[{"language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","ec_funded":1,"date_published":"2016-12-01T00:00:00Z","month":"12","scopus_import":"1","title":"Lifelong learning with weighted majority votes","intvolume":"        29","_id":"1098","year":"2016","pubrep_id":"775","date_updated":"2025-06-03T11:35:58Z","project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_created":"2018-12-11T11:50:08Z","author":[{"full_name":"Pentina, Anastasia","first_name":"Anastasia","last_name":"Pentina","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Urner","first_name":"Ruth","full_name":"Urner, Ruth"}],"abstract":[{"lang":"eng","text":"Better understanding of the potential benefits of information transfer and representation learning is an important step towards the goal of building intelligent systems that are able to persist in the world and learn over time. In this work, we consider a setting where the learner encounters a stream of tasks but is able to retain only limited information from each encountered task, such as a learned predictor. In contrast to most previous works analyzing this scenario, we do not make any distributional assumptions on the task generating process. Instead, we formulate a complexity measure that captures the diversity of the observed tasks. We provide a lifelong learning algorithm with error guarantees for every observed task (rather than on average). We show sample complexity reductions in comparison to solving every task in isolation in terms of our task complexity measure. Further, our algorithmic framework can naturally be viewed as learning a representation from encountered tasks with a neural network."}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":29,"oa":1,"file_date_updated":"2018-12-12T10:12:43Z","page":"3619-3627","conference":{"start_date":"2016-12-05","location":"Barcelona, Spain","name":"NIPS: Neural Information Processing Systems","end_date":"2016-12-10"},"acknowledgement":"This work was in parts funded by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 308036.\r\n\r\n","publist_id":"6277","day":"01","citation":{"mla":"Pentina, Anastasia, and Ruth Urner. <i>Lifelong Learning with Weighted Majority Votes</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 3619–27.","ista":"Pentina A, Urner R. 2016. Lifelong learning with weighted majority votes. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3619–3627.","chicago":"Pentina, Anastasia, and Ruth Urner. “Lifelong Learning with Weighted Majority Votes,” 29:3619–27. Neural Information Processing Systems Foundation, 2016.","ama":"Pentina A, Urner R. Lifelong learning with weighted majority votes. In: Vol 29. Neural Information Processing Systems Foundation; 2016:3619-3627.","apa":"Pentina, A., &#38; Urner, R. (2016). Lifelong learning with weighted majority votes (Vol. 29, pp. 3619–3627). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems Foundation.","short":"A. Pentina, R. Urner, in:, Neural Information Processing Systems Foundation, 2016, pp. 3619–3627.","ieee":"A. Pentina and R. Urner, “Lifelong learning with weighted majority votes,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 3619–3627."},"department":[{"_id":"ChLa"}],"file":[{"access_level":"open_access","creator":"system","date_updated":"2018-12-12T10:12:42Z","file_name":"IST-2017-775-v1+1_main.pdf","date_created":"2018-12-12T10:12:42Z","relation":"main_file","file_size":237111,"content_type":"application/pdf","file_id":"4961"},{"content_type":"application/pdf","file_size":185818,"file_id":"4962","creator":"system","access_level":"open_access","file_name":"IST-2017-775-v1+2_supplementary.pdf","date_updated":"2018-12-12T10:12:43Z","date_created":"2018-12-12T10:12:43Z","relation":"main_file"}],"alternative_title":["Advances in Neural Information Processing Systems"],"publication_status":"published","type":"conference","quality_controlled":"1","ddc":["006"],"publisher":"Neural Information Processing Systems Foundation","has_accepted_license":"1"},{"file_date_updated":"2018-12-12T10:12:01Z","conference":{"end_date":"2016-12-08","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","location":"Macao, China","start_date":"2016-12-05"},"acknowledgement":"The armadillo, bunny and dragon models are courtesy of the Stanford  3D  Scanning  Repository.   The  bimba,  fertility  and  elephant models are courtesy of the AIM@SHAPE Shape Repository.  \r\nThis project has received funding from the European Union’s Horizon 2020  research  and  innovation  programme  under  grant  agreement\r\nNo. 645599.","doi":"10.1145/2980179.2982397","issue":"6","article_number":"223","citation":{"mla":"Malomo, Luigi, et al. <i>FlexMolds: Automatic Design of Flexible Shells for Molding</i>. Vol. 35, no. 6, 223, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2980179.2982397\">10.1145/2980179.2982397</a>.","chicago":"Malomo, Luigi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “FlexMolds: Automatic Design of Flexible Shells for Molding,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2980179.2982397\">https://doi.org/10.1145/2980179.2982397</a>.","ista":"Malomo L, Pietroni N, Bickel B, Cignoni P. 2016. FlexMolds: Automatic design of flexible shells for molding. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 223.","apa":"Malomo, L., Pietroni, N., Bickel, B., &#38; Cignoni, P. (2016). FlexMolds: Automatic design of flexible shells for molding (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. <a href=\"https://doi.org/10.1145/2980179.2982397\">https://doi.org/10.1145/2980179.2982397</a>","ama":"Malomo L, Pietroni N, Bickel B, Cignoni P. FlexMolds: Automatic design of flexible shells for molding. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2980179.2982397\">10.1145/2980179.2982397</a>","short":"L. Malomo, N. Pietroni, B. Bickel, P. Cignoni, in:, ACM, 2016.","ieee":"L. Malomo, N. Pietroni, B. Bickel, and P. Cignoni, “FlexMolds: Automatic design of flexible shells for molding,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6."},"day":"01","publist_id":"6276","isi":1,"file":[{"content_type":"application/pdf","file_size":11122029,"file_id":"4918","access_level":"open_access","creator":"system","date_updated":"2018-12-12T10:12:01Z","file_name":"IST-2017-760-v1+1_flexmolds.pdf","date_created":"2018-12-12T10:12:01Z","relation":"main_file"}],"alternative_title":["ACM Transactions on Graphics"],"department":[{"_id":"BeBi"}],"quality_controlled":"1","type":"conference","publication_status":"published","ddc":["000","005"],"has_accepted_license":"1","publisher":"ACM","article_processing_charge":"No","language":[{"iso":"eng"}],"ec_funded":1,"status":"public","title":"FlexMolds: Automatic design of flexible shells for molding","month":"11","scopus_import":"1","date_published":"2016-11-01T00:00:00Z","_id":"1099","pubrep_id":"760","year":"2016","intvolume":"        35","date_updated":"2025-09-22T14:16:02Z","author":[{"full_name":"Malomo, Luigi","first_name":"Luigi","last_name":"Malomo"},{"last_name":"Pietroni","first_name":"Nico","full_name":"Pietroni, Nico"},{"first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"full_name":"Cignoni, Paolo","first_name":"Paolo","last_name":"Cignoni"}],"date_created":"2018-12-11T11:50:08Z","project":[{"call_identifier":"H2020","_id":"25082902-B435-11E9-9278-68D0E5697425","grant_number":"645599","name":"Soft-bodied intelligence for Manipulation"}],"oa_version":"Submitted Version","abstract":[{"text":"We present FlexMolds, a novel computational approach to automatically design flexible, reusable molds that, once 3D printed, allow us to physically fabricate, by means of liquid casting, multiple copies of complex shapes with rich surface details and complex topology. The approach to design such flexible molds is based on a greedy bottom-up search of possible cuts over an object, evaluating for each possible cut the feasibility of the resulting mold. We use a dynamic simulation approach to evaluate candidate molds, providing a heuristic to generate forces that are able to open, detach, and remove a complex mold from the object it surrounds. We have tested the approach with a number of objects with nontrivial shapes and topologies.","lang":"eng"}],"volume":35,"oa":1,"external_id":{"isi":["000388446200065"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"date_updated":"2025-09-22T14:14:58Z","author":[{"first_name":"Joshua","last_name":"Mitchell","full_name":"Mitchell, Joshua"},{"last_name":"Whitfield","first_name":"Jason","full_name":"Whitfield, Jason"},{"last_name":"Zhang","first_name":"William","full_name":"Zhang, William"},{"full_name":"Henneberger, Christian","last_name":"Henneberger","first_name":"Christian"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"},{"first_name":"Megan","last_name":"O'Mara","full_name":"O'Mara, Megan"},{"full_name":"Jackson, Colin","first_name":"Colin","last_name":"Jackson"}],"date_created":"2018-12-11T11:50:09Z","oa_version":"None","abstract":[{"text":"Optical sensors based on the phenomenon of Förster resonance energy transfer (FRET) are powerful tools that have advanced the study of small molecules in biological systems. However, sensor construction is not trivial and often requires multiple rounds of engineering or an ability to screen large numbers of variants. A method that would allow the accurate rational design of FRET sensors would expedite the production of biologically useful sensors. Here, we present Rangefinder, a computational algorithm that allows rapid in silico screening of dye attachment sites in a ligand-binding protein for the conjugation of a dye molecule to act as a Förster acceptor for a fused fluorescent protein. We present three ratiometric fluorescent sensors designed with Rangefinder, including a maltose sensor with a dynamic range of &gt;300% and the first sensors for the most abundant sialic acid in human cells, N-acetylneuraminic acid. Provided a ligand-binding protein exists, it is our expectation that this model will facilitate the design of an optical sensor for any small molecule of interest.","lang":"eng"}],"volume":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000388914800003"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","title":"Rangefinder: A semisynthetic FRET sensor design algorithm","month":"11","scopus_import":"1","date_published":"2016-11-10T00:00:00Z","_id":"1101","year":"2016","intvolume":"         1","department":[{"_id":"HaJa"}],"quality_controlled":"1","type":"journal_article","publication_status":"published","publication":"ACS SENSORS","publisher":"American Chemical Society","page":"1286 - 1290","acknowledgement":"J.A.M., J.H.W., and W.H.Z. were supported by Australian\r\nPostgraduate Awards (APA), AS Sargeson Supplementary\r\nscholarships, and RSC supplementary scholarships. C.J.J.\r\nacknowledges support from a Human Frontiers in Science\r\nYoung Investigator Award and a Discovery Project and Future\r\nFellowship from the Australian Research Council. M.L.O. is\r\nsupported by an Australian Research Council Discovery Project\r\n(DP130102153) and the Merit Allocation Scheme of the\r\nNational Computational Infrastructure.","issue":"11","doi":"10.1021/acssensors.6b00576","citation":{"ama":"Mitchell J, Whitfield J, Zhang W, et al. Rangefinder: A semisynthetic FRET sensor design algorithm. <i>ACS SENSORS</i>. 