[{"month":"09","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-34059-8_20","conference":{"name":"Monterey Workshop 2012","location":"Oxford, UK","start_date":"2012-03-19","end_date":"2012-03-21"},"ec_funded":1,"publist_id":"3791","department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2012","acknowledgement":"ERC Advanced Grant QUAREM (Quantitative Reactive Modeling), FWF National Research Network RISE (Rigorous Systems Engineering)","volume":7539,"date_updated":"2021-01-12T07:39:56Z","date_created":"2018-12-11T12:00:28Z","author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":1,"day":"16","page":"380 - 395","citation":{"short":"T.A. Henzinger, D. Nickovic, in:, Conference Proceedings Monterey Workshop 2012, Springer, 2012, pp. 380–395.","mla":"Henzinger, Thomas A., and Dejan Nickovic. “Independent Implementability of Viewpoints.” Conference Proceedings Monterey Workshop 2012, vol. 7539, Springer, 2012, pp. 380–95, doi:10.1007/978-3-642-34059-8_20.","chicago":"Henzinger, Thomas A, and Dejan Nickovic. “Independent Implementability of Viewpoints.” In Conference Proceedings Monterey Workshop 2012, 7539:380–95. Springer, 2012. https://doi.org/10.1007/978-3-642-34059-8_20.","ama":"Henzinger TA, Nickovic D. Independent implementability of viewpoints. In: Conference Proceedings Monterey Workshop 2012. Vol 7539. Springer; 2012:380-395. doi:10.1007/978-3-642-34059-8_20","ieee":"T. A. Henzinger and D. Nickovic, “Independent implementability of viewpoints,” in Conference proceedings Monterey Workshop 2012, Oxford, UK, 2012, vol. 7539, pp. 380–395.","apa":"Henzinger, T. A., & Nickovic, D. (2012). Independent implementability of viewpoints. In Conference proceedings Monterey Workshop 2012 (Vol. 7539, pp. 380–395). Oxford, UK: Springer. https://doi.org/10.1007/978-3-642-34059-8_20","ista":"Henzinger TA, Nickovic D. 2012. Independent implementability of viewpoints. Conference proceedings Monterey Workshop 2012. Monterey Workshop 2012, LNCS, vol. 7539, 380–395."},"publication":" Conference proceedings Monterey Workshop 2012","date_published":"2012-09-16T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Interface theories provide a formal framework for component-based development of software and hardware which supports the incremental design of systems and the independent implementability of components. These capabilities are ensured through mathematical properties of the parallel composition operator and the refinement relation for components. More recently, a conjunction operation was added to interface theories in order to provide support for handling multiple viewpoints, requirements engineering, and component reuse. Unfortunately, the conjunction operator does not allow independent implementability in general. In this paper, we study conditions that need to be imposed on interface models in order to enforce independent implementability with respect to conjunction. We focus on multiple viewpoint specifications and propose a new compatibility criterion between two interfaces, which we call orthogonality. We show that orthogonal interfaces can be refined separately, while preserving both orthogonality and composability with other interfaces. We illustrate the independent implementability of different viewpoints with a FIFO buffer example."}],"intvolume":" 7539","title":"Independent implementability of viewpoints","status":"public","_id":"2942","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None"},{"date_created":"2018-12-11T12:00:28Z","date_updated":"2021-01-12T07:39:56Z","volume":86,"author":[{"full_name":"Hadizadeh Yazdi, Nastaran","first_name":"Nastaran","last_name":"Hadizadeh Yazdi"},{"full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johnson, Reid","first_name":"Reid","last_name":"Johnson"},{"first_name":"John","last_name":"Marko","full_name":"Marko, John"}],"publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Wiley-Blackwell","year":"2012","acknowledgement":"We thank Professor Philippe Cluzel and Mr Lance Min for providing advice and materials. Jeannette Chau provided technical support. Work at NU was supported by NSF Grants DMR-0715099, MCB-1022117, DMR-1206868, DMR-0520513 and DMR-1121262 (NU-MRSEC), by NIH-NCI Grant U54CA143869-01 (NU-PS-OC) and by the Chicago Biomedical Consortium with support from the Searle Funds at the Chicago Community Trust. Work at UCLA was supported by NIH Grant GM038509.","publist_id":"3790","language":[{"iso":"eng"}],"doi":"10.1111/mmi.12071","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://europepmc.org/articles/pmc3524407"}],"month":"11","oa_version":"Submitted