"06","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Two generalizations of Itô formula to infinite-dimensional spaces are given.\r\nThe first one, in Hilbert spaces, extends the classical one by taking advantage of\r\ncancellations when they occur in examples and it is applied to the case of a group\r\ngenerator. The second one, based on the previous one and a limit procedure, is an Itô\r\nformula in a special class of Banach spaces having a product structure with the noise\r\nin a Hilbert component; again the key point is the extension due to a cancellation. This\r\nextension to Banach spaces and in particular the specific cancellation are motivated\r\nby path-dependent Itô calculus.","lang":"eng"}],"issue":"2","volume":31,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5266","checksum":"47686d58ec21c164540f1a980ff2163f","file_size":671125,"date_updated":"2020-07-14T12:44:39Z","creator":"system","file_name":"IST-2016-712-v1+1_s10959-016-0724-2.pdf","date_created":"2018-12-12T10:17:13Z"}],"publication_status":"published","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"title":"Infinite-dimensional calculus under weak spatial regularity of the processes","article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Flandoli, Franco","last_name":"Flandoli","first_name":"Franco"},{"first_name":"Francesco","full_name":"Russo, Francesco","last_name":"Russo"},{"id":"47491882-F248-11E8-B48F-1D18A9856A87","first_name":"Giovanni A","full_name":"Zanco, Giovanni A","last_name":"Zanco"}],"publist_id":"6119","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Flandoli, Franco, Francesco Russo, and Giovanni A Zanco. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability. Springer, 2018. https://doi.org/10.1007/s10959-016-0724-2.","ista":"Flandoli F, Russo F, Zanco GA. 2018. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 31(2), 789–826.","mla":"Flandoli, Franco, et al. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability, vol. 31, no. 2, Springer, 2018, pp. 789–826, doi:10.1007/s10959-016-0724-2.","apa":"Flandoli, F., Russo, F., & Zanco, G. A. (2018). Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. Springer. https://doi.org/10.1007/s10959-016-0724-2","ama":"Flandoli F, Russo F, Zanco GA. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 2018;31(2):789-826. doi:10.1007/s10959-016-0724-2","short":"F. Flandoli, F. Russo, G.A. Zanco, Journal of Theoretical Probability 31 (2018) 789–826.","ieee":"F. Flandoli, F. Russo, and G. A. Zanco, “Infinite-dimensional calculus under weak spatial regularity of the processes,” Journal of Theoretical Probability, vol. 31, no. 2. Springer, pp. 789–826, 2018."},"oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The second named author benefited partially from the support of the “FMJH Program Gaspard Monge in Optimization and Operations Research” (Project 2014-1607H). He is also grateful for the invitation to the Department of Mathematics of the University of Pisa. The third named author is grateful for the invitation to ENSTA.","date_created":"2018-12-11T11:50:45Z","date_published":"2018-06-01T00:00:00Z","doi":"10.1007/s10959-016-0724-2","page":"789-826","publication":"Journal of Theoretical Probability","day":"01","year":"2018","has_accepted_license":"1"},{"project":[{"call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs"}],"article_number":"39","publist_id":"7735","author":[{"last_name":"Fulek","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kynčl","full_name":"Kynčl, Jan","first_name":"Jan"}],"title":"Hanani-Tutte for approximating maps of graphs","citation":{"short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ieee":"R. Fulek and J. Kynčl, “Hanani-Tutte for approximating maps of graphs,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","apa":"Fulek, R., & Kynčl, J. (2018). Hanani-Tutte for approximating maps of graphs (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.39","ama":"Fulek R, Kynčl J. Hanani-Tutte for approximating maps of graphs. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.39","mla":"Fulek, Radoslav, and Jan Kynčl. Hanani-Tutte for Approximating Maps of Graphs. Vol. 99, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.39.","ista":"Fulek R, Kynčl J. 2018. Hanani-Tutte for approximating maps of graphs. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 39.","chicago":"Fulek, Radoslav, and Jan Kynčl. “Hanani-Tutte for Approximating Maps of Graphs,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.39."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"date_published":"2018-01-01T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2018.39","date_created":"2018-12-11T11:45:04Z","has_accepted_license":"1","year":"2018","day":"01","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2018-06-11","end_date":"2018-06-14","location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry"},"status":"public","_id":"185","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"UlWa"}],"date_updated":"2021-01-12T06:53:36Z","ddc":["510"],"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"scopus_import":1,"month":"01","intvolume":" 99","abstract":[{"text":"We resolve in the affirmative conjectures of A. Skopenkov and Repovš (1998), and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the setting of approximating maps of graphs on 2-dimensional surfaces by embeddings. Our proof of this result is constructive and almost immediately implies an efficient algorithm for testing whether a given piecewise linear map of a graph in a surface is approximable by an embedding. More precisely, an instance of this problem consists of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact surface M given as the union of a set of pairwise disjoint discs corresponding to the clusters and a set of pairwise disjoint "pipes" corresponding to the bundles, connecting certain pairs of these discs. We are to decide whether G can be embedded inside M so that the vertices in every cluster are drawn in the corresponding disc, the edges in every bundle pass only through its corresponding pipe, and every edge crosses the boundary of each disc at most once.","lang":"eng"}],"oa_version":"Published Version","volume":99,"publication_identifier":{"isbn":["978-3-95977-066-8"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-07-14T12:45:19Z","file_size":718857,"date_created":"2018-12-17T12:33:52Z","file_name":"2018_LIPIcs_Fulek.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"f1b94f1a75b37c414a1f61d59fb2cd4c","file_id":"5701"}],"language":[{"iso":"eng"}]},{"project":[{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:35:1-35:13. doi:10.4230/LIPIcs.SoCG.2018.35","apa":"Edelsbrunner, H., Virk, Z., & Wagner, H. (2018). Smallest enclosing spheres and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.35","short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13.","ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Smallest enclosing spheres and Chernoff points in Bregman geometry,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 35:1-35:13.","mla":"Edelsbrunner, Herbert, et al. Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13, doi:10.4230/LIPIcs.SoCG.2018.35.","ista":"Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13.","chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.35."},"title":"Smallest enclosing spheres and Chernoff points in Bregman geometry","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"last_name":"Virk","full_name":"Virk, Ziga","first_name":"Ziga"},{"first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","full_name":"Wagner, Hubert"}],"publist_id":"7733","acknowledgement":"This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"day":"11","has_accepted_license":"1","year":"2018","doi":"10.4230/LIPIcs.SoCG.2018.35","date_published":"2018-06-11T00:00:00Z","date_created":"2018-12-11T11:45:05Z","page":"35:1 - 35:13","_id":"188","status":"public","type":"conference","conference":{"start_date":"2018-06-11","end_date":"2018-06-14","location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"date_updated":"2021-01-12T06:53:48Z","file_date_updated":"2020-07-14T12:45:20Z","department":[{"_id":"HeEd"}],"oa_version":"Published Version","abstract":[{"text":"Smallest enclosing spheres of finite point sets are central to methods in topological data analysis. Focusing on Bregman divergences to measure dissimilarity, we prove bounds on the location of the center of a smallest enclosing sphere. These bounds depend on the range of radii for which Bregman balls are convex.","lang":"eng"}],"month":"06","intvolume":" 99","scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"7509403803b3ac1aee94bbc2ad293d21","file_id":"5724","date_updated":"2020-07-14T12:45:20Z","file_size":489080,"creator":"dernst","date_created":"2018-12-17T16:31:31Z","file_name":"2018_LIPIcs_Edelsbrunner.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":99},{"date_updated":"2021-01-12T07:40:46Z","ddc":["530"],"department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:59Z","_id":"306","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"2018_Heliyon_DeMartino.pdf","date_created":"2019-02-06T07:36:24Z","file_size":994490,"date_updated":"2020-07-14T12:45:59Z","creator":"dernst","file_id":"5929","checksum":"67010cf5e3b3e0637c659371714a715a","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"ec_funded":1,"issue":"4","volume":4,"abstract":[{"text":"A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 4","month":"04","citation":{"mla":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon, vol. 4, no. 4, e00596, Elsevier, 2018, doi:10.1016/j.heliyon.2018.e00596.","ieee":"A. De Martino and D. De Martino, “An introduction to the maximum entropy approach and its application to inference problems in biology,” Heliyon, vol. 4, no. 4. Elsevier, 2018.","short":"A. De Martino, D. De Martino, Heliyon 4 (2018).","ama":"De Martino A, De Martino D. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 2018;4(4). doi:10.1016/j.heliyon.2018.e00596","apa":"De Martino, A., & De Martino, D. (2018). An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. Elsevier. https://doi.org/10.1016/j.heliyon.2018.e00596","chicago":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon. Elsevier, 2018. https://doi.org/10.1016/j.heliyon.2018.e00596.","ista":"De Martino A, De Martino D. 2018. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 4(4), e00596."