[{"date_published":"2012-03-22T00:00:00Z","publication_status":"published","day":"22","publisher":"BioMed Central","date_created":"2018-12-11T11:55:33Z","intvolume":"        13","publist_id":"4965","extern":1,"author":[{"full_name":"Zhou, Qi","last_name":"Zhou","first_name":"Qi"},{"full_name":"Zhu, Hongmei","last_name":"Zhu","first_name":"Hongmei"},{"last_name":"Huang","first_name":"Quanfei","full_name":"Huang, Quanfei"},{"first_name":"Li","last_name":"Zhao","full_name":"Zhao, Li"},{"full_name":"Zhang, Guo J","first_name":"Guo","last_name":"Zhang"},{"full_name":"Roy, Scott W","first_name":"Scott","last_name":"Roy"},{"first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Beatriz Vicoso"},{"last_name":"Xuan","first_name":"Zhaolin","full_name":"Xuan, Zhaolin"},{"full_name":"Ruan, Jue","last_name":"Ruan","first_name":"Jue"},{"first_name":"Yue","last_name":"Zhang","full_name":"Zhang, Yue"},{"last_name":"Zhao","first_name":"Ruoping","full_name":"Zhao, Ruoping"},{"full_name":"Ye, Chen","last_name":"Ye","first_name":"Chen"},{"first_name":"Xiuqing","last_name":"Zhang","full_name":"Zhang, Xiuqing"},{"first_name":"Jùn","last_name":"Wang","full_name":"Wang, Jùn"},{"first_name":"Wen","last_name":"Wang","full_name":"Wang, Wen"},{"last_name":"Bachtrog","first_name":"Doris","full_name":"Bachtrog, Doris"}],"year":"2012","month":"03","_id":"2073","status":"public","issue":"1","quality_controlled":0,"license":"https://creativecommons.org/licenses/by/4.0/","title":"Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1186/1471-2164-13-109","citation":{"mla":"Zhou, Qi, et al. “Deciphering Neo-Sex and B Chromosome Evolution by the Draft Genome of Drosophila Albomicans.” <i>BMC Genomics</i>, vol. 13, no. 1, BioMed Central, 2012, doi:<a href=\"https://doi.org/10.1186/1471-2164-13-109\">10.1186/1471-2164-13-109</a>.","ama":"Zhou Q, Zhu H, Huang Q, et al. Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans. <i>BMC Genomics</i>. 2012;13(1). doi:<a href=\"https://doi.org/10.1186/1471-2164-13-109\">10.1186/1471-2164-13-109</a>","short":"Q. Zhou, H. Zhu, Q. Huang, L. Zhao, G. Zhang, S. Roy, B. Vicoso, Z. Xuan, J. Ruan, Y. Zhang, R. Zhao, C. Ye, X. Zhang, J. Wang, W. Wang, D. Bachtrog, BMC Genomics 13 (2012).","chicago":"Zhou, Qi, Hongmei Zhu, Quanfei Huang, Li Zhao, Guo Zhang, Scott Roy, Beatriz Vicoso, et al. “Deciphering Neo-Sex and B Chromosome Evolution by the Draft Genome of Drosophila Albomicans.” <i>BMC Genomics</i>. BioMed Central, 2012. <a href=\"https://doi.org/10.1186/1471-2164-13-109\">https://doi.org/10.1186/1471-2164-13-109</a>.","ieee":"Q. Zhou <i>et al.</i>, “Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans,” <i>BMC Genomics</i>, vol. 13, no. 1. BioMed Central, 2012.","apa":"Zhou, Q., Zhu, H., Huang, Q., Zhao, L., Zhang, G., Roy, S., … Bachtrog, D. (2012). Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans. <i>BMC Genomics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2164-13-109\">https://doi.org/10.1186/1471-2164-13-109</a>","ista":"Zhou Q, Zhu H, Huang Q, Zhao L, Zhang G, Roy S, Vicoso B, Xuan Z, Ruan J, Zhang Y, Zhao R, Ye C, Zhang X, Wang J, Wang W, Bachtrog D. 2012. Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans. BMC Genomics. 13(1)."},"date_updated":"2021-01-12T06:55:08Z","abstract":[{"lang":"eng","text":"Background: Drosophila albomicans is a unique model organism for studying both sex chromosome and B chromosome evolution. A pair of its autosomes comprising roughly 40% of the whole genome has fused to the ancient X and Y chromosomes only about 0.12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses recently derived B chromosomes that show non-Mendelian inheritance and significantly influence fertility.Methods: We sequenced male flies with B chromosomes at 124.5-fold genome coverage using next-generation sequencing. To characterize neo-Y specific changes and B chromosome sequences, we also sequenced inbred female flies derived from the same strain but without B's at 28.5-fold.Results: We assembled a female genome and placed 53% of the sequence and 85% of the annotated proteins into specific chromosomes, by comparison with the 12 Drosophila genomes. Despite its very recent origin, the non-recombining neo-Y chromosome shows various signs of degeneration, including a significant enrichment of non-functional genes compared to the neo-X, and an excess of tandem duplications relative to other chromosomes. We also characterized a B-chromosome linked scaffold that contains an actively transcribed unit and shows sequence similarity to the subcentromeric regions of both the ancient X and the neo-X chromosome.Conclusions: Our results provide novel insights into the very early stages of sex chromosome evolution and B chromosome origination, and suggest an unprecedented connection between the births of these two systems in D. albomicans."}],"publication":"BMC Genomics","volume":13,"type":"journal_article"},{"quality_controlled":0,"title":"crdbrd: Shape fabrication by sliding planar slices","issue":"2pt3","doi":"10.1111/j.1467-8659.2012.03037.x","citation":{"ieee":"K. Hildebrand, B. Bickel, and M. Alexa, “crdbrd: Shape fabrication by sliding planar slices,” <i>Computer Graphics Forum</i>, vol. 31, no. 2pt3. Wiley-Blackwell, pp. 583–592, 2012.","chicago":"Hildebrand, Kristian, Bernd Bickel, and Marc Alexa. “Crdbrd: Shape Fabrication by Sliding Planar Slices.” <i>Computer Graphics Forum</i>. Wiley-Blackwell, 2012. <a href=\"https://doi.org/10.1111/j.1467-8659.2012.03037.x\">https://doi.org/10.1111/j.1467-8659.2012.03037.x</a>.","apa":"Hildebrand, K., Bickel, B., &#38; Alexa, M. (2012). crdbrd: Shape fabrication by sliding planar slices. <i>Computer Graphics Forum</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1467-8659.2012.03037.x\">https://doi.org/10.1111/j.1467-8659.2012.03037.x</a>","ista":"Hildebrand K, Bickel B, Alexa M. 2012. crdbrd: Shape fabrication by sliding planar slices. Computer Graphics Forum. 31(2pt3), 583–592.","mla":"Hildebrand, Kristian, et al. “Crdbrd: Shape Fabrication by Sliding Planar Slices.” <i>Computer Graphics Forum</i>, vol. 31, no. 2pt3, Wiley-Blackwell, 2012, pp. 583–92, doi:<a href=\"https://doi.org/10.1111/j.1467-8659.2012.03037.x\">10.1111/j.1467-8659.2012.03037.x</a>.","ama":"Hildebrand K, Bickel B, Alexa M. crdbrd: Shape fabrication by sliding planar slices. <i>Computer Graphics Forum</i>. 2012;31(2pt3):583-592. doi:<a href=\"https://doi.org/10.1111/j.1467-8659.2012.03037.x\">10.1111/j.1467-8659.2012.03037.x</a>","short":"K. Hildebrand, B. Bickel, M. Alexa, Computer Graphics Forum 31 (2012) 583–592."},"publication":"Computer Graphics Forum","abstract":[{"text":"We introduce an algorithm and representation for fabricating 3D shape abstractions using mutually intersecting planar cut-outs. The planes have prefabricated slits at their intersections and are assembled by sliding them together. Often such abstractions are used as a sculptural art form or in architecture and are colloquially called ‘cardboard sculptures’. Based on an analysis of construction rules, we propose an extended binary space partitioning tree as an efficient representation of such cardboard models which allows us to quickly evaluate the feasibility of newly added planar elements. The complexity of insertion order quickly increases with the number of planar elements and manual analysis becomes intractable. We provide tools for generating cardboard sculptures with guaranteed constructibility. In combination with a simple optimization and sampling strategy for new elements, planar shape abstraction models can be designed by iteratively adding elements. As an output, we obtain a fabrication plan that can be printed or sent to a laser cutter. We demonstrate the complete process by designing and fabricating cardboard models of various well-known 3D shapes.","lang":"eng"}],"date_updated":"2021-01-12T06:55:10Z","volume":31,"type":"journal_article","date_published":"2012-05-01T00:00:00Z","page":"583 - 592","publication_status":"published","publist_id":"4959","intvolume":"        31","author":[{"first_name":"Kristian","last_name":"Hildebrand","full_name":"Hildebrand, Kristian"},{"first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bernd Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alexa, Marc","first_name":"Marc","last_name":"Alexa"}],"extern":1,"publisher":"Wiley-Blackwell","day":"01","date_created":"2018-12-11T11:55:35Z","_id":"2079","month":"05","status":"public","year":"2012"},{"volume":178,"type":"journal_article","publication":"Journal of Structural Biology","abstract":[{"lang":"eng","text":"Outer membrane protein F, a major component of the Escherichia coli outer membrane, was crystallized for the first time in lipidic mesophase of monoolein in novel space groups, P1 and H32. Due to ease of its purification and crystallization OmpF can be used as a benchmark protein for establishing membrane protein crystallization in meso, as a &quot;membrane lyzozyme&quot; The packing of porin trimers in the crystals of space group H32 is similar to natural outer membranes, providing the first high-resolution insight into the close to native packing of OmpF. Surprisingly, interaction between trimers is mediated exclusively by lipids, without direct protein-protein contacts. Multiple ordered lipids are observed and many of them occupy identical positions independently of the space group, identifying preferential interaction sites of lipid acyl chains. Presence of ordered aliphatic chains close to a positively charged area on the porin surface suggests a position for a lipopolysaccharide binding site on the surface of the major E. coli porins."