Version","title":"Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions","status":"public","intvolume":" 86","_id":"2943","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We examine whether the Escherichia coli chromosome is folded into a self-adherent nucleoprotein complex, or alternately is a confined but otherwise unconstrained self-avoiding polymer. We address this through in vivo visualization, using an inducible GFP fusion to the nucleoid-associated protein Fis to non-specifically decorate the entire chromosome. For a range of different growth conditions, the chromosome is a compact structure that does not fill the volume of the cell, and which moves from the new pole to the cell centre. During rapid growth, chromosome segregation occurs well before cell division, with daughter chromosomes coupled by a thin inter-daughter filament before complete segregation, whereas during slow growth chromosomes stay adjacent until cell division occurs. Image correlation analysis indicates that sub-nucleoid structure is stable on a 1min timescale, comparable to the timescale for redistribution time measured for GFP-Fis after photobleaching. Optical deconvolution and writhe calculation analysis indicate that the nucleoid has a large-scale coiled organization rather than being an amorphous mass. Our observations are consistent with the chromosome having a self-adherent filament organization.","lang":"eng"}],"issue":"6","type":"journal_article","date_published":"2012-11-09T00:00:00Z","page":"1318 - 1333","publication":"Molecular Microbiology","citation":{"ista":"Hadizadeh Yazdi N, Guet CC, Johnson R, Marko J. 2012. Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Molecular Microbiology. 86(6), 1318–1333.","ieee":"N. Hadizadeh Yazdi, C. C. Guet, R. Johnson, and J. Marko, “Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions,” Molecular Microbiology, vol. 86, no. 6. Wiley-Blackwell, pp. 1318–1333, 2012.","apa":"Hadizadeh Yazdi, N., Guet, C. C., Johnson, R., & Marko, J. (2012). Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Molecular Microbiology. Wiley-Blackwell. https://doi.org/10.1111/mmi.12071","ama":"Hadizadeh Yazdi N, Guet CC, Johnson R, Marko J. Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Molecular Microbiology. 2012;86(6):1318-1333. doi:10.1111/mmi.12071","chicago":"Hadizadeh Yazdi, Nastaran, Calin C Guet, Reid Johnson, and John Marko. “Variation of the Folding and Dynamics of the Escherichia Coli Chromosome with Growth Conditions.” Molecular Microbiology. Wiley-Blackwell, 2012. https://doi.org/10.1111/mmi.12071.","mla":"Hadizadeh Yazdi, Nastaran, et al. “Variation of the Folding and Dynamics of the Escherichia Coli Chromosome with Growth Conditions.” Molecular Microbiology, vol. 86, no. 6, Wiley-Blackwell, 2012, pp. 1318–33, doi:10.1111/mmi.12071.","short":"N. Hadizadeh Yazdi, C.C. Guet, R. Johnson, J. Marko, Molecular Microbiology 86 (2012) 1318–1333."},"day":"09","scopus_import":1},{"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2012-11-01T00:00:00Z","citation":{"ieee":"N. Dolbilin, H. Edelsbrunner, and O. Musin, “On the optimality of functionals over triangulations of Delaunay sets,” Russian Mathematical Surveys, vol. 67, no. 4. IOP Publishing, pp. 781–783, 2012.","apa":"Dolbilin, N., Edelsbrunner, H., & Musin, O. (2012). On the optimality of functionals over triangulations of Delaunay sets. Russian Mathematical Surveys. IOP Publishing. https://doi.org/10.1070/RM2012v067n04ABEH004807","ista":"Dolbilin N, Edelsbrunner H, Musin O. 2012. On the optimality of functionals over triangulations of Delaunay sets. Russian Mathematical Surveys. 67(4), 781–783.","ama":"Dolbilin N, Edelsbrunner H, Musin O. On the optimality of functionals over triangulations of Delaunay sets. Russian Mathematical Surveys. 2012;67(4):781-783. doi:10.1070/RM2012v067n04ABEH004807","chicago":"Dolbilin, Nikolai, Herbert Edelsbrunner, and Oleg Musin. “On the Optimality of Functionals over Triangulations of Delaunay Sets.” Russian Mathematical Surveys. IOP Publishing, 2012. https://doi.org/10.1070/RM2012v067n04ABEH004807.","short":"N. Dolbilin, H. Edelsbrunner, O. Musin, Russian Mathematical Surveys 67 (2012) 781–783.","mla":"Dolbilin, Nikolai, et al. “On the Optimality of Functionals over Triangulations of Delaunay Sets.” Russian Mathematical Surveys, vol. 67, no. 4, IOP Publishing, 2012, pp. 781–83, doi:10.1070/RM2012v067n04ABEH004807."