[{"_id":"1607","type":"conference","conference":{"name":"CAV: Computer Aided Verification","start_date":"2015-07-18","end_date":"2015-07-24","location":"San Francisco, CA, USA"},"status":"public","date_updated":"2023-09-07T12:01:59Z","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff property, the ratio property, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let n denote the number of nodes of a graph, m the number of edges (for constant treewidth graphs m=O(n)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a multiplicative factor of ϵ in time O(n⋅log(n/ϵ)) and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time O(n⋅log(|a⋅b|))=O(n⋅log(n⋅W)), when the output is ab, as compared to the previously best known algorithm with running time O(n2⋅log(n⋅W)). Third, for the minimum initial credit problem we show that (i) for general graphs the problem can be solved in O(n2⋅m) time and the associated decision problem can be solved in O(n⋅m) time, improving the previous known O(n3⋅m⋅log(n⋅W)) and O(n2⋅m) bounds, respectively; and (ii) for constant treewidth graphs we present an algorithm that requires O(n⋅logn) time, improving the previous known O(n4⋅log(n⋅W)) bound. We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks."}],"oa_version":"Preprint","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.07384"}],"month":"07","intvolume":" 9206","publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5430"},{"status":"public","id":"5437","relation":"earlier_version"},{"id":"821","status":"public","relation":"dissertation_contains"}]},"volume":9206,"ec_funded":1,"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"citation":{"ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs. CAV: Computer Aided Verification, LNCS, vol. 9206, 140–157.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs,” 9206:140–57. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_9.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative verification in constant treewidth graphs. In: Vol 9206. Springer; 2015:140-157. doi:10.1007/978-3-319-21690-4_9","apa":"Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms for quantitative verification in constant treewidth graphs (Vol. 9206, pp. 140–157). Presented at the CAV: Computer Aided Verification, San Francisco, CA, USA: Springer. https://doi.org/10.1007/978-3-319-21690-4_9","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for quantitative verification in constant treewidth graphs,” presented at the CAV: Computer Aided Verification, San Francisco, CA, USA, 2015, vol. 9206, pp. 140–157.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Springer, 2015, pp. 140–157.","mla":"Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. Vol. 9206, Springer, 2015, pp. 140–57, doi:10.1007/978-3-319-21690-4_9."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"}],"publist_id":"5560","title":"Faster algorithms for quantitative verification in constant treewidth graphs","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","publisher":"Springer","quality_controlled":"1","oa":1,"year":"2015","day":"16","page":"140 - 157","date_published":"2015-07-16T00:00:00Z","doi":"10.1007/978-3-319-21690-4_9","date_created":"2018-12-11T11:52:59Z"},{"day":"15","publication":"Real-Time Systems Symposium","year":"2015","doi":"10.1109/RTSS.2014.9","date_published":"2015-01-15T00:00:00Z","date_created":"2018-12-11T11:53:37Z","page":"118 - 127","publisher":"IEEE","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Alexander Kößler, and Ulrich Schmid. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” In Real-Time Systems Symposium, 2015:118–27. IEEE, 2015. https://doi.org/10.1109/RTSS.2014.9.","ista":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. 2015. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. Real-Time Systems Symposium. RTSS: Real-Time Systems Symposium vol. 2015, 118–127.","mla":"Chatterjee, Krishnendu, et al. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” Real-Time Systems Symposium, vol. 2015, no. January, IEEE, 2015, pp. 118–27, doi:10.1109/RTSS.2014.9.","short":"K. Chatterjee, A. Pavlogiannis, A. Kößler, U. Schmid, in:, Real-Time Systems Symposium, IEEE, 2015, pp. 118–127.","ieee":"K. Chatterjee, A. Pavlogiannis, A. Kößler, and U. Schmid, “A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks,” in Real-Time Systems Symposium, Rome, Italy, 2015, vol. 2015, no. January, pp. 118–127.","apa":"Chatterjee, K., Pavlogiannis, A., Kößler, A., & Schmid, U. (2015). A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In Real-Time Systems Symposium (Vol. 2015, pp. 118–127). Rome, Italy: IEEE. https://doi.org/10.1109/RTSS.2014.9","ama":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In: Real-Time Systems Symposium. Vol 2015. IEEE; 2015:118-127. doi:10.1109/RTSS.2014.9"},"title":"A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kößler","full_name":"Kößler, Alexander","first_name":"Alexander"},{"first_name":"Ulrich","full_name":"Schmid, Ulrich","last_name":"Schmid"}],"publist_id":"5417","article_processing_charge":"No","language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"earlier_version","id":"5423","status":"public"},{"relation":"dissertation_contains","id":"821","status":"public"}]},"issue":"January","volume":2015,"oa_version":"None","abstract":[{"lang":"eng","text":"We present a flexible framework for the automated competitive analysis of on-line scheduling algorithms for firm-deadline real-time tasks based on multi-objective graphs: Given a task set and an on-line scheduling algorithm specified as a labeled transition system, along with some optional safety, liveness, and/or limit-average constraints for the adversary, we automatically compute the competitive ratio of the algorithm w.r.t. A clairvoyant scheduler. We demonstrate the flexibility and power of our approach by comparing the competitive ratio of several on-line algorithms, including Dover, that have been proposed in the past, for various task sets. Our experimental results reveal that none of these algorithms is universally optimal, in the sense that there are task sets where other schedulers provide better performance. Our framework is hence a very useful design tool for selecting optimal algorithms for a given application."}],"month":"01","intvolume":" 2015","scopus_import":1,"date_updated":"2023-09-07T12:01:59Z","department":[{"_id":"KrCh"}],"_id":"1714","status":"public","type":"conference","conference":{"name":"RTSS: Real-Time Systems Symposium","end_date":"2014-12-05","location":"Rome, Italy","start_date":"2014-12-02"}},{"_id":"1633","conference":{"end_date":"2015-08-13","location":"Los Angeles, CA, United States","start_date":"2015-08-09","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"type":"conference","pubrep_id":"609","status":"public","date_updated":"2023-09-07T12:02:56Z","ddc":["000"],"file_date_updated":"2020-07-14T12:45:07Z","department":[{"_id":"ChWo"}],"abstract":[{"lang":"eng","text":"We present a method for simulating brittle fracture under the assumptions of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture surfaces. The computational cost of the BEM is alleviated by using a low-resolution mesh and interpolating the resulting stress intensity factors when propagating the high-resolution crack-front.\r\n\r\nOur system produces physics-based fracture surfaces with high spatial and temporal resolution, taking spatial variation of material toughness and/or strength into account. It also allows for crack initiation to be handled separately from crack propagation, which is not only more reasonable from a physics perspective, but can also be used to control the simulation.\r\n\r\nSeparating the resolution of the crack-front from the resolution of the computational mesh increases the efficiency and therefore the amount of visual detail on the resulting fracture surfaces. The BEM also allows us to re-use previously computed blocks of the system matrix."}],"oa_version":"Submitted Version","scopus_import":1,"intvolume":" 34","month":"07","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:15:13Z","file_name":"IST-2016-609-v1+1_FractureBEM.pdf","creator":"system","date_updated":"2020-07-14T12:45:07Z","file_size":20154270,"checksum":"955aee971983f6b6152bcc1c9b4a7c20","file_id":"5131","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"volume":34,"issue":"4","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"839"}]},"article_number":"151","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"citation":{"ista":"Hahn D, Wojtan C. 2015. High-resolution brittle fracture simulation with boundary elements. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 151.","chicago":"Hahn, David, and Chris Wojtan. “High-Resolution Brittle Fracture Simulation with Boundary Elements,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766896.","ieee":"D. Hahn and C. Wojtan, “High-resolution brittle fracture simulation with boundary elements,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","short":"D. Hahn, C. Wojtan, in:, ACM, 2015.","apa":"Hahn, D., & Wojtan, C. (2015). High-resolution brittle fracture simulation with boundary elements (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766896","ama":"Hahn D, Wojtan C. High-resolution brittle fracture simulation with boundary elements. In: Vol 34. ACM; 2015. doi:10.1145/2766896","mla":"Hahn, David, and Chris Wojtan. High-Resolution Brittle Fracture Simulation with Boundary Elements. Vol. 34, no. 4, 151, ACM, 2015, doi:10.1145/2766896."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"357A6A66-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Hahn, David","last_name":"Hahn"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"publist_id":"5522","title":"High-resolution brittle fracture simulation with boundary elements","oa":1,"quality_controlled":"1","publisher":"ACM","year":"2015","has_accepted_license":"1","day":"27","date_created":"2018-12-11T11:53:09Z","date_published":"2015-07-27T00:00:00Z","doi":"10.1145/2766896"},{"ddc":["570"],"date_updated":"2023-09-07T12:05:08Z","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:45:01Z","_id":"1537","status":"public","pubrep_id":"484","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5003","checksum":"228d3edf40627d897b3875088a0ac51f","creator":"system","file_size":4362653,"date_updated":"2020-07-14T12:45:01Z","file_name":"IST-2016-484-v1+1_1-s2.0-S0092867415000094-main.pdf","date_created":"2018-12-12T10:13:21Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":160,"related_material":{"record":[{"id":"961","status":"public","relation":"dissertation_contains"}]},"issue":"4","oa_version":"Published Version","abstract":[{"lang":"eng","text":"3D amoeboid cell migration is central to many developmental and disease-related processes such as cancer metastasis. Here, we identify a unique prototypic amoeboid cell migration mode in early zebrafish embryos, termed stable-bleb migration. Stable-bleb cells display an invariant polarized balloon-like shape with exceptional migration speed and persistence. Progenitor cells can be reversibly transformed into stable-bleb cells irrespective of their primary fate and motile characteristics by increasing myosin II activity through biochemical or mechanical stimuli. Using a combination of theory and experiments, we show that, in stable-bleb cells, cortical contractility fluctuations trigger a stochastic switch into amoeboid motility, and a positive feedback between cortical flows and gradients in contractility maintains stable-bleb cell polarization. We further show that rearward cortical flows drive stable-bleb cell migration in various adhesive and non-adhesive environments, unraveling a highly versatile amoeboid migration phenotype."}],"acknowledged_ssus":[{"_id":"SSU"}],"month":"02","intvolume":" 160","scopus_import":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Ruprecht, Verena, Stefan Wieser, Andrew Callan Jones, Michael Smutny, Hitoshi Morita, Keisuke Sako, Vanessa Barone, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.01.008.","ista":"Ruprecht V, Wieser S, Callan Jones A, Smutny M, Morita H, Sako K, Barone V, Ritsch Marte M, Sixt MK, Voituriez R, Heisenberg C-PJ. 2015. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 160(4), 673–685.","mla":"Ruprecht, Verena, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” Cell, vol. 160, no. 4, Cell Press, 2015, pp. 673–85, doi:10.1016/j.cell.2015.01.008.","short":"V. Ruprecht, S. Wieser, A. Callan Jones, M. Smutny, H. Morita, K. Sako, V. Barone, M. Ritsch Marte, M.K. Sixt, R. Voituriez, C.-P.J. Heisenberg, Cell 160 (2015) 673–685.","ieee":"V. Ruprecht et al., “Cortical contractility triggers a stochastic switch to fast amoeboid cell motility,” Cell, vol. 160, no. 4. Cell Press, pp. 673–685, 2015.","apa":"Ruprecht, V., Wieser, S., Callan Jones, A., Smutny, M., Morita, H., Sako, K., … Heisenberg, C.-P. J. (2015). Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.01.008","ama":"Ruprecht V, Wieser S, Callan Jones A, et al. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 2015;160(4):673-685. doi:10.1016/j.cell.2015.01.008"},"title":"Cortical contractility triggers a stochastic switch to fast amoeboid cell motility","publist_id":"5634","author":[{"id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","first_name":"Verena","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","last_name":"Ruprecht"},{"id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Wieser","orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan"},{"last_name":"Callan Jones","full_name":"Callan Jones, Andrew","first_name":"Andrew"},{"last_name":"Smutny","orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"},{"first_name":"Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","last_name":"Morita","full_name":"Morita, Hitoshi"},{"id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","first_name":"Keisuke","full_name":"Sako, Keisuke","orcid":"0000-0002-6453-8075","last_name":"Sako"},{"full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa"},{"first_name":"Monika","full_name":"Ritsch Marte, Monika","last_name":"Ritsch Marte"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Voituriez","full_name":"Voituriez, Raphaël","first_name":"Raphaël"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"project":[{"_id":"2529486C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"T 560-B17","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation"},{"call_identifier":"FWF","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","grant_number":"I 812-B12"}],"day":"12","publication":"Cell","has_accepted_license":"1","year":"2015","date_published":"2015-02-12T00:00:00Z","doi":"10.1016/j.cell.2015.01.008","date_created":"2018-12-11T11:52:35Z","page":"673 - 685","acknowledgement":"We would like to thank R. Hausschild and E. Papusheva for technical assistance and the service facilities at the IST Austria for continuous support. The caRhoA plasmid was a kind gift of T. Kudoh and A. Takesono. We thank M. Piel and E. Paluch for exchanging unpublished data. ","quality_controlled":"1","publisher":"Cell Press","oa":1},{"oa":1,"quality_controlled":"1","publisher":"American Society of Plant Biologists","page":"20 - 32","date_created":"2018-12-11T11:52:54Z","date_published":"2015-01-20T00:00:00Z","doi":"10.1105/tpc.114.134874","year":"2015","publication":"Plant Cell","day":"20","external_id":{"pmid":["25604445"]},"publist_id":"5580","author":[{"first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","last_name":"Adamowski"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"title":"PIN-dependent auxin transport: Action, regulation, and evolution","citation":{"chicago":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell. American Society of Plant Biologists, 2015. https://doi.org/10.1105/tpc.114.134874.","ista":"Adamowski M, Friml J. 2015. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 27(1), 20–32.","mla":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 20–32, doi:10.1105/tpc.114.134874.","ieee":"M. Adamowski and J. Friml, “PIN-dependent auxin transport: Action, regulation, and evolution,” Plant Cell, vol. 27, no. 1. American Society of Plant Biologists, pp. 20–32, 2015.","short":"M. Adamowski, J. Friml, Plant Cell 27 (2015) 20–32.","apa":"Adamowski, M., & Friml, J. (2015). PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.134874","ama":"Adamowski M, Friml J. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 2015;27(1):20-32. doi:10.1105/tpc.114.134874"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330589/"}],"scopus_import":1,"intvolume":" 27","month":"01","abstract":[{"lang":"eng","text":"Auxin participates in a multitude of developmental processes, as well as responses to environmental cues. Compared with other plant hormones, auxin exhibits a unique property, as it undergoes directional, cell-to-cell transport facilitated by plasma membrane-localized transport proteins. Among them, a prominent role has been ascribed to the PIN family of auxin efflux facilitators. PIN proteins direct polar auxin transport on account of their asymmetric subcellular localizations. In this review, we provide an overview of the multiple developmental roles of PIN proteins, including the atypical endoplasmic reticulum-localized members of the family, and look at the family from an evolutionary perspective. Next, we cover the cell biological and molecular aspects of PIN function, in particular the establishment of their polar subcellular localization. Hormonal and environmental inputs into the regulation of PIN action are summarized as well."}],"oa_version":"Submitted Version","pmid":1,"issue":"1","volume":27,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"938"}]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1591","department":[{"_id":"JiFr"}],"date_updated":"2023-09-07T12:06:09Z"},{"date_updated":"2023-09-07T12:38:08Z","department":[{"_id":"LaEr"}],"_id":"1677","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"149"}]},"volume":56,"issue":"10","ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider real symmetric and complex Hermitian random matrices with the additional symmetry hxy = hN-y,N-x. The matrix elements are independent (up to the fourfold symmetry) and not necessarily identically distributed. This ensemble naturally arises as the Fourier transform of a Gaussian orthogonal ensemble. Italso occurs as the flip matrix model - an approximation of the two-dimensional Anderson model at small disorder. We show that the density of states converges to the Wigner semicircle law despite the new symmetry type. We also prove the local version of the semicircle law on the optimal scale."}],"month":"10","intvolume":" 56","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1506.04683","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Alt J. 2015. The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. 56(10), 103301.","chicago":"Alt, Johannes. “The Local Semicircle Law for Random Matrices with a Fourfold Symmetry.” Journal of Mathematical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4932606.","short":"J. Alt, Journal of Mathematical Physics 56 (2015).","ieee":"J. Alt, “The local semicircle law for random matrices with a fourfold symmetry,” Journal of Mathematical Physics, vol. 56, no. 10. American Institute of Physics, 2015.","apa":"Alt, J. (2015). The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4932606","ama":"Alt J. The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. 2015;56(10). doi:10.1063/1.4932606","mla":"Alt, Johannes. “The Local Semicircle Law for Random Matrices with a Fourfold Symmetry.” Journal of Mathematical Physics, vol. 56, no. 10, 103301, American Institute of Physics, 2015, doi:10.1063/1.4932606."},"title":"The local semicircle law for random matrices with a fourfold symmetry","author":[{"last_name":"Alt","full_name":"Alt, Johannes","first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5472","article_number":"103301","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"day":"09","publication":"Journal of Mathematical Physics","year":"2015","date_published":"2015-10-09T00:00:00Z","doi":"10.1063/1.4932606","date_created":"2018-12-11T11:53:25Z","publisher":"American Institute of Physics","quality_controlled":"1","oa":1},{"abstract":[{"lang":"eng","text":"High-throughput live-cell screens are intricate elements of systems biology studies and drug discovery pipelines. Here, we demonstrate an optogenetics-assisted method that avoids the need for chemical activators and reporters, reduces the number of operational steps and increases information content in a cell-based small-molecule screen against human protein kinases, including an orphan receptor tyrosine kinase. This blueprint for all-optical screening can be adapted to many drug targets and cellular processes."}],"oa_version":"Submitted Version","scopus_import":1,"intvolume":" 11","month":"10","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"4842","checksum":"e9fb251dfcb7cd209b83f17867e61321","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:10:51Z","file_name":"IST-2017-837-v1+1_ingles-prieto.pdf","date_updated":"2020-07-14T12:45:12Z","file_size":1308364,"creator":"system"}],"ec_funded":1,"issue":"12","volume":11,"related_material":{"record":[{"id":"418","status":"public","relation":"dissertation_contains"}]},"_id":"1678","type":"journal_article","pubrep_id":"837","status":"public","date_updated":"2023-09-07T12:49:09Z","ddc":["571"],"file_date_updated":"2020-07-14T12:45:12Z","department":[{"_id":"HaJa"},{"_id":"LifeSc"}],"acknowledgement":"This work was supported by grants from the European Union Seventh Framework Programme (CIG-303564 to H.J. and ERC-StG-311166 to S.M.B.N.), the Human Frontier Science Program (RGY0084_2012 to H.J.) and the Herzfelder Foundation (to M.G.). A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W 1232) and a FemTech fellowship (3580812 Austrian Research Promotion Agency).","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","year":"2015","has_accepted_license":"1","publication":"Nature Chemical Biology","day":"12","page":"952 - 954","date_created":"2018-12-11T11:53:25Z","doi":"10.1038/nchembio.1933","date_published":"2015-10-12T00:00:00Z","project":[{"call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564"},{"grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"255A6082-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24"}],"citation":{"short":"Á. Inglés Prieto, E. Gschaider-Reichhart, M. Muellner, M. Nowak, S. Nijman, M. Grusch, H.L. Janovjak, Nature Chemical Biology 11 (2015) 952–954.","ieee":"Á. Inglés Prieto et al., “Light-assisted small-molecule screening against protein kinases,” Nature Chemical Biology, vol. 11, no. 12. Nature Publishing Group, pp. 952–954, 2015.","ama":"Inglés Prieto Á, Gschaider-Reichhart E, Muellner M, et al. Light-assisted small-molecule screening against protein kinases. Nature Chemical Biology. 