}],"date_updated":"2021-01-12T06:54:26Z","acknowledgement":"This work was funded by the Medical Research Council.","citation":{"apa":"Efremov, R., &#38; Sazanov, L. A. (2012). Structure of Escherichia coli OmpF porin from lipidic mesophase. <i>Journal of Structural Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jsb.2012.03.005\">https://doi.org/10.1016/j.jsb.2012.03.005</a>","chicago":"Efremov, Rouslan, and Leonid A Sazanov. “Structure of Escherichia Coli OmpF Porin from Lipidic Mesophase.” <i>Journal of Structural Biology</i>. Academic Press, 2012. <a href=\"https://doi.org/10.1016/j.jsb.2012.03.005\">https://doi.org/10.1016/j.jsb.2012.03.005</a>.","ieee":"R. Efremov and L. A. Sazanov, “Structure of Escherichia coli OmpF porin from lipidic mesophase,” <i>Journal of Structural Biology</i>, vol. 178, no. 3. Academic Press, pp. 311–318, 2012.","ista":"Efremov R, Sazanov LA. 2012. Structure of Escherichia coli OmpF porin from lipidic mesophase. Journal of Structural Biology. 178(3), 311–318.","mla":"Efremov, Rouslan, and Leonid A. Sazanov. “Structure of Escherichia Coli OmpF Porin from Lipidic Mesophase.” <i>Journal of Structural Biology</i>, vol. 178, no. 3, Academic Press, 2012, pp. 311–18, doi:<a href=\"https://doi.org/10.1016/j.jsb.2012.03.005\">10.1016/j.jsb.2012.03.005</a>.","short":"R. Efremov, L.A. Sazanov, Journal of Structural Biology 178 (2012) 311–318.","ama":"Efremov R, Sazanov LA. Structure of Escherichia coli OmpF porin from lipidic mesophase. <i>Journal of Structural Biology</i>. 2012;178(3):311-318. doi:<a href=\"https://doi.org/10.1016/j.jsb.2012.03.005\">10.1016/j.jsb.2012.03.005</a>"},"doi":"10.1016/j.jsb.2012.03.005","title":"Structure of Escherichia coli OmpF porin from lipidic mesophase","quality_controlled":0,"issue":"3","status":"public","_id":"1972","month":"06","year":"2012","author":[{"last_name":"Efremov","first_name":"Rouslan","full_name":"Efremov, Rouslan G"},{"first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Leonid Sazanov"}],"extern":1,"publist_id":"5109","intvolume":"       178","date_created":"2018-12-11T11:54:59Z","publisher":"Academic Press","day":"01","publication_status":"published","page":"311 - 318","date_published":"2012-06-01T00:00:00Z"},{"type":"review","volume":1817,"publication":"Biochimica et Biophysica Acta - Bioenergetics","abstract":[{"text":"Complex I is a key enzyme of the respiratory chain in many organisms. This multi-protein complex with an intricate evolutionary history originated from the unification of prebuilt modules of hydrogenases and transporters. Using recently determined crystallographic structures of complex I we reanalyzed evolutionarily related complexes that couple oxidoreduction to trans-membrane ion translocation. Our analysis points to the previously unnoticed structural homology of the electron input module of formate dehydrogenlyases and subunit NuoG of complex I. We also show that all related to complex I hydrogenases likely operate via a conformation driven mechanism with structural changes generated in the conserved coupling site located at the interface of subunits NuoB/D/H. The coupling apparently originated once in evolutionary history, together with subunit NuoH joining hydrogenase and transport modules. Analysis of quinone oxidoreduction properties and the structure of complex I allows us to suggest a fully reversible coupling mechanism. Our model predicts that: 1) proton access to the ketone groups of the bound quinone is rigorously controlled by the protein, 2) the negative electric charge of the anionic ubiquinol head group is a major driving force for conformational changes.","lang":"eng"}],"acknowledgement":"The work in authors' laboratory was funded by the Medical Research Council.","date_updated":"2019-04-26T07:22:06Z","doi":"10.1016/j.bbabio.2012.02.015","citation":{"chicago":"Efremov, Rouslan, and Leonid A Sazanov. “The Coupling Mechanism of Respiratory Complex i - A Structural and Evolutionary Perspective.” <i>Biochimica et Biophysica Acta - Bioenergetics</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.bbabio.2012.02.015\">https://doi.org/10.1016/j.bbabio.2012.02.015</a>.","ieee":"R. Efremov and L. A. Sazanov, “The coupling mechanism of respiratory complex i - A structural and evolutionary perspective,” <i>Biochimica et Biophysica Acta - Bioenergetics</i>, vol. 1817, no. 10. Elsevier, pp. 1785–1795, 2012.","apa":"Efremov, R., &#38; Sazanov, L. A. (2012). The coupling mechanism of respiratory complex i - A structural and evolutionary perspective. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbabio.2012.02.015\">https://doi.org/10.1016/j.bbabio.2012.02.015</a>","ista":"Efremov R, Sazanov LA. 2012. The coupling mechanism of respiratory complex i - A structural and evolutionary perspective. Biochimica et Biophysica Acta - Bioenergetics. 1817(10), 1785–1795.","mla":"Efremov, Rouslan, and Leonid A. Sazanov. “The Coupling Mechanism of Respiratory Complex i - A Structural and Evolutionary Perspective.” <i>Biochimica et Biophysica Acta - Bioenergetics</i>, vol. 1817, no. 10, Elsevier, 2012, pp. 1785–95, doi:<a href=\"https://doi.org/10.1016/j.bbabio.2012.02.015\">10.1016/j.bbabio.2012.02.015</a>.","ama":"Efremov R, Sazanov LA. The coupling mechanism of respiratory complex i - A structural and evolutionary perspective. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. 2012;1817(10):1785-1795. doi:<a href=\"https://doi.org/10.1016/j.bbabio.2012.02.015\">10.1016/j.bbabio.2012.02.015</a>","short":"R. Efremov, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1817 (2012) 1785–1795."},"quality_controlled":0,"title":"The coupling mechanism of respiratory complex i - A structural and evolutionary perspective","issue":"10","_id":"1976","month":"10","status":"public","year":"2012","publist_id":"5108","intvolume":"      1817","extern":1,"author":[{"first_name":"Rouslan","last_name":"Efremov","full_name":"Efremov, Rouslan G"},{"last_name":"Sazanov","first_name":"Leonid A","full_name":"Leonid Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989"}],"publisher":"Elsevier","day":"01","date_created":"2018-12-11T11:55:00Z","publication_status":"published","page":"1785 - 1795","date_published":"2012-10-01T00:00:00Z"},{"article_processing_charge":"No","publication":"Physical Review Letters","acknowledgement":"We are indebted to R. Grimm for generous support. We thank J. von Stecher, P. Johnson, and E. Tiesinga for fruitful discussions. We gratefully acknowledge funding by the Austrian Science Fund (FWF) within Project No. I153-N16 and within the framework of the European Science Foundation (ESF) EuroQUASAR collective research project QuDeGPM, and by the European Research Council (ERC) under Project No. 278417.","oa_version":"Preprint","external_id":{"arxiv":["1201.1008"]},"doi":"10.1103/PhysRevLett.108.215302","title":"Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions","month":"05","status":"public","year":"2012","publist_id":"6334","intvolume":"       108","author":[{"full_name":"Mark, Manfred","first_name":"Manfred","last_name":"Mark"},{"full_name":"Haller, Elmar","last_name":"Haller","first_name":"Elmar"},{"first_name":"Katharina","last_name":"Lauber","full_name":"Lauber, Katharina"},{"orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl"},{"first_name":"Alexander","last_name":"Janisch","full_name":"Janisch, Alexander"},{"last_name":"Büchler","first_name":"Hans","full_name":"Büchler, Hans"},{"full_name":"Daley, Andrew","last_name":"Daley","first_name":"Andrew"},{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"}],"arxiv":1,"date_created":"2018-12-11T11:49:55Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1201.1008"}],"date_published":"2012-05-25T00:00:00Z","type":"journal_article","volume":108,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We prepare and study a metastable attractive Mott-insulator state formed with bosonic atoms in a three-dimensional optical lattice. Starting from a Mott insulator with Cs atoms at weak repulsive interactions, we use a magnetic Feshbach resonance to tune the interactions to large attractive values and produce a metastable state pinned by attractive interactions with a lifetime on the order of 10 s. We probe the (de)excitation spectrum via lattice modulation spectroscopy, measuring the interaction dependence of two- and three-body bound-state energies. As a result of increased on-site three-body loss we observe resonance broadening and suppression of tunneling processes that produce three-body occupation."}],"date_updated":"2021-01-12T06:47:58Z","citation":{"ieee":"M. Mark <i>et al.</i>, “Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions,” <i>Physical Review Letters</i>, vol. 108, no. 21. American Physical Society, 2012.","chicago":"Mark, Manfred, Elmar Haller, Katharina Lauber, Johann G Danzl, Alexander Janisch, Hans Büchler, Andrew Daley, and Hanns Nägerl. “Preparation and Spectroscopy of a Metastable Mott-Insulator State with Attractive Interactions.” <i>Physical Review Letters</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/PhysRevLett.108.215302\">https://doi.org/10.1103/PhysRevLett.108.215302</a>.","apa":"Mark, M., Haller, E., Lauber, K., Danzl, J. G., Janisch, A., Büchler, H., … Nägerl, H. (2012). Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.108.215302\">https://doi.org/10.1103/PhysRevLett.108.215302</a>","ista":"Mark M, Haller E, Lauber K, Danzl JG, Janisch A, Büchler H, Daley A, Nägerl H. 2012. Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions. Physical Review Letters. 