},"publication":"Russian Mathematical Surveys","page":"781 - 783","issue":"4","type":"journal_article","pubrep_id":"132","oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":253816,"creator":"system","file_name":"IST-2013-132-v1+1_2012-J-04-Functional-E.pdf","access_level":"open_access","date_created":"2018-12-12T10:16:49Z","date_updated":"2020-07-14T12:45:55Z","checksum":"389a5ae53d6347de36c3468034f2821d","relation":"main_file","file_id":"5239"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2941","intvolume":" 67","status":"public","title":"On the optimality of functionals over triangulations of Delaunay sets","ddc":["510"],"month":"11","doi":"10.1070/RM2012v067n04ABEH004807","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","publist_id":"3792","file_date_updated":"2020-07-14T12:45:55Z","author":[{"last_name":"Dolbilin","first_name":"Nikolai","full_name":"Dolbilin, Nikolai"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"full_name":"Musin, Oleg","first_name":"Oleg","last_name":"Musin"}],"volume":67,"date_created":"2018-12-11T12:00:28Z","date_updated":"2021-01-12T07:39:55Z","year":"2012","publisher":"IOP Publishing","department":[{"_id":"HeEd"}],"publication_status":"published"},{"publication":"Nucleic Acids Research","citation":{"ama":"Dueck A, Ziegler C, Eichner A, Berezikov E, Meister G. MicroRNAs associated with the different human Argonaute proteins. Nucleic Acids Research. 2012;40(19):9850-9862. doi:10.1093/nar/gks705","ieee":"A. Dueck, C. Ziegler, A. Eichner, E. Berezikov, and G. Meister, “MicroRNAs associated with the different human Argonaute proteins,” Nucleic Acids Research, vol. 40, no. 19. Oxford University Press, pp. 9850–9862, 2012.","apa":"Dueck, A., Ziegler, C., Eichner, A., Berezikov, E., & Meister, G. (2012). MicroRNAs associated with the different human Argonaute proteins. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gks705","ista":"Dueck A, Ziegler C, Eichner A, Berezikov E, Meister G. 2012. MicroRNAs associated with the different human Argonaute proteins. Nucleic Acids Research. 40(19), 9850–9862.","short":"A. Dueck, C. Ziegler, A. Eichner, E. Berezikov, G. Meister, Nucleic Acids Research 40 (2012) 9850–9862.","mla":"Dueck, Anne, et al. “MicroRNAs Associated with the Different Human Argonaute Proteins.” Nucleic Acids Research, vol. 40, no. 19, Oxford University Press, 2012, pp. 9850–62, doi:10.1093/nar/gks705.","chicago":"Dueck, Anne, Christian Ziegler, Alexander Eichner, Eugène Berezikov, and Gunter Meister. “MicroRNAs Associated with the Different Human Argonaute Proteins.” Nucleic Acids Research. Oxford University Press, 2012. https://doi.org/10.1093/nar/gks705."},"page":"9850 - 9862","date_published":"2012-10-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","_id":"2946","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"MicroRNAs associated with the different human Argonaute proteins","ddc":["570"],"status":"public","intvolume":" 40","pubrep_id":"383","oa_version":"Published Version","file":[{"checksum":"1bb8d1ff894014b481657a21083c941c","date_updated":"2020-07-14T12:45:55Z","date_created":"2018-12-12T10:13:12Z","file_id":"4993","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":8126936,"access_level":"open_access","file_name":"IST-2015-383-v1+1_Nucl._Acids_Res.-2012-Dueck-9850-62.pdf"}],"type":"journal_article","abstract":[{"text":"MicroRNAs (miRNAs) are small noncoding RNAs that function in literally all cellular processes. miRNAs interact with Argonaute (Ago) proteins and guide them to specific target sites located in the 3′-untranslated region (3′-UTR) of target mRNAs leading to translational repression and deadenylation-induced mRNA degradation. Most miRNAs are processed from hairpin-structured precursors by the consecutive action of the RNase III enzymes Drosha and Dicer. However, processing of miR-451 is Dicer independent and cleavage is mediated by the endonuclease Ago2. Here we have characterized miR-451 sequence and structure requirements for processing as well as sorting of miRNAs into different Ago proteins. Pre-miR-451 appears to be optimized for Ago2 cleavage and changes result in reduced processing. In addition, we show that the mature miR-451 only associates with Ago2 suggesting that mature miRNAs are not exchanged between different members of the Ago protein family. Based on cloning and deep sequencing of endogenous miRNAs associated with Ago1-3, we do not find evidence for miRNA sorting in human cells. However, Ago identity appears to influence the length of some miRNAs, while others remain unaffected.","lang":"eng"}],"issue":"19","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","doi":"10.1093/nar/gks705","language":[{"iso":"eng"}],"month":"10","year":"2012","acknowledgement":"Deutsche