[{"author":[{"full_name":"Leonid Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","last_name":"Sazanov"},{"full_name":"Baradaran, Rozbeh ","first_name":"Rozbeh","last_name":"Baradaran"},{"full_name":"Efremov, Rouslan G","first_name":"Rouslan","last_name":"Efremov"},{"first_name":"John","full_name":"Berrisford, John M","last_name":"Berrisford"},{"first_name":"Gurdeep","full_name":"Minhas, Gurdeep S","last_name":"Minhas"}],"abstract":[{"lang":"eng","text":"Complex I (NADH:ubiquinone oxidoreductase) is central to cellular energy production, being the first and largest enzyme of the respiratory chain in mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the inner mitochondrial membrane and is involved in a wide range of human neurodegenerative disorders. Mammalian complex I is composed of 44 different subunits, whereas the 'minimal' bacterial version contains 14 highly conserved 'core' subunits. The L-shaped assembly consists of hydrophilic and membrane domains. We have determined all known atomic structures of complex I, starting from the hydrophilic domain of Thermus thermophilus enzyme (eight subunits, nine Fe-S clusters), followed by the membrane domains of the Escherichia coli (six subunits, 55 transmembrane helices) and T. thermophilus (seven subunits, 64 transmembrane helices) enzymes, and finally culminating in a recent crystal structure of the entire intact complex I from T. thermophilus (536 kDa, 16 subunits, nine Fe-S clusters, 64 transmembrane helices). The structure suggests an unusual and unique coupling mechanism via longrange conformational changes. Determination of the structure of the entire complex was possible only through this step-by-step approach, building on from smaller subcomplexes towards the entire assembly. Large membrane proteins are notoriously difficult to crystallize, and so various non-standard and sometimes counterintuitive approaches were employed in order to achieve crystal diffraction to high resolution and solve the structures. These steps, as well as the implications from the final structure, are discussed in the present review."}],"quality_controlled":0,"publisher":"Portland Press","date_created":"2018-12-11T11:55:00Z","month":"10","publication":"Biochemical Society Transactions","doi":"10.1042/BST20130193","extern":1,"citation":{"ieee":"L. A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, and G. Minhas, “A long road towards the structure of respiratory complex I, a giant molecular proton pump,” <i>Biochemical Society Transactions</i>, vol. 41, no. 5. Portland Press, pp. 1265–1271, 2013.","apa":"Sazanov, L. A., Baradaran, R., Efremov, R., Berrisford, J., &#38; Minhas, G. (2013). A long road towards the structure of respiratory complex I, a giant molecular proton pump. <i>Biochemical Society Transactions</i>. Portland Press. <a href=\"https://doi.org/10.1042/BST20130193\">https://doi.org/10.1042/BST20130193</a>","chicago":"Sazanov, Leonid A, Rozbeh Baradaran, Rouslan Efremov, John Berrisford, and Gurdeep Minhas. “A Long Road towards the Structure of Respiratory Complex I, a Giant Molecular Proton Pump.” <i>Biochemical Society Transactions</i>. Portland Press, 2013. <a href=\"https://doi.org/10.1042/BST20130193\">https://doi.org/10.1042/BST20130193</a>.","ama":"Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. A long road towards the structure of respiratory complex I, a giant molecular proton pump. <i>Biochemical Society Transactions</i>. 2013;41(5):1265-1271. doi:<a href=\"https://doi.org/10.1042/BST20130193\">10.1042/BST20130193</a>","short":"L.A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, G. Minhas, Biochemical Society Transactions 41 (2013) 1265–1271.","mla":"Sazanov, Leonid A., et al. “A Long Road towards the Structure of Respiratory Complex I, a Giant Molecular Proton Pump.” <i>Biochemical Society Transactions</i>, vol. 41, no. 5, Portland Press, 2013, pp. 1265–71, doi:<a href=\"https://doi.org/10.1042/BST20130193\">10.1042/BST20130193</a>.","ista":"Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. 2013. A long road towards the structure of respiratory complex I, a giant molecular proton pump. Biochemical Society Transactions. 41(5), 1265–1271."},"_id":"1977","publication_status":"published","intvolume":"        41","type":"journal_article","date_updated":"2021-01-12T06:54:28Z","issue":"5","page":"1265 - 1271","title":"A long road towards the structure of respiratory complex I, a giant molecular proton pump","day":"01","year":"2013","volume":41,"acknowledgement":"This work was funded by the Medical Research Council.","publist_id":"5106","status":"public","date_published":"2013-10-01T00:00:00Z"},{"publication_identifier":{"eissn":["1742-2051"],"issn":["1742-206X"]},"article_number":"2604","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2013-08-20T00:00:00Z","publication":"Molecular BioSystems","date_created":"2024-03-21T07:58:57Z","month":"08","scopus_import":"1","abstract":[{"lang":"eng","text":"Cytological profiling (CP) is an unbiased image-based screening technique that uses automated microscopy and image analysis to profile compounds based on numerous quantifiable phenotypic features. We used CP to evaluate a library of nearly 500 compounds with documented mechanisms of action (MOAs) spanning a wide range of biological pathways. We developed informatics techniques for generating dosage-independent phenotypic “fingerprints” for each compound, and for quantifying the likelihood that a compound's CP fingerprint corresponds to its annotated MOA. We identified groups of features that distinguish classes with closely related phenotypes, such as microtubule poisons vs. HSP90 inhibitors, and DNA synthesis vs. proteasome inhibitors. We tested several cases in which cytological profiles indicated novel mechanisms, including a tyrphostin kinase inhibitor involved in mitochondrial uncoupling, novel microtubule poisons, and a nominal PPAR-gamma ligand that acts as a proteasome inhibitor, using independent biochemical assays to confirm the MOAs predicted by the CP signatures. We also applied maximal-information statistics to identify correlations between cytological features and kinase inhibitory activities by combining the CP fingerprints of 24 kinase inhibitors with published data on their specificities against a diverse panel of kinases. The resulting analysis suggests a strategy for probing the biological functions of specific kinases by compiling cytological data from inhibitors of varying specificities."}],"language":[{"iso":"eng"}],"oa_version":"None","doi":"10.1039/c3mb70245f","citation":{"chicago":"Woehrmann, Marcos H., Walter M. Bray, James K. Durbin, Sean C. Nisam, Alicia K. Michael, Emerson Glassey, Joshua M. Stuart, and R. Scott Lokey. “Large-Scale Cytological Profiling for Functional Analysis of Bioactive Compounds.” <i>Molecular BioSystems</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3mb70245f\">https://doi.org/10.1039/c3mb70245f</a>.","apa":"Woehrmann, M. H., Bray, W. M., Durbin, J. K., Nisam, S. C., Michael, A. K., Glassey, E., … Lokey, R. S. (2013). Large-scale cytological profiling for functional analysis of bioactive compounds. <i>Molecular BioSystems</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3mb70245f\">https://doi.org/10.1039/c3mb70245f</a>","ieee":"M. H. Woehrmann <i>et al.</i>, “Large-scale cytological profiling for functional analysis of bioactive compounds,” <i>Molecular BioSystems</i>, vol. 9, no. 11. Royal Society of Chemistry, 2013.","ama":"Woehrmann MH, Bray WM, Durbin JK, et al. Large-scale cytological profiling for functional analysis of bioactive compounds. <i>Molecular BioSystems</i>. 2013;9(11). doi:<a href=\"https://doi.org/10.1039/c3mb70245f\">10.1039/c3mb70245f</a>","short":"M.H. Woehrmann, W.M. Bray, J.K. Durbin, S.C. Nisam, A.K. Michael, E. Glassey, J.M. Stuart, R.S. Lokey, Molecular BioSystems 9 (2013).","mla":"Woehrmann, Marcos H., et al. “Large-Scale Cytological Profiling for Functional Analysis of Bioactive Compounds.” <i>Molecular BioSystems</i>, vol. 9, no. 11, 2604, Royal Society of Chemistry, 2013, doi:<a href=\"https://doi.org/10.1039/c3mb70245f\">10.1039/c3mb70245f</a>.","ista":"Woehrmann MH, Bray WM, Durbin JK, Nisam SC, Michael AK, Glassey E, Stuart JM, Lokey RS. 2013. Large-scale cytological profiling for functional analysis of bioactive compounds. Molecular BioSystems. 9(11), 2604."},"_id":"15162","intvolume":"         9","day":"20","year":"2013","volume":9,"keyword":["Molecular Biology","Biotechnology"],"article_type":"original","publisher":"Royal Society of Chemistry","author":[{"last_name":"Woehrmann","full_name":"Woehrmann, Marcos H.","first_name":"Marcos H."},{"last_name":"Bray","first_name":"Walter M.","full_name":"Bray, Walter M."},{"last_name":"Durbin","first_name":"James K.","full_name":"Durbin, James K."