2016;1(11):1286-1290. doi:<a href=\"https://doi.org/10.1021/acssensors.6b00576\">10.1021/acssensors.6b00576</a>","apa":"Mitchell, J., Whitfield, J., Zhang, W., Henneberger, C., Janovjak, H. L., O’Mara, M., &#38; Jackson, C. (2016). Rangefinder: A semisynthetic FRET sensor design algorithm. <i>ACS SENSORS</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssensors.6b00576\">https://doi.org/10.1021/acssensors.6b00576</a>","chicago":"Mitchell, Joshua, Jason Whitfield, William Zhang, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” <i>ACS SENSORS</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acssensors.6b00576\">https://doi.org/10.1021/acssensors.6b00576</a>.","ista":"Mitchell J, Whitfield J, Zhang W, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2016. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. 1(11), 1286–1290.","mla":"Mitchell, Joshua, et al. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” <i>ACS SENSORS</i>, vol. 1, no. 11, American Chemical Society, 2016, pp. 1286–90, doi:<a href=\"https://doi.org/10.1021/acssensors.6b00576\">10.1021/acssensors.6b00576</a>.","ieee":"J. Mitchell <i>et al.</i>, “Rangefinder: A semisynthetic FRET sensor design algorithm,” <i>ACS SENSORS</i>, vol. 1, no. 11. American Chemical Society, pp. 1286–1290, 2016.","short":"J. Mitchell, J. Whitfield, W. Zhang, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, ACS SENSORS 1 (2016) 1286–1290."},"publist_id":"6274","day":"10","isi":1},{"date_published":"2016-09-01T00:00:00Z","scopus_import":1,"month":"09","title":"Improving weakly-supervised object localization by micro-annotation","year":"2016","_id":"1102","language":[{"iso":"eng"}],"status":"public","ec_funded":1,"abstract":[{"lang":"eng","text":"Weakly-supervised object localization methods tend to fail for object classes that consistently co-occur with the same background elements, e.g. trains on tracks. We propose a method to overcome these failures by adding a very small amount of model-specific additional annotation. The main idea is to cluster a deep network\\'s mid-level representations and assign object or distractor labels to each cluster. Experiments show substantially improved localization results on the challenging ILSVC2014 dataset for bounding box detection and the PASCAL VOC2012 dataset for semantic segmentation."}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":"2016-September","oa":1,"date_updated":"2021-01-12T06:48:18Z","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"}],"date_created":"2018-12-11T11:50:09Z","author":[{"full_name":"Kolesnikov, Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","first_name":"Alexander"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"doi":"10.5244/C.30.92","acknowledgement":"This work was funded in parts by the European Research Council\r\nunder the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant\r\nagreement no 308036. We gratefully acknowledge the support of NVIDIA Corporation with\r\nthe donation of the GPUs used for this research.","day":"01","publist_id":"6273","main_file_link":[{"url":"http://www.bmva.org/bmvc/2016/papers/paper092/paper092.pdf","open_access":"1"}],"citation":{"short":"A. Kolesnikov, C. Lampert, in:, Proceedings of the British Machine Vision Conference 2016, BMVA Press, 2016, p. 92.1-92.12.","ieee":"A. Kolesnikov and C. Lampert, “Improving weakly-supervised object localization by micro-annotation,” in <i>Proceedings of the British Machine Vision Conference 2016</i>, York, United Kingdom, 2016, vol. 2016–September, p. 92.1-92.12.","mla":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” <i>Proceedings of the British Machine Vision Conference 2016</i>, vol. 2016–September, BMVA Press, 2016, p. 92.1-92.12, doi:<a href=\"https://doi.org/10.5244/C.30.92\">10.5244/C.30.92</a>.","ista":"Kolesnikov A, Lampert C. 2016. Improving weakly-supervised object localization by micro-annotation. Proceedings of the British Machine Vision Conference 2016. BMVC: British Machine Vision Conference vol. 2016–September, 92.1-92.12.","chicago":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” In <i>Proceedings of the British Machine Vision Conference 2016</i>, 2016–September:92.1-92.12. BMVA Press, 2016. <a href=\"https://doi.org/10.5244/C.30.92\">https://doi.org/10.5244/C.30.92</a>.","apa":"Kolesnikov, A., &#38; Lampert, C. (2016). Improving weakly-supervised object localization by micro-annotation. In <i>Proceedings of the British Machine Vision Conference 2016</i> (Vol. 2016–September, p. 92.1-92.12). York, United Kingdom: BMVA Press. <a href=\"https://doi.org/10.5244/C.30.92\">https://doi.org/10.5244/C.30.92</a>","ama":"Kolesnikov A, Lampert C. Improving weakly-supervised object localization by micro-annotation. In: <i>Proceedings of the British Machine Vision Conference 2016</i>. Vol 2016-September. BMVA Press; 2016:92.1-92.12. doi:<a href=\"https://doi.org/10.5244/C.30.92\">10.5244/C.30.92</a>"},"page":"92.1-92.12","conference":{"location":"York, United Kingdom","end_date":"2016-09-22","name":"BMVC: British Machine Vision Conference","start_date":"2016-09-19"},"publication":"Proceedings of the British Machine Vision Conference 2016","publisher":"BMVA Press","department":[{"_id":"ChLa"}],"publication_status":"published","type":"conference","quality_controlled":"1"},{"publisher":"IEEE","department":[{"_id":"ToHe"}],"type":"conference","publication_status":"published","quality_controlled":"1","article_number":"7797741","acknowledgement":"This work was supported in part by DST-SERB, GoI under Project No. YSS/2014/000623 and by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","doi":"10.1109/MEMCOD.2016.7797741","main_file_link":[{"url":"https://arxiv.org/abs/1606.05473","open_access":"1"}],"citation":{"mla":"Gurung, Amit, et al. <i>Parallel Reachability Analysis for Hybrid Systems</i>. 7797741, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">10.1109/MEMCOD.2016.7797741</a>.","ista":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. 2016. Parallel reachability analysis for hybrid systems. MEMOCODE: Conference on Formal Methods and Models for System Design, 7797741.","chicago":"Gurung, Amit, Arup Deka, Ezio Bartocci, Sergiy Bogomolov, Radu Grosu, and Rajarshi Ray. “Parallel Reachability Analysis for Hybrid Systems.” IEEE, 2016. <a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">https://doi.org/10.1109/MEMCOD.2016.7797741</a>.","ama":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. Parallel reachability analysis for hybrid systems. In: IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">10.1109/MEMCOD.2016.7797741</a>","apa":"Gurung, A., Deka, A., Bartocci, E., Bogomolov, S., Grosu, R., &#38; Ray, R. (2016). Parallel reachability analysis for hybrid systems. Presented at the MEMOCODE: Conference on Formal Methods and Models for System Design, Kanpur, India : IEEE. <a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">https://doi.org/10.1109/MEMCOD.2016.7797741</a>","short":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, R. Ray, in:, IEEE, 2016.","ieee":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, and R. Ray, “Parallel reachability analysis for hybrid systems,” presented at the MEMOCODE: Conference on Formal Methods and Models for System Design, Kanpur, India , 2016."},"day":"27","publist_id":"6272","conference":{"start_date":"2016-11-18","location":"Kanpur, India ","name":"MEMOCODE: Conference on Formal Methods and Models for System Design","end_date":"2016-11-20"},"abstract":[{"lang":"eng","text":"We propose two parallel state-space-exploration algorithms for hybrid automaton (HA), with the goal of enhancing performance on multi-core shared-memory systems. The first uses the parallel, breadth-first-search algorithm (PBFS) of the SPIN model checker, when traversing the discrete modes of the HA, and enhances it with a parallel exploration of the continuous states within each mode. We show that this simple-minded extension of PBFS does not provide the desired load balancing in many HA benchmarks. The second algorithm is a task-parallel BFS algorithm (TP-BFS), which uses a cheap precomputation of the cost associated with the post operations (both continuous and discrete) in order to improve load balancing. We illustrate the TP-BFS and the cost precomputation of the post operators on a support-function-based algorithm for state-space exploration. The performance comparison of the two algorithms shows that, in general, TP-BFS provides a better utilization/load-balancing of the CPU. Both algorithms are implemented in the model checker XSpeed. Our experiments show a maximum speed-up of more than 2000 χ on a navigation benchmark, with respect to SpaceEx LGG scenario. In order to make the comparison fair, we employed an equal number of post operations in both tools. To the best of our knowledge, this paper represents the first attempt to provide parallel, reachability-analysis algorithms for HA."}],"oa_version":"Preprint","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1606.05473"]},"oa":1,"date_updated":"2025-06-04T11:52:29Z","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"author":[{"last_name":"Gurung","first_name":"Amit","full_name":"Gurung, Amit"},{"full_name":"Deka, Arup","first_name":"Arup","last_name":"Deka"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","last_name":"Bogomolov","first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grosu, Radu","last_name":"Grosu","first_name":"Radu"},{"full_name":"Ray, Rajarshi","last_name":"Ray","first_name":"Rajarshi"}],"date_created":"2018-12-11T11:50:09Z","date_published":"2016-12-27T00:00:00Z","title":"Parallel reachability analysis for hybrid systems","scopus_import":"1","month":"12","_id":"1103","year":"2016","language":[{"iso":"eng"}],"article_processing_charge":"No","ec_funded":1,"status":"public"},{"publisher":"Neural Information Processing Systems Foundation","department":[{"_id":"GaTk"}],"alternative_title":["Advances in Neural Information Processing Systems"],"corr_author":"1","type":"conference","publication_status":"published","quality_controlled":"1","acknowledgement":"We  thank  Jozsef  Csicsvari  for  kindly  sharing  the  CA1  data.\r\nThis work was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no. 291734.","citation":{"apa":"Savin, C., &#38; Tkačik, G. (2016). Estimating nonlinear neural response functions using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information Processing Systems Foundation.","ama":"Savin C, Tkačik G. Estimating nonlinear neural response functions using GP priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems Foundation; 2016:3610-3618.","chicago":"Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information Processing Systems Foundation, 2016.","ista":"Savin C, Tkačik G. 2016. Estimating nonlinear neural response functions using GP priors and Kronecker methods. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3610–3618.","mla":"Savin, Cristina, and Gašper Tkačik. <i>Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 3610–18.","ieee":"C. Savin and G. Tkačik, “Estimating nonlinear neural response functions using GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.","short":"C. Savin, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, pp. 3610–3618."