[{"article_processing_charge":"No","type":"dissertation","language":[{"iso":"eng"}],"author":[{"last_name":"Tarrach","full_name":"Tarrach, Thorsten","first_name":"Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4409-8487"}],"month":"07","date_created":"2018-12-11T11:50:19Z","page":"151","related_material":{"record":[{"relation":"part_of_dissertation","id":"1729","status":"public"},{"id":"2218","relation":"part_of_dissertation","status":"public"},{"id":"2445","relation":"part_of_dissertation","status":"public"}]},"file_date_updated":"2021-11-17T13:46:55Z","ddc":["000"],"publist_id":"6230","ec_funded":1,"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"}],"main_file_link":[{"url":"http://thorstent.github.io/theses/phd_thorsten_tarrach.pdf","open_access":"1"}],"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"_id":"1130","abstract":[{"lang":"eng","text":"In this thesis we present a computer-aided programming approach to concurrency. Our approach helps the programmer by automatically fixing concurrency-related bugs, i.e. bugs that occur when the program is executed using an aggressive preemptive scheduler, but not when using a non-preemptive (cooperative) scheduler. Bugs are program behaviours that are incorrect w.r.t. a specification. We consider both user-provided explicit specifications in the form of assertion\r\nstatements in the code as well as an implicit specification. The implicit specification is inferred from the non-preemptive behaviour. Let us consider sequences of calls that the program makes to an external interface. The implicit specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We consider several semantics-preserving fixes that go beyond atomic sections typically explored in the synchronisation synthesis literature. Our synthesis is able to place locks, barriers and wait-signal statements and last, but not least reorder independent statements. The latter may be useful if a thread is released to early, e.g., before some initialisation is completed. We guarantee that our synthesis does not introduce deadlocks and that the synchronisation inserted is optimal w.r.t. a given objective function. We dub our solution trace-based synchronisation synthesis and it is loosely based on counterexample-guided inductive synthesis (CEGIS). The synthesis works by discovering a trace that is incorrect w.r.t. the specification and identifying ordering constraints crucial to trigger the specification violation. Synchronisation may be placed immediately (greedy approach) or delayed until all incorrect traces are found (non-greedy approach). For the non-greedy approach we construct a set of global constraints over synchronisation placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronisation placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronisation solution. We evaluate our approach on a number of realistic (albeit simplified) Linux device-driver\r\nbenchmarks. The benchmarks are versions of the drivers with known concurrency-related bugs. For the experiments with an explicit specification we added assertions that would detect the bugs in the experiments. Device drivers lend themselves to implicit specification, where the device and the operating system are the external interfaces. Our experiments demonstrate that our synthesis method is precise and efficient. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronisation placements are produced for our experiments, favouring e.g. a minimal number of synchronisation operations or maximum concurrency."}],"status":"public","date_updated":"2023-09-07T11:57:01Z","supervisor":[{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"degree_awarded":"PhD","year":"2016","day":"07","doi":"10.15479/at:ista:1130","title":"Automatic synthesis of synchronisation primitives for concurrent programs","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"date_published":"2016-07-07T00:00:00Z","file":[{"date_updated":"2021-02-22T11:39:32Z","checksum":"319a506831650327e85376db41fc1094","file_size":1523935,"relation":"main_file","access_level":"open_access","file_name":"2016_Tarrach_Thesis.pdf","success":1,"date_created":"2021-02-22T11:39:32Z","content_type":"application/pdf","file_id":"9179","creator":"dernst"},{"relation":"main_file","access_level":"closed","checksum":"39efcd789f0ad859ff15652cb7afc412","file_size":1306068,"file_name":"2016_Tarrach_Thesispdfa.pdf","date_updated":"2021-11-17T13:46:55Z","creator":"cchlebak","date_created":"2021-11-16T14:14:38Z","file_id":"10296","content_type":"application/pdf"}],"oa_version":"Published Version","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"publication_status":"published","citation":{"chicago":"Tarrach, Thorsten. “Automatic Synthesis of Synchronisation Primitives for Concurrent Programs.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/at:ista:1130\">https://doi.org/10.15479/at:ista:1130</a>.","ama":"Tarrach T. Automatic synthesis of synchronisation primitives for concurrent programs. 2016. doi:<a href=\"https://doi.org/10.15479/at:ista:1130\">10.15479/at:ista:1130</a>","apa":"Tarrach, T. (2016). <i>Automatic synthesis of synchronisation primitives for concurrent programs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:1130\">https://doi.org/10.15479/at:ista:1130</a>","ista":"Tarrach T. 2016. Automatic synthesis of synchronisation primitives for concurrent programs. Institute of Science and Technology Austria.","mla":"Tarrach, Thorsten. <i>Automatic Synthesis of Synchronisation Primitives for Concurrent Programs</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/at:ista:1130\">10.15479/at:ista:1130</a>.","short":"T. Tarrach, Automatic Synthesis of Synchronisation Primitives for Concurrent Programs, Institute of Science and Technology Austria, 2016.","ieee":"T. Tarrach, “Automatic synthesis of synchronisation primitives for concurrent programs,” Institute of Science and Technology Austria, 2016."}},{"degree_awarded":"PhD","year":"2016","has_accepted_license":"1","title":"Evolution of transcriptional regulatory sequences","publication_identifier":{"issn":["2663-337X"]},"day":"01","date_updated":"2025-05-28T11:57:04Z","status":"public","oa":1,"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"publication_status":"published","citation":{"ista":"Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","mla":"Tugrul, Murat. <i>Evolution of Transcriptional Regulatory Sequences</i>. Institute of Science and Technology Austria, 2016.","short":"M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of Science and Technology Austria, 2016.","ieee":"M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute of Science and Technology Austria, 2016.","chicago":"Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute of Science and Technology Austria, 2016.","apa":"Tugrul, M. (2016). <i>Evolution of transcriptional regulatory sequences</i>. Institute of Science and Technology Austria.","ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016."},"date_published":"2016-07-01T00:00:00Z","department":[{"_id":"NiBa"}],"file":[{"date_updated":"2019-08-13T08:53:52Z","file_name":"Tugrul_thesis_w_signature_page.pdf","checksum":"66cb61a59943e4fb7447c6a86be5ef51","file_size":3695257,"access_level":"closed","relation":"main_file","content_type":"application/pdf","file_id":"6810","date_created":"2019-08-13T08:53:52Z","creator":"dernst"},{"file_name":"2016_Tugrul_Thesis.pdf","access_level":"open_access","relation":"main_file","checksum":"293e388d70563760f6b24c3e66283dda","file_size":3880811,"date_updated":"2021-02-22T11:45:20Z","creator":"dernst","file_id":"9182","content_type":"application/pdf","date_created":"2021-02-22T11:45:20Z","success":1}],"oa_version":"Published Version","page":"89","date_created":"2018-12-11T11:50:19Z","ddc":["576"],"file_date_updated":"2021-02-22T11:45:20Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"5554"},{"id":"1666","relation":"part_of_dissertation","status":"public"}]},"article_processing_charge":"No","month":"07","language":[{"iso":"eng"}],"author":[{"last_name":"Tugrul","full_name":"Tugrul, Murat","first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758"}],"type":"dissertation","_id":"1131","alternative_title":["ISTA Thesis"],"acknowledgement":"This PhD thesis may not have been completed without the help and care I received from some peo- ple during my PhD life. I am especially grateful to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices but also for their patience and support. I thank Calin Guet and Jonathan Bollback for allowing me to “play around” in their labs and get some experience on experimental evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and sharing their experimental data with me. I thank Johannes Jaeger for reviewing my thesis. I thank all members of Barton group (aka bartonians) for their feedback, and all workers of IST Austria for making the best working conditions. Lastly, I thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous support and encouragement. I truly had a great chance of having right people around me.","abstract":[{"text":"Evolution of gene regulation is important for phenotypic evolution and diversity. Sequence-specific binding of regulatory proteins is one of the key regulatory mechanisms determining gene expression. Although there has been intense interest in evolution of regulatory binding sites in the last decades, a theoretical understanding is far from being complete. In this thesis, I aim at a better understanding of the evolution of transcriptional regulatory binding sequences by using biophysical and population genetic models.