[{"title":"Differentiation","status":"public","scopus_import":"1","department":[{"_id":"NiBa"}],"publication":"Encyclopedia of Biodiversity","_id":"10899","citation":{"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>","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>.","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>.","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>","ista":"Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515.","short":"N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515.","ieee":"N. H. Barton, “Differentiation,” in <i>Encyclopedia of Biodiversity</i>, 2nd ed., Elsevier, 2013, pp. 508–515."},"doi":"10.1016/b978-0-12-384719-5.00031-9","publisher":"Elsevier","article_processing_charge":"No","language":[{"iso":"eng"}],"date_updated":"2024-10-09T21:02:37Z","date_published":"2013-01-01T00:00:00Z","page":"508-515","author":[{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","keyword":["Adaptive landscape","Cline","Coalescent process","Gene flow","Hybrid zone","Local adaptation","Natural selection","Neutral theory","Population structure","Speciation"],"month":"01","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","publication_identifier":{"isbn":["978-0-12-384720-1"]},"day":"01","corr_author":"1","quality_controlled":"1","edition":"2","oa_version":"None","date_created":"2022-03-21T07:46:22Z"},{"date_published":"2013-04-03T00:00:00Z","page":"215-226","author":[{"full_name":"Weber, Michele","first_name":"Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","last_name":"Weber"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K"}],"publisher":"Humana Press","article_processing_charge":"No","language":[{"iso":"eng"}],"series_title":"MIMB","_id":"10900","editor":[{"last_name":"Cardona","full_name":"Cardona, Astrid","first_name":"Astrid"},{"full_name":"Ubogu, Eroboghene","first_name":"Eroboghene","last_name":"Ubogu"}],"alternative_title":["Methods in Molecular Biology"],"scopus_import":"1","date_created":"2022-03-21T07:47:41Z","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_identifier":{"issn":["1064-3745"],"eisbn":["9781627034265"],"isbn":["9781627034258"],"eissn":["1940-6029"]},"intvolume":"      1013","volume":1013,"date_updated":"2024-10-09T21:02:37Z","publication":"Chemokines","citation":{"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>.","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>.","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>","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.","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>","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.","short":"M. Weber, M.K. Sixt, in:, A. Cardona, E. Ubogu (Eds.), Chemokines, Humana Press, Totowa, NJ, 2013, pp. 215–226."},"doi":"10.1007/978-1-62703-426-5_14","title":"Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations","external_id":{"pmid":["23625502"]},"status":"public","department":[{"_id":"MiSi"}],"pmid":1,"oa_version":"None","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"}],"type":"book_chapter","day":"03","place":"Totowa, NJ","quality_controlled":"1","corr_author":"1","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"04","year":"2013"},{"intvolume":"      7810","date_updated":"2025-07-10T11:50:03Z","volume":7810,"doi":"10.1007/978-3-642-37064-9_20","citation":{"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>","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>.","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.","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.","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>","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."},"publication":"7th International Conference on Language and Automata Theory and Applications","ec_funded":1,"department":[{"_id":"KrCh"}],"status":"public","title":"How to travel between languages","oa_version":"None","quality_controlled":"1","corr_author":"1","day":"15","place":"Berlin, Heidelberg","type":"conference","abstract":[{"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.","lang":"eng"}],"year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","publication_status":"published","page":"214-225","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","full_name":"Chaubal, Siddhesh","first_name":"Siddhesh"},{"full_name":"Rubin, Sasha","first_name":"Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","last_name":"Rubin"}],"conference":{"start_date":"2013-04-02","end_date":"2013-04-05","location":"Bilbao, Spain","name":"LATA: Language and Automata Theory and Applications"},"date_published":"2013-04-15T00:00:00Z","series_title":"LNCS","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Springer Nature","_id":"10902","scopus_import":"1","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"alternative_title":["LNCS"],"date_created":"2022-03-21T07:56:21Z","publication_identifier":{"isbn":["9783642370632"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["9783642370649"]},"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."