[{"publication":"Advanced Materials","date_created":"2019-02-14T12:14:26Z","type":"journal_article","department":[{"_id":"GeKa"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","volume":30,"quality_controlled":"1","external_id":{"arxiv":["1809.08487"],"isi":["000450232800015"]},"day":"02","author":[{"full_name":"Ridderbos, Joost","first_name":"Joost","last_name":"Ridderbos"},{"first_name":"Matthias","last_name":"Brauns","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","full_name":"Brauns, Matthias"},{"first_name":"Jie","last_name":"Shen","full_name":"Shen, Jie"},{"full_name":"de Vries, Folkert K.","first_name":"Folkert K.","last_name":"de Vries"},{"first_name":"Ang","last_name":"Li","full_name":"Li, Ang"},{"full_name":"Bakkers, Erik P. A. M.","last_name":"Bakkers","first_name":"Erik P. A. M."},{"full_name":"Brinkman, Alexander","last_name":"Brinkman","first_name":"Alexander"},{"full_name":"Zwanenburg, Floris A.","last_name":"Zwanenburg","first_name":"Floris A."}],"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","title":"Josephson effect in a few-hole quantum dot","doi":"10.1002/adma.201802257","publication_status":"published","oa_version":"Preprint","date_published":"2018-11-02T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.08487"}],"scopus_import":"1","intvolume":" 30","citation":{"chicago":"Ridderbos, Joost, Matthias Brauns, Jie Shen, Folkert K. de Vries, Ang Li, Erik P. A. M. Bakkers, Alexander Brinkman, and Floris A. Zwanenburg. “Josephson Effect in a Few-Hole Quantum Dot.” Advanced Materials. Wiley, 2018. https://doi.org/10.1002/adma.201802257.","apa":"Ridderbos, J., Brauns, M., Shen, J., de Vries, F. K., Li, A., Bakkers, E. P. A. M., … Zwanenburg, F. A. (2018). Josephson effect in a few-hole quantum dot. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201802257","ista":"Ridderbos J, Brauns M, Shen J, de Vries FK, Li A, Bakkers EPAM, Brinkman A, Zwanenburg FA. 2018. Josephson effect in a few-hole quantum dot. Advanced Materials. 30(44), 1802257.","mla":"Ridderbos, Joost, et al. “Josephson Effect in a Few-Hole Quantum Dot.” Advanced Materials, vol. 30, no. 44, 1802257, Wiley, 2018, doi:10.1002/adma.201802257.","short":"J. Ridderbos, M. Brauns, J. Shen, F.K. de Vries, A. Li, E.P.A.M. Bakkers, A. Brinkman, F.A. Zwanenburg, Advanced Materials 30 (2018).","ieee":"J. Ridderbos et al., “Josephson effect in a few-hole quantum dot,” Advanced Materials, vol. 30, no. 44. Wiley, 2018.","ama":"Ridderbos J, Brauns M, Shen J, et al. Josephson effect in a few-hole quantum dot. Advanced Materials. 2018;30(44). doi:10.1002/adma.201802257"},"issue":"44","abstract":[{"text":"A Ge–Si core–shell nanowire is used to realize a Josephson field‐effect transistor with highly transparent contacts to superconducting leads. By changing the electric field, access to two distinct regimes, not combined before in a single device, is gained: in the accumulation mode the device is highly transparent and the supercurrent is carried by multiple subbands, while near depletion, the supercurrent is carried by single‐particle levels of a strongly coupled quantum dot operating in the few‐hole regime. These results establish Ge–Si nanowires as an important platform for hybrid superconductor–semiconductor physics and Majorana fermions.","lang":"eng"}],"arxiv":1,"date_updated":"2023-09-19T14:29:58Z","year":"2018","article_number":"1802257","_id":"5990","status":"public","publication_identifier":{"issn":["0935-9648"]},"oa":1,"month":"11"},{"title":"On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility","publisher":"American Society for Cell Biology ","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"pmid":1,"file":[{"file_size":6668971,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"e98465b4416b3e804c47f40086932af2","creator":"kschuh","file_id":"5994","date_created":"2019-02-14T12:34:29Z","file_name":"2018_ASCB_Dolati.pdf","date_updated":"2020-07-14T12:47:15Z"}],"isi":1,"author":[{"first_name":"Setareh","last_name":"Dolati","full_name":"Dolati, Setareh"},{"first_name":"Frieda","last_name":"Kage","full_name":"Kage, Frieda"},{"full_name":"Mueller, Jan","last_name":"Mueller","first_name":"Jan"},{"last_name":"Müsken","first_name":"Mathias","full_name":"Müsken, Mathias"},{"last_name":"Kirchner","first_name":"Marieluise","full_name":"Kirchner, Marieluise"},{"full_name":"Dittmar, Gunnar","last_name":"Dittmar","first_name":"Gunnar"},{"full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179"},{"full_name":"Rottner, Klemens","first_name":"Klemens","last_name":"Rottner"},{"full_name":"Falcke, Martin","last_name":"Falcke","first_name":"Martin"}],"article_processing_charge":"No","external_id":{"pmid":["30156465"],"isi":["000455641000011"]},"volume":29,"quality_controlled":"1","page":"2674-2686","date_created":"2019-02-14T12:25:47Z","publication":"Molecular Biology of the Cell","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"}],"type":"journal_article","publication_identifier":{"eissn":["1939-4586"]},"oa":1,"status":"public","month":"11","year":"2018","date_updated":"2023-09-19T14:30:23Z","issue":"22","abstract":[{"lang":"eng","text":"Lamellipodia are flat membrane protrusions formed during mesenchymal motion. Polymerization at the leading edge assembles the actin filament network and generates protrusion force. How this force is supported by the network and how the assembly rate is shared between protrusion and network retrograde flow determines the protrusion rate. We use mathematical modeling to understand experiments changing the F-actin density in lamellipodia of B16-F1 melanoma cells by modulation of Arp2/3 complex activity or knockout of the formins FMNL2 and FMNL3. Cells respond to a reduction of density with a decrease of protrusion velocity, an increase in the ratio of force to filament number, but constant network assembly rate. The relation between protrusion force and tension gradient in the F-actin network and the density dependency of friction, elasticity, and viscosity of the network explain the experimental observations. The formins act as filament nucleators and elongators with differential rates. Modulation of their activity suggests an effect on network assembly rate. Contrary to these expectations, the effect of changes in elongator composition is much weaker than the consequences of the density change. We conclude that the force acting on the leading edge membrane is the force required to drive F-actin network retrograde flow."}],"_id":"5992","ddc":["570"],"scopus_import":"1","file_date_updated":"2020-07-14T12:47:15Z","citation":{"ieee":"S. Dolati et al., “On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility,” Molecular Biology of the Cell, vol. 29, no. 22. American Society for Cell Biology , pp. 2674–2686, 2018.","ama":"Dolati S, Kage F, Mueller J, et al. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 2018;29(22):2674-2686. doi:10.1091/mbc.e18-02-0082","short":"S. Dolati, F. Kage, J. Mueller, M. Müsken, M. Kirchner, G. Dittmar, M.K. Sixt, K. Rottner, M. Falcke, Molecular Biology of the Cell 29 (2018) 2674–2686.","chicago":"Dolati, Setareh, Frieda Kage, Jan Mueller, Mathias Müsken, Marieluise Kirchner, Gunnar Dittmar, Michael K Sixt, Klemens Rottner, and Martin Falcke. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” Molecular Biology of the Cell. American Society for Cell Biology , 2018. https://doi.org/10.1091/mbc.e18-02-0082.","mla":"Dolati, Setareh, et al. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” Molecular Biology of the Cell, vol. 29, no. 22, American Society for Cell Biology , 2018, pp. 2674–86, doi:10.1091/mbc.e18-02-0082.","ista":"Dolati S, Kage F, Mueller J, Müsken M, Kirchner M, Dittmar G, Sixt MK, Rottner K, Falcke M. 2018. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 29(22), 2674–2686.","apa":"Dolati, S., Kage, F., Mueller, J., Müsken, M., Kirchner, M., Dittmar, G., … Falcke, M. (2018). On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. American Society for Cell Biology . https://doi.org/10.1091/mbc.e18-02-0082"},"intvolume":" 29","publication_status":"published","doi":"10.1091/mbc.e18-02-0082","date_published":"2018-11-01T00:00:00Z","oa_version":"Published Version"},{"ec_funded":1,"month":"06","publication_identifier":{"issn":["0164-0925"]},"oa":1,"status":"public","_id":"5993","article_number":"7","year":"2018","issue":"2","arxiv":1,"abstract":[{"lang":"eng","text":"In this article, we consider the termination problem of probabilistic programs with real-valued variables. Thequestions concerned are: qualitative ones that ask (i) whether the program terminates with probability 1(almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); andquantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) tocompute a boundBsuch that the probability not to terminate afterBsteps decreases exponentially (con-centration problem). To solve these questions, we utilize the notion of ranking supermartingales, which isa powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmicsynthesis of linear ranking-supermartingales over affine probabilistic programs (Apps) with both angelic anddemonic non-determinism. An important subclass of Apps is LRApp which is defined as the class of all Appsover which a linear ranking-supermartingale exists.Our main contributions are as follows. Firstly, we show that the membership problem of LRApp (i) canbe decided in polynomial time for Apps with at most demonic non-determinism, and (ii) isNP-hard and inPSPACEfor Apps with angelic non-determinism. Moreover, theNP-hardness result holds already for Appswithout probability and demonic non-determinism. Secondly, we show that the concentration problem overLRApp can be solved in the same complexity as for the membership problem of LRApp. Finally, we show thatthe expectation problem over LRApp can be solved in2EXPTIMEand isPSPACE-hard even for Apps withoutprobability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate theeffectiveness of our approach to answer the qualitative and quantitative questions over Apps with at mostdemonic non-determinism."}],"date_updated":"2023-09-19T14:38:42Z","intvolume":" 40","citation":{"chicago":"Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs.” ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3174800.","apa":"Chatterjee, K., Fu, H., Novotný, P., & Hasheminezhad, R. (2018). Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM). https://doi.org/10.1145/3174800","mla":"Chatterjee, Krishnendu, et al. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs.” ACM Transactions on Programming Languages and Systems, vol. 40, no. 2, 7, Association for Computing Machinery (ACM), 2018, doi:10.1145/3174800.","ista":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2018. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. 40(2), 7.","short":"K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, ACM Transactions on Programming Languages and Systems 40 (2018).","ama":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. 2018;40(2). doi:10.1145/3174800","ieee":"K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs,” ACM Transactions on Programming Languages and Systems, vol. 40, no. 2. Association for Computing Machinery (ACM), 2018."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1510.08517"}],"scopus_import":"1","date_published":"2018-06-01T00:00:00Z","oa_version":"Submitted Version","doi":"10.1145/3174800","publication_status":"published","title":"Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Association for Computing Machinery (ACM)","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"full_name":"Fu, Hongfei","first_name":"Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu"},{"full_name":"Novotný, Petr","last_name":"Novotný","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"full_name":"Hasheminezhad, Rouzbeh","first_name":"Rouzbeh","last_name":"Hasheminezhad"}],"isi":1,"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"day":"01","related_material":{"record":[{"id":"1438","relation":"earlier_version","status":"public"}]},"quality_controlled":"1","volume":40,"external_id":{"arxiv":["1510.08517"],"isi":["000434634500003"]},"article_processing_charge":"No","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"ACM Transactions on Programming Languages and Systems","date_created":"2019-02-14T12:29:10Z"},{"project":[{"call_identifier":"FP7","name":"Systematic investigation of epistasis in molecular evolution","_id":"26120F5C-B435-11E9-9278-68D0E5697425","grant_number":"335980"}],"isi":1,"author":[{"last_name":"Usmanova","first_name":"Dinara R","full_name":"Usmanova, Dinara R"},{"full_name":"Bogatyreva, Natalya S","last_name":"Bogatyreva","first_name":"Natalya S"},{"full_name":"Ariño Bernad, Joan","last_name":"Ariño Bernad","first_name":"Joan"},{"last_name":"Eremina","first_name":"Aleksandra A","full_name":"Eremina, Aleksandra A"},{"full_name":"Gorshkova, Anastasiya A","first_name":"Anastasiya A","last_name":"Gorshkova"},{"full_name":"Kanevskiy, German M","last_name":"Kanevskiy","first_name":"German M"},{"full_name":"Lonishin, Lyubov R","first_name":"Lyubov R","last_name":"Lonishin"},{"full_name":"Meister, Alexander V","last_name":"Meister","first_name":"Alexander V"},{"full_name":"Yakupova, Alisa G","first_name":"Alisa G","last_name":"Yakupova"},{"last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","last_name":"Ivankov","full_name":"Ivankov, Dmitry"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_size":291969,"file_id":"5997","creator":"kschuh","checksum":"7e0495153f44211479674601d7f6ee03","access_level":"open_access","date_updated":"2020-07-14T12:47:15Z","file_name":"2018_Oxford_Usmanova.pdf","date_created":"2019-02-14T13:00:55Z"}],"pmid":1,"day":"01","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"publisher":"Oxford University Press ","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"FyKo"}],"has_accepted_license":"1","date_created":"2019-02-14T12:48:00Z","page":"3653-3658","publication":"Bioinformatics","external_id":{"isi":["000450038900008"],"pmid":["29722803"]},"quality_controlled":"1","volume":34,"article_processing_charge":"No","_id":"5995","date_updated":"2023-09-19T14:31:13Z","abstract":[{"lang":"eng","text":"Motivation\r\nComputational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations.\r\n\r\nResults\r\nHere we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a self-consistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. Authors using algorithms for predicting effects of mutations should be aware of the bias described here."}],"issue":"21","year":"2018","month":"11","ec_funded":1,"status":"public","oa":1,"publication_identifier":{"issn":["1367-4803","1460-2059"]},"oa_version":"Published Version","date_published":"2018-11-01T00:00:00Z","publication_status":"published","doi":"10.1093/bioinformatics/bty340","intvolume":" 34","citation":{"ieee":"D. R. Usmanova et al., “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” Bioinformatics, vol. 34, no. 21. Oxford University Press , pp. 3653–3658, 2018.","ama":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, et al. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 2018;34(21):3653-3658. doi:10.1093/bioinformatics/bty340","short":"D.R. Usmanova, N.S. Bogatyreva, J. Ariño Bernad, A.A. Eremina, A.A. Gorshkova, G.M. Kanevskiy, L.R. Lonishin, A.V. Meister, A.G. Yakupova, F. Kondrashov, D. Ivankov, Bioinformatics 34 (2018) 3653–3658.","chicago":"Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics. Oxford University Press , 2018. https://doi.org/10.1093/bioinformatics/bty340.","mla":"Usmanova, Dinara R., et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics, vol. 34, no. 21, Oxford University Press , 2018, pp. 3653–58, doi:10.1093/bioinformatics/bty340.","ista":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov F, Ivankov D. 2018. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 34(21), 3653–3658.","apa":"Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova, A. A., Kanevskiy, G. M., … Ivankov, D. (2018). Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. Oxford University Press . https://doi.org/10.1093/bioinformatics/bty340"},"scopus_import":"1","file_date_updated":"2020-07-14T12:47:15Z","ddc":["570"]},{"intvolume":" 839","citation":{"apa":"Vasudevan, M., & Hof, B. (2018). The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.923","mla":"Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to Turbulence in Pipe Flow.” Journal of Fluid Mechanics, vol. 839, Cambridge University Press, 2018, pp. 76–94, doi:10.1017/jfm.2017.923.","ista":"Vasudevan M, Hof B. 2018. The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. 839, 76–94.","chicago":"Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to Turbulence in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2018. https://doi.org/10.1017/jfm.2017.923.","ieee":"M. Vasudevan and B. Hof, “The critical point of the transition to turbulence in pipe flow,” Journal of Fluid Mechanics, vol. 839. Cambridge University Press, pp. 76–94, 2018.","ama":"Vasudevan M, Hof B. The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. 2018;839:76-94. doi:10.1017/jfm.2017.923","short":"M. Vasudevan, B. Hof, Journal of Fluid Mechanics 839 (2018) 76–94."