},{"full_name":"Nisam, Sean C.","first_name":"Sean C.","last_name":"Nisam"},{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael","full_name":"Michael, Alicia Kathleen","first_name":"Alicia Kathleen"},{"first_name":"Emerson","full_name":"Glassey, Emerson","last_name":"Glassey"},{"full_name":"Stuart, Joshua M.","first_name":"Joshua M.","last_name":"Stuart"},{"last_name":"Lokey","first_name":"R. Scott","full_name":"Lokey, R. Scott"}],"quality_controlled":"1","date_updated":"2024-03-25T11:45:46Z","issue":"11","article_processing_charge":"No","title":"Large-scale cytological profiling for functional analysis of bioactive compounds","extern":"1","publication_status":"published","type":"journal_article"},{"publication_identifier":{"issn":["0003-0503"]},"date_published":"2013-03-01T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","article_number":"N36.00001","abstract":[{"text":"Fluxoid quantization provides a direct means to study phase coherence. In cuprate superconductors, there have been observations which suggest that phase coherent superconducting fluctuations may persist at temperatures significantly above Tc. The focus of this work is to study the vortex states in mesoscopic cuprate superconducting samples to directly probe phase coherence over a wide range of temperatures. We present cantilever torque susceptometry measurements of micron and sub-micron size Bi2212 rings and disks. The high sensitivity of this technique allowed observation of transitions between different fluxoid states of a single ring, and the discrete vortex states of micron size disks. The dependence of magnetic susceptibility on diameter and wall thickness of the ring was investigated. Measurements were made at different values of the in-plane magnetic field, and over a wide range of temperatures.","lang":"eng"}],"publication":"APS March Meeting 2013","date_created":"2022-02-08T10:34:29Z","month":"03","oa":1,"_id":"10749","intvolume":"        58","oa_version":"Published Version","citation":{"ista":"Polshyn H, Budakian R, Gu G. 2013. Cantilever micro-susceptometry of mesoscopic Bi2212 samples. APS March Meeting 2013. APS: American Physical Society, Bulletin of the American Physical Society, vol. 58, N36.00001.","mla":"Polshyn, Hryhoriy, et al. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212 Samples.” <i>APS March Meeting 2013</i>, vol. 58, no. 1, N36.00001, American Physical Society, 2013.","short":"H. Polshyn, R. Budakian, G. Gu, in:, APS March Meeting 2013, American Physical Society, 2013.","ama":"Polshyn H, Budakian R, Gu G. Cantilever micro-susceptometry of mesoscopic Bi2212 samples. In: <i>APS March Meeting 2013</i>. Vol 58. American Physical Society; 2013.","apa":"Polshyn, H., Budakian, R., &#38; Gu, G. (2013). Cantilever micro-susceptometry of mesoscopic Bi2212 samples. In <i>APS March Meeting 2013</i> (Vol. 58). Baltimore, MD, United States: American Physical Society.","chicago":"Polshyn, Hryhoriy, Raffi Budakian, and Genda Gu. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212 Samples.” In <i>APS March Meeting 2013</i>, Vol. 58. American Physical Society, 2013.","ieee":"H. Polshyn, R. Budakian, and G. Gu, “Cantilever micro-susceptometry of mesoscopic Bi2212 samples,” in <i>APS March Meeting 2013</i>, Baltimore, MD, United States, 2013, vol. 58, no. 1."},"language":[{"iso":"eng"}],"year":"2013","volume":58,"day":"01","acknowledgement":"This work was supported by the Center for Emergent Superconductivity, an Energy Frontier Research Center funded by the US DOE, Office of Science.","alternative_title":["Bulletin of the American Physical Society"],"conference":{"start_date":"2013-03-18","name":"APS: American Physical Society","end_date":"2013-03-22","location":"Baltimore, MD, United States"},"author":[{"last_name":"Polshyn","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy"},{"last_name":"Budakian","first_name":"Raffi","full_name":"Budakian, Raffi"},{"last_name":"Gu","first_name":"Genda","full_name":"Gu, Genda"}],"main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR13/Event/186873","open_access":"1"}],"quality_controlled":"1","publisher":"American Physical Society","publication_status":"published","type":"conference","extern":"1","article_processing_charge":"No","title":"Cantilever micro-susceptometry of mesoscopic Bi2212 samples","date_updated":"2022-02-08T10:48:06Z","issue":"1"},{"file":[{"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_name":"2013_Plants_Vanneste.pdf","success":1,"file_size":670188,"date_created":"2022-03-21T12:12:56Z","file_id":"10916","access_level":"open_access","checksum":"fb4ff2e820e344e253c9197544610be6","date_updated":"2022-03-21T12:12:56Z"}],"publication_status":"published","type":"journal_article","date_updated":"2024-10-09T21:01:52Z","has_accepted_license":"1","issue":"4","article_processing_charge":"No","department":[{"_id":"JiFr"}],"title":"Calcium: The missing link in auxin action","author":[{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","ddc":["580"],"publisher":"MDPI","file_date_updated":"2022-03-21T12:12:56Z","external_id":{"pmid":["27137397"]},"keyword":["Plant Science","Ecology","Ecology","Evolution","Behavior and Systematics"],"article_type":"original","license":"https://creativecommons.org/licenses/by/3.0/","day":"21","year":"2013","volume":2,"oa_version":"Published Version","doi":"10.3390/plants2040650","citation":{"short":"S. Vanneste, J. Friml, Plants 2 (2013) 650–675.","mla":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” <i>Plants</i>, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:<a href=\"https://doi.org/10.3390/plants2040650\">10.3390/plants2040650</a>.","ista":"Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants. 2(4), 650–675.","ieee":"S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” <i>Plants</i>, vol. 2, no. 4. MDPI, pp. 650–675, 2013.","apa":"Vanneste, S., &#38; Friml, J. (2013). Calcium: The missing link in auxin action. <i>Plants</i>. MDPI. <a href=\"https://doi.org/10.3390/plants2040650\">https://doi.org/10.3390/plants2040650</a>","chicago":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” <i>Plants</i>. MDPI, 2013. <a href=\"https://doi.org/10.3390/plants2040650\">https://doi.org/10.3390/plants2040650</a>.","ama":"Vanneste S, Friml J. Calcium: The missing link in auxin action. <i>Plants</i>. 2013;2(4):650-675. doi:<a href=\"https://doi.org/10.3390/plants2040650\">10.3390/plants2040650</a>"},"corr_author":"1","_id":"10895","intvolume":"         2","language":[{"iso":"eng"}],"page":"650-675","scopus_import":"1","abstract":[{"lang":"eng","text":"Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. "}],"oa":1,"pmid":1,"month":"10","date_created":"2022-03-21T07:13:49Z","publication":"Plants","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2013-10-21T00:00:00Z","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"publication_identifier":{"issn":["2223-7747"]}},{"conference":{"location":"Vienna, Austria","end_date":"2013-05-17","name":"GbRPR: Graph-based Representations in Pattern Recognition","start_date":"2013-05-15"},"project":[{"grant_number":"318493","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems"}],"volume":7877,"year":"2013","day":"01","acknowledgement":"This research is partially supported by the European Science Foundation (ESF) under the Research Network Programme, the European Union under the Toposys Project FP7-ICT-318493-STREP, the Russian Government under the Mega Project 11.G34.31.0053.","type":"conference","publication_status":"published","department":[{"_id":"HeEd"}],"title":"Persistent homology in image processing","article_processing_charge":"No","date_updated":"2025-04-15T08:37:54Z","quality_controlled":"1","author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"}],"publisher":"Springer Nature","series_title":"LNCS","date_published":"2013-06-01T00:00:00Z","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eisbn":["9783642382215"],"eissn":["1611-3349"],"isbn":["9783642382208"],"issn":["0302-9743"]},"intvolume":"      7877","corr_author":"1","_id":"10897","citation":{"apa":"Edelsbrunner, H. (2013). Persistent homology in image processing. In <i>Graph-Based Representations in Pattern Recognition</i> (Vol. 7877, pp. 182–183). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">https://doi.org/10.1007/978-3-642-38221-5_19</a>","chicago":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” In <i>Graph-Based Representations in Pattern Recognition</i>, 7877:182–83. LNCS. Berlin, Heidelberg: Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">https://doi.org/10.1007/978-3-642-38221-5_19</a>.","ieee":"H. Edelsbrunner, “Persistent homology in image processing,” in <i>Graph-Based Representations in Pattern Recognition</i>, Vienna, Austria, 2013, vol. 7877, pp. 182–183.","ama":"Edelsbrunner H. Persistent homology in image processing. In: <i>Graph-Based Representations in Pattern Recognition</i>. Vol 7877. LNCS. Berlin, Heidelberg: Springer Nature; 2013:182-183. doi:<a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">10.1007/978-3-642-38221-5_19</a>","short":"H. Edelsbrunner, in:, Graph-Based Representations in Pattern Recognition, Springer Nature, Berlin, Heidelberg, 2013, pp. 182–183.","mla":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” <i>Graph-Based Representations in Pattern Recognition</i>, vol. 7877, Springer Nature, 2013, pp. 182–83, doi:<a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">10.1007/978-3-642-38221-5_19</a>.","ista":"Edelsbrunner H. 2013. Persistent homology in image processing. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNCS vol. 7877, 182–183."},"doi":"10.1007/978-3-642-38221-5_19","oa_version":"None","page":"182-183","place":"Berlin, Heidelberg","language":[{"iso":"eng"}],"ec_funded":1,"scopus_import":"1","abstract":[{"text":"Taking images is an efficient way to collect data about the physical world. It can be done fast and in exquisite detail. By definition, image processing is the field that concerns itself with the computation aimed at harnessing the information contained in images [10]. This talk is concerned with topological information. Our main thesis is that persistent homology [5] is a useful method to quantify and summarize topological information, building a bridge that connects algebraic topology with applications. We provide supporting evidence for this thesis by touching upon four technical developments in the overlap between persistent homology and image processing.","lang":"eng"}],"publication":"Graph-Based Representations in Pattern Recognition","date_created":"2022-03-21T07:30:33Z","month":"06"},{"date_published":"2013-05-14T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","article_number":"17","publication_identifier":{"isbn":["978-145032053-5"]},"_id":"10898","oa_version":"None","doi":"10.1145/2482767.2482789","citation":{"ama":"Haas A, Lippautz M, Henzinger TA, et al. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In: <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. ACM; 2013. doi:<a href=\"https://doi.org/10.1145/2482767.2482789\">10.1145/2482767.2482789</a>","chicago":"Haas, Andreas, Michael Lippautz, Thomas A Henzinger, Hannes Payer, Ana Sokolova, Christoph M. Kirsch, and Ali Sezgin. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” In <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2482767.2482789\">https://doi.org/10.1145/2482767.2482789</a>.","ieee":"A. Haas <i>et al.</i>, “Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation,” in <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>, Ischia, Italy, 2013, no. 5.","apa":"Haas, A., Lippautz, M., Henzinger, T. A., Payer, H., Sokolova, A., Kirsch, C. M., &#38; Sezgin, A. (2013). Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. Ischia, Italy: ACM. <a href=\"https://doi.org/10.1145/2482767.2482789\">https://doi.org/10.1145/2482767.2482789</a>","short":"A. Haas, M. Lippautz, T.A. Henzinger, H. Payer, A. Sokolova, C.M. Kirsch, A. Sezgin, in:, Proceedings of the ACM International Conference on Computing Frontiers - CF ’13, ACM, 2013.","mla":"Haas, Andreas, et al. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>, no. 5, 17, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2482767.2482789\">10.1145/2482767.2482789</a>.","ista":"Haas A, Lippautz M, Henzinger TA, Payer H, Sokolova A, Kirsch CM, Sezgin A. 2013. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. CF: Conference on Computing Frontiers, 17."},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered."}],"ec_funded":1,"scopus_import":"1","month":"05","publication":"Proceedings of the ACM International Conference on Computing Frontiers - CF '13","date_created":"2022-03-21T07:33:22Z","conference":{"start_date":"2013-05-14","name":"CF: Conference on Computing Frontiers","end_date":"2013-05-16","location":"Ischia, Italy"},"project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"}],"year":"2013","day":"14","acknowledgement":"This work has been supported by the European Research Council advanced grant on Quantitative Reactive Modeling (QUAREM) and the National Research Network RiSE on Rigorous Systems Engineering (Austrian Science Fund S11402-N23 and S11404-N23).","publication_status":"published","type":"conference","article_processing_charge":"No","title":"Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation","department":[{"_id":"ToHe"}],"date_updated":"2025-05-14T11:23:58Z","issue":"5","author":[{"full_name":"Haas, Andreas","first_name":"Andreas","last_name":"Haas"},{"full_name":"Lippautz, Michael","first_name":"Michael","last_name":"Lippautz"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000-0002-2985-7724"},{"full_name":"Payer, Hannes","first_name":"Hannes","last_name":"Payer"},{"first_name":"Ana","full_name":"Sokolova, Ana","last_name":"Sokolova"},{"full_name":"Kirsch, Christoph M.","first_name":"Christoph M.","last_name":"Kirsch"},{"first_name":"Ali","full_name":"Sezgin, Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","publisher":"ACM"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2013-01-01T00:00:00Z","keyword":["Adaptive landscape","Cline","Coalescent process","Gene flow","Hybrid zone","Local adaptation","Natural selection","Neutral theory","Population structure","Speciation"],"day":"01","year":"2013","publication_identifier":{"isbn":["978-0-12-384720-1"]},"oa_version":"None","doi":"10.1016/b978-0-12-384719-5.00031-9","citation":{"ista":"Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515.","mla":"Barton, Nicholas H. “Differentiation.” <i>Encyclopedia of Biodiversity</i>, 2nd ed., Elsevier, 2013, pp. 508–15, doi:<a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">10.1016/b978-0-12-384719-5.00031-9</a>.","short":"N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515.","apa":"Barton, N. H. (2013). Differentiation. In <i>Encyclopedia of Biodiversity</i> (2nd ed., pp. 508–515). Elsevier. <a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">https://doi.org/10.1016/b978-0-12-384719-5.00031-9</a>","ieee":"N. H. Barton, “Differentiation,” in <i>Encyclopedia of Biodiversity</i>, 2nd ed., Elsevier, 2013, pp. 508–515.","chicago":"Barton, Nicholas H. “Differentiation.” In <i>Encyclopedia of Biodiversity</i>, 2nd ed., 508–15. Elsevier, 2013. <a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">https://doi.org/10.1016/b978-0-12-384719-5.00031-9</a>.","ama":"Barton NH. Differentiation. In: <i>Encyclopedia of Biodiversity</i>. 2nd ed. Elsevier; 2013:508-515. doi:<a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">10.1016/b978-0-12-384719-5.00031-9</a>"},"corr_author":"1","_id":"10899","publication_status":"published","type":"book_chapter","language":[{"iso":"eng"}],"date_updated":"2024-10-09T21:02:37Z","edition":"2","article_processing_charge":"No","department":[{"_id":"NiBa"}],"title":"Differentiation","page":"508-515","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"scopus_import":"1","quality_controlled":"1","publisher":"Elsevier","publication":"Encyclopedia of Biodiversity","month":"01","date_created":"2022-03-21T07:46:22Z"},{"external_id":{"pmid":["23625502"]},"year":"2013","volume":1013,"day":"03","alternative_title":["Methods in Molecular Biology"],"acknowledgement":"We would like to thank Alexander Eichner and Ingrid de Vries for discussion and critical reading of the manuscript, and Mary Frank for assistance with the recording of videos and images in Fig. 1. M.S. is supported through funding from the German Research Foundation (DFG). M.W. acknowledges the Alexander von Humboldt Foundation for funding.","publication_status":"published","type":"book_chapter","article_processing_charge":"No","title":"Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations","department":[{"_id":"MiSi"}],"date_updated":"2024-10-09T21:02:37Z","author":[{"first_name":"Michele","full_name":"Weber, Michele","last_name":"Weber","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K"}],"quality_controlled":"1","publisher":"Humana Press","series_title":"MIMB","editor":[{"last_name":"Cardona","full_name":"Cardona, Astrid","first_name":"Astrid"},{"last_name":"Ubogu","full_name":"Ubogu, Eroboghene","first_name":"Eroboghene"}],"date_published":"2013-04-03T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","publication_identifier":{"eissn":["1940-6029"],"eisbn":["9781627034265"],"isbn":["9781627034258"],"issn":["1064-3745"]},"corr_author":"1","_id":"10900","intvolume":"      1013","oa_version":"None","doi":"10.1007/978-1-62703-426-5_14","citation":{"short":"M. Weber, M.K. Sixt, in:, A. Cardona, E. Ubogu (Eds.), Chemokines, Humana Press, Totowa, NJ, 2013, pp. 215–226.","mla":"Weber, Michele, and Michael K. Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” <i>Chemokines</i>, edited by Astrid Cardona and Eroboghene Ubogu, vol. 1013, Humana Press, 2013, pp. 215–26, doi:<a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">10.1007/978-1-62703-426-5_14</a>.","ista":"Weber M, Sixt MK. 2013.Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Chemokines. Methods in Molecular Biology, vol. 1013, 215–226.","chicago":"Weber, Michele, and Michael K Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” In <i>Chemokines</i>, edited by Astrid Cardona and Eroboghene Ubogu, 1013:215–26. MIMB. Totowa, NJ: Humana Press, 2013. <a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">https://doi.org/10.1007/978-1-62703-426-5_14</a>.","apa":"Weber, M., &#38; Sixt, M. K. (2013). Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In A. Cardona &#38; E. Ubogu (Eds.), <i>Chemokines</i> (Vol. 1013, pp. 215–226). Totowa, NJ: Humana Press. <a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">https://doi.org/10.1007/978-1-62703-426-5_14</a>","ieee":"M. Weber and M. K. Sixt, “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations,” in <i>Chemokines</i>, vol. 1013, A. Cardona and E. Ubogu, Eds. Totowa, NJ: Humana Press, 2013, pp. 215–226.","ama":"Weber M, Sixt MK. Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Cardona A, Ubogu E, eds. <i>Chemokines</i>. Vol 1013. MIMB. Totowa, NJ: Humana Press; 2013:215-226. doi:<a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">10.1007/978-1-62703-426-5_14</a>"},"place":"Totowa, NJ","page":"215-226","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"text":"Leukocyte migration through the interstitial space is crucial for the maintenance of tolerance and immunity. The main cues for leukocyte trafficking are chemokines thought to directionally guide these cells towards their targets. However, model systems that facilitate quantification of chemokine-guided leukocyte migration in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted mouse ears that allows the visualization of chemokine-dependent dendritic cell (DC) motility in the dermal interstitium in real time. We present methods for the preparation of mouse ear sheets and their use in multidimensional confocal imaging experiments to monitor and analyze the directional migration of fluorescently labelled DCs through the dermis and into afferent lymphatic vessels. The assay provides a more physiological approach to study leukocyte migration than in vitro three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen gels and transwell assays.","lang":"eng"}],"pmid":1,"date_created":"2022-03-21T07:47:41Z","month":"04","publication":"Chemokines"},{"conference":{"location":"Bilbao, Spain","name":"LATA: Language and Automata Theory and Applications","start_date":"2013-04-02","end_date":"2013-04-05"},"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23"},{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"alternative_title":["LNCS"],"acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award. Thanks to Gabriele Puppis for suggesting the problem of identifying a deterministic transducer to compute the optimal cost, and to Martin Chmelik for his comments on the introduction.","year":"2013","volume":7810,"day":"15","article_processing_charge":"No","title":"How to travel between languages","department":[{"_id":"KrCh"}],"date_updated":"2025-07-10T11:50:03Z","publication_status":"published","type":"conference","series_title":"LNCS","publisher":"Springer Nature","author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chaubal","first_name":"Siddhesh","full_name":"Chaubal, Siddhesh"},{"last_name":"Rubin","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha","full_name":"Rubin, Sasha"}],"quality_controlled":"1","date_published":"2013-04-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_identifier":{"isbn":["9783642370632"],"eisbn":["9783642370649"],"eissn":["1611-3349"],"issn":["0302-9743"]},"place":"Berlin, Heidelberg","page":"214-225","language":[{"iso":"eng"}],"_id":"10902","corr_author":"1","intvolume":"      7810","oa_version":"None","doi":"10.1007/978-3-642-37064-9_20","citation":{"ama":"Chatterjee K, Chaubal S, Rubin S. How to travel between languages. In: <i>7th International Conference on Language and Automata Theory and Applications</i>. Vol 7810. LNCS. Berlin, Heidelberg: Springer Nature; 2013:214-225. doi:<a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">10.1007/978-3-642-37064-9_20</a>","ieee":"K. Chatterjee, S. Chaubal, and S. Rubin, “How to travel between languages,” in <i>7th International Conference on Language and Automata Theory and Applications</i>, Bilbao, Spain, 2013, vol. 7810, pp. 214–225.","apa":"Chatterjee, K., Chaubal, S., &#38; Rubin, S. (2013). How to travel between languages. In <i>7th International Conference on Language and Automata Theory and Applications</i> (Vol. 7810, pp. 214–225). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">https://doi.org/10.1007/978-3-642-37064-9_20</a>","chicago":"Chatterjee, Krishnendu, Siddhesh Chaubal, and Sasha Rubin. “How to Travel between Languages.” In <i>7th International Conference on Language and Automata Theory and Applications</i>, 7810:214–25. LNCS. Berlin, Heidelberg: Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">https://doi.org/10.1007/978-3-642-37064-9_20</a>.","short":"K. Chatterjee, S. Chaubal, S. Rubin, in:, 7th International Conference on Language and Automata Theory and Applications, Springer Nature, Berlin, Heidelberg, 2013, pp. 214–225.","mla":"Chatterjee, Krishnendu, et al. “How to Travel between Languages.” <i>7th International Conference on Language and Automata Theory and Applications</i>, vol. 7810, Springer Nature, 2013, pp. 214–25, doi:<a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">10.1007/978-3-642-37064-9_20</a>.","ista":"Chatterjee K, Chaubal S, Rubin S. 2013. How to travel between languages. 7th International Conference on Language and Automata Theory and Applications. LATA: Language and Automata Theory and ApplicationsLNCS, LNCS, vol. 7810, 214–225."},"month":"04","publication":"7th International Conference on Language and Automata Theory and Applications","date_created":"2022-03-21T07:56:21Z","ec_funded":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"We consider how to edit strings from a source language so that the edited strings belong to a target language, where the languages are given as deterministic finite automata. Non-streaming (or offline) transducers perform edits given the whole source string. We show that the class of deterministic one-pass transducers with registers along with increment and min operation suffices for computing optimal edit distance, whereas the same class of transducers without the min operation is not sufficient. Streaming (or online) transducers perform edits as the letters of the source string are received. We present a polynomial time algorithm for the partial-repair problem that given a bound α asks for the construction of a deterministic streaming transducer (if one exists) that ensures that the ‘maximum fraction’ η of the strings of the source language are edited, within cost α, to the target language."}]},{"author":[{"full_name":"Franks, Tobias M.","first_name":"Tobias M.","last_name":"Franks"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","first_name":"Martin W"}],"quality_controlled":"1","publisher":"Elsevier","extern":"1","publication_status":"published","type":"journal_article","date_updated":"2024-10-14T11:23:44Z","issue":"3","article_processing_charge":"No","title":"The role of Nup98 in transcription regulation in healthy and diseased cells","day":"01","year":"2013","volume":23,"external_id":{"pmid":["23246429"]},"keyword":["Cell Biology"],"article_type":"letter_note","abstract":[{"text":"Nuclear pore complex (NPC) proteins are known for their critical roles in regulating nucleocytoplasmic traffic of macromolecules across the nuclear envelope. However, recent findings suggest that some nucleoporins (Nups), including Nup98, have additional functions in developmental gene regulation. Nup98, which exhibits transcription-dependent mobility at the NPC but can also bind chromatin away from the nuclear envelope, is frequently involved in chromosomal translocations in a subset of patients suffering from acute myeloid leukemia (AML). A common paradigm suggests that Nup98 translocations cause aberrant transcription when they are recuited to aberrant genomic loci. Importantly, this model fails to account for the potential loss of wild type (WT) Nup98 function in the presence of Nup98 translocation mutants. Here we examine how the cell might regulate Nup98 nucleoplasmic protein levels to control transcription in healthy cells. In addition, we discuss the possibility that dominant negative Nup98 fusion proteins disrupt the transcriptional activity of WT Nup98 in the nucleoplasm to drive AML.","lang":"eng"}],"scopus_import":"1","pmid":1,"date_created":"2022-04-07T07:50:33Z","publication":"Trends in Cell Biology","month":"03","doi":"10.1016/j.tcb.2012.10.013","oa_version":"None","citation":{"short":"T.M. Franks, M. Hetzer, Trends in Cell Biology 23 (2013) 112–117.","mla":"Franks, Tobias M., and Martin Hetzer. “The Role of Nup98 in Transcription Regulation in Healthy and Diseased Cells.” <i>Trends in Cell Biology</i>, vol. 23, no. 3, Elsevier, 2013, pp. 112–17, doi:<a href=\"https://doi.org/10.1016/j.tcb.2012.10.013\">10.1016/j.tcb.2012.10.013</a>.","ista":"Franks TM, Hetzer M. 2013. The role of Nup98 in transcription regulation in healthy and diseased cells. Trends in Cell Biology. 