2015;11(12):952-954. doi:10.1038/nchembio.1933","apa":"Inglés Prieto, Á., Gschaider-Reichhart, E., Muellner, M., Nowak, M., Nijman, S., Grusch, M., & Janovjak, H. L. (2015). Light-assisted small-molecule screening against protein kinases. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.1933","mla":"Inglés Prieto, Álvaro, et al. “Light-Assisted Small-Molecule Screening against Protein Kinases.” Nature Chemical Biology, vol. 11, no. 12, Nature Publishing Group, 2015, pp. 952–54, doi:10.1038/nchembio.1933.","ista":"Inglés Prieto Á, Gschaider-Reichhart E, Muellner M, Nowak M, Nijman S, Grusch M, Janovjak HL. 2015. Light-assisted small-molecule screening against protein kinases. Nature Chemical Biology. 11(12), 952–954.","chicago":"Inglés Prieto, Álvaro, Eva Gschaider-Reichhart, Markus Muellner, Matthias Nowak, Sebastian Nijman, Michael Grusch, and Harald L Janovjak. “Light-Assisted Small-Molecule Screening against Protein Kinases.” Nature Chemical Biology. Nature Publishing Group, 2015. https://doi.org/10.1038/nchembio.1933."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5471","author":[{"full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro"},{"orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart","first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Muellner","full_name":"Muellner, Markus","first_name":"Markus"},{"id":"30845DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","full_name":"Nowak, Matthias","last_name":"Nowak"},{"first_name":"Sebastian","last_name":"Nijman","full_name":"Nijman, Sebastian"},{"last_name":"Grusch","full_name":"Grusch, Michael","first_name":"Michael"},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"}],"title":"Light-assisted small-molecule screening against protein kinases"},{"department":[{"_id":"GaTk"}],"date_updated":"2023-09-07T12:55:21Z","type":"journal_article","status":"public","_id":"1576","related_material":{"record":[{"relation":"part_of_dissertation","id":"6473","status":"public"}]},"issue":"24","volume":115,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1504.05716","open_access":"1"}],"month":"12","intvolume":" 115","abstract":[{"text":"Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect regulatory crosstalk: the possibility that noncognate TFs could initiate transcription, with potentially disastrous effects for the cell. Here, we estimate the importance of crosstalk, suggest that its avoidance strongly constrains equilibrium models of TF binding, and propose an alternative nonequilibrium scheme that implements kinetic proofreading to suppress erroneous initiation. This proposal is consistent with the observed covalent modifications of the transcriptional apparatus and predicts increased noise in gene expression as a trade-off for improved specificity. Using information theory, we quantify this trade-off to find when optimal proofreading architectures are favored over their equilibrium counterparts. Such architectures exhibit significant super-Poisson noise at low expression in steady state.","lang":"eng"}],"oa_version":"Preprint","publist_id":"5595","author":[{"id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarah A","full_name":"Cepeda Humerez, Sarah A","last_name":"Cepeda Humerez"},{"last_name":"Rieckh","full_name":"Rieckh, Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"title":"Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation","citation":{"ista":"Cepeda Humerez SA, Rieckh G, Tkačik G. 2015. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 115(24), 248101.","chicago":"Cepeda Humerez, Sarah A, Georg Rieckh, and Gašper Tkačik. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.115.248101.","ieee":"S. A. Cepeda Humerez, G. Rieckh, and G. Tkačik, “Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation,” Physical Review Letters, vol. 115, no. 24. American Physical Society, 2015.","short":"S.A. Cepeda Humerez, G. Rieckh, G. Tkačik, Physical Review Letters 115 (2015).","ama":"Cepeda Humerez SA, Rieckh G, Tkačik G. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 2015;115(24). doi:10.1103/PhysRevLett.115.248101","apa":"Cepeda Humerez, S. A., Rieckh, G., & Tkačik, G. (2015). Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.115.248101","mla":"Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters, vol. 115, no. 24, 248101, American Physical Society, 2015, doi:10.1103/PhysRevLett.115.248101."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"article_number":"248101","doi":"10.1103/PhysRevLett.115.248101","date_published":"2015-12-08T00:00:00Z","date_created":"2018-12-11T11:52:49Z","year":"2015","day":"08","publication":"Physical Review Letters","publisher":"American Physical Society","quality_controlled":"1","oa":1},{"abstract":[{"lang":"eng","text":"We study conditions under which a finite simplicial complex $K$ can be mapped to $\\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding is a map $f: K\\to \\mathbb R^d$ such that the images of any $r$\r\npairwise disjoint simplices of $K$ do not have a common point. We show that if $r$ is not a prime power and $d\\geq 2r+1$, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost $r$-embedding of\r\nthe $(d+1)(r-1)$-simplex in $\\mathbb R^d$. This improves on previous constructions of counterexamples (for $d\\geq 3r$) based on a series of papers by M. \\\"Ozaydin, M. Gromov, P. Blagojevi\\'c, F. Frick, G. Ziegler, and the second and fourth present authors. The counterexamples are obtained by proving the following algebraic criterion in codimension 2: If $r\\ge3$ and if $K$ is a finite $2(r-1)$-complex then there exists an almost $r$-embedding $K\\to \\mathbb R^{2r}$ if and only if there exists a general position PL map $f:K\\to \\mathbb R^{2r}$ such that the algebraic intersection number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero. This result can be restated in terms of cohomological obstructions or equivariant maps, and extends an analogous codimension 3 criterion by the second and fourth authors. As another application we classify ornaments $f:S^3 \\sqcup S^3\\sqcup S^3\\to \\mathbb R^5$ up to ornament\r\nconcordance. It follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample."}],"acknowledgement":"We would like to thank A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful discussions.","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1511.03501","open_access":"1"}],"oa":1,"month":"11","year":"2015","publication_status":"submitted","language":[{"iso":"eng"}],"publication":"arXiv","day":"15","date_created":"2020-07-30T10:45:19Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"9308"},{"relation":"later_version","id":"10220","status":"public"},{"status":"public","id":"8156","relation":"dissertation_contains"}]},"date_published":"2015-11-15T00:00:00Z","_id":"8183","article_number":"1511.03501","type":"preprint","status":"public","citation":{"mla":"Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” ArXiv, 1511.03501.","short":"S. Avvakumov, I. Mabillard, A. Skopenkov, U. Wagner, ArXiv (n.d.).","ieee":"S. Avvakumov, I. Mabillard, A. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections, III. Codimension 2,” arXiv. .","ama":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv.","apa":"Avvakumov, S., Mabillard, I., Skopenkov, A., & Wagner, U. (n.d.). Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv.","chicago":"Avvakumov, Sergey, Isaac Mabillard, A. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” ArXiv, n.d.","ista":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv, 1511.03501."},"date_updated":"2023-09-07T13:12:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1511.03501"]},"author":[{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey","last_name":"Avvakumov","full_name":"Avvakumov, Sergey"},{"full_name":"Mabillard, Isaac","last_name":"Mabillard","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac"},{"last_name":"Skopenkov","full_name":"Skopenkov, A.","first_name":"A."},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"department":[{"_id":"UlWa"}],"title":"Eliminating higher-multiplicity intersections, III. Codimension 2"},{"_id":"5441","type":"technical_report","pubrep_id":"340","status":"public","date_updated":"2023-09-19T14:36:19Z","citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria; 2015. doi:10.15479/AT:IST-2015-340-v1-1","apa":"Chatterjee, K., Ibsen-Jensen, R., Goharshady, A. K., & Pavlogiannis, A. (2015). Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria. https://doi.org/10.15479/AT:IST-2015-340-v1-1","ieee":"K. Chatterjee, R. Ibsen-Jensen, A. K. Goharshady, and A. Pavlogiannis, Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria, 2015.","short":"K. Chatterjee, R. Ibsen-Jensen, A.K. Goharshady, A. Pavlogiannis, Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components, IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015, doi:10.15479/AT:IST-2015-340-v1-1.","ista":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. 2015. Algorithms for algebraic path properties in concurrent systems of constant treewidth components, IST Austria, 24p.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-340-v1-1."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir","first_name":"Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"}],"file_date_updated":"2020-07-14T12:46:56Z","department":[{"_id":"KrCh"}],"title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","abstract":[{"text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.","lang":"eng"}],"oa_version":"Published Version","oa":1,"alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","month":"07","year":"2015","publication_status":"published","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:46:56Z","file_size":861396,"date_created":"2018-12-12T11:54:09Z","file_name":"IST-2015-340-v1+1_main.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"df383dc62c94d7b2ea639aba088a76c6","file_id":"5531"}],"day":"11","page":"24","date_created":"2018-12-12T11:39:21Z","doi":"10.15479/AT:IST-2015-340-v1-1","related_material":{"record":[{"relation":"later_version","id":"1437","status":"public"},{"id":"5442","status":"public","relation":"earlier_version"},{"relation":"later_version","status":"public","id":"6009"}]},"date_published":"2015-07-11T00:00:00Z"},{"_id":"5442","pubrep_id":"344","status":"public","type":"technical_report","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"date_updated":"2023-09-19T14:36:19Z","citation":{"ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2015. Algorithms for algebraic path properties in concurrent systems of constant treewidth components, IST Austria, 22p.","chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components, IST Austria, 2015.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria, 2015.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, & Anonymous, 4. (2015). Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria; 2015.","mla":"Anonymous, 1, et al. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015."},"title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","file_date_updated":"2020-07-14T12:46:57Z","author":[{"first_name":"1","full_name":"Anonymous, 1","last_name":"Anonymous"},{"first_name":"2","last_name":"Anonymous","full_name":"Anonymous, 2"},{"full_name":"Anonymous, 3","last_name":"Anonymous","first_name":"3"},{"first_name":"4","last_name":"Anonymous","full_name":"Anonymous, 4"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural properties that arise in program analysis.\r\nWe consider that each component of the concurrent system is a graph with constant treewidth, and it is known that the controlflow graphs of most programs have constant treewidth. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis problems (e.g., alias analysis). The study of multiple queries allows us to consider the tradeoff between the resource usage of the \\emph{one-time} preprocessing and for \\emph{each individual} query. The traditional approaches construct the product graph of all components and apply the best-known graph algorithm on the product. In the traditional approach, even the answer to a single query requires the transitive closure computation (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time.\r\n\r\nOur main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, \r\neach subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results that show that the worst-case running times of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (such as improving \r\nthe worst-case bounds for the shortest path problem in general graphs whose current best-known bound has not been improved in five decades). Finally, we provide a prototype implementation of our algorithms which significantly outperforms the existing algorithmic methods on several benchmarks."}],"month":"07","oa":1,"publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"scopus_import":1,"language":[{"iso":"eng"}],"day":"14","file":[{"date_updated":"2020-07-14T12:46:57Z","file_size":658747,"creator":"system","date_created":"2018-12-12T11:53:37Z","file_name":"IST-2015-343-v2+1_main.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5498","checksum":"98fd936102f3e057fc321ef6d316001d"},{"date_created":"2019-04-16T12:36:08Z","file_name":"IST-2015-343-v2+2_anonymous.txt","date_updated":"2020-07-14T12:46:57Z","file_size":139,"creator":"dernst","file_id":"6316","checksum":"b31d09b1241b59c75e1f42dadf09d258","content_type":"text/plain","access_level":"closed","relation":"main_file"}],"year":"2015","publication_status":"published","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"date_created":"2018-12-12T11:39:21Z","related_material":{"record":[{"relation":"later_version","id":"1437","status":"public"},{"id":"5441","status":"public","relation":"later_version"},{"relation":"later_version","id":"6009","status":"public"}]},"date_published":"2015-07-14T00:00:00Z","page":"22"},{"_id":"1689","type":"conference","conference":{"end_date":"2015-04-16","location":"Seattle, WA, United States","start_date":"2015-04-14","name":"HSCC: Hybrid Systems - Computation and Control"},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"}],"status":"public","date_updated":"2023-09-20T09:43:09Z","citation":{"chicago":"Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, 259–68. ACM, 2015. https://doi.org/10.1145/2728606.2728608.","ista":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2015. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 259–268.","mla":"Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 259–68, doi:10.1145/2728606.2728608.","apa":"Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., & Belta, C. (2015). Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control (pp. 259–268). Seattle, WA, United States: ACM. https://doi.org/10.1145/2728606.2728608","ama":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. In: Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. ACM; 2015:259-268. doi:10.1145/2728606.2728608","ieee":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta, “Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games,” in Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, Seattle, WA, United States, 2015, pp. 259–268.","short":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, in:, Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 259–268."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5456","author":[{"full_name":"Svoreňová, Mária","last_name":"Svoreňová","first_name":"Mária"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chmelik, Martin","last_name":"Chmelik","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Cěrná","full_name":"Cěrná, Ivana","first_name":"Ivana"},{"last_name":"Belta","full_name":"Belta, Cǎlin","first_name":"Cǎlin"}],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"title":"Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games","abstract":[{"text":"We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. We demonstrate our approach on an illustrative case study.","lang":"eng"}],"oa_version":"Preprint","publisher":"ACM","scopus_import":1,"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.5387"}],"month":"04","year":"2015","publication_status":"published","day":"14","language":[{"iso":"eng"}],"publication":"Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control","page":"259 - 268","doi":"10.1145/2728606.2728608","related_material":{"record":[{"relation":"later_version","status":"public","id":"1407"}]},"date_published":"2015-04-14T00:00:00Z","ec_funded":1,"date_created":"2018-12-11T11:53:29Z"},{"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"From non-preemptive to preemptive scheduling using synchronization synthesis","author":[{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","full_name":"Cerny, Pavol","last_name":"Cerny"},{"full_name":"Clarke, Edmund","last_name":"Clarke","first_name":"Edmund"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna"},{"last_name":"Ryzhyk","full_name":"Ryzhyk, Leonid","first_name":"Leonid"},{"first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","last_name":"Samanta","full_name":"Samanta, Roopsha"},{"last_name":"Tarrach","full_name":"Tarrach, Thorsten","orcid":"0000-0003-4409-8487","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","first_name":"Thorsten"}],"publist_id":"5398","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-21668-3_11.","ista":"Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2015. From non-preemptive to preemptive scheduling using synchronization synthesis. 9207, 180–197.","mla":"Cerny, Pavol, et al. From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis. Vol. 9207, Springer, 2015, pp. 180–97, doi:10.1007/978-3-319-21668-3_11.","apa":"Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., & Tarrach, T. (2015). From non-preemptive to preemptive scheduling using synchronization synthesis. Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21668-3_11","ama":"Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. 2015;9207:180-197. doi:10.1007/978-3-319-21668-3_11","ieee":"P. Cerny et al., “From non-preemptive to preemptive scheduling using synchronization synthesis,” vol. 9207. Springer, pp. 180–197, 2015.","short":"P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, 9207 (2015) 180–197."},"quality_controlled":"1","publisher":"Springer","date_created":"2018-12-11T11:53:42Z","doi":"10.1007/978-3-319-21668-3_11","date_published":"2015-07-01T00:00:00Z","page":"180 - 197","day":"01","year":"2015","has_accepted_license":"1","pubrep_id":"336","status":"public","conference":{"location":"San Francisco, CA, United States","end_date":"2015-07-24","start_date":"2015-07-18","name":"CAV: Computer Aided Verification"},"type":"conference","series_title":"Lecture Notes in Computer Science","_id":"1729","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:13Z","ddc":["000"],"date_updated":"2023-09-20T11:13:50Z","intvolume":" 9207","month":"07","scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"text":"We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of such sequences produced under a non-preemptive scheduler. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and rules for inserting synchronization. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient, and, since it does not require explicit specifications, is more practical than the conventional approach based on user-provided assertions.","lang":"eng"}],"ec_funded":1,"volume":9207,"related_material":{"record":[{"id":"1130","status":"public","relation":"dissertation_contains"},{"relation":"later_version","status":"public","id":"1338"}]},"language":[{"iso":"eng"}],"file":[{"checksum":"6ff58ac220e2f20cb001ba35d4924495","file_id":"4715","relation":"main_file","access_level":"local","content_type":"application/pdf","file_name":"IST-2015-336-v1+1_long_version.pdf","date_created":"2018-12-12T10:08:53Z","creator":"system","file_size":481922,"date_updated":"2020-07-14T12:45:13Z"}],"publication_status":"published"},{"citation":{"mla":"Giacobbe, Mirco, et al. Model Checking Gene Regulatory Networks. Vol. 9035, Springer, 2015, pp. 469–83, doi:10.1007/978-3-662-46681-0_47.","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035 (2015) 469–483.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_47","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking gene regulatory networks. 2015;9035:469-483. doi:10.1007/978-3-662-46681-0_47","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_47.","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5267","author":[{"first_name":"Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","last_name":"Giacobbe","full_name":"Giacobbe, Mirco","orcid":"0000-0001-8180-0904"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh","last_name":"Gupta"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"last_name":"Petrov","orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"}],"title":"Model checking gene regulatory networks","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"year":"2015","day":"01","page":"469 - 483","date_published":"2015-04-01T00:00:00Z","doi":"10.1007/978-3-662-46681-0_47","date_created":"2018-12-11T11:54:16Z","acknowledgement":"SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2 148797.\r\n","quality_controlled":"1","publisher":"Springer","oa":1,"date_updated":"2023-09-20T11:06:03Z","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"_id":"1835","series_title":"Lecture Notes in Computer Science","type":"conference","conference":{"end_date":"2015-04-18","location":"London, United Kingdom","start_date":"2015-04-11","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"status":"public","publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"1351","status":"public","relation":"later_version"}]},"volume":9035,"ec_funded":1,"abstract":[{"text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs –an important problem of interest in evolutionary biology– more efficiently than the classical simulation method. We specify the property in linear temporal logics. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights.","lang":"eng"}],"oa_version":"Preprint","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"url":"http://arxiv.org/abs/1410.7704","open_access":"1"}],"month":"04","intvolume":" 9035"},{"publisher":"F1000 Research","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG-20101109-PSDP to JF). JM internship was supported by the grant “Action Austria – Slovakia”.