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Andrea","full_name":"De Martino, Andrea","last_name":"De Martino"},{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"}],"title":"An introduction to the maximum entropy approach and its application to inference problems in biology","article_number":"e00596","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"year":"2018","has_accepted_license":"1","publication":"Heliyon","day":"01","date_created":"2018-12-11T11:45:44Z","date_published":"2018-04-01T00:00:00Z","doi":"10.1016/j.heliyon.2018.e00596","oa":1,"publisher":"Elsevier","quality_controlled":"1"},{"publication_status":"published","year":"2018","publication_identifier":{"isbn":["978-3-319-10574-1"],"eisbn":["978-3-319-10575-8"]},"language":[{"iso":"eng"}],"day":"08","page":"XLVIII, 1212","date_created":"2018-12-11T12:02:32Z","doi":"10.1007/978-3-319-10575-8","date_published":"2018-06-08T00:00:00Z","abstract":[{"text":"This book first explores the origins of this idea, grounded in theoretical work on temporal logic and automata. The editors and authors are among the world's leading researchers in this domain, and they contributed 32 chapters representing a thorough view of the development and application of the technique. Topics covered include binary decision diagrams, symbolic model checking, satisfiability modulo theories, partial-order reduction, abstraction, interpolation, concurrency, security protocols, games, probabilistic model checking, and process algebra, and chapters on the transfer of theory to industrial practice, property specification languages for hardware, and verification of real-time systems and hybrid systems.\r\n\r\nThe book will be valuable for researchers and graduate students engaged with the development of formal methods and verification tools.","lang":"eng"}],"oa_version":"None","edition":"1","publisher":"Springer Nature","scopus_import":"1","quality_controlled":"1","month":"06","place":"Cham","date_updated":"2021-12-21T10:49:36Z","citation":{"chicago":"Clarke, Edmund M., Thomas A Henzinger, Helmut Veith, and Roderick Bloem. Handbook of Model Checking. 1st ed. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-10575-8.","ista":"Clarke EM, Henzinger TA, Veith H, Bloem R. 2018. Handbook of Model Checking 1st ed., Cham: Springer Nature, XLVIII, 1212p.","mla":"Clarke, Edmund M., et al. Handbook of Model Checking. 1st ed., Springer Nature, 2018, doi:10.1007/978-3-319-10575-8.","short":"E.M. Clarke, T.A. Henzinger, H. Veith, R. Bloem, Handbook of Model Checking, 1st ed., Springer Nature, Cham, 2018.","ieee":"E. M. Clarke, T. A. Henzinger, H. Veith, and R. Bloem, Handbook of Model Checking, 1st ed. Cham: Springer Nature, 2018.","apa":"Clarke, E. M., Henzinger, T. A., Veith, H., & Bloem, R. (2018). Handbook of Model Checking (1st ed.). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-10575-8","ama":"Clarke EM, Henzinger TA, Veith H, Bloem R. Handbook of Model Checking. 1st ed. Cham: Springer Nature; 2018. doi:10.1007/978-3-319-10575-8"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","publist_id":"3340","author":[{"first_name":"Edmund M.","full_name":"Clarke, Edmund M.","last_name":"Clarke"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Veith, Helmut","last_name":"Veith","first_name":"Helmut"},{"last_name":"Bloem","full_name":"Bloem, Roderick","first_name":"Roderick"}],"title":"Handbook of Model Checking","department":[{"_id":"ToHe"}],"_id":"3300","type":"book","status":"public"},{"project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"}],"publist_id":"8018","author":[{"last_name":"Zagórski","orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"}],"article_processing_charge":"No","title":"Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube","citation":{"mla":"Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63, doi:10.1007/978-1-4939-8772-6_4.","apa":"Zagórski, M. P., & Kicheva, A. (2018). Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In Morphogen Gradients (Vol. 1863, pp. 47–63). Springer Nature. https://doi.org/10.1007/978-1-4939-8772-6_4","ama":"Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Vol 1863. MIMB. Springer Nature; 2018:47-63. doi:10.1007/978-1-4939-8772-6_4","short":"M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63.","ieee":"M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube,” in Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63.","chicago":"Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” In Morphogen Gradients , 1863:47–63. MIMB. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-8772-6_4.","ista":"Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods in Molecular Biology, vol. 1863, 47–63."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Springer Nature","oa":1,"page":"47 - 63","date_published":"2018-10-16T00:00:00Z","doi":"10.1007/978-1-4939-8772-6_4","date_created":"2018-12-11T11:44:17Z","has_accepted_license":"1","year":"2018","day":"16","publication":"Morphogen Gradients ","type":"book_chapter","status":"public","series_title":"MIMB","_id":"37","department":[{"_id":"AnKi"}],"file_date_updated":"2020-10-13T14:20:37Z","date_updated":"2021-01-12T07:49:03Z","ddc":["570"],"scopus_import":"1","alternative_title":["Methods in Molecular Biology"],"month":"10","intvolume":" 1863","abstract":[{"lang":"eng","text":"Developmental processes are inherently dynamic and understanding them requires quantitative measurements of gene and protein expression levels in space and time. While live imaging is a powerful approach for obtaining such data, it is still a challenge to apply it over long periods of time to large tissues, such as the embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression and signaling activity patterns in this organ can be studied by collecting tissue sections at different developmental stages. In combination with immunohistochemistry, this allows for measuring the levels of multiple developmental regulators in a quantitative manner with high spatiotemporal resolution. The mean protein expression levels over time, as well as embryo-to-embryo variability can be analyzed. A key aspect of the approach is the ability to compare protein levels across different samples. This requires a number of considerations in sample preparation, imaging and data analysis. Here we present a protocol for obtaining time course data of dorsoventral expression patterns from mouse and chick neural tube in the first 3 days of neural tube development. The described workflow starts from embryo dissection and ends with a processed dataset. Software scripts for data analysis are included. The protocol is adaptable and instructions that allow the user to modify different steps are provided. Thus, the procedure can be altered for analysis of time-lapse images and applied to systems other than the neural tube."}],"oa_version":"Submitted Version","volume":1863,"ec_funded":1,"publication_identifier":{"issn":["1064-3745"],"isbn":["978-1-4939-8771-9"]},"publication_status":"published","file":[{"creator":"dernst","file_size":4906815,"date_updated":"2020-10-13T14:20:37Z","file_name":"2018_MIMB_Zagorski.pdf","date_created":"2020-10-13T14:20:37Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8656","checksum":"2a97d0649fdcfcf1bdca7c8ad1dce71b"}],"language":[{"iso":"eng"}]},{"_id":"305","status":"public","type":"journal_article","date_updated":"2021-01-12T07:40:42Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"oa_version":"None","abstract":[{"lang":"eng","text":"The hanging-drop network (HDN) is a technology platform based on a completely open microfluidic network at the bottom of an inverted, surface-patterned substrate. The platform is predominantly used for the formation, culturing, and interaction of self-assembled spherical microtissues (spheroids) under precisely controlled flow conditions. Here, we describe design, fabrication, and operation of microfluidic hanging-drop networks."}],"intvolume":" 1771","month":"01","scopus_import":1,"alternative_title":["MIMB"],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":1771,"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology. Springer, 2018. https://doi.org/10.1007/978-1-4939-7792-5_15.","ista":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. 2018. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 1771, 183–202.","mla":"Misun, Patrick, et al. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology, vol. 1771, Springer, 2018, pp. 183–202, doi:10.1007/978-1-4939-7792-5_15.","ama":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 2018;1771:183-202. doi:10.1007/978-1-4939-7792-5_15","apa":"Misun, P., Birchler, A., Lang, M., Hierlemann, A., & Frey, O. (2018). Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-4939-7792-5_15","short":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular Biology 1771 (2018) 183–202.","ieee":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, and O. Frey, “Fabrication and operation of microfluidic hanging drop networks,” Methods in Molecular Biology, vol. 1771. Springer, pp. 183–202, 2018."},"title":"Fabrication and operation of microfluidic hanging drop networks","author":[{"full_name":"Misun, Patrick","last_name":"Misun","first_name":"Patrick"},{"full_name":"Birchler, Axel","last_name":"Birchler","first_name":"Axel"},{"last_name":"Lang","full_name":"Lang, Moritz","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hierlemann, Andreas","last_name":"Hierlemann","first_name":"Andreas"},{"first_name":"Olivier","last_name":"Frey","full_name":"Frey, Olivier"}],"publist_id":"7574","acknowledgement":"This work was financially supported by FP7 of the EU through the project “Body on a chip,” ICT-FET-296257, and the ERC Advanced Grant “NeuroCMOS” (contract 267351), as well as by an individual Ambizione Grant 142440 from the Swiss National Science Foundation for Olivier Frey. The research leading to these results also received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734]. We would like to thank Alexander Stettler, ETH Zurich for his expertise and support in the cleanroom, and we acknowledge the Single Cell Unit of D-BSSE, ETH Zurich for assistance in microscopy issues. M.L. is grateful to the members of the Guet and Tkačik groups, IST Austria, for valuable comments and support.","quality_controlled":"1","publisher":"Springer","publication":"Methods in Molecular Biology","day":"01","year":"2018","date_created":"2018-12-11T11:45:43Z","doi":"10.1007/978-1-4939-7792-5_15","date_published":"2018-01-01T00:00:00Z","page":"183 - 202"},{"language":[{"iso":"eng"}],"publication_status":"published","issue":"POPL","volume":2,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Probabilistic programs extend classical imperative programs with real-valued random variables and random branching. The most basic liveness property for such programs is the termination property. The qualitative (aka almost-sure) termination problem asks whether a given program program terminates with probability 1. While ranking functions provide a sound and complete method for non-probabilistic programs, the extension of them to probabilistic programs is achieved via ranking supermartingales (RSMs). Although deep theoretical results have been established about RSMs, their application to probabilistic programs with nondeterminism has been limited only to programs of restricted control-flow structure. For non-probabilistic programs, lexicographic ranking functions provide a compositional and practical approach for termination analysis of real-world programs. In this work we introduce lexicographic RSMs and show that they present a sound method for almost-sure termination of probabilistic programs with nondeterminism. We show that lexicographic RSMs provide a tool for compositional reasoning about almost-sure termination, and for probabilistic programs with linear arithmetic they can be synthesized efficiently (in polynomial time). We also show that with additional restrictions even asymptotic bounds on expected termination time can be obtained through lexicographic RSMs. Finally, we present experimental results on benchmarks adapted from previous work to demonstrate the effectiveness of our approach."