\r\nIn the first part of the thesis, I discuss how to formulate the evolutionary dynamics of binding se- quences in a single isolated binding site and in promoter/enhancer regions. I develop a theoretical framework bridging between a thermodynamical model for transcription and a mutation-selection-drift model for monomorphic populations. I mainly address the typical evolutionary rates, and how they de- pend on biophysical parameters (e.g. binding length and specificity) and population genetic parameters (e.g. population size and selection strength).\r\nIn the second part of the thesis, I analyse empirical data for a better evolutionary and biophysical understanding of sequence-specific binding of bacterial RNA polymerase. First, I infer selection on regulatory and non-regulatory binding sites of RNA polymerase in the E. coli K12 genome. Second, I infer the chemical potential of RNA polymerase, an important but unknown physical parameter defining the threshold energy for strong binding. Furthermore, I try to understand the relation between the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial isolates by constructing a simple but biophysically motivated gene expression model. Lastly, I lay out a statistical framework to predict adaptive point mutations in de novo promoter evolution in a selection experiment.","lang":"eng"}],"publist_id":"6229","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria"},{"type":"conference","language":[{"iso":"eng"}],"author":[{"full_name":"Duggirala, Parasara","first_name":"Parasara","last_name":"Duggirala"},{"full_name":"Fan, Chuchu","first_name":"Chuchu","last_name":"Fan"},{"full_name":"Potok, Matthew","first_name":"Matthew","last_name":"Potok"},{"last_name":"Qi","full_name":"Qi, Bolun","first_name":"Bolun"},{"first_name":"Sayan","full_name":"Mitra, Sayan","last_name":"Mitra"},{"last_name":"Viswanathan","full_name":"Viswanathan, Mahesh","first_name":"Mahesh"},{"last_name":"Bak","first_name":"Stanley","full_name":"Bak, Stanley"},{"last_name":"Bogomolov","first_name":"Sergiy","full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365"},{"full_name":"Johnson, Taylor","first_name":"Taylor","last_name":"Johnson"},{"full_name":"Nguyen, Luan","first_name":"Luan","last_name":"Nguyen"},{"last_name":"Schilling","full_name":"Schilling, Christian","first_name":"Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sogokon","full_name":"Sogokon, Andrew","first_name":"Andrew"},{"first_name":"Hoang","full_name":"Tran, Hoang","last_name":"Tran"},{"full_name":"Xiang, Weiming","first_name":"Weiming","last_name":"Xiang"}],"month":"10","conference":{"end_date":"2016-09-22","start_date":"2016-09-19","location":"Buenos Aires, Argentina ","name":"CCA: Control Applications "},"scopus_import":1,"status":"public","date_updated":"2021-01-12T06:48:32Z","publication":"2016 IEEE Conference on Control Applications","doi":"10.1109/CCA.2016.7587948","article_number":"7587948","day":"10","title":"Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP","date_created":"2018-12-11T11:50:20Z","year":"2016","publisher":"IEEE","oa_version":"None","department":[{"_id":"ToHe"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6224","date_published":"2016-10-10T00:00:00Z","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_status":"published","citation":{"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.","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>.","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.","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.","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>","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>","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>."},"_id":"1134","quality_controlled":"1"},{"file_date_updated":"2018-12-12T10:09:31Z","ddc":["000"],"date_created":"2018-12-11T11:50:20Z","type":"conference","month":"10","language":[{"iso":"eng"}],"author":[{"last_name":"Avni","first_name":"Guy","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287"},{"full_name":"Guha, Shibashis","first_name":"Shibashis","last_name":"Guha"},{"first_name":"Guillermo","full_name":"Rodríguez Navas, Guillermo","last_name":"Rodríguez Navas"}],"conference":{"location":"Pittsburgh, PA, USA","name":"EMSOFT: Embedded Software ","start_date":"2016-10-01","end_date":"2016-10-07"},"publication":"Proceedings of the 13th International Conference on Embedded Software ","scopus_import":1,"abstract":[{"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.","lang":"eng"}],"_id":"1135","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"publisher":"ACM","ec_funded":1,"publist_id":"6223","has_accepted_license":"1","title":"Synthesizing time triggered schedules for switched networks with faulty links","doi":"10.1145/2968478.2968499","day":"01","article_number":"26","year":"2016","oa":1,"date_updated":"2021-01-12T06:48:33Z","pubrep_id":"644","status":"public","publication_status":"published","citation":{"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>","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>","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>.","short":"G. Avni, S. Guha, G. Rodríguez Navas, in:, Proceedings of the 13th International Conference on Embedded Software , ACM, 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>.","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.","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."},"quality_controlled":"1","department":[{"_id":"ToHe"}],"file":[{"file_id":"4755","content_type":"application/pdf","date_created":"2018-12-12T10:09:31Z","creator":"system","date_updated":"2018-12-12T10:09:31Z","file_name":"IST-2016-644-v1+1_emsoft-no-format.pdf","access_level":"open_access","relation":"main_file","file_size":279240}],"oa_version":"Submitted Version","date_published":"2016-10-01T00:00:00Z"},{"publist_id":"6222","ec_funded":1,"main_file_link":[{"url":"https://hal.inria.fr/hal-01367181","open_access":"1"}],"project":[{"grant_number":"638176","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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).","_id":"1136","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)."}],"scopus_import":"1","publication":"Proceedings of the 9th International Conference on Motion in Games ","article_processing_charge":"No","type":"conference","conference":{"end_date":"2016-10-12","start_date":"2016-10-10","name":"MIG: Motion in Games","location":"San Francisco, CA, USA"},"language":[{"iso":"eng"}],"author":[{"last_name":"Manteaux","full_name":"Manteaux, Pierre","first_name":"Pierre"},{"full_name":"Vimont, Ulysse","first_name":"Ulysse","last_name":"Vimont"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rohmer","full_name":"Rohmer, Damien","first_name":"Damien"},{"first_name":"Marie","full_name":"Cani, Marie","last_name":"Cani"}],"month":"10","date_created":"2018-12-11T11:50:20Z","ddc":["004"],"date_published":"2016-10-10T00:00:00Z","oa_version":"Submitted Version","department":[{"_id":"ChWo"}],"quality_controlled":"1","citation":{"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>","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>","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>.","short":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, M. Cani, in:, Proceedings of the 9th International Conference on Motion in Games , ACM, 2016.","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.","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."