},"main_file_link":[{"url":"http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods","open_access":"1"}],"publist_id":"6265","day":"01","conference":{"start_date":"2016-12-05","location":"Barcelona; Spain","name":"NIPS: Neural Information Processing Systems","end_date":"2016-12-10"},"page":"3610-3618","abstract":[{"lang":"eng","text":"Jointly characterizing neural responses in terms of several external variables promises novel insights into circuit function, but remains computationally prohibitive in practice. Here we use gaussian process (GP) priors and exploit recent advances in fast GP inference and learning based on Kronecker methods, to efficiently estimate multidimensional nonlinear tuning functions. Our estimator require considerably less data than traditional methods and further provides principled uncertainty estimates. We apply these tools to hippocampal recordings during open field exploration and use them to characterize the joint dependence of CA1 responses on the position of the animal and several other variables, including the animal\\'s speed, direction of motion, and network oscillations.Our results provide an unprecedentedly detailed quantification of the tuning of hippocampal neurons. The model\\'s generality suggests that our approach can be used to estimate neural response properties in other brain regions."}],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":29,"oa":1,"date_updated":"2025-06-03T11:36:49Z","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"author":[{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","first_name":"Cristina","full_name":"Savin, Cristina"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"}],"date_created":"2018-12-11T11:50:10Z","date_published":"2016-12-01T00:00:00Z","title":"Estimating nonlinear neural response functions using GP priors and Kronecker methods","scopus_import":"1","month":"12","intvolume":"        29","year":"2016","_id":"1105","language":[{"iso":"eng"}],"article_processing_charge":"No","ec_funded":1,"status":"public"},{"date_updated":"2025-04-22T13:41:54Z","author":[{"last_name":"Rueda","first_name":"Alfredo","full_name":"Rueda, Alfredo"},{"full_name":"Sedlmeir, Florian","first_name":"Florian","last_name":"Sedlmeir"},{"full_name":"Collodo, Michele","first_name":"Michele","last_name":"Collodo"},{"first_name":"Ulrich","last_name":"Vogl","full_name":"Vogl, Ulrich"},{"full_name":"Stiller, Birgit","first_name":"Birgit","last_name":"Stiller"},{"full_name":"Schunk, Georg","last_name":"Schunk","first_name":"Georg"},{"last_name":"Strekalov","first_name":"Dimitry","full_name":"Strekalov, Dimitry"},{"first_name":"Christoph","last_name":"Marquardt","full_name":"Marquardt, Christoph"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Oskar","last_name":"Painter","full_name":"Painter, Oskar"},{"last_name":"Leuchs","first_name":"Gerd","full_name":"Leuchs, Gerd"},{"first_name":"Harald","last_name":"Schwefel","full_name":"Schwefel, Harald"}],"date_created":"2018-12-11T11:50:14Z","oa_version":"Preprint","arxiv":1,"abstract":[{"lang":"eng","text":"We present a coherent microwave to telecom signal converter based on the electro-optical effect using a crystalline WGM-resonator coupled to a 3D microwave cavity, achieving high photon conversion efficiency of 0.1% with MHz bandwidth."}],"oa":1,"external_id":{"arxiv":["1601.07261"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","title":"Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator","scopus_import":"1","month":"12","date_published":"2016-12-16T00:00:00Z","_id":"1115","year":"2016","department":[{"_id":"JoFi"}],"quality_controlled":"1","type":"conference","publication_status":"published","related_material":{"link":[{"url":"http://ieeexplore.ieee.org/document/7788479/","relation":"other"}]},"publisher":"IEEE","conference":{"start_date":"2016-06-05","name":"CLEO: Conference on Lasers and Electro Optics","end_date":"2016-06-10","location":"San Jose, CA, USA"},"doi":"10.1364/CLEO_SI.2016.SF2G.3","article_number":"7788479","citation":{"ieee":"A. Rueda <i>et al.</i>, “Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator,” presented at the CLEO: Conference on Lasers and Electro Optics, San Jose, CA, USA, 2016.","short":"A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov, C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, in:, IEEE, 2016.","ama":"Rueda A, Sedlmeir F, Collodo M, et al. Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. In: IEEE; 2016. doi:<a href=\"https://doi.org/10.1364/CLEO_SI.2016.SF2G.3\">10.1364/CLEO_SI.2016.SF2G.3</a>","apa":"Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., … Schwefel, H. (2016). Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. Presented at the CLEO: Conference on Lasers and Electro Optics, San Jose, CA, USA: IEEE. <a href=\"https://doi.org/10.1364/CLEO_SI.2016.SF2G.3\">https://doi.org/10.1364/CLEO_SI.2016.SF2G.3</a>","ista":"Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D, Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. CLEO: Conference on Lasers and Electro Optics, 7788479.","chicago":"Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit Stiller, Georg Schunk, Dimitry Strekalov, et al. “Efficient Single Sideband Microwave to Optical Conversion Using a LiNbO₃ WGM-Resonator.” IEEE, 2016. <a href=\"https://doi.org/10.1364/CLEO_SI.2016.SF2G.3\">https://doi.org/10.1364/CLEO_SI.2016.SF2G.3</a>.","mla":"Rueda, Alfredo, et al. <i>Efficient Single Sideband Microwave to Optical Conversion Using a LiNbO₃ WGM-Resonator</i>. 7788479, IEEE, 2016, doi:<a href=\"https://doi.org/10.1364/CLEO_SI.2016.SF2G.3\">10.1364/CLEO_SI.2016.SF2G.3</a>."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.07261"}],"publist_id":"6251","day":"16"},{"date_updated":"2021-01-12T06:48:32Z","department":[{"_id":"ToHe"}],"author":[{"full_name":"Duggirala, Parasara","first_name":"Parasara","last_name":"Duggirala"},{"last_name":"Fan","first_name":"Chuchu","full_name":"Fan, Chuchu"},{"full_name":"Potok, Matthew","last_name":"Potok","first_name":"Matthew"},{"full_name":"Qi, Bolun","first_name":"Bolun","last_name":"Qi"},{"first_name":"Sayan","last_name":"Mitra","full_name":"Mitra, Sayan"},{"last_name":"Viswanathan","first_name":"Mahesh","full_name":"Viswanathan, Mahesh"},{"first_name":"Stanley","last_name":"Bak","full_name":"Bak, Stanley"},{"full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","last_name":"Bogomolov","first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Johnson","first_name":"Taylor","full_name":"Johnson, Taylor"},{"full_name":"Nguyen, Luan","first_name":"Luan","last_name":"Nguyen"},{"orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","first_name":"Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sogokon, Andrew","first_name":"Andrew","last_name":"Sogokon"},{"first_name":"Hoang","last_name":"Tran","full_name":"Tran, Hoang"},{"last_name":"Xiang","first_name":"Weiming","full_name":"Xiang, Weiming"}],"quality_controlled":"1","date_created":"2018-12-11T11:50:20Z","type":"conference","publication_status":"published","oa_version":"None","abstract":[{"text":"Hybrid systems have both continuous and discrete dynamics and are useful for modeling a variety of control systems, from air traffic control protocols to robotic maneuvers and beyond. Recently, numerous powerful and scalable tools for analyzing hybrid systems have emerged. Several of these tools implement automated formal methods for mathematically proving a system meets a specification. This tutorial session will present three recent hybrid systems tools: C2E2, HyST, and TuLiP. C2E2 is a simulated-based verification tool for hybrid systems, and uses validated numerical solvers and bloating of simulation traces to verify systems meet specifications. HyST is a hybrid systems model transformation and translation tool, and uses a canonical intermediate representation to support most of the recent verification tools, as well as automated sound abstractions that simplify verification of a given hybrid system. TuLiP is a controller synthesis tool for hybrid systems, where given a temporal logic specification to be satisfied for a system (plant) model, TuLiP will find a controller that meets a given specification. © 2016 IEEE.","lang":"eng"}],"publication":"2016 IEEE Conference on Control Applications","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","language":[{"iso":"eng"}],"status":"public","conference":{"end_date":"2016-09-22","name":"CCA: Control Applications ","location":"Buenos Aires, Argentina ","start_date":"2016-09-19"},"title":"Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP","scopus_import":1,"doi":"10.1109/CCA.2016.7587948","month":"10","date_published":"2016-10-10T00:00:00Z","article_number":"7587948","_id":"1134","year":"2016","citation":{"mla":"Duggirala, Parasara, et al. “Tutorial: Software Tools for Hybrid Systems Verification Transformation and Synthesis C2E2 HyST and TuLiP.” <i>2016 IEEE Conference on Control Applications</i>, 7587948, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/CCA.2016.7587948\">10.1109/CCA.2016.7587948</a>.","chicago":"Duggirala, Parasara, Chuchu Fan, Matthew Potok, Bolun Qi, Sayan Mitra, Mahesh Viswanathan, Stanley Bak, et al. “Tutorial: Software Tools for Hybrid Systems Verification Transformation and Synthesis C2E2 HyST and TuLiP.” In <i>2016 IEEE Conference on Control Applications</i>. IEEE, 2016. <a href=\"https://doi.org/10.1109/CCA.2016.7587948\">https://doi.org/10.1109/CCA.2016.7587948</a>.","ista":"Duggirala P, Fan C, Potok M, Qi B, Mitra S, Viswanathan M, Bak S, Bogomolov S, Johnson T, Nguyen L, Schilling C, Sogokon A, Tran H, Xiang W. 2016. Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP. 2016 IEEE Conference on Control Applications. CCA: Control Applications , 7587948.","ama":"Duggirala P, Fan C, Potok M, et al. Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP. In: <i>2016 IEEE Conference on Control Applications</i>. IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/CCA.2016.7587948\">10.1109/CCA.2016.7587948</a>","apa":"Duggirala, P., Fan, C., Potok, M., Qi, B., Mitra, S., Viswanathan, M., … Xiang, W. (2016). Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP. In <i>2016 IEEE Conference on Control Applications</i>. Buenos Aires, Argentina : IEEE. <a href=\"https://doi.org/10.1109/CCA.2016.7587948\">https://doi.org/10.1109/CCA.2016.7587948</a>","short":"P. Duggirala, C. Fan, M. Potok, B. Qi, S. Mitra, M. Viswanathan, S. Bak, S. Bogomolov, T. Johnson, L. Nguyen, C. Schilling, A. Sogokon, H. Tran, W. Xiang, in:, 2016 IEEE Conference on Control Applications, IEEE, 2016.","ieee":"P. Duggirala <i>et al.</i>, “Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP,” in <i>2016 IEEE Conference on Control Applications</i>, Buenos Aires, Argentina , 2016."