Forschungsgemeinschaft (DFG) (SFB 960 and FOR855); European Research Council (ERC grant ‘sRNAs’); European Union (FP7 project ‘ONCOMIRs’); German Bundesministerium für Bildung und Forschung (BMBF, NGFN+, FKZ PIM-01GS0804-5); Bavarian Genome Research Network (BayGene to G.M.); The Netherlands Organization for Scientific Research (NWO, VIDI grant to E.B.). Funding for open access charge: DFG via the open access publishing program. \r\n\r\nWe thank Sigrun Ammon and Corinna Friederich for technical assistance and Sebastian Petri and Daniel Schraivogel for helpful discussions.","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Oxford University Press","author":[{"full_name":"Dueck, Anne","last_name":"Dueck","first_name":"Anne"},{"last_name":"Ziegler","first_name":"Christian","full_name":"Ziegler, Christian"},{"id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","last_name":"Eichner","first_name":"Alexander","full_name":"Eichner, Alexander"},{"last_name":"Berezikov","first_name":"Eugène","full_name":"Berezikov, Eugène"},{"full_name":"Meister, Gunter","last_name":"Meister","first_name":"Gunter"}],"date_created":"2018-12-11T12:00:29Z","date_updated":"2021-01-12T07:39:57Z","volume":40,"file_date_updated":"2020-07-14T12:45:55Z","publist_id":"3786"},{"quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1202.4140"}],"language":[{"iso":"eng"}],"conference":{"name":" ATVA: Automated Technology for Verification and Analysis","start_date":"2012-10-03","location":"Thiruvananthapuram, India","end_date":"2012-10-06"},"doi":"10.1007/978-3-642-33386-6_30","month":"06","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer","year":"2012","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","date_updated":"2021-01-12T07:39:58Z","date_created":"2018-12-11T12:00:29Z","volume":7561,"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"},{"first_name":"Ritankar","last_name":"Majumdar","full_name":"Majumdar, Ritankar"}],"ec_funded":1,"publist_id":"3785","page":"385 - 399","citation":{"ieee":"K. Chatterjee, M. Chmelik, and R. Majumdar, “Equivalence of games with probabilistic uncertainty and partial observation games,” presented at the ATVA: Automated Technology for Verification and Analysis, Thiruvananthapuram, India, 2012, vol. 7561, pp. 385–399.","apa":"Chatterjee, K., Chmelik, M., & Majumdar, R. (2012). Equivalence of games with probabilistic uncertainty and partial observation games (Vol. 7561, pp. 385–399). Presented at the ATVA: Automated Technology for Verification and Analysis, Thiruvananthapuram, India: Springer. https://doi.org/10.1007/978-3-642-33386-6_30","ista":"Chatterjee K, Chmelik M, Majumdar R. 2012. Equivalence of games with probabilistic uncertainty and partial observation games. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 7561, 385–399.","ama":"Chatterjee K, Chmelik M, Majumdar R. Equivalence of games with probabilistic uncertainty and partial observation games. In: Vol 7561. Springer; 2012:385-399. doi:10.1007/978-3-642-33386-6_30","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Ritankar Majumdar. “Equivalence of Games with Probabilistic Uncertainty and Partial Observation Games,” 7561:385–99. Springer, 2012. https://doi.org/10.1007/978-3-642-33386-6_30.","short":"K. Chatterjee, M. Chmelik, R. Majumdar, in:, Springer, 2012, pp. 385–399.","mla":"Chatterjee, Krishnendu, et al. Equivalence of Games with Probabilistic Uncertainty and Partial Observation Games. Vol. 7561, Springer, 2012, pp. 385–99, doi:10.1007/978-3-642-33386-6_30."},"date_published":"2012-06-01T00:00:00Z","scopus_import":1,"day":"01","title":"Equivalence of games with probabilistic uncertainty and partial observation games","status":"public","intvolume":" 7561","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2947","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"We introduce games with probabilistic uncertainty, a model for controller synthesis in which the controller observes the state through imprecise sensors that provide correct information about the current state with a fixed probability. That is, in each step, the sensors return an observed state, and given the observed state, there is a probability distribution (due to the estimation error) over the actual current state. The controller must base its decision on the observed state (rather than the actual current state, which it does not know). On the other hand, we assume that the environment can perfectly observe the current state. We show