},{"issue":"3","extern":"1","date_created":"2022-04-07T07:50:33Z","publication_identifier":{"issn":["0962-8924"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Elsevier","page":"112-117","author":[{"first_name":"Tobias M.","full_name":"Franks, Tobias M.","last_name":"Franks"},{"full_name":"HETZER, Martin W","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","last_name":"HETZER"}],"date_published":"2013-03-01T00:00:00Z","scopus_import":"1","_id":"11083","oa_version":"None","pmid":1,"year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","publication_status":"published","keyword":["Cell Biology"],"quality_controlled":"1","day":"01","type":"journal_article","abstract":[{"lang":"eng","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."}],"date_updated":"2024-10-14T11:23:44Z","volume":23,"article_type":"letter_note","intvolume":"        23","status":"public","title":"The role of Nup98 in transcription regulation in healthy and diseased cells","external_id":{"pmid":["23246429"]},"citation":{"short":"T.M. Franks, M. Hetzer, Trends in Cell Biology 23 (2013) 112–117.","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.","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>","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.","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>","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>.","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>."},"doi":"10.1016/j.tcb.2012.10.013","publication":"Trends in Cell Biology"},{"external_id":{"pmid":["23258296"]},"title":"Protein homeostasis: Live long, won't prosper","status":"public","publication":"Nature Reviews Molecular Cell Biology","doi":"10.1038/nrm3496","citation":{"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>","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>.","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>","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.","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."},"article_type":"original","volume":14,"date_updated":"2024-10-14T11:24:09Z","intvolume":"        14","keyword":["Cell Biology","Molecular Biology"],"publication_status":"published","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","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."}],"type":"journal_article","day":"01","quality_controlled":"1","pmid":1,"oa_version":"None","scopus_import":"1","_id":"11084","publisher":"Springer Nature","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2013-01-01T00:00:00Z","page":"55-61","author":[{"last_name":"Toyama","full_name":"Toyama, Brandon H.","first_name":"Brandon H."},{"orcid":"0000-0002-2111-992X","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","full_name":"HETZER, Martin W"}],"publication_identifier":{"issn":["1471-0072","1471-0080"]},"extern":"1","date_created":"2022-04-07T07:50:43Z"},{"year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","publication_status":"published","keyword":["General Biochemistry","Genetics and Molecular Biology"],"quality_controlled":"1","day":"03","type":"journal_article","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"status":"public","external_id":{"pmid":["23827674"]},"title":"Catastrophic nuclear envelope collapse in cancer cell micronuclei","citation":{"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>","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>.","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>.","short":"E.M. Hatch, A.H. Fischer, T.J. Deerinck, M. Hetzer, Cell 154 (2013) 47–60.","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.","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>","ista":"Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. 2013. Catastrophic nuclear envelope collapse in cancer cell micronuclei. Cell. 154(1), 47–60."},"doi":"10.1016/j.cell.2013.06.007","publication":"Cell","date_updated":"2024-10-14T11:24:29Z","oa":1,"volume":154,"article_type":"original","intvolume":"       154","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2013.06.007"}],"publication_identifier":{"issn":["0092-8674"]},"issue":"1","extern":"1","date_created":"2022-04-07T07:50:51Z","scopus_import":"1","_id":"11085","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Elsevier","page":"47-60","author":[{"full_name":"Hatch, Emily M.","first_name":"Emily M.","last_name":"Hatch"},{"first_name":"Andrew H.","full_name":"Fischer, Andrew H.","last_name":"Fischer"},{"first_name":"Thomas J.","full_name":"Deerinck, Thomas J.","last_name":"Deerinck"},{"full_name":"HETZER, Martin W","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","orcid":"0000-0002-2111-992X"}],"date_published":"2013-07-03T00:00:00Z"},{"oa_version":"Published Version","pmid":1,"year":"2013","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"publication_status":"published","quality_controlled":"1","day":"28","type":"journal_article","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"}],"date_updated":"2024-10-14T11:24:40Z","oa":1,"volume":9,"article_type":"original","intvolume":"         9","status":"public","title":"Dynamic association of NUP98 with the human genome","external_id":{"pmid":["23468646"]},"citation":{"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>","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>.","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>.","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>","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.","short":"Y. Liang, T.M. Franks, M.C. Marchetto, F.H. Gage, M. Hetzer, PLoS Genetics 9 (2013).","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."