108(21).","mla":"Mark, Manfred, et al. “Preparation and Spectroscopy of a Metastable Mott-Insulator State with Attractive Interactions.” <i>Physical Review Letters</i>, vol. 108, no. 21, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.108.215302\">10.1103/PhysRevLett.108.215302</a>.","ama":"Mark M, Haller E, Lauber K, et al. Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions. <i>Physical Review Letters</i>. 2012;108(21). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.108.215302\">10.1103/PhysRevLett.108.215302</a>","short":"M. Mark, E. Haller, K. Lauber, J.G. Danzl, A. Janisch, H. Büchler, A. Daley, H. Nägerl, Physical Review Letters 108 (2012)."},"issue":"21","_id":"1056","extern":"1","day":"25","publisher":"American Physical Society"},{"date_published":"2012-02-01T00:00:00Z","main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR12/Event/167014","open_access":"1"}],"publication_status":"published","date_created":"2022-02-08T10:39:08Z","author":[{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","last_name":"Polshyn","first_name":"Hryhoriy"},{"full_name":"Budakian, Raffi","last_name":"Budakian","first_name":"Raffi"}],"publication_identifier":{"issn":["0003-0503"]},"intvolume":"        57","year":"2012","status":"public","month":"02","alternative_title":["Bulletin of the American Physical Society"],"title":"Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc","quality_controlled":"1","oa_version":"Published Version","acknowledgement":"This work was supported by the Center for Emergent Superconductivity, an Energy Frontier Research Center funded by the U.S. DOE, Office of Science, under Award No. DE-AC0298CH1088.","publication":"APS March Meeting 2012","article_processing_charge":"No","publisher":"American Physical Society","day":"01","extern":"1","_id":"10750","issue":"1","conference":{"start_date":"2012-02-27","end_date":"2012-03-02","name":"APS: American Physical Society","location":"Boston, MA, United States"},"article_number":"X21.00008","citation":{"ista":"Polshyn H, Budakian R. 2012. Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc. APS March Meeting 2012. APS: American Physical Society, Bulletin of the American Physical Society, vol. 57, X21.00008.","apa":"Polshyn, H., &#38; Budakian, R. (2012). Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc. In <i>APS March Meeting 2012</i> (Vol. 57). Boston, MA, United States: American Physical Society.","chicago":"Polshyn, Hryhoriy, and Raffi Budakian. “Cantilever Torque Magnetometry Study of Multiply Connected BSCCO Arrays near Tc.” In <i>APS March Meeting 2012</i>, Vol. 57. American Physical Society, 2012.","ieee":"H. Polshyn and R. Budakian, “Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc,” in <i>APS March Meeting 2012</i>, Boston, MA, United States, 2012, vol. 57, no. 1.","short":"H. Polshyn, R. Budakian, in:, APS March Meeting 2012, American Physical Society, 2012.","ama":"Polshyn H, Budakian R. Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc. In: <i>APS March Meeting 2012</i>. Vol 57. American Physical Society; 2012.","mla":"Polshyn, Hryhoriy, and Raffi Budakian. “Cantilever Torque Magnetometry Study of Multiply Connected BSCCO Arrays near Tc.” <i>APS March Meeting 2012</i>, vol. 57, no. 1, X21.00008, American Physical Society, 2012."},"date_updated":"2022-02-08T10:48:01Z","abstract":[{"lang":"eng","text":"The goal of this work is to study the superconducting coherence length in the fluctuation regime in cuprate superconductors. In this work we present cantilever torque magnetometry measurements of micron-size BSCCO flakes patterned with arrays of nanometer scale rings or holes. Using ultrasensitive dynamic torque magnetometry, oscillations in magnetization are observed near Tc as a function of the applied magnetic flux threading the array. Special effort was made to detect the oscillations in magnetization at temperatures above Tc, where the Nernst effect and magnetization measurements suggest the possibility of pairing. To constrain the magnitude of the coherence length in the fluctuation regime, we will present the dependence of the amplitude of the h/2e period oscillations as a function of temperature and hole size."}],"language":[{"iso":"eng"}],"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":57,"type":"conference"},{"year":"2012","place":"New York","_id":"10896","month":"07","status":"public","publisher":"Springer","day":"23","date_created":"2022-03-21T07:16:12Z","publication_identifier":{"eisbn":["9781461439035"],"isbn":["9781461439028"]},"author":[{"id":"3C77F464-F248-11E8-B48F-1D18A9856A87","full_name":"zur Nedden, Stephanie","last_name":"zur Nedden","first_name":"Stephanie"},{"full_name":"Doney, Alexander S.","last_name":"Doney","first_name":"Alexander S."},{"last_name":"Frenguelli","first_name":"Bruno G.","full_name":"Frenguelli, Bruno G."}],"page":"109-129","publication_status":"published","department":[{"_id":"HaJa"}],"editor":[{"first_name":"Susan","last_name":"Masino","full_name":"Masino, Susan"},{"first_name":"Detlev","last_name":"Boison","full_name":"Boison, Detlev"}],"date_published":"2012-07-23T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","type":"book_chapter","acknowledgement":"We are grateful to Research into Ageing/Ageing UK and The Dunhill Trust for funding SzN’s graduate studies, and to Prof Nicholas Dale for his valuable input.","date_updated":"2022-06-21T11:51:58Z","language":[{"iso":"eng"}],"publication":"Adenosine","abstract":[{"text":"Under physiological conditions the brain, via the purine salvage pathway, reuses the preformed purine bases hypoxanthine, derived from ATP degradation, and adenine (Ade), derived from polyamine synthesis, to restore its ATP pool. However, the massive degradation of ATP during ischemia, although providing valuable neuroprotective adenosine, results in the accumulation and loss of diffusible purine metabolites and thereby leads to a protracted reduction in the post-ischemic ATP pool size. In vivo, this may both limit the ability to deploy ATP-dependent reparative mechanisms and reduce the subsequent availability of adenosine, whilst in brain slices results in tissue with substantially lower levels of ATP than in vivo. In the present review, we describe the mechanisms by which brain tissue replenishes its ATP, how this can be improved with the clinically tolerated chemicals D-ribose and adenine, and the functional, and potential therapeutic, implications of doing so.","lang":"eng"}],"oa_version":"None","citation":{"mla":"zur Nedden, Stephanie, et al. “The Double-Edged Sword: Gaining Adenosine at the Expense of ATP. How to Balance the Books.” <i>Adenosine</i>, edited by Susan Masino and Detlev Boison, 1st ed., Springer, 2012, pp. 109–29, doi:<a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">10.1007/978-1-4614-3903-5_6</a>.","short":"S. zur Nedden, A.S. Doney, B.G. Frenguelli, in:, S. Masino, D. Boison (Eds.), Adenosine, 1st ed., Springer, New York, 2012, pp. 109–129.","ama":"zur Nedden S, Doney AS, Frenguelli BG. The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In: Masino S, Boison D, eds. <i>Adenosine</i>. 1st ed. New York: Springer; 2012:109-129. doi:<a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">10.1007/978-1-4614-3903-5_6</a>","apa":"zur Nedden, S., Doney, A. S., &#38; Frenguelli, B. G. (2012). The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In S. Masino &#38; D. Boison (Eds.), <i>Adenosine</i> (1st ed., pp. 109–129). New York: Springer. <a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">https://doi.org/10.1007/978-1-4614-3903-5_6</a>","chicago":"Nedden, Stephanie zur, Alexander S. Doney, and Bruno G. Frenguelli. “The Double-Edged Sword: Gaining Adenosine at the Expense of ATP. How to Balance the Books.” In <i>Adenosine</i>, edited by Susan Masino and Detlev Boison, 1st ed., 109–29. New York: Springer, 2012. <a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">https://doi.org/10.1007/978-1-4614-3903-5_6</a>.","ieee":"S. zur Nedden, A. S. Doney, and B. G. Frenguelli, “The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books,” in <i>Adenosine</i>, 1st ed., S. Masino and D. Boison, Eds. New York: Springer, 2012, pp. 109–129.","ista":"zur Nedden S, Doney AS, Frenguelli BG. 2012.The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In: Adenosine. , 109–129."},"doi":"10.1007/978-1-4614-3903-5_6","edition":"1","scopus_import":"1","quality_controlled":"1","title":"The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books"},{"title":"Accurate invariant checking for programs manipulating lists and arrays with infinite data","quality_controlled":"1","scopus_import":"1","alternative_title":["LNCS"],"oa_version":"None","doi":"10.1007/978-3-642-33386-6_14","publication":"Automated Technology for Verification and Analysis","acknowledgement":"This work has been partially supported by the French ANR project Veridyc","article_processing_charge":"No","date_published":"2012-10-15T00:00:00Z","series_title":"LNCS","corr_author":"1","department":[{"_id":"ToHe"}],"publication_status":"published","author":[{"first_name":"Ahmed","last_name":"Bouajjani","full_name":"Bouajjani, Ahmed"},{"full_name":"Dragoi, Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","first_name":"Cezara","last_name":"Dragoi"},{"last_name":"Enea","first_name":"Constantin","full_name":"Enea, Constantin"},{"full_name":"Sighireanu, Mihaela","last_name":"Sighireanu","first_name":"Mihaela"}],"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783642333859"],"eisbn":["9783642333866"]},"intvolume":"      7561","date_created":"2022-03-21T07:58:39Z","status":"public","month":"10","year":"2012","conference":{"start_date":"2012-10-03","location":"Thiruvananthapuram, India","end_date":"2012-10-06","name":"ATVA: Automated Technology for Verification and Analysis"},"citation":{"apa":"Bouajjani, A., Dragoi, C., Enea, C., &#38; Sighireanu, M. (2012). Accurate invariant checking for programs manipulating lists and arrays with infinite data. In <i>Automated Technology for Verification and Analysis</i> (Vol. 7561, pp. 167–182). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">https://doi.org/10.1007/978-3-642-33386-6_14</a>","ieee":"A. Bouajjani, C. Dragoi, C. Enea, and M. Sighireanu, “Accurate invariant checking for programs manipulating lists and arrays with infinite data,” in <i>Automated Technology for Verification and Analysis</i>, Thiruvananthapuram, India, 2012, vol. 7561, pp. 167–182.","chicago":"Bouajjani, Ahmed, Cezara Dragoi, Constantin Enea, and Mihaela Sighireanu. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” In <i>Automated Technology for Verification and Analysis</i>, 7561:167–82. LNCS. Berlin, Heidelberg: Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">https://doi.org/10.1007/978-3-642-33386-6_14</a>.","ista":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. 2012. Accurate invariant checking for programs manipulating lists and arrays with infinite data. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and AnalysisLNCS, LNCS, vol. 7561, 167–182.","mla":"Bouajjani, Ahmed, et al. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” <i>Automated Technology for Verification and Analysis</i>, vol. 7561, Springer, 2012, pp. 167–82, doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">10.1007/978-3-642-33386-6_14</a>.","short":"A. Bouajjani, C. Dragoi, C. Enea, M. Sighireanu, in:, Automated Technology for Verification and Analysis, Springer, Berlin, Heidelberg, 2012, pp. 167–182.","ama":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. Accurate invariant checking for programs manipulating lists and arrays with infinite data. In: <i>Automated Technology for Verification and Analysis</i>. Vol 7561. LNCS. Berlin, Heidelberg: Springer; 2012:167-182. doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">10.1007/978-3-642-33386-6_14</a>"},"abstract":[{"text":"We propose a logic-based framework for automated reasoning about sequential programs manipulating singly-linked lists and arrays with unbounded data. We introduce the logic SLAD, which allows combining shape constraints, written in a fragment of Separation Logic, with data and size constraints. We address the problem of checking the entailment between SLAD formulas, which is crucial in performing pre-post condition reasoning. Although this problem is undecidable in general for SLAD, we propose a sound and powerful procedure that is able to solve this problem for a large class of formulas, beyond the capabilities of existing techniques and tools. We prove that this procedure is complete, i.e., it is actually a decision procedure for this problem, for an important fragment of SLAD including known decidable logics. We implemented this procedure and shown its preciseness and its efficiency on a significant benchmark of formulas.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2024-10-09T21:02:34Z","volume":7561,"type":"conference","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"167-182","day":"15","publisher":"Springer","_id":"10903","place":"Berlin, Heidelberg"},{"conference":{"end_date":"2012-09-07","name":"CONCUR: Conference on Concurrency Theory","location":"Newcastle upon Tyne, United Kingdom","start_date":"2012-09-04"},"citation":{"apa":"Chatterjee, K., Randour, M., &#38; Raskin, J.-F. (2012). Strategy synthesis for multi-dimensional quantitative objectives. In M. Koutny &#38; I. Ulidowski (Eds.), <i>CONCUR 2012 - Concurrency Theory</i> (Vol. 7454, pp. 115–131). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">https://doi.org/10.1007/978-3-642-32940-1_10</a>","ieee":"K. Chatterjee, M. Randour, and J.-F. Raskin, “Strategy synthesis for multi-dimensional quantitative objectives,” in <i>CONCUR 2012 - Concurrency Theory</i>, Newcastle upon Tyne, United Kingdom, 2012, vol. 7454, pp. 115–131.","chicago":"Chatterjee, Krishnendu, Mickael Randour, and Jean-François Raskin. “Strategy Synthesis for Multi-Dimensional Quantitative Objectives.” In <i>CONCUR 2012 - Concurrency Theory</i>, edited by Maciej Koutny and Irek Ulidowski, 7454:115–31. Berlin, Heidelberg: Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">https://doi.org/10.1007/978-3-642-32940-1_10</a>.","ista":"Chatterjee K, Randour M, Raskin J-F. 2012. Strategy synthesis for multi-dimensional quantitative objectives. CONCUR 2012 - Concurrency Theory. CONCUR: Conference on Concurrency Theory, LNCS, vol. 7454, 115–131.","mla":"Chatterjee, Krishnendu, et al. “Strategy Synthesis for Multi-Dimensional Quantitative Objectives.” <i>CONCUR 2012 - Concurrency Theory</i>, edited by Maciej Koutny and Irek Ulidowski, vol. 7454, Springer, 2012, pp. 115–31, doi:<a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">10.1007/978-3-642-32940-1_10</a>.","short":"K. Chatterjee, M. Randour, J.-F. Raskin, in:, M. Koutny, I. Ulidowski (Eds.), CONCUR 2012 - Concurrency Theory, Springer, Berlin, Heidelberg, 2012, pp. 115–131.","ama":"Chatterjee K, Randour M, Raskin J-F. Strategy synthesis for multi-dimensional quantitative objectives. In: Koutny M, Ulidowski I, eds. <i>CONCUR 2012 - Concurrency Theory</i>. Vol 7454. Berlin, Heidelberg: Springer; 2012:115-131. doi:<a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">10.1007/978-3-642-32940-1_10</a>"},"date_updated":"2025-09-29T11:10:44Z","abstract":[{"lang":"eng","text":"Multi-dimensional mean-payoff and energy games provide the mathematical foundation for the quantitative study of reactive systems, and play a central role in the emerging quantitative theory of verification and synthesis. In this work, we study the strategy synthesis problem for games with such multi-dimensional objectives along with a parity condition, a canonical way to express ω-regular conditions. While in general, the winning strategies in such games may require infinite memory, for synthesis the most relevant problem is the construction of a finite-memory winning strategy (if one exists). Our main contributions are as follows. First, we show a tight exponential bound (matching upper and lower bounds) on the memory required for finite-memory winning strategies in both multi-dimensional mean-payoff and energy games along with parity objectives. This significantly improves the triple exponential upper bound for multi energy games (without parity) that could be derived from results in literature for games on VASS (vector addition systems with states). Second, we present an optimal symbolic and incremental algorithm to compute a finite-memory winning strategy (if one exists) in such games. Finally, we give a complete characterization of when finite memory of strategies can be traded off for randomness. In particular, we show that for one-dimension mean-payoff parity games, randomized memoryless strategies are as powerful as their pure finite-memory counterparts."}],"language":[{"iso":"eng"}],"oa":1,"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","volume":7454,"OA_type":"green","page":"115-131","publisher":"Springer","day":"15","related_material":{"record":[{"relation":"later_version","status":"public","id":"2716"}]},"place":"Berlin, Heidelberg","_id":"10904","scopus_import":"1","alternative_title":["LNCS"],"title":"Strategy synthesis for multi-dimensional quantitative objectives","quality_controlled":"1","OA_place":"repository","external_id":{"arxiv":["1201.5073"]},"oa_version":"Preprint","doi":"10.1007/978-3-642-32940-1_10","acknowledgement":"Author supported by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407 (RiSE), ERC Start Grant (279307: Graph Games), Microsoft faculty fellowship.","publication":"CONCUR 2012 - Concurrency Theory","article_processing_charge":"No","corr_author":"1","ec_funded":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1201.5073","open_access":"1"}],"date_published":"2012-09-15T00:00:00Z","publication_status":"published","editor":[{"full_name":"Koutny, Maciej","last_name":"Koutny","first_name":"Maciej"},{"full_name":"Ulidowski, Irek","last_name":"Ulidowski","first_name":"Irek"}],"department":[{"_id":"KrCh"}],"date_created":"2022-03-21T08:00:21Z","arxiv":1,"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Mickael","last_name":"Randour","full_name":"Randour, Mickael"},{"first_name":"Jean-François","last_name":"Raskin","full_name":"Raskin, Jean-François"}],"publication_identifier":{"eisbn":["9783642329401"],"isbn":["9783642329395"],"issn":["0302-9743"],"eissn":["1611-3349"]},"intvolume":"      7454","year":"2012","status":"public","month":"09"},{"conference":{"start_date":"2012-09-10","location":"Ljubljana, Slovenia","name":"ESA: European Symposium on Algorithms","end_date":"2012-09-12"},"citation":{"ista":"Chatterjee K, Henzinger M, Krinninger S, Nanongkai D. 2012. Polynomial-time algorithms for energy games with special weight structures. Algorithms – ESA 2012. ESA: European Symposium on Algorithms, LNCS, vol. 7501, 301–312.","apa":"Chatterjee, K., Henzinger, M., Krinninger, S., &#38; Nanongkai, D. (2012). Polynomial-time algorithms for energy games with special weight structures. In <i>Algorithms – ESA 2012</i> (Vol. 7501, pp. 301–312). Ljubljana, Slovenia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-33090-2_27\">https://doi.org/10.1007/978-3-642-33090-2_27</a>","ieee":"K. Chatterjee, M. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time algorithms for energy games with special weight structures,” in <i>Algorithms – ESA 2012</i>, Ljubljana, Slovenia, 2012, vol. 7501, pp. 301–312.","chicago":"Chatterjee, Krishnendu, Monika Henzinger, Sebastian Krinninger, and Danupon Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” In <i>Algorithms – ESA 2012</i>, 7501:301–12. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33090-2_27\">https://doi.org/10.1007/978-3-642-33090-2_27</a>.","short":"K. Chatterjee, M. Henzinger, S. Krinninger, D. Nanongkai, in:, Algorithms – ESA 2012, Springer, 2012, pp. 301–312.","ama":"Chatterjee K, Henzinger M, Krinninger S, Nanongkai D. Polynomial-time algorithms for energy games with special weight structures. In: <i>Algorithms – ESA 2012</i>. Vol 7501. Springer; 2012:301-312. doi:<a href=\"https://doi.org/10.1007/978-3-642-33090-2_27\">10.1007/978-3-642-33090-2_27</a>","mla":"Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” <i>Algorithms – ESA 2012</i>, vol. 7501, Springer, 2012, pp. 301–12, doi:<a href=\"https://doi.org/10.1007/978-3-642-33090-2_27\">10.1007/978-3-642-33090-2_27</a>."},"date_updated":"2025-09-29T13:18:37Z","abstract":[{"lang":"eng","text":"Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP ∩ co−NP, but are not known to be in P. While the existence of polynomial-time algorithms has been a major open problem for decades, there is no algorithm that solves any non-trivial subclass in polynomial time.\r\nIn this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several counter examples that show that many previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting graph structures need not help."}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"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"}],"type":"conference","volume":7501,"page":"301-312","day":"01","publisher":"Springer","related_material":{"record":[{"relation":"later_version","id":"535","status":"public"}]},"_id":"10905","scopus_import":"1","alternative_title":["LNCS"],"title":"Polynomial-time algorithms for energy games with special weight structures","quality_controlled":"1","doi":"10.1007/978-3-642-33090-2_27","external_id":{"arxiv":["1604.08234"]},"oa_version":"Preprint","acknowledgement":"Supported by the Austrian Science Fund (FWF): P23499-N23, the Austrian Science Fund (FWF): S11407-N23 (RiSE), an ERC Start Grant (279307: Graph Games), and a Microsoft Faculty Fellows Award","publication":"Algorithms – ESA 2012","article_processing_charge":"No","corr_author":"1","ec_funded":1,"date_published":"2012-10-01T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1604.08234","open_access":"1"}],"publication_status":"published","department":[{"_id":"KrCh"}],"date_created":"2022-03-21T08:01:45Z","arxiv":1,"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H"},{"full_name":"Krinninger, Sebastian","last_name":"Krinninger","first_name":"Sebastian"},{"last_name":"Nanongkai","first_name":"Danupon","full_name":"Nanongkai, Danupon"}],"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783642330896"],"eisbn":["9783642330902"]},"intvolume":"      7501","year":"2012","status":"public","month":"10"},{"article_processing_charge":"No","publication":"Tools and Algorithms for the Construction and Analysis of Systems","doi":"10.1007/978-3-642-28756-5_46","oa_version":"Published Version","quality_controlled":"1","title":"HSF(C): A software verifier based on Horn clauses","alternative_title":["LNCS"],"scopus_import":"1","month":"04","status":"public","year":"2012","publication_identifier":{"eisbn":["9783642287565"],"isbn":["9783642287558"],"issn":["0302-9743"],"eissn":["1611-3349"]},"intvolume":"      7214","author":[{"full_name":"Grebenshchikov, Sergey","first_name":"Sergey","last_name":"Grebenshchikov"},{"last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh"},{"full_name":"Lopes, Nuno P.","first_name":"Nuno P.","last_name":"Lopes"},{"full_name":"Popeea, Corneliu","last_name":"Popeea","first_name":"Corneliu"},{"first_name":"Andrey","last_name":"Rybalchenko","full_name":"Rybalchenko, Andrey"}],"date_created":"2022-03-21T08:03:30Z","department":[{"_id":"ToHe"}],"editor":[{"last_name":"Flanagan","first_name":"Cormac","full_name":"Flanagan, Cormac"},{"first_name":"Barbara","last_name":"König","full_name":"König, Barbara"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/978-3-642-28756-5_46"}],"date_published":"2012-04-01T00:00:00Z","corr_author":"1","series_title":"LNCS","volume":7214,"type":"conference","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"HSF(C) is a tool that automates verification of safety and liveness properties for C programs. This paper describes the verification approach taken by HSF(C) and provides instructions on how to install and use the tool.","lang":"eng"}],"date_updated":"2024-10-09T21:02:32Z","citation":{"ama":"Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. HSF(C): A software verifier based on Horn clauses. In: Flanagan C, König B, eds. <i>Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 7214. LNCS. Berlin, Heidelberg: Springer; 2012:549-551. doi:<a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">10.1007/978-3-642-28756-5_46</a>","short":"S. Grebenshchikov, A. Gupta, N.P. Lopes, C. Popeea, A. Rybalchenko, in:, C. Flanagan, B. König (Eds.), Tools and Algorithms for the Construction and Analysis of Systems, Springer, Berlin, Heidelberg, 2012, pp. 549–551.","mla":"Grebenshchikov, Sergey, et al. “HSF(C): A Software Verifier Based on Horn Clauses.” <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, edited by Cormac Flanagan and Barbara König, vol. 7214, Springer, 2012, pp. 549–51, doi:<a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">10.1007/978-3-642-28756-5_46</a>.","ista":"Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. 2012. HSF(C): A software verifier based on Horn clauses. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of SystemsLNCS, LNCS, vol. 7214, 549–551.","ieee":"S. Grebenshchikov, A. Gupta, N. P. Lopes, C. Popeea, and A. Rybalchenko, “HSF(C): A software verifier based on Horn clauses,” in <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, Tallinn, Estonia, 2012, vol. 7214, pp. 549–551.","chicago":"Grebenshchikov, Sergey, Ashutosh Gupta, Nuno P. Lopes, Corneliu Popeea, and Andrey Rybalchenko. “HSF(C): A Software Verifier Based on Horn Clauses.” In <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, edited by Cormac Flanagan and Barbara König, 7214:549–51. LNCS. Berlin, Heidelberg: Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">https://doi.org/10.1007/978-3-642-28756-5_46</a>.","apa":"Grebenshchikov, S., Gupta, A., Lopes, N. P., Popeea, C., &#38; Rybalchenko, A. (2012). HSF(C): A software verifier based on Horn clauses. In C. Flanagan &#38; B. König (Eds.), <i>Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 7214, pp. 549–551). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">https://doi.org/10.1007/978-3-642-28756-5_46</a>"},"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2012-04-01","location":"Tallinn, Estonia","start_date":"2012-03-24"},"_id":"10906","place":"Berlin, Heidelberg","day":"01","publisher":"Springer","page":"549-551"},{"citation":{"chicago":"Gomez-Cavazos, J Sebastian, and Martin Hetzer. “Outfits for Different Occasions: Tissue-Specific Roles of Nuclear Envelope Proteins.” <i>Current Opinion in Cell Biology</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.ceb.2012.08.008\">https://doi.org/10.1016/j.ceb.2012.08.008</a>.","ieee":"J. S. Gomez-Cavazos and M. Hetzer, “Outfits for different occasions: tissue-specific roles of Nuclear Envelope proteins,” <i>Current Opinion in Cell Biology</i>, vol. 24, no. 6. Elsevier, pp. 775–783, 2012.","apa":"Gomez-Cavazos, J. S., &#38; Hetzer, M. (2012). Outfits for different occasions: tissue-specific roles of Nuclear Envelope proteins. <i>Current Opinion in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ceb.2012.08.008\">https://doi.org/10.1016/j.ceb.2012.08.008</a>","ista":"Gomez-Cavazos JS, Hetzer M. 2012. Outfits for different occasions: tissue-specific roles of Nuclear Envelope proteins. Current Opinion in Cell Biology. 24(6), 775–783.","mla":"Gomez-Cavazos, J. Sebastian, and Martin Hetzer. “Outfits for Different Occasions: Tissue-Specific Roles of Nuclear Envelope Proteins.” <i>Current Opinion in Cell Biology</i>, vol. 24, no. 6, Elsevier, 2012, pp. 775–83, doi:<a href=\"https://doi.org/10.1016/j.ceb.2012.08.008\">10.1016/j.ceb.2012.08.008</a>.","ama":"Gomez-Cavazos JS, Hetzer M. Outfits for different occasions: tissue-specific roles of Nuclear Envelope proteins. <i>Current Opinion in Cell Biology</i>. 2012;24(6):775-783. doi:<a href=\"https://doi.org/10.1016/j.ceb.2012.08.008\">10.1016/j.ceb.2012.08.008</a>","short":"J.S. Gomez-Cavazos, M. Hetzer, Current Opinion in Cell Biology 24 (2012) 775–783."