}],"month":"01","intvolume":" 2","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.04037"}],"date_updated":"2021-01-12T07:42:07Z","department":[{"_id":"KrCh"}],"_id":"325","status":"public","type":"conference","conference":{"end_date":"2018-01-13","location":"Los Angeles, CA, USA","start_date":"2018-01-07","name":"POPL: Principles of Programming Languages"},"day":"01","year":"2018","doi":"10.1145/3158122","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:45:50Z","quality_controlled":"1","publisher":"ACM","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Agrawal S, Chatterjee K, Novotný P. 2018. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. POPL: Principles of Programming Languages vol. 2, 34.","chicago":"Agrawal, Sheshansh, Krishnendu Chatterjee, and Petr Novotný. “Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs,” Vol. 2. ACM, 2018. https://doi.org/10.1145/3158122.","ama":"Agrawal S, Chatterjee K, Novotný P. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. In: Vol 2. ACM; 2018. doi:10.1145/3158122","apa":"Agrawal, S., Chatterjee, K., & Novotný, P. (2018). Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs (Vol. 2). Presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/3158122","ieee":"S. Agrawal, K. Chatterjee, and P. Novotný, “Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs,” presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA, 2018, vol. 2, no. POPL.","short":"S. Agrawal, K. Chatterjee, P. Novotný, in:, ACM, 2018.","mla":"Agrawal, Sheshansh, et al. Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs. Vol. 2, no. POPL, 34, ACM, 2018, doi:10.1145/3158122."},"title":"Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs","publist_id":"7540","author":[{"first_name":"Sheshansh","full_name":"Agrawal, Sheshansh","last_name":"Agrawal"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Novotny, Petr","last_name":"Novotny","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"}],"external_id":{"arxiv":["1709.04037"]},"article_number":"34","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"publication_identifier":{"issn":["1064-3745"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":1761,"abstract":[{"lang":"eng","text":"Adventitious roots (AR) are de novo formed roots that emerge from any part of the plant or from callus in tissue culture, except root tissue. The plant tissue origin and the method by which they are induced determine the physiological properties of emerged ARs. Hence, a standard method encompassing all types of AR does not exist. Here we describe a method for the induction and analysis of AR that emerge from the etiolated hypocotyl of dicot plants. The hypocotyl is formed during embryogenesis and shows a determined developmental pattern which usually does not involve AR formation. However, the hypocotyl shows propensity to form de novo roots under specific circumstances such as removal of the root system, high humidity or flooding, or during de-etiolation. The hypocotyl AR emerge from a pericycle-like cell layer surrounding the vascular tissue of the central cylinder, which is reminiscent to the developmental program of lateral roots. Here we propose an easy protocol for in vitro hypocotyl AR induction from etiolated Arabidopsis seedlings."}],"oa_version":"None","pmid":1,"scopus_import":"1","alternative_title":["MIMB"],"month":"03","intvolume":" 1761","date_updated":"2021-01-12T07:54:21Z","department":[{"_id":"JiFr"}],"_id":"408","type":"book_chapter","status":"public","year":"2018","day":"01","publication":"Root Development ","page":"95 - 102","date_published":"2018-03-01T00:00:00Z","doi":"10.1007/978-1-4939-7747-5_7","date_created":"2018-12-11T11:46:18Z","quality_controlled":"1","publisher":"Springer Nature","citation":{"apa":"Trinh, H., Verstraeten, I., & Geelen, D. (2018). In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In Root Development (Vol. 1761, pp. 95–102). Springer Nature. https://doi.org/10.1007/978-1-4939-7747-5_7","ama":"Trinh H, Verstraeten I, Geelen D. In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . Vol 1761. Springer Nature; 2018:95-102. doi:10.1007/978-1-4939-7747-5_7","short":"H. Trinh, I. Verstraeten, D. Geelen, in:, Root Development , Springer Nature, 2018, pp. 95–102.","ieee":"H. Trinh, I. Verstraeten, and D. Geelen, “In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls,” in Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102.","mla":"Trinh, Hoang, et al. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102, doi:10.1007/978-1-4939-7747-5_7.","ista":"Trinh H, Verstraeten I, Geelen D. 2018.In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . MIMB, vol. 1761, 95–102.","chicago":"Trinh, Hoang, Inge Verstraeten, and Danny Geelen. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” In Root Development , 1761:95–102. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-7747-5_7."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7421","author":[{"last_name":"Trinh","full_name":"Trinh, Hoang","first_name":"Hoang"},{"first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","last_name":"Verstraeten"},{"full_name":"Geelen, Danny","last_name":"Geelen","first_name":"Danny"}],"external_id":{"pmid":["29525951"]},"article_processing_charge":"No","title":"In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls"},{"title":"Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia","department":[{"_id":"JiFr"}],"editor":[{"full_name":"Ristova, Daniela","last_name":"Ristova","first_name":"Daniela"},{"last_name":"Barbez","full_name":"Barbez, Elke","first_name":"Elke"}],"author":[{"full_name":"Karampelias, Michael","last_name":"Karampelias","first_name":"Michael"},{"last_name":"Tejos","full_name":"Tejos, Ricardo","first_name":"Ricardo"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"}],"publist_id":"7418","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:54:34Z","citation":{"ista":"Karampelias M, Tejos R, Friml J, Vanneste S. 2018.Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Root Development. Methods and Protocols. Methods in Molecular Biology, vol. 1761, 131–143.","chicago":"Karampelias, Michael, Ricardo Tejos, Jiří Friml, and Steffen Vanneste. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” In Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, 1761:131–43. MIMB. Springer, 2018. https://doi.org/10.1007/978-1-4939-7747-5_10.","ieee":"M. Karampelias, R. Tejos, J. Friml, and S. Vanneste, “Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia,” in Root Development. Methods and Protocols, vol. 1761, D. Ristova and E. Barbez, Eds. Springer, 2018, pp. 131–143.","short":"M. Karampelias, R. Tejos, J. Friml, S. Vanneste, in:, D. Ristova, E. Barbez (Eds.), Root Development. Methods and Protocols, Springer, 2018, pp. 131–143.","ama":"Karampelias M, Tejos R, Friml J, Vanneste S. Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Ristova D, Barbez E, eds. Root Development. Methods and Protocols. Vol 1761. MIMB. Springer; 2018:131-143. doi:10.1007/978-1-4939-7747-5_10","apa":"Karampelias, M., Tejos, R., Friml, J., & Vanneste, S. (2018). Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In D. Ristova & E. Barbez (Eds.), Root Development. Methods and Protocols (Vol. 1761, pp. 131–143). Springer. https://doi.org/10.1007/978-1-4939-7747-5_10","mla":"Karampelias, Michael, et al. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, vol. 1761, Springer, 2018, pp. 131–43, doi:10.1007/978-1-4939-7747-5_10."},"status":"public","type":"book_chapter","_id":"411","series_title":"MIMB","date_created":"2018-12-11T11:46:20Z","date_published":"2018-03-11T00:00:00Z","doi":"10.1007/978-1-4939-7747-5_10","volume":1761,"page":"131 - 143","publication":"Root Development. Methods and Protocols","language":[{"iso":"eng"}],"day":"11","year":"2018","publication_status":"published","intvolume":" 1761","month":"03","publisher":"Springer","alternative_title":["Methods in Molecular Biology"],"quality_controlled":"1","scopus_import":1,"oa_version":"None","abstract":[{"text":"Immunolocalization is a valuable tool for cell biology research that allows to rapidly determine the localization and expression levels of endogenous proteins. In plants, whole-mount in situ immunolocalization remains a challenging method, especially in tissues protected by waxy layers and complex cell wall carbohydrates. Here, we present a robust method for whole-mount in situ immunolocalization in primary root meristems and lateral root primordia in Arabidopsis thaliana. For good epitope preservation, fixation is done in an alkaline paraformaldehyde/glutaraldehyde mixture. This fixative is suitable for detecting a wide range of proteins, including integral transmembrane proteins and proteins peripherally attached to the plasma membrane. From initiation until emergence from the primary root, lateral root primordia are surrounded by several layers of differentiated tissues with a complex cell wall composition that interferes with the efficient penetration of all buffers. Therefore, immunolocalization in early lateral root primordia requires a modified method, including a strong solvent treatment for removal of hydrophobic barriers and a specific cocktail of cell wall-degrading enzymes. The presented method allows for easy, reliable, and high-quality in situ detection of the subcellular localization of endogenous proteins in primary and lateral root meristems without the need of time-consuming crosses or making translational fusions to fluorescent proteins.","lang":"eng"}]},{"_id":"456","article_number":"eaar7514","type":"journal_article","status":"public","date_updated":"2021-01-12T07:59:42Z","citation":{"chicago":"Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” Science Translational Medicine. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/scitranslmed.aar7514.","ista":"Novarino G. 2018. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 10(423), eaar7514.","mla":"Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” Science Translational Medicine, vol. 10, no. 423, eaar7514, American Association for the Advancement of Science, 2018, doi:10.1126/scitranslmed.aar7514.","ama":"Novarino G. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 2018;10(423). doi:10.1126/scitranslmed.aar7514","apa":"Novarino, G. (2018). Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aar7514","ieee":"G. Novarino, “Zika-associated microcephaly: Reduce the stress and race for the treatment,” Science Translational Medicine, vol. 10, no. 423. American Association for the Advancement of Science, 2018.","short":"G. Novarino, Science Translational Medicine 10 (2018)."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7365","title":"Zika-associated microcephaly: Reduce the stress and race for the treatment","department":[{"_id":"GaNo"}],"abstract":[{"lang":"eng","text":"Inhibition of the endoplasmic reticulum stress pathway may hold the key to Zika virus-associated microcephaly treatment. "}],"oa_version":"None","quality_controlled":"1","scopus_import":1,"publisher":"American Association for the Advancement of Science","month":"01","intvolume":" 10","year":"2018","publication_status":"published","day":"10","language":[{"iso":"eng"}],"publication":"Science Translational Medicine","volume":10,"doi":"10.1126/scitranslmed.aar7514","date_published":"2018-01-10T00:00:00Z","issue":"423","date_created":"2018-12-11T11:46:34Z"},{"citation":{"short":"B. Petritsch, J. Porsche, VÖB Mitteilungen 71 (2018) 199–206.","ieee":"B. Petritsch and J. Porsche, “IST PubRep and IST DataRep: the institutional repositories at IST Austria,” VÖB Mitteilungen, vol. 71, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 199–206, 2018.","apa":"Petritsch, B., & Porsche, J. (2018). IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v71i1.1993","ama":"Petritsch B, Porsche J. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 2018;71(1):199-206. doi:10.31263/voebm.v71i1.1993","mla":"Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen, vol. 71, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018, pp. 199–206, doi:10.31263/voebm.v71i1.1993.","ista":"Petritsch B, Porsche J. 2018. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 71(1), 199–206.","chicago":"Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018. https://doi.org/10.31263/voebm.v71i1.1993."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"8001","author":[{"last_name":"Petritsch","full_name":"Petritsch, Barbara","orcid":"0000-0003-2724-4614","first_name":"Barbara","id":"406048EC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Porsche","full_name":"Porsche, Jana","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87","first_name":"Jana"}],"title":"IST PubRep and IST DataRep: the institutional repositories at IST Austria","has_accepted_license":"1","year":"2018","day":"01","publication":"VÖB Mitteilungen","page":"199 - 206","date_published":"2018-10-01T00:00:00Z","doi":"10.31263/voebm.v71i1.1993","date_created":"2018-12-11T11:44:22Z","publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","oa":1,"date_updated":"2021-01-12T08:01:26Z","ddc":["020"],"department":[{"_id":"E-Lib"}],"file_date_updated":"2020-07-14T12:46:38Z","_id":"53","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_status":"published","file":[{"file_name":"2018_VOEB_Petritsch.pdf","date_created":"2018-12-17T12:40:27Z","creator":"dernst","file_size":509434,"date_updated":"2020-07-14T12:46:38Z","checksum":"7ac61bade5f37db011ca435ebcf86797","file_id":"5702","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":71,"issue":"1","abstract":[{"text":"In 2013, a publication repository was implemented at IST Austria and 2015 after a thorough preparation phase a data repository was implemented - both based on the Open Source Software EPrints. In this text, designed as field report, we will reflect on our experiences with Open Source Software in general and specifically with EPrints regarding technical aspects but also regarding their characteristics of the user community. The second part is a pleading for including the end users in the process of implementation, adaption and evaluation.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"10","intvolume":" 71"},{"volume":31,"issue":"6","publication_status":"published","publication_identifier":{"issn":["01782770"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5867","checksum":"69b46e537acdcac745237ddb853fcbb5","file_size":595707,"date_updated":"2020-07-14T12:46:38Z","creator":"dernst","file_name":"2017_DistribComp_Alistarh.pdf","date_created":"2019-01-22T07:25:51Z"}],"scopus_import":1,"intvolume":" 31","month":"11","abstract":[{"text":"We consider the problem of consensus in the challenging classic model. In this model, the adversary is adaptive; it can choose which processors crash at any point during the course of the algorithm. Further, communication is via asynchronous message passing: there is no known upper bound on the time to send a message from one processor to another, and all messages and coin flips are seen by the adversary. We describe a new randomized consensus protocol with expected message complexity O(n2log2n) when fewer than n / 2 processes may fail by crashing. This is an almost-linear improvement over the best previously known protocol, and within logarithmic factors of a known Ω(n2) message lower bound. The protocol further ensures that no process sends more than O(nlog3n) messages in expectation, which is again within logarithmic factors of optimal. We also present a generalization of the algorithm to an arbitrary number of failures t, which uses expected O(nt+t2log2t) total messages. Our approach is to build a message-efficient, resilient mechanism for aggregating individual processor votes, implementing the message-passing equivalent of a weak shared coin. Roughly, in our protocol, a processor first announces its votes to small groups, then propagates them to increasingly larger groups as it generates more and more votes. To bound the number of messages that an individual process might have to send or receive, the protocol progressively increases the weight of generated votes. The main technical challenge is bounding the impact of votes that are still “in flight” (generated, but not fully propagated) on the final outcome of the shared coin, especially since such votes might have different weights. We achieve this by leveraging the structure of the algorithm, and a technical argument based on martingale concentration bounds. Overall, we show that it is possible to build an efficient message-passing implementation of a shared coin, and in the process (almost-optimally) solve the classic consensus problem in the asynchronous message-passing model.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:46:38Z","date_updated":"2023-02-23T12:23:25Z","ddc":["000"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"536","page":"489-501","date_created":"2018-12-11T11:47:01Z","doi":"10.1007/s00446-017-0315-1","date_published":"2018-11-01T00:00:00Z","year":"2018","has_accepted_license":"1","publication":"Distributed Computing","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer","article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"James","full_name":"Aspnes, James","last_name":"Aspnes"},{"full_name":"King, Valerie","last_name":"King","first_name":"Valerie"},{"full_name":"Saia, Jared","last_name":"Saia","first_name":"Jared"}],"publist_id":"7281","title":"Communication-efficient randomized consensus","citation":{"chicago":"Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient Randomized Consensus.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-017-0315-1.","ista":"Alistarh D-A, Aspnes J, King V, Saia J. 2018. Communication-efficient randomized consensus. Distributed Computing. 31(6), 489–501.","mla":"Alistarh, Dan-Adrian, et al. “Communication-Efficient Randomized Consensus.” Distributed Computing, vol. 31, no. 6, Springer, 2018, pp. 489–501, doi:10.1007/s00446-017-0315-1.","ieee":"D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient randomized consensus,” Distributed Computing, vol. 31, no. 6. Springer, pp. 489–501, 2018.","short":"D.-A. Alistarh, J. Aspnes, V. King, J. Saia, Distributed Computing 31 (2018) 489–501.","apa":"Alistarh, D.-A., Aspnes, J., King, V., & Saia, J. (2018). Communication-efficient randomized consensus. Distributed Computing. Springer. https://doi.org/10.1007/s00446-017-0315-1","ama":"Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized consensus. Distributed Computing. 2018;31(6):489-501. doi:10.1007/s00446-017-0315-1"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}]},{"page":"347-403","date_created":"2018-12-11T11:47:09Z","doi":"10.1007/s00220-017-3064-x","date_published":"2018-05-01T00:00:00Z","year":"2018","publication":"Communications in Mathematical Physics","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer","external_id":{"arxiv":["1511.05953"]},"author":[{"last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin M"},{"first_name":"Robin","full_name":"Reuvers, Robin","last_name":"Reuvers"},{"first_name":"Jan","full_name":"Solovej, Jan","last_name":"Solovej"}],"publist_id":"7260","title":"The Bogoliubov free energy functional II: The dilute Limit","citation":{"mla":"Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” Communications in Mathematical Physics, vol. 360, no. 1, Springer, 2018, pp. 347–403, doi:10.1007/s00220-017-3064-x.","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-017-3064-x","ama":"Napiórkowski MM, Reuvers R, Solovej J. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 2018;360(1):347-403. doi:10.1007/s00220-017-3064-x","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical Physics 360 (2018) 347–403.","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “The Bogoliubov free energy functional II: The dilute Limit,” Communications in Mathematical Physics, vol. 360, no. 1. Springer, pp. 347–403, 2018.","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” Communications in Mathematical Physics. Springer, 2018. https://doi.org/10.1007/s00220-017-3064-x.","ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 360(1), 347–403."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"}],"issue":"1","volume":360,"publication_status":"published","publication_identifier":{"issn":["00103616"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1511.05953","open_access":"1"}],"scopus_import":1,"intvolume":" 360","month":"05","abstract":[{"text":"We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a first-order phase transition and, in the limit (Formula presented.), we determine the critical temperature to be (Formula presented.) to leading order. Here, (Formula presented.) is the critical temperature of the free Bose gas, ρ is the density of the gas and a is the scattering length of the pair-interaction potential V. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula in the limit (Formula presented.).","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T08:02:35Z","type":"journal_article","status":"public","_id":"554"},{"oa":1,"quality_controlled":"1","publisher":"Springer","publication":"Neurotrophic Factors","day":"01","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:47:11Z","date_published":"2018-01-01T00:00:00Z","doi":"10.1007/978-1-4939-7571-6_15","page":"201 - 215","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. 2018.Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Neurotrophic Factors. Methods in Molecular Biology, vol. 1727, 201–215.","chicago":"Dimitrov, Dimitar, Laurent Guillaud, Kohgaku Eguchi, and Tomoyuki Takahashi. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” In Neurotrophic Factors, edited by Stephen D. Skaper, 1727:201–15. Springer, 2018. https://doi.org/10.1007/978-1-4939-7571-6_15.","short":"D. Dimitrov, L. Guillaud, K. Eguchi, T. Takahashi, in:, S.D. Skaper (Ed.), Neurotrophic Factors, Springer, 2018, pp. 201–215.","ieee":"D. Dimitrov, L. Guillaud, K. Eguchi, and T. Takahashi, “Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses,” in Neurotrophic Factors, vol. 1727, S. D. Skaper, Ed. Springer, 2018, pp. 201–215.","ama":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Skaper SD, ed. Neurotrophic Factors. Vol 1727. Springer; 2018:201-215. doi:10.1007/978-1-4939-7571-6_15","apa":"Dimitrov, D., Guillaud, L., Eguchi, K., & Takahashi, T. (2018). Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In S. D. Skaper (Ed.), Neurotrophic Factors (Vol. 1727, pp. 201–215). Springer. https://doi.org/10.1007/978-1-4939-7571-6_15","mla":"Dimitrov, Dimitar, et al. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” Neurotrophic Factors, edited by Stephen D. Skaper, vol. 1727, Springer, 2018, pp. 201–15, doi:10.1007/978-1-4939-7571-6_15."},"title":"Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses","editor":[{"first_name":"Stephen D.","full_name":"Skaper, Stephen D.","last_name":"Skaper"}],"article_processing_charge":"No","external_id":{"pmid":["29222783"]},"author":[{"first_name":"Dimitar","last_name":"Dimitrov","full_name":"Dimitrov, Dimitar"},{"first_name":"Laurent","last_name":"Guillaud","full_name":"Guillaud, Laurent"},{"full_name":"Eguchi, Kohgaku","orcid":"0000-0002-6170-2546","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku"},{"last_name":"Takahashi","full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki"}],"publist_id":"7252","pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Primary neuronal cell culture preparations are widely used to investigate synaptic functions. This chapter describes a detailed protocol for the preparation of a neuronal cell culture in which giant calyx-type synaptic terminals are formed. This chapter also presents detailed protocols for utilizing the main technical advantages provided by such a preparation, namely, labeling and imaging of synaptic organelles and electrophysiological recordings directly from presynaptic terminals.","lang":"eng"}],"intvolume":" 1727","month":"01","alternative_title":["Methods in Molecular Biology"],"scopus_import":1,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7046","checksum":"8aa174ca65a56fbb19e9f88cff3ac3fd","file_size":787407,"date_updated":"2020-07-14T12:47:09Z","creator":"dernst","file_name":"2018_NeurotrophicFactors_Dimitrov.pdf","date_created":"2019-11-19T07:47:43Z"}],"publication_status":"published","volume":1727,"_id":"562","status":"public","type":"book_chapter","ddc":["570"],"date_updated":"2021-01-12T08:03:05Z","department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:47:09Z"},{"_id":"59","status":"public","type":"book_chapter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bloem, Roderick, et al. “Graph Games and Reactive Synthesis.” Handbook of Model Checking, edited by Thomas A Henzinger et al., 1st ed., Springer, 2018, pp. 921–62, doi:10.1007/978-3-319-10575-8_27.","short":"R. Bloem, K. Chatterjee, B. Jobstmann, in:, T.A. Henzinger, E.M. Clarke, H. Veith, R. Bloem (Eds.), Handbook of Model Checking, 1st ed., Springer, 2018, pp. 921–962.","ieee":"R. Bloem, K. Chatterjee, and B. Jobstmann, “Graph games and reactive synthesis,” in Handbook of Model Checking, 1st ed., T. A. Henzinger, E. M. Clarke, H. Veith, and R. Bloem, Eds. Springer, 2018, pp. 921–962.","apa":"Bloem, R., Chatterjee, K., & Jobstmann, B. (2018). Graph games and reactive synthesis. In T. A. Henzinger, E. M. Clarke, H. Veith, & R. Bloem (Eds.), Handbook of Model Checking (1st ed., pp. 921–962). Springer. https://doi.org/10.1007/978-3-319-10575-8_27","ama":"Bloem R, Chatterjee K, Jobstmann B. Graph games and reactive synthesis. In: Henzinger TA, Clarke EM, Veith H, Bloem R, eds. Handbook of Model Checking. 1st ed. Springer; 2018:921-962. doi:10.1007/978-3-319-10575-8_27","chicago":"Bloem, Roderick, Krishnendu Chatterjee, and Barbara Jobstmann. “Graph Games and Reactive Synthesis.” In Handbook of Model Checking, edited by Thomas A Henzinger, Edmund M. Clarke, Helmut Veith, and Roderick Bloem, 1st ed., 921–62. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_27.","ista":"Bloem R, Chatterjee K, Jobstmann B. 2018.Graph games and reactive synthesis. In: Handbook of Model Checking. , 921–962."},"date_updated":"2021-01-12T08:05:10Z","department":[{"_id":"KrCh"}],"title":"Graph games and reactive synthesis","editor":[{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Edmund M.","full_name":"Clarke, Edmund M.","last_name":"Clarke"},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"},{"last_name":"Bloem","full_name":"Bloem, Roderick","first_name":"Roderick"}],"publist_id":"7995","author":[{"last_name":"Bloem","full_name":"Bloem, Roderick","first_name":"Roderick"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Jobstmann, Barbara","last_name":"Jobstmann","first_name":"Barbara"}],"oa_version":"None","abstract":[{"lang":"eng","text":"Graph-based games are an important tool in computer science. They have applications in synthesis, verification, refinement, and far beyond. We review graphbased games with objectives on infinite plays. We give definitions and algorithms to solve the games and to give a winning strategy. The objectives we consider are mostly Boolean, but we also look at quantitative graph-based games and their objectives. Synthesis aims to turn temporal logic specifications into correct reactive systems. We explain the reduction of synthesis to graph-based games (or equivalently tree automata) using synthesis of LTL specifications as an example. We treat the classical approach that uses determinization of parity automata and more modern approaches."}],"month":"05","publisher":"Springer","scopus_import":1,"quality_controlled":"1","edition":"1","day":"19","publication":"Handbook of Model Checking","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-319-10574-1"]},"year":"2018","publication_status":"published","date_published":"2018-05-19T00:00:00Z","doi":"10.1007/978-3-319-10575-8_27","date_created":"2018-12-11T11:44:24Z","page":"921 - 962"},{"publication":"Handbook of Model Checking","language":[{"iso":"eng"}],"day":"19","year":"2018","publication_status":"published","date_created":"2018-12-11T11:44:25Z","date_published":"2018-05-19T00:00:00Z","doi":"10.1007/978-3-319-10575-8_1","page":"1 - 26","oa_version":"None","abstract":[{"text":"Model checking is a computer-assisted method for the analysis of dynamical systems that can be modeled by state-transition systems. Drawing from research traditions in mathematical logic, programming languages, hardware design, and theoretical computer science, model checking is now widely used for the verification of hardware and software in industry. This chapter is an introduction and short survey of model checking. The chapter aims to motivate and link the individual chapters of the handbook, and to provide context for readers who are not familiar with model checking.","lang":"eng"}],"month":"05","quality_controlled":"1","scopus_import":1,"publisher":"Springer","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Clarke E, Henzinger TA, Veith H. 2018.Introduction to model checking. In: Handbook of Model Checking. , 1–26.","chicago":"Clarke, Edmund, Thomas A Henzinger, and Helmut Veith. “Introduction to Model Checking.” In Handbook of Model Checking, edited by Thomas A Henzinger, 1–26. Handbook of Model Checking. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_1.","ama":"Clarke E, Henzinger TA, Veith H. Introduction to model checking. In: Henzinger TA, ed. Handbook of Model Checking. Handbook of Model Checking. Springer; 2018:1-26. doi:10.1007/978-3-319-10575-8_1","apa":"Clarke, E., Henzinger, T. A., & Veith, H. (2018). Introduction to model checking. In T. A. Henzinger (Ed.), Handbook of Model Checking (pp. 1–26). Springer. https://doi.org/10.1007/978-3-319-10575-8_1","short":"E. Clarke, T.A. Henzinger, H. Veith, in:, T.A. Henzinger (Ed.), Handbook of Model Checking, Springer, 2018, pp. 1–26.","ieee":"E. Clarke, T. A. Henzinger, and H. Veith, “Introduction to model checking,” in Handbook of Model Checking, T. A. Henzinger, Ed. Springer, 2018, pp. 1–26.","mla":"Clarke, Edmund, et al. “Introduction to Model Checking.” Handbook of Model Checking, edited by Thomas A Henzinger, Springer, 2018, pp. 1–26, doi:10.1007/978-3-319-10575-8_1."