},"day":"10","publist_id":"6224"},{"title":"Synthesizing time triggered schedules for switched networks with faulty links","scopus_import":"1","month":"10","date_published":"2016-10-01T00:00:00Z","pubrep_id":"644","_id":"1135","year":"2016","article_processing_charge":"No","language":[{"iso":"eng"}],"ec_funded":1,"status":"public","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Time-triggered (TT) switched networks are a deterministic communication infrastructure used by real-time distributed embedded systems. These networks rely on the notion of globally discretized time (i.e. time slots) and a static TT schedule that prescribes which message is sent through which link at every time slot, such that all messages reach their destination before a global timeout. These schedules are generated offline, assuming a static network with fault-free links, and entrusting all error-handling functions to the end user. Assuming the network is static is an over-optimistic view, and indeed links tend to fail in practice. We study synthesis of TT schedules on a network in which links fail over time and we assume the switches run a very simple error-recovery protocol once they detect a crashed link. We address the problem of finding a pk; qresistant schedule; namely, one that, assuming the switches run a fixed error-recovery protocol, guarantees that the number of messages that arrive at their destination by the timeout is at least no matter what sequence of at most k links fail. Thus, we maintain the simplicity of the switches while giving a guarantee on the number of messages that meet the timeout. We show how a pk; q-resistant schedule can be obtained using a CEGAR-like approach: find a schedule, decide whether it is pk; q-resistant, and if it is not, use the witnessing fault sequence to generate a constraint that is added to the program. The newly added constraint disallows the schedule to be regenerated in a future iteration while also eliminating several other schedules that are not pk; q-resistant. We illustrate the applicability of our approach using an SMT-based implementation. © 2016 ACM."}],"oa":1,"external_id":{"isi":["000414220100026"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:14:05Z","author":[{"orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","first_name":"Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shibashis","last_name":"Guha","full_name":"Guha, Shibashis"},{"first_name":"Guillermo","last_name":"Rodríguez Navas","full_name":"Rodríguez Navas, Guillermo"}],"date_created":"2018-12-11T11:50:20Z","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems"}],"doi":"10.1145/2968478.2968499","article_number":"26","citation":{"short":"G. Avni, S. Guha, G. Rodríguez Navas, in:, Proceedings of the 13th International Conference on Embedded Software , ACM, 2016.","ieee":"G. Avni, S. Guha, and G. Rodríguez Navas, “Synthesizing time triggered schedules for switched networks with faulty links,” in <i>Proceedings of the 13th International Conference on Embedded Software </i>, Pittsburgh, PA, USA, 2016.","mla":"Avni, Guy, et al. “Synthesizing Time Triggered Schedules for Switched Networks with Faulty Links.” <i>Proceedings of the 13th International Conference on Embedded Software </i>, 26, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2968478.2968499\">10.1145/2968478.2968499</a>.","chicago":"Avni, Guy, Shibashis Guha, and Guillermo Rodríguez Navas. “Synthesizing Time Triggered Schedules for Switched Networks with Faulty Links.” In <i>Proceedings of the 13th International Conference on Embedded Software </i>. ACM, 2016. <a href=\"https://doi.org/10.1145/2968478.2968499\">https://doi.org/10.1145/2968478.2968499</a>.","ista":"Avni G, Guha S, Rodríguez Navas G. 2016. Synthesizing time triggered schedules for switched networks with faulty links. Proceedings of the 13th International Conference on Embedded Software . EMSOFT: Embedded Software , 26.","apa":"Avni, G., Guha, S., &#38; Rodríguez Navas, G. (2016). Synthesizing time triggered schedules for switched networks with faulty links. In <i>Proceedings of the 13th International Conference on Embedded Software </i>. Pittsburgh, PA, USA: ACM. <a href=\"https://doi.org/10.1145/2968478.2968499\">https://doi.org/10.1145/2968478.2968499</a>","ama":"Avni G, Guha S, Rodríguez Navas G. Synthesizing time triggered schedules for switched networks with faulty links. In: <i>Proceedings of the 13th International Conference on Embedded Software </i>. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2968478.2968499\">10.1145/2968478.2968499</a>"},"isi":1,"day":"01","publist_id":"6223","file_date_updated":"2018-12-12T10:09:31Z","conference":{"start_date":"2016-10-01","location":"Pittsburgh, PA, USA","name":"EMSOFT: Embedded Software ","end_date":"2016-10-07"},"publication":"Proceedings of the 13th International Conference on Embedded Software ","ddc":["000"],"has_accepted_license":"1","publisher":"ACM","file":[{"access_level":"open_access","creator":"system","file_name":"IST-2016-644-v1+1_emsoft-no-format.pdf","date_updated":"2018-12-12T10:09:31Z","date_created":"2018-12-12T10:09:31Z","relation":"main_file","file_size":279240,"content_type":"application/pdf","file_id":"4755"}],"department":[{"_id":"ToHe"}],"quality_controlled":"1","type":"conference","publication_status":"published"},{"department":[{"_id":"ChWo"}],"publication_status":"published","type":"conference","quality_controlled":"1","publication":"Proceedings of the 9th International Conference on Motion in Games ","ddc":["004"],"publisher":"ACM","has_accepted_license":"1","conference":{"start_date":"2016-10-10","end_date":"2016-10-12","name":"MIG: Motion in Games","location":"San Francisco, CA, USA"},"article_number":"2994261","doi":"10.1145/2994258.2994261","acknowledgement":"This work was partly supported by the starting grant BigSplash, as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2014-StG 638176 , and ERC-2011-ADG 20110209).","publist_id":"6222","day":"10","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01367181"}],"citation":{"ama":"Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. Space-time sculpting of liquid animation. In: <i>Proceedings of the 9th International Conference on Motion in Games </i>. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2994258.2994261\">10.1145/2994258.2994261</a>","apa":"Manteaux, P., Vimont, U., Wojtan, C., Rohmer, D., &#38; Cani, M. (2016). Space-time sculpting of liquid animation. In <i>Proceedings of the 9th International Conference on Motion in Games </i>. San Francisco, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2994258.2994261\">https://doi.org/10.1145/2994258.2994261</a>","ista":"Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. 2016. Space-time sculpting of liquid animation. Proceedings of the 9th International Conference on Motion in Games . MIG: Motion in Games, 2994261.","chicago":"Manteaux, Pierre, Ulysse Vimont, Chris Wojtan, Damien Rohmer, and Marie Cani. “Space-Time Sculpting of Liquid Animation.” In <i>Proceedings of the 9th International Conference on Motion in Games </i>. ACM, 2016. <a href=\"https://doi.org/10.1145/2994258.2994261\">https://doi.org/10.1145/2994258.2994261</a>.","mla":"Manteaux, Pierre, et al. “Space-Time Sculpting of Liquid Animation.” <i>Proceedings of the 9th International Conference on Motion in Games </i>, 2994261, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2994258.2994261\">10.1145/2994258.2994261</a>.","ieee":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, and M. Cani, “Space-time sculpting of liquid animation,” in <i>Proceedings of the 9th International Conference on Motion in Games </i>, San Francisco, CA, USA, 2016.","short":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, M. Cani, in:, Proceedings of the 9th International Conference on Motion in Games , ACM, 2016."},"date_updated":"2024-10-22T09:58:18Z","project":[{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_created":"2018-12-11T11:50:20Z","author":[{"full_name":"Manteaux, Pierre","last_name":"Manteaux","first_name":"Pierre"},{"full_name":"Vimont, Ulysse","first_name":"Ulysse","last_name":"Vimont"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"},{"last_name":"Rohmer","first_name":"Damien","full_name":"Rohmer, Damien"},{"last_name":"Cani","first_name":"Marie","full_name":"Cani, Marie"}],"abstract":[{"lang":"eng","text":"We propose an interactive sculpting system for seamlessly editing pre-computed animations of liquid, without the need for any resimulation. The input is a sequence of meshes without correspondences representing the liquid surface over time. Our method enables the efficient selection of consistent space-time parts of this animation, such as moving waves or droplets, which we call space-time features. Once selected, a feature can be copied, edited, or duplicated and then pasted back anywhere in space and time in the same or in another liquid animation sequence. Our method circumvents tedious user interactions by automatically computing the spatial and temporal ranges of the selected feature. We also provide space-time shape editing tools for non-uniform scaling, rotation, trajectory changes, and temporal editing to locally speed up or slow down motion. Using our tools, the user can edit and progressively refine any input simulation result, possibly using a library of precomputed space-time features extracted from other animations. In contrast to the trial-and-error loop usually required to edit animation results through the tuning of indirect simulation parameters, our method gives the user full control over the edited space-time behaviors. © 2016 Copyright held by the owner/author(s)."}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","ec_funded":1,"date_published":"2016-10-10T00:00:00Z","month":"10","scopus_import":"1","title":"Space-time sculpting of liquid animation","year":"2016","_id":"1136"},{"date_updated":"2025-09-22T14:13:22Z","date_created":"2018-12-11T11:50:21Z","author":[{"full_name":"Salzer, Elisabeth","first_name":"Elisabeth","last_name":"Salzer"},{"full_name":"Çaǧdaş, Deniz","last_name":"Çaǧdaş","first_name":"Deniz"},{"id":"4167FE56-F248-11E8-B48F-1D18A9856A87","first_name":"Miroslav","last_name":"Hons","orcid":"0000-0002-6625-3348","full_name":"Hons, Miroslav"},{"first_name":"Emily","last_name":"Mace","full_name":"Mace, Emily"},{"first_name":"Wojciech","last_name":"Garncarz","full_name":"Garncarz, Wojciech"},{"full_name":"Petronczki, Oezlem","last_name":"Petronczki","first_name":"Oezlem"},{"full_name":"Platzer, René","first_name":"René","last_name":"Platzer"},{"first_name":"Laurène","last_name":"Pfajfer","full_name":"Pfajfer, Laurène"},{"full_name":"Bilic, Ivan","last_name":"Bilic","first_name":"Ivan"},{"last_name":"Ban","first_name":"Sol","full_name":"Ban, Sol"},{"full_name":"Willmann, Katharina","first_name":"Katharina","last_name":"Willmann"},{"first_name":"Malini","last_name":"Mukherjee","full_name":"Mukherjee, Malini"},{"first_name":"Verena","last_name":"Supper","full_name":"Supper, Verena"},{"full_name":"Hsu, Hsiangting","first_name":"Hsiangting","last_name":"Hsu"},{"last_name":"Banerjee","first_name":"Pinaki","full_name":"Banerjee, Pinaki"},{"first_name":"Papiya","last_name":"Sinha","full_name":"Sinha, Papiya"},{"full_name":"Mcclanahan, Fabienne","first_name":"Fabienne","last_name":"Mcclanahan"},{"last_name":"Zlabinger","first_name":"Gerhard","full_name":"Zlabinger, Gerhard"},{"full_name":"Pickl, Winfried","last_name":"Pickl","first_name":"Winfried"},{"full_name":"Gribben, John","last_name":"Gribben","first_name":"John"},{"full_name":"Stockinger, Hannes","first_name":"Hannes","last_name":"Stockinger"},{"full_name":"Bennett, Keiryn","last_name":"Bennett","first_name":"Keiryn"},{"last_name":"Huppa","first_name":"Johannes","full_name":"Huppa, Johannes"},{"full_name":"Dupré, Loï̈C","first_name":"Loï̈C","last_name":"Dupré"},{"last_name":"Sanal","first_name":"Özden","full_name":"Sanal, Özden"},{"last_name":"Jäger","first_name":"Ulrich","full_name":"Jäger, Ulrich"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ilhan","last_name":"Tezcan","full_name":"Tezcan, Ilhan"},{"last_name":"Orange","first_name":"Jordan","full_name":"Orange, Jordan"},{"last_name":"Boztug","first_name":"Kaan","full_name":"Boztug, Kaan"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"RASGRP1 is an important guanine nucleotide exchange factor and activator of the RAS-MAPK pathway following T cell antigen receptor (TCR) signaling. The consequences of RASGRP1 mutations in humans are unknown. In a patient with recurrent bacterial and viral infections, born to healthy consanguineous parents, we used homozygosity mapping and exome sequencing to identify a biallelic stop-gain variant in RASGRP1. This variant segregated perfectly with the disease and has not been reported in genetic databases. RASGRP1 deficiency was associated in T cells and B cells with decreased phosphorylation of the extracellular-signal-regulated serine kinase ERK, which was restored following expression of wild-type RASGRP1. RASGRP1 deficiency also resulted in defective proliferation, activation and motility of T cells and B cells. RASGRP1-deficient natural killer (NK) cells exhibited impaired cytotoxicity with defective granule convergence and actin accumulation. Interaction proteomics identified the dynein light chain DYNLL1 as interacting with RASGRP1, which links RASGRP1 to cytoskeletal dynamics. RASGRP1-deficient cells showed decreased activation of the GTPase RhoA. Treatment with lenalidomide increased RhoA activity and reversed the migration and activation defects of RASGRP1-deficient lymphocytes."