},"publication_status":"published","status":"public","date_updated":"2023-02-21T09:49:49Z","oa":1,"year":"2016","article_number":"2994261","day":"10","doi":"10.1145/2994258.2994261","title":"Space-time sculpting of liquid animation","has_accepted_license":"1"},{"title":"RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics","issue":"12","doi":"10.1038/ni.3575","day":"01","year":"2016","oa":1,"external_id":{"pmid":["27776107"]},"date_updated":"2021-01-12T06:48:33Z","intvolume":"        17","status":"public","publication_status":"published","citation":{"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.","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.","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>.","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.","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>.","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>","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>"},"quality_controlled":"1","department":[{"_id":"MiSi"}],"oa_version":"Submitted Version","article_type":"original","date_published":"2016-12-01T00:00:00Z","volume":17,"page":"1352 - 1360","date_created":"2018-12-11T11:50:21Z","type":"journal_article","month":"12","language":[{"iso":"eng"}],"author":[{"last_name":"Salzer","first_name":"Elisabeth","full_name":"Salzer, Elisabeth"},{"full_name":"Çaǧdaş, Deniz","first_name":"Deniz","last_name":"Çaǧdaş"},{"full_name":"Hons, Miroslav","first_name":"Miroslav","last_name":"Hons","orcid":"0000-0002-6625-3348","id":"4167FE56-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mace, Emily","first_name":"Emily","last_name":"Mace"},{"last_name":"Garncarz","full_name":"Garncarz, Wojciech","first_name":"Wojciech"},{"first_name":"Oezlem","full_name":"Petronczki, Oezlem","last_name":"Petronczki"},{"full_name":"Platzer, René","first_name":"René","last_name":"Platzer"},{"last_name":"Pfajfer","full_name":"Pfajfer, Laurène","first_name":"Laurène"},{"first_name":"Ivan","full_name":"Bilic, Ivan","last_name":"Bilic"},{"full_name":"Ban, Sol","first_name":"Sol","last_name":"Ban"},{"full_name":"Willmann, Katharina","first_name":"Katharina","last_name":"Willmann"},{"first_name":"Malini","full_name":"Mukherjee, Malini","last_name":"Mukherjee"},{"full_name":"Supper, Verena","first_name":"Verena","last_name":"Supper"},{"last_name":"Hsu","full_name":"Hsu, Hsiangting","first_name":"Hsiangting"},{"last_name":"Banerjee","first_name":"Pinaki","full_name":"Banerjee, Pinaki"},{"full_name":"Sinha, Papiya","first_name":"Papiya","last_name":"Sinha"},{"last_name":"Mcclanahan","full_name":"Mcclanahan, Fabienne","first_name":"Fabienne"},{"last_name":"Zlabinger","first_name":"Gerhard","full_name":"Zlabinger, Gerhard"},{"last_name":"Pickl","full_name":"Pickl, Winfried","first_name":"Winfried"},{"first_name":"John","full_name":"Gribben, John","last_name":"Gribben"},{"last_name":"Stockinger","first_name":"Hannes","full_name":"Stockinger, Hannes"},{"last_name":"Bennett","first_name":"Keiryn","full_name":"Bennett, Keiryn"},{"first_name":"Johannes","full_name":"Huppa, Johannes","last_name":"Huppa"},{"last_name":"Dupré","full_name":"Dupré, Loï̈C","first_name":"Loï̈C"},{"last_name":"Sanal","first_name":"Özden","full_name":"Sanal, Özden"},{"last_name":"Jäger","first_name":"Ulrich","full_name":"Jäger, Ulrich"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt"},{"last_name":"Tezcan","first_name":"Ilhan","full_name":"Tezcan, Ilhan"},{"full_name":"Orange, Jordan","first_name":"Jordan","last_name":"Orange"},{"first_name":"Kaan","full_name":"Boztug, Kaan","last_name":"Boztug"}],"publication":"Nature Immunology","article_processing_charge":"No","scopus_import":1,"abstract":[{"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.","lang":"eng"}],"pmid":1,"_id":"1137","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400263","open_access":"1"}],"publisher":"Nature Publishing Group","publist_id":"6221"},{"year":"2016","doi":"10.1145/2933575.2933588","day":"05","title":"Quantitative automata under probabilistic semantics","status":"public","date_updated":"2021-01-12T06:48:34Z","external_id":{"arxiv":["1604.06764"]},"oa":1,"quality_controlled":"1","arxiv":1,"publication_status":"published","citation":{"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.","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>.","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.","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>","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>."},"date_published":"2016-07-05T00:00:00Z","oa_version":"Preprint","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_created":"2018-12-11T11:50:21Z","page":"76 - 85","scopus_import":1,"publication":"Proceedings of the 31st Annual ACM/IEEE Symposium","type":"conference","author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Otop","full_name":"Otop, Jan","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"conference":{"location":"New York, NY, USA","name":"LICS: Logic in Computer Science","start_date":"2016-07-05","end_date":"2016-07-08"},"language":[{"iso":"eng"}],"month":"07","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","_id":"1138","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."}],"publist_id":"6220","ec_funded":1,"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.06764"}],"publisher":"IEEE","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","date_updated":"2025-06-02T08:53:44Z","external_id":{"arxiv":["1602.02670"]},"oa":1,"year":"2016","day":"05","doi":"10.1145/2933575.2935304","title":"Model and objective separation with conditional lower bounds: disjunction is harder than conjunction","date_published":"2016-07-05T00:00:00Z","oa_version":"Preprint","department":[{"_id":"KrCh"}],"arxiv":1,"quality_controlled":"1","publication_status":"published","citation":{"short":"K. Chatterjee, W. Dvoák, M.H. Henzinger, V. Loitzenbauer, in:, Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2016, pp. 197–206.","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>.","ieee":"K. Chatterjee, W. Dvoák, M. H. 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.","ista":"Chatterjee K, Dvoák W, Henzinger MH, 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.","apa":"Chatterjee, K., Dvoák, W., Henzinger, M. H., &#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 MH, 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>","chicago":"Chatterjee, Krishnendu, Wolfgang Dvoák, Monika H 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>."},"scopus_import":"1","article_processing_charge":"No","publication":"Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science","month":"07","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dvoák","first_name":"Wolfgang","full_name":"Dvoák, Wolfgang"},{"first_name":"Monika H","full_name":"Henzinger, Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Veronika","full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer"}],"language":[{"iso":"eng"}],"conference":{"name":"LICS: Logic in Computer Science","location":"New York, NY, USA","end_date":"2016-07-08","start_date":"2016-07-05"},"type":"conference","date_created":"2018-12-11T11:50:22Z","page":"197 - 206","publist_id":"6219","publisher":"IEEE","main_file_link":[{"url":"https://arxiv.org/abs/1602.02670","open_access":"1"}],"project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1140","alternative_title":["Proceedings Symposium on Logic in Computer Science"],"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.","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"}]},{"publist_id":"6217","date_published":"2016-11-01T00:00:00Z","oa_version":"None","publisher":"Elsevier","department":[{"_id":"ChWo"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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.","_id":"1141","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"publication_status":"published","citation":{"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>","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>","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>.","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>.","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."},"scopus_import":1,"intvolume":"        17","status":"public","publication":"Journal of Computational Science","date_updated":"2021-01-12T06:48:35Z","type":"journal_article","language":[{"iso":"eng"}],"month":"11","author":[{"full_name":"Łazarz, Radosław","first_name":"Radosław","last_name":"Łazarz"},{"last_name":"Idzik","full_name":"Idzik, Michał","first_name":"Michał"},{"full_name":"Gądek, Konrad","first_name":"Konrad","last_name":"Gądek"},{"last_name":"Gajda-Zagorska","full_name":"Gajda-Zagorska, Ewa P","first_name":"Ewa P","id":"47794CF0-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:50:22Z","year":"2016","page":"249 - 260","doi":"10.1016/j.jocs.2016.03.004","day":"01","issue":"1","title":"Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization","volume":17},{"page":"1361 - 1372","date_created":"2018-12-11T11:50:22Z","volume":17,"publication":"Nature Immunology","scopus_import":1,"type":"journal_article","month":"12","language":[{"iso":"eng"}],"author":[{"last_name":"Martins","first_name":"Rui","full_name":"Martins, Rui"},{"first_name":"Julia","full_name":"Maier, Julia","last_name":"Maier"},{"first_name":"Anna","full_name":"Gorki, Anna","last_name":"Gorki"},{"first_name":"Kilian","full_name":"Huber, Kilian","last_name":"Huber"},{"first_name":"Omar","full_name":"Sharif, Omar","last_name":"Sharif"},{"first_name":"Philipp","full_name":"Starkl, Philipp","last_name":"Starkl"},{"first_name":"Simona","full_name":"Saluzzo, Simona","last_name":"Saluzzo"},{"last_name":"Quattrone","full_name":"Quattrone, Federica","first_name":"Federica"},{"first_name":"Riem","full_name":"Gawish, Riem","last_name":"Gawish"},{"last_name":"Lakovits","full_name":"Lakovits, Karin","first_name":"Karin"},{"full_name":"Aichinger, Michael","first_name":"Michael","last_name":"Aichinger"},{"last_name":"Radic