},"date_updated":"2021-01-12T08:05:35Z","editor":[{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"department":[{"_id":"ToHe"}],"title":"Introduction to model checking","author":[{"last_name":"Clarke","full_name":"Clarke, Edmund","first_name":"Edmund"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Helmut","full_name":"Veith, Helmut","last_name":"Veith"}],"publist_id":"7994","_id":"60","series_title":"Handbook of Model Checking","status":"public","type":"book_chapter"},{"page":"131 - 134","doi":"10.1007/978-3-319-72456-0_7","date_published":"2018-05-23T00:00:00Z","date_created":"2018-12-11T11:44:25Z","year":"2018","publication_status":"published","day":"23","publication":"Contemporary Computational Mathematics","language":[{"iso":"eng"}],"publisher":"Springer","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1509.06286","open_access":"1"}],"oa":1,"month":"05","abstract":[{"lang":"eng","text":"We prove that there is no strongly regular graph (SRG) with parameters (460; 153; 32; 60). The proof is based on a recent lower bound on the number of 4-cliques in a SRG and some applications of Euclidean representation of SRGs. "}],"oa_version":"Preprint","publist_id":"7993","author":[{"first_name":"Andriy","full_name":"Bondarenko, Andriy","last_name":"Bondarenko"},{"last_name":"Mellit","full_name":"Mellit, Anton","id":"388D3134-F248-11E8-B48F-1D18A9856A87","first_name":"Anton"},{"full_name":"Prymak, Andriy","last_name":"Prymak","first_name":"Andriy"},{"first_name":"Danylo","last_name":"Radchenko","full_name":"Radchenko, Danylo"},{"full_name":"Viazovska, Maryna","last_name":"Viazovska","first_name":"Maryna"}],"article_processing_charge":"No","external_id":{"arxiv":["1509.06286"]},"department":[{"_id":"TaHa"}],"title":"There is no strongly regular graph with parameters (460; 153; 32; 60)","citation":{"mla":"Bondarenko, Andriy, et al. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” Contemporary Computational Mathematics, Springer, 2018, pp. 131–34, doi:10.1007/978-3-319-72456-0_7.","apa":"Bondarenko, A., Mellit, A., Prymak, A., Radchenko, D., & Viazovska, M. (2018). There is no strongly regular graph with parameters (460; 153; 32; 60). In Contemporary Computational Mathematics (pp. 131–134). Springer. https://doi.org/10.1007/978-3-319-72456-0_7","ama":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. Springer; 2018:131-134. doi:10.1007/978-3-319-72456-0_7","ieee":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, and M. Viazovska, “There is no strongly regular graph with parameters (460; 153; 32; 60),” in Contemporary Computational Mathematics, Springer, 2018, pp. 131–134.","short":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, M. Viazovska, in:, Contemporary Computational Mathematics, Springer, 2018, pp. 131–134.","chicago":"Bondarenko, Andriy, Anton Mellit, Andriy Prymak, Danylo Radchenko, and Maryna Viazovska. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” In Contemporary Computational Mathematics, 131–34. Springer, 2018. https://doi.org/10.1007/978-3-319-72456-0_7.","ista":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. 2018.There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. , 131–134."},"date_updated":"2021-01-12T08:06:06Z","extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","status":"public","_id":"61"},{"abstract":[{"text":"Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow.","lang":"eng"}],"oa_version":"Published Version","intvolume":" 8","month":"09","publication_status":"published","publication_identifier":{"issn":["2331-8325"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:28Z","file_size":2928337,"creator":"dernst","date_created":"2019-04-30T08:04:33Z","file_name":"2018_BioProtocol_Fan.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"d4588377e789da7f360b553ae02c5119","file_id":"6360"}],"ec_funded":1,"volume":8,"issue":"18","_id":"6354","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","keyword":["Platelets","Cell migration","Bacteria","Shear flow","Fibrinogen","E. coli"],"status":"public","date_updated":"2021-01-12T08:07:12Z","ddc":["570"],"department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:47:28Z","acknowledgement":" FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.)","oa":1,"quality_controlled":"1","publisher":"Bio-Protocol","year":"2018","has_accepted_license":"1","publication":"Bio-Protocol","day":"20","date_created":"2019-04-29T09:40:33Z","doi":"10.21769/bioprotoc.3018","date_published":"2018-09-20T00:00:00Z","article_number":"e3018","project":[{"grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 8(18), e3018.","chicago":"Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol, 2018. https://doi.org/10.21769/bioprotoc.3018.","short":"S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018).","ieee":"S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol, 2018.","apa":"Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018","ama":"Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018","mla":"Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Shuxia","full_name":"Fan, Shuxia","last_name":"Fan"},{"full_name":"Lorenz, Michael","last_name":"Lorenz","first_name":"Michael"},{"full_name":"Massberg, Steffen","last_name":"Massberg","first_name":"Steffen"},{"id":"397A88EE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian R","orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R","last_name":"Gärtner"}],"title":"Platelet migration and bacterial trapping assay under flow"},{"author":[{"orcid":"0000-0003-2724-4614","full_name":"Petritsch, Barbara","last_name":"Petritsch","first_name":"Barbara","id":"406048EC-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:30Z","title":"Open Access at IST Austria 2009-2017","department":[{"_id":"E-Lib"}],"date_updated":"2020-07-14T23:06:21Z","citation":{"chicago":"Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018. https://doi.org/10.5281/zenodo.1410279.","ista":"Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p.","mla":"Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018, doi:10.5281/zenodo.1410279.","apa":"Petritsch, B. (2018). Open Access at IST Austria 2009-2017. Presented at the Open-Access-Tage, Graz, Austria: IST Austria. https://doi.org/10.5281/zenodo.1410279","ama":"Petritsch B. Open Access at IST Austria 2009-2017. IST Austria; 2018. doi:10.5281/zenodo.1410279","short":"B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018.","ieee":"B. Petritsch, Open Access at IST Austria 2009-2017. IST Austria, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["020"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2018-09-24","location":"Graz, Austria","end_date":"2018-09-26","name":"Open-Access-Tage"},"type":"conference_poster","keyword":["Open Access","Publication Analysis"],"status":"public","_id":"6459","date_created":"2019-05-16T07:27:14Z","date_published":"2018-09-24T00:00:00Z","doi":"10.5281/zenodo.1410279","year":"2018","publication_status":"published","has_accepted_license":"1","language":[{"iso":"eng"}],"day":"24","file":[{"file_size":1967778,"date_updated":"2020-07-14T12:47:30Z","creator":"dernst","file_name":"Poster_Beitrag_125_Petritsch.pdf","date_created":"2019-05-16T07:26:25Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"9063ab4d10ea93353c3a03bbf53fbcf1","file_id":"6460"}],"oa":1,"publisher":"IST Austria","month":"09","oa_version":"Published Version"},{"month":"01","scopus_import":1,"publisher":"Oxford University Press","quality_controlled":"1","oa_version":"None","abstract":[{"text":"This chapter finds an agreement of equivariant indices of semi-classical homomorphisms between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface. On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs bundles, whose mirror was proposed by Hitchin to be certain even exterior powers of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present. The agreement arises from a mysterious functional equation. This gives strong computational evidence for Hitchin’s proposal.","lang":"eng"}],"doi":"10.1093/oso/9780198802013.003.0009","date_published":"2018-01-01T00:00:00Z","date_created":"2019-06-06T12:42:01Z","page":"189-218","day":"01","language":[{"iso":"eng"}],"publication":"Geometry and Physics: Volume I","publication_identifier":{"isbn":["9780198802013","9780191840500"]},"publication_status":"published","year":"2018","status":"public","type":"book_chapter","_id":"6525","title":"Mirror symmetry with branes by equivariant verlinde formulas","department":[{"_id":"TaHa"}],"author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamás","last_name":"Hausel","full_name":"Hausel, Tamás"},{"id":"388D3134-F248-11E8-B48F-1D18A9856A87","first_name":"Anton","last_name":"Mellit","full_name":"Mellit, Anton"},{"first_name":"Du","full_name":"Pei, Du","last_name":"Pei"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Hausel T, Mellit A, Pei D. Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. Oxford University Press; 2018:189-218. doi:10.1093/oso/9780198802013.003.0009","apa":"Hausel, T., Mellit, A., & Pei, D. (2018). Mirror symmetry with branes by equivariant verlinde formulas. In Geometry and Physics: Volume I (pp. 189–218). Oxford University Press. https://doi.org/10.1093/oso/9780198802013.003.0009","ieee":"T. Hausel, A. Mellit, and D. Pei, “Mirror symmetry with branes by equivariant verlinde formulas,” in Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.","short":"T. Hausel, A. Mellit, D. Pei, in:, Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.","mla":"Hausel, Tamás, et al. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218, doi:10.1093/oso/9780198802013.003.0009.","ista":"Hausel T, Mellit A, Pei D. 2018.Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. , 189–218.","chicago":"Hausel, Tamás, Anton Mellit, and Du Pei. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” In Geometry and Physics: Volume I, 189–218. Oxford University Press, 2018. https://doi.org/10.1093/oso/9780198802013.003.0009."