}],"volume":17,"oa":1,"pmid":1,"external_id":{"isi":["000388056400005"],"pmid":["27776107"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"status":"public","month":"12","scopus_import":"1","title":"RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics","date_published":"2016-12-01T00:00:00Z","_id":"1137","year":"2016","intvolume":"        17","department":[{"_id":"MiSi"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","publication":"Nature Immunology","publisher":"Nature Publishing Group","page":"1352 - 1360","doi":"10.1038/ni.3575","issue":"12","isi":1,"publist_id":"6221","day":"01","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400263","open_access":"1"}],"citation":{"short":"E. Salzer, D. Çaǧdaş, M. Hons, E. Mace, W. Garncarz, O. Petronczki, R. Platzer, L. Pfajfer, I. Bilic, S. Ban, K. Willmann, M. Mukherjee, V. Supper, H. Hsu, P. Banerjee, P. Sinha, F. Mcclanahan, G. Zlabinger, W. Pickl, J. Gribben, H. Stockinger, K. Bennett, J. Huppa, L. Dupré, Ö. Sanal, U. Jäger, M.K. Sixt, I. Tezcan, J. Orange, K. Boztug, Nature Immunology 17 (2016) 1352–1360.","ieee":"E. Salzer <i>et al.</i>, “RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics,” <i>Nature Immunology</i>, vol. 17, no. 12. Nature Publishing Group, pp. 1352–1360, 2016.","mla":"Salzer, Elisabeth, et al. “RASGRP1 Deficiency Causes Immunodeficiency with Impaired Cytoskeletal Dynamics.” <i>Nature Immunology</i>, vol. 17, no. 12, Nature Publishing Group, 2016, pp. 1352–60, doi:<a href=\"https://doi.org/10.1038/ni.3575\">10.1038/ni.3575</a>.","chicago":"Salzer, Elisabeth, Deniz Çaǧdaş, Miroslav Hons, Emily Mace, Wojciech Garncarz, Oezlem Petronczki, René Platzer, et al. “RASGRP1 Deficiency Causes Immunodeficiency with Impaired Cytoskeletal Dynamics.” <i>Nature Immunology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ni.3575\">https://doi.org/10.1038/ni.3575</a>.","ista":"Salzer E, Çaǧdaş D, Hons M, Mace E, Garncarz W, Petronczki O, Platzer R, Pfajfer L, Bilic I, Ban S, Willmann K, Mukherjee M, Supper V, Hsu H, Banerjee P, Sinha P, Mcclanahan F, Zlabinger G, Pickl W, Gribben J, Stockinger H, Bennett K, Huppa J, Dupré L, Sanal Ö, Jäger U, Sixt MK, Tezcan I, Orange J, Boztug K. 2016. RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. Nature Immunology. 17(12), 1352–1360.","apa":"Salzer, E., Çaǧdaş, D., Hons, M., Mace, E., Garncarz, W., Petronczki, O., … Boztug, K. (2016). RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ni.3575\">https://doi.org/10.1038/ni.3575</a>","ama":"Salzer E, Çaǧdaş D, Hons M, et al. RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. <i>Nature Immunology</i>. 2016;17(12):1352-1360. doi:<a href=\"https://doi.org/10.1038/ni.3575\">10.1038/ni.3575</a>"}},{"type":"conference","publication_status":"published","quality_controlled":"1","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"IEEE","publication":"Proceedings of the 31st Annual ACM/IEEE Symposium","conference":{"end_date":"2016-07-08","name":"LICS: Logic in Computer Science","location":"New York, NY, USA","start_date":"2016-07-05"},"page":"76 - 85","citation":{"mla":"Chatterjee, Krishnendu, et al. “Quantitative Automata under Probabilistic Semantics.” <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, IEEE, 2016, pp. 76–85, doi:<a href=\"https://doi.org/10.1145/2933575.2933588\">10.1145/2933575.2933588</a>.","ama":"Chatterjee K, Henzinger TA, Otop J. Quantitative automata under probabilistic semantics. In: <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>. IEEE; 2016:76-85. doi:<a href=\"https://doi.org/10.1145/2933575.2933588\">10.1145/2933575.2933588</a>","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2016). Quantitative automata under probabilistic semantics. In <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i> (pp. 76–85). New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2933588\">https://doi.org/10.1145/2933575.2933588</a>","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative automata under probabilistic semantics. Proceedings of the 31st Annual ACM/IEEE Symposium. LICS: Logic in Computer Science, 76–85.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Automata under Probabilistic Semantics.” In <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, 76–85. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2933588\">https://doi.org/10.1145/2933575.2933588</a>.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative automata under probabilistic semantics,” in <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, New York, NY, USA, 2016, pp. 76–85.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings of the 31st Annual ACM/IEEE Symposium, IEEE, 2016, pp. 76–85."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.06764"}],"isi":1,"day":"05","publist_id":"6220","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), FWF Grant No P23499- N23, FWF NFN Grant No S114","doi":"10.1145/2933575.2933588","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"}],"date_created":"2018-12-11T11:50:21Z","date_updated":"2025-09-22T14:12:47Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000387609200008"],"arxiv":["1604.06764"]},"oa":1,"abstract":[{"lang":"eng","text":"Automata with monitor counters, where the transitions do not depend on counter values, and nested weighted automata are two expressive automata-theoretic frameworks for quantitative properties. For a well-studied and wide class of quantitative functions, we establish that automata with monitor counters and nested weighted automata are equivalent. We study for the first time such quantitative automata under probabilistic semantics. We show that several problems that are undecidable for the classical questions of emptiness and universality become decidable under the probabilistic semantics. We present a complete picture of decidability for such automata, and even an almost-complete picture of computational complexity, for the probabilistic questions we consider. © 2016 ACM."}],"arxiv":1,"oa_version":"Preprint","ec_funded":1,"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","year":"2016","_id":"1138","date_published":"2016-07-05T00:00:00Z","title":"Quantitative automata under probabilistic semantics","month":"07","scopus_import":"1"},{"date_updated":"2025-09-22T14:12:05Z","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dvoák","first_name":"Wolfgang","full_name":"Dvoák, Wolfgang"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"last_name":"Loitzenbauer","first_name":"Veronika","full_name":"Loitzenbauer, Veronika"}],"date_created":"2018-12-11T11:50:22Z","abstract":[{"text":"Given a model of a system and an objective, the model-checking question asks whether the model satisfies the objective. We study polynomial-time problems in two classical models, graphs and Markov Decision Processes (MDPs), with respect to several fundamental -regular objectives, e.g., Rabin and Streett objectives. For many of these problems the best-known upper bounds are quadratic or cubic, yet no super-linear lower bounds are known. In this work our contributions are two-fold: First, we present several improved algorithms, and second, we present the first conditional super-linear lower bounds based on widely believed assumptions about the complexity of CNF-SAT and combinatorial Boolean matrix multiplication. A separation result for two models with respect to an objective means a conditional lower bound for one model that is strictly higher than the existing upper bound for the other model, and similarly for two objectives with respect to a model. Our results establish the following separation results: (1) A separation of models (graphs and MDPs) for disjunctive queries of reachability and Büchi objectives. (2) Two kinds of separations of objectives, both for graphs and MDPs, namely, (2a) the separation of dual objectives such as Streett/Rabin objectives, and (2b) the separation of conjunction and disjunction of multiple objectives of the same type such as safety, Büchi, and coBüchi. In summary, our results establish the first model and objective separation results for graphs and MDPs for various classical -regular objectives. Quite strikingly, we establish conditional lower bounds for the disjunction of objectives that are strictly higher than the existing upper bounds for the conjunction of the same objectives. © 2016 ACM.","lang":"eng"}],"oa_version":"Preprint","arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"arxiv":["1602.02670"],"isi":["000387609200020"]},"oa":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","date_published":"2016-07-05T00:00:00Z","title":"Model and objective separation with conditional lower bounds: disjunction is harder than conjunction","scopus_import":"1","month":"07","_id":"1140","year":"2016","department":[{"_id":"KrCh"}],"alternative_title":["Proceedings Symposium on Logic in Computer Science"],"type":"conference","publication_status":"published","quality_controlled":"1","publication":"Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science","publisher":"IEEE","page":"197 - 206","conference":{"start_date":"2016-07-05","location":"New York, NY, USA","name":"LICS: Logic in Computer Science","end_date":"2016-07-08"},"acknowledgement":"K.  C.,  M.  H.,  and  W.  D.  are  partially  supported  by  the  Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003.\r\nK. C. is partially supported by the Austrian Science Fund (FWF)\r\nNFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Start grant\r\n(279307: Graph Games). For W. D., M. H., and V. L. the research\r\nleading to these results has received funding from the European\r\nResearch Council under the European Union’s Seventh Framework\r\nProgramme (FP/2007-2013) / ERC Grant Agreement no. 340506.","doi":"10.1145/2933575.2935304","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.02670"}],"citation":{"ista":"Chatterjee K, Dvoák W, Henzinger M, Loitzenbauer V. 2016. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, Proceedings Symposium on Logic in Computer Science, , 197–206.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvoák, Monika Henzinger, and Veronika Loitzenbauer. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” In <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, 197–206. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2935304\">https://doi.org/10.1145/2933575.2935304</a>.","apa":"Chatterjee, K., Dvoák, W., Henzinger, M., &#38; Loitzenbauer, V. (2016). Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i> (pp. 197–206). New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2935304\">https://doi.org/10.1145/2933575.2935304</a>","ama":"Chatterjee K, Dvoák W, Henzinger M, Loitzenbauer V. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In: <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>. IEEE; 2016:197-206. doi:<a href=\"https://doi.org/10.1145/2933575.2935304\">10.1145/2933575.2935304</a>","mla":"Chatterjee, Krishnendu, et al. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, IEEE, 2016, pp. 197–206, doi:<a href=\"https://doi.org/10.1145/2933575.2935304\">10.1145/2933575.2935304</a>.","short":"K. Chatterjee, W. Dvoák, M. Henzinger, V. Loitzenbauer, in:, Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2016, pp. 197–206.","ieee":"K. Chatterjee, W. Dvoák, M. Henzinger, and V. Loitzenbauer, “Model and objective separation with conditional lower bounds: disjunction is harder than conjunction,” in <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, New York, NY, USA, 2016, pp. 197–206."},"isi":1,"day":"05","publist_id":"6219"},{"title":"Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization","scopus_import":"1","month":"11","date_published":"2016-11-01T00:00:00Z","_id":"1141","year":"2016","intvolume":"        17","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"None","abstract":[{"lang":"eng","text":"In this paper we introduce the Multiobjective Optimization Hierarchic Genetic Strategy with maturing (MO-mHGS), a meta-algorithm that performs evolutionary optimization in a hierarchy of populations. The maturing mechanism improves growth and reduces redundancy. The performance of MO-mHGS with selected state-of-the-art multiobjective evolutionary algorithms as internal algorithms is analysed on benchmark problems and their modifications for which single fitness evaluation time depends on the solution accuracy. We compare the proposed algorithm with the Island Model Genetic Algorithm as well as with single-deme methods, and discuss the impact of internal algorithms on the MO-mHGS meta-algorithm. © 2016 Elsevier B.V."}],"volume":17,"external_id":{"isi":["000390625600021"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:11:23Z","author":[{"first_name":"Radosław","last_name":"Łazarz","full_name":"Łazarz, Radosław"},{"last_name":"Idzik","first_name":"Michał","full_name":"Idzik, Michał"},{"full_name":"Gądek, Konrad","first_name":"Konrad","last_name":"Gądek"},{"full_name":"Gajda-Zagorska, Ewa P","id":"47794CF0-F248-11E8-B48F-1D18A9856A87","last_name":"Gajda-Zagorska","first_name":"Ewa P"}],"date_created":"2018-12-11T11:50:22Z","acknowledgement":"The work presented in this paper was partially supported by Polish National Science Centre grant nos. DEC-2012/05/N/ST6/03433 and DEC-2011/03/B/ST6/01393. Radosław Łazarz was supported by Polish National Science Centre grant no. DEC-2013/10/M/ST6/00531.","doi":"10.1016/j.jocs.2016.03.004","issue":"1","citation":{"short":"R. Łazarz, M. Idzik, K. Gądek, E.P. Gajda-Zagorska, Journal of Computational Science 17 (2016) 249–260.","ieee":"R. Łazarz, M. Idzik, K. Gądek, and E. P. Gajda-Zagorska, “Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization,” <i>Journal of Computational Science</i>, vol. 17, no. 1. Elsevier, pp. 249–260, 2016.","ista":"Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. 2016. Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. Journal of Computational Science. 17(1), 249–260.","chicago":"Łazarz, Radosław, Michał Idzik, Konrad Gądek, and Ewa P Gajda-Zagorska. “Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective Optimization.” <i>Journal of Computational Science</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">https://doi.org/10.1016/j.jocs.2016.03.004</a>.","ama":"Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. <i>Journal of Computational Science</i>. 2016;17(1):249-260. doi:<a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">10.1016/j.jocs.2016.03.004</a>","apa":"Łazarz, R., Idzik, M., Gądek, K., &#38; Gajda-Zagorska, E. P. (2016). Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. <i>Journal of Computational Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">https://doi.org/10.1016/j.jocs.2016.03.004</a>","mla":"Łazarz, Radosław, et al. “Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective Optimization.” <i>Journal of Computational Science</i>, vol. 17, no. 1, Elsevier, 2016, pp. 249–60, doi:<a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">10.1016/j.jocs.2016.03.004</a>."},"isi":1,"publist_id":"6217","day":"01","page":"249 - 260","publication":"Journal of Computational Science","publisher":"Elsevier","department":[{"_id":"ChWo"}],"quality_controlled":"1","type":"journal_article","publication_status":"published"},{"date_updated":"2025-09-22T14:10:50Z","date_created":"2018-12-11T11:50:22Z","author":[{"full_name":"Martins, Rui","first_name":"Rui","last_name":"Martins"},{"full_name":"Maier, Julia","last_name":"Maier","first_name":"Julia"},{"last_name":"Gorki","first_name":"Anna","full_name":"Gorki, Anna"},{"last_name":"Huber","first_name":"Kilian","full_name":"Huber, Kilian"},{"full_name":"Sharif, Omar","last_name":"Sharif","first_name":"Omar"},{"first_name":"Philipp","last_name":"Starkl","full_name":"Starkl, Philipp"},{"first_name":"Simona","last_name":"Saluzzo","full_name":"Saluzzo, Simona"},{"last_name":"Quattrone","first_name":"Federica","full_name":"Quattrone, Federica"},{"last_name":"Gawish","first_name":"Riem","full_name":"Gawish, Riem"},{"full_name":"Lakovits, Karin","last_name":"Lakovits","first_name":"Karin"},{"last_name":"Aichinger","first_name":"Michael","full_name":"Aichinger, Michael"},{"first_name":"Branka","last_name":"Radic Sarikas","full_name":"Radic Sarikas, Branka"},{"full_name":"Lardeau, Charles","last_name":"Lardeau","first_name":"Charles"},{"first_name":"Anastasiya","last_name":"Hladik","full_name":"Hladik, Anastasiya"},{"full_name":"Korosec, Ana","last_name":"Korosec","first_name":"Ana"},{"first_name":"Markus","last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus"},{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","first_name":"Kari","full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518"},{"last_name":"Duggan","first_name":"Michelle","id":"2EDEA62C-F248-11E8-B48F-1D18A9856A87","full_name":"Duggan, Michelle"},{"full_name":"Kerjaschki, Dontscho","first_name":"Dontscho","last_name":"Kerjaschki"},{"last_name":"Esterbauer","first_name":"Harald","full_name":"Esterbauer, Harald"},{"first_name":"Jacques","last_name":"Colinge","full_name":"Colinge, Jacques"},{"full_name":"Eisenbarth, Stephanie","last_name":"Eisenbarth","first_name":"Stephanie"},{"first_name":"Thomas","last_name":"Decker","full_name":"Decker, Thomas"},{"first_name":"Keiryn","last_name":"Bennett","full_name":"Bennett, Keiryn"},{"last_name":"Kubicek","first_name":"Stefan","full_name":"Kubicek, Stefan"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Giulio","last_name":"Superti Furga","full_name":"Superti Furga, Giulio"},{"last_name":"Knapp","first_name":"Sylvia","full_name":"Knapp, Sylvia"}],"oa_version":"Submitted Version","abstract":[{"text":"Hemolysis drives susceptibility to bacterial infections and predicts poor outcome from sepsis. These detrimental effects are commonly considered to be a consequence of heme-iron serving as a nutrient for bacteria. We employed a Gram-negative sepsis model and found that elevated heme levels impaired the control of bacterial proliferation independently of heme-iron acquisition by pathogens. Heme strongly inhibited phagocytosis and the migration of human and mouse phagocytes by disrupting actin cytoskeletal dynamics via activation of the GTP-binding Rho family protein Cdc42 by the guanine nucleotide exchange factor DOCK8. A chemical screening approach revealed that quinine effectively prevented heme effects on the cytoskeleton, restored phagocytosis and improved survival in sepsis. These mechanistic insights provide potential therapeutic targets for patients with sepsis or hemolytic disorders.","lang":"eng"}],"oa":1,"volume":17,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000388056400006"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","scopus_import":"1","month":"12","title":"Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions","date_published":"2016-12-01T00:00:00Z","year":"2016","_id":"1142","intvolume":"        17","department":[{"_id":"MiSi"},{"_id":"PeJo"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","publication":"Nature Immunology","publisher":"Nature Publishing Group","page":"1361 - 1372","issue":"12","doi":"10.1038/ni.3590","acknowledgement":"Y. Fukui (Medical Institute of Bioregulation, Kyushu University) and J. Stein (Theodor Kocher Institute, University of Bern) are acknowledged for providing the DOCK8 deficient bone marrow. and H. Häcker (St. Judes Children's Research Hospital) for providing the ERHBD-HoxB8-encoding retroviral construct. pSpCas9(BB)-2a-Puro (PX459) was a gift from F. Zhang (Massachusetts Institute of Technology) (Addgene plasmid # 48139) and pGRG36 was a gift from N. Craig (Johns Hopkins University School of Medicine) (Addgene plasmid # 16666). LifeAct-GFP-encoding retrovirus was kindly provided by A. Leithner (Institute of Science and Technology Austria). pSIM8 and TKC E. coli were gifts from D.L. Court (Center for Cancer Research, National Cancer Institute). We acknowledge M. Gröger and S. Rauscher for excellent technical support (Core imaging facility, Medical University of Vienna). We thank D.P. Barlow and L.R. Cheever for critical reading of the manuscript. This work was supported by the Austrian Academy of Sciences, the Science Fund of the Austrian National Bank (14107) and the Austrian Science Fund FWF (I1620-B22) in the Infect-ERA framework (to S.Knapp).","isi":1,"day":"01","publist_id":"6216","citation":{"ieee":"R. Martins <i>et al.</i>, “Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions,” <i>Nature Immunology</i>, vol. 17, no. 12. Nature Publishing Group, pp. 1361–1372, 2016.","short":"R. Martins, J. Maier, A. Gorki, K. Huber, O. Sharif, P. Starkl, S. Saluzzo, F. Quattrone, R. Gawish, K. Lakovits, M. Aichinger, B. Radic Sarikas, C. Lardeau, A. Hladik, A. Korosec, M. Brown, K. Vaahtomeri, M. Duggan, D. Kerjaschki, H. Esterbauer, J. Colinge, S. Eisenbarth, T. Decker, K. Bennett, S. Kubicek, M.K. Sixt, G. Superti Furga, S. Knapp, Nature Immunology 17 (2016) 1361–1372.","apa":"Martins, R., Maier, J., Gorki, A., Huber, K., Sharif, O., Starkl, P., … Knapp, S. (2016). Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ni.3590\">https://doi.org/10.1038/ni.3590</a>","ama":"Martins R, Maier J, Gorki A, et al. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. <i>Nature Immunology</i>. 