Sarikas","full_name":"Radic Sarikas, Branka","first_name":"Branka"},{"first_name":"Charles","full_name":"Lardeau, Charles","last_name":"Lardeau"},{"last_name":"Hladik","full_name":"Hladik, Anastasiya","first_name":"Anastasiya"},{"full_name":"Korosec, Ana","first_name":"Ana","last_name":"Korosec"},{"id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus","first_name":"Markus","last_name":"Brown"},{"orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari","first_name":"Kari"},{"id":"2EDEA62C-F248-11E8-B48F-1D18A9856A87","full_name":"Duggan, Michelle","first_name":"Michelle","last_name":"Duggan"},{"last_name":"Kerjaschki","first_name":"Dontscho","full_name":"Kerjaschki, Dontscho"},{"first_name":"Harald","full_name":"Esterbauer, Harald","last_name":"Esterbauer"},{"full_name":"Colinge, Jacques","first_name":"Jacques","last_name":"Colinge"},{"first_name":"Stephanie","full_name":"Eisenbarth, Stephanie","last_name":"Eisenbarth"},{"full_name":"Decker, Thomas","first_name":"Thomas","last_name":"Decker"},{"full_name":"Bennett, Keiryn","first_name":"Keiryn","last_name":"Bennett"},{"first_name":"Stefan","full_name":"Kubicek, Stefan","last_name":"Kubicek"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"first_name":"Giulio","full_name":"Superti Furga, Giulio","last_name":"Superti Furga"},{"last_name":"Knapp","full_name":"Knapp, Sylvia","first_name":"Sylvia"}],"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).","_id":"1142","abstract":[{"lang":"eng","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."}],"publist_id":"6216","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://ora.ox.ac.uk/objects/uuid:f53a464e-1e5b-4f08-a7d8-b6749b852b9d","open_access":"1"}],"publisher":"Nature Publishing Group","year":"2016","title":"Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions","issue":"12","doi":"10.1038/ni.3590","day":"01","date_updated":"2021-01-12T06:48:36Z","intvolume":"        17","status":"public","oa":1,"quality_controlled":"1","publication_status":"published","citation":{"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.","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.","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>.","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.","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>.","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>"},"date_published":"2016-12-01T00:00:00Z","department":[{"_id":"MiSi"},{"_id":"PeJo"}],"oa_version":"Submitted Version"},{"type":"journal_article","language":[{"iso":"eng"}],"month":"03","author":[{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","full_name":"Nam, Phan","first_name":"Phan","last_name":"Nam"},{"last_name":"Rougerie","full_name":"Rougerie, Nicolas","first_name":"Nicolas"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer"}],"publication":"Analysis and PDE","scopus_import":1,"volume":9,"page":"459 - 485","date_created":"2018-12-11T11:50:23Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"main_file_link":[{"url":"https://arxiv.org/abs/1503.07061","open_access":"1"}],"publisher":"Mathematical Sciences Publishers","ec_funded":1,"publist_id":"6215","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."}],"_id":"1143","oa":1,"date_updated":"2021-01-12T06:48:36Z","intvolume":"         9","status":"public","issue":"2","title":"Ground states of large bosonic systems: The gross Pitaevskii limit revisited","day":"24","doi":"10.2140/apde.2016.9.459","year":"2016","department":[{"_id":"RoSe"}],"oa_version":"Preprint","date_published":"2016-03-24T00:00:00Z","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.","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>.","short":"P. Nam, N. Rougerie, R. Seiringer, Analysis and PDE 9 (2016) 459–485.","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.","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>","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>","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>."},"publication_status":"published","quality_controlled":"1"},{"abstract":[{"lang":"eng","text":"Auxin directs plant ontogenesis via differential accumulation within tissues depending largely on the activity of PIN proteins that mediate auxin efflux from cells and its directional cell-to-cell transport. Regardless of the developmental importance of PINs, the structure of these transporters is poorly characterized. Here, we present experimental data concerning protein topology of plasma membrane-localized PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters combined with immunolocalization techniques, we mapped the membrane topology of PINs and further cross-validated our results using available topology modeling software. We delineated the topology of PIN1 with two transmembrane (TM) bundles of five α-helices linked by a large intracellular loop and a C-terminus positioned outside the cytoplasm. Using constraints derived from our experimental data, we also provide an updated position of helical regions generating a verisimilitude model of PIN1. Since the canonical long PINs show a high degree of conservation in TM domains and auxin transport capacity has been demonstrated for Arabidopsis representatives of this group, this empirically enhanced topological model of PIN1 will be an important starting point for further studies on PIN structure–function relationships. In addition, we have established protocols that can be used to probe the topology of other plasma membrane proteins in plants. © 2016 The Authors"}],"acknowledgement":"This research has been financially supported by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) (T.N., M.Z., M.P., J.H.), Czech Science Foundation (13-40637S [J.F., M.Z.], 13-39982S [J.H.]); Research Foundation Flanders (Grant number FWO09/PDO/196) (S.V.) and the European Research Council (project ERC-2011-StG-20101109-PSDP) (J.F.). We thank David G. Robinson and Ranjan Swarup for sharing published material; Maria Šimášková, Mamoona Khan, Eva Benková for technical assistance; and R. Tejos, J. Kleine-Vehn, and E. Feraru for helpful discussions.","_id":"1145","project":[{"name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300"}],"publisher":"Cell Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6213","ec_funded":1,"file_date_updated":"2018-12-12T10:13:22Z","ddc":["581"],"volume":9,"date_created":"2018-12-11T11:50:23Z","page":"1504 - 1519","type":"journal_article","month":"11","language":[{"iso":"eng"}],"author":[{"last_name":"Nodzyński","first_name":"Tomasz","full_name":"Nodzyński, Tomasz"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"first_name":"Marta","full_name":"Zwiewka, Marta","last_name":"Zwiewka"},{"last_name":"Pernisová","first_name":"Markéta","full_name":"Pernisová, Markéta"},{"last_name":"Hejátko","full_name":"Hejátko, Jan","first_name":"Jan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml"}],"scopus_import":1,"publication":"Molecular Plant","citation":{"apa":"Nodzyński, T., Vanneste, S., Zwiewka, M., Pernisová, M., Hejátko, J., &#38; Friml, J. (2016). Enquiry into the topology of plasma membrane localized PIN auxin transport components. <i>Molecular Plant</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">https://doi.org/10.1016/j.molp.2016.08.010</a>","ama":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. Enquiry into the topology of plasma membrane localized PIN auxin transport components. <i>Molecular Plant</i>. 2016;9(11):1504-1519. doi:<a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">10.1016/j.molp.2016.08.010</a>","chicago":"Nodzyński, Tomasz, Steffen Vanneste, Marta Zwiewka, Markéta Pernisová, Jan Hejátko, and Jiří Friml. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” <i>Molecular Plant</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">https://doi.org/10.1016/j.molp.2016.08.010</a>.","ieee":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, and J. Friml, “Enquiry into the topology of plasma membrane localized PIN auxin transport components,” <i>Molecular Plant</i>, vol. 9, no. 11. Cell Press, pp. 1504–1519, 2016.","short":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, J. Friml, Molecular Plant 9 (2016) 1504–1519.","mla":"Nodzyński, Tomasz, et al. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” <i>Molecular Plant</i>, vol. 9, no. 11, Cell Press, 2016, pp. 1504–19, doi:<a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">10.1016/j.molp.2016.08.010</a>.","ista":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. 2016. Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. 9(11), 1504–1519."