\r\nData associated with the article are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication). \r\n\r\nData availability: \r\nF1000Research: Dataset 1. Dataset 1, 10.5256/f1000research.7143.d104552\r\n\r\nF1000Research: Dataset 2. Dataset 2, 10.5256/f1000research.7143.d104553\r\n\r\nF1000Research: Dataset 3. Dataset 3, 10.5256/f1000research.7143.d104554","doi":"10.12688/f1000research.7143.1","date_published":"2015-10-01T00:00:00Z","date_created":"2018-12-11T11:52:26Z","day":"01","publication":"F1000 Research ","has_accepted_license":"1","year":"2015","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene","publist_id":"5668","author":[{"first_name":"Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","full_name":"Michalko, Jaroslav","last_name":"Michalko"},{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","last_name":"Dravecka","full_name":"Dravecka, Marta","orcid":"0000-0002-2519-8004"},{"first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias","last_name":"Bollenbach"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. 2015. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 4.","chicago":"Michalko, Jaroslav, Marta Lukacisinova, Mark Tobias Bollenbach, and Jiří Friml. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” F1000 Research . F1000 Research, 2015. https://doi.org/10.12688/f1000research.7143.1.","ama":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 2015;4. doi:10.12688/f1000research.7143.1","apa":"Michalko, J., Lukacisinova, M., Bollenbach, M. T., & Friml, J. (2015). Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . F1000 Research. https://doi.org/10.12688/f1000research.7143.1","ieee":"J. Michalko, M. Lukacisinova, M. T. Bollenbach, and J. Friml, “Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene,” F1000 Research , vol. 4. F1000 Research, 2015.","short":"J. Michalko, M. Lukacisinova, M.T. Bollenbach, J. Friml, F1000 Research 4 (2015).","mla":"Michalko, Jaroslav, et al. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” F1000 Research , vol. 4, F1000 Research, 2015, doi:10.12688/f1000research.7143.1."},"month":"10","intvolume":" 4","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The Auxin Binding Protein1 (ABP1) has been identified based on its ability to bind auxin with high affinity and studied for a long time as a prime candidate for the extracellular auxin receptor responsible for mediating in particular the fast non-transcriptional auxin responses. However, the contradiction between the embryo-lethal phenotypes of the originally described Arabidopsis T-DNA insertional knock-out alleles (abp1-1 and abp1-1s) and the wild type-like phenotypes of other recently described loss-of-function alleles (abp1-c1 and abp1-TD1) questions the biological importance of ABP1 and relevance of the previous genetic studies. Here we show that there is no hidden copy of the ABP1 gene in the Arabidopsis genome but the embryo-lethal phenotypes of abp1-1 and abp1-1s alleles are very similar to the knock-out phenotypes of the neighboring gene, BELAYA SMERT (BSM). Furthermore, the allelic complementation test between bsm and abp1 alleles shows that the embryo-lethality in the abp1-1 and abp1-1s alleles is caused by the off-target disruption of the BSM locus by the T-DNA insertions. This clarifies the controversy of different phenotypes among published abp1 knock-out alleles and asks for reflections on the developmental role of ABP1."}],"volume":4,"ec_funded":1,"file":[{"file_name":"IST-2016-497-v1+1_10.12688_f1000research.7143.1_20151102.pdf","date_created":"2018-12-12T10:16:12Z","creator":"system","file_size":4414248,"date_updated":"2020-07-14T12:44:59Z","checksum":"8beae5cbe988e1060265ae7de2ee8306","file_id":"5198","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"497","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1509","department":[{"_id":"JiFr"},{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:44:59Z","ddc":["570"],"date_updated":"2023-10-10T14:10:24Z"},{"publist_id":"5467","author":[{"first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","last_name":"Priklopil","full_name":"Priklopil, Tadeas"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Evolution of decisions in population games with sequentially searching individuals","citation":{"chicago":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games. MDPI, 2015. https://doi.org/10.3390/g6040413.","ista":"Priklopil T, Chatterjee K. 2015. Evolution of decisions in population games with sequentially searching individuals. Games. 6(4), 413–437.","mla":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games, vol. 6, no. 4, MDPI, 2015, pp. 413–37, doi:10.3390/g6040413.","apa":"Priklopil, T., & Chatterjee, K. (2015). Evolution of decisions in population games with sequentially searching individuals. Games. MDPI. https://doi.org/10.3390/g6040413","ama":"Priklopil T, Chatterjee K. Evolution of decisions in population games with sequentially searching individuals. Games. 2015;6(4):413-437. doi:10.3390/g6040413","ieee":"T. Priklopil and K. Chatterjee, “Evolution of decisions in population games with sequentially searching individuals,” Games, vol. 6, no. 4. MDPI, pp. 413–437, 2015.","short":"T. Priklopil, K. Chatterjee, Games 6 (2015) 413–437."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"page":"413 - 437","doi":"10.3390/g6040413","date_published":"2015-09-29T00:00:00Z","date_created":"2018-12-11T11:53:26Z","has_accepted_license":"1","year":"2015","day":"29","publication":"Games","quality_controlled":"1","publisher":"MDPI","oa":1,"department":[{"_id":"NiBa"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:12Z","date_updated":"2023-10-17T11:42:52Z","ddc":["000"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"448","_id":"1681","issue":"4","volume":6,"ec_funded":1,"publication_identifier":{"eissn":["2073-4336"]},"publication_status":"published","file":[{"file_name":"IST-2016-448-v1+1_games-06-00413.pdf","date_created":"2018-12-12T10:12:41Z","file_size":518832,"date_updated":"2020-07-14T12:45:12Z","creator":"system","file_id":"4959","checksum":"912e1acbaf201100f447a43e4d5958bd","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"09","intvolume":" 6","abstract":[{"lang":"eng","text":"In many social situations, individuals endeavor to find the single best possible partner, but are constrained to evaluate the candidates in sequence. Examples include the search for mates, economic partnerships, or any other long-term ties where the choice to interact involves two parties. Surprisingly, however, previous theoretical work on mutual choice problems focuses on finding equilibrium solutions, while ignoring the evolutionary dynamics of decisions. Empirically, this may be of high importance, as some equilibrium solutions can never be reached unless the population undergoes radical changes and a sufficient number of individuals change their decisions simultaneously. To address this question, we apply a mutual choice sequential search problem in an evolutionary game-theoretical model that allows one to find solutions that are favored by evolution. As an example, we study the influence of sequential search on the evolutionary dynamics of cooperation. For this, we focus on the classic snowdrift game and the prisoner’s dilemma game."}],"oa_version":"Published Version"},{"title":"Quantifying emergent behavior of autonomous robots","author":[{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","last_name":"Martius","full_name":"Martius, Georg S"},{"first_name":"Eckehard","last_name":"Olbrich","full_name":"Olbrich, Eckehard"}],"publist_id":"5495","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"G. S. Martius and E. Olbrich, “Quantifying emergent behavior of autonomous robots,” Entropy, vol. 17, no. 10. MDPI, pp. 7266–7297, 2015.","short":"G.S. Martius, E. Olbrich, Entropy 17 (2015) 7266–7297.","apa":"Martius, G. S., & Olbrich, E. (2015). Quantifying emergent behavior of autonomous robots. Entropy. MDPI. https://doi.org/10.3390/e17107266","ama":"Martius GS, Olbrich E. Quantifying emergent behavior of autonomous robots. Entropy. 2015;17(10):7266-7297. doi:10.3390/e17107266","mla":"Martius, Georg S., and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.” Entropy, vol. 17, no. 10, MDPI, 2015, pp. 7266–97, doi:10.3390/e17107266.","ista":"Martius GS, Olbrich E. 2015. Quantifying emergent behavior of autonomous robots. Entropy. 17(10), 7266–7297.","chicago":"Martius, Georg S, and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.” Entropy. MDPI, 2015. https://doi.org/10.3390/e17107266."},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"date_published":"2015-10-23T00:00:00Z","doi":"10.3390/e17107266","date_created":"2018-12-11T11:53:17Z","page":"7266 - 7297","day":"23","publication":"Entropy","has_accepted_license":"1","year":"2015","quality_controlled":"1","publisher":"MDPI","oa":1,"acknowledgement":"This work was supported by the DFG priority program 1527 (Autonomous Learning) and by the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 318723 (MatheMACS) and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734.","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:08Z","ddc":["000"],"date_updated":"2023-10-17T11:42:00Z","status":"public","pubrep_id":"464","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1655","issue":"10","volume":17,"ec_funded":1,"file":[{"checksum":"945d99631a96e0315acb26dc8541dcf9","file_id":"4943","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:12:25Z","file_name":"IST-2016-464-v1+1_entropy-17-07266.pdf","date_updated":"2020-07-14T12:45:08Z","file_size":6455007,"creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 17","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Quantifying behaviors of robots which were generated autonomously from task-independent objective functions is an important prerequisite for objective comparisons of algorithms and movements of animals. The temporal sequence of such a behavior can be considered as a time series and hence complexity measures developed for time series are natural candidates for its quantification. The predictive information and the excess entropy are such complexity measures. They measure the amount of information the past contains about the future and thus quantify the nonrandom structure in the temporal sequence. However, when using these measures for systems with continuous states one has to deal with the fact that their values will depend on the resolution with which the systems states are observed. For deterministic systems both measures will diverge with increasing resolution. We therefore propose a new decomposition of the excess entropy in resolution dependent and resolution independent parts and discuss how they depend on the dimensionality of the dynamics, correlations and the noise level. For the practical estimation we propose to use estimates based on the correlation integral instead of the direct estimation of the mutual information based on next neighbor statistics because the latter allows less control of the scale dependencies. Using our algorithm we are able to show how autonomous learning generates behavior of increasing complexity with increasing learning duration.","lang":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chen C, Wang C, Zhao X, Zhou T, Xu D, Wang Z, Wang Y. 2015. Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. 7(2).","chicago":"Chen, Chong, Chao Wang, Xuan Zhao, Tao Zhou, Dao Xu, Zhi Wang, and Ying Wang. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis and Facilitates the Development of Dentate Gyrus-Dependent Learning in Neonatal Rats.” ASN Neuro. SAGE Publications, 2015. https://doi.org/10.1177/1759091415575845.","apa":"Chen, C., Wang, C., Zhao, X., Zhou, T., Xu, D., Wang, Z., & Wang, Y. (2015). Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. SAGE Publications. https://doi.org/10.1177/1759091415575845","ama":"Chen C, Wang C, Zhao X, et al. Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. 2015;7(2). doi:10.1177/1759091415575845","ieee":"C. Chen et al., “Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats,” ASN Neuro, vol. 7, no. 2. SAGE Publications, 2015.","short":"C. Chen, C. Wang, X. Zhao, T. Zhou, D. Xu, Z. Wang, Y. Wang, ASN Neuro 7 (2015).","mla":"Chen, Chong, et al. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis and Facilitates the Development of Dentate Gyrus-Dependent Learning in Neonatal Rats.” ASN Neuro, vol. 7, no. 2, SAGE Publications, 2015, doi:10.1177/1759091415575845."},"title":"Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats","author":[{"full_name":"Chen, Chong","last_name":"Chen","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","first_name":"Chong"},{"first_name":"Chao","full_name":"Wang, Chao","last_name":"Wang"},{"first_name":"Xuan","last_name":"Zhao","full_name":"Zhao, Xuan"},{"first_name":"Tao","full_name":"Zhou, Tao","last_name":"Zhou"},{"first_name":"Dao","full_name":"Xu, Dao","last_name":"Xu"},{"first_name":"Zhi","full_name":"Wang, Zhi","last_name":"Wang"},{"full_name":"Wang, Ying","last_name":"Wang","first_name":"Ying"}],"publist_id":"5269","article_processing_charge":"No","quality_controlled":"1","publisher":"SAGE Publications","oa":1,"day":"13","publication":"ASN Neuro","has_accepted_license":"1","year":"2015","date_published":"2015-04-13T00:00:00Z","doi":"10.1177/1759091415575845","date_created":"2018-12-11T11:54:16Z","_id":"1834","status":"public","pubrep_id":"456","type":"journal_article","article_type":"original","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"ddc":["570"],"date_updated":"2023-10-18T06:47:30Z","department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:18Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Huge body of evidences demonstrated that volatile anesthetics affect the hippocampal neurogenesis and neurocognitive functions, and most of them showed impairment at anesthetic dose. Here, we investigated the effect of low dose (1.8%) sevoflurane on hippocampal neurogenesis and dentate gyrus-dependent learning. Neonatal rats at postnatal day 4 to 6 (P4-6) were treated with 1.8% sevoflurane for 6 hours. Neurogenesis was quantified by bromodeoxyuridine labeling and electrophysiology recording. Four and seven weeks after treatment, the Morris water maze and contextual-fear discrimination learning tests were performed to determine the influence on spatial learning and pattern separation. A 6-hour treatment with 1.8% sevoflurane promoted hippocampal neurogenesis and increased the survival of newborn cells and the proportion of immature granular cells in the dentate gyrus of neonatal rats. Sevoflurane-treated rats performed better during the training days of the Morris water maze test and in contextual-fear discrimination learning test. These results suggest that a subanesthetic dose of sevoflurane promotes hippocampal neurogenesis in neonatal rats and facilitates their performance in dentate gyrus-dependent learning tasks."}],"month":"04","intvolume":" 7","scopus_import":"1","file":[{"date_updated":"2020-07-14T12:45:18Z","file_size":1146814,"creator":"system","date_created":"2018-12-12T10:14:08Z","file_name":"IST-2016-456-v1+1_ASN_Neuro-2015-Chen-.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5057","checksum":"53e16bd3fc2ae2c0d7de9164626c37aa"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":7,"issue":"2","license":"https://creativecommons.org/licenses/by/3.0/"},{"date_created":"2018-12-11T11:53:10Z","date_published":"2015-01-01T00:00:00Z","doi":"10.5802/afst.1464","page":"781 - 800","publication":"Annales de la faculté des sciences de Toulouse","day":"01","year":"2015","oa":1,"quality_controlled":"1","publisher":"Faculté des sciences de Toulouse","title":"Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models","article_processing_charge":"No","external_id":{"arxiv":["1409.8605"]},"author":[{"first_name":"Matthias","full_name":"Erbar, Matthias","last_name":"Erbar"},{"orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Prasad","full_name":"Tetali, Prasad","last_name":"Tetali"}],"publist_id":"5520","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Erbar, Matthias, et al. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” Annales de La Faculté Des Sciences de Toulouse, vol. 24, no. 4, Faculté des sciences de Toulouse, 2015, pp. 781–800, doi:10.5802/afst.1464.","ama":"Erbar M, Maas J, Tetali P. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de la faculté des sciences de Toulouse. 2015;24(4):781-800. doi:10.5802/afst.1464","apa":"Erbar, M., Maas, J., & Tetali, P. (2015). Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de La Faculté Des Sciences de Toulouse. Faculté des sciences de Toulouse. https://doi.org/10.5802/afst.1464","short":"M. Erbar, J. Maas, P. Tetali, Annales de La Faculté Des Sciences de Toulouse 24 (2015) 781–800.","ieee":"M. Erbar, J. Maas, and P. Tetali, “Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models,” Annales de la faculté des sciences de Toulouse, vol. 24, no. 4. Faculté des sciences de Toulouse, pp. 781–800, 2015.","chicago":"Erbar, Matthias, Jan Maas, and Prasad Tetali. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” Annales de La Faculté Des Sciences de Toulouse. Faculté des sciences de Toulouse, 2015. https://doi.org/10.5802/afst.1464.","ista":"Erbar M, Maas J, Tetali P. 2015. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de la faculté des sciences de Toulouse. 24(4), 781–800."},"volume":24,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 24","month":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1409.8605"}],"oa_version":"Preprint","abstract":[{"text":"We calculate a Ricci curvature lower bound for some classical examples of random walks, namely, a chain on a slice of the n-dimensional discrete cube (the so-called Bernoulli-Laplace model) and the random transposition shuffle of the symmetric group of permutations on n letters.","lang":"eng"}],"department":[{"_id":"JaMa"}],"date_updated":"2023-10-18T07:48:28Z","status":"public","article_type":"original","type":"journal_article","_id":"1635"},{"article_type":"letter_note","type":"journal_article","status":"public","_id":"14303","date_updated":"2023-11-07T11:56:32Z","extern":"1","main_file_link":[{"url":"https://doi.org/10.1021/acs.nanolett.5b01461","open_access":"1"}],"intvolume":" 15","month":"06","abstract":[{"text":"Scaffolded DNA origami enables the fabrication of a variety of complex nanostructures that promise utility in diverse fields of application, ranging from biosensing over advanced therapeutics to metamaterials. The broad applicability of DNA origami as a material beyond the level of proof-of-concept studies critically depends, among other factors, on the availability of large amounts of pure single-stranded scaffold DNA. Here, we present a method for the efficient production of M13 bacteriophage-derived genomic DNA using high-cell-density fermentation of Escherichia coli in stirred-tank bioreactors. We achieve phage titers of up to 1.6 × 1014 plaque-forming units per mL. Downstream processing yields up to 410 mg of high-quality single-stranded DNA per one liter reaction volume, thus upgrading DNA origami-based nanotechnology from the milligram to the gram scale.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","issue":"7","volume":15,"publication_status":"published","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"language":[{"iso":"eng"}],"external_id":{"pmid":["26028443"]},"article_processing_charge":"No","author":[{"first_name":"B","full_name":"Kick, B","last_name":"Kick"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M","full_name":"Praetorius, Florian M","last_name":"Praetorius"},{"first_name":"H","last_name":"Dietz","full_name":"Dietz, H"},{"full_name":"Weuster-Botz, D","last_name":"Weuster-Botz","first_name":"D"}],"title":"Efficient production of single-stranded phage DNA as scaffolds for DNA origami","citation":{"chicago":"Kick, B, Florian M Praetorius, H Dietz, and D Weuster-Botz. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” Nano Letters. ACS Publications, 2015. https://doi.org/10.1021/acs.nanolett.5b01461.","ista":"Kick B, Praetorius FM, Dietz H, Weuster-Botz D. 2015. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 15(7), 4672–4676.","mla":"Kick, B., et al. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” Nano Letters, vol. 15, no. 7, ACS Publications, 2015, pp. 4672–76, doi:10.1021/acs.nanolett.5b01461.","apa":"Kick, B., Praetorius, F. M., Dietz, H., & Weuster-Botz, D. (2015). Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. ACS Publications. https://doi.org/10.1021/acs.nanolett.5b01461","ama":"Kick B, Praetorius FM, Dietz H, Weuster-Botz D. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 2015;15(7):4672-4676. doi:10.1021/acs.nanolett.5b01461","short":"B. Kick, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Nano Letters 15 (2015) 4672–4676.","ieee":"B. Kick, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Efficient production of single-stranded phage DNA as scaffolds for DNA origami,” Nano Letters, vol. 15, no. 7. ACS Publications, pp. 4672–4676, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"ACS Publications","page":"4672-4676","date_created":"2023-09-06T12:52:47Z","doi":"10.1021/acs.nanolett.5b01461","date_published":"2015-06-01T00:00:00Z","year":"2015","publication":"Nano Letters","day":"01"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. 2015. Counterexample explanation by learning small strategies in Markov decision processes. CAV: Computer Aided Verification, LNCS, vol. 9206, 158–177.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Andreas Fellner, and Jan Kretinsky. “Counterexample Explanation by Learning Small Strategies in Markov Decision Processes,” 9206:158–77. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_10.","short":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, J. Kretinsky, in:, Springer, 2015, pp. 158–177.","ieee":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, and J. Kretinsky, “Counterexample explanation by learning small strategies in Markov decision processes,” presented at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015, vol. 9206, pp. 158–177.","ama":"Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. Counterexample explanation by learning small strategies in Markov decision processes. In: Vol 9206. Springer; 2015:158-177. doi:10.1007/978-3-319-21690-4_10","apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Fellner, A., & Kretinsky, J. (2015). Counterexample explanation by learning small strategies in Markov decision processes (Vol. 9206, pp. 158–177). Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21690-4_10","mla":"Brázdil, Tomáš, et al. Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Vol. 9206, Springer, 2015, pp. 158–77, doi:10.1007/978-3-319-21690-4_10."},"title":"Counterexample explanation by learning small strategies in Markov decision processes","publist_id":"5564","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"full_name":"Fellner, Andreas","last_name":"Fellner","id":"42BABFB4-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"}],"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"day":"16","year":"2015","date_created":"2018-12-11T11:52:58Z","date_published":"2015-07-16T00:00:00Z","doi":"10.1007/978-3-319-21690-4_10","page":"158 - 177","acknowledgement":"This research was funded in part by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE) and Z211-N23 (Wittgenstein Award), European Research Council (ERC) Grant No 279307 (Graph Games), ERC Grant No 267989 (QUAREM), the Czech Science Foundation Grant No P202/12/G061, and People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) REA Grant No 291734.","oa":1,"quality_controlled":"1","publisher":"Springer","date_updated":"2024-02-21T13:52:07Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"_id":"1603","status":"public","conference":{"name":"CAV: Computer Aided Verification","location":"San Francisco, CA, United States","end_date":"2015-07-24","start_date":"2015-07-18"},"type":"conference","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eisbn":["978-3-319-21690-4"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"5549","relation":"research_paper"}]},"volume":9206,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"For deterministic systems, a counterexample to a property can simply be an error trace, whereas counterexamples in probabilistic systems are necessarily more complex. For instance, a set of erroneous traces with a sufficient cumulative probability mass can be used. Since these are too large objects to understand and manipulate, compact representations such as subchains have been considered. In the case of probabilistic systems with non-determinism, the situation is even more complex. While a subchain for a given strategy (or scheduler, resolving non-determinism) is a straightforward choice, we take a different approach. Instead, we focus on the strategy itself, and extract the most important decisions it makes, and present its succinct representation.\r\nThe key tools we employ to achieve this are (1) introducing a concept of importance of a state w.r.t. the strategy, and (2) learning using decision trees. There are three main consequent advantages of our approach. Firstly, it exploits the quantitative information on states, stressing the more important decisions. Secondly, it leads to a greater variability and degree of freedom in representing the strategies. Thirdly, the representation uses a self-explanatory data structure. In summary, our approach produces more succinct and more explainable strategies, as opposed to e.g. binary decision diagrams. Finally, our experimental results show that we can extract several rules describing the strategy even for very large systems that do not fit in memory, and based on the rules explain the erroneous behaviour."}],"intvolume":" 9206","month":"07","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1502.02834"}],"alternative_title":["LNCS"],"scopus_import":1},{"file_date_updated":"2020-07-14T12:47:00Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2024-02-21T13:52:07Z","ddc":["004"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","keyword":["Markov Decision Process","Decision Tree","Probabilistic Verification","Counterexample Explanation"],"_id":"5549","related_material":{"record":[{"relation":"popular_science","status":"public","id":"1603"}]},"contributor":[{"last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","ec_funded":1,"datarep_id":"28","file":[{"creator":"system","date_updated":"2020-07-14T12:47:00Z","file_size":49557109,"date_created":"2018-12-12T13:02:31Z","file_name":"IST-2015-28-v1+2_Fellner_DataRep.zip","access_level":"open_access","relation":"main_file","content_type":"application/zip","checksum":"b8bcb43c0893023cda66c1b69c16ac62","file_id":"5597"}],"month":"08","abstract":[{"lang":"eng","text":"This repository contains the experimental part of the CAV 2015 publication Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.\r\nWe extended the probabilistic model checker PRISM to represent strategies of Markov Decision Processes as Decision Trees.\r\nThe archive contains a java executable version of the extended tool (prism_dectree.jar) together with a few examples of the PRISM benchmark library.\r\nTo execute the program, please have a look at the README.txt, which provides instructions and further information on the archive.\r\nThe archive contains scripts that (if run often enough) reproduces the data presented in the publication."}],"oa_version":"Published Version","author":[{"id":"42BABFB4-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Fellner, Andreas","last_name":"Fellner"}],"publist_id":"5564","article_processing_charge":"No","title":"Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes","citation":{"ama":"Fellner A. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. 2015. doi:10.15479/AT:ISTA:28","apa":"Fellner, A. (2015). Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:28","short":"A. Fellner, (2015).","ieee":"A. Fellner, “Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015.","mla":"Fellner, Andreas. Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria, 2015, doi:10.15479/AT:ISTA:28.","ista":"Fellner A. 2015. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:28.","chicago":"Fellner, Andreas. “Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015. https://doi.org/10.15479/AT:ISTA:28."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"date_published":"2015-08-13T00:00:00Z","doi":"10.15479/AT:ISTA:28","date_created":"2018-12-12T12:31:29Z","has_accepted_license":"1","year":"2015","day":"13","publisher":"Institute of Science and Technology Austria","oa":1},{"status":"public","pubrep_id":"501","type":"conference","conference":{"location":"Eindhoven, Netherlands","end_date":"2015-06-25","start_date":"2015-06-22","name":"SoCG: Symposium on Computational Geometry"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1512","file_date_updated":"2020-07-14T12:45:00Z","department":[{"_id":"UlWa"}],"ddc":["510"],"date_updated":"2024-02-28T12:59:37Z","month":"01","intvolume":" 34","alternative_title":["LIPIcs"],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b,d) such that the following holds. If F is a finite family of subsets of R^d such that the ith reduced Betti number (with Z_2 coefficients in singular homology) of the intersection of any proper subfamily G of F is at most b for every non-negative integer i less or equal to (d-1)/2, then F has Helly number at most h(b,d). These topological conditions are sharp: not controlling any of these first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map from C_*(K) to C_*(R^d). Both techniques are of independent interest.","lang":"eng"}],"related_material":{"record":[{"id":"424","status":"public","relation":"later_version"}]},"volume":34,"file":[{"file_name":"IST-2016-501-v1+1_46.pdf","date_created":"2018-12-12T10:10:09Z","file_size":633712,"date_updated":"2020-07-14T12:45:00Z","creator":"system","checksum":"e6881df44d87fe0c2529c9f7b2724614","file_id":"4794","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","title":"Bounding Helly numbers via Betti numbers","publist_id":"5665","author":[{"first_name":"Xavier","full_name":"Goaoc, Xavier","last_name":"Goaoc"},{"full_name":"Paták, Pavel","last_name":"Paták","first_name":"Pavel"},{"last_name":"Patakova","orcid":"0000-0002-3975-1683","full_name":"Patakova, Zuzana","first_name":"Zuzana"},{"first_name":"Martin","full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714","last_name":"Tancer"},{"last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–521.","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Bounding Helly numbers via Betti numbers,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 507–521.","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Bounding Helly numbers via Betti numbers. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:507-521. doi:10.4230/LIPIcs.SOCG.2015.507","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2015). Bounding Helly numbers via Betti numbers (Vol. 34, pp. 507–521). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.507","mla":"Goaoc, Xavier, et al. Bounding Helly Numbers via Betti Numbers. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–21, doi:10.4230/LIPIcs.SOCG.2015.507.","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2015. Bounding Helly numbers via Betti numbers. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 507–521.","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Bounding Helly Numbers via Betti Numbers,” 34:507–21. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.507."},"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"acknowledgement":"PP, ZP and MT were partially supported by the Charles University Grant GAUK 421511. ZP was\r\npartially supported by the Charles University Grant SVV-2014-260103. ZP and MT were partially\r\nsupported by the ERC Advanced Grant No. 267165 and by the project CE-ITI (GACR P202/12/G061)\r\nof the Czech Science Foundation. UW was partially supported by the Swiss National Science Foundation\r\n(grants SNSF-200020-138230 and SNSF-PP00P2-138948). Part of this work was done when XG was affiliated with INRIA Nancy Grand-Est and when MT was affiliated with Institutionen för matematik, Kungliga Tekniska Högskolan, then IST Austria.","date_published":"2015-01-01T00:00:00Z","doi":"10.4230/LIPIcs.SOCG.2015.507","date_created":"2018-12-11T11:52:27Z","page":"507 - 521","day":"01","has_accepted_license":"1","year":"2015"},{"publisher":"Walter de Gruyter","quality_controlled":"1","oa":1,"acknowledgement":"While working on this paper the authors were supported by the Leverhulme Trust and ERC grant 306457.","date_published":"2015-02-20T00:00:00Z","doi":"10.1515/crelle-2014-0122","date_created":"2018-12-11T11:45:32Z","page":"203 - 234","day":"20","publication":"Journal fur die Reine und Angewandte Mathematik","year":"2015","title":"Improvements in Birch's theorem on forms in many variables","author":[{"first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D"},{"full_name":"Prendiville, Sean","last_name":"Prendiville","first_name":"Sean"}],"publist_id":"7631","article_processing_charge":"No","external_id":{"arxiv":["1402.4489"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Browning TD, Prendiville S. Improvements in Birch’s theorem on forms in many variables. Journal fur die Reine und Angewandte Mathematik. 2017(731):203-234. doi:10.1515/crelle-2014-0122","apa":"Browning, T. D., & Prendiville, S. (n.d.). Improvements in Birch’s theorem on forms in many variables. Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter. https://doi.org/10.1515/crelle-2014-0122","short":"T.D. Browning, S. Prendiville, Journal Fur Die Reine Und Angewandte Mathematik 2017 (n.d.) 203–234.","ieee":"T. D. Browning and S. Prendiville, “Improvements in Birch’s theorem on forms in many variables,” Journal fur die Reine und Angewandte Mathematik, vol. 2017, no. 731. Walter de Gruyter, pp. 203–234.","mla":"Browning, Timothy D., and Sean Prendiville. “Improvements in Birch’s Theorem on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik, vol. 2017, no. 731, Walter de Gruyter, pp. 203–34, doi:10.1515/crelle-2014-0122.","ista":"Browning TD, Prendiville S. Improvements in Birch’s theorem on forms in many variables. Journal fur die Reine und Angewandte Mathematik. 2017(731), 203–234.","chicago":"Browning, Timothy D, and Sean Prendiville. “Improvements in Birch’s Theorem on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter, n.d. https://doi.org/10.1515/crelle-2014-0122."},"month":"02","intvolume":" 2017","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1402.4489"}],"oa_version":"Preprint","abstract":[{"text":"We show that a non-singular integral form of degree d is soluble non-trivially over the integers if and only if it is soluble non-trivially over the reals and the p-adic numbers, provided that the form has at least (d-\\sqrt{d}/2)2^d variables. This improves on a longstanding result of Birch.","lang":"eng"}],"volume":2017,"related_material":{"record":[{"relation":"later_version","status":"public","id":"256"}]},"issue":"731","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0075-4102"]},"publication_status":"submitted","status":"public","type":"journal_article","article_type":"original","_id":"271","extern":"1","date_updated":"2024-03-05T12:09:22Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Dziembowski, Stefan, et al. “Proofs of Space.” 35th Annual Cryptology Conference, vol. 9216, Springer, 2015, pp. 585–605, doi:10.1007/978-3-662-48000-7_29.","ieee":"S. Dziembowski, S. Faust, V. Kolmogorov, and K. Z. Pietrzak, “Proofs of space,” in 35th Annual Cryptology Conference, Santa Barbara, CA, United States, 2015, vol. 9216, pp. 585–605.","short":"S. Dziembowski, S. Faust, V. Kolmogorov, K.Z. Pietrzak, in:, 35th Annual Cryptology Conference, Springer, 2015, pp. 585–605.","ama":"Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. Proofs of space. In: 35th Annual Cryptology Conference. Vol 9216. Springer; 2015:585-605. doi:10.1007/978-3-662-48000-7_29","apa":"Dziembowski, S., Faust, S., Kolmogorov, V., & Pietrzak, K. Z. (2015). Proofs of space. In 35th Annual Cryptology Conference (Vol. 9216, pp. 585–605). Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-48000-7_29","chicago":"Dziembowski, Stefan, Sebastian Faust, Vladimir Kolmogorov, and Krzysztof Z Pietrzak. “Proofs of Space.” In 35th Annual Cryptology Conference, 9216:585–605. Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_29.","ista":"Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. 2015. Proofs of space. 35th Annual Cryptology Conference. CRYPTO: International Cryptology Conference, LNCS, vol. 9216, 585–605."},"title":"Proofs of space","article_processing_charge":"No","author":[{"first_name":"Stefan","last_name":"Dziembowski","full_name":"Dziembowski, Stefan"},{"last_name":"Faust","full_name":"Faust, Sebastian","first_name":"Sebastian"},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"publist_id":"5474","project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"},{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668"}],"publication":"35th Annual Cryptology Conference","day":"01","year":"2015","date_created":"2018-12-11T11:53:24Z","doi":"10.1007/978-3-662-48000-7_29","date_published":"2015-08-01T00:00:00Z","page":"585 - 605","oa":1,"quality_controlled":"1","publisher":"Springer","date_updated":"2024-03-20T08:31:49Z","department":[{"_id":"VlKo"},{"_id":"KrPi"}],"_id":"1675","pubrep_id":"671","status":"public","conference":{"location":"Santa Barbara, CA, United States","end_date":"2015-08-20","start_date":"2015-08-16","name":"CRYPTO: International Cryptology Conference"},"type":"conference","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"isbn":["9783662479995"]},"ec_funded":1,"related_material":{"record":[{"id":"2274","status":"public","relation":"earlier_version"}]},"volume":9216,"oa_version":"Preprint","abstract":[{"text":"Proofs of work (PoW) have been suggested by Dwork and Naor (Crypto’92) as protection to a shared resource. The basic idea is to ask the service requestor to dedicate some non-trivial amount of computational work to every request. The original applications included prevention of spam and protection against denial of service attacks. More recently, PoWs have been used to prevent double spending in the Bitcoin digital currency system. In this work, we put forward an alternative concept for PoWs - so-called proofs of space (PoS), where a service requestor must dedicate a significant amount of disk space as opposed to computation. We construct secure PoS schemes in the random oracle model (with one additional mild assumption required for the proof to go through), using graphs with high “pebbling complexity” and Merkle hash-trees. We discuss some applications, including follow-up work where a decentralized digital currency scheme called Spacecoin is constructed that uses PoS (instead of wasteful PoW like in Bitcoin) to prevent double spending. The main technical contribution of this work is the construction of (directed, loop-free) graphs on N vertices with in-degree O(log logN) such that even if one places Θ(N) pebbles on the nodes of the graph, there’s a constant fraction of nodes that needs Θ(N) steps to be pebbled (where in every step one can put a pebble on a node if all its parents have a pebble).","lang":"eng"}],"intvolume":" 9216","month":"08","main_file_link":[{"url":"https://eprint.iacr.org/2013/796.pdf","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":"1"},{"date_updated":"2024-03-25T11:52:26Z","extern":"1","_id":"15160","type":"journal_article","article_type":"original","keyword":["Cell Biology","Molecular Biology"],"status":"public","publication_status":"published","publication_identifier":{"issn":["1097-2765"]},"language":[{"iso":"eng"}],"issue":"5","volume":58,"abstract":[{"lang":"eng","text":"The circadian clock orchestrates global changes in transcriptional regulation on a daily basis via the bHLH-PAS transcription factor CLOCK:BMAL1. Pathways driven by other bHLH-PAS transcription factors have a homologous repressor that modulates activity on a tissue-specific basis, but none have been identified for CLOCK:BMAL1. We show here that the cancer/testis antigen PASD1 fulfills this role to suppress circadian rhythms. PASD1 is evolutionarily related to CLOCK and interacts with the CLOCK:BMAL1 complex to repress transcriptional activation. Expression of PASD1 is restricted to germline tissues in healthy individuals but can be induced in cells of somatic origin upon oncogenic transformation. Reducing PASD1 in human cancer cells significantly increases the amplitude of transcriptional oscillations to generate more robust circadian rhythms. Our results describe a function for a germline-specific protein in regulation of the circadian clock and provide a molecular link from oncogenic transformation to suppression of circadian rhythms."}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.molcel.2015.03.031"}],"scopus_import":"1","intvolume":" 58","month":"06","citation":{"chicago":"Michael, Alicia K., Stacy L. Harvey, Patrick J. Sammons, Amanda P. Anderson, Hema M. Kopalle, Alison H. Banham, and Carrie L. Partch. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” Molecular Cell. Elsevier, 2015. https://doi.org/10.1016/j.molcel.2015.03.031.","ista":"Michael AK, Harvey SL, Sammons PJ, Anderson AP, Kopalle HM, Banham AH, Partch CL. 2015. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. 58(5), 743–754.","mla":"Michael, Alicia K., et al. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” Molecular Cell, vol. 58, no. 5, Elsevier, 2015, pp. 743–54, doi:10.1016/j.molcel.2015.03.031.","apa":"Michael, A. K., Harvey, S. L., Sammons, P. J., Anderson, A. P., Kopalle, H. M., Banham, A. H., & Partch, C. L. (2015). Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2015.03.031","ama":"Michael AK, Harvey SL, Sammons PJ, et al. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. 2015;58(5):743-754. doi:10.1016/j.molcel.2015.03.031","short":"A.K. Michael, S.L. Harvey, P.J. Sammons, A.P. Anderson, H.M. Kopalle, A.H. Banham, C.L. Partch, Molecular Cell 58 (2015) 743–754.","ieee":"A. K. Michael et al., “Cancer/Testis antigen PASD1 silences the circadian clock,” Molecular Cell, vol. 58, no. 5. Elsevier, pp. 743–754, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia Kathleen","last_name":"Michael","full_name":"Michael, Alicia Kathleen"},{"last_name":"Harvey","full_name":"Harvey, Stacy L.","first_name":"Stacy L."},{"first_name":"Patrick J.","last_name":"Sammons","full_name":"Sammons, Patrick J."},{"full_name":"Anderson, Amanda P.","last_name":"Anderson","first_name":"Amanda P."},{"last_name":"Kopalle","full_name":"Kopalle, Hema M.","first_name":"Hema M."},{"first_name":"Alison H.","last_name":"Banham","full_name":"Banham, Alison H."},{"first_name":"Carrie L.","last_name":"Partch","full_name":"Partch, Carrie L."}],"title":"Cancer/Testis antigen PASD1 silences the circadian clock","year":"2015","publication":"Molecular Cell","day":"04","page":"743-754","date_created":"2024-03-21T07:58:08Z","date_published":"2015-06-04T00:00:00Z","doi":"10.1016/j.molcel.2015.03.031","oa":1,"quality_controlled":"1","publisher":"Elsevier"},{"issue":"9","volume":40,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0968-0004"]},"intvolume":" 40","month":"09","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"It is widely recognized that BMAL1 is an essential subunit of the primary transcription factor that drives rhythmic circadian transcription in the nucleus. In a surprising turn, Lipton et al. now show that BMAL1 rhythmically interacts with translational machinery in the cytosol to stimulate protein synthesis in response to mTOR signaling."}],"extern":"1","date_updated":"2024-03-25T11:53:58Z","keyword":["Molecular Biology","Biochemistry"],"status":"public","article_type":"original","type":"journal_article","_id":"15159","date_created":"2024-03-21T07:57:44Z","doi":"10.1016/j.tibs.2015.07.006","date_published":"2015-09-01T00:00:00Z","page":"489-490","publication":"Trends in Biochemical Sciences","day":"01","year":"2015","publisher":"Elsevier","quality_controlled":"1","title":"Cytosolic BMAL1 moonlights as a translation factor","article_processing_charge":"No","author":[{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia Kathleen","last_name":"Michael","full_name":"Michael, Alicia Kathleen"},{"first_name":"Hande","full_name":"Asimgil, Hande","last_name":"Asimgil"},{"first_name":"Carrie L.","last_name":"Partch","full_name":"Partch, Carrie L."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Michael, Alicia K., Hande Asimgil, and Carrie L. Partch. “Cytosolic BMAL1 Moonlights as a Translation Factor.” Trends in Biochemical Sciences. Elsevier, 2015. https://doi.org/10.1016/j.tibs.2015.07.006.","ista":"Michael AK, Asimgil H, Partch CL. 2015. Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. 40(9), 489–490.","mla":"Michael, Alicia K., et al. “Cytosolic BMAL1 Moonlights as a Translation Factor.” Trends in Biochemical Sciences, vol. 40, no. 9, Elsevier, 2015, pp. 489–90, doi:10.1016/j.tibs.2015.07.006.","short":"A.K. Michael, H. Asimgil, C.L. Partch, Trends in Biochemical Sciences 40 (2015) 489–490.","ieee":"A. K. Michael, H. Asimgil, and C. L. Partch, “Cytosolic BMAL1 moonlights as a translation factor,” Trends in Biochemical Sciences, vol. 40, no. 9. Elsevier, pp. 489–490, 2015.","ama":"Michael AK, Asimgil H, Partch CL. Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. 2015;40(9):489-490. doi:10.1016/j.tibs.2015.07.006","apa":"Michael, A. K., Asimgil, H., & Partch, C. L. (2015). Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. Elsevier. https://doi.org/10.1016/j.tibs.2015.07.006"}},{"publication":"PLoS Biology","day":"18","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:53:04Z","date_published":"2015-11-18T00:00:00Z","doi":"10.1371/journal.pbio.1002299","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 13(11), e1002299.","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak, M.T. Bollenbach, PLoS Biology 13 (2015).","ieee":"G. Chevereau et al., “Quantifying the determinants of evolutionary dynamics leading to drug resistance,” PLoS Biology, vol. 13, no. 11. Public Library of Science, 2015.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak, E., & Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 2015;13(11). doi:10.1371/journal.pbio.1002299","mla":"Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology, vol. 13, no. 11, e1002299, Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299."},"title":"Quantifying the determinants of evolutionary dynamics leading to drug resistance","author":[{"first_name":"Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","full_name":"Chevereau, Guillaume","last_name":"Chevereau"},{"first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Dravecka","orcid":"0000-0002-2519-8004","full_name":"Dravecka, Marta"},{"first_name":"Tugce","full_name":"Batur, Tugce","last_name":"Batur"},{"last_name":"Guvenek","full_name":"Guvenek, Aysegul","first_name":"Aysegul"},{"last_name":"Ayhan","full_name":"Ayhan, Dilay","first_name":"Dilay"},{"first_name":"Erdal","full_name":"Toprak, Erdal","last_name":"Toprak"},{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5547","article_number":"e1002299","project":[{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"},{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","grant_number":"303507"}],"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-468-v1+1_journal.pbio.1002299.pdf","date_created":"2018-12-12T10:09:00Z","file_size":1387760,"date_updated":"2020-07-14T12:45:07Z","creator":"system","checksum":"0e82e3279f50b15c6c170c042627802b","file_id":"4723","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","ec_funded":1,"volume":13,"related_material":{"record":[{"status":"public","id":"9711","relation":"research_data"},{"relation":"research_data","status":"public","id":"9765"},{"relation":"dissertation_contains","id":"6263","status":"public"}]},"issue":"11","oa_version":"Published Version","abstract":[{"text":"The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the “morbidostat”, a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations—an almost paradoxical behavior since this drug causes DNA damage and increases the mutation rate. Overall, we identified novel quantitative characteristics of the evolutionary landscape that provide the conceptual foundation for predicting the dynamics of drug resistance evolution.","lang":"eng"}],"intvolume":" 13","month":"11","scopus_import":1,"ddc":["570"],"date_updated":"2024-03-27T23:30:28Z","department":[{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:45:07Z","_id":"1619","pubrep_id":"468","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article"},{"oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","acknowledgement":"We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs, for helpful discussions. A.Š. acknowledges support from the Human Frontier Science Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology and Biological Sciences Research Council. D.F. acknowledges European Research Council Advanced Grant 227758.","page":"17869-17874","date_created":"2021-11-29T13:09:53Z","date_published":"2014-12-01T00:00:00Z","doi":"10.1073/pnas.1410159111","year":"2014","publication":"Proceedings of the National Academy of Sciences","day":"01","article_processing_charge":"No","external_id":{"arxiv":["1412.0897"],"pmid":["25453085"]},"author":[{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić"},{"last_name":"Chebaro","full_name":"Chebaro, Yassmine C.","first_name":"Yassmine C."},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."},{"first_name":"Daan","full_name":"Frenkel, Daan","last_name":"Frenkel"}],"title":"Crucial role of nonspecific interactions in amyloid nucleation","citation":{"mla":"Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings of the National Academy of Sciences, vol. 111, no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:10.1073/pnas.1410159111.","ieee":"A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of nonspecific interactions in amyloid nucleation,” Proceedings of the National Academy of Sciences, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874, 2014.","short":"A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National Academy of Sciences 111 (2014) 17869–17874.","apa":"Šarić, A., Chebaro, Y. C., Knowles, T. P. J., & Frenkel, D. (2014). Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1410159111","ama":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 2014;111(50):17869-17874. doi:10.1073/pnas.1410159111","chicago":"Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410159111.","ista":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 111(50), 17869–17874."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"url":"https://www.pnas.org/content/111/50/17869","open_access":"1"}],"scopus_import":"1","intvolume":" 111","month":"12","abstract":[{"lang":"eng","text":"Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical one-step nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory."}],"pmid":1,"oa_version":"Published Version","issue":"50","volume":111,"publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","keyword":["multidisciplinary"],"status":"public","_id":"10382","date_updated":"2021-11-29T13:29:05Z","extern":"1"},{"article_type":"original","type":"journal_article","status":"public","_id":"10383","date_updated":"2021-11-29T13:29:01Z","extern":"1","main_file_link":[{"url":"https://arxiv.org/abs/1310.0826","open_access":"1"}],"scopus_import":"1","intvolume":" 89","month":"05","abstract":[{"text":"We use numerical simulations to compute the equation of state of a suspension of spherical self-propelled nanoparticles in two and three dimensions. We study in detail the effect of excluded volume interactions and confinement as a function of the system's temperature, concentration, and strength of the propulsion. We find a striking nonmonotonic dependence of the pressure on the temperature and provide simple scaling arguments to predict and explain the occurrence of such anomalous behavior. We explicitly show how our results have important implications for the effective forces on passive components suspended in a bath of active particles.","lang":"eng"}],"oa_version":"Preprint","pmid":1,"volume":89,"issue":"5","publication_status":"published","publication_identifier":{"eissn":["1550-2376"],"issn":["1539-3755"]},"language":[{"iso":"eng"}],"article_number":"052303","external_id":{"arxiv":["1310.0826"],"pmid":["25353796"]},"article_processing_charge":"No","author":[{"full_name":"Mallory, S. A.","last_name":"Mallory","first_name":"S. A."},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"first_name":"C.","full_name":"Valeriani, C.","last_name":"Valeriani"},{"first_name":"A.","last_name":"Cacciuto","full_name":"Cacciuto, A."}],"title":"Anomalous thermomechanical properties of a self-propelled colloidal fluid","citation":{"chicago":"Mallory, S. A., Anđela Šarić, C. Valeriani, and A. Cacciuto. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.89.052303.","ista":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. 2014. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 89(5), 052303.","mla":"Mallory, S. A., et al. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical Review E, vol. 89, no. 5, 052303, American Physical Society, 2014, doi:10.1103/physreve.89.052303.","ama":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 2014;89(5). doi:10.1103/physreve.89.052303","apa":"Mallory, S. A., Šarić, A., Valeriani, C., & Cacciuto, A. (2014). Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.89.052303","ieee":"S. A. Mallory, A. Šarić, C. Valeriani, and A. Cacciuto, “Anomalous thermomechanical properties of a self-propelled colloidal fluid,” Physical Review E, vol. 89, no. 5. American Physical Society, 2014.","short":"S.A. Mallory, A. Šarić, C. Valeriani, A. Cacciuto, Physical Review E 89 (2014)."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_created":"2021-11-29T13:10:33Z","doi":"10.1103/physreve.89.052303","date_published":"2014-05-06T00:00:00Z","year":"2014","publication":"Physical Review E","day":"06"},{"month":"03","intvolume":" 15","publisher":"Wiley-Blackwell","oa_version":"None","abstract":[{"lang":"eng","text":"Diffraction-unlimited far-field super-resolution fluorescence (nanoscopy) methods typically rely on transiently transferring fluorophores between two states, whereby this transfer is usually laid out as a switch. However, depending on whether this is induced in a spatially controlled manner using a pattern of light (coordinate-targeted) or stochastically on a single-molecule basis, specific requirements on the fluorophores are imposed. Therefore, the fluorophores are usually utilized just for one class of methods only. In this study we demonstrate that the reversibly switchable fluorescent protein Dreiklang enables live-cell recordings in both spatially controlled and stochastic modes. We show that the Dreiklang chromophore entails three different light-induced switching mechanisms, namely a reversible photochemical one, off-switching by stimulated emission, and a reversible transfer to a long-lived dark state from the S1 state, all of which can be utilized to overcome the diffraction barrier. We also find that for the single-molecule- based stochastic GSDIM approach (ground-state depletion followed by individual molecule return), Dreiklang provides a larger number of on-off localization events as compared to its progenitor Citrine. Altogether, Dreiklang is a versatile probe for essentially all popular forms of live-cell fluorescence nanoscopy."}],"issue":"4","date_published":"2014-03-17T00:00:00Z","doi":"10.1002/cphc.201301034","volume":15,"date_created":"2018-12-11T11:49:55Z","page":"756 - 762","day":"17","publication":"ChemPhysChem","language":[{"iso":"eng"}],"year":"2014","publication_status":"published","status":"public","type":"journal_article","_id":"1058","title":"Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang","publist_id":"6332","author":[{"last_name":"Jensen","full_name":"Jensen, Nickels","first_name":"Nickels"},{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"},{"first_name":"Katrin","full_name":"Willig, Katrin","last_name":"Willig"},{"first_name":"Flavie","last_name":"Lavoie Cardinal","full_name":"Lavoie Cardinal, Flavie"},{"last_name":"Brakemann","full_name":"Brakemann, Tanja","first_name":"Tanja"},{"last_name":"Hell","full_name":"Hell, Stefan","first_name":"Stefan"},{"last_name":"Jakobs","full_name":"Jakobs, Stefan","first_name":"Stefan"}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Jensen N, Danzl JG, Willig K, Lavoie Cardinal F, Brakemann T, Hell S, Jakobs S. 2014. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 15(4), 756–762.","chicago":"Jensen, Nickels, Johann G Danzl, Katrin Willig, Flavie Lavoie Cardinal, Tanja Brakemann, Stefan Hell, and Stefan Jakobs. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem. Wiley-Blackwell, 2014. https://doi.org/10.1002/cphc.201301034.","short":"N. Jensen, J.G. Danzl, K. Willig, F. Lavoie Cardinal, T. Brakemann, S. Hell, S. Jakobs, ChemPhysChem 15 (2014) 756–762.","ieee":"N. Jensen et al., “Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang,” ChemPhysChem, vol. 15, no. 4. Wiley-Blackwell, pp. 756–762, 2014.","ama":"Jensen N, Danzl JG, Willig K, et al. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 2014;15(4):756-762. doi:10.1002/cphc.201301034","apa":"Jensen, N., Danzl, J. G., Willig, K., Lavoie Cardinal, F., Brakemann, T., Hell, S., & Jakobs, S. (2014). Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. Wiley-Blackwell. https://doi.org/10.1002/cphc.201301034","mla":"Jensen, Nickels, et al. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem, vol. 15, no. 4, Wiley-Blackwell, 2014, pp. 756–62, doi:10.1002/cphc.201301034."},"date_updated":"2021-01-12T06:47:58Z"},{"date_published":"2014-02-01T00:00:00Z","doi":"10.1111/cga.12039","date_created":"2022-03-04T08:17:25Z","page":"1-7","day":"01","publication":"Congenital Anomalies","year":"2014","publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"The authors thank all the members of the Division of Morphogenesis, National Institute for Basic Biology, for their contributions to the research, their encouragement, and helpful discussions, particularly Dr M. Suzuki for his critical reading of the manuscript. We also thank the Model Animal Research and Spectrography and Bioimaging Facilities, NIBB Core Research Facilities, for technical support. M.H. was supported by a research fellowship from the Japan Society for the Promotion of Science (JSPS). Our work introduced in this review was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan, to N.U.","title":"Molecular and cellular mechanisms of development underlying congenital diseases","author":[{"first_name":"Masakazu","full_name":"Hashimoto, Masakazu","last_name":"Hashimoto"},{"full_name":"Morita, Hitoshi","last_name":"Morita","first_name":"Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ueno, Naoto","last_name":"Ueno","first_name":"Naoto"}],"article_processing_charge":"No","external_id":{"pmid":["24666178"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Hashimoto M, Morita H, Ueno N. Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. 2014;54(1):1-7. doi:10.1111/cga.12039","apa":"Hashimoto, M., Morita, H., & Ueno, N. (2014). Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. Wiley. https://doi.org/10.1111/cga.12039","ieee":"M. Hashimoto, H. Morita, and N. Ueno, “Molecular and cellular mechanisms of development underlying congenital diseases,” Congenital Anomalies, vol. 54, no. 1. Wiley, pp. 1–7, 2014.","short":"M. Hashimoto, H. Morita, N. Ueno, Congenital Anomalies 54 (2014) 1–7.","mla":"Hashimoto, Masakazu, et al. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” Congenital Anomalies, vol. 54, no. 1, Wiley, 2014, pp. 1–7, doi:10.1111/cga.12039.","ista":"Hashimoto M, Morita H, Ueno N. 2014. Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. 54(1), 1–7.","chicago":"Hashimoto, Masakazu, Hitoshi Morita, and Naoto Ueno. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” Congenital Anomalies. Wiley, 2014. https://doi.org/10.1111/cga.12039."},"issue":"1","volume":54,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0914-3505"]},"publication_status":"published","month":"02","intvolume":" 54","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/cga.12039"}],"pmid":1,"oa_version":"None","abstract":[{"text":"In the last several decades, developmental biology has clarified the molecular mechanisms of embryogenesis and organogenesis. In particular, it has demonstrated that the “tool-kit genes” essential for regulating developmental processes are not only highly conserved among species, but are also used as systems at various times and places in an organism to control distinct developmental events. Therefore, mutations in many of these tool-kit genes may cause congenital diseases involving morphological abnormalities. This link between genes and abnormal morphological phenotypes underscores the importance of understanding how cells behave and contribute to morphogenesis as a result of gene function. Recent improvements in live imaging and in quantitative analyses of cellular dynamics will advance our understanding of the cellular pathogenesis of congenital diseases associated with aberrant morphologies. In these studies, it is critical to select an appropriate model organism for the particular phenomenon of interest.","lang":"eng"}],"department":[{"_id":"CaHe"}],"date_updated":"2022-03-04T08:26:05Z","status":"public","keyword":["Developmental Biology","Embryology","General Medicine","Pediatrics","Perinatology","and Child Health"],"type":"journal_article","article_type":"original","_id":"10815"},{"citation":{"ista":"Zažímalová E, Petrášek J, Benková E eds. 2014. Auxin and Its Role in Plant Development 1st ed., Vienna: Springer Nature, 444p.","chicago":"Zažímalová, Eva, Jan Petrášek, and Eva Benková, eds. Auxin and Its Role in Plant Development. 1st ed. Vienna: Springer Nature, 2014. https://doi.org/10.1007/978-3-7091-1526-8.","short":"E. Zažímalová, J. Petrášek, E. Benková, eds., Auxin and Its Role in Plant Development, 1st ed., Springer Nature, Vienna, 2014.","ieee":"E. Zažímalová, J. Petrášek, and E. Benková, Eds., Auxin and Its Role in Plant Development, 1st ed. Vienna: Springer Nature, 2014.","apa":"Zažímalová, E., Petrášek, J., & Benková, E. (Eds.). (2014). Auxin and Its Role in Plant Development (1st ed.). Vienna: Springer Nature. https://doi.org/10.1007/978-3-7091-1526-8","ama":"Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development. 1st ed. Vienna: Springer Nature; 2014. doi:10.1007/978-3-7091-1526-8","mla":"Zažímalová, Eva, et al., editors. Auxin and Its Role in Plant Development. 1st ed., Springer Nature, 2014, doi:10.1007/978-3-7091-1526-8."},"date_updated":"2022-03-04T07:38:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"EvBe"}],"title":"Auxin and Its Role in Plant Development","editor":[{"first_name":"Eva","full_name":"Zažímalová, Eva","last_name":"Zažímalová"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"_id":"10811","type":"book_editor","status":"public","publication_identifier":{"eisbn":["9783709115268"],"isbn":["9783709115251"]},"publication_status":"published","year":"2014","day":"01","language":[{"iso":"eng"}],"page":"444","date_published":"2014-04-01T00:00:00Z","doi":"10.1007/978-3-7091-1526-8","date_created":"2022-03-03T11:52:44Z","abstract":[{"text":"Auxin is an important signaling compound in plants and vital for plant development and growth. The present book, Auxin and its Role in Plant Development, provides the reader with detailed and comprehensive insight into the functioning of the molecule on the whole and specifically in plant development. In the first part, the functioning, metabolism and signaling pathways of auxin in plants are explained, the second part depicts the specific role of auxin in plant development and the third part describes the interaction and functioning of the signaling compound upon stimuli of the environment. Each chapter is written by international experts in the respective field and designed for scientists and researchers in plant biology, plant development and cell biology to summarize the recent progress in understanding the role of auxin and suggest future perspectives for auxin research.","lang":"eng"}],"oa_version":"None","publisher":"Springer Nature","quality_controlled":"1","scopus_import":"1","edition":"1","month":"04","place":"Vienna"},{"external_id":{"arxiv":["1311.4425"]},"article_processing_charge":"No","author":[{"full_name":"Aminof, Benjamin","last_name":"Aminof","first_name":"Benjamin","id":"4A55BD00-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Swen","full_name":"Jacobs, Swen","last_name":"Jacobs"},{"last_name":"Khalimov","full_name":"Khalimov, Ayrat","first_name":"Ayrat"},{"first_name":"Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","full_name":"Rubin, Sasha","last_name":"Rubin"}],"title":"Parameterized model checking of token-passing systems","citation":{"mla":"Aminof, Benjamin, et al. “Parameterized Model Checking of Token-Passing Systems.” Verification, Model Checking, and Abstract Interpretation, vol. 8318, Springer Nature, 2014, pp. 262–81, doi:10.1007/978-3-642-54013-4_15.","apa":"Aminof, B., Jacobs, S., Khalimov, A., & Rubin, S. (2014). Parameterized model checking of token-passing systems. In Verification, Model Checking, and Abstract Interpretation (Vol. 8318, pp. 262–281). San Diego, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-642-54013-4_15","ama":"Aminof B, Jacobs S, Khalimov A, Rubin S. Parameterized model checking of token-passing systems. In: Verification, Model Checking, and Abstract Interpretation. Vol 8318. Springer Nature; 2014:262-281. doi:10.1007/978-3-642-54013-4_15","ieee":"B. Aminof, S. Jacobs, A. Khalimov, and S. Rubin, “Parameterized model checking of token-passing systems,” in Verification, Model Checking, and Abstract Interpretation, San Diego, CA, United States, 2014, vol. 8318, pp. 262–281.","short":"B. Aminof, S. Jacobs, A. Khalimov, S. Rubin, in:, Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 262–281.","chicago":"Aminof, Benjamin, Swen Jacobs, Ayrat Khalimov, and Sasha Rubin. “Parameterized Model Checking of Token-Passing Systems.” In Verification, Model Checking, and Abstract Interpretation, 8318:262–81. Springer Nature, 2014. https://doi.org/10.1007/978-3-642-54013-4_15.","ista":"Aminof B, Jacobs S, Khalimov A, Rubin S. 2014. Parameterized model checking of token-passing systems. Verification, Model Checking, and Abstract Interpretation. VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318, 262–281."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"page":"262-281","date_created":"2022-03-18T13:01:22Z","date_published":"2014-01-30T00:00:00Z","doi":"10.1007/978-3-642-54013-4_15","year":"2014","publication":"Verification, Model Checking, and Abstract Interpretation","day":"30","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"This work was supported by the Austrian Science Fund through grant P23499-N23\r\nand through the RiSE network (S11403, S11405, S11406, S11407-N23); ERC Starting Grant (279307: Graph Games); Vienna Science and Technology Fund (WWTF)\r\ngrants PROSEED, ICT12-059, and VRG11-005.","department":[{"_id":"KrCh"}],"date_updated":"2022-05-17T08:36:01Z","conference":{"name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation","location":"San Diego, CA, United States","end_date":"2014-01-21","start_date":"2014-01-19"},"type":"conference","status":"public","_id":"10884","ec_funded":1,"volume":8318,"publication_status":"published","publication_identifier":{"eisbn":["9783642540134"],"eissn":["1611-3349"],"isbn":["9783642540127"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1311.4425","open_access":"1"}],"scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 8318","month":"01","abstract":[{"lang":"eng","text":"We revisit the parameterized model checking problem for token-passing systems and specifications in indexed CTL ∗ \\X. Emerson and Namjoshi (1995, 2003) have shown that parameterized model checking of indexed CTL ∗ \\X in uni-directional token rings can be reduced to checking rings up to some cutoff size. Clarke et al. (2004) have shown a similar result for general topologies and indexed LTL \\X, provided processes cannot choose the directions for sending or receiving the token.