2016;17(12):1361-1372. doi:<a href=\"https://doi.org/10.1038/ni.3590\">10.1038/ni.3590</a>","chicago":"Martins, Rui, Julia Maier, Anna Gorki, Kilian Huber, Omar Sharif, Philipp Starkl, Simona Saluzzo, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” <i>Nature Immunology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ni.3590\">https://doi.org/10.1038/ni.3590</a>.","ista":"Martins R, Maier J, Gorki A, Huber K, Sharif O, Starkl P, Saluzzo S, Quattrone F, Gawish R, Lakovits K, Aichinger M, Radic Sarikas B, Lardeau C, Hladik A, Korosec A, Brown M, Vaahtomeri K, Duggan M, Kerjaschki D, Esterbauer H, Colinge J, Eisenbarth S, Decker T, Bennett K, Kubicek S, Sixt MK, Superti Furga G, Knapp S. 2016. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nature Immunology. 17(12), 1361–1372.","mla":"Martins, Rui, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” <i>Nature Immunology</i>, vol. 17, no. 12, Nature Publishing Group, 2016, pp. 1361–72, doi:<a href=\"https://doi.org/10.1038/ni.3590\">10.1038/ni.3590</a>."},"main_file_link":[{"open_access":"1","url":"https://ora.ox.ac.uk/objects/uuid:f53a464e-1e5b-4f08-a7d8-b6749b852b9d"}]},{"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"date_created":"2018-12-11T11:50:23Z","author":[{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","last_name":"Nam","full_name":"Nam, Phan"},{"full_name":"Rougerie, Nicolas","last_name":"Rougerie","first_name":"Nicolas"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer"}],"date_updated":"2025-09-22T14:10:16Z","external_id":{"arxiv":["1503.07061"],"isi":["000378287000006"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":9,"oa":1,"abstract":[{"lang":"eng","text":"We study the ground state of a dilute Bose gas in a scaling limit where the Gross-Pitaevskii functional emerges. This is a repulsive nonlinear Schrödinger functional whose quartic term is proportional to the scattering length of the interparticle interaction potential. We propose a new derivation of this limit problem, with a method that bypasses some of the technical difficulties that previous derivations had to face. The new method is based on a combination of Dyson\\'s lemma, the quantum de Finetti theorem and a second moment estimate for ground states of the effective Dyson Hamiltonian. It applies equally well to the case where magnetic fields or rotation are present."}],"oa_version":"Preprint","arxiv":1,"status":"public","ec_funded":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","intvolume":"         9","year":"2016","_id":"1143","date_published":"2016-03-24T00:00:00Z","month":"03","scopus_import":"1","title":"Ground states of large bosonic systems: The gross Pitaevskii limit revisited","publication_status":"published","type":"journal_article","quality_controlled":"1","department":[{"_id":"RoSe"}],"publisher":"Mathematical Sciences Publishers","publication":"Analysis and PDE","page":"459 - 485","day":"24","publist_id":"6215","isi":1,"citation":{"ieee":"P. Nam, N. Rougerie, and R. Seiringer, “Ground states of large bosonic systems: The gross Pitaevskii limit revisited,” <i>Analysis and PDE</i>, vol. 9, no. 2. Mathematical Sciences Publishers, pp. 459–485, 2016.","short":"P. Nam, N. Rougerie, R. Seiringer, Analysis and PDE 9 (2016) 459–485.","ama":"Nam P, Rougerie N, Seiringer R. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. <i>Analysis and PDE</i>. 2016;9(2):459-485. doi:<a href=\"https://doi.org/10.2140/apde.2016.9.459\">10.2140/apde.2016.9.459</a>","apa":"Nam, P., Rougerie, N., &#38; Seiringer, R. (2016). Ground states of large bosonic systems: The gross Pitaevskii limit revisited. <i>Analysis and PDE</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/apde.2016.9.459\">https://doi.org/10.2140/apde.2016.9.459</a>","ista":"Nam P, Rougerie N, Seiringer R. 2016. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. Analysis and PDE. 9(2), 459–485.","chicago":"Nam, Phan, Nicolas Rougerie, and Robert Seiringer. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” <i>Analysis and PDE</i>. Mathematical Sciences Publishers, 2016. <a href=\"https://doi.org/10.2140/apde.2016.9.459\">https://doi.org/10.2140/apde.2016.9.459</a>.","mla":"Nam, Phan, et al. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” <i>Analysis and PDE</i>, vol. 9, no. 2, Mathematical Sciences Publishers, 2016, pp. 459–85, doi:<a href=\"https://doi.org/10.2140/apde.2016.9.459\">10.2140/apde.2016.9.459</a>."},"main_file_link":[{"url":"https://arxiv.org/abs/1503.07061","open_access":"1"}],"doi":"10.2140/apde.2016.9.459","issue":"2"},{"abstract":[{"lang":"eng","text":"Feedback loops in biological networks, among others, enable differentiation and cell cycle progression, and increase robustness in signal transduction. In natural networks, feedback loops are often complex and intertwined, making it challenging to identify which loops are mainly responsible for an observed behavior. However, minimal synthetic replicas could allow for such identification. Here, we engineered a synthetic permease-inducer-repressor system in Saccharomyces cerevisiae to analyze if a transport-mediated positive feedback loop could be a core mechanism for the switch-like behavior in the regulation of metabolic gene networks such as the S. cerevisiae GAL system or the Escherichia coli lac operon. We characterized the synthetic circuit using deterministic and stochastic mathematical models. Similar to its natural counterparts, our synthetic system shows bistable and hysteretic behavior, and the inducer concentration range for bistability as well as the switching rates between the two stable states depend on the repressor concentration. Our results indicate that a generic permease–inducer–repressor circuit with a single feedback loop is sufficient to explain the experimentally observed bistable behavior of the natural systems. We anticipate that the approach of reimplementing natural systems with orthogonal parts to identify crucial network components is applicable to other natural systems such as signaling pathways."}],"oa_version":"None","external_id":{"isi":["000386196100008"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":5,"date_updated":"2025-09-22T14:20:45Z","date_created":"2018-12-11T11:49:40Z","author":[{"last_name":"Gnügge","first_name":"Robert","full_name":"Gnügge, Robert"},{"full_name":"Dharmarajan, Lekshmi","last_name":"Dharmarajan","first_name":"Lekshmi"},{"last_name":"Lang","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz"},{"full_name":"Stelling, Jörg","last_name":"Stelling","first_name":"Jörg"}],"date_published":"2016-05-05T00:00:00Z","month":"05","title":"An orthogonal permease–inducer–repressor feedback loop shows bistability","intvolume":"         5","year":"2016","_id":"1008","language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","publication":"ACS Synthetic Biology","publisher":"American Chemical Society","department":[{"_id":"CaGu"}],"publication_status":"published","type":"journal_article","quality_controlled":"1","issue":"10","doi":"10.1021/acssynbio.6b00013","acknowledgement":"We thank Julio Polaina (Instituto de Agroqu ı ́ mica y Tecnolog ı ́ a de Alimentos, C.S.I.C., Paterna, Spain) for the gift of plasmid pMR4, Gregor W. Schmidt for provision of and support with the micro fl uidic device, Markus Du ̈ rr for the cell tracking R script, and Lukas Widmer for the script for MEIGO using “ parfor ” in MATLAB. We acknowledge the members of the Stelling group for discussions, comments, and support.","day":"05","isi":1,"publist_id":"6390","citation":{"ista":"Gnügge R, Dharmarajan L, Lang M, Stelling J. 2016. An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. 5(10), 1098–1107.","chicago":"Gnügge, Robert, Lekshmi Dharmarajan, Moritz Lang, and Jörg Stelling. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” <i>ACS Synthetic Biology</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acssynbio.6b00013\">https://doi.org/10.1021/acssynbio.6b00013</a>.","apa":"Gnügge, R., Dharmarajan, L., Lang, M., &#38; Stelling, J. (2016). An orthogonal permease–inducer–repressor feedback loop shows bistability. <i>ACS Synthetic Biology</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssynbio.6b00013\">https://doi.org/10.1021/acssynbio.6b00013</a>","ama":"Gnügge R, Dharmarajan L, Lang M, Stelling J. An orthogonal permease–inducer–repressor feedback loop shows bistability. <i>ACS Synthetic Biology</i>. 2016;5(10):1098-1107. doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00013\">10.1021/acssynbio.6b00013</a>","mla":"Gnügge, Robert, et al. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” <i>ACS Synthetic Biology</i>, vol. 5, no. 10, American Chemical Society, 2016, pp. 1098–107, doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00013\">10.1021/acssynbio.6b00013</a>.","short":"R. Gnügge, L. Dharmarajan, M. Lang, J. Stelling, ACS Synthetic Biology 5 (2016) 1098–1107.","ieee":"R. Gnügge, L. Dharmarajan, M. Lang, and J. Stelling, “An orthogonal permease–inducer–repressor feedback loop shows bistability,” <i>ACS Synthetic Biology</i>, vol. 5, no. 10. American Chemical Society, pp. 1098–1107, 2016."},"page":"1098 - 1107"},{"date_updated":"2025-09-18T11:03:28Z","date_created":"2018-12-11T11:52:40Z","author":[{"orcid":"0000-0002-6148-2416","full_name":"Qi, Qin","first_name":"Qin","last_name":"Qi","id":"3B22D412-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Toll Riera, Macarena","last_name":"Toll Riera","first_name":"Macarena"},{"full_name":"Heilbron, Karl","first_name":"Karl","last_name":"Heilbron"},{"first_name":"Gail","last_name":"Preston","full_name":"Preston, Gail"},{"first_name":"R Craig","last_name":"Maclean","full_name":"Maclean, R Craig"}],"abstract":[{"text":"Antibiotic resistance carries a fitness cost that must be overcome in order for resistance to persist over the long term. Compensatory mutations that recover the functional defects associated with resistance mutations have been argued to play a key role in overcoming the cost of resistance, but compensatory mutations are expected to be rare relative to generally beneficial mutations that increase fitness, irrespective of antibiotic resistance. Given this asymmetry, population genetics theory predicts that populations should adapt by compensatory mutations when the cost of resistance is large, whereas generally beneficial mutations should drive adaptation when the cost of resistance is small. We tested this prediction by determining the genomic mechanisms underpinning adaptation to antibiotic-free conditions in populations of the pathogenic bacterium Pseudomonas aeruginosa that carry costly antibiotic resistance mutations. Whole-genome sequencing revealed that populations founded by high-cost rifampicin-resistant mutants adapted via compensatory mutations in three genes of the RNA polymerase core enzyme, whereas populations founded by low-cost mutants adapted by generally beneficial mutations, predominantly in the quorum-sensing transcriptional regulator gene lasR. Even though the importance of compensatory evolution in maintaining resistance has been widely recognized, our study shows that the roles of general adaptation in maintaining resistance should not be underestimated and highlights the need to understand how selection at other sites in the genome influences the dynamics of resistance alleles in clinical settings.","lang":"eng"}],"oa_version":"Published Version","external_id":{"isi":["000368441200022"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"volume":283,"language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","date_published":"2016-01-13T00:00:00Z","scopus_import":"1","month":"01","title":"The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa","intvolume":"       283","_id":"1552","pubrep_id":"488","year":"2016","department":[{"_id":"ToBo"}],"file":[{"relation":"main_file","date_created":"2018-12-12T10:11:43Z","date_updated":"2020-07-14T12:45:02Z","file_name":"IST-2016-488-v1+1_20152452.full.pdf","access_level":"open_access","creator":"system","checksum":"78ffe70c1c88af3856d31ca6b7195a27","file_id":"4899","file_size":626804,"content_type":"application/pdf"}],"publication_status":"published","type":"journal_article","quality_controlled":"1","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","ddc":["570"],"publisher":"Royal Society, The","has_accepted_license":"1","file_date_updated":"2020-07-14T12:45:02Z","article_number":"20152452","doi":"10.1098/rspb.2015.2452","issue":"1822","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics funded by Wellcome\r\nTrust grant reference 090532/Z/09/Z and Medical Research Council Hub grant no. G0900747 91070 for generation of the high-throughput sequencing data. We thank Wook Kim and two anonymous reviewers for their constructive feedback on previous versions of our manuscript.","day":"13","isi":1,"publist_id":"5619","citation":{"mla":"Qi, Qin, et al. “The Genomic Basis of Adaptation to the Fitness Cost of Rifampicin Resistance in Pseudomonas Aeruginosa.