},"date_updated":"2021-01-12T08:07:52Z"},{"department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T08:09:33Z","status":"public","type":"journal_article","_id":"690","ec_funded":1,"volume":171,"issue":"1-2","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 171","month":"06","main_file_link":[{"url":"https://arxiv.org/abs/1605.08767","open_access":"1"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"We consider spectral properties and the edge universality of sparse random matrices, the class of random matrices that includes the adjacency matrices of the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density up to the spectral edges. Under a suitable condition on the sparsity, we also prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations if a deterministic shift of the spectral edge due to the sparsity is included. For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom fluctuations of the second largest eigenvalue when p is much larger than N−2/3 with a deterministic shift of order (Np)−1.","lang":"eng"}],"title":"Local law and Tracy–Widom limit for sparse random matrices","external_id":{"arxiv":["1605.08767"]},"author":[{"first_name":"Jii","last_name":"Lee","full_name":"Lee, Jii"},{"orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","last_name":"Schnelli","first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields, vol. 171, no. 1–2, 543–616, Springer, 2018, doi:10.1007/s00440-017-0787-8.","ieee":"J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random matrices,” Probability Theory and Related Fields, vol. 171, no. 1–2. Springer, 2018.","short":"J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018).","apa":"Lee, J., & Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-017-0787-8","ama":"Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 2018;171(1-2). doi:10.1007/s00440-017-0787-8","chicago":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields. Springer, 2018. https://doi.org/10.1007/s00440-017-0787-8.","ista":"Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 171(1–2), 543–616."},"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"article_number":"543-616","date_created":"2018-12-11T11:47:56Z","date_published":"2018-06-14T00:00:00Z","doi":"10.1007/s00440-017-0787-8","publication":"Probability Theory and Related Fields","day":"14","year":"2018","oa":1,"quality_controlled":"1","publisher":"Springer"},{"title":"Maximum persistency via iterative relaxed inference with graphical models","author":[{"full_name":"Shekhovtsov, Alexander","last_name":"Shekhovtsov","first_name":"Alexander"},{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","last_name":"Swoboda","full_name":"Swoboda, Paul"},{"last_name":"Savchynskyy","full_name":"Savchynskyy, Bogdan","first_name":"Bogdan"}],"publist_id":"6992","external_id":{"arxiv":["1508.07902"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Shekhovtsov, Alexander, et al. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7, IEEE, 2018, pp. 1668–82, doi:10.1109/TPAMI.2017.2730884.","ama":"Shekhovtsov A, Swoboda P, Savchynskyy B. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2018;40(7):1668-1682. doi:10.1109/TPAMI.2017.2730884","apa":"Shekhovtsov, A., Swoboda, P., & Savchynskyy, B. (2018). Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2017.2730884","ieee":"A. Shekhovtsov, P. Swoboda, and B. Savchynskyy, “Maximum persistency via iterative relaxed inference with graphical models,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7. IEEE, pp. 1668–1682, 2018.","short":"A. Shekhovtsov, P. Swoboda, B. Savchynskyy, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1668–1682.","chicago":"Shekhovtsov, Alexander, Paul Swoboda, and Bogdan Savchynskyy. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2017.2730884.","ista":"Shekhovtsov A, Swoboda P, Savchynskyy B. 2018. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(7), 1668–1682."},"date_published":"2018-07-01T00:00:00Z","doi":"10.1109/TPAMI.2017.2730884","date_created":"2018-12-11T11:48:01Z","page":"1668-1682","day":"01","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","year":"2018","publisher":"IEEE","quality_controlled":"1","oa":1,"department":[{"_id":"VlKo"}],"date_updated":"2021-01-12T08:11:32Z","status":"public","type":"journal_article","_id":"703","volume":40,"issue":"7","language":[{"iso":"eng"}],"publication_identifier":{"issn":["01628828"]},"publication_status":"published","month":"07","intvolume":" 40","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1508.07902","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"We consider the NP-hard problem of MAP-inference for undirected discrete graphical models. We propose a polynomial time and practically efficient algorithm for finding a part of its optimal solution. Specifically, our algorithm marks some labels of the considered graphical model either as (i) optimal, meaning that they belong to all optimal solutions of the inference problem; (ii) non-optimal if they provably do not belong to any solution. With access to an exact solver of a linear programming relaxation to the MAP-inference problem, our algorithm marks the maximal possible (in a specified sense) number of labels. We also present a version of the algorithm, which has access to a suboptimal dual solver only and still can ensure the (non-)optimality for the marked labels, although the overall number of the marked labels may decrease. We propose an efficient implementation, which runs in time comparable to a single run of a suboptimal dual solver. Our method is well-scalable and shows state-of-the-art results on computational benchmarks from machine learning and computer vision.","lang":"eng"}]},{"date_created":"2019-11-26T14:19:11Z","doi":"10.5441/002/EDBT.2018.14","date_published":"2018-03-26T00:00:00Z","page":"145-156","publication":"Proceedings of the 21st International Conference on Extending Database Technology","day":"26","year":"2018","has_accepted_license":"1","oa":1,"publisher":"OpenProceedings","quality_controlled":"1","title":"Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study","article_processing_charge":"No","author":[{"full_name":"Grubic, Demjan","last_name":"Grubic","first_name":"Demjan"},{"full_name":"Tam, Leo","last_name":"Tam","first_name":"Leo"},{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"Ce","last_name":"Zhang","full_name":"Zhang, Ce"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Grubic D, Tam L, Alistarh D-A, Zhang C. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In: Proceedings of the 21st International Conference on Extending Database Technology. OpenProceedings; 2018:145-156. doi:10.5441/002/EDBT.2018.14","apa":"Grubic, D., Tam, L., Alistarh, D.-A., & Zhang, C. (2018). Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In Proceedings of the 21st International Conference on Extending Database Technology (pp. 145–156). Vienna, Austria: OpenProceedings. https://doi.org/10.5441/002/EDBT.2018.14","short":"D. Grubic, L. Tam, D.-A. Alistarh, C. Zhang, in:, Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–156.","ieee":"D. Grubic, L. Tam, D.-A. Alistarh, and C. Zhang, “Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study,” in Proceedings of the 21st International Conference on Extending Database Technology, Vienna, Austria, 2018, pp. 145–156.","mla":"Grubic, Demjan, et al. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–56, doi:10.5441/002/EDBT.2018.14.","ista":"Grubic D, Tam L, Alistarh D-A, Zhang C. 2018. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. Proceedings of the 21st International Conference on Extending Database Technology. EDBT: Conference on Extending Database Technology, 145–156.","chicago":"Grubic, Demjan, Leo Tam, Dan-Adrian Alistarh, and Ce Zhang. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” In Proceedings of the 21st International Conference on Extending Database Technology, 145–56. OpenProceedings, 2018. https://doi.org/10.5441/002/EDBT.2018.14."},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","language":[{"iso":"eng"}],"file":[{"file_size":1603204,"date_updated":"2020-07-14T12:47:49Z","creator":"dernst","file_name":"2018_OpenProceedings_Grubic.pdf","date_created":"2019-11-26T14:23:04Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7118","checksum":"ec979b56abc71016d6e6adfdadbb4afe"}],"publication_status":"published","publication_identifier":{"issn":["2367-2005"],"isbn":["9783893180783"]},"month":"03","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Training deep learning models has received tremendous research interest recently. In particular, there has been intensive research on reducing the communication cost of training when using multiple computational devices, through reducing the precision of the underlying data representation. Naturally, such methods induce system trade-offs—lowering communication precision could de-crease communication overheads and improve scalability; but, on the other hand, it can also reduce the accuracy of training. In this paper, we study this trade-off space, and ask:Can low-precision communication consistently improve the end-to-end performance of training modern neural networks, with no accuracy loss?From the performance point of view, the answer to this question may appear deceptively easy: compressing communication through low precision should help when the ratio between communication and computation is high. However, this answer is less straightforward when we try to generalize this principle across various neural network architectures (e.g., AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g., EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL), and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is not clear how a realistic realization of all these factors maps to the speed up provided by low-precision communication. In this paper, we conduct an empirical study to answer this question and report the insights."