23(3), 112–117.","chicago":"Franks, Tobias M., and Martin Hetzer. “The Role of Nup98 in Transcription Regulation in Healthy and Diseased Cells.” <i>Trends in Cell Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.tcb.2012.10.013\">https://doi.org/10.1016/j.tcb.2012.10.013</a>.","ieee":"T. M. Franks and M. Hetzer, “The role of Nup98 in transcription regulation in healthy and diseased cells,” <i>Trends in Cell Biology</i>, vol. 23, no. 3. Elsevier, pp. 112–117, 2013.","apa":"Franks, T. M., &#38; Hetzer, M. (2013). The role of Nup98 in transcription regulation in healthy and diseased cells. <i>Trends in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcb.2012.10.013\">https://doi.org/10.1016/j.tcb.2012.10.013</a>","ama":"Franks TM, Hetzer M. The role of Nup98 in transcription regulation in healthy and diseased cells. <i>Trends in Cell Biology</i>. 2013;23(3):112-117. doi:<a href=\"https://doi.org/10.1016/j.tcb.2012.10.013\">10.1016/j.tcb.2012.10.013</a>"},"_id":"11083","intvolume":"        23","language":[{"iso":"eng"}],"page":"112-117","publication_identifier":{"issn":["0962-8924"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2013-03-01T00:00:00Z"},{"_id":"11084","intvolume":"        14","oa_version":"None","doi":"10.1038/nrm3496","citation":{"ieee":"B. H. Toyama and M. Hetzer, “Protein homeostasis: Live long, won’t prosper,” <i>Nature Reviews Molecular Cell Biology</i>, vol. 14. Springer Nature, pp. 55–61, 2013.","apa":"Toyama, B. H., &#38; Hetzer, M. (2013). Protein homeostasis: Live long, won’t prosper. <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nrm3496\">https://doi.org/10.1038/nrm3496</a>","chicago":"Toyama, Brandon H., and Martin Hetzer. “Protein Homeostasis: Live Long, Won’t Prosper.” <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature, 2013. <a href=\"https://doi.org/10.1038/nrm3496\">https://doi.org/10.1038/nrm3496</a>.","ama":"Toyama BH, Hetzer M. Protein homeostasis: Live long, won’t prosper. <i>Nature Reviews Molecular Cell Biology</i>. 2013;14:55-61. doi:<a href=\"https://doi.org/10.1038/nrm3496\">10.1038/nrm3496</a>","mla":"Toyama, Brandon H., and Martin Hetzer. “Protein Homeostasis: Live Long, Won’t Prosper.” <i>Nature Reviews Molecular Cell Biology</i>, vol. 14, Springer Nature, 2013, pp. 55–61, doi:<a href=\"https://doi.org/10.1038/nrm3496\">10.1038/nrm3496</a>.","ista":"Toyama BH, Hetzer M. 2013. Protein homeostasis: Live long, won’t prosper. Nature Reviews Molecular Cell Biology. 14, 55–61.","short":"B.H. Toyama, M. Hetzer, Nature Reviews Molecular Cell Biology 14 (2013) 55–61."},"page":"55-61","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Protein turnover is an effective way of maintaining a functional proteome, as old and potentially damaged polypeptides are destroyed and replaced by newly synthesized copies. An increasing number of intracellular proteins, however, have been identified that evade this turnover process and instead are maintained over a cell's lifetime. This diverse group of long-lived proteins might be particularly prone to accumulation of damage and thus have a crucial role in the functional deterioration of key regulatory processes during ageing."}],"scopus_import":"1","pmid":1,"publication":"Nature Reviews Molecular Cell Biology","date_created":"2022-04-07T07:50:43Z","month":"01","date_published":"2013-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_identifier":{"issn":["1471-0072","1471-0080"]},"publication_status":"published","type":"journal_article","extern":"1","article_processing_charge":"No","title":"Protein homeostasis: Live long, won't prosper","date_updated":"2024-10-14T11:24:09Z","author":[{"last_name":"Toyama","full_name":"Toyama, Brandon H.","first_name":"Brandon H."},{"full_name":"HETZER, Martin W","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","last_name":"HETZER"}],"quality_controlled":"1","publisher":"Springer Nature","article_type":"original","external_id":{"pmid":["23258296"]},"keyword":["Cell Biology","Molecular Biology"],"year":"2013","volume":14,"day":"01"},{"publication_identifier":{"issn":["0092-8674"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2013-07-03T00:00:00Z","oa":1,"date_created":"2022-04-07T07:50:51Z","publication":"Cell","month":"07","pmid":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"During mitotic exit, missegregated chromosomes can recruit their own nuclear envelope (NE) to form micronuclei (MN). MN have reduced functioning compared to primary nuclei in the same cell, although the two compartments appear to be structurally comparable. Here we show that over 60% of MN undergo an irreversible loss of compartmentalization during interphase due to NE collapse. This disruption of the MN, which is induced by defects in nuclear lamina assembly, drastically reduces nuclear functions and can trigger massive DNA damage. MN disruption is associated with chromatin compaction and invasion of endoplasmic reticulum (ER) tubules into the chromatin. We identified disrupted MN in both major subtypes of human non-small-cell lung cancer, suggesting that disrupted MN could be a useful objective biomarker for genomic instability in solid tumors. Our study shows that NE collapse is a key event underlying MN dysfunction and establishes a link between aberrant NE organization and aneuploidy."}],"language":[{"iso":"eng"}],"page":"47-60","citation":{"short":"E.M. Hatch, A.H. Fischer, T.J. Deerinck, M. Hetzer, Cell 154 (2013) 47–60.","mla":"Hatch, Emily M., et al. “Catastrophic Nuclear Envelope Collapse in Cancer Cell Micronuclei.” <i>Cell</i>, vol. 154, no. 1, Elsevier, 2013, pp. 47–60, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.06.007\">10.1016/j.cell.2013.06.007</a>.","ista":"Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. 2013. Catastrophic nuclear envelope collapse in cancer cell micronuclei. Cell. 154(1), 47–60.","ama":"Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. Catastrophic nuclear envelope collapse in cancer cell micronuclei. <i>Cell</i>. 2013;154(1):47-60. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.06.007\">10.1016/j.cell.2013.06.007</a>","apa":"Hatch, E. M., Fischer, A. H., Deerinck, T. J., &#38; Hetzer, M. (2013). Catastrophic nuclear envelope collapse in cancer cell micronuclei. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.06.007\">https://doi.org/10.1016/j.cell.2013.06.007</a>","chicago":"Hatch, Emily M., Andrew H. Fischer, Thomas J. Deerinck, and Martin Hetzer. “Catastrophic Nuclear Envelope Collapse in Cancer Cell Micronuclei.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.06.007\">https://doi.org/10.1016/j.cell.2013.06.007</a>.","ieee":"E. M. Hatch, A. H. Fischer, T. J. Deerinck, and M. Hetzer, “Catastrophic nuclear envelope collapse in cancer cell micronuclei,” <i>Cell</i>, vol. 154, no. 1. Elsevier, pp. 47–60, 2013."},"oa_version":"Published Version","doi":"10.1016/j.cell.2013.06.007","intvolume":"       154","_id":"11085","day":"03","volume":154,"year":"2013","keyword":["General Biochemistry","Genetics and Molecular Biology"],"external_id":{"pmid":["23827674"]},"article_type":"original","publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2013.06.007"}],"quality_controlled":"1","author":[{"last_name":"Hatch","full_name":"Hatch, Emily M.","first_name":"Emily M."},{"last_name":"Fischer","full_name":"Fischer, Andrew H.","first_name":"Andrew H."},{"full_name":"Deerinck, Thomas J.","first_name":"Thomas J.","last_name":"Deerinck"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","first_name":"Martin W"}],"issue":"1","date_updated":"2024-10-14T11:24:29Z","title":"Catastrophic nuclear envelope collapse in cancer cell micronuclei","article_processing_charge":"No","extern":"1","type":"journal_article","publication_status":"published"},{"citation":{"chicago":"Liang, Yun, Tobias M. Franks, Maria C. Marchetto, Fred H. Gage, and Martin Hetzer. “Dynamic Association of NUP98 with the Human Genome.” <i>PLoS Genetics</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pgen.1003308\">https://doi.org/10.1371/journal.pgen.1003308</a>.","ieee":"Y. Liang, T. M. Franks, M. C. Marchetto, F. H. Gage, and M. Hetzer, “Dynamic association of NUP98 with the human genome,” <i>PLoS Genetics</i>, vol. 9, no. 2. Public Library of Science, 2013.","apa":"Liang, Y., Franks, T. M., Marchetto, M. C., Gage, F. H., &#38; Hetzer, M. (2013). Dynamic association of NUP98 with the human genome. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1003308\">https://doi.org/10.1371/journal.pgen.1003308</a>","ama":"Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. Dynamic association of NUP98 with the human genome. <i>PLoS Genetics</i>. 2013;9(2). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1003308\">10.1371/journal.pgen.1003308</a>","short":"Y. Liang, T.M. Franks, M.C. Marchetto, F.H. Gage, M. Hetzer, PLoS Genetics 9 (2013).","mla":"Liang, Yun, et al. “Dynamic Association of NUP98 with the Human Genome.” <i>PLoS Genetics</i>, vol. 9, no. 2, e1003308, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1003308\">10.1371/journal.pgen.1003308</a>.","ista":"Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. 2013. Dynamic association of NUP98 with the human genome. PLoS Genetics. 9(2), e1003308."},"oa_version":"Published Version","doi":"10.1371/journal.pgen.1003308","intvolume":"         9","_id":"11086","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"text":"Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs.","lang":"eng"}],"oa":1,"date_created":"2022-04-07T07:50:59Z","month":"02","publication":"PLoS Genetics","pmid":1,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2013-02-28T00:00:00Z","article_number":"e1003308","publication_identifier":{"issn":["1553-7404"]},"extern":"1","type":"journal_article","publication_status":"published","issue":"2","date_updated":"2024-10-14T11:24:40Z","title":"Dynamic association of NUP98 with the human genome","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pgen.1003308"}],"quality_controlled":"1","author":[{"first_name":"Yun","full_name":"Liang, Yun","last_name":"Liang"},{"last_name":"Franks","first_name":"Tobias M.","full_name":"Franks, Tobias M."},{"last_name":"Marchetto","full_name":"Marchetto, Maria C.","first_name":"Maria C."},{"first_name":"Fred H.","full_name":"Gage, Fred H.","last_name":"Gage"},{"full_name":"HETZER, Martin W","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","orcid":"0000-0002-2111-992X"}],"publisher":"Public Library of Science","keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"external_id":{"pmid":["23468646"]},"article_type":"original","day":"28","volume":9,"year":"2013"},{"author":[{"last_name":"Toyama","first_name":"Brandon H.","full_name":"Toyama, Brandon H."},{"full_name":"Savas, Jeffrey N.","first_name":"Jeffrey N.","last_name":"Savas"},{"last_name":"Park","full_name":"Park, Sung Kyu","first_name":"Sung Kyu"},{"first_name":"Michael S.","full_name":"Harris, Michael S.","last_name":"Harris"},{"first_name":"Nicholas T.","full_name":"Ingolia, Nicholas T.","last_name":"Ingolia"},{"last_name":"Yates","first_name":"John R.","full_name":"Yates, John R."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","last_name":"HETZER","full_name":"HETZER, Martin W","first_name":"Martin W"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2013.07.037"}],"quality_controlled":"1","publisher":"Elsevier","publication_status":"published","type":"journal_article","extern":"1","article_processing_charge":"No","department":[{"_id":"MaHe"}],"title":"Identification of long-lived proteins reveals exceptional stability of essential cellular structures","date_updated":"2025-12-15T10:02:46Z","issue":"5","year":"2013","volume":154,"day":"29","article_type":"original","external_id":{"pmid":["23993091"]},"keyword":["General Biochemistry","Genetics and Molecular Biology"],"abstract":[{"text":"Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process.","lang":"eng"}],"scopus_import":"1","pmid":1,"month":"08","date_created":"2022-04-07T07:51:08Z","publication":"Cell","oa":1,"_id":"11087","intvolume":"       154","oa_version":"Published Version","doi":"10.1016/j.cell.2013.07.037","citation":{"chicago":"Toyama, Brandon H., Jeffrey N. Savas, Sung Kyu Park, Michael S. Harris, Nicholas T. Ingolia, John R. Yates, and Martin Hetzer. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">https://doi.org/10.1016/j.cell.2013.07.037</a>.","ieee":"B. H. Toyama <i>et al.</i>, “Identification of long-lived proteins reveals exceptional stability of essential cellular structures,” <i>Cell</i>, vol. 154, no. 5. Elsevier, pp. 971–982, 2013.","apa":"Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates, J. R., &#38; Hetzer, M. (2013). Identification of long-lived proteins reveals exceptional stability of essential cellular structures. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">https://doi.org/10.1016/j.cell.2013.07.037</a>","ama":"Toyama BH, Savas JN, Park SK, et al. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. <i>Cell</i>. 2013;154(5):971-982. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">10.1016/j.cell.2013.07.037</a>","short":"B.H. Toyama, J.N. Savas, S.K. Park, M.S. Harris, N.T. Ingolia, J.R. Yates, M. Hetzer, Cell 154 (2013) 971–982.","mla":"Toyama, Brandon H., et al. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” <i>Cell</i>, vol. 154, no. 5, Elsevier, 2013, pp. 971–82, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">10.1016/j.cell.2013.07.037</a>.","ista":"Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR, Hetzer M. 2013. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell. 154(5), 971–982."},"page":"971-982","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0092-8674"]},"date_published":"2013-08-29T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public"},{"day":"16","year":"2013","volume":104,"external_id":{"pmid":["23601312"]},"keyword":["Biophysics"],"article_type":"original","publisher":"Elsevier","author":[{"last_name":"Regner","full_name":"Regner, Benjamin M.","first_name":"Benjamin M."},{"first_name":"Dejan","full_name":"Vučinić, Dejan","last_name":"Vučinić"},{"last_name":"Domnisoru","full_name":"Domnisoru, Cristina","first_name":"Cristina"},{"last_name":"Bartol","first_name":"Thomas M.","full_name":"Bartol, Thomas M."},{"last_name":"HETZER","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","full_name":"HETZER, Martin W"},{"first_name":"Daniel M.","full_name":"Tartakovsky, Daniel M.","last_name":"Tartakovsky"},{"last_name":"Sejnowski","full_name":"Sejnowski, Terrence J.","first_name":"Terrence J."}],"main_file_link":[{"url":"https://doi.org/10.1016/j.bpj.2013.01.049","open_access":"1"}],"quality_controlled":"1","date_updated":"2022-07-18T08:51:01Z","issue":"8","article_processing_charge":"No","title":"Anomalous diffusion of single particles in cytoplasm","extern":"1","publication_status":"published","type":"journal_article","publication_identifier":{"issn":["0006-3495"]},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","status":"public","date_published":"2013-04-16T00:00:00Z","oa":1,"pmid":1,"month":"04","date_created":"2022-04-07T07:51:26Z","publication":"Biophysical Journal","scopus_import":"1","abstract":[{"lang":"eng","text":"The crowded intracellular environment poses a formidable challenge to experimental and theoretical analyses of intracellular transport mechanisms. Our measurements of single-particle trajectories in cytoplasm and their random-walk interpretations elucidate two of these mechanisms: molecular diffusion in crowded environments and cytoskeletal transport along microtubules. We employed acousto-optic deflector microscopy to map out the three-dimensional trajectories of microspheres migrating in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM), continuous time random walk, and fractional BM were alternatively used to represent these trajectories. The comparison of the experimental and numerical data demonstrates that cytoskeletal transport along microtubules and diffusion in the cytosolic fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct signatures. Among the three random-walk models used, continuous time random walk provides the best representation of diffusion, whereas microtubular transport is accurately modeled with fractional BM."}],"language":[{"iso":"eng"}],"page":"1652-1660","doi":"10.1016/j.bpj.2013.01.049","oa_version":"Published Version","citation":{"mla":"Regner, Benjamin M., et al. “Anomalous Diffusion of Single Particles in Cytoplasm.” <i>Biophysical Journal</i>, vol. 104, no. 8, Elsevier, 2013, pp. 1652–60, doi:<a href=\"https://doi.org/10.1016/j.bpj.2013.01.049\">10.1016/j.bpj.2013.01.049</a>.","ista":"Regner BM, Vučinić D, Domnisoru C, Bartol TM, Hetzer M, Tartakovsky DM, Sejnowski TJ. 2013. Anomalous diffusion of single particles in cytoplasm. Biophysical Journal. 104(8), 1652–1660.","short":"B.M. Regner, D. Vučinić, C. Domnisoru, T.M. Bartol, M. Hetzer, D.M. Tartakovsky, T.J. Sejnowski, Biophysical Journal 104 (2013) 1652–1660.","ama":"Regner BM, Vučinić D, Domnisoru C, et al. Anomalous diffusion of single particles in cytoplasm. <i>Biophysical Journal</i>. 