},"main_file_link":[{"url":"https://arxiv.org/abs/1709.06372","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","date_published":"2018-03-25T00:00:00Z","doi":"10.1017/jfm.2017.923","publication_status":"published","month":"03","ec_funded":1,"status":"public","publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"oa":1,"_id":"5996","abstract":[{"text":"In pipes, turbulence sets in despite the linear stability of the laminar Hagen–Poiseuille flow. The Reynolds number ( ) for which turbulence first appears in a given experiment – the ‘natural transition point’ – depends on imperfections of the set-up, or, more precisely, on the magnitude of finite amplitude perturbations. At onset, turbulence typically only occupies a certain fraction of the flow, and this fraction equally is found to differ from experiment to experiment. Despite these findings, Reynolds proposed that after sufficiently long times, flows may settle to steady conditions: below a critical velocity, flows should (regardless of initial conditions) always return to laminar, while above this velocity, eddying motion should persist. As will be shown, even in pipes several thousand diameters long, the spatio-temporal intermittent flow patterns observed at the end of the pipe strongly depend on the initial conditions, and there is no indication that different flow patterns would eventually settle to a (statistical) steady state. Exploiting the fact that turbulent puffs do not age (i.e. they are memoryless), we continuously recreate the puff sequence exiting the pipe at the pipe entrance, and in doing so introduce periodic boundary conditions for the puff pattern. This procedure allows us to study the evolution of the flow patterns for arbitrary long times, and we find that after times in excess of advective time units, indeed a statistical steady state is reached. Although the resulting flows remain spatio-temporally intermittent, puff splitting and decay rates eventually reach a balance, so that the turbulent fraction fluctuates around a well-defined level which only depends on . In accordance with Reynolds’ proposition, we find that at lower (here 2020), flows eventually always resume to laminar, while for higher ( ), turbulence persists. The critical point for pipe flow hence falls in the interval of $2020 , which is in very good agreement with the recently proposed value of . The latter estimate was based on single-puff statistics and entirely neglected puff interactions. Unlike in typical contact processes where such interactions strongly affect the percolation threshold, in pipe flow, the critical point is only marginally influenced. Interactions, on the other hand, are responsible for the approach to the statistical steady state. As shown, they strongly affect the resulting flow patterns, where they cause ‘puff clustering’, and these regions of large puff densities are observed to travel across the puff pattern in a wave-like fashion.","lang":"eng"}],"arxiv":1,"date_updated":"2023-09-19T14:37:49Z","year":"2018","quality_controlled":"1","volume":839,"external_id":{"arxiv":["1709.06372"],"isi":["000437858300003"]},"article_processing_charge":"No","article_type":"original","type":"journal_article","department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"publication":"Journal of Fluid Mechanics","page":"76-94","date_created":"2019-02-14T12:50:50Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Cambridge University Press","title":"The critical point of the transition to turbulence in pipe flow","isi":1,"author":[{"full_name":"Vasudevan, Mukund","first_name":"Mukund","id":"3C5A959A-F248-11E8-B48F-1D18A9856A87","last_name":"Vasudevan"},{"full_name":"Hof, Björn","first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"acknowledgement":" We also thank Philipp Maier and the IST Austria workshop for theirdedicated technical support","day":"25"},{"has_accepted_license":"1","date_created":"2019-02-14T13:07:45Z","publication":"PLOS Genetics","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JoDa"}],"article_processing_charge":"No","external_id":{"isi":["000449328500025"]},"volume":14,"quality_controlled":"1","day":"12","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","first_name":"Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gudrun","last_name":"Meinhardt","full_name":"Meinhardt, Gudrun"},{"full_name":"Plessl, Kerstin","first_name":"Kerstin","last_name":"Plessl"},{"full_name":"Vondra, Sigrid","last_name":"Vondra","first_name":"Sigrid"},{"full_name":"Weiss, Tamara","first_name":"Tamara","last_name":"Weiss"},{"full_name":"Haslinger, Peter","first_name":"Peter","last_name":"Haslinger"},{"last_name":"Lendl","first_name":"Thomas","full_name":"Lendl, Thomas"},{"last_name":"Aumayr","first_name":"Karin","full_name":"Aumayr, Karin"},{"first_name":"Mario","last_name":"Mairhofer","full_name":"Mairhofer, Mario"},{"full_name":"Zhu, Xiaowei","first_name":"Xiaowei","last_name":"Zhu"},{"full_name":"Schütz, Birgit","first_name":"Birgit","last_name":"Schütz"},{"last_name":"Hannibal","first_name":"Roberta L.","full_name":"Hannibal, Roberta L."},{"full_name":"Lindau, Robert","last_name":"Lindau","first_name":"Robert"},{"full_name":"Weil, Beatrix","last_name":"Weil","first_name":"Beatrix"},{"first_name":"Jan","last_name":"Ernerudh","full_name":"Ernerudh, Jan"},{"first_name":"Jürgen","last_name":"Neesen","full_name":"Neesen, Jürgen"},{"first_name":"Gerda","last_name":"Egger","full_name":"Egger, Gerda"},{"first_name":"Mario","last_name":"Mikula","full_name":"Mikula, Mario"},{"full_name":"Röhrl, Clemens","last_name":"Röhrl","first_name":"Clemens"},{"last_name":"Urban","first_name":"Alexander E.","full_name":"Urban, Alexander E."},{"full_name":"Baker, Julie","last_name":"Baker","first_name":"Julie"},{"full_name":"Knöfler, Martin","last_name":"Knöfler","first_name":"Martin"},{"last_name":"Pollheimer","first_name":"Jürgen","full_name":"Pollheimer, Jürgen"}],"isi":1,"file":[{"relation":"main_file","content_type":"application/pdf","file_size":4592947,"date_updated":"2020-07-14T12:47:15Z","file_name":"2018_PLOS_Velicky.pdf","date_created":"2019-02-14T13:14:35Z","checksum":"34aa9a5972f61889c19f18be8ee787a0","creator":"kschuh","file_id":"6000","access_level":"open_access"}],"publisher":"Public Library of Science","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Genome amplification and cellular senescence are hallmarks of human placenta development","publication_status":"published","doi":"10.1371/journal.pgen.1007698","oa_version":"Published Version","date_published":"2018-10-12T00:00:00Z","scopus_import":"1","file_date_updated":"2020-07-14T12:47:15Z","ddc":["570"],"intvolume":" 14","citation":{"ama":"Velicky P, Meinhardt G, Plessl K, et al. Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. 2018;14(10). doi:10.1371/journal.pgen.1007698","ieee":"P. Velicky et al., “Genome amplification and cellular senescence are hallmarks of human placenta development,” PLOS Genetics, vol. 14, no. 10. Public Library of Science, 2018.","short":"P. Velicky, G. Meinhardt, K. Plessl, S. Vondra, T. Weiss, P. Haslinger, T. Lendl, K. Aumayr, M. Mairhofer, X. Zhu, B. Schütz, R.L. Hannibal, R. Lindau, B. Weil, J. Ernerudh, J. Neesen, G. Egger, M. Mikula, C. Röhrl, A.E. Urban, J. Baker, M. Knöfler, J. Pollheimer, PLOS Genetics 14 (2018).","chicago":"Velicky, Philipp, Gudrun Meinhardt, Kerstin Plessl, Sigrid Vondra, Tamara Weiss, Peter Haslinger, Thomas Lendl, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” PLOS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007698.","ista":"Velicky P, Meinhardt G, Plessl K, Vondra S, Weiss T, Haslinger P, Lendl T, Aumayr K, Mairhofer M, Zhu X, Schütz B, Hannibal RL, Lindau R, Weil B, Ernerudh J, Neesen J, Egger G, Mikula M, Röhrl C, Urban AE, Baker J, Knöfler M, Pollheimer J. 2018. Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. 14(10), e1007698.","apa":"Velicky, P., Meinhardt, G., Plessl, K., Vondra, S., Weiss, T., Haslinger, P., … Pollheimer, J. (2018). Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007698","mla":"Velicky, Philipp, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” PLOS Genetics, vol. 14, no. 10, e1007698, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007698."},"date_updated":"2023-09-19T14:31:43Z","issue":"10","abstract":[{"lang":"eng","text":"Genome amplification and cellular senescence are commonly associated with pathological processes. While physiological roles for polyploidization and senescence have been described in mouse development, controversy exists over their significance in humans. Here, we describe tetraploidization and senescence as phenomena of normal human placenta development. During pregnancy, placental extravillous trophoblasts (EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted microenvironment required for the developing embryo. This process is critically dependent on continuous cell proliferation and differentiation, which is thought to follow the classical model of cell cycle arrest prior to terminal differentiation. Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied with a genome-wide polyploidization, independent of mitotic cycles. DNA replication in these cells was analysed by a fluorescent cell-cycle indicator reporter system, cell cycle marker expression and EdU incorporation. Upon invasion into the decidua, EVTs widely lose their replicative potential and enter a senescent state characterized by high senescence-associated (SA) β-galactosidase activity, induction of a SA secretory phenotype as well as typical metabolic alterations. Furthermore, we show that the shift from endocycle-dependent genome amplification to growth arrest is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy disorder associated with increased risk of developing choriocarinoma. Senescence is decreased in CHM-EVTs, accompanied by exacerbated endoreduplication and hyperploidy. We propose induction of cellular senescence as a ploidy-limiting mechanism during normal human placentation and unravel a link between excessive polyploidization and reduced senescence in CHM."}],"year":"2018","article_number":"e1007698","_id":"5998","status":"public","publication_identifier":{"issn":["1553-7404"]},"oa":1,"month":"10"},{"_id":"5999","date_updated":"2023-09-19T14:37:19Z","arxiv":1,"abstract":[{"text":"We introduce for each quiver Q and each algebraic oriented cohomology theory A, the cohomological Hall algebra (CoHA) of Q, as the A-homology of the moduli of representations of the preprojective algebra of Q. This generalizes the K-theoretic Hall algebra of commuting varieties defined by Schiffmann-Vasserot. When A is the Morava K-theory, we show evidence that this algebra is a candidate for Lusztig's reformulated conjecture on modular representations of algebraic groups.\r\nWe construct an action of the preprojective CoHA on the A-homology of Nakajima quiver varieties. We compare this with the action of the Borel subalgebra of Yangian when A is the intersection theory. We also give a shuffle algebra description of this CoHA in terms of the underlying formal group law of A. As applications, we obtain a shuffle description of the Yangian. ","lang":"eng"}],"issue":"5","year":"2018","month":"05","status":"public","oa":1,"publication_identifier":{"issn":["0024-6115"]},"oa_version":"Preprint","date_published":"2018-05-01T00:00:00Z","publication_status":"published","doi":"10.1112/plms.12111","citation":{"short":"Y. Yang, G. Zhao, Proceedings of the London Mathematical Society 116 (2018) 1029–1074.","ieee":"Y. Yang and G. Zhao, “The cohomological Hall algebra of a preprojective algebra,” Proceedings of the London Mathematical Society, vol. 116, no. 5. Oxford University Press, pp. 1029–1074, 2018.","ama":"Yang Y, Zhao G. The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. 2018;116(5):1029-1074. doi:10.1112/plms.12111","chicago":"Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective Algebra.” Proceedings of the London Mathematical Society. Oxford University Press, 2018. https://doi.org/10.1112/plms.12111.","ista":"Yang Y, Zhao G. 2018. The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. 116(5), 1029–1074.","mla":"Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective Algebra.” Proceedings of the London Mathematical Society, vol. 116, no. 5, Oxford University Press, 2018, pp. 1029–74, doi:10.1112/plms.12111.","apa":"Yang, Y., & Zhao, G. (2018). The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. Oxford University Press. https://doi.org/10.1112/plms.12111"},"intvolume":" 116","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1407.7994"}],"author":[{"full_name":"Yang, Yaping","first_name":"Yaping","last_name":"Yang"},{"full_name":"Zhao, Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","last_name":"Zhao","first_name":"Gufang"}],"isi":1,"day":"01","publisher":"Oxford University Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"The cohomological Hall algebra of a preprojective algebra","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"TaHa"}],"page":"1029-1074","date_created":"2019-02-14T13:14:22Z","publication":"Proceedings of the London Mathematical Society","external_id":{"isi":["000431506400001"],"arxiv":["1407.7994"]},"quality_controlled":"1","volume":116,"article_processing_charge":"No"},{"title":"A micro-CT-based method for characterising lesions and locating electrodes in small animal brains","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"MyJove Corporation","status":"public","month":"11","year":"2018","day":"08","abstract":[{"lang":"eng","text":"Lesion and electrode location verification are traditionally done via histological examination of stained brain slices, a time-consuming procedure that requires manual estimation. Here, we describe a simple, straightforward method for quantifying lesions and locating electrodes in the brain that is less laborious and yields more detailed results. Whole brains are stained with osmium tetroxide, embedded in resin, and imaged with a micro-CT scanner. The scans result in 3D digital volumes of the brains with resolutions and virtual section thicknesses dependent on the sample size (12-15 and 5-6 µm per voxel for rat and zebra finch brains, respectively). Surface and deep lesions can be characterized, and single tetrodes, tetrode arrays, electrolytic lesions, and silicon probes can also be localized. Free and proprietary software allows experimenters to examine the sample volume from any plane and segment the volume manually or automatically. Because this method generates whole brain volume, lesions and electrodes can be quantified to a much higher degree than in current methods, which will help standardize comparisons within and across studies."}],"date_updated":"2023-10-17T11:49:25Z","_id":"6","isi":1,"author":[{"full_name":"Masís, Javier","last_name":"Masís","first_name":"Javier"},{"first_name":"David","last_name":"Mankus","full_name":"Mankus, David"},{"first_name":"Steffen","last_name":"Wolff","full_name":"Wolff, Steffen"},{"full_name":"Guitchounts, Grigori","last_name":"Guitchounts","first_name":"Grigori"},{"last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"},{"full_name":"Cox, David","last_name":"Cox","first_name":"David"}],"article_processing_charge":"No","scopus_import":"1","publist_id":"8050","quality_controlled":"1","citation":{"ista":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of visualized experiments. 141.","mla":"Masís, Javier, et al. “A Micro-CT-Based Method for Characterising Lesions and Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments, vol. 141, MyJove Corporation, 2018, doi:10.3791/58585.","apa":"Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox, D. (2018). A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of Visualized Experiments. MyJove Corporation. https://doi.org/10.3791/58585","chicago":"Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian A Jösch, and David Cox. “A Micro-CT-Based Method for Characterising Lesions and Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments. MyJove Corporation, 2018. https://doi.org/10.3791/58585.","short":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Journal of Visualized Experiments 141 (2018).","ama":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of visualized experiments. 2018;141. doi:10.3791/58585","ieee":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A micro-CT-based method for characterising lesions and locating electrodes in small animal brains,” Journal of visualized experiments, vol. 141. MyJove Corporation, 2018."},"intvolume":" 141","volume":141,"external_id":{"isi":["000456469400103"]},"publication":"Journal of visualized experiments","date_created":"2018-12-11T11:44:07Z","doi":"10.3791/58585","publication_status":"published","date_published":"2018-11-08T00:00:00Z","department":[{"_id":"MaJö"}],"language":[{"iso":"eng"}],"oa_version":"None","type":"journal_article"},{"author":[{"full_name":"Clarke, Edmund","first_name":"Edmund","last_name":"Clarke"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Veith, Helmut","first_name":"Helmut","last_name":"Veith"}],"_id":"60","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"}],"date_updated":"2021-01-12T08:05:35Z","year":"2018","day":"19","month":"05","series_title":"Handbook of Model Checking","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Springer","title":"Introduction to model checking","oa_version":"None","type":"book_chapter","department":[{"_id":"ToHe"}],"date_published":"2018-05-19T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-10575-8_1","publication_status":"published","publication":"Handbook of Model Checking","date_created":"2018-12-11T11:44:25Z","page":"1 - 26","editor":[{"first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"citation":{"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.","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.","ista":"Clarke E, Henzinger TA, Veith H. 2018.Introduction to model checking. In: Handbook of Model Checking. , 1–26.","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","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","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.","short":"E. Clarke, T.A. Henzinger, H. Veith, in:, T.A. Henzinger (Ed.), Handbook of Model Checking, Springer, 2018, pp. 1–26."