},"issue":"6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Cell Biology"],"volume":24,"type":"journal_article","date_updated":"2024-10-14T11:25:04Z","abstract":[{"text":"The Nuclear Envelope (NE) contains over 100 different proteins that associate with nuclear components such as chromatin, the lamina and the transcription machinery. Mutations in genes encoding NE proteins have been shown to result in tissue-specific defects and disease, suggesting cell-type specific differences in NE composition and function. Consistent with these observations, recent studies have revealed unexpected functions for numerous NE associated proteins during cell differentiation and development. Here we review the latest insights into the roles played by the NE in cell differentiation, development, disease and aging, focusing primarily on inner nuclear membrane (INM) proteins and nuclear pore components.","lang":"eng"}],"language":[{"iso":"eng"}],"page":"775-783","article_type":"original","_id":"11089","publisher":"Elsevier","day":"01","extern":"1","external_id":{"pmid":["22995343"]},"oa_version":"None","doi":"10.1016/j.ceb.2012.08.008","scopus_import":"1","title":"Outfits for different occasions: tissue-specific roles of Nuclear Envelope proteins","quality_controlled":"1","article_processing_charge":"No","publication":"Current Opinion in Cell Biology","pmid":1,"publication_status":"published","date_published":"2012-12-01T00:00:00Z","year":"2012","status":"public","month":"12","date_created":"2022-04-07T07:51:37Z","author":[{"last_name":"Gomez-Cavazos","first_name":"J Sebastian","full_name":"Gomez-Cavazos, J Sebastian"},{"last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}],"publication_identifier":{"issn":["0955-0674"]},"intvolume":"        24"},{"page":"733-735","_id":"11090","article_type":"letter_note","publisher":"Elsevier","day":"11","extern":"1","citation":{"apa":"Hatch, E. M., &#38; Hetzer, M. (2012). RNP export by nuclear envelope budding. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2012.04.018\">https://doi.org/10.1016/j.cell.2012.04.018</a>","ieee":"E. M. Hatch and M. Hetzer, “RNP export by nuclear envelope budding,” <i>Cell</i>, vol. 149, no. 4. Elsevier, pp. 733–735, 2012.","chicago":"Hatch, Emily M., and Martin Hetzer. “RNP Export by Nuclear Envelope Budding.” <i>Cell</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.cell.2012.04.018\">https://doi.org/10.1016/j.cell.2012.04.018</a>.","ista":"Hatch EM, Hetzer M. 2012. RNP export by nuclear envelope budding. Cell. 149(4), 733–735.","mla":"Hatch, Emily M., and Martin Hetzer. “RNP Export by Nuclear Envelope Budding.” <i>Cell</i>, vol. 149, no. 4, Elsevier, 2012, pp. 733–35, doi:<a href=\"https://doi.org/10.1016/j.cell.2012.04.018\">10.1016/j.cell.2012.04.018</a>.","short":"E.M. Hatch, M. Hetzer, Cell 149 (2012) 733–735.","ama":"Hatch EM, Hetzer M. RNP export by nuclear envelope budding. <i>Cell</i>. 2012;149(4):733-735. doi:<a href=\"https://doi.org/10.1016/j.cell.2012.04.018\">10.1016/j.cell.2012.04.018</a>"},"issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"volume":149,"type":"journal_article","keyword":["General Biochemistry","Genetics and Molecular Biology"],"date_updated":"2024-10-14T11:25:24Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Nuclear export of mRNAs is thought to occur exclusively through nuclear pore complexes. In this issue of Cell, Speese et al. identify an alternate pathway for mRNA export in muscle cells where ribonucleoprotein complexes involved in forming neuromuscular junctions transit the nuclear envelope by fusing with and budding through the nuclear membrane."}],"publication_status":"published","date_published":"2012-05-11T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2012.04.018"}],"year":"2012","month":"05","status":"public","date_created":"2022-04-07T07:51:45Z","intvolume":"       149","publication_identifier":{"issn":["0092-8674"]},"author":[{"full_name":"Hatch, Emily M.","last_name":"Hatch","first_name":"Emily M."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W"}],"doi":"10.1016/j.cell.2012.04.018","oa_version":"Published Version","external_id":{"pmid":["22579277"]},"scopus_import":"1","quality_controlled":"1","title":"RNP export by nuclear envelope budding","article_processing_charge":"No","pmid":1,"publication":"Cell"},{"page":"88-100","extern":"1","day":"01","publisher":"Taylor & Francis","_id":"11091","article_type":"original","issue":"1","citation":{"ama":"Vargas JD, Hatch EM, Anderson DJ, Hetzer M. Transient nuclear envelope rupturing during interphase in human cancer cells. <i>Nucleus</i>. 2012;3(1):88-100. doi:<a href=\"https://doi.org/10.4161/nucl.18954\">10.4161/nucl.18954</a>","short":"J.D. Vargas, E.M. Hatch, D.J. Anderson, M. Hetzer, Nucleus 3 (2012) 88–100.","mla":"Vargas, Jesse D., et al. “Transient Nuclear Envelope Rupturing during Interphase in Human Cancer Cells.” <i>Nucleus</i>, vol. 3, no. 1, Taylor &#38; Francis, 2012, pp. 88–100, doi:<a href=\"https://doi.org/10.4161/nucl.18954\">10.4161/nucl.18954</a>.","ista":"Vargas JD, Hatch EM, Anderson DJ, Hetzer M. 2012. Transient nuclear envelope rupturing during interphase in human cancer cells. Nucleus. 3(1), 88–100.","chicago":"Vargas, Jesse D., Emily M. Hatch, Daniel J. Anderson, and Martin Hetzer. “Transient Nuclear Envelope Rupturing during Interphase in Human Cancer Cells.” <i>Nucleus</i>. Taylor &#38; Francis, 2012. <a href=\"https://doi.org/10.4161/nucl.18954\">https://doi.org/10.4161/nucl.18954</a>.","ieee":"J. D. Vargas, E. M. Hatch, D. J. Anderson, and M. Hetzer, “Transient nuclear envelope rupturing during interphase in human cancer cells,” <i>Nucleus</i>, vol. 3, no. 1. Taylor &#38; Francis, pp. 88–100, 2012.","apa":"Vargas, J. D., Hatch, E. M., Anderson, D. J., &#38; Hetzer, M. (2012). Transient nuclear envelope rupturing during interphase in human cancer cells. <i>Nucleus</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.4161/nucl.18954\">https://doi.org/10.4161/nucl.18954</a>"},"abstract":[{"lang":"eng","text":"Neoplastic cells are often characterized by specific morphological abnormalities of the nuclear envelope (NE), which have been used for cancer diagnosis for more than a century. The NE is a double phospholipid bilayer that encapsulates the nuclear genome, regulates all nuclear trafficking of RNAs and proteins and prevents the passive diffusion of macromolecules between the nucleoplasm and the cytoplasm. Whether there is a consequence to the proper functioning of the cell and loss of structural integrity of the nucleus remains unclear. Using live cell imaging, we characterize a phenomenon wherein nuclei of several proliferating human cancer cell lines become temporarily ruptured during interphase. Strikingly, NE rupturing was associated with the mislocalization of nucleoplasmic and cytoplasmic proteins and, in the most extreme cases, the entrapment of cytoplasmic organelles in the nuclear interior. In addition, we observed the formation of micronuclei-like structures during interphase and the movement of chromatin out of the nuclear space. The frequency of these NE rupturing events was higher in cells in which the nuclear lamina, a network of intermediate filaments providing mechanical support to the NE, was not properly formed. Our data uncover the existence of a NE instability that has the potential to change the genomic landscape of cancer cells."}],"language":[{"iso":"eng"}],"date_updated":"2024-10-14T11:25:37Z","keyword":["Cell Biology"],"volume":3,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2012-01-01T00:00:00Z","publication_status":"published","author":[{"full_name":"Vargas, Jesse D.","first_name":"Jesse D.","last_name":"Vargas"},{"full_name":"Hatch, Emily M.","last_name":"Hatch","first_name":"Emily M."},{"first_name":"Daniel J.","last_name":"Anderson","full_name":"Anderson, Daniel J."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W"}],"publication_identifier":{"eissn":["1949-1042"],"issn":["1949-1034"]},"intvolume":"         3","date_created":"2022-04-07T07:51:53Z","status":"public","month":"01","year":"2012","title":"Transient nuclear envelope rupturing during interphase in human cancer cells","quality_controlled":"1","scopus_import":"1","oa_version":"None","external_id":{"pmid":["22567193"]},"doi":"10.4161/nucl.18954","pmid":1,"publication":"Nucleus","article_processing_charge":"No"},{"scopus_import":"1","quality_controlled":"1","title":"Extremely long-lived nuclear pore proteins in the rat brain","external_id":{"pmid":["22300851"]},"doi":"10.1126/science.1217421","oa_version":"None","publication":"Science","pmid":1,"article_processing_charge":"No","date_published":"2012-02-02T00:00:00Z","publication_status":"published","department":[{"_id":"MaHe"}],"date_created":"2022-04-07T07:52:01Z","intvolume":"       335","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"author":[{"full_name":"Savas, Jeffrey N.","first_name":"Jeffrey N.","last_name":"Savas"},{"full_name":"Toyama, Brandon H.","first_name":"Brandon H.","last_name":"Toyama"},{"last_name":"Xu","first_name":"Tao","full_name":"Xu, Tao"},{"full_name":"Yates, John R.","last_name":"Yates","first_name":"John R."},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER"}],"year":"2012","month":"02","status":"public","issue":"6071","citation":{"apa":"Savas, J. N., Toyama, B. H., Xu, T., Yates, J. R., &#38; Hetzer, M. (2012). Extremely long-lived nuclear pore proteins in the rat brain. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1217421\">https://doi.org/10.1126/science.1217421</a>","ieee":"J. N. Savas, B. H. Toyama, T. Xu, J. R. Yates, and M. Hetzer, “Extremely long-lived nuclear pore proteins in the rat brain,” <i>Science</i>, vol. 335, no. 6071. American Association for the Advancement of Science, pp. 942–942, 2012.","chicago":"Savas, Jeffrey N., Brandon H. Toyama, Tao Xu, John R. Yates, and Martin Hetzer. “Extremely Long-Lived Nuclear Pore Proteins in the Rat Brain.” <i>Science</i>. American Association for the Advancement of Science, 2012. <a href=\"https://doi.org/10.1126/science.1217421\">https://doi.org/10.1126/science.1217421</a>.","ista":"Savas JN, Toyama BH, Xu T, Yates JR, Hetzer M. 2012. Extremely long-lived nuclear pore proteins in the rat brain. Science. 335(6071), 942–942.","mla":"Savas, Jeffrey N., et al. “Extremely Long-Lived Nuclear Pore Proteins in the Rat Brain.” <i>Science</i>, vol. 335, no. 6071, American Association for the Advancement of Science, 2012, pp. 942–942, doi:<a href=\"https://doi.org/10.1126/science.1217421\">10.1126/science.1217421</a>.","short":"J.N. Savas, B.H. Toyama, T. Xu, J.R. Yates, M. Hetzer, Science 335 (2012) 942–942.","ama":"Savas JN, Toyama BH, Xu T, Yates JR, Hetzer M. Extremely long-lived nuclear pore proteins in the rat brain. <i>Science</i>. 