2013;104(8):1652-1660. doi:<a href=\"https://doi.org/10.1016/j.bpj.2013.01.049\">10.1016/j.bpj.2013.01.049</a>","chicago":"Regner, Benjamin M., Dejan Vučinić, Cristina Domnisoru, Thomas M. Bartol, Martin Hetzer, Daniel M. Tartakovsky, and Terrence J. Sejnowski. “Anomalous Diffusion of Single Particles in Cytoplasm.” <i>Biophysical Journal</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.bpj.2013.01.049\">https://doi.org/10.1016/j.bpj.2013.01.049</a>.","apa":"Regner, B. M., Vučinić, D., Domnisoru, C., Bartol, T. M., Hetzer, M., Tartakovsky, D. M., &#38; Sejnowski, T. J. (2013). Anomalous diffusion of single particles in cytoplasm. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2013.01.049\">https://doi.org/10.1016/j.bpj.2013.01.049</a>","ieee":"B. M. Regner <i>et al.</i>, “Anomalous diffusion of single particles in cytoplasm,” <i>Biophysical Journal</i>, vol. 104, no. 8. Elsevier, pp. 1652–1660, 2013."},"_id":"11088","intvolume":"       104"},{"issue":"24","date_updated":"2021-11-29T14:05:19Z","title":"Living clusters and crystals from low-density suspensions of active colloids","article_processing_charge":"No","extern":"1","type":"journal_article","publication_status":"published","publisher":"American Physical Society","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.4681"}],"author":[{"last_name":"Mognetti","full_name":"Mognetti, B. M.","first_name":"B. M."},{"first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Angioletti-Uberti, S.","first_name":"S.","last_name":"Angioletti-Uberti"},{"full_name":"Cacciuto, A.","first_name":"A.","last_name":"Cacciuto"},{"last_name":"Valeriani","full_name":"Valeriani, C.","first_name":"C."},{"last_name":"Frenkel","first_name":"D.","full_name":"Frenkel, D."}],"keyword":["general physics and astronomy"],"external_id":{"pmid":["24483677"],"arxiv":["1311.4681"]},"article_type":"original","acknowledgement":"This work was supported by the ERC Advanced Grant 227758, the National Science Foundation under Career Grant No. DMR-0846426, the Wolfson Merit Award 2007/R3 of the Royal Society of London and the EPSRC Programme Grant EP/I001352/1. BMM acknowledge T. Curk and A. Ballard for useful discussions. C. V. acknowledges financial support from a Juan de la Cierva Fellowship, from the Marie Curie Integration Grant PCIG-GA-2011-303941 ANISOKINEQ, and from the National Project FIS2010- 16159. S. A-U acknowledges support from the Alexander von Humboldt Foundation.","day":"11","volume":111,"year":"2013","language":[{"iso":"eng"}],"citation":{"chicago":"Mognetti, B. M., Anđela Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, and D. Frenkel. “Living Clusters and Crystals from Low-Density Suspensions of Active Colloids.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/physrevlett.111.245702\">https://doi.org/10.1103/physrevlett.111.245702</a>.","apa":"Mognetti, B. M., Šarić, A., Angioletti-Uberti, S., Cacciuto, A., Valeriani, C., &#38; Frenkel, D. (2013). Living clusters and crystals from low-density suspensions of active colloids. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.111.245702\">https://doi.org/10.1103/physrevlett.111.245702</a>","ieee":"B. M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, and D. Frenkel, “Living clusters and crystals from low-density suspensions of active colloids,” <i>Physical Review Letters</i>, vol. 111, no. 24. American Physical Society, 2013.","ama":"Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel D. Living clusters and crystals from low-density suspensions of active colloids. <i>Physical Review Letters</i>. 2013;111(24). doi:<a href=\"https://doi.org/10.1103/physrevlett.111.245702\">10.1103/physrevlett.111.245702</a>","short":"B.M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, D. Frenkel, Physical Review Letters 111 (2013).","mla":"Mognetti, B. M., et al. “Living Clusters and Crystals from Low-Density Suspensions of Active Colloids.” <i>Physical Review Letters</i>, vol. 111, no. 24, 245702, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/physrevlett.111.245702\">10.1103/physrevlett.111.245702</a>.","ista":"Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel D. 2013. Living clusters and crystals from low-density suspensions of active colloids. Physical Review Letters. 111(24), 245702."},"doi":"10.1103/physrevlett.111.245702","oa_version":"Preprint","intvolume":"       111","_id":"10384","oa":1,"publication":"Physical Review Letters","month":"12","date_created":"2021-11-29T13:29:31Z","pmid":1,"scopus_import":"1","abstract":[{"text":"Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter, we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move toward each other as a result of active agents (e.g., by molecular motors). In both cases, fluidlike “living” clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behavior onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation.","lang":"eng"}],"article_number":"245702","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2013-12-11T00:00:00Z","arxiv":1,"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]}},{"volume":9,"year":"2013","day":"08","acknowledgement":"This work was supported by the National Science Foundation under Career Grant no. DMR-0846426.","article_type":"original","keyword":["condensed matter physics","general chemistry"],"quality_controlled":"1","author":[{"full_name":"Napoli, Joseph A.","first_name":"Joseph A.","last_name":"Napoli"},{"full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"first_name":"Angelo","full_name":"Cacciuto, Angelo","last_name":"Cacciuto"}],"publisher":"Royal Society of Chemistry","type":"journal_article","publication_status":"published","extern":"1","title":"Collapsing nanoparticle-laden nanotubes","article_processing_charge":"No","issue":"37","date_updated":"2021-11-29T14:05:23Z","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"date_published":"2013-08-08T00:00:00Z","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","scopus_import":"1","abstract":[{"text":"We show how self-assembly of sticky nanoparticles can drive radial collapse of thin-walled nanotubes. Using numerical simulations, we study the transition as a function of the geometric and elastic parameters of the nanotube and the binding strength of the nanoparticles. We find that it is possible to derive a simple scaling law relating all these parameters, and estimate bounds for the onset conditions leading to the collapse of the nanotube. We also study the reverse process – the nanoparticle release from the folded state – and find that the stability of the collapsed state can be greatly improved by increasing the bending rigidity of the nanotubes. Our results suggest ways to strengthen the mechanical properties of nanotubes, but also indicate that the control of nanoparticle self-assembly on these nanotubes can lead to nanoparticle-laden responsive materials.","lang":"eng"}],"month":"08","publication":"Soft Matter","date_created":"2021-11-29T13:31:24Z","intvolume":"         9","_id":"10385","citation":{"ama":"Napoli JA, Šarić A, Cacciuto A. Collapsing nanoparticle-laden nanotubes. <i>Soft Matter</i>. 2013;9(37):8881-8886. doi:<a href=\"https://doi.org/10.1039/c3sm51495a\">10.1039/c3sm51495a</a>","chicago":"Napoli, Joseph A., Anđela Šarić, and Angelo Cacciuto. “Collapsing Nanoparticle-Laden Nanotubes.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm51495a\">https://doi.org/10.1039/c3sm51495a</a>.","ieee":"J. A. Napoli, A. Šarić, and A. Cacciuto, “Collapsing nanoparticle-laden nanotubes,” <i>Soft Matter</i>, vol. 9, no. 37. Royal Society of Chemistry, pp. 8881–8886, 2013.","apa":"Napoli, J. A., Šarić, A., &#38; Cacciuto, A. (2013). Collapsing nanoparticle-laden nanotubes. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm51495a\">https://doi.org/10.1039/c3sm51495a</a>","mla":"Napoli, Joseph A., et al. “Collapsing Nanoparticle-Laden Nanotubes.” <i>Soft Matter</i>, vol. 9, no. 37, Royal Society of Chemistry, 2013, pp. 8881–86, doi:<a href=\"https://doi.org/10.1039/c3sm51495a\">10.1039/c3sm51495a</a>.","ista":"Napoli JA, Šarić A, Cacciuto A. 2013. Collapsing nanoparticle-laden nanotubes. Soft Matter. 9(37), 8881–8886.","short":"J.A. Napoli, A. Šarić, A. Cacciuto, Soft Matter 9 (2013) 8881–8886."},"doi":"10.1039/c3sm51495a","oa_version":"None","page":"8881-8886","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"In this paper we review recent numerical and theoretical developments of particle self-assembly on fluid and elastic membranes and compare them to available experimental realizations. We discuss the problem and its applications in biology and materials science, and give an overview of numerical models and strategies to study these systems across all length-scales. As this is a very broad field, this review focuses exclusively on surface-driven aggregation of nanoparticles that are at least one order of magnitude larger than the surface thickness and are adsorbed onto it. In this regime, all chemical details of the surface can be ignored in favor of a coarse-grained representation, and the collective behavior of many particles can be monitored and analyzed. We review the existing literature on how the mechanical properties and the geometry of the surface affect the structure of the particle aggregates and how these can drive shape deformation on the surface."