},"publication_status":"published","quality_controlled":"1","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:13:22Z","file_id":"5004","content_type":"application/pdf","creator":"system","date_updated":"2018-12-12T10:13:22Z","access_level":"open_access","relation":"main_file","file_size":5005876,"file_name":"IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf"}],"department":[{"_id":"JiFr"}],"date_published":"2016-11-07T00:00:00Z","day":"07","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"doi":"10.1016/j.molp.2016.08.010","title":"Enquiry into the topology of plasma membrane localized PIN auxin transport components","issue":"11","has_accepted_license":"1","year":"2016","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa":1,"intvolume":"         9","status":"public","date_updated":"2021-01-12T06:48:37Z","pubrep_id":"746"},{"department":[{"_id":"JiFr"}],"oa_version":"Published Version","file":[{"file_id":"4752","content_type":"application/pdf","date_created":"2018-12-12T10:09:28Z","creator":"system","date_updated":"2018-12-12T10:09:28Z","file_name":"IST-2017-745-v1+1_srep35955.pdf","relation":"main_file","access_level":"open_access","file_size":1587544}],"date_published":"2016-11-08T00:00:00Z","citation":{"chicago":"Balla, Jozef, Zuzana Medved’Ová, Petr Kalousek, Natálie Matiješčuková, Jiří Friml, Vilém Reinöhl, and Stanislav Procházka. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep35955\">https://doi.org/10.1038/srep35955</a>.","ama":"Balla J, Medved’Ová Z, Kalousek P, et al. Auxin flow mediated competition between axillary buds to restore apical dominance. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep35955\">10.1038/srep35955</a>","apa":"Balla, J., Medved’Ová, Z., Kalousek, P., Matiješčuková, N., Friml, J., Reinöhl, V., &#38; Procházka, S. (2016). Auxin flow mediated competition between axillary buds to restore apical dominance. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep35955\">https://doi.org/10.1038/srep35955</a>","ista":"Balla J, Medved’Ová Z, Kalousek P, Matiješčuková N, Friml J, Reinöhl V, Procházka S. 2016. Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. 6, 35955.","short":"J. Balla, Z. Medved’Ová, P. Kalousek, N. Matiješčuková, J. Friml, V. Reinöhl, S. Procházka, Scientific Reports 6 (2016).","mla":"Balla, Jozef, et al. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” <i>Scientific Reports</i>, vol. 6, 35955, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep35955\">10.1038/srep35955</a>.","ieee":"J. Balla <i>et al.</i>, “Auxin flow mediated competition between axillary buds to restore apical dominance,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016."},"publication_status":"published","quality_controlled":"1","oa":1,"license":"https://creativecommons.org/licenses/by/4.0/","date_updated":"2021-01-12T06:48:38Z","pubrep_id":"745","intvolume":"         6","status":"public","has_accepted_license":"1","title":"Auxin flow mediated competition between axillary buds to restore apical dominance","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"08","doi":"10.1038/srep35955","article_number":"35955","year":"2016","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Publishing Group","publist_id":"6211","abstract":[{"lang":"eng","text":"Apical dominance is one of the fundamental developmental phenomena in plant biology, which determines the overall architecture of aerial plant parts. Here we show apex decapitation activated competition for dominance in adjacent upper and lower axillary buds. A two-nodal-bud pea (Pisum sativum L.) was used as a model system to monitor and assess auxin flow, auxin transport channels, and dormancy and initiation status of axillary buds. Auxin flow was manipulated by lateral stem wounds or chemically by auxin efflux inhibitors 2,3,5-triiodobenzoic acid (TIBA), 1-N-naphtylphtalamic acid (NPA), or protein synthesis inhibitor cycloheximide (CHX) treatments, which served to interfere with axillary bud competition. Redirecting auxin flow to different points influenced which bud formed the outgrowing and dominant shoot. The obtained results proved that competition between upper and lower axillary buds as secondary auxin sources is based on the same auxin canalization principle that operates between the shoot apex and axillary bud. © The Author(s) 2016."}],"acknowledgement":"This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II., supported by the project “CEITEC–Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) and the Agronomy faculty grant from Mendel University “IGA AF MENDELU” (IP 14/2013).","_id":"1147","type":"journal_article","language":[{"iso":"eng"}],"author":[{"full_name":"Balla, Jozef","first_name":"Jozef","last_name":"Balla"},{"last_name":"Medved'Ová","first_name":"Zuzana","full_name":"Medved'Ová, Zuzana"},{"last_name":"Kalousek","first_name":"Petr","full_name":"Kalousek, Petr"},{"full_name":"Matiješčuková, Natálie","first_name":"Natálie","last_name":"Matiješčuková"},{"first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Reinöhl","first_name":"Vilém","full_name":"Reinöhl, Vilém"},{"full_name":"Procházka, Stanislav","first_name":"Stanislav","last_name":"Procházka"}],"month":"11","publication":"Scientific Reports","scopus_import":1,"file_date_updated":"2018-12-12T10:09:28Z","ddc":["581"],"volume":6,"date_created":"2018-12-11T11:50:24Z"},{"citation":{"ieee":"C. Schilling, S. Bogomolov, T. A. Henzinger, A. Podelski, and J. Ruess, “Adaptive moment closure for parameter inference of biochemical reaction networks,” <i>Biosystems</i>, vol. 149. Elsevier, pp. 15–25, 2016.","mla":"Schilling, Christian, et al. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” <i>Biosystems</i>, vol. 149, Elsevier, 2016, pp. 15–25, doi:<a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">10.1016/j.biosystems.2016.07.005</a>.","short":"C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems 149 (2016) 15–25.","ista":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. 2016. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. 149, 15–25.","apa":"Schilling, C., Bogomolov, S., Henzinger, T. A., Podelski, A., &#38; Ruess, J. (2016). Adaptive moment closure for parameter inference of biochemical reaction networks. <i>Biosystems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">https://doi.org/10.1016/j.biosystems.2016.07.005</a>","ama":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. Adaptive moment closure for parameter inference of biochemical reaction networks. <i>Biosystems</i>. 2016;149:15-25. doi:<a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">10.1016/j.biosystems.2016.07.005</a>","chicago":"Schilling, Christian, Sergiy Bogomolov, Thomas A Henzinger, Andreas Podelski, and Jakob Ruess. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” <i>Biosystems</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">https://doi.org/10.1016/j.biosystems.2016.07.005</a>."},"publication_status":"published","quality_controlled":"1","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"oa_version":"None","date_published":"2016-11-01T00:00:00Z","title":"Adaptive moment closure for parameter inference of biochemical reaction networks","doi":"10.1016/j.biosystems.2016.07.005","day":"01","year":"2016","date_updated":"2023-02-23T10:08:46Z","status":"public","intvolume":"       149","abstract":[{"text":"Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space. © 2016 Elsevier Ireland Ltd","lang":"eng"}],"_id":"1148","acknowledgement":"This work is based on the CMSB 2015 paper “Adaptive moment closure for parameter inference of biochemical reaction networks” (Bogomolov et al., 2015). The work was partly supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS1), by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award). J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"ec_funded":1,"publist_id":"6210","volume":149,"related_material":{"record":[{"status":"public","id":"1658","relation":"earlier_version"}]},"page":"15 - 25","date_created":"2018-12-11T11:50:24Z","language":[{"iso":"eng"}],"author":[{"last_name":"Schilling","full_name":"Schilling, Christian","first_name":"Christian"},{"orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy","first_name":"Sergiy"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Andreas","full_name":"Podelski, Andreas","last_name":"Podelski"},{"id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282","last_name":"Ruess","full_name":"Ruess, Jakob","first_name":"Jakob"}],"month":"11","type":"journal_article","publication":"Biosystems","scopus_import":1},{"volume":107,"title":"A study of rigorous ODE integrators for multi scale set oriented computations","day":"01","doi":"10.1016/j.apnum.2016.04.005","page":"34 - 47","year":"2016","date_created":"2018-12-11T11:50:25Z","month":"09","author":[{"last_name":"Miyaji","first_name":"Tomoyuki","full_name":"Miyaji, Tomoyuki"},{"id":"3768D56A-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk"},{"full_name":"Gameiro, Marcio","first_name":"Marcio","last_name":"Gameiro"},{"full_name":"Kokubu, Hiroshi","first_name":"Hiroshi","last_name":"Kokubu"},{"last_name":"Mischaikow","full_name":"Mischaikow, Konstantin","first_name":"Konstantin"}],"language":[{"iso":"eng"}],"type":"journal_article","date_updated":"2021-01-12T06:48:38Z","publication":"Applied Numerical Mathematics","status":"public","intvolume":"       107","scopus_import":1,"citation":{"apa":"Miyaji, T., Pilarczyk, P., Gameiro, M., Kokubu, H., &#38; Mischaikow, K. (2016). A study of rigorous ODE integrators for multi scale set oriented computations. <i>Applied Numerical Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">https://doi.org/10.1016/j.apnum.2016.04.005</a>","ama":"Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. A study of rigorous ODE integrators for multi scale set oriented computations. <i>Applied Numerical Mathematics</i>. 