2012;335(6071):942-942. doi:<a href=\"https://doi.org/10.1126/science.1217421\">10.1126/science.1217421</a>"},"date_updated":"2025-12-15T10:03:06Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"To combat the functional decline of the proteome, cells use the process of protein turnover to replace potentially impaired polypeptides with new functional copies. We found that extremely long-lived proteins (ELLPs) did not turn over in postmitotic cells of the rat central nervous system. These ELLPs were associated with chromatin and the nuclear pore complex, the central transport channels that mediate all molecular trafficking in and out of the nucleus. The longevity of these proteins would be expected to expose them to potentially harmful metabolites, putting them at risk of accumulating damage over extended periods of time. Thus, it is possible that failure to maintain proper levels and functional integrity of ELLPs in nonproliferative cells might contribute to age-related deterioration in cell and tissue function."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":335,"page":"942-942","day":"02","publisher":"American Association for the Advancement of Science","extern":"1","_id":"11092","article_type":"letter_note"},{"quality_controlled":"1","title":"A change in nuclear pore complex composition regulates cell differentiation","scopus_import":"1","external_id":{"pmid":["22264802"]},"doi":"10.1016/j.devcel.2011.11.021","oa_version":"Published Version","publication":"Developmental Cell","pmid":1,"article_processing_charge":"No","date_published":"2012-01-19T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2011.11.021","open_access":"1"}],"publication_status":"published","publication_identifier":{"issn":["1534-5807"]},"intvolume":"        22","author":[{"first_name":"Maximiliano A.","last_name":"D'Angelo","full_name":"D'Angelo, Maximiliano A."},{"full_name":"Gomez-Cavazos, J. Sebastian","last_name":"Gomez-Cavazos","first_name":"J. Sebastian"},{"last_name":"Mei","first_name":"Arianna","full_name":"Mei, Arianna"},{"first_name":"Daniel H.","last_name":"Lackner","full_name":"Lackner, Daniel H."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W"}],"date_created":"2022-04-07T07:52:10Z","month":"01","status":"public","year":"2012","issue":"2","citation":{"ista":"D’Angelo MA, Gomez-Cavazos JS, Mei A, Lackner DH, Hetzer M. 2012. A change in nuclear pore complex composition regulates cell differentiation. Developmental Cell. 22(2), 446–458.","apa":"D’Angelo, M. A., Gomez-Cavazos, J. S., Mei, A., Lackner, D. H., &#38; Hetzer, M. (2012). A change in nuclear pore complex composition regulates cell differentiation. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2011.11.021\">https://doi.org/10.1016/j.devcel.2011.11.021</a>","ieee":"M. A. D’Angelo, J. S. Gomez-Cavazos, A. Mei, D. H. Lackner, and M. Hetzer, “A change in nuclear pore complex composition regulates cell differentiation,” <i>Developmental Cell</i>, vol. 22, no. 2. Elsevier, pp. 446–458, 2012.","chicago":"D’Angelo, Maximiliano A., J. Sebastian Gomez-Cavazos, Arianna Mei, Daniel H. Lackner, and Martin Hetzer. “A Change in Nuclear Pore Complex Composition Regulates Cell Differentiation.” <i>Developmental Cell</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.devcel.2011.11.021\">https://doi.org/10.1016/j.devcel.2011.11.021</a>.","short":"M.A. D’Angelo, J.S. Gomez-Cavazos, A. Mei, D.H. Lackner, M. Hetzer, Developmental Cell 22 (2012) 446–458.","ama":"D’Angelo MA, Gomez-Cavazos JS, Mei A, Lackner DH, Hetzer M. A change in nuclear pore complex composition regulates cell differentiation. <i>Developmental Cell</i>. 2012;22(2):446-458. doi:<a href=\"https://doi.org/10.1016/j.devcel.2011.11.021\">10.1016/j.devcel.2011.11.021</a>","mla":"D’Angelo, Maximiliano A., et al. “A Change in Nuclear Pore Complex Composition Regulates Cell Differentiation.” <i>Developmental Cell</i>, vol. 22, no. 2, Elsevier, 2012, pp. 446–58, doi:<a href=\"https://doi.org/10.1016/j.devcel.2011.11.021\">10.1016/j.devcel.2011.11.021</a>."},"language":[{"iso":"eng"}],"abstract":[{"text":"Nuclear pore complexes (NPCs) are built from ∼30 different proteins called nucleoporins or Nups. Previous studies have shown that several Nups exhibit cell-type-specific expression and that mutations in NPC components result in tissue-specific diseases. Here we show that a specific change in NPC composition is required for both myogenic and neuronal differentiation. The transmembrane nucleoporin Nup210 is absent in proliferating myoblasts and embryonic stem cells (ESCs) but becomes expressed and incorporated into NPCs during cell differentiation. Preventing Nup210 production by RNAi blocks myogenesis and the differentiation of ESCs into neuroprogenitors. We found that the addition of Nup210 to NPCs does not affect nuclear transport but is required for the induction of genes that are essential for cell differentiation. Our results identify a single change in NPC composition as an essential step in cell differentiation and establish a role for Nup210 in gene expression regulation and cell fate determination.","lang":"eng"}],"date_updated":"2024-10-14T11:26:00Z","volume":22,"type":"journal_article","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"page":"446-458","extern":"1","day":"19","publisher":"Elsevier","_id":"11093","article_type":"original"},{"publication_status":"published","page":"205 - 209","date_published":"2012-07-12T00:00:00Z","_id":"113","month":"07","status":"public","year":"2012","publist_id":"7941","intvolume":"       487","extern":"1","author":[{"last_name":"Waitukaitis","first_name":"Scott R","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176"},{"first_name":"Heinrich","last_name":"Jaeger","full_name":"Jaeger, Heinrich"}],"day":"12","publisher":"Nature Publishing Group","date_created":"2018-12-11T11:44:42Z","citation":{"ista":"Waitukaitis SR, Jaeger H. 2012. Impact-activated solidification of dense suspensions via dynamic jamming fronts. Nature. 487(7406), 205–209.","apa":"Waitukaitis, S. R., &#38; Jaeger, H. (2012). Impact-activated solidification of dense suspensions via dynamic jamming fronts. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature11187\">https://doi.org/10.1038/nature11187</a>","ieee":"S. R. Waitukaitis and H. Jaeger, “Impact-activated solidification of dense suspensions via dynamic jamming fronts,” <i>Nature</i>, vol. 487, no. 7406. Nature Publishing Group, pp. 205–209, 2012.","chicago":"Waitukaitis, Scott R, and Heinrich Jaeger. “Impact-Activated Solidification of Dense Suspensions via Dynamic Jamming Fronts.” <i>Nature</i>. Nature Publishing Group, 2012. <a href=\"https://doi.org/10.1038/nature11187\">https://doi.org/10.1038/nature11187</a>.","short":"S.R. Waitukaitis, H. Jaeger, Nature 487 (2012) 205–209.","ama":"Waitukaitis SR, Jaeger H. Impact-activated solidification of dense suspensions via dynamic jamming fronts. <i>Nature</i>. 2012;487(7406):205-209. doi:<a href=\"https://doi.org/10.1038/nature11187\">10.1038/nature11187</a>","mla":"Waitukaitis, Scott R., and Heinrich Jaeger. “Impact-Activated Solidification of Dense Suspensions via Dynamic Jamming Fronts.” <i>Nature</i>, vol. 487, no. 7406, Nature Publishing Group, 2012, pp. 205–09, doi:<a href=\"https://doi.org/10.1038/nature11187\">10.1038/nature11187</a>."},"doi":"10.1038/nature11187","oa_version":"None","title":"Impact-activated solidification of dense suspensions via dynamic jamming fronts","issue":"7406","type":"journal_article","volume":487,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"Nature","abstract":[{"text":"Although liquids typically flow around intruding objects, a counterintuitive phenomenon occurs in dense suspensions of micrometre-sized particles: they become liquid-like when perturbed lightly, but harden when driven strongly. Rheological experiments have investigated how such thickening arises under shear, and linked it to hydrodynamic interactions or granular dilation. However, neither of these mechanisms alone can explain the ability of suspensions to generate very large, positive normal stresses under impact. To illustrate the phenomenon, such stresses can be large enough to allow a person to run across a suspension without sinking, and far exceed the upper limit observed under shear or extension. Here we show that these stresses originate from an impact-generated solidification front that transforms an initially compressible particle matrix into a rapidly growing jammed region, ultimately leading to extraordinary amounts of momentum absorption. Using high-speed videography, embedded force sensing and X-ray imaging, we capture the detailed dynamics of this process as it decelerates a metal rod hitting a suspension of cornflour (cornstarch) in water. We develop a model for the dynamic solidification and its effect on the surrounding suspension that reproduces the observed behaviour quantitatively. Our findings suggest that prior interpretations of the impact resistance as dominated by shear thickening need to be revisited.","lang":"eng"}],"acknowledgement":"This work was supported by NSF through its MRSEC programme (DMR-0820054) and by the US Army Research Office through grant number W911NF-12-1-0182. S.R.W. acknowledges support from a Millikan fellowship.","date_updated":"2021-01-12T06:48:30Z"},{"title":"Solidification of a cornstarch and water suspension","quality_controlled":"1","file":[{"creator":"kschuh","content_type":"application/pdf","file_id":"6461","file_size":589776,"success":1,"file_name":"2012_RCF_Waitukaitis.pdf","access_level":"open_access","date_updated":"2019-05-16T11:08:52Z","date_created":"2019-05-16T11:08:52Z","relation":"main_file"}],"file_date_updated":"2019-05-16T11:08:52Z","oa_version":"Published Version","ddc":["530"],"acknowledgement":"This work was supported by the NSF through its MRSEC program (DMR-0820054). S. R. W. acknowledges support from a Millikan fellowship.","publication":"Revista Cubana de Fisica","date_published":"2012-08-14T00:00:00Z","publication_status":"published","date_created":"2018-12-11T11:44:42Z","author":[{"orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","full_name":"Waitukaitis, Scott R","first_name":"Scott R","last_name":"Waitukaitis"},{"full_name":"Jaeger, Heinrich","first_name":"Heinrich","last_name":"Jaeger"}],"intvolume":"        29","publist_id":"7940","year":"2012","status":"public","month":"08","issue":"1E","license":"https://creativecommons.org/licenses/by-nc/4.0/","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"has_accepted_license":"1","citation":{"mla":"Waitukaitis, Scott R., and Heinrich Jaeger. “Solidification of a Cornstarch and Water Suspension.” <i>Revista Cubana de Fisica</i>, vol. 29, no. 1E, Universidad de La Habana, 2012, p. 1E31-1E33.","ama":"Waitukaitis SR, Jaeger H. Solidification of a cornstarch and water suspension. <i>Revista Cubana de Fisica</i>. 