},"quality_controlled":"1","scopus_import":1,"publist_id":"7994"},{"oa_version":"None","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2018-09-01T00:00:00Z","department":[{"_id":"DaAl"}],"publication_status":"published","doi":"10.1145/3201897","date_created":"2019-02-14T13:24:11Z","publication":"ACM Transactions on Parallel Computing","citation":{"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.","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.","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","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.","short":"D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, ACM Transactions on Parallel Computing 4 (2018).","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","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."},"quality_controlled":"1","intvolume":" 4","volume":4,"related_material":{"record":[{"id":"779","relation":"earlier_version","status":"public"}]},"scopus_import":1,"article_number":"18","author":[{"last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Leiserson","first_name":"William","full_name":"Leiserson, William"},{"last_name":"Matveev","first_name":"Alexander","full_name":"Matveev, Alexander"},{"last_name":"Shavit","first_name":"Nir","full_name":"Shavit, Nir"}],"_id":"6001","date_updated":"2023-02-23T13:17:54Z","issue":"4","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"}],"day":"01","year":"2018","month":"09","publisher":"Association for Computing Machinery","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"ThreadScan: Automatic and scalable memory reclamation","publication_identifier":{"issn":["2329-4949"]}},{"article_processing_charge":"No","external_id":{"arxiv":["1511.05935"],"isi":["000435367300003"]},"quality_controlled":"1","volume":229,"date_created":"2019-02-14T13:40:53Z","page":"1037-1090","publication":"Archive for Rational Mechanics and Analysis","language":[{"iso":"eng"}],"department":[{"_id":"RoSe"}],"type":"journal_article","title":"The Bogoliubov free energy functional I: Existence of minimizers and phase diagram","publisher":"Springer Nature","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"author":[{"first_name":"Marcin M","last_name":"Napiórkowski","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","full_name":"Napiórkowski, Marcin M"},{"full_name":"Reuvers, Robin","first_name":"Robin","last_name":"Reuvers"},{"last_name":"Solovej","first_name":"Jan Philip","full_name":"Solovej, Jan Philip"}],"isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.05935"}],"scopus_import":"1","citation":{"ama":"Napiórkowski MM, Reuvers R, Solovej JP. The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. 2018;229(3):1037-1090. doi:10.1007/s00205-018-1232-6","ieee":"M. M. Napiórkowski, R. Reuvers, and J. P. Solovej, “The Bogoliubov free energy functional I: Existence of minimizers and phase diagram,” Archive for Rational Mechanics and Analysis, vol. 229, no. 3. Springer Nature, pp. 1037–1090, 2018.","short":"M.M. Napiórkowski, R. Reuvers, J.P. Solovej, Archive for Rational Mechanics and Analysis 229 (2018) 1037–1090.","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. P. (2018). The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-018-1232-6","mla":"Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional I: Existence of Minimizers and Phase Diagram.” Archive for Rational Mechanics and Analysis, vol. 229, no. 3, Springer Nature, 2018, pp. 1037–90, doi:10.1007/s00205-018-1232-6.","ista":"Napiórkowski MM, Reuvers R, Solovej JP. 2018. The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. 229(3), 1037–1090.","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Philip Solovej. “The Bogoliubov Free Energy Functional I: Existence of Minimizers and Phase Diagram.” Archive for Rational Mechanics and Analysis. Springer Nature, 2018. https://doi.org/10.1007/s00205-018-1232-6."},"intvolume":" 229","publication_status":"published","doi":"10.1007/s00205-018-1232-6","date_published":"2018-09-01T00:00:00Z","oa_version":"Preprint","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"oa":1,"status":"public","month":"09","year":"2018","date_updated":"2023-09-19T14:33:12Z","abstract":[{"text":"The Bogoliubov free energy functional is analysed. The functional serves as a model of a translation-invariant Bose gas at positive temperature. We prove the existence of minimizers in the case of repulsive interactions given by a sufficiently regular two-body potential. Furthermore, we prove the existence of a phase transition in this model and provide its phase diagram.","lang":"eng"}],"arxiv":1,"issue":"3","_id":"6002"},{"doi":"10.1111/cgf.13327","publication_status":"published","date_published":"2018-09-01T00:00:00Z","oa_version":"Submitted Version","ddc":["004"],"scopus_import":"1","file_date_updated":"2020-07-14T12:47:15Z","citation":{"ama":"Bickel B, Cignoni P, Malomo L, Pietroni N. State of the art on stylized fabrication. Computer Graphics Forum. 2018;37(6):325-342. doi:10.1111/cgf.13327","ieee":"B. Bickel, P. Cignoni, L. Malomo, and N. Pietroni, “State of the art on stylized fabrication,” Computer Graphics Forum, vol. 37, no. 6. Wiley, pp. 325–342, 2018.","short":"B. Bickel, P. Cignoni, L. Malomo, N. Pietroni, Computer Graphics Forum 37 (2018) 325–342.","chicago":"Bickel, Bernd, Paolo Cignoni, Luigi Malomo, and Nico Pietroni. “State of the Art on Stylized Fabrication.” Computer Graphics Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13327.","apa":"Bickel, B., Cignoni, P., Malomo, L., & Pietroni, N. (2018). State of the art on stylized fabrication. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13327","mla":"Bickel, Bernd, et al. “State of the Art on Stylized Fabrication.” Computer Graphics Forum, vol. 37, no. 6, Wiley, 2018, pp. 325–42, doi:10.1111/cgf.13327.","ista":"Bickel B, Cignoni P, Malomo L, Pietroni N. 2018. State of the art on stylized fabrication. Computer Graphics Forum. 37(6), 325–342."},"intvolume":" 37","year":"2018","issue":"6","abstract":[{"lang":"eng","text":"Digital fabrication devices are powerful tools for creating tangible reproductions of 3D digital models. Most available printing technologies aim at producing an accurate copy of a tridimensional shape. However, fabrication technologies can also be used to create a stylistic representation of a digital shape. We refer to this class of methods as ‘stylized fabrication methods’. These methods abstract geometric and physical features of a given shape to create an unconventional representation, to produce an optical illusion or to devise a particular interaction with the fabricated model. In this state‐of‐the‐art report, we classify and overview this broad and emerging class of approaches and also propose possible directions for future research."}],"date_updated":"2023-09-19T14:33:40Z","_id":"6003","publication_identifier":{"issn":["0167-7055"]},"oa":1,"status":"public","ec_funded":1,"month":"09","publication":"Computer Graphics Forum","date_created":"2019-02-14T13:52:25Z","page":"325-342","has_accepted_license":"1","department":[{"_id":"BeBi"}],"language":[{"iso":"eng"}],"type":"journal_article","pubrep_id":"1051","article_processing_charge":"No","volume":37,"quality_controlled":"1","external_id":{"isi":["000437272800019"]},"day":"01","file":[{"access_level":"open_access","checksum":"d2bbe5c658d8159fbe9016a4f5e82b19","file_id":"6004","creator":"kschuh","date_created":"2019-02-14T14:09:28Z","date_updated":"2020-07-14T12:47:15Z","file_name":"StylizedFabricationSTAR-Personal.pdf","file_size":6209349,"relation":"main_file","content_type":"application/pdf"}],"author":[{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"},{"full_name":"Cignoni, Paolo","last_name":"Cignoni","first_name":"Paolo"},{"first_name":"Luigi","last_name":"Malomo","full_name":"Malomo, Luigi"},{"last_name":"Pietroni","first_name":"Nico","full_name":"Pietroni, Nico"}],"isi":1,"project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"title":"State of the art on stylized fabrication","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley"},{"type":"conference","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","date_created":"2019-02-14T14:12:09Z","volume":117,"quality_controlled":"1","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"963"}]},"article_processing_charge":"No","author":[{"full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","orcid":"0000-0001-5588-8287","first_name":"Guy"},{"full_name":"Guha, Shibashis","first_name":"Shibashis","last_name":"Guha"},{"full_name":"Kupferman, Orna","first_name":"Orna","last_name":"Kupferman"}],"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory"}],"file":[{"file_size":542889,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_id":"6007","checksum":"41ab2ae9b63f5eb49fa995250c0ba128","date_created":"2019-02-14T14:22:04Z","date_updated":"2020-07-14T12:47:15Z","file_name":"2018_LIPIcs_Avni.pdf"}],"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"alternative_title":["LIPIcs"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","title":"Timed network games with clocks","oa_version":"Published Version","date_published":"2018-08-01T00:00:00Z","doi":"10.4230/LIPICS.MFCS.2018.23","conference":{"name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2018-08-27","location":"Liverpool, United Kingdom","end_date":"2018-08-31"},"publication_status":"published","citation":{"short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom, 2018, vol. 117.