\r\nWe unify and substantially extend these results by systematically exploring fragments of indexed CTL ∗ \\X with respect to general topologies. For each fragment we establish whether a cutoff exists, and for some concrete topologies, such as rings, cliques and stars, we infer small cutoffs. Finally, we show that the problem becomes undecidable, and thus no cutoffs exist, if processes are allowed to choose the directions in which they send or from which they receive the token."}],"oa_version":"Preprint"},{"intvolume":" 1","place":"Cham","month":"03","scopus_import":"1","oa_version":"None","abstract":[{"text":"Saddle periodic orbits are an essential and stable part of the topological skeleton of a 3D vector field. Nevertheless, there is currently no efficient algorithm to robustly extract these features. In this chapter, we present a novel technique to extract saddle periodic orbits. Exploiting the analytic properties of such an orbit, we propose a scalar measure based on the finite-time Lyapunov exponent (FTLE) that indicates its presence. Using persistent homology, we can then extract the robust cycles of this field. These cycles thereby represent the saddle periodic orbits of the given vector field. We discuss the different existing FTLE approximation schemes regarding their applicability to this specific problem and propose an adapted version of FTLE called Normalized Velocity Separation. Finally, we evaluate our method using simple analytic vector field data.","lang":"eng"}],"ec_funded":1,"volume":1,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eisbn":["9783319040998"],"issn":["1612-3786"],"eissn":["2197-666X"],"isbn":["9783319040981"]},"status":"public","type":"book_chapter","_id":"10893","series_title":"Mathematics and Visualization","department":[{"_id":"HeEd"}],"date_updated":"2022-06-21T12:01:47Z","quality_controlled":"1","publisher":"Springer","acknowledgement":"First, we thank the reviewers of this paper for their ideas and critical comments. In addition, we thank Ronny Peikert and Filip Sadlo for a fruitful discussions. This research is supported by the European Commission under the TOPOSYS project FP7-ICT-318493-STREP, the European Social Fund (ESF App. No. 100098251), and the European Science Foundation under the ACAT Research Network Program.","date_created":"2022-03-21T07:11:23Z","date_published":"2014-03-19T00:00:00Z","doi":"10.1007/978-3-319-04099-8_4","page":"55-69","publication":"Topological Methods in Data Analysis and Visualization III ","day":"19","year":"2014","project":[{"grant_number":"318493","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Toward the extraction of saddle periodic orbits","editor":[{"first_name":"Peer-Timo","last_name":"Bremer","full_name":"Bremer, Peer-Timo"},{"full_name":"Hotz, Ingrid","last_name":"Hotz","first_name":"Ingrid"},{"full_name":"Pascucci, Valerio","last_name":"Pascucci","first_name":"Valerio"},{"first_name":"Ronald","full_name":"Peikert, Ronald","last_name":"Peikert"}],"article_processing_charge":"No","author":[{"first_name":"Jens","full_name":"Kasten, Jens","last_name":"Kasten"},{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"first_name":"Wieland","last_name":"Reich","full_name":"Reich, Wieland"},{"last_name":"Scheuermann","full_name":"Scheuermann, Gerik","first_name":"Gerik"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"J. Kasten, J. Reininghaus, W. Reich, G. Scheuermann, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III , Springer, Cham, 2014, pp. 55–69.","ieee":"J. Kasten, J. Reininghaus, W. Reich, and G. Scheuermann, “Toward the extraction of saddle periodic orbits,” in Topological Methods in Data Analysis and Visualization III , vol. 1, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Cham: Springer, 2014, pp. 55–69.","ama":"Kasten J, Reininghaus J, Reich W, Scheuermann G. Toward the extraction of saddle periodic orbits. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III . Vol 1. Mathematics and Visualization. Cham: Springer; 2014:55-69. doi:10.1007/978-3-319-04099-8_4","apa":"Kasten, J., Reininghaus, J., Reich, W., & Scheuermann, G. (2014). Toward the extraction of saddle periodic orbits. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III (Vol. 1, pp. 55–69). Cham: Springer. https://doi.org/10.1007/978-3-319-04099-8_4","mla":"Kasten, Jens, et al. “Toward the Extraction of Saddle Periodic Orbits.” Topological Methods in Data Analysis and Visualization III , edited by Peer-Timo Bremer et al., vol. 1, Springer, 2014, pp. 55–69, doi:10.1007/978-3-319-04099-8_4.","ista":"Kasten J, Reininghaus J, Reich W, Scheuermann G. 2014.Toward the extraction of saddle periodic orbits. In: Topological Methods in Data Analysis and Visualization III . vol. 1, 55–69.","chicago":"Kasten, Jens, Jan Reininghaus, Wieland Reich, and Gerik Scheuermann. “Toward the Extraction of Saddle Periodic Orbits.” In Topological Methods in Data Analysis and Visualization III , edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 1:55–69. Mathematics and Visualization. Cham: Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_4."}},{"_id":"11080","article_type":"original","type":"journal_article","keyword":["General Biochemistry","Genetics and Molecular Biology"],"status":"public","date_updated":"2022-07-18T08:44:33Z","extern":"1","abstract":[{"lang":"eng","text":"The spindle assembly checkpoint prevents separation of sister chromatids until each kinetochore is attached to the mitotic spindle. Rodriguez-Bravo et al. report that the nuclear pore complex scaffolds spindle assembly checkpoint signaling in interphase, providing a store of inhibitory signals that limits the speed of the subsequent mitosis."}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2014.02.004","open_access":"1"}],"scopus_import":"1","intvolume":" 156","month":"02","publication_status":"published","publication_identifier":{"issn":["0092-8674"]},"language":[{"iso":"eng"}],"issue":"5","volume":156,"citation":{"ista":"Buchwalter A, Hetzer M. 2014. Nuclear pores set the speed limit for mitosis. Cell. 156(5), 868–869.","chicago":"Buchwalter, Abigail, and Martin Hetzer. “Nuclear Pores Set the Speed Limit for Mitosis.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2014.02.004.","ama":"Buchwalter A, Hetzer M. Nuclear pores set the speed limit for mitosis. Cell. 2014;156(5):868-869. doi:10.1016/j.cell.2014.02.004","apa":"Buchwalter, A., & Hetzer, M. (2014). Nuclear pores set the speed limit for mitosis. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.02.004","ieee":"A. Buchwalter and M. Hetzer, “Nuclear pores set the speed limit for mitosis,” Cell, vol. 156, no. 5. Elsevier, pp. 868–869, 2014.","short":"A. Buchwalter, M. Hetzer, Cell 156 (2014) 868–869.","mla":"Buchwalter, Abigail, and Martin Hetzer. “Nuclear Pores Set the Speed Limit for Mitosis.” Cell, vol. 156, no. 5, Elsevier, 2014, pp. 868–69, doi:10.1016/j.cell.2014.02.004."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","external_id":{"pmid":["24581486"]},"article_processing_charge":"No","author":[{"last_name":"Buchwalter","full_name":"Buchwalter, Abigail","first_name":"Abigail"},{"last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W"}],"title":"Nuclear pores set the speed limit for mitosis","oa":1,"quality_controlled":"1","publisher":"Elsevier","year":"2014","publication":"Cell","day":"27","page":"868-869","date_created":"2022-04-07T07:50:04Z","doi":"10.1016/j.cell.2014.02.004","date_published":"2014-02-27T00:00:00Z"},{"intvolume":" 25","month":"08","main_file_link":[{"url":"https://doi.org/10.1091/mbc.e14-04-0865","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The nuclear pore complex (NPC) plays a critical role in gene expression by mediating import of transcription regulators into the nucleus and export of RNA transcripts to the cytoplasm. Emerging evidence suggests that in addition to mediating transport, a subset of nucleoporins (Nups) engage in transcriptional activation and elongation at genomic loci that are not associated with NPCs. The underlying mechanism and regulation of Nup mobility on and off nuclear pores remain unclear. Here we show that Nup50 is a mobile Nup with a pronounced presence both at the NPC and in the nucleoplasm that can move between these different localizations. Strikingly, the dynamic behavior of Nup50 in both locations is dependent on active transcription by RNA polymerase II and requires the N-terminal half of the protein, which contains importin α– and Nup153-binding domains. However, Nup50 dynamics are independent of importin α, Nup153, and Nup98, even though the latter two proteins also exhibit transcription-dependent mobility. Of interest, depletion of Nup50 from C2C12 myoblasts does not affect cell proliferation but inhibits differentiation into myotubes. Taken together, our results suggest a transport-independent role for Nup50 in chromatin biology that occurs away from the NPC."}],"volume":25,"issue":"16","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1059-1524","1939-4586"]},"keyword":["Cell Biology","Molecular Biology"],"status":"public","article_type":"original","type":"journal_article","_id":"11082","extern":"1","date_updated":"2022-07-18T08:45:20Z","oa":1,"quality_controlled":"1","publisher":"American Society for Cell Biology","date_created":"2022-04-07T07:50:24Z","doi":"10.1091/mbc.e14-04-0865","date_published":"2014-08-15T00:00:00Z","page":"2472-2484","publication":"Molecular Biology of the Cell","day":"15","year":"2014","title":"Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics","article_processing_charge":"No","author":[{"first_name":"Abigail L.","full_name":"Buchwalter, Abigail L.","last_name":"Buchwalter"},{"full_name":"Liang, Yun","last_name":"Liang","first_name":"Yun"},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"ama":"Buchwalter AL, Liang Y, Hetzer M. Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Molecular Biology of the Cell. 2014;25(16):2472-2484. doi:10.1091/mbc.e14-04-0865","apa":"Buchwalter, A. L., Liang, Y., & Hetzer, M. (2014). Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.e14-04-0865","ieee":"A. L. Buchwalter, Y. Liang, and M. Hetzer, “Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics,” Molecular Biology of the Cell, vol. 25, no. 16. American Society for Cell Biology, pp. 2472–2484, 2014.","short":"A.L. Buchwalter, Y. Liang, M. Hetzer, Molecular Biology of the Cell 25 (2014) 2472–2484.","mla":"Buchwalter, Abigail L., et al. “Nup50 Is Required for Cell Differentiation and Exhibits Transcription-Dependent Dynamics.” Molecular Biology of the Cell, vol. 25, no. 16, American Society for Cell Biology, 2014, pp. 2472–84, doi:10.1091/mbc.e14-04-0865.","ista":"Buchwalter AL, Liang Y, Hetzer M. 2014. Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Molecular Biology of the Cell. 25(16), 2472–2484.","chicago":"Buchwalter, Abigail L., Yun Liang, and Martin Hetzer. “Nup50 Is Required for Cell Differentiation and Exhibits Transcription-Dependent Dynamics.” Molecular Biology of the Cell. American Society for Cell Biology, 2014. https://doi.org/10.1091/mbc.e14-04-0865."}},{"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"chicago":"Hatch, Emily, and Martin Hetzer. “Breaching the Nuclear Envelope in Development and Disease.” Journal of Cell Biology. Rockefeller University Press, 2014. https://doi.org/10.1083/jcb.201402003.","ista":"Hatch E, Hetzer M. 2014. Breaching the nuclear envelope in development and disease. Journal of Cell Biology. 205(2), 133–141.","mla":"Hatch, Emily, and Martin Hetzer. “Breaching the Nuclear Envelope in Development and Disease.” Journal of Cell Biology, vol. 205, no. 2, Rockefeller University Press, 2014, pp. 133–41, doi:10.1083/jcb.201402003.","ama":"Hatch E, Hetzer M. Breaching the nuclear envelope in development and disease. Journal of Cell Biology. 2014;205(2):133-141. doi:10.1083/jcb.201402003","apa":"Hatch, E., & Hetzer, M. (2014). Breaching the nuclear envelope in development and disease. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201402003","ieee":"E. Hatch and M. Hetzer, “Breaching the nuclear envelope in development and disease,” Journal of Cell Biology, vol. 205, no. 2. Rockefeller University Press, pp. 133–141, 2014.","short":"E. Hatch, M. Hetzer, Journal of Cell Biology 205 (2014) 133–141."},"title":"Breaching the nuclear envelope in development and disease","article_processing_charge":"No","external_id":{"pmid":["24751535"]},"author":[{"first_name":"Emily","full_name":"Hatch, Emily","last_name":"Hatch"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER"}],"oa":1,"quality_controlled":"1","publisher":"Rockefeller University Press","publication":"Journal of Cell Biology","day":"21","year":"2014","date_created":"2022-04-07T07:50:13Z","date_published":"2014-04-21T00:00:00Z","doi":"10.1083/jcb.201402003","page":"133-141","_id":"11081","keyword":["Cell Biology"],"status":"public","type":"journal_article","article_type":"review","extern":"1","date_updated":"2022-07-18T08:45:09Z","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In eukaryotic cells the nuclear genome is enclosed by the nuclear envelope (NE). In metazoans, the NE breaks down in mitosis and it has been assumed that the physical barrier separating nucleoplasm and cytoplasm remains intact during the rest of the cell cycle and cell differentiation. However, recent studies suggest that nonmitotic NE remodeling plays a critical role in development, virus infection, laminopathies, and cancer. Although the mechanisms underlying these NE restructuring events are currently being defined, one common theme is activation of protein kinase C family members in the interphase nucleus to disrupt the nuclear lamina, demonstrating the importance of the lamina in maintaining nuclear integrity."}],"intvolume":" 205","month":"04","main_file_link":[{"url":"https://doi.org/10.1083/jcb.201402003","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1540-8140","0021-9525"]},"volume":205,"issue":"2"},{"date_updated":"2022-08-19T08:30:30Z","extern":"1","article_type":"original","type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","cosmology: observations","dark ages","reionization","first stars"],"status":"public","_id":"11583","volume":440,"issue":"3","publication_status":"published","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1402.6697"}],"scopus_import":"1","intvolume":" 440","month":"05","abstract":[{"lang":"eng","text":"Candidate galaxies at redshifts of z ∼ 10 are now being found in extremely deep surveys, probing very small areas. As a consequence, candidates are very faint, making spectroscopic confirmation practically impossible. In order to overcome such limitations, we have undertaken the CF-HiZELS survey, which is a large-area, medium-depth near-infrared narrow-band survey targeted at z = 8.8 Lyman α (Lyα) emitters (LAEs) and covering 10 deg2 in part of the SSA22 field with the Canada–France–Hawaii Telescope (CFHT). We surveyed a comoving volume of 4.7 × 106 Mpc3 to a Lyα luminosity limit of 6.3 × 1043舁erg舁s−1. We look for Lyα candidates by applying the following criteria: (i) clear emission-line source, (ii) no optical detections (ugriz from CFHTLS), (iii) no visible detection in the optical stack (ugriz > 27), (iv) visually checked reliable NBJ and J detections and (v) J − K ≤ 0. We compute photometric redshifts and remove a significant amount of dusty lower redshift line-emitters at z ∼ 1.4 or 2.2. A total of 13 Lyα candidates were found, of which two are marked as strong candidates, but the majority have very weak constraints on their spectral energy distributions. Using follow-up observations with SINFONI/VLT, we are able to exclude the most robust candidates as LAEs. We put a strong constraint on the Lyα luminosity function at z ∼ 9 and make realistic predictions for ongoing and future surveys. Our results show that surveys for the highest redshift LAEs are susceptible of multiple contaminations and that spectroscopic follow-up is absolutely necessary."}],"oa_version":"Preprint","external_id":{"arxiv":["1402.6697"]},"article_processing_charge":"No","author":[{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee"},{"first_name":"David","last_name":"Sobral","full_name":"Sobral, David"},{"first_name":"A. M.","last_name":"Swinbank","full_name":"Swinbank, A. M."},{"first_name":"Ian","full_name":"Smail, Ian","last_name":"Smail"},{"last_name":"Best","full_name":"Best, P. N.","first_name":"P. N."},{"first_name":"Jae-Woo","full_name":"Kim, Jae-Woo","last_name":"Kim"},{"last_name":"Franx","full_name":"Franx, Marijn","first_name":"Marijn"},{"first_name":"Bo","full_name":"Milvang-Jensen, Bo","last_name":"Milvang-Jensen"},{"first_name":"Johan","full_name":"Fynbo, Johan","last_name":"Fynbo"}],"title":"A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys","citation":{"ista":"Matthee JJ, Sobral D, Swinbank AM, Smail I, Best PN, Kim J-W, Franx M, Milvang-Jensen B, Fynbo J. 2014. A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys. Monthly Notices of the Royal Astronomical Society. 440(3), 2375–2387.","chicago":"Matthee, Jorryt J, David Sobral, A. M. Swinbank, Ian Smail, P. N. Best, Jae-Woo Kim, Marijn Franx, Bo Milvang-Jensen, and Johan Fynbo. “A 10 Deg2 Lyman α Survey at Z=8.8 with Spectroscopic Follow-up: Strong Constraints on the Luminosity Function and Implications for Other Surveys.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2014. https://doi.org/10.1093/mnras/stu392.","ama":"Matthee JJ, Sobral D, Swinbank AM, et al. A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys. Monthly Notices of the Royal Astronomical Society. 2014;440(3):2375-2387. doi:10.1093/mnras/stu392","apa":"Matthee, J. J., Sobral, D., Swinbank, A. M., Smail, I., Best, P. N., Kim, J.-W., … Fynbo, J. (2014). A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stu392","ieee":"J. J. Matthee et al., “A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys,” Monthly Notices of the Royal Astronomical Society, vol. 440, no. 3. Oxford University Press, pp. 2375–2387, 2014.","short":"J.J. Matthee, D. Sobral, A.M. Swinbank, I. Smail, P.N. Best, J.-W. Kim, M. Franx, B. Milvang-Jensen, J. Fynbo, Monthly Notices of the Royal Astronomical Society 440 (2014) 2375–2387.","mla":"Matthee, Jorryt J., et al. “A 10 Deg2 Lyman α Survey at Z=8.8 with Spectroscopic Follow-up: Strong Constraints on the Luminosity Function and Implications for Other Surveys.” Monthly Notices of the Royal Astronomical Society, vol. 440, no. 3, Oxford University Press, 2014, pp. 2375–87, doi:10.1093/mnras/stu392."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"2375-2387","date_created":"2022-07-14T12:33:24Z","date_published":"2014-05-21T00:00:00Z","doi":"10.1093/mnras/stu392","year":"2014","publication":"Monthly Notices of the Royal Astronomical Society","day":"21","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"We thank the anonymous referee for the comments and suggestions which improved both the quality and clarity of this work. DS acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a Veni fellowship. IRS acknowledges support from STFC (ST/I001573/1), a Leverhulme Fellowship, the ERC Advanced Investigator programme DUSTYGAL 321334 and a Royal Society/Wolfson Merit Award. PNB acknowledges support from the Leverhulme Trust. JWK acknowledges the support from the Creative Research Initiative Program, no. 2008- 0060544, of the National Research Foundation of Korea (NRF) funded by the Korean government (MSIP). JPUF and BMJ acknowledge support from the ERC-StG grant EGGS-278202. The Dark Cosmology Centre is funded by the Danish National Research Foundation. This work is based in part on data obtained as part of the UKIRT Infrared Deep Sky Survey. Based on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and CEA/IRFU, at the Canada–France–Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de l’Univers of the Centre National de la Recherche Scientifique (CNRS) of France and the University of Hawaii. This work is based in part on data products produced at Terapix available at the Canadian Astronomy Data Centre as part of the Canada-France-Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. This work was only possible due to OPTICON/FP7 and the access that it granted to the CFHT telescope. The authors also wish to acknowledge the CFHTLS and UKIDSS surveys for their excellent legacy and complementary value – without such high-quality data sets, this research would not have been possible."},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1407.1047"}],"scopus_import":"1","intvolume":" 443","month":"09","abstract":[{"text":"We have observed a sample of typical z ∼ 1 star-forming galaxies, selected from the HiZELS survey, with the new K-band Multi-Object Spectrograph (KMOS) near-infrared, multi-integral field unit instrument on the Very Large Telescope (VLT), in order to obtain their dynamics and metallicity gradients. The majority of our galaxies have a metallicity gradient consistent with being flat or negative (i.e. higher metallicity cores than outskirts). Intriguingly, we find a trend between metallicity gradient and specific star formation rate (sSFR), such that galaxies with a high sSFR tend to have relatively metal poor centres, a result which is strengthened when combined with data sets from the literature. This result appears to explain the discrepancies reported between different high-redshift studies and varying claims for evolution. From a galaxy evolution perspective, the trend we see would mean that a galaxy's sSFR is governed by the amount of metal-poor gas that can be funnelled into its core, triggered either by merging or through efficient accretion. In fact, merging may play a significant role as it is the starburst galaxies at all epochs, which have the more positive metallicity gradients. Our results may help to explain the origin of the fundamental metallicity relation, in which galaxies at a fixed mass are observed to have lower metallicities at higher star formation rates, especially if the metallicity is measured in an aperture encompassing only the central regions of the galaxy. Finally, we note that this study demonstrates the power of KMOS as an efficient instrument for large-scale resolved galaxy surveys.","lang":"eng"}],"oa_version":"Preprint","issue":"3","volume":443,"publication_status":"published","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: abundances","galaxies: evolution","galaxies: kinematics and dynamics"],"status":"public","_id":"11582","date_updated":"2022-08-19T08:27:25Z","extern":"1","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","acknowledgement":"First, we acknowledge the referee for their comments, which have improved the clarity of this paper. JPS and IRS acknowledge support from STFC (ST/I001573/1). IRS also acknowledges support from the ERC Advanced Investigator programme DUSTYGAL and a Royal Society/Wolfson Merit Award. DS acknowledges financial support from NWO through a Veni fellowship and from FCT through the award of an FCT-IF starting grant. PNB acknowledges STFC for financial support.","page":"2695-2704","date_created":"2022-07-14T12:16:10Z","date_published":"2014-09-21T00:00:00Z","doi":"10.1093/mnras/stu1343","year":"2014","publication":"Monthly Notices of the Royal Astronomical Society","day":"21","article_processing_charge":"No","external_id":{"arxiv":["1407.1047"]},"author":[{"first_name":"John P.","full_name":"Stott, John P.","last_name":"Stott"},{"full_name":"Sobral, David","last_name":"Sobral","first_name":"David"},{"first_name":"A. M.","last_name":"Swinbank","full_name":"Swinbank, A. M."