2016;107:34-47. doi:<a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">10.1016/j.apnum.2016.04.005</a>","chicago":"Miyaji, Tomoyuki, Pawel Pilarczyk, Marcio Gameiro, Hiroshi Kokubu, and Konstantin Mischaikow. “A Study of Rigorous ODE Integrators for Multi Scale Set Oriented Computations.” <i>Applied Numerical Mathematics</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">https://doi.org/10.1016/j.apnum.2016.04.005</a>.","ieee":"T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, and K. Mischaikow, “A study of rigorous ODE integrators for multi scale set oriented computations,” <i>Applied Numerical Mathematics</i>, vol. 107. Elsevier, pp. 34–47, 2016.","mla":"Miyaji, Tomoyuki, et al. “A Study of Rigorous ODE Integrators for Multi Scale Set Oriented Computations.” <i>Applied Numerical Mathematics</i>, vol. 107, Elsevier, 2016, pp. 34–47, doi:<a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">10.1016/j.apnum.2016.04.005</a>.","short":"T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, K. Mischaikow, Applied Numerical Mathematics 107 (2016) 34–47.","ista":"Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. 2016. A study of rigorous ODE integrators for multi scale set oriented computations. Applied Numerical Mathematics. 107, 34–47."},"publication_status":"published","abstract":[{"lang":"eng","text":"We study the usefulness of two most prominent publicly available rigorous ODE integrators: one provided by the CAPD group (capd.ii.uj.edu.pl), the other based on the COSY Infinity project (cosyinfinity.org). Both integrators are capable of handling entire sets of initial conditions and provide tight rigorous outer enclosures of the images under a time-T map. We conduct extensive benchmark computations using the well-known Lorenz system, and compare the computation time against the final accuracy achieved. We also discuss the effect of a few technical parameters, such as the order of the numerical integration method, the value of T, and the phase space resolution. We conclude that COSY may provide more precise results due to its ability of avoiding the variable dependency problem. However, the overall cost of computations conducted using CAPD is typically lower, especially when intervals of parameters are involved. Moreover, access to COSY is limited (registration required) and the rigorous ODE integrators are not publicly available, while CAPD is an open source free software project. Therefore, we recommend the latter integrator for this kind of computations. Nevertheless, proper choice of the various integration parameters turns out to be of even greater importance than the choice of the integrator itself. © 2016 IMACS. Published by Elsevier B.V. All rights reserved."}],"quality_controlled":"1","_id":"1149","acknowledgement":"MG was partially supported by FAPESP grants 2013/07460-7 and 2010/00875-9, and by CNPq grants 305860/2013-5 and 306453/2009-6, Brazil. The work of HK was partially supported by Grant-in-Aid for Scientific Research (Nos.24654022, 25287029), Ministry of Education, Science, Technology, Culture and Sports, Japan. KM was supported by NSF grants NSF-DMS-0835621, 0915019, 1125174, 1248071, and contracts from AFOSR and DARPA. TM was supported by Grant-in-Aid for JSPS Fellows No. 245312. A part of the research of TM and HK was also supported by JST, CREST.\r\n\r\nResearch conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE – Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (Ref. FCT PTDC/MAT/098871/2008); from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. 622033; and from the same sources as HK.\r\n\r\nThe authors express their gratitude to the Department of Mathematics of Kyoto University for making their server available for conducting the computations described in the paper, and to the reviewers for helpful comments that contributed towards increasing the quality of the paper.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"oa_version":"None","publisher":"Elsevier","project":[{"_id":"255F06BE-B435-11E9-9278-68D0E5697425","name":"Persistent Homology - Images, Data and Maps","grant_number":"622033","call_identifier":"FP7"}],"date_published":"2016-09-01T00:00:00Z","ec_funded":1,"publist_id":"6209"},{"date_published":"2016-09-12T00:00:00Z","publist_id":"6208","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiSi"}],"oa_version":"None","publisher":"Cell Press","quality_controlled":"1","_id":"1150","citation":{"ista":"Renkawitz J, Sixt MK. 2016. A Radical Break Restraining Neutrophil Migration. Developmental Cell. 38(5), 448–450.","ieee":"J. Renkawitz and M. K. Sixt, “A Radical Break Restraining Neutrophil Migration,” <i>Developmental Cell</i>, vol. 38, no. 5. Cell Press, pp. 448–450, 2016.","short":"J. Renkawitz, M.K. Sixt, Developmental Cell 38 (2016) 448–450.","mla":"Renkawitz, Jörg, and Michael K. Sixt. “A Radical Break Restraining Neutrophil Migration.” <i>Developmental Cell</i>, vol. 38, no. 5, Cell Press, 2016, pp. 448–50, doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">10.1016/j.devcel.2016.08.017</a>.","chicago":"Renkawitz, Jörg, and Michael K Sixt. “A Radical Break Restraining Neutrophil Migration.” <i>Developmental Cell</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">https://doi.org/10.1016/j.devcel.2016.08.017</a>.","apa":"Renkawitz, J., &#38; Sixt, M. K. (2016). A Radical Break Restraining Neutrophil Migration. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">https://doi.org/10.1016/j.devcel.2016.08.017</a>","ama":"Renkawitz J, Sixt MK. A Radical Break Restraining Neutrophil Migration. <i>Developmental Cell</i>. 2016;38(5):448-450. doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">10.1016/j.devcel.2016.08.017</a>"},"publication_status":"published","abstract":[{"lang":"eng","text":"When neutrophils infiltrate a site of inflammation, they have to stop at the right place to exert their effector function. In this issue of Developmental Cell, Wang et al. (2016) show that neutrophils sense reactive oxygen species via the TRPM2 channel to arrest migration at their target site. © 2016 Elsevier Inc."}],"publication":"Developmental Cell","date_updated":"2021-01-12T06:48:39Z","status":"public","intvolume":"        38","scopus_import":1,"author":[{"first_name":"Jörg","full_name":"Renkawitz, Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"}],"month":"09","language":[{"iso":"eng"}],"type":"journal_article","page":"448 - 450","year":"2016","date_created":"2018-12-11T11:50:25Z","volume":38,"issue":"5","title":"A Radical Break Restraining Neutrophil Migration","day":"12","doi":"10.1016/j.devcel.2016.08.017"},{"oa":1,"external_id":{"pmid":["27898393"]},"date_updated":"2021-01-12T06:48:39Z","intvolume":"        30","status":"public","issue":"20","has_accepted_license":"1","title":"A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis","day":"15","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1101/gad.285361.116","year":"2016","department":[{"_id":"JiFr"}],"file":[{"creator":"dernst","file_id":"5882","content_type":"application/pdf","date_created":"2019-01-25T09:32:55Z","success":1,"file_name":"2016_GeneDev_Simonini.pdf","access_level":"open_access","relation":"main_file","file_size":1419263,"date_updated":"2019-01-25T09:32:55Z"}],"oa_version":"Published Version","date_published":"2016-10-15T00:00:00Z","citation":{"ista":"Simonini S, Deb J, Moubayidin L, Stephenson P, Valluru M, Freire Rios A, Sorefan K, Weijers D, Friml J, Östergaard L. 2016. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. 30(20), 2286–2296.","ieee":"S. Simonini <i>et al.</i>, “A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis,” <i>Genes and Development</i>, vol. 30, no. 20. Cold Spring Harbor Laboratory Press, pp. 2286–2296, 2016.","mla":"Simonini, Sara, et al. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” <i>Genes and Development</i>, vol. 30, no. 20, Cold Spring Harbor Laboratory Press, 2016, pp. 2286–96, doi:<a href=\"https://doi.org/10.1101/gad.285361.116\">10.1101/gad.285361.116</a>.","short":"S. Simonini, J. Deb, L. Moubayidin, P. Stephenson, M. Valluru, A. Freire Rios, K. Sorefan, D. Weijers, J. Friml, L. Östergaard, Genes and Development 30 (2016) 2286–2296.","chicago":"Simonini, Sara, Joyita Deb, Laila Moubayidin, Pauline Stephenson, Manoj Valluru, Alejandra Freire Rios, Karim Sorefan, Dolf Weijers, Jiří Friml, and Lars Östergaard. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2016. <a href=\"https://doi.org/10.1101/gad.285361.116\">https://doi.org/10.1101/gad.285361.116</a>.","apa":"Simonini, S., Deb, J., Moubayidin, L., Stephenson, P., Valluru, M., Freire Rios, A., … Östergaard, L. (2016). A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.285361.116\">https://doi.org/10.1101/gad.285361.116</a>","ama":"Simonini S, Deb J, Moubayidin L, et al. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. <i>Genes and Development</i>. 2016;30(20):2286-2296. doi:<a href=\"https://doi.org/10.1101/gad.285361.116\">10.1101/gad.285361.116</a>"},"publication_status":"published","quality_controlled":"1","type":"journal_article","author":[{"first_name":"Sara","full_name":"Simonini, Sara","last_name":"Simonini"},{"first_name":"Joyita","full_name":"Deb, Joyita","last_name":"Deb"},{"full_name":"Moubayidin, Laila","first_name":"Laila","last_name":"Moubayidin"},{"first_name":"Pauline","full_name":"Stephenson, Pauline","last_name":"Stephenson"},{"last_name":"Valluru","first_name":"Manoj","full_name":"Valluru, Manoj"},{"full_name":"Freire Rios, Alejandra","first_name":"Alejandra","last_name":"Freire Rios"},{"last_name":"Sorefan","full_name":"Sorefan, Karim","first_name":"Karim"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Östergaard, Lars","first_name":"Lars","last_name":"Östergaard"}],"language":[{"iso":"eng"}],"month":"10","publication":"Genes and Development","scopus_import":1,"file_date_updated":"2019-01-25T09:32:55Z","volume":30,"ddc":["570"],"page":"2286 - 2296","date_created":"2018-12-11T11:50:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Cold Spring Harbor Laboratory Press","publist_id":"6207","abstract":[{"text":"Tissue patterning in multicellular organisms is the output of precise spatio–temporal regulation of gene expression coupled with changes in hormone dynamics. In plants, the hormone auxin regulates growth and development at every stage of a plant’s life cycle. Auxin signaling occurs through binding of the auxin molecule to a TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional repressor proteins. These are subsequently ubiquitinated and degraded via the 26S proteasome, leading to derepression of auxin response factors (ARFs). How auxin is able to elicit such a diverse range of developmental responses through a single signaling module has not yet been resolved. Here we present an alternative auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through interactions with process-specific transcription factors. This noncanonical hormonesensing mechanism exhibits strong preference for the naturally occurring auxin indole 3-acetic acid (IAA) and is important for coordinating growth and patterning in diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence, ovule development, and primary branch formation. Disrupting this IAA-sensing ability induces morphological aberrations with consequences for plant fitness. Therefore, our findings introduce a novel transcription factor-based mechanism of hormone perception in plants. © 2016 Simonini et al.","lang":"eng"}],"pmid":1,"acknowledgement":"We thank Norwich Research Park Bioimaging, Grant Calder, Roy\r\nDunford, Caroline Smith, Paul Thomas, and Mark Youles for\r\ntechnical support; Charlie Scutt, Alejandro Ferrando, and George\r\nLomonossoff for plasmids; Toshiro Ito for seeds; Brendan Davies\r\nand Barry Causier for the REGIA library; and Mark Buttner,\r\nSimona Masiero, Fabio Rossi, Doris Wagner, and Jun Xiao for\r\nhelp and material. We are also grateful to Stefano Bencivenga,\r\nMarie Brüser, Friederike Jantzen, Lukasz Langowski, Xinran Li,\r\nand Nicola Stacey for discussions and helpful comments on the\r\nmanuscript. This work was supported by grants BB/M004112/1\r\nand BB/I017232/1 (Crop Improvement Research Club) to L.Ø.\r\nfrom the Biotechnological and Biological Sciences Research\r\nCouncil, and Institute Strategic Programme grant (BB/J004553/\r\n1) to the John Innes Centre. S.S., J.D., and L.Ø conceived the ex-\r\nperiments. ","_id":"1151"},{"year":"2016","issue":"10","title":"A model of differential growth guided apical hook formation in plants","doi":"10.1105/tpc.15.00569","day":"01","date_updated":"2021-01-12T06:48:40Z","intvolume":"        28","status":"public","oa":1,"quality_controlled":"1","publication_status":"published","citation":{"ista":"Žádníková P, Wabnik KT, Abuzeineh A, Gallemí M, Van Der Straeten D, Smith R, Inze D, Friml J, Prusinkiewicz P, Benková E. 2016. A model of differential growth guided apical hook formation in plants. Plant Cell. 28(10), 2464–2477.","ieee":"P. Žádníková <i>et al.</i>, “A model of differential growth guided apical hook formation in plants,” <i>Plant Cell</i>, vol. 28, no. 10. American Society of Plant Biologists, pp. 2464–2477, 2016.","mla":"Žádníková, Petra, et al. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” <i>Plant Cell</i>, vol. 28, no. 10, American Society of Plant Biologists, 2016, pp. 2464–77, doi:<a href=\"https://doi.org/10.1105/tpc.15.00569\">10.1105/tpc.15.00569</a>.","short":"P. Žádníková, K.T. Wabnik, A. Abuzeineh, M. Gallemí, D. Van Der Straeten, R. Smith, D. Inze, J. Friml, P. Prusinkiewicz, E. Benková, Plant Cell 28 (2016) 2464–2477.","chicago":"Žádníková, Petra, Krzysztof T Wabnik, Anas Abuzeineh, Marçal Gallemí, Dominique Van Der Straeten, Richard Smith, Dirk Inze, Jiří Friml, Przemysław Prusinkiewicz, and Eva Benková. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” <i>Plant Cell</i>. American Society of Plant Biologists, 2016. <a href=\"https://doi.org/10.1105/tpc.15.00569\">https://doi.org/10.1105/tpc.15.00569</a>.","ama":"Žádníková P, Wabnik KT, Abuzeineh A, et al. A model of differential growth guided apical hook formation in plants. <i>Plant Cell</i>. 2016;28(10):2464-2477. doi:<a href=\"https://doi.org/10.1105/tpc.15.00569\">10.1105/tpc.15.00569</a>","apa":"Žádníková, P., Wabnik, K. T., Abuzeineh, A., Gallemí, M., Van Der Straeten, D., Smith, R., … Benková, E. (2016). A model of differential growth guided apical hook formation in plants. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.15.00569\">https://doi.org/10.1105/tpc.15.00569</a>"},"date_published":"2016-10-01T00:00:00Z","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"oa_version":"Submitted Version","page":"2464 - 2477","date_created":"2018-12-11T11:50:26Z","volume":28,"publication":"Plant Cell","scopus_import":1,"type":"journal_article","month":"10","author":[{"last_name":"Žádníková","first_name":"Petra","full_name":"Žádníková, Petra"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","last_name":"Wabnik","first_name":"Krzysztof T","full_name":"Wabnik, Krzysztof T"},{"first_name":"Anas","full_name":"Abuzeineh, Anas","last_name":"Abuzeineh"},{"first_name":"Marçal","full_name":"Gallemí, Marçal","last_name":"Gallemí"},{"first_name":"Dominique","full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten"},{"full_name":"Smith, Richard","first_name":"Richard","last_name":"Smith"},{"last_name":"Inze","full_name":"Inze, Dirk","first_name":"Dirk"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml"},{"first_name":"Przemysław","full_name":"Prusinkiewicz, Przemysław","last_name":"Prusinkiewicz"},{"full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"language":[{"iso":"eng"}],"acknowledgement":"We thank Martine De Cock and Annick Bleys for help in preparing the manuscript, Daniel Van Damme for sharing material and stimulating discussion, and Rudiger Simon for support during revision of the manuscript.\r\nThis work was supported by grants from the European Research Council (StartingIndependentResearchGrantERC-2007-Stg-207362-HCPO)and the Czech Science Foundation (GACR CZ.1.07/2.3.00/20.0043) to E.B.\r\nand Natural Sciences and Engineering Research Council of Canada Discovery Grant 2014-05325 to P.P. K.W. acknowledges funding from a Human Frontier Science Program Long-Term Fellowship (LT-000209-2014).","_id":"1153","abstract":[{"lang":"eng","text":"Differential cell growth enables flexible organ bending in the presence of environmental signals such as light or gravity. A prominent example of the developmental processes based on differential cell growth is the formation of the apical hook that protects the fragile shoot apical meristem when it breaks through the soil during germination. Here, we combined in silico and in vivo approaches to identify a minimal mechanism producing auxin gradient-guided differential growth during the establishment of the apical hook in the model plant Arabidopsis thaliana. Computer simulation models based on experimental data demonstrate that asymmetric expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus convex (outer) side of the hook suffices to establish an auxin maximum in the epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism that translates this maximum into differential growth, and thus curvature, of the apical hook. Through a combination of experimental and in silico computational approaches, we have identified the individual contributions of differential cell elongation and proliferation to defining the apical hook and reveal the role of auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society of Plant Biologists. All rights reserved."