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23.","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks (Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2018.23","ista":"Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23."},"intvolume":" 117","file_date_updated":"2020-07-14T12:47:15Z","scopus_import":"1","ddc":["000"],"article_number":"23","_id":"6005","abstract":[{"lang":"eng","text":"Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting."}],"date_updated":"2023-02-23T14:02:58Z","year":"2018","month":"08","status":"public","oa":1,"publication_identifier":{"issn":["1868-8969"]}},{"status":"public","oa":1,"publication_identifier":{"issn":["2073-4336"]},"month":"09","date_updated":"2023-09-22T09:48:59Z","issue":"3","abstract":[{"text":"Network games (NGs) are played on directed graphs and are extensively used in network design and analysis. Search problems for NGs include finding special strategy profiles such as a Nash equilibrium and a globally-optimal solution. The networks modeled by NGs may be huge. In formal verification, abstraction has proven to be an extremely effective technique for reasoning about systems with big and even infinite state spaces. We describe an abstraction-refinement methodology for reasoning about NGs. Our methodology is based on an abstraction function that maps the state space of an NG to a much smaller state space. We search for a global optimum and a Nash equilibrium by reasoning on an under- and an over-approximation defined on top of this smaller state space. When the approximations are too coarse to find such profiles, we refine the abstraction function. We extend the abstraction-refinement methodology to labeled networks, where the objectives of the players are regular languages. Our experimental results demonstrate the effectiveness of the methodology. ","lang":"eng"}],"year":"2018","article_number":"39","_id":"6006","file_date_updated":"2020-07-14T12:47:16Z","scopus_import":1,"ddc":["004"],"citation":{"ieee":"G. Avni, S. Guha, and O. Kupferman, “An abstraction-refinement methodology for reasoning about network games,” Games, vol. 9, no. 3. MDPI AG, 2018.","ama":"Avni G, Guha S, Kupferman O. An abstraction-refinement methodology for reasoning about network games. Games. 2018;9(3). doi:10.3390/g9030039","short":"G. Avni, S. Guha, O. Kupferman, Games 9 (2018).","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “An Abstraction-Refinement Methodology for Reasoning about Network Games.” Games. MDPI AG, 2018. https://doi.org/10.3390/g9030039.","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). An abstraction-refinement methodology for reasoning about network games. Games. MDPI AG. https://doi.org/10.3390/g9030039","mla":"Avni, Guy, et al. “An Abstraction-Refinement Methodology for Reasoning about Network Games.” Games, vol. 9, no. 3, 39, MDPI AG, 2018, doi:10.3390/g9030039.","ista":"Avni G, Guha S, Kupferman O. 2018. An abstraction-refinement methodology for reasoning about network games. Games. 9(3), 39."},"intvolume":" 9","publication_status":"published","doi":"10.3390/g9030039","oa_version":"Published Version","date_published":"2018-09-01T00:00:00Z","publisher":"MDPI AG","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"An abstraction-refinement methodology for reasoning about network games","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","project":[{"name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"author":[{"full_name":"Avni, Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy"},{"full_name":"Guha, Shibashis","first_name":"Shibashis","last_name":"Guha"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":505155,"file_name":"2018_MDPI_Avni.pdf","date_updated":"2020-07-14T12:47:16Z","date_created":"2019-02-14T14:20:31Z","file_id":"6008","creator":"kschuh","checksum":"749d65ca4ce74256a029d9644a1b1cb0","access_level":"open_access"}],"quality_controlled":"1","volume":9,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1003"}]},"has_accepted_license":"1","date_created":"2019-02-14T14:17:54Z","publication":"Games","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}]},{"day":"01","isi":1,"author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584"},{"first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"}],"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Association for Computing Machinery (ACM)","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","publication":"ACM Transactions on Programming Languages and Systems","date_created":"2019-02-14T14:31:52Z","type":"journal_article","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","volume":40,"quality_controlled":"1","external_id":{"arxiv":["1510.07565"],"isi":["000444694800001"]},"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1437"},{"id":"5441","relation":"earlier_version","status":"public"},{"id":"5442","status":"public","relation":"earlier_version"},{"status":"public","relation":"dissertation_contains","id":"8934"}]},"issue":"3","arxiv":1,"abstract":[{"text":"We study algorithmic questions wrt algebraic path properties in concurrent systems, where the transitions of the system are labeled from a complete, closed semiring. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time.\r\nOur main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.\r\n","lang":"eng"}],"date_updated":"2024-03-25T23:30:19Z","year":"2018","article_number":"9","_id":"6009","status":"public","oa":1,"publication_identifier":{"issn":["0164-0925"]},"month":"08","ec_funded":1,"doi":"10.1145/3210257","publication_status":"published","oa_version":"Preprint","date_published":"2018-08-01T00:00:00Z","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1510.07565","open_access":"1"}],"intvolume":" 40","citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components.” ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3210257.","apa":"Chatterjee, K., Ibsen-Jensen, R., Goharshady, A. K., & Pavlogiannis, A. (2018). Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM). https://doi.org/10.1145/3210257","ista":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. 2018. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. 40(3), 9.","mla":"Chatterjee, Krishnendu, et al. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components.” ACM Transactions on Programming Languages and Systems, vol. 40, no. 3, 9, Association for Computing Machinery (ACM), 2018, doi:10.1145/3210257.","ieee":"K. Chatterjee, R. Ibsen-Jensen, A. K. Goharshady, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” ACM Transactions on Programming Languages and Systems, vol. 40, no. 3. Association for Computing Machinery (ACM), 2018.","ama":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. 2018;40(3). doi:10.1145/3210257","short":"K. Chatterjee, R. Ibsen-Jensen, A.K. Goharshady, A. Pavlogiannis, ACM Transactions on Programming Languages and Systems 40 (2018)."}},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30026198"}],"citation":{"ama":"Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, et al. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. 2018;115(32):E7615-E7623. doi:10.1073/pnas.1804517115","ieee":"F. Garrido-Charad et al., ““Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network,” Proceedings of the National Academy of Sciences, vol. 115, no. 32. National Academy of Sciences, pp. E7615–E7623, 2018.","short":"F. Garrido-Charad, T.A. Vega Zuniga, C. Gutiérrez-Ibáñez, P. Fernandez, L. López-Jury, C. González-Cabrera, H.J. Karten, H. Luksch, G.J. Marín, Proceedings of the National Academy of Sciences 115 (2018) E7615–E7623.","mla":"Garrido-Charad, Florencia, et al. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” Proceedings of the National Academy of Sciences, vol. 115, no. 32, National Academy of Sciences, 2018, pp. E7615–23, doi:10.1073/pnas.1804517115.","ista":"Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, Fernandez P, López-Jury L, González-Cabrera C, Karten HJ, Luksch H, Marín GJ. 2018. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. 