that controller synthesis for qualitative ω-regular objectives in our model can be reduced in polynomial time to standard partial-observation stochastic games, and vice-versa. As a consequence we establish the precise decidability frontier for the new class of games, and establish optimal complexity results for all the decidable problems.","lang":"eng"}]},{"page":"762 - 773","quality_controlled":"1","citation":{"mla":"Girard, Jean, et al. “HEVs, Lymphatics and Homeostatic Immune Cell Trafficking in Lymph Nodes.” Nature Reviews Immunology, vol. 12, no. 11, Nature Publishing Group, 2012, pp. 762–73, doi:10.1038/nri3298.","short":"J. Girard, C. Moussion, R. Förster, Nature Reviews Immunology 12 (2012) 762–773.","chicago":"Girard, Jean, Christine Moussion, and Reinhold Förster. “HEVs, Lymphatics and Homeostatic Immune Cell Trafficking in Lymph Nodes.” Nature Reviews Immunology. Nature Publishing Group, 2012. https://doi.org/10.1038/nri3298.","ama":"Girard J, Moussion C, Förster R. HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes. Nature Reviews Immunology. 2012;12(11):762-773. doi:10.1038/nri3298","ista":"Girard J, Moussion C, Förster R. 2012. HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes. Nature Reviews Immunology. 12(11), 762–773.","ieee":"J. Girard, C. Moussion, and R. Förster, “HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes,” Nature Reviews Immunology, vol. 12, no. 11. Nature Publishing Group, pp. 762–773, 2012.","apa":"Girard, J., Moussion, C., & Förster, R. (2012). HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes. Nature Reviews Immunology. Nature Publishing Group. https://doi.org/10.1038/nri3298"},"publication":"Nature Reviews Immunology","language":[{"iso":"eng"}],"doi":"10.1038/nri3298","date_published":"2012-11-01T00:00:00Z","scopus_import":1,"month":"11","day":"01","department":[{"_id":"MiSi"}],"publisher":"Nature Publishing Group","intvolume":" 12","title":"HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes","status":"public","publication_status":"published","_id":"2945","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank M. Sixt and A. Peixoto for helpful comments on the manuscript. Work in the laboratory of J.-P.G. is supported by grants from Fondation ARC pour la Recherche sur le Cancer, Agence Nationale de la Recherche (ANR), Institut National du Cancer (INCA), Fondation RITC and Région Midi-Pyrénées. Research by R.F. is supported by Deutsche Forschungsgemeinschaft (DFG) grants SFB621-A1, SFB738-B5, SFB587-B3, SFB900-B1 and KFO 250-FO 334/2-1. We regret that, owing to space limitations, we could not always quote the work of colleagues who have contributed to the field.","volume":12,"oa_version":"None","date_created":"2018-12-11T12:00:29Z","date_updated":"2021-01-12T07:39:57Z","author":[{"full_name":"Girard, Jean","first_name":"Jean","last_name":"Girard"},{"full_name":"Moussion, Christine","id":"3356F664-F248-11E8-B48F-1D18A9856A87","last_name":"Moussion","first_name":"Christine"},{"last_name":"Förster","first_name":"Reinhold","full_name":"Förster, Reinhold"}],"type":"journal_article","publist_id":"3787","issue":"11","abstract":[{"text":"In search of foreign antigens, lymphocytes recirculate from the blood, through lymph nodes, into lymphatics and back to the blood. Dendritic cells also migrate to lymph nodes for optimal interaction with lymphocytes. This continuous trafficking of immune cells into and out of lymph nodes is essential for immune surveillance of foreign invaders. In this article, we review our current understanding of the functions of high endothelial venules (HEVs), stroma and lymphatics in the entry, positioning and exit of immune cells in lymph nodes during homeostasis, and we highlight the unexpected role of dendritic cells in the control of lymphocyte homing through HEVs.","lang":"eng"}]},{"publication":"Nature Neuroscience","main_file_link":[{"url":"http://www.mrcbndu.ox.ac.uk/publications/medial-entorhinal-cortex-keeps"}],"citation":{"mla":"Dupret, David, and Jozsef L. Csicsvari. “The Medial Entorhinal Cortex Keeps Up.” Nature Neuroscience, vol. 15, no. 11, Nature Publishing Group, 2012, pp. 1471–72, doi:10.1038/nn.3245.","short":"D. Dupret, J.L. Csicsvari, Nature Neuroscience 15 (2012) 1471–1472.","chicago":"Dupret, David, and Jozsef L Csicsvari. “The Medial Entorhinal Cortex Keeps Up.” Nature Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3245.","ama":"Dupret D, Csicsvari JL. The medial entorhinal cortex keeps Up. Nature Neuroscience. 