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 283, no. 1822, 20152452, Royal Society, The, 2016, doi:<a href=\"https://doi.org/10.1098/rspb.2015.2452\">10.1098/rspb.2015.2452</a>.","ama":"Qi Q, Toll Riera M, Heilbron K, Preston G, Maclean RC. The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2016;283(1822). doi:<a href=\"https://doi.org/10.1098/rspb.2015.2452\">10.1098/rspb.2015.2452</a>","apa":"Qi, Q., Toll Riera, M., Heilbron, K., Preston, G., &#38; Maclean, R. C. (2016). The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rspb.2015.2452\">https://doi.org/10.1098/rspb.2015.2452</a>","chicago":"Qi, Qin, Macarena Toll Riera, Karl Heilbron, Gail Preston, and R Craig Maclean. “The Genomic Basis of Adaptation to the Fitness Cost of Rifampicin Resistance in Pseudomonas Aeruginosa.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The, 2016. <a href=\"https://doi.org/10.1098/rspb.2015.2452\">https://doi.org/10.1098/rspb.2015.2452</a>.","ista":"Qi Q, Toll Riera M, Heilbron K, Preston G, Maclean RC. 2016. The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa. Proceedings of the Royal Society of London Series B Biological Sciences. 283(1822), 20152452.","ieee":"Q. Qi, M. Toll Riera, K. Heilbron, G. Preston, and R. C. Maclean, “The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 283, no. 1822. Royal Society, The, 2016.","short":"Q. Qi, M. Toll Riera, K. Heilbron, G. Preston, R.C. Maclean, Proceedings of the Royal Society of London Series B Biological Sciences 283 (2016)."}},{"publisher":"Springer","publication":"Journal of Cryptology","type":"journal_article","publication_status":"published","quality_controlled":"1","department":[{"_id":"KrPi"}],"citation":{"short":"M. Abe, G. Fuchsbauer, J. Groth, K. Haralambiev, M. Ohkubo, Journal of Cryptology 29 (2016) 363–421.","ieee":"M. Abe, G. Fuchsbauer, J. Groth, K. Haralambiev, and M. Ohkubo, “Structure preserving signatures and commitments to group elements,” <i>Journal of Cryptology</i>, vol. 29, no. 2. Springer, pp. 363–421, 2016.","chicago":"Abe, Masayuki, Georg Fuchsbauer, Jens Groth, Kristiyan Haralambiev, and Miyako Ohkubo. “Structure Preserving Signatures and Commitments to Group Elements.” <i>Journal of Cryptology</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00145-014-9196-7\">https://doi.org/10.1007/s00145-014-9196-7</a>.","ista":"Abe M, Fuchsbauer G, Groth J, Haralambiev K, Ohkubo M. 2016. Structure preserving signatures and commitments to group elements. Journal of Cryptology. 29(2), 363–421.","ama":"Abe M, Fuchsbauer G, Groth J, Haralambiev K, Ohkubo M. Structure preserving signatures and commitments to group elements. <i>Journal of Cryptology</i>. 2016;29(2):363-421. doi:<a href=\"https://doi.org/10.1007/s00145-014-9196-7\">10.1007/s00145-014-9196-7</a>","apa":"Abe, M., Fuchsbauer, G., Groth, J., Haralambiev, K., &#38; Ohkubo, M. (2016). Structure preserving signatures and commitments to group elements. <i>Journal of Cryptology</i>. Springer. <a href=\"https://doi.org/10.1007/s00145-014-9196-7\">https://doi.org/10.1007/s00145-014-9196-7</a>","mla":"Abe, Masayuki, et al. “Structure Preserving Signatures and Commitments to Group Elements.” <i>Journal of Cryptology</i>, vol. 29, no. 2, Springer, 2016, pp. 363–421, doi:<a href=\"https://doi.org/10.1007/s00145-014-9196-7\">10.1007/s00145-014-9196-7</a>."},"day":"01","publist_id":"5579","isi":1,"acknowledgement":"The authors would like to thank the anonymous reviewers of this paper. We also would like to express our appreciation to the program committee and the anonymous reviewers for CRYPTO 2010. The first author thanks Sherman S. M. Chow for his comment on group signatures in Sect. 7.1.","issue":"2","doi":"10.1007/s00145-014-9196-7","page":"363 - 421","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000371077900004"]},"volume":29,"abstract":[{"lang":"eng","text":"A modular approach to constructing cryptographic protocols leads to simple designs but often inefficient instantiations. On the other hand, ad hoc constructions may yield efficient protocols at the cost of losing conceptual simplicity. We suggest a new design paradigm, structure-preserving cryptography, that provides a way to construct modular protocols with reasonable efficiency while retaining conceptual simplicity. A cryptographic scheme over a bilinear group is called structure-preserving if its public inputs and outputs consist of elements from the bilinear groups and their consistency can be verified by evaluating pairing-product equations. As structure-preserving schemes smoothly interoperate with each other, they are useful as building blocks in modular design of cryptographic applications. This paper introduces structure-preserving commitment and signature schemes over bilinear groups with several desirable properties. The commitment schemes include homomorphic, trapdoor and length-reducing commitments to group elements, and the structure-preserving signature schemes are the first ones that yield constant-size signatures on multiple group elements. A structure-preserving signature scheme is called automorphic if the public keys lie in the message space, which cannot be achieved by compressing inputs via a cryptographic hash function, as this would destroy the mathematical structure we are trying to preserve. Automorphic signatures can be used for building certification chains underlying privacy-preserving protocols. Among a vast number of applications of structure-preserving protocols, we present an efficient round-optimal blind-signature scheme and a group signature scheme with an efficient and concurrently secure protocol for enrolling new members."}],"oa_version":"None","author":[{"first_name":"Masayuki","last_name":"Abe","full_name":"Abe, Masayuki"},{"full_name":"Fuchsbauer, Georg","first_name":"Georg","last_name":"Fuchsbauer","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Groth, Jens","last_name":"Groth","first_name":"Jens"},{"last_name":"Haralambiev","first_name":"Kristiyan","full_name":"Haralambiev, Kristiyan"},{"full_name":"Ohkubo, Miyako","first_name":"Miyako","last_name":"Ohkubo"}],"date_created":"2018-12-11T11:52:54Z","date_updated":"2025-09-18T11:02:49Z","intvolume":"        29","_id":"1592","year":"2016","date_published":"2016-04-01T00:00:00Z","title":"Structure preserving signatures and commitments to group elements","scopus_import":"1","month":"04","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No"},{"page":"567 - 581","acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.1016/bs.mie.2015.11.004","acknowledgement":"This work was supported by the Boehringer Ingelheim Fonds, the European Research Council (ERC StG 281556), and a START Award of the Austrian Science Foundation (FWF). We thank Robert Hauschild, Anne Reversat, and Jack Merrin for valuable input and the Imaging Facility of IST Austria for excellent support.","isi":1,"day":"01","publist_id":"5573","citation":{"mla":"Schwarz, Jan, and Michael K. Sixt. “Quantitative Analysis of Dendritic Cell Haptotaxis.” <i>Methods in Enzymology</i>, vol. 570, Elsevier, 2016, pp. 567–81, doi:<a href=\"https://doi.org/10.1016/bs.mie.2015.11.004\">10.1016/bs.mie.2015.11.004</a>.","chicago":"Schwarz, Jan, and Michael K Sixt. “Quantitative Analysis of Dendritic Cell Haptotaxis.” <i>Methods in Enzymology</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/bs.mie.2015.11.004\">https://doi.org/10.1016/bs.mie.2015.11.004</a>.","ista":"Schwarz J, Sixt MK. 2016. Quantitative analysis of dendritic cell haptotaxis. Methods in Enzymology. 570, 567–581.","ama":"Schwarz J, Sixt MK. Quantitative analysis of dendritic cell haptotaxis. <i>Methods in Enzymology</i>. 2016;570:567-581. doi:<a href=\"https://doi.org/10.1016/bs.mie.2015.11.004\">10.1016/bs.mie.2015.11.004</a>","apa":"Schwarz, J., &#38; Sixt, M. K. (2016). Quantitative analysis of dendritic cell haptotaxis. <i>Methods in Enzymology</i>. Elsevier. <a href=\"https://doi.org/10.1016/bs.mie.2015.11.004\">https://doi.org/10.1016/bs.mie.2015.11.004</a>","short":"J. Schwarz, M.K. Sixt, Methods in Enzymology 570 (2016) 567–581.","ieee":"J. Schwarz and M. K. Sixt, “Quantitative analysis of dendritic cell haptotaxis,” <i>Methods in Enzymology</i>, vol. 570. Elsevier, pp. 567–581, 2016."},"department":[{"_id":"MiSi"}],"corr_author":"1","publication_status":"published","type":"journal_article","quality_controlled":"1","publication":"Methods in Enzymology","publisher":"Elsevier","language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","status":"public","ec_funded":1,"date_published":"2016-01-01T00:00:00Z","scopus_import":"1","month":"01","title":"Quantitative analysis of dendritic cell haptotaxis","intvolume":"       570","_id":"1597","year":"2016","date_updated":"2025-09-18T11:02:13Z","project":[{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"Y 564-B12","call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:52:56Z","author":[{"full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Jan"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"Chemokines are the main guidance cues directing leukocyte migration. Opposed to early assumptions, chemokines do not necessarily act as soluble cues but are often immobilized within tissues, e.g., dendritic cell migration toward lymphatic vessels is guided by a haptotactic gradient of the chemokine CCL21. Controlled assay systems to quantitatively study haptotaxis in vitro are still missing. In this chapter, we describe an in vitro haptotaxis assay optimized for the unique properties of dendritic cells. The chemokine CCL21 is immobilized in a bioactive state, using laser-assisted protein adsorption by photobleaching. The cells follow this immobilized CCL21 gradient in a haptotaxis chamber, which provides three dimensionally confined migration conditions."}],"oa_version":"None","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000375648700025"],"pmid":["26921962"]},"pmid":1,"volume":570}]