115(32), E7615–E7623.","apa":"Garrido-Charad, F., Vega Zuniga, T. A., Gutiérrez-Ibáñez, C., Fernandez, P., López-Jury, L., González-Cabrera, C., … Marín, G. J. (2018). “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1804517115","chicago":"Garrido-Charad, Florencia, Tomas A Vega Zuniga, Cristián Gutiérrez-Ibáñez, Pedro Fernandez, Luciana López-Jury, Cristian González-Cabrera, Harvey J. Karten, Harald Luksch, and Gonzalo J. Marín. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1804517115."},"intvolume":" 115","doi":"10.1073/pnas.1804517115","publication_status":"published","oa_version":"Submitted Version","date_published":"2018-08-07T00:00:00Z","status":"public","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"oa":1,"month":"08","abstract":[{"lang":"eng","text":"The optic tectum (TeO), or superior colliculus, is a multisensory midbrain center that organizes spatially orienting responses to relevant stimuli. To define the stimulus with the highest priority at each moment, a network of reciprocal connections between the TeO and the isthmi promotes competition between concurrent tectal inputs. In the avian midbrain, the neurons mediating enhancement and suppression of tectal inputs are located in separate isthmic nuclei, facilitating the analysis of the neural processes that mediate competition. A specific subset of radial neurons in the intermediate tectal layers relay retinal inputs to the isthmi, but at present it is unclear whether separate neurons innervate individual nuclei or a single neural type sends a common input to several of them. In this study, we used in vitro neural tracing and cell-filling experiments in chickens to show that single neurons innervate, via axon collaterals, the three nuclei that comprise the isthmotectal network. This demonstrates that the input signals representing the strength of the incoming stimuli are simultaneously relayed to the mechanisms promoting both enhancement and suppression of the input signals. By performing in vivo recordings in anesthetized chicks, we also show that this common input generates synchrony between both antagonistic mechanisms, demonstrating that activity enhancement and suppression are closely coordinated. From a computational point of view, these results suggest that these tectal neurons constitute integrative nodes that combine inputs from different sources to drive in parallel several concurrent neural processes, each performing complementary functions within the network through different firing patterns and connectivity."}],"issue":"32","date_updated":"2023-09-19T14:35:36Z","year":"2018","_id":"6010","article_processing_charge":"No","volume":115,"quality_controlled":"1","external_id":{"isi":["000440982000020"],"pmid":["30026198"]},"publication":"Proceedings of the National Academy of Sciences","date_created":"2019-02-14T14:33:34Z","page":"E7615-E7623","type":"journal_article","department":[{"_id":"MaJö"}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"National Academy of Sciences","title":"“Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network","pmid":1,"day":"07","author":[{"first_name":"Florencia","last_name":"Garrido-Charad","full_name":"Garrido-Charad, Florencia"},{"last_name":"Vega Zuniga","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas A","full_name":"Vega Zuniga, Tomas A"},{"first_name":"Cristián","last_name":"Gutiérrez-Ibáñez","full_name":"Gutiérrez-Ibáñez, Cristián"},{"last_name":"Fernandez","first_name":"Pedro","full_name":"Fernandez, Pedro"},{"full_name":"López-Jury, Luciana","last_name":"López-Jury","first_name":"Luciana"},{"full_name":"González-Cabrera, Cristian","last_name":"González-Cabrera","first_name":"Cristian"},{"first_name":"Harvey J.","last_name":"Karten","full_name":"Karten, Harvey J."},{"full_name":"Luksch, Harald","first_name":"Harald","last_name":"Luksch"},{"first_name":"Gonzalo J.","last_name":"Marín","full_name":"Marín, Gonzalo J."}],"isi":1},{"external_id":{"isi":["000683379202095"],"arxiv":["1703.01678"]},"quality_controlled":"1","volume":80,"article_processing_charge":"No","type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"ChLa"}],"date_created":"2019-02-14T14:51:57Z","page":"2815-2824","publication":"Proceedings of the 35 th International Conference on Machine Learning","publisher":"ML Research Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Data-dependent stability of stochastic gradient descent","project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"isi":1,"author":[{"last_name":"Kuzborskij","first_name":"Ilja","full_name":"Kuzborskij, Ilja"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"day":"01","intvolume":" 80","citation":{"chicago":"Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic Gradient Descent.” In Proceedings of the 35 Th International Conference on Machine Learning, 80:2815–24. ML Research Press, 2018.","mla":"Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic Gradient Descent.” Proceedings of the 35 Th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 2815–24.","apa":"Kuzborskij, I., & Lampert, C. (2018). Data-dependent stability of stochastic gradient descent. In Proceedings of the 35 th International Conference on Machine Learning (Vol. 80, pp. 2815–2824). Stockholm, Sweden: ML Research Press.","ista":"Kuzborskij I, Lampert C. 2018. Data-dependent stability of stochastic gradient descent. Proceedings of the 35 th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 80, 2815–2824.","ieee":"I. Kuzborskij and C. Lampert, “Data-dependent stability of stochastic gradient descent,” in Proceedings of the 35 th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 2815–2824.","ama":"Kuzborskij I, Lampert C. Data-dependent stability of stochastic gradient descent. In: Proceedings of the 35 Th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:2815-2824.","short":"I. Kuzborskij, C. Lampert, in:, Proceedings of the 35 Th International Conference on Machine Learning, ML Research Press, 2018, pp. 2815–2824."},"main_file_link":[{"url":"https://arxiv.org/abs/1703.01678","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","date_published":"2018-02-01T00:00:00Z","publication_status":"published","conference":{"location":"Stockholm, Sweden","end_date":"2018-07-15","name":"ICML: International Conference on Machine Learning","start_date":"2018-07-10"},"month":"02","ec_funded":1,"status":"public","oa":1,"_id":"6011","date_updated":"2023-10-17T09:51:13Z","arxiv":1,"abstract":[{"text":"We establish a data-dependent notion of algorithmic stability for Stochastic Gradient Descent (SGD), and employ it to develop novel generalization bounds. This is in contrast to previous distribution-free algorithmic stability results for SGD which depend on the worst-case constants. By virtue of the data-dependent argument, our bounds provide new insights into learning with SGD on convex and non-convex problems. In the convex case, we show that the bound on the generalization error depends on the risk at the initialization point. In the non-convex case, we prove that the expected curvature of the objective function around the initialization point has crucial influence on the generalization error. In both cases, our results suggest a simple data-driven strategy to stabilize SGD by pre-screening its initialization. As a corollary, our results allow us to show optimistic generalization bounds that exhibit fast convergence rates for SGD subject to a vanishing empirical risk and low noise of stochastic gradient. ","lang":"eng"}],"year":"2018"},{"intvolume":" 80","citation":{"chicago":"Sahoo, Subham, Christoph Lampert, and Georg S Martius. “Learning Equations for Extrapolation and Control.” In Proceedings of the 35th International Conference on Machine Learning, 80:4442–50. ML Research Press, 2018.","ista":"Sahoo S, Lampert C, Martius GS. 2018. Learning equations for extrapolation and control. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 80, 4442–4450.","apa":"Sahoo, S., Lampert, C., & Martius, G. S. (2018). Learning equations for extrapolation and control. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 4442–4450). Stockholm, Sweden: ML Research Press.","mla":"Sahoo, Subham, et al. “Learning Equations for Extrapolation and Control.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 4442–50.","ieee":"S. Sahoo, C. Lampert, and G. S. Martius, “Learning equations for extrapolation and control,” in Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 4442–4450.","ama":"Sahoo S, Lampert C, Martius GS. Learning equations for extrapolation and control. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:4442-4450.","short":"S. Sahoo, C. Lampert, G.S. Martius, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 4442–4450."