2012;15(11):1471-1472. doi:10.1038/nn.3245","ista":"Dupret D, Csicsvari JL. 2012. The medial entorhinal cortex keeps Up. Nature Neuroscience. 15(11), 1471–1472.","ieee":"D. Dupret and J. L. Csicsvari, “The medial entorhinal cortex keeps Up,” Nature Neuroscience, vol. 15, no. 11. Nature Publishing Group, pp. 1471–1472, 2012.","apa":"Dupret, D., & Csicsvari, J. L. (2012). The medial entorhinal cortex keeps Up. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3245"},"quality_controlled":"1","page":"1471 - 1472","date_published":"2012-11-01T00:00:00Z","doi":"10.1038/nn.3245","language":[{"iso":"eng"}],"scopus_import":1,"month":"11","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2949","year":"2012","publication_status":"published","title":"The medial entorhinal cortex keeps Up","status":"public","publisher":"Nature Publishing Group","intvolume":" 15","department":[{"_id":"JoCs"}],"author":[{"full_name":"Dupret, David","last_name":"Dupret","first_name":"David"},{"last_name":"Csicsvari","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L"}],"date_updated":"2021-01-12T07:39:59Z","date_created":"2018-12-11T12:00:30Z","volume":15,"oa_version":"None","type":"journal_article","issue":"11","publist_id":"3782"},{"month":"10","doi":"10.1016/j.bpj.2012.08.039","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3471482/","open_access":"1"}],"oa":1,"external_id":{"pmid":["23062335"]},"project":[{"name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen","grant_number":"SFB-TR3-TP10B","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publist_id":"3774","author":[{"id":"36963E98-F248-11E8-B48F-1D18A9856A87","last_name":"Pernia-Andrade","first_name":"Alejandro","full_name":"Pernia-Andrade, Alejandro"},{"full_name":"Goswami, Sarit","id":"3A578F32-F248-11E8-B48F-1D18A9856A87","first_name":"Sarit","last_name":"Goswami"},{"full_name":"Stickler, Yvonne","first_name":"Yvonne","last_name":"Stickler","id":"63B76600-E9CC-11E9-9B5F-82450873F7A1"},{"last_name":"Fröbe","first_name":"Ulrich","full_name":"Fröbe, Ulrich"},{"last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"}],"volume":103,"date_created":"2018-12-11T12:00:32Z","date_updated":"2021-01-12T07:40:01Z","pmid":1,"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (TR3/B10) and a European Research Council Advanced grant to P.J.\r\nWe thank H. Hu, S. J. Guzman, and C. Schmidt-Hieber for critically reading the manuscript, I. Koeva and F. Marr for technical support, and E. Kramberger for editorial assistance.\r\n","year":"2012","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"publisher":"Biophysical","publication_status":"published","day":"03","scopus_import":1,"date_published":"2012-10-03T00:00:00Z","citation":{"ama":"Pernia-Andrade A, Goswami S, Stickler Y, Fröbe U, Schlögl A, Jonas PM. A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo. Biophysical Journal. 2012;103(7):1429-1439. doi:10.1016/j.bpj.2012.08.039","ista":"Pernia-Andrade A, Goswami S, Stickler Y, Fröbe U, Schlögl A, Jonas PM. 2012. A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo. Biophysical Journal. 103(7), 1429–1439.","apa":"Pernia-Andrade, A., Goswami, S., Stickler, Y., Fröbe, U., Schlögl, A., & Jonas, P. M. (2012). A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo. Biophysical Journal. Biophysical. https://doi.org/10.1016/j.bpj.2012.08.039","ieee":"A. Pernia-Andrade, S. Goswami, Y. Stickler, U. Fröbe, A. Schlögl, and P. M. Jonas, “A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo,” Biophysical Journal, vol. 103, no. 7. Biophysical, pp. 1429–1439, 2012.","mla":"Pernia-Andrade, Alejandro, et al. “A Deconvolution Based Method with High Sensitivity and Temporal Resolution for Detection of Spontaneous Synaptic Currents in Vitro and in Vivo.” Biophysical Journal, vol. 103, no. 7, Biophysical, 2012, pp. 1429–39, doi:10.1016/j.bpj.2012.08.039.","short":"A. Pernia-Andrade, S. Goswami, Y. Stickler, U. Fröbe, A. Schlögl, P.M. Jonas, Biophysical Journal 103 (2012) 1429–1439.","chicago":"Pernia-Andrade, Alejandro, Sarit Goswami, Yvonne Stickler, Ulrich Fröbe, Alois Schlögl, and Peter M Jonas. “A Deconvolution Based Method with High Sensitivity and Temporal Resolution for Detection of Spontaneous Synaptic Currents in Vitro and in Vivo.” Biophysical Journal. Biophysical, 2012. https://doi.org/10.1016/j.bpj.2012.08.039."