}],"ec_funded":1,"publist_id":"6205","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/"}],"project":[{"grant_number":"207362","call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis"}],"publisher":"American Society of Plant Biologists"},{"type":"journal_article","author":[{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Jan","full_name":"Schwarz, Jan"},{"last_name":"Bierbaum","first_name":"Veronika","full_name":"Bierbaum, Veronika","id":"3FD04378-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"last_name":"Frank","first_name":"Tino","full_name":"Frank, Tino"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"},{"first_name":"Savaş","full_name":"Tay, Savaş","last_name":"Tay"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K"},{"full_name":"Mehling, Matthias","first_name":"Matthias","last_name":"Mehling","orcid":"0000-0001-8599-1226","id":"3C23B994-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"month":"11","scopus_import":1,"publication":"Scientific Reports","file_date_updated":"2018-12-12T10:09:32Z","volume":6,"ddc":["579"],"date_created":"2018-12-11T11:50:27Z","project":[{"call_identifier":"FP7","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Y 564-B12","call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)"}],"publisher":"Nature Publishing Group","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6204","ec_funded":1,"abstract":[{"lang":"eng","text":"Cellular locomotion is a central hallmark of eukaryotic life. It is governed by cell-extrinsic molecular factors, which can either emerge in the soluble phase or as immobilized, often adhesive ligands. To encode for direction, every cue must be present as a spatial or temporal gradient. Here, we developed a microfluidic chamber that allows measurement of cell migration in combined response to surface immobilized and soluble molecular gradients. As a proof of principle we study the response of dendritic cells to their major guidance cues, chemokines. The majority of data on chemokine gradient sensing is based on in vitro studies employing soluble gradients. Despite evidence suggesting that in vivo chemokines are often immobilized to sugar residues, limited information is available how cells respond to immobilized chemokines. We tracked migration of dendritic cells towards immobilized gradients of the chemokine CCL21 and varying superimposed soluble gradients of CCL19. Differential migratory patterns illustrate the potential of our setup to quantitatively study the competitive response to both types of gradients. Beyond chemokines our approach is broadly applicable to alternative systems of chemo- and haptotaxis such as cells migrating along gradients of adhesion receptor ligands vs. any soluble cue. \r\n"}],"acknowledgement":"This work was supported by the Swiss National Science Foundation (Ambizione fellowship; PZ00P3-154733 to M.M.), the Swiss Multiple Sclerosis Society (research support to M.M.), a fellowship from the Boehringer Ingelheim Fonds (BIF) to J.S., the European Research Council (grant ERC GA 281556) and a START award from the Austrian Science Foundation (FWF) to M.S. #BioimagingFacility","_id":"1154","oa":1,"intvolume":"         6","status":"public","date_updated":"2021-01-12T06:48:41Z","pubrep_id":"744","article_number":"36440","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"07","doi":"10.1038/srep36440","has_accepted_license":"1","title":"A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients","year":"2016","oa_version":"Published Version","file":[{"creator":"system","file_id":"4756","content_type":"application/pdf","date_created":"2018-12-12T10:09:32Z","file_name":"IST-2017-744-v1+1_srep36440.pdf","relation":"main_file","access_level":"open_access","file_size":2353456,"date_updated":"2018-12-12T10:09:32Z"}],"department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"ToBo"}],"date_published":"2016-11-07T00:00:00Z","publication_status":"published","citation":{"chicago":"Schwarz, Jan, Veronika Bierbaum, Jack Merrin, Tino Frank, Robert Hauschild, Mark Tobias Bollenbach, Savaş Tay, Michael K Sixt, and Matthias Mehling. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep36440\">https://doi.org/10.1038/srep36440</a>.","ama":"Schwarz J, Bierbaum V, Merrin J, et al. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep36440\">10.1038/srep36440</a>","apa":"Schwarz, J., Bierbaum, V., Merrin, J., Frank, T., Hauschild, R., Bollenbach, M. T., … Mehling, M. (2016). A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep36440\">https://doi.org/10.1038/srep36440</a>","ista":"Schwarz J, Bierbaum V, Merrin J, Frank T, Hauschild R, Bollenbach MT, Tay S, Sixt MK, Mehling M. 2016. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. 6, 36440.","mla":"Schwarz, Jan, et al. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” <i>Scientific Reports</i>, vol. 6, 36440, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep36440\">10.1038/srep36440</a>.","short":"J. Schwarz, V. Bierbaum, J. Merrin, T. Frank, R. Hauschild, M.T. Bollenbach, S. Tay, M.K. Sixt, M. Mehling, Scientific Reports 6 (2016).","ieee":"J. Schwarz <i>et al.</i>, “A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016."},"quality_controlled":"1"},{"day":"15","doi":"10.1214/16-AAP1193","title":"Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population","issue":"6","year":"2016","oa":1,"intvolume":"        26","status":"public","date_updated":"2021-01-12T06:48:43Z","citation":{"ista":"Lee J, Schnelli K. 2016. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. Annals of Applied Probability. 26(6), 3786–3839.","mla":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” <i>Annals of Applied Probability</i>, vol. 26, no. 6, Institute of Mathematical Statistics, 2016, pp. 3786–839, doi:<a href=\"https://doi.org/10.1214/16-AAP1193\">10.1214/16-AAP1193</a>.","short":"J. Lee, K. Schnelli, Annals of Applied Probability 26 (2016) 3786–3839.","ieee":"J. Lee and K. Schnelli, “Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population,” <i>Annals of Applied Probability</i>, vol. 26, no. 6. Institute of Mathematical Statistics, pp. 3786–3839, 2016.","chicago":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2016. <a href=\"https://doi.org/10.1214/16-AAP1193\">https://doi.org/10.1214/16-AAP1193</a>.","apa":"Lee, J., &#38; Schnelli, K. (2016). Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/16-AAP1193\">https://doi.org/10.1214/16-AAP1193</a>","ama":"Lee J, Schnelli K. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. <i>Annals of Applied Probability</i>. 2016;26(6):3786-3839. doi:<a href=\"https://doi.org/10.1214/16-AAP1193\">10.1214/16-AAP1193</a>"},"publication_status":"published","quality_controlled":"1","oa_version":"Preprint","department":[{"_id":"LaEr"}],"date_published":"2016-12-15T00:00:00Z","volume":26,"date_created":"2018-12-11T11:50:27Z","page":"3786 - 3839","type":"journal_article","language":[{"iso":"eng"}],"author":[{"full_name":"Lee, Ji","first_name":"Ji","last_name":"Lee"},{"id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231","first_name":"Kevin","full_name":"Schnelli, Kevin","last_name":"Schnelli"}],"month":"12","scopus_import":1,"publication":"Annals of Applied Probability","abstract":[{"lang":"eng","text":"We consider sample covariance matrices of the form Q = ( σ1/2X)(σ1/2X)∗, where the sample X is an M ×N random matrix whose entries are real independent random variables with variance 1/N and whereσ is an M × M positive-definite deterministic matrix. We analyze the asymptotic fluctuations of the largest rescaled eigenvalue of Q when both M and N tend to infinity with N/M →d ϵ (0,∞). For a large class of populations σ in the sub-critical regime, we show that the distribution of the largest rescaled eigenvalue of Q is given by the type-1 Tracy-Widom distribution under the additional assumptions that (1) either the entries of X are i.i.d. Gaussians or (2) that σ is diagonal and that the entries of X have a sub-exponential decay."}],"acknowledgement":"We thank Horng-Tzer Yau for numerous discussions and remarks. We are grateful to Ben Adlam, Jinho Baik, Zhigang Bao, Paul Bourgade, László Erd ̋os, Iain Johnstone and Antti Knowles for comments. We are also grate-\r\nful to the anonymous referee for carefully reading our manuscript and suggesting several improvements.","_id":"1157","main_file_link":[{"url":"https://arxiv.org/abs/1409.4979","open_access":"1"}],"project":[{"call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"publisher":"Institute of Mathematical Statistics","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6201","ec_funded":1}]