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.07259"}],"scopus_import":"1","date_published":"2018-02-01T00:00:00Z","oa_version":"Preprint","publication_status":"published","conference":{"start_date":"2018-07-10","name":"ICML: International Conference on Machine Learning","end_date":"2018-07-15","location":"Stockholm, Sweden"},"ec_funded":1,"month":"02","oa":1,"status":"public","_id":"6012","year":"2018","date_updated":"2023-10-17T09:50:53Z","arxiv":1,"abstract":[{"text":"We present an approach to identify concise equations from data using a shallow neural network approach. In contrast to ordinary black-box regression, this approach allows understanding functional relations and generalizing them from observed data to unseen parts of the parameter space. We show how to extend the class of learnable equations for a recently proposed equation learning network to include divisions, and we improve the learning and model selection strategy to be useful for challenging real-world data. For systems governed by analytical expressions, our method can in many cases identify the true underlying equation and extrapolate to unseen domains. We demonstrate its effectiveness by experiments on a cart-pendulum system, where only 2 random rollouts are required to learn the forward dynamics and successfully achieve the swing-up task.","lang":"eng"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/first-machine-learning-method-capable-of-accurate-extrapolation/","relation":"press_release","description":"News on IST Homepage"}]},"external_id":{"isi":["000683379204058"],"arxiv":["1806.07259"]},"volume":80,"quality_controlled":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"department":[{"_id":"ChLa"}],"type":"conference","date_created":"2019-02-14T15:21:07Z","page":"4442-4450","publication":"Proceedings of the 35th International Conference on Machine Learning","title":"Learning equations for extrapolation and control","publisher":"ML Research Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Sahoo","first_name":"Subham","full_name":"Sahoo, Subham"},{"first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph"},{"full_name":"Martius, Georg S","first_name":"Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"day":"01"},{"language":[{"iso":"eng"}],"department":[{"_id":"DaAl"}],"date_published":"2018-12-31T00:00:00Z","type":"conference","oa_version":"None","date_created":"2019-02-17T22:59:25Z","publication":"2018 IEEE International Workshop on Signal Processing Systems","conference":{"start_date":"2018-10-21","name":"SiPS: Workshop on Signal Processing Systems","end_date":"2018-10-24","location":"Cape Town, South Africa"},"publication_status":"published","doi":"10.1109/SiPS.2018.8598402","external_id":{"isi":["000465106800060"]},"citation":{"apa":"Stojanov, A., Smith, T. M., Alistarh, D.-A., & Puschel, M. (2018). Fast quantized arithmetic on x86: Trading compute for data movement. In 2018 IEEE International Workshop on Signal Processing Systems (Vol. 2018–October). Cape Town, South Africa: IEEE. https://doi.org/10.1109/SiPS.2018.8598402","mla":"Stojanov, Alen, et al. “Fast Quantized Arithmetic on X86: Trading Compute for Data Movement.” 2018 IEEE International Workshop on Signal Processing Systems, vol. 2018–October, 8598402, IEEE, 2018, doi:10.1109/SiPS.2018.8598402.","ista":"Stojanov A, Smith TM, Alistarh D-A, Puschel M. 2018. Fast quantized arithmetic on x86: Trading compute for data movement. 2018 IEEE International Workshop on Signal Processing Systems. SiPS: Workshop on Signal Processing Systems vol. 2018–October, 8598402.","chicago":"Stojanov, Alen, Tyler Michael Smith, Dan-Adrian Alistarh, and Markus Puschel. “Fast Quantized Arithmetic on X86: Trading Compute for Data Movement.” In 2018 IEEE International Workshop on Signal Processing Systems, Vol. 2018–October. IEEE, 2018. https://doi.org/10.1109/SiPS.2018.8598402.","short":"A. Stojanov, T.M. Smith, D.-A. Alistarh, M. Puschel, in:, 2018 IEEE International Workshop on Signal Processing Systems, IEEE, 2018.","ieee":"A. Stojanov, T. M. Smith, D.-A. Alistarh, and M. Puschel, “Fast quantized arithmetic on x86: Trading compute for data movement,” in 2018 IEEE International Workshop on Signal Processing Systems, Cape Town, South Africa, 2018, vol. 2018–October.","ama":"Stojanov A, Smith TM, Alistarh D-A, Puschel M. Fast quantized arithmetic on x86: Trading compute for data movement. In: 2018 IEEE International Workshop on Signal Processing Systems. Vol 2018-October. IEEE; 2018. doi:10.1109/SiPS.2018.8598402"},"quality_controlled":"1","volume":"2018-October","scopus_import":"1","article_processing_charge":"No","_id":"6031","article_number":"8598402","isi":1,"author":[{"full_name":"Stojanov, Alen","last_name":"Stojanov","first_name":"Alen"},{"first_name":"Tyler Michael","last_name":"Smith","full_name":"Smith, Tyler Michael"},{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Markus","last_name":"Puschel","full_name":"Puschel, Markus"}],"day":"31","year":"2018","date_updated":"2023-09-19T14:41:51Z","abstract":[{"lang":"eng","text":"We introduce Clover, a new library for efficient computation using low-precision data, providing mathematical routines required by fundamental methods in optimization and sparse recovery. Our library faithfully implements variants of stochastic quantization that guarantee convergence at low precision, and supports data formats from 4-bit quantized to 32-bit IEEE-754 on current Intel processors. In particular, we show that 4-bit can be implemented efficiently using Intel AVX despite the lack of native support for this data format. Experimental results with dot product, matrix-vector multiplication (MVM), gradient descent (GD), and iterative hard thresholding (IHT) demonstrate that the attainable speedups are in many cases close to linear with respect to the reduction of precision due to reduced data movement. Finally, for GD and IHT, we show examples of absolute speedup achieved by 4-bit versus 32-bit, by iterating until a given target error is achieved."}],"month":"12","title":"Fast quantized arithmetic on x86: Trading compute for data movement","publisher":"IEEE","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"VlKo"}],"date_created":"2019-02-17T22:59:25Z","publication":"ACM Transactions on Algorithms","external_id":{"arxiv":["1602.03124"],"isi":["000468036500007"]},"quality_controlled":"1","volume":15,"related_material":{"record":[{"id":"1192","relation":"earlier_version","status":"public"}]},"article_processing_charge":"No","article_type":"original","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"isi":1,"author":[{"full_name":"Kazda, Alexandr","last_name":"Kazda","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandr"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"},{"last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Rolinek, Michal"}],"day":"01","publisher":"ACM","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Even delta-matroids and the complexity of planar boolean CSPs","oa_version":"Preprint","date_published":"2018-12-01T00:00:00Z","publication_status":"published","doi":"10.1145/3230649","citation":{"ama":"Kazda A, Kolmogorov V, Rolinek M. Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. 2018;15(2). doi:10.1145/3230649","ieee":"A. Kazda, V. Kolmogorov, and M. Rolinek, “Even delta-matroids and the complexity of planar boolean CSPs,” ACM Transactions on Algorithms, vol. 15, no. 2. ACM, 2018.","short":"A. Kazda, V. Kolmogorov, M. Rolinek, ACM Transactions on Algorithms 15 (2018).","ista":"Kazda A, Kolmogorov V, Rolinek M. 2018. Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. 15(2), 22.","apa":"Kazda, A., Kolmogorov, V., & Rolinek, M. (2018). Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. ACM. https://doi.org/10.1145/3230649","mla":"Kazda, Alexandr, et al. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs.” ACM Transactions on Algorithms, vol. 15, no. 2, 22, ACM, 2018, doi:10.1145/3230649.","chicago":"Kazda, Alexandr, Vladimir Kolmogorov, and Michal Rolinek. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs.” ACM Transactions on Algorithms. ACM, 2018. https://doi.org/10.1145/3230649."},"intvolume":" 15","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.03124"}],"article_number":"22","_id":"6032","date_updated":"2023-09-20T11:20:26Z","abstract":[{"text":"The main result of this article is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Using a reduction to even Δ-matroids, we then extend the tractability result to larger classes of Δ-matroids that we call efficiently coverable. It properly includes classes that were known to be tractable before, namely, co-independent, compact, local, linear, and binary, with the following caveat:We represent Δ-matroids by lists of tuples, while the last two use a representation by matrices. Since an n ×n matrix can represent exponentially many tuples, our tractability result is not strictly stronger than the known algorithm for linear and binary Δ-matroids.","lang":"eng"}],"issue":"2","arxiv":1,"year":"2018","month":"12","ec_funded":1,"status":"public","oa":1}]