},"publication":"Biophysical Journal","page":"1429 - 1439","issue":"7","abstract":[{"text":"Spontaneous postsynaptic currents (PSCs) provide key information about the mechanisms of synaptic transmission and the activity modes of neuronal networks. However, detecting spontaneous PSCs in vitro and in vivo has been challenging, because of the small amplitude, the variable kinetics, and the undefined time of generation of these events. Here, we describe a, to our knowledge, new method for detecting spontaneous synaptic events by deconvolution, using a template that approximates the average time course of spontaneous PSCs. A recorded PSC trace is deconvolved from the template, resulting in a series of delta-like functions. The maxima of these delta-like events are reliably detected, revealing the precise onset times of the spontaneous PSCs. Among all detection methods, the deconvolution-based method has a unique temporal resolution, allowing the detection of individual events in high-frequency bursts. Furthermore, the deconvolution-based method has a high amplitude resolution, because deconvolution can substantially increase the signal/noise ratio. When tested against previously published methods using experimental data, the deconvolution-based method was superior for spontaneous PSCs recorded in vivo. Using the high-resolution deconvolution-based detection algorithm, we show that the frequency of spontaneous excitatory postsynaptic currents in dentate gyrus granule cells is 4.5 times higher in vivo than in vitro.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2954","intvolume":" 103","title":"A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo","status":"public"},{"scopus_import":1,"day":"12","citation":{"chicago":"Behrndt, Martin, Guillaume Salbreux, Pedro Campinho, Robert Hauschild, Felix Oswald, Julia Roensch, Stephan Grill, and Carl-Philipp J Heisenberg. “Forces Driving Epithelial Spreading in Zebrafish Gastrulation.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224143.","mla":"Behrndt, Martin, et al. “Forces Driving Epithelial Spreading in Zebrafish Gastrulation.” Science, vol. 338, no. 6104, American Association for the Advancement of Science, 2012, pp. 257–60, doi:10.1126/science.1224143.","short":"M. Behrndt, G. Salbreux, P. Campinho, R. Hauschild, F. Oswald, J. Roensch, S. Grill, C.-P.J. Heisenberg, Science 338 (2012) 257–260.","ista":"Behrndt M, Salbreux G, Campinho P, Hauschild R, Oswald F, Roensch J, Grill S, Heisenberg C-PJ. 2012. Forces driving epithelial spreading in zebrafish gastrulation. Science. 338(6104), 257–260.","apa":"Behrndt, M., Salbreux, G., Campinho, P., Hauschild, R., Oswald, F., Roensch, J., … Heisenberg, C.-P. J. (2012). Forces driving epithelial spreading in zebrafish gastrulation. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1224143","ieee":"M. Behrndt et al., “Forces driving epithelial spreading in zebrafish gastrulation,” Science, vol. 338, no. 6104. American Association for the Advancement of Science, pp. 257–260, 2012.","ama":"Behrndt M, Salbreux G, Campinho P, et al. Forces driving epithelial spreading in zebrafish gastrulation. Science. 2012;338(6104):257-260. doi:10.1126/science.1224143"},"publication":"Science","page":"257 - 260","date_published":"2012-10-12T00:00:00Z","type":"journal_article","issue":"6104","abstract":[{"lang":"eng","text":"Contractile actomyosin rings drive various fundamental morphogenetic processes ranging from cytokinesis to wound healing. Actomyosin rings are generally thought to function by circumferential contraction. Here, we show that the spreading of the enveloping cell layer (EVL) over the yolk cell during zebrafish gastrulation is driven by a contractile actomyosin ring. In contrast to previous suggestions, we find that this ring functions not only by circumferential contraction but also by a flow-friction mechanism. This generates a pulling force through resistance against retrograde actomyosin flow. EVL spreading proceeds normally in situations where circumferential contraction is unproductive, indicating that the flow-friction mechanism is sufficient. Thus, actomyosin rings can function in epithelial morphogenesis through a combination of cable-constriction and flow-friction mechanisms."