}],"file_date_updated":"2020-07-14T12:47:49Z","department":[{"_id":"DaAl"}],"ddc":["000"],"date_updated":"2023-02-23T12:59:17Z","status":"public","conference":{"start_date":"2018-03-26","location":"Vienna, Austria","end_date":"2018-03-29","name":"EDBT: Conference on Extending Database Technology"},"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"conference","_id":"7116"},{"month":"12","intvolume":" 124","scopus_import":1,"alternative_title":["LIPIcs"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/194"}],"oa_version":"Published Version","abstract":[{"text":"Proofs of space (PoS) [Dziembowski et al., CRYPTO'15] are proof systems where a prover can convince a verifier that he \"wastes\" disk space. PoS were introduced as a more ecological and economical replacement for proofs of work which are currently used to secure blockchains like Bitcoin. In this work we investigate extensions of PoS which allow the prover to embed useful data into the dedicated space, which later can be recovered. Our first contribution is a security proof for the original PoS from CRYPTO'15 in the random oracle model (the original proof only applied to a restricted class of adversaries which can store a subset of the data an honest prover would store). When this PoS is instantiated with recent constructions of maximally depth robust graphs, our proof implies basically optimal security. As a second contribution we show three different extensions of this PoS where useful data can be embedded into the space required by the prover. Our security proof for the PoS extends (non-trivially) to these constructions. We discuss how some of these variants can be used as proofs of catalytic space (PoCS), a notion we put forward in this work, and which basically is a PoS where most of the space required by the prover can be used to backup useful data. Finally we discuss how one of the extensions is a candidate construction for a proof of replication (PoR), a proof system recently suggested in the Filecoin whitepaper. ","lang":"eng"}],"volume":124,"ec_funded":1,"file":[{"file_id":"7443","checksum":"5cebb7f7849a3beda898f697d755dd96","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-02-04T08:17:52Z","file_name":"2018_LIPIcs_Pietrzak.pdf","date_updated":"2020-07-14T12:47:57Z","file_size":822884,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-095-8"]},"publication_status":"published","status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2019-01-10","end_date":"2019-01-12","location":"San Diego, CA, United States","name":"ITCS: Innovations in theoretical Computer Science Conference"},"_id":"7407","file_date_updated":"2020-07-14T12:47:57Z","department":[{"_id":"KrPi"}],"ddc":["000"],"date_updated":"2021-01-12T08:13:26Z","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"date_published":"2018-12-31T00:00:00Z","doi":"10.4230/LIPICS.ITCS.2019.59","date_created":"2020-01-30T09:16:05Z","page":"59:1-59:25","day":"31","publication":"10th Innovations in Theoretical Computer Science Conference (ITCS 2019)","has_accepted_license":"1","year":"2018","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"title":"Proofs of catalytic space","author":[{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), 124:59:1-59:25. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ITCS.2019.59.","ista":"Pietrzak KZ. 2018. Proofs of catalytic space. 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). ITCS: Innovations in theoretical Computer Science Conference, LIPIcs, vol. 124, 59:1-59:25.","mla":"Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), vol. 124, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25, doi:10.4230/LIPICS.ITCS.2019.59.","ieee":"K. Z. Pietrzak, “Proofs of catalytic space,” in 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), San Diego, CA, United States, 2018, vol. 124, p. 59:1-59:25.","short":"K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25.","apa":"Pietrzak, K. Z. (2018). Proofs of catalytic space. In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019) (Vol. 124, p. 59:1-59:25). San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.59","ama":"Pietrzak KZ. Proofs of catalytic space. In: 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:59:1-59:25. doi:10.4230/LIPICS.ITCS.2019.59"}},{"day":"01","publication":"ACM Transactions on Parallel Computing","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2329-4949"]},"publication_status":"published","year":"2018","issue":"4","related_material":{"record":[{"relation":"earlier_version","id":"779","status":"public"}]},"doi":"10.1145/3201897","date_published":"2018-09-01T00:00:00Z","volume":4,"date_created":"2019-02-14T13:24:11Z","oa_version":"None","abstract":[{"text":"The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem; existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU are either prohibitively expensive or require significant programming expertise to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated.\r\nIn this article, we take a new approach to concurrent memory reclamation. Instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm, called ThreadScan, leverages operating system signaling to automatically detect which memory locations are being accessed by concurrent threads.\r\nInitial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free.","lang":"eng"}],"month":"09","intvolume":" 4","scopus_import":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T13:17:54Z","citation":{"chicago":"Alistarh, Dan-Adrian, William Leiserson, Alexander Matveev, and Nir Shavit. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing. Association for Computing Machinery, 2018. https://doi.org/10.1145/3201897.","ista":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. 2018. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 4(4), 18.","mla":"Alistarh, Dan-Adrian, et al. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing, vol. 4, no. 4, 18, Association for Computing Machinery, 2018, doi:10.1145/3201897.","apa":"Alistarh, D.-A., Leiserson, W., Matveev, A., & Shavit, N. (2018). ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. Association for Computing Machinery. https://doi.org/10.1145/3201897","ama":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 2018;4(4). doi:10.1145/3201897","short":"D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, ACM Transactions on Parallel Computing 4 (2018).","ieee":"D.-A. Alistarh, W. Leiserson, A. Matveev, and N. Shavit, “ThreadScan: Automatic and scalable memory reclamation,” ACM Transactions on Parallel Computing, vol. 4, no. 4. Association for Computing Machinery, 2018."},"department":[{"_id":"DaAl"}],"title":"ThreadScan: Automatic and scalable memory reclamation","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"first_name":"William","last_name":"Leiserson","full_name":"Leiserson, William"},{"first_name":"Alexander","last_name":"Matveev","full_name":"Matveev, Alexander"},{"first_name":"Nir","full_name":"Shavit, Nir","last_name":"Shavit"}],"article_number":"18","_id":"6001","status":"public","type":"journal_article"},{"date_created":"2020-05-10T22:00:51Z","date_published":"2018-05-01T00:00:00Z","publication":"6th International Conference on Learning Representations","language":[{"iso":"eng"}],"day":"01","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7894","checksum":"a4336c167978e81891970e4e4517a8c3","date_updated":"2020-07-14T12:48:03Z","file_size":308339,"creator":"dernst","date_created":"2020-05-26T13:02:00Z","file_name":"2018_ICLR_Polino.pdf"}],"publication_status":"published","year":"2018","has_accepted_license":"1","month":"05","oa":1,"scopus_import":1,"quality_controlled":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method, differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model. We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices."}],"file_date_updated":"2020-07-14T12:48:03Z","title":"Model compression via distillation and quantization","department":[{"_id":"DaAl"}],"article_processing_charge":"No","external_id":{"arxiv":["1802.05668"]},"author":[{"last_name":"Polino","full_name":"Polino, Antonio","first_name":"Antonio"},{"first_name":"Razvan","last_name":"Pascanu","full_name":"Pascanu, Razvan"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"date_updated":"2023-02-23T13:18:41Z","citation":{"ista":"Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation and quantization. 6th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","chicago":"Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In 6th International Conference on Learning Representations, 2018.","apa":"Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via distillation and quantization. In 6th International Conference on Learning Representations. Vancouver, Canada.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: 6th International Conference on Learning Representations. ; 2018.","short":"A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018.","ieee":"A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018.","mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” 6th International Conference on Learning Representations, 2018."},"status":"public","conference":{"start_date":"2018-04-30","end_date":"2018-05-03","location":"Vancouver, Canada","name":"ICLR: International Conference on Learning Representations"},"type":"conference","_id":"7812"},{"acknowledgement":"We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme.","oa_version":"Preprint","abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex."}],"month":"12","oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/494088","open_access":"1"}],"publisher":"Cold Spring Harbor Laboratory","publication":"bioRxiv","language":[{"iso":"eng"}],"day":"13","year":"2018","publication_status":"submitted","ec_funded":1,"date_created":"2020-09-21T12:01:50Z","doi":"10.1101/494088","date_published":"2018-12-13T00:00:00Z","_id":"8547","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02416","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex"}],"status":"public","type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, 10.1101/494088.","mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/494088.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.).","ieee":"A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor Laboratory.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/494088","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088"},"date_updated":"2021-01-12T08:20:00Z","title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","department":[{"_id":"SiHi"}],"article_processing_charge":"No","author":[{"first_name":"Alfredo","full_name":"Llorca, Alfredo","last_name":"Llorca"},{"first_name":"Gabriele","last_name":"Ciceri","full_name":"Ciceri, Gabriele"},{"first_name":"Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J"},{"last_name":"Wong","full_name":"Wong, Fong K.","first_name":"Fong K."},{"last_name":"Diana","full_name":"Diana, Giovanni","first_name":"Giovanni"},{"first_name":"Eleni","last_name":"Serafeimidou","full_name":"Serafeimidou, Eleni"},{"first_name":"Marian","full_name":"Fernández-Otero, Marian","last_name":"Fernández-Otero"},{"last_name":"Streicher","full_name":"Streicher, Carmen","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Arnold","full_name":"Arnold, Sebastian J.","first_name":"Sebastian J."},{"first_name":"Martin","full_name":"Meyer, Martin","last_name":"Meyer"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"full_name":"Maravall, Miguel","last_name":"Maravall","first_name":"Miguel"},{"full_name":"Marín, Oscar","last_name":"Marín","first_name":"Oscar"}]}]