},{"full_name":"Smail, Ian","last_name":"Smail","first_name":"Ian"},{"first_name":"Richard","full_name":"Bower, Richard","last_name":"Bower"},{"first_name":"Philip N.","last_name":"Best","full_name":"Best, Philip N."},{"first_name":"Ray M.","last_name":"Sharples","full_name":"Sharples, Ray M."},{"last_name":"Geach","full_name":"Geach, James E.","first_name":"James E."},{"full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"}],"title":"A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS","citation":{"chicago":"Stott, John P., David Sobral, A. M. Swinbank, Ian Smail, Richard Bower, Philip N. Best, Ray M. Sharples, James E. Geach, and Jorryt J Matthee. “A Relationship between Specific Star Formation Rate and Metallicity Gradient within z ∼ 1 Galaxies from KMOS-HiZELS.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2014. https://doi.org/10.1093/mnras/stu1343.","ista":"Stott JP, Sobral D, Swinbank AM, Smail I, Bower R, Best PN, Sharples RM, Geach JE, Matthee JJ. 2014. A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of the Royal Astronomical Society. 443(3), 2695–2704.","mla":"Stott, John P., et al. “A Relationship between Specific Star Formation Rate and Metallicity Gradient within z ∼ 1 Galaxies from KMOS-HiZELS.” Monthly Notices of the Royal Astronomical Society, vol. 443, no. 3, Oxford University Press, 2014, pp. 2695–704, doi:10.1093/mnras/stu1343.","apa":"Stott, J. P., Sobral, D., Swinbank, A. M., Smail, I., Bower, R., Best, P. N., … Matthee, J. J. (2014). A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stu1343","ama":"Stott JP, Sobral D, Swinbank AM, et al. A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of the Royal Astronomical Society. 2014;443(3):2695-2704. doi:10.1093/mnras/stu1343","ieee":"J. P. Stott et al., “A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS,” Monthly Notices of the Royal Astronomical Society, vol. 443, no. 3. Oxford University Press, pp. 2695–2704, 2014.","short":"J.P. Stott, D. Sobral, A.M. Swinbank, I. Smail, R. Bower, P.N. Best, R.M. Sharples, J.E. Geach, J.J. Matthee, Monthly Notices of the Royal Astronomical Society 443 (2014) 2695–2704."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","article_type":"original","status":"public","_id":"11750","date_updated":"2022-08-11T09:51:22Z","extern":"1","scopus_import":"1","intvolume":" 50","month":"05","abstract":[{"text":"We report on the magnetic properties of a hot-pressed FeSb 2 sample. We find a significant increase in the magnetic susceptibility in our sample when compared with the values previously reported for the polycrystalline sample. The pronounced Curie tail at low temperature corresponds to 0.2% of Fe 2+ impurities per mole. In the intrinsic conductivity region, the susceptibility due to free carriers shows thermally activated behavior and is consistent with the data reported for single crystal FeSb 2 . Based on our data and analysis, while the enhanced magnetic susceptibility in our sample comes mainly from a small amount of unreacted Fe, the contribution from the enhanced carrier density due to lattice and strain defects arising from the ball milling process is also significant. Existence of an unreacted Fe phase is evidenced by small coercivity values of ~100 observed at 50 and 300 K.","lang":"eng"}],"oa_version":"None","issue":"5","volume":50,"publication_status":"published","publication_identifier":{"eissn":["1941-0069"],"issn":["0018-9464"]},"language":[{"iso":"eng"}],"article_number":"6675864","article_processing_charge":"No","author":[{"full_name":"Pokharel, Mani","last_name":"Pokharel","first_name":"Mani"},{"last_name":"Zhao","full_name":"Zhao, Huaizhou","first_name":"Huaizhou"},{"first_name":"Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","orcid":"0000-0001-9760-3147","full_name":"Modic, Kimberly A","last_name":"Modic"},{"first_name":"Zhifeng","full_name":"Ren, Zhifeng","last_name":"Ren"},{"full_name":"Opeil, Cyril","last_name":"Opeil","first_name":"Cyril"}],"title":"Magnetic properties of hot-pressed FeSb2","citation":{"ama":"Pokharel M, Zhao H, Modic KA, Ren Z, Opeil C. Magnetic properties of hot-pressed FeSb2. IEEE Transactions on Magnetics. 2014;50(5). doi:10.1109/TMAG.2013.2292607","apa":"Pokharel, M., Zhao, H., Modic, K. A., Ren, Z., & Opeil, C. (2014). Magnetic properties of hot-pressed FeSb2. IEEE Transactions on Magnetics. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/TMAG.2013.2292607","short":"M. Pokharel, H. Zhao, K.A. Modic, Z. Ren, C. Opeil, IEEE Transactions on Magnetics 50 (2014).","ieee":"M. Pokharel, H. Zhao, K. A. Modic, Z. Ren, and C. Opeil, “Magnetic properties of hot-pressed FeSb2,” IEEE Transactions on Magnetics, vol. 50, no. 5. Institute of Electrical and Electronics Engineers, 2014.","mla":"Pokharel, Mani, et al. “Magnetic Properties of Hot-Pressed FeSb2.” IEEE Transactions on Magnetics, vol. 50, no. 5, 6675864, Institute of Electrical and Electronics Engineers, 2014, doi:10.1109/TMAG.2013.2292607.","ista":"Pokharel M, Zhao H, Modic KA, Ren Z, Opeil C. 2014. Magnetic properties of hot-pressed FeSb2. IEEE Transactions on Magnetics. 50(5), 6675864.","chicago":"Pokharel, Mani, Huaizhou Zhao, Kimberly A Modic, Zhifeng Ren, and Cyril Opeil. “Magnetic Properties of Hot-Pressed FeSb2.” IEEE Transactions on Magnetics. Institute of Electrical and Electronics Engineers, 2014. https://doi.org/10.1109/TMAG.2013.2292607."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Institute of Electrical and Electronics Engineers","date_created":"2022-08-08T08:26:02Z","doi":"10.1109/TMAG.2013.2292607","date_published":"2014-05-01T00:00:00Z","year":"2014","publication":"IEEE Transactions on Magnetics","day":"01"},{"date_created":"2022-08-11T10:41:47Z","doi":"10.1007/978-3-662-44777-2_22","date_published":"2014-09-01T00:00:00Z","page":"260 - 271","publication":"22nd Annual European Symposium on Algorithms","day":"01","year":"2014","oa":1,"publisher":"Springer Nature","quality_controlled":"1","title":"Online bipartite matching with decomposable weights","article_processing_charge":"No","external_id":{"arxiv":["1409.2139"]},"author":[{"last_name":"Charikar","full_name":"Charikar, Moses","first_name":"Moses"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"last_name":"Nguyễn","full_name":"Nguyễn, Huy L.","first_name":"Huy L."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Charikar, Moses, Monika H Henzinger, and Huy L. Nguyễn. “Online Bipartite Matching with Decomposable Weights.” In 22nd Annual European Symposium on Algorithms, 8737:260–71. Springer Nature, 2014. https://doi.org/10.1007/978-3-662-44777-2_22.","ista":"Charikar M, Henzinger MH, Nguyễn HL. 2014. Online bipartite matching with decomposable weights. 22nd Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LNCS, vol. 8737, 260–271.","mla":"Charikar, Moses, et al. “Online Bipartite Matching with Decomposable Weights.” 22nd Annual European Symposium on Algorithms, vol. 8737, Springer Nature, 2014, pp. 260–71, doi:10.1007/978-3-662-44777-2_22.","apa":"Charikar, M., Henzinger, M. H., & Nguyễn, H. L. (2014). Online bipartite matching with decomposable weights. In 22nd Annual European Symposium on Algorithms (Vol. 8737, pp. 260–271). Wroclaw, Poland: Springer Nature. https://doi.org/10.1007/978-3-662-44777-2_22","ama":"Charikar M, Henzinger MH, Nguyễn HL. Online bipartite matching with decomposable weights. In: 22nd Annual European Symposium on Algorithms. Vol 8737. Springer Nature; 2014:260-271. doi:10.1007/978-3-662-44777-2_22","short":"M. Charikar, M.H. Henzinger, H.L. Nguyễn, in:, 22nd Annual European Symposium on Algorithms, Springer Nature, 2014, pp. 260–271.","ieee":"M. Charikar, M. H. Henzinger, and H. L. Nguyễn, “Online bipartite matching with decomposable weights,” in 22nd Annual European Symposium on Algorithms, Wroclaw, Poland, 2014, vol. 8737, pp. 260–271."},"volume":8737,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-366244776-5"],"issn":["0302-9743"]},"intvolume":" 8737","month":"09","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1409.2139"}],"scopus_import":"1","alternative_title":["LNCS"],"oa_version":"Preprint","abstract":[{"text":"We study a weighted online bipartite matching problem: G(V 1, V 2, E) is a weighted bipartite graph where V 1 is known beforehand and the vertices of V 2 arrive online. The goal is to match vertices of V 2 as they arrive to vertices in V 1, so as to maximize the sum of weights of edges in the matching. If assignments to V 1 cannot be changed, no bounded competitive ratio is achievable. We study the weighted online matching problem with free disposal, where vertices in V 1 can be assigned multiple times, but only get credit for the maximum weight edge assigned to them over the course of the algorithm. For this problem, the greedy algorithm is 0.5-competitive and determining whether a better competitive ratio is achievable is a well known open problem.\r\n\r\nWe identify an interesting special case where the edge weights are decomposable as the product of two factors, one corresponding to each end point of the edge. This is analogous to the well studied related machines model in the scheduling literature, although the objective functions are different. For this case of decomposable edge weights, we design a 0.5664 competitive randomized algorithm in complete bipartite graphs. We show that such instances with decomposable weights are non-trivial by establishing upper bounds of 0.618 for deterministic and 0.8 for randomized algorithms.\r\n\r\nA tight competitive ratio of 1 − 1/e ≈ 0.632 was known previously for both the 0-1 case as well as the case where edge weights depend on the offline vertices only, but for these cases, reassignments cannot change the quality of the solution. Beating 0.5 for weighted matching where reassignments are necessary has been a significant challenge. We thus give the first online algorithm with competitive ratio strictly better than 0.5 for a non-trivial case of weighted matching with free disposal.","lang":"eng"}],"extern":"1","date_updated":"2023-02-13T11:16:24Z","status":"public","conference":{"end_date":"2014-09-10","location":"Wroclaw, Poland","start_date":"2014-09-08","name":"ESA: Annual European Symposium on Algorithms"},"type":"conference","_id":"11789"},{"publication":"10th International Conference of Web and Internet Economics","language":[{"iso":"eng"}],"day":"01","year":"2014","publication_status":"published","publication_identifier":{"issn":["0302-9743"]},"date_created":"2022-08-11T10:58:44Z","date_published":"2014-12-01T00:00:00Z","doi":"10.1007/978-3-319-13129-0_4","volume":8877,"page":"44 - 57","oa_version":"None","abstract":[{"lang":"eng","text":"Assume a seller wants to sell a digital product in a social network where a buyer’s valuation of the item has positive network externalities from her neighbors that already have the item. The goal of the seller is to maximize his revenue. Previous work on this problem [7] studies the case where clients are offered the item in sequence and have to pay personalized prices. This is highly infeasible in large scale networks such as the Facebook graph: (1) Offering items to the clients one after the other consumes a large amount of time, and (2) price-discrimination of clients could appear unfair to them and result in negative client reaction or could conflict with legal requirements.\r\n\r\nWe study a setting dealing with these issues. Specifically, the item is offered in parallel to multiple clients at the same time and at the same price. This is called a round. We show that with O(logn) rounds, where n is the number of clients, a constant factor of the revenue with price discrimination can be achieved and that this is not possible with o(logn) rounds. Moreover we show that it is APX-hard to maximize the revenue and we give constant factor approximation algorithms for various further settings of limited price discrimination."}],"intvolume":" 8877","month":"12","quality_controlled":"1","alternative_title":["LNCS"],"publisher":"Springer Nature","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2023-02-13T11:18:30Z","citation":{"ama":"Cigler L, Dvořák W, Henzinger MH, Starnberger M. Limiting price discrimination when selling products with positive network externalities. In: 10th International Conference of Web and Internet Economics. Vol 8877. Springer Nature; 2014:44-57. doi:10.1007/978-3-319-13129-0_4","apa":"Cigler, L., Dvořák, W., Henzinger, M. H., & Starnberger, M. (2014). Limiting price discrimination when selling products with positive network externalities. In 10th International Conference of Web and Internet Economics (Vol. 8877, pp. 44–57). Beijing, China: Springer Nature. https://doi.org/10.1007/978-3-319-13129-0_4","short":"L. Cigler, W. Dvořák, M.H. Henzinger, M. Starnberger, in:, 10th International Conference of Web and Internet Economics, Springer Nature, 2014, pp. 44–57.","ieee":"L. Cigler, W. Dvořák, M. H. Henzinger, and M. Starnberger, “Limiting price discrimination when selling products with positive network externalities,” in 10th International Conference of Web and Internet Economics, Beijing, China, 2014, vol. 8877, pp. 44–57.","mla":"Cigler, Luděk, et al. “Limiting Price Discrimination When Selling Products with Positive Network Externalities.” 10th International Conference of Web and Internet Economics, vol. 8877, Springer Nature, 2014, pp. 44–57, doi:10.1007/978-3-319-13129-0_4.","ista":"Cigler L, Dvořák W, Henzinger MH, Starnberger M. 2014. Limiting price discrimination when selling products with positive network externalities. 10th International Conference of Web and Internet Economics. WINE: International Conference on Web and Internet Economics, LNCS, vol. 8877, 44–57.","chicago":"Cigler, Luděk, Wolfgang Dvořák, Monika H Henzinger, and Martin Starnberger. “Limiting Price Discrimination When Selling Products with Positive Network Externalities.” In 10th International Conference of Web and Internet Economics, 8877:44–57. Springer Nature, 2014. https://doi.org/10.1007/978-3-319-13129-0_4."},"title":"Limiting price discrimination when selling products with positive network externalities","article_processing_charge":"No","author":[{"first_name":"Luděk","last_name":"Cigler","full_name":"Cigler, Luděk"},{"last_name":"Dvořák","full_name":"Dvořák, Wolfgang","first_name":"Wolfgang"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Starnberger, Martin","last_name":"Starnberger","first_name":"Martin"}],"_id":"11790","status":"public","conference":{"name":"WINE: International Conference on Web and Internet Economics","location":"Beijing, China","end_date":"2014-12-17","start_date":"2014-12-14"},"type":"conference"},{"author":[{"last_name":"Altshuler","full_name":"Altshuler, Ernesto","first_name":"Ernesto"},{"full_name":"Torres, H","last_name":"Torres","first_name":"H"},{"full_name":"González_Pita, A","last_name":"González_Pita","first_name":"A"},{"last_name":"Sánchez","full_name":"Sánchez, Colina G","first_name":"Colina G"},{"last_name":"Pérez Penichet","full_name":"Pérez Penichet, Carlos","first_name":"Carlos"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis"},{"first_name":"Rauól","last_name":"Hidalgo","full_name":"Hidalgo, Rauól"}],"publist_id":"7936","title":"Settling into dry granular media in different gravities","citation":{"mla":"Altshuler, Ernesto, et al. “Settling into Dry Granular Media in Different Gravities.” Geophysical Research Letters, vol. 41, no. 9, Wiley-Blackwell, 2014, pp. 3032–37, doi:10.1002/2014GL059229.","short":"E. Altshuler, H. Torres, A. González_Pita, C.G. Sánchez, C. Pérez Penichet, S.R. Waitukaitis, R. Hidalgo, Geophysical Research Letters 41 (2014) 3032–3037.","ieee":"E. Altshuler et al., “Settling into dry granular media in different gravities,” Geophysical Research Letters, vol. 41, no. 9. Wiley-Blackwell, pp. 3032–3037, 2014.","ama":"Altshuler E, Torres H, González_Pita A, et al. Settling into dry granular media in different gravities. Geophysical Research Letters. 2014;41(9):3032-3037. doi:10.1002/2014GL059229","apa":"Altshuler, E., Torres, H., González_Pita, A., Sánchez, C. G., Pérez Penichet, C., Waitukaitis, S. R., & Hidalgo, R. (2014). Settling into dry granular media in different gravities. Geophysical Research Letters. Wiley-Blackwell. https://doi.org/10.1002/2014GL059229","chicago":"Altshuler, Ernesto, H Torres, A González_Pita, Colina G Sánchez, Carlos Pérez Penichet, Scott R Waitukaitis, and Rauól Hidalgo. “Settling into Dry Granular Media in Different Gravities.” Geophysical Research Letters. Wiley-Blackwell, 2014. https://doi.org/10.1002/2014GL059229.","ista":"Altshuler E, Torres H, González_Pita A, Sánchez CG, Pérez Penichet C, Waitukaitis SR, Hidalgo R. 2014. Settling into dry granular media in different gravities. Geophysical Research Letters. 41(9), 3032–3037."},"date_updated":"2021-01-12T06:48:53Z","extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"118","page":"3032 - 3037","doi":"10.1002/2014GL059229","date_published":"2014-05-16T00:00:00Z","issue":"9","volume":41,"date_created":"2018-12-11T11:44:43Z","publication_status":"published","year":"2014","day":"16","publication":"Geophysical Research Letters","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Wiley-Blackwell","month":"05","intvolume":" 41","abstract":[{"lang":"eng","text":"While the penetration of objects into granular media is well-studied, there is little understanding of how objects settle in gravities, geff, different from that of Earth - a scenario potentially relevant to the geomorphology of planets and asteroids and also to their exploration using man-made devices. By conducting experiments in an accelerating frame, we explore geff ranging from 0.4 g to 1.2 g. Surprisingly, we find that the rest depth is independent of geff and also that the time required for the object to come to rest scales like geff-1/2. With discrete element modeling simulations, we reproduce the experimental results and extend the range of geff to objects as small as asteroids and as large as Jupiter. Our results shed light on the initial stage of sedimentation into dry granular media across a range of celestial bodies and also have implications for the design of man-made, extraterrestrial vehicles and structures. Key Points The settling depth in granular media is independent of gravity The settling time scales like g-1/2 Layering driven by granular sedimentation should be similar."}],"oa_version":"None","acknowledgement":"The Spanish MINECO project FIS2011-26675, the PIUNA program (U. Navarra), and the Project 29942WL (Fonds de Solidarité Prioritaire France-Cuba) have partially supported this research. "},{"citation":{"mla":"Henzinger, Monika H., et al. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” 55th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2014, pp. 146–55, doi:10.1109/focs.2014.24.","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Decremental single-source shortest paths on undirected graphs in near-linear total update time,” in 55th Annual Symposium on Foundations of Computer Science, Philadelphia, PA, United States, 2014, pp. 146–155.","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 55th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2014, pp. 146–155.","ama":"Henzinger MH, Krinninger S, Nanongkai D. Decremental single-source shortest paths on undirected graphs in near-linear total update time. In: 55th Annual Symposium on Foundations of Computer Science. Institute of Electrical and Electronics Engineers; 2014:146-155. doi:10.1109/focs.2014.24","apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Decremental single-source shortest paths on undirected graphs in near-linear total update time. In 55th Annual Symposium on Foundations of Computer Science (pp. 146–155). Philadelphia, PA, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/focs.2014.24","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” In 55th Annual Symposium on Foundations of Computer Science, 146–55. Institute of Electrical and Electronics Engineers, 2014. https://doi.org/10.1109/focs.2014.24.","ista":"Henzinger MH, Krinninger S, Nanongkai D. 2014. Decremental single-source shortest paths on undirected graphs in near-linear total update time. 55th Annual Symposium on Foundations of Computer Science. FOCS: Annual Symposium on Foundations of Computer Science, 146–155."