2012;29(1E):1E31-1E33.","short":"S.R. Waitukaitis, H. Jaeger, Revista Cubana de Fisica 29 (2012) 1E31-1E33.","chicago":"Waitukaitis, Scott R, and Heinrich Jaeger. “Solidification of a Cornstarch and Water Suspension.” <i>Revista Cubana de Fisica</i>. Universidad de La Habana, 2012.","ieee":"S. R. Waitukaitis and H. Jaeger, “Solidification of a cornstarch and water suspension,” <i>Revista Cubana de Fisica</i>, vol. 29, no. 1E. Universidad de La Habana, p. 1E31-1E33, 2012.","apa":"Waitukaitis, S. R., &#38; Jaeger, H. (2012). Solidification of a cornstarch and water suspension. <i>Revista Cubana de Fisica</i>. Universidad de La Habana.","ista":"Waitukaitis SR, Jaeger H. 2012. Solidification of a cornstarch and water suspension. Revista Cubana de Fisica. 29(1E), 1E31-1E33."},"date_updated":"2021-01-12T06:48:34Z","abstract":[{"lang":"eng","text":"We report on an investigation of the solidification of a cornstarch and water suspension during normal impact on its surface. We find that a finite time after impact, the suspension displays characteristics reminiscent of a solid, including localized stress transmission, the development of a yield stress, and some elastic energy storage. The time dependence of these characteristics depends on the thickness of the cornstarch layer, showing that the solidification is a dynamic process driven by the impacting object. These findings confirm previous speculations that rapidly applied normal stress transforms the normally fluid-like suspension into a temporarily jammed solid and draw a clear distinction between the effects of normal stress and shear stress in dense suspensions."}],"language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":29,"page":"1E31 - 1E33","publisher":"Universidad de La Habana","day":"14","extern":"1","_id":"114"},{"date_updated":"2021-11-29T14:29:25Z","abstract":[{"text":"We report numerical simulations of membrane tubulation driven by large colloidal particles. Using Monte Carlo simulations we study how the process depends on particle size and binding strength, and present accurate free energy calculations to sort out how tube formation compares with the competing budding process. We find that tube formation is a result of the collective behavior of the particles adhering on the surface, and it occurs for binding strengths that are smaller than those required for budding. We also find that long linear aggregates of particles forming on the membrane surface act as nucleation seeds for tubulation by lowering the free energy barrier associated to the process.","lang":"eng"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","keyword":["general physics and astronomy"],"volume":109,"type":"journal_article","issue":"18","article_number":"188101","citation":{"short":"A. Šarić, A. Cacciuto, Physical Review Letters 109 (2012).","ama":"Šarić A, Cacciuto A. Mechanism of membrane tube formation induced by adhesive nanocomponents. <i>Physical Review Letters</i>. 2012;109(18). doi:<a href=\"https://doi.org/10.1103/physrevlett.109.188101\">10.1103/physrevlett.109.188101</a>","mla":"Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation Induced by Adhesive Nanocomponents.” <i>Physical Review Letters</i>, vol. 109, no. 18, 188101, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/physrevlett.109.188101\">10.1103/physrevlett.109.188101</a>.","ista":"Šarić A, Cacciuto A. 2012. Mechanism of membrane tube formation induced by adhesive nanocomponents. Physical Review Letters. 109(18), 188101.","apa":"Šarić, A., &#38; Cacciuto, A. (2012). Mechanism of membrane tube formation induced by adhesive nanocomponents. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.109.188101\">https://doi.org/10.1103/physrevlett.109.188101</a>","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation Induced by Adhesive Nanocomponents.” <i>Physical Review Letters</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/physrevlett.109.188101\">https://doi.org/10.1103/physrevlett.109.188101</a>.","ieee":"A. Šarić and A. Cacciuto, “Mechanism of membrane tube formation induced by adhesive nanocomponents,” <i>Physical Review Letters</i>, vol. 109, no. 18. American Physical Society, 2012."},"publisher":"American Physical Society","day":"31","extern":"1","article_type":"original","_id":"10387","pmid":1,"publication":"Physical Review Letters","article_processing_charge":"No","scopus_import":"1","title":"Mechanism of membrane tube formation induced by adhesive nanocomponents","quality_controlled":"1","external_id":{"arxiv":["1206.3528"],"pmid":["23215334"]},"oa_version":"Preprint","doi":"10.1103/physrevlett.109.188101","date_created":"2021-11-29T14:08:00Z","arxiv":1,"author":[{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić"},{"full_name":"Cacciuto, Angelo","first_name":"Angelo","last_name":"Cacciuto"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"intvolume":"       109","year":"2012","status":"public","month":"10","date_published":"2012-10-31T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1206.3528","open_access":"1"}],"publication_status":"published"},{"abstract":[{"text":"Using computer simulations, we show that lipid membranes can mediate linear aggregation of spherical nanoparticles binding to it for a wide range of biologically relevant bending rigidities. This result is in net contrast with the isotropic aggregation of nanoparticles on fluid interfaces or the expected clustering of isotropic insertions in biological membranes. We present a phase diagram indicating where linear aggregation is expected and compute explicitly the free-energy barriers associated with linear and isotropic aggregation. Finally, we provide simple scaling arguments to explain this phenomenology.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2021-11-29T15:12:13Z","keyword":["general physics and astronomy"],"type":"journal_article","volume":108,"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"11","article_number":"118101","citation":{"ama":"Šarić A, Cacciuto A. Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. <i>Physical Review Letters</i>. 2012;108(11). doi:<a href=\"https://doi.org/10.1103/physrevlett.108.118101\">10.1103/physrevlett.108.118101</a>","short":"A. Šarić, A. Cacciuto, Physical Review Letters 108 (2012).","mla":"Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation of Adsorbed Spherical Nanoparticles.” <i>Physical Review Letters</i>, vol. 108, no. 11, 118101, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/physrevlett.108.118101\">10.1103/physrevlett.108.118101</a>.","ista":"Šarić A, Cacciuto A. 2012. Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. Physical Review Letters. 108(11), 118101.","ieee":"A. Šarić and A. Cacciuto, “Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles,” <i>Physical Review Letters</i>, vol. 108, no. 11. American Physical Society, 2012.","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation of Adsorbed Spherical Nanoparticles.” <i>Physical Review Letters</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/physrevlett.108.118101\">https://doi.org/10.1103/physrevlett.108.118101</a>.","apa":"Šarić, A., &#38; Cacciuto, A. (2012). Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.108.118101\">https://doi.org/10.1103/physrevlett.108.118101</a>"},"extern":"1","day":"14","publisher":"American Physical Society","article_type":"original","_id":"10388","publication":"Physical Review Letters","pmid":1,"acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR-0846426.\r\n","article_processing_charge":"No","title":"Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles","quality_controlled":"1","scopus_import":"1","doi":"10.1103/physrevlett.108.118101","oa_version":"Preprint","external_id":{"arxiv":["1201.0036"],"pmid":["22540513"]},"author":[{"first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"first_name":"Angelo","last_name":"Cacciuto","full_name":"Cacciuto, Angelo"}],"intvolume":"       108","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"date_created":"2021-11-29T14:30:05Z","arxiv":1,"status":"public","month":"03","year":"2012","main_file_link":[{"url":"https://arxiv.org/abs/1201.0036","open_access":"1"}],"date_published":"2012-03-14T00:00:00Z","publication_status":"published"}]