}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2950","intvolume":" 338","status":"public","title":"Forces driving epithelial spreading in zebrafish gastrulation","oa_version":"None","month":"10","project":[{"name":"Control of Epithelial Cell Layer Spreading in Zebrafish","call_identifier":"FWF","grant_number":"I 930-B20","_id":"252ABD0A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1126/science.1224143","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"publist_id":"3778","year":"2012","publisher":"American Association for the Advancement of Science","department":[{"_id":"CaHe"},{"_id":"Bio"}],"publication_status":"published","related_material":{"record":[{"id":"1403","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Behrndt","full_name":"Behrndt, Martin"},{"full_name":"Salbreux, Guillaume","last_name":"Salbreux","first_name":"Guillaume"},{"id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8526-5416","first_name":"Pedro","last_name":"Campinho","full_name":"Campinho, Pedro"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"full_name":"Oswald, Felix","first_name":"Felix","last_name":"Oswald"},{"full_name":"Roensch, Julia","id":"4220E59C-F248-11E8-B48F-1D18A9856A87","last_name":"Roensch","first_name":"Julia"},{"full_name":"Grill, Stephan","last_name":"Grill","first_name":"Stephan"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"volume":338,"date_updated":"2023-02-21T17:02:44Z","date_created":"2018-12-11T12:00:30Z"},{"department":[{"_id":"CaHe"}],"intvolume":" 338","publisher":"American Association for the Advancement of Science","status":"public","publication_status":"published","title":"Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells","_id":"2951","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2012","volume":338,"oa_version":"None","date_created":"2018-12-11T12:00:31Z","date_updated":"2021-01-12T07:40:00Z","author":[{"full_name":"Maître, Jean-Léon","orcid":"0000-0002-3688-1474","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","last_name":"Maître","first_name":"Jean-Léon"},{"full_name":"Berthoumieux, Hélène","first_name":"Hélène","last_name":"Berthoumieux"},{"full_name":"Krens, Gabriel","last_name":"Krens","first_name":"Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Salbreux, Guillaume","first_name":"Guillaume","last_name":"Salbreux"},{"full_name":"Julicher, Frank","first_name":"Frank","last_name":"Julicher"},{"full_name":"Paluch, Ewa","first_name":"Ewa","last_name":"Paluch"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"type":"journal_article","issue":"6104","publist_id":"3777","abstract":[{"text":"Differential cell adhesion and cortex tension are thought to drive cell sorting by controlling cell-cell contact formation. Here, we show that cell adhesion and cortex tension have different mechanical functions in controlling progenitor cell-cell contact formation and sorting during zebrafish gastrulation. Cortex tension controls cell-cell contact expansion by modulating interfacial tension at the contact. By contrast, adhesion has little direct function in contact expansion, but instead is needed to mechanically couple the cortices of adhering cells at their contacts, allowing cortex tension to control contact expansion. The coupling function of adhesion is mediated by E-cadherin and limited by the mechanical anchoring of E-cadherin to the cortex. Thus, cell adhesion provides the mechanical scaffold for cell cortex tension to drive cell sorting during gastrulation.","lang":"eng"}],"page":"253 - 256","quality_controlled":"1","citation":{"short":"J.-L. Maître, H. Berthoumieux, G. Krens, G. Salbreux, F. Julicher, E. Paluch, C.-P.J. Heisenberg, Science 338 (2012) 253–256.","mla":"Maître, Jean-Léon, et al. “Adhesion Functions in Cell Sorting by Mechanically Coupling the Cortices of Adhering Cells.” Science, vol. 338, no. 6104, American Association for the Advancement of Science, 2012, pp. 253–56, doi:10.1126/science.1225399.","chicago":"Maître, Jean-Léon, Hélène Berthoumieux, Gabriel Krens, Guillaume Salbreux, Frank Julicher, Ewa Paluch, and Carl-Philipp J Heisenberg. “Adhesion Functions in Cell Sorting by Mechanically Coupling the Cortices of Adhering Cells.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1225399.","ama":"Maître J-L, Berthoumieux H, Krens G, et al. Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells. Science. 2012;338(6104):253-256. doi:10.1126/science.1225399","ieee":"J.-L. Maître et al., “Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells,” Science, vol. 338, no. 6104. American Association for the Advancement of Science, pp. 253–256, 2012.","apa":"Maître, J.-L., Berthoumieux, H., Krens, G., Salbreux, G., Julicher, F., Paluch, E., & Heisenberg, C.-P. J. (2012). Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1225399","ista":"Maître J-L, Berthoumieux H, Krens G, Salbreux G, Julicher F, Paluch E, Heisenberg C-PJ. 2012. Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells. Science. 338(6104), 253–256."},"publication":"Science","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"doi":"10.1126/science.1225399","date_published":"2012-10-12T00:00:00Z","scopus_import":1,"day":"12","month":"10"}]