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"first_name":"Sebastian","last_name":"Krinninger","full_name":"Krinninger, Sebastian"},{"first_name":"Danupon","full_name":"Nanongkai, Danupon","last_name":"Nanongkai"}],"external_id":{"arxiv":["1402.0054"]},"article_processing_charge":"No","title":"Decremental single-source shortest paths on undirected graphs in near-linear total update time","year":"2014","day":"01","publication":"55th Annual Symposium on Foundations of Computer Science","page":"146-155","date_published":"2014-10-01T00:00:00Z","doi":"10.1109/focs.2014.24","date_created":"2022-08-16T08:14:33Z","publisher":"Institute of Electrical and Electronics Engineers","quality_controlled":"1","oa":1,"date_updated":"2023-02-21T16:27:34Z","extern":"1","_id":"11855","type":"conference","conference":{"start_date":"2014-10-18","location":"Philadelphia, PA, United States","end_date":"2014-10-21","name":"FOCS: Annual Symposium on Foundations of Computer Science"},"status":"public","publication_identifier":{"issn":["0272-5428"],"eisbn":["978-1-4799-6517-5"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"11768","relation":"later_version"}]},"abstract":[{"lang":"eng","text":"The decremental single-source shortest paths (SSSP) problem concerns maintaining the distances between a given source node s to every node in an n-node m-edge graph G undergoing edge deletions. While its static counterpart can be easily solved in near-linear time, this decremental problem is much more challenging even in the undirected unweighted case. In this case, the classic O(mn) total update time of Even and Shiloach (JACM 1981) has been the fastest known algorithm for three decades. With the loss of a (1 + ε)-approximation factor, the running time was recently improved to O(n 2+o(1) ) by Bernstein and Roditty (SODA 2011), and more recently to O(n 1.8+o(1) + m 1+o(1) ) by Henzinger, Krinninger, and Nanongkai (SODA 2014). In this paper, we finally bring the running time of this case down to near-linear: We give a (1 + ε)-approximation algorithm with O(m 1+o(1) ) total update time, thus obtaining near-linear time. Moreover, we obtain O(m 1+o(1) log W) time for the weighted case, where the edge weights are integers from 1 to W. The only prior work on weighted graphs in o(mn log W) time is the O(mn 0.986 log W)-time algorithm by Henzinger, Krinninger, and Nanongkai (STOC 2014) which works for the general weighted directed case. In contrast to the previous results which rely on maintaining a sparse emulator, our algorithm relies on maintaining a so-called sparse (d, ε)-hop set introduced by Cohen (JACM 2000) in the PRAM literature. A (d, ε)-hop set of a graph G = (V, E) is a set E' of weighted edges such that the distance between any pair of nodes in G can be (1 + ε)-approximated by their d-hop distance (given by a path containing at most d edges) on G'=(V, E∪E'). Our algorithm can maintain an (n o(1) , ε)-hop set of near-linear size in near-linear time under edge deletions. It is the first of its kind to the best of our knowledge. To maintain the distances on this hop set, we develop a monotone bounded-hop Even-Shiloach tree. It results from extending and combining the monotone Even-Shiloach tree of Henzinger, Krinninger, and Nanongkai (FOCS 2013) with the bounded-hop SSSP technique of Bernstein (STOC 2013). These two new tools might be of independent interest."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1402.0054","open_access":"1"}],"month":"10"},{"status":"public","type":"conference","conference":{"end_date":"2014-06-03","location":"New York, NY, United States","start_date":"2014-05-31","name":"STOC: Symposium on Theory of Computing"},"article_number":"674 - 683","_id":"11870","title":"Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs","author":[{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Krinninger","full_name":"Krinninger, Sebastian","first_name":"Sebastian"},{"full_name":"Nanongkai, Danupon","last_name":"Nanongkai","first_name":"Danupon"}],"article_processing_charge":"No","external_id":{"arxiv":["1504.07959"]},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs,” in 46th Annual ACM Symposium on Theory of Computing, New York, NY, United States, 2014.","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 46th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2014.","ama":"Henzinger MH, Krinninger S, Nanongkai D. Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. In: 46th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2014. doi:10.1145/2591796.2591869","apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. In 46th Annual ACM Symposium on Theory of Computing. New York, NY, United States: Association for Computing Machinery. https://doi.org/10.1145/2591796.2591869","mla":"Henzinger, Monika H., et al. “Sublinear-Time Decremental Algorithms for Single-Source Reachability and Shortest Paths on Directed Graphs.” 46th Annual ACM Symposium on Theory of Computing, 674–683, Association for Computing Machinery, 2014, doi:10.1145/2591796.2591869.","ista":"Henzinger MH, Krinninger S, Nanongkai D. 2014. Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. 46th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 674–683.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Sublinear-Time Decremental Algorithms for Single-Source Reachability and Shortest Paths on Directed Graphs.” In 46th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery, 2014. https://doi.org/10.1145/2591796.2591869."},"date_updated":"2023-02-17T11:18:52Z","month":"05","scopus_import":"1","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.07959"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider dynamic algorithms for maintaining Single-Source Reachability (SSR) and approximate Single-Source Shortest Paths (SSSP) on n-node m-edge directed graphs under edge deletions (decremental algorithms). The previous fastest algorithm for SSR and SSSP goes back three decades to Even and Shiloach (JACM 1981); it has O(1) query time and O(mn) total update time (i.e., linear amortized update time if all edges are deleted). This algorithm serves as a building block for several other dynamic algorithms. The question whether its total update time can be improved is a major, long standing, open problem.\r\n\r\nIn this paper, we answer this question affirmatively. We obtain a randomized algorithm which, in a simplified form, achieves an Õ(mn0.984) expected total update time for SSR and (1 + ε)-approximate SSSP, where Õ(·) hides poly log n. We also extend our algorithm to achieve roughly the same running time for Strongly Connected Components (SCC), improving the algorithm of Roditty and Zwick (FOCS 2002), and an algorithm that improves the Õ (mn log W)-time algorithm of Bernstein (STOC 2013) for approximating SSSP on weighted directed graphs, where the edge weights are integers from 1 to W. All our algorithms have constant query time in the worst case."}],"date_published":"2014-05-01T00:00:00Z","doi":"10.1145/2591796.2591869","date_created":"2022-08-16T09:41:57Z","day":"01","language":[{"iso":"eng"}],"publication":"46th Annual ACM Symposium on Theory of Computing","publication_identifier":{"issn":["0737-8017"],"isbn":["978-145032710-7"]},"publication_status":"published","year":"2014"},{"abstract":[{"lang":"eng","text":"We study dynamic (1 + ∊)-approximation algorithms for the single-source shortest paths problem in an unweighted undirected n-node m-edge graph under edge deletions. The fastest algorithm for this problem is an algorithm with O(n2+o(1)) total update time and constant query time by Bernstein and Roditty (SODA 2011). In this paper, we improve the total update time to O(n1.8+o(1) + m1+o(1)) while keeping the query time constant. This running time is essentially tight when m = Ω(n1.8) since we need Ω(m) time even in the static setting. For smaller values of m, the running time of our algorithm is subquadratic, and is the first that breaks through the quadratic time barrier.\r\n\r\nIn obtaining this result, we develop a fast algorithm for what we call center cover data structure. We also make non-trivial extensions to our previous techniques called lazy-update and monotone Even-Shiloach trees (ICALP 2013 and FOCS 2013). As by-products of our new techniques, we obtain two new results for the decremental all-pairs shortest-paths problem. Our first result is the first approximation algorithm whose total update time is faster than Õ(mn) for all values of m. Our second result is a new trade-off between the total update time and the additive approximation guarantee."}],"oa_version":"Published Version","scopus_import":"1","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics","main_file_link":[{"url":"https://doi.org/10.1137/1.9781611973402.79","open_access":"1"}],"oa":1,"month":"01","publication_identifier":{"isbn":["978-1-61197-338-9"],"eisbn":["978-1-61197-340-2"]},"year":"2014","publication_status":"published","day":"01","publication":"25th Annual ACM-SIAM Symposium on Discrete Algorithms","language":[{"iso":"eng"}],"page":"1053-1072","date_published":"2014-01-01T00:00:00Z","doi":"10.1137/1.9781611973402.79","date_created":"2022-08-16T12:58:31Z","_id":"11876","type":"conference","conference":{"name":"SODA: Symposium on Discrete Algorithms","location":"Portland, OR, United States","end_date":"2014-01-07","start_date":"2014-01-05"},"status":"public","date_updated":"2023-02-17T11:58:42Z","citation":{"ista":"Henzinger MH, Krinninger S, Nanongkai D. 2014. A subquadratic-time algorithm for decremental single-source shortest paths. 25th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1053–1072.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “A Subquadratic-Time Algorithm for Decremental Single-Source Shortest Paths.” In 25th Annual ACM-SIAM Symposium on Discrete Algorithms, 1053–72. Society for Industrial and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973402.79.","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “A subquadratic-time algorithm for decremental single-source shortest paths,” in 25th Annual ACM-SIAM Symposium on Discrete Algorithms, Portland, OR, United States, 2014, pp. 1053–1072.","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 25th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 1053–1072.","apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). A subquadratic-time algorithm for decremental single-source shortest paths. In 25th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1053–1072). Portland, OR, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973402.79","ama":"Henzinger MH, Krinninger S, Nanongkai D. A subquadratic-time algorithm for decremental single-source shortest paths. In: 25th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2014:1053-1072. doi:10.1137/1.9781611973402.79","mla":"Henzinger, Monika H., et al. “A Subquadratic-Time Algorithm for Decremental Single-Source Shortest Paths.” 25th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 1053–72, doi:10.1137/1.9781611973402.79."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"full_name":"Krinninger, Sebastian","last_name":"Krinninger","first_name":"Sebastian"},{"first_name":"Danupon","full_name":"Nanongkai, Danupon","last_name":"Nanongkai"}],"article_processing_charge":"No","title":"A subquadratic-time algorithm for decremental single-source shortest paths"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"S. Bhattacharya, M.H. Henzinger, G.F. Italiano, in:, 26th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 785–804.","ieee":"S. Bhattacharya, M. H. Henzinger, and G. F. Italiano, “Deterministic fully dynamic data structures for vertex cover and matching,” in 26th Annual ACM-SIAM Symposium on Discrete Algorithms, San Diego, CA, United States, 2014, pp. 785–804.","ama":"Bhattacharya S, Henzinger MH, Italiano GF. Deterministic fully dynamic data structures for vertex cover and matching. In: 26th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2014:785-804. doi:10.1137/1.9781611973730.54","apa":"Bhattacharya, S., Henzinger, M. H., & Italiano, G. F. (2014). Deterministic fully dynamic data structures for vertex cover and matching. In 26th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 785–804). San Diego, CA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973730.54","mla":"Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” 26th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 785–804, doi:10.1137/1.9781611973730.54.","ista":"Bhattacharya S, Henzinger MH, Italiano GF. 2014. Deterministic fully dynamic data structures for vertex cover and matching. 26th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 785–804.","chicago":"Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe F. Italiano. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” In 26th Annual ACM-SIAM Symposium on Discrete Algorithms, 785–804. Society for Industrial and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973730.54."},"title":"Deterministic fully dynamic data structures for vertex cover and matching","author":[{"full_name":"Bhattacharya, Sayan","last_name":"Bhattacharya","first_name":"Sayan"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger"},{"first_name":"Giuseppe F.","last_name":"Italiano","full_name":"Italiano, Giuseppe F."}],"external_id":{"arxiv":["1412.1318"]},"article_processing_charge":"No","publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","oa":1,"day":"01","publication":"26th Annual ACM-SIAM Symposium on Discrete Algorithms","year":"2014","doi":"10.1137/1.9781611973730.54","date_published":"2014-01-01T00:00:00Z","date_created":"2022-08-16T12:36:42Z","page":"785-804","_id":"11875","status":"public","type":"conference","conference":{"start_date":"2015-01-04","location":"San Diego, CA, United States","end_date":"2015-01-06","name":"SODA: Symposium on Discrete Algorithms"},"extern":"1","date_updated":"2023-02-21T16:32:06Z","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We present the first deterministic data structures for maintaining approximate minimum vertex cover and maximum matching in a fully dynamic graph in time per update. In particular, for minimum vertex cover we provide deterministic data structures for maintaining a (2 + ε) approximation in O(log n/ε2) amortized time per update. For maximum matching, we show how to maintain a (3 + e) approximation in O(m1/3/ε2) amortized time per update, and a (4 + ε) approximation in O(m1/3/ε2) worst-case time per update. Our data structure for fully dynamic minimum vertex cover is essentially near-optimal and settles an open problem by Onak and Rubinfeld [13]."}],"month":"01","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1412.1318"}],"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["978-1-61197-373-0"],"isbn":["978-1-61197-374-7"]},"publication_status":"published","related_material":{"record":[{"relation":"later_version","status":"public","id":"11890"}]}},{"acknowledgement":"This work was supported by the NSF through DMR-1309611. Access to the shared experimental facilities provided by the NSF-supported Chicago MRSEC (DMR-0820054) is gratefully acknowledged. S. L. F. and J. L. P. acknowledge funding from UIC NSF Grants No. 0850830 and No. 0602308. S. R. W. acknowledges support from a University of Chicago Millikan Fellowship and from Mrs. Joan Winstein through the Winstein Prize for Instrumentation.","publisher":"American Physical Society","quality_controlled":"1","oa":1,"day":"30","publication":"APS Physics, Physical Review Letters","year":"2014","date_published":"2014-05-30T00:00:00Z","doi":"10.1103/PhysRevLett.112.218001","date_created":"2018-12-11T11:44:44Z","article_number":"218001","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Waitukaitis SR, Lee V, Pierson J, Forman S, Jaeger H. 2014. Size-dependent same-material tribocharging in insulating grains. APS Physics, Physical Review Letters. 112(21), 218001.","chicago":"Waitukaitis, Scott R, Victor Lee, James Pierson, Steven Forman, and Heinrich Jaeger. “Size-Dependent Same-Material Tribocharging in Insulating Grains.” APS Physics, Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.112.218001.","apa":"Waitukaitis, S. R., Lee, V., Pierson, J., Forman, S., & Jaeger, H. (2014). Size-dependent same-material tribocharging in insulating grains. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.112.218001","ama":"Waitukaitis SR, Lee V, Pierson J, Forman S, Jaeger H. Size-dependent same-material tribocharging in insulating grains. APS Physics, Physical Review Letters. 2014;112(21). doi:10.1103/PhysRevLett.112.218001","ieee":"S. R. Waitukaitis, V. Lee, J. Pierson, S. Forman, and H. Jaeger, “Size-dependent same-material tribocharging in insulating grains,” APS Physics, Physical Review Letters, vol. 112, no. 21. American Physical Society, 2014.","short":"S.R. Waitukaitis, V. Lee, J. Pierson, S. Forman, H. Jaeger, APS Physics, Physical Review Letters 112 (2014).","mla":"Waitukaitis, Scott R., et al. “Size-Dependent Same-Material Tribocharging in Insulating Grains.” APS Physics, Physical Review Letters, vol. 112, no. 21, 218001, American Physical Society, 2014, doi:10.1103/PhysRevLett.112.218001."},"title":"Size-dependent same-material tribocharging in insulating grains","publist_id":"7935","author":[{"last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R"},{"last_name":"Lee","full_name":"Lee, Victor","first_name":"Victor"},{"full_name":"Pierson, James","last_name":"Pierson","first_name":"James"},{"full_name":"Forman, Steven","last_name":"Forman","first_name":"Steven"},{"full_name":"Jaeger, Heinrich","last_name":"Jaeger","first_name":"Heinrich"}],"external_id":{"arxiv":["1309.2578"]},"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Observations of flowing granular matter have suggested that same-material tribocharging depends on particle size, typically rendering large grains positive and small ones negative. Models assuming the transfer of trapped electrons can account for this trend, but have not been validated. Tracking individual grains in an electric field, we show quantitatively that charge is transferred based on size between materially identical grains. However, the surface density of trapped electrons, measured independently by thermoluminescence techniques, is orders of magnitude too small to account for the scale of charge transferred. This reveals that trapped electrons are not a necessary ingredient for same-material tribocharging."}],"month":"05","intvolume":" 112","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.2578"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"21","volume":112,"_id":"119","status":"public","type":"journal_article","extern":"1","date_updated":"2021-01-12T06:48:58Z"},{"publisher":"Elsevier","quality_controlled":"1","oa":1,"doi":"10.1016/j.devcel.2014.04.025","date_published":"2014-06-23T00:00:00Z","date_created":"2022-08-25T08:42:42Z","page":"P729-739","day":"23","publication":"Developmental Cell","year":"2014","title":"Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids","author":[{"last_name":"Hofbauer","full_name":"Hofbauer, Harald F.","first_name":"Harald F."},{"first_name":"Florian H.","last_name":"Schopf","full_name":"Schopf, Florian H."},{"first_name":"Hannes","last_name":"Schleifer","full_name":"Schleifer, Hannes"},{"last_name":"Knittelfelder","full_name":"Knittelfelder, Oskar L.","first_name":"Oskar L."},{"id":"93e5e5b2-0da6-11ed-8a41-af589a024726","first_name":"Bartholomäus","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus","last_name":"Pieber"},{"last_name":"Rechberger","full_name":"Rechberger, Gerald N.","first_name":"Gerald N."},{"first_name":"Heimo","full_name":"Wolinski, Heimo","last_name":"Wolinski"},{"full_name":"Gaspar, Maria L.","last_name":"Gaspar","first_name":"Maria L."},{"first_name":"C. Oliver","full_name":"Kappe, C. Oliver","last_name":"Kappe"},{"full_name":"Stadlmann, Johannes","last_name":"Stadlmann","first_name":"Johannes"},{"last_name":"Mechtler","full_name":"Mechtler, Karl","first_name":"Karl"},{"first_name":"Alexandra","full_name":"Zenz, Alexandra","last_name":"Zenz"},{"full_name":"Lohner, Karl","last_name":"Lohner","first_name":"Karl"},{"full_name":"Tehlivets, Oksana","last_name":"Tehlivets","first_name":"Oksana"},{"last_name":"Henry","full_name":"Henry, Susan A.","first_name":"Susan A."},{"full_name":"Kohlwein, Sepp D.","last_name":"Kohlwein","first_name":"Sepp D."}],"article_processing_charge":"No","external_id":{"pmid":["24960695"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Hofbauer HF, Schopf FH, Schleifer H, Knittelfelder OL, Pieber B, Rechberger GN, Wolinski H, Gaspar ML, Kappe CO, Stadlmann J, Mechtler K, Zenz A, Lohner K, Tehlivets O, Henry SA, Kohlwein SD. 2014. Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Developmental Cell. 29(6), P729-739.","chicago":"Hofbauer, Harald F., Florian H. Schopf, Hannes Schleifer, Oskar L. Knittelfelder, Bartholomäus Pieber, Gerald N. Rechberger, Heimo Wolinski, et al. “Regulation of Gene Expression through a Transcriptional Repressor That Senses Acyl-Chain Length in Membrane Phospholipids.” Developmental Cell. Elsevier, 2014. https://doi.org/10.1016/j.devcel.2014.04.025.","apa":"Hofbauer, H. F., Schopf, F. H., Schleifer, H., Knittelfelder, O. L., Pieber, B., Rechberger, G. N., … Kohlwein, S. D. (2014). Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2014.04.025","ama":"Hofbauer HF, Schopf FH, Schleifer H, et al. Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Developmental Cell. 2014;29(6):P729-739. doi:10.1016/j.devcel.2014.04.025","ieee":"H. F. Hofbauer et al., “Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids,” Developmental Cell, vol. 29, no. 6. Elsevier, pp. P729-739, 2014.","short":"H.F. Hofbauer, F.H. Schopf, H. Schleifer, O.L. Knittelfelder, B. Pieber, G.N. Rechberger, H. Wolinski, M.L. Gaspar, C.O. Kappe, J. Stadlmann, K. Mechtler, A. Zenz, K. Lohner, O. Tehlivets, S.A. Henry, S.D. Kohlwein, Developmental Cell 29 (2014) P729-739.","mla":"Hofbauer, Harald F., et al. “Regulation of Gene Expression through a Transcriptional Repressor That Senses Acyl-Chain Length in Membrane Phospholipids.” Developmental Cell, vol. 29, no. 6, Elsevier, 2014, pp. P729-739, doi:10.1016/j.devcel.2014.04.025."},"month":"06","intvolume":" 29","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2014.04.025"}],"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Membrane phospholipids typically contain fatty acids (FAs) of 16 and 18 carbon atoms. This particular chain length is evolutionarily highly conserved and presumably provides maximum stability and dynamic properties to biological membranes in response to nutritional or environmental cues. Here, we show that the relative proportion of C16 versus C18 FAs is regulated by the activity of acetyl-CoA carboxylase (Acc1), the first and rate-limiting enzyme of FA de novo synthesis. Acc1 activity is attenuated by AMPK/Snf1-dependent phosphorylation, which is required to maintain an appropriate acyl-chain length distribution. Moreover, we find that the transcriptional repressor Opi1 preferentially binds to C16 over C18 phosphatidic acid (PA) species: thus, C16-chain containing PA sequesters Opi1 more effectively to the ER, enabling AMPK/Snf1 control of PA acyl-chain length to determine the degree of derepression of Opi1 target genes. These findings reveal an unexpected regulatory link between the major energy-sensing kinase, membrane lipid composition, and transcription.","lang":"eng"}],"issue":"6","volume":29,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"11968","extern":"1","date_updated":"2023-02-21T10:09:45Z"}]