}],"scopus_import":"1","month":"05","publication":"Soft Matter","date_created":"2021-11-29T14:06:32Z","intvolume":"         9","_id":"10386","citation":{"ama":"Šarić A, Cacciuto A. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. <i>Soft Matter</i>. 2013;9(29). doi:<a href=\"https://doi.org/10.1039/c3sm50188d\">10.1039/c3sm50188d</a>","ieee":"A. Šarić and A. Cacciuto, “Self-assembly of nanoparticles adsorbed on fluid and elastic membranes,” <i>Soft Matter</i>, vol. 9, no. 29. Royal Society of Chemistry, 2013.","apa":"Šarić, A., &#38; Cacciuto, A. (2013). Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm50188d\">https://doi.org/10.1039/c3sm50188d</a>","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm50188d\">https://doi.org/10.1039/c3sm50188d</a>.","short":"A. Šarić, A. Cacciuto, Soft Matter 9 (2013).","mla":"Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” <i>Soft Matter</i>, vol. 9, no. 29, 6677, Royal Society of Chemistry, 2013, doi:<a href=\"https://doi.org/10.1039/c3sm50188d\">10.1039/c3sm50188d</a>.","ista":"Šarić A, Cacciuto A. 2013. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. Soft Matter. 9(29), 6677."},"doi":"10.1039/c3sm50188d","oa_version":"None","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"date_published":"2013-05-03T00:00:00Z","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_number":"6677","quality_controlled":"1","main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2013/sm/c3sm50188d"}],"author":[{"first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Cacciuto, Angelo","first_name":"Angelo","last_name":"Cacciuto"}],"publisher":"Royal Society of Chemistry","type":"journal_article","publication_status":"published","extern":"1","title":"Self-assembly of nanoparticles adsorbed on fluid and elastic membranes","article_processing_charge":"No","issue":"29","date_updated":"2021-11-29T14:29:31Z","volume":9,"year":"2013","day":"03","acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR 0846426. The authors thank J. C. Pàmies for many fruitful discussions on the subject.","article_type":"original","keyword":["condensed matter physics","general chemistry"]},{"publisher":"De Gruyter","ddc":["005","610"],"author":[{"first_name":"Alois","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804"},{"full_name":"Schmidt-Hieber, C.","first_name":"C.","last_name":"Schmidt-Hieber"},{"full_name":"Guzman, S. J.","first_name":"S. J.","last_name":"Guzman"}],"quality_controlled":"1","article_processing_charge":"No","title":"Stimfit: A fast visualization and analysis environment for cellular neurophysiology","department":[{"_id":"PeJo"}],"date_updated":"2025-09-30T07:31:23Z","issue":"SI-1-Track-G","has_accepted_license":"1","publication_status":"published","type":"journal_article","file":[{"access_level":"open_access","checksum":"cdfc5339b530a25d6079f7223f0b1f16","date_updated":"2021-12-01T14:38:08Z","relation":"main_file","file_name":"Schloegl_Abstract-BMT2013.pdf","content_type":"application/pdf","creator":"schloegl","file_size":149825,"success":1,"file_id":"10397","date_created":"2021-12-01T14:38:08Z"}],"isi":1,"year":"2013","volume":58,"day":"01","article_type":"original","conference":{"start_date":"2013-09-19","name":"BMT: Biomedizinische Technik ","end_date":"2013-09-21","location":"Graz, Austria"},"external_id":{"isi":["000497714000034"],"pmid":["24042795"]},"keyword":["biomedical engineering","data analysis","free software"],"file_date_updated":"2021-12-01T14:38:08Z","pmid":1,"month":"08","publication":"Biomedical Engineering / Biomedizinische Technik","date_created":"2021-12-01T14:35:35Z","oa":1,"abstract":[{"lang":"eng","text":"Stimfit is a free cross-platform software package for viewing and analyzing electrophysiological data. It supports most standard file types for cellular neurophysiology and other biomedical formats. Its analysis algorithms have been used and validated in several experimental laboratories. Its embedded Python scripting interface makes Stimfit highly extensible and customizable."}],"language":[{"iso":"eng"}],"corr_author":"1","_id":"10396","intvolume":"        58","doi":"10.1515/bmt-2013-4181","oa_version":"Submitted Version","citation":{"mla":"Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>.","ista":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181.","short":"A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering / Biomedizinische Technik 58 (2013).","apa":"Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., &#38; Guzman, S. J. (2013). Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. Graz, Austria: De Gruyter. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>","chicago":"Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>. De Gruyter, 2013. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>.","ieee":"A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A fast visualization and analysis environment for cellular neurophysiology,” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G. De Gruyter, 2013.","ama":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. 2013;58(SI-1-Track-G). doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>"},"publication_identifier":{"eissn":["1862-278X"],"issn":["0013-5585"]},"article_number":"000010151520134181","date_published":"2013-08-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public"},{"date_published":"2013-07-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","article_number":"82","year":"2013","volume":32,"day":"01","acknowledgement":"This work was partly funded by the NCCR Co-Me of the Swiss NSF","publist_id":"4926","_id":"2107","publication_status":"published","type":"journal_article","intvolume":"        32","oa_version":"None","doi":"10.1145/2461912.2461979","citation":{"mla":"Skouras, Mélina, et al. “Computational Design of Actuated Deformable Characters.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, 82, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461979\">10.1145/2461912.2461979</a>.","ista":"Skouras M, Thomaszewski B, Coros S, Bickel B, Groß M. 2013. Computational design of actuated deformable characters. ACM Transactions on Graphics. 32(4), 82.","short":"M. Skouras, B. Thomaszewski, S. Coros, B. Bickel, M. Groß, ACM Transactions on Graphics 32 (2013).","ama":"Skouras M, Thomaszewski B, Coros S, Bickel B, Groß M. Computational design of actuated deformable characters. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461979\">10.1145/2461912.2461979</a>","ieee":"M. Skouras, B. Thomaszewski, S. Coros, B. Bickel, and M. Groß, “Computational design of actuated deformable characters,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","chicago":"Skouras, Mélina, Bernhard Thomaszewski, Stelian Coros, Bernd Bickel, and Markus Groß. “Computational Design of Actuated Deformable Characters.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461979\">https://doi.org/10.1145/2461912.2461979</a>.","apa":"Skouras, M., Thomaszewski, B., Coros, S., Bickel, B., &#38; Groß, M. (2013). Computational design of actuated deformable characters. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461979\">https://doi.org/10.1145/2461912.2461979</a>"},"extern":"1","article_processing_charge":"No","title":"Computational design of actuated deformable characters","date_updated":"2025-10-01T08:08:25Z","language":[{"iso":"eng"}],"issue":"4","author":[{"full_name":"Skouras, Mélina","first_name":"Mélina","last_name":"Skouras"},{"full_name":"Thomaszewski, Bernhard","first_name":"Bernhard","last_name":"Thomaszewski"},{"last_name":"Coros","full_name":"Coros, Stelian","first_name":"Stelian"},{"first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Groß","full_name":"Groß, Markus","first_name":"Markus"}],"abstract":[{"lang":"eng","text":"We present a method for fabrication-oriented design of actuated deformable characters that allows a user to automatically create physical replicas of digitally designed characters using rapid manufacturing technologies. Given a deformable character and a set of target poses as input, our method computes a small set of actuators along with their locations on the surface and optimizes the internal material distribution such that the resulting character exhibits the desired deformation behavior. We approach this problem with a dedicated algorithm that combines finite-element analysis, sparse regularization, and constrained optimization. We validate our pipeline on a set of two- and three-dimensional example characters and present results in simulation and physically-fabricated prototypes."}],"publisher":"ACM","date_created":"2018-12-11T11:55:45Z","month":"07","publication":"ACM Transactions on Graphics"}]