},"doi":"10.1371/journal.pgen.1003308","publication":"PLoS Genetics","issue":"2","extern":"1","date_created":"2022-04-07T07:50:59Z","main_file_link":[{"url":"https://doi.org/10.1371/journal.pgen.1003308","open_access":"1"}],"publication_identifier":{"issn":["1553-7404"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Public Library of Science","author":[{"last_name":"Liang","first_name":"Yun","full_name":"Liang, Yun"},{"first_name":"Tobias M.","full_name":"Franks, Tobias M.","last_name":"Franks"},{"first_name":"Maria C.","full_name":"Marchetto, Maria C.","last_name":"Marchetto"},{"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","orcid":"0000-0002-2111-992X","last_name":"HETZER"}],"date_published":"2013-02-28T00:00:00Z","scopus_import":"1","article_number":"e1003308","_id":"11086"},{"intvolume":"       154","volume":154,"oa":1,"date_updated":"2025-12-15T10:02:46Z","article_type":"original","publication":"Cell","doi":"10.1016/j.cell.2013.07.037","citation":{"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.","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.","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.","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>","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>.","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>.","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>"},"department":[{"_id":"MaHe"}],"external_id":{"pmid":["23993091"]},"title":"Identification of long-lived proteins reveals exceptional stability of essential cellular structures","status":"public","oa_version":"Published Version","pmid":1,"day":"29","quality_controlled":"1","abstract":[{"lang":"eng","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."}],"type":"journal_article","keyword":["General Biochemistry","Genetics and Molecular Biology"],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","year":"2013","date_published":"2013-08-29T00:00:00Z","author":[{"full_name":"Toyama, Brandon H.","first_name":"Brandon H.","last_name":"Toyama"},{"full_name":"Savas, Jeffrey N.","first_name":"Jeffrey N.","last_name":"Savas"},{"last_name":"Park","first_name":"Sung Kyu","full_name":"Park, Sung Kyu"},{"last_name":"Harris","full_name":"Harris, Michael S.","first_name":"Michael S."},{"last_name":"Ingolia","first_name":"Nicholas T.","full_name":"Ingolia, Nicholas T."},{"last_name":"Yates","first_name":"John R.","full_name":"Yates, John R."},{"full_name":"HETZER, Martin W","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","last_name":"HETZER"}],"page":"971-982","publisher":"Elsevier","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"11087","scopus_import":"1","date_created":"2022-04-07T07:51:08Z","issue":"5","extern":"1","publication_identifier":{"issn":["0092-8674"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2013.07.037"}]},{"day":"16","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"type":"journal_article","keyword":["Biophysics"],"publication_status":"published","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","year":"2013","month":"04","oa_version":"Published Version","pmid":1,"publication":"Biophysical Journal","doi":"10.1016/j.bpj.2013.01.049","citation":{"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.","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.","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.","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>.","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>.","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>"},"external_id":{"pmid":["23601312"]},"title":"Anomalous diffusion of single particles in cytoplasm","status":"public","intvolume":"       104","volume":104,"oa":1,"date_updated":"2022-07-18T08:51:01Z","article_type":"original","publication_identifier":{"issn":["0006-3495"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.bpj.2013.01.049","open_access":"1"}],"date_created":"2022-04-07T07:51:26Z","issue":"8","extern":"1","_id":"11088","scopus_import":"1","date_published":"2013-04-16T00:00:00Z","page":"1652-1660","author":[{"full_name":"Regner, Benjamin M.","first_name":"Benjamin M.","last_name":"Regner"},{"last_name":"Vučinić","full_name":"Vučinić, Dejan","first_name":"Dejan"},{"first_name":"Cristina","full_name":"Domnisoru, Cristina","last_name":"Domnisoru"},{"full_name":"Bartol, Thomas M.","first_name":"Thomas M.","last_name":"Bartol"},{"full_name":"HETZER, Martin W","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","orcid":"0000-0002-2111-992X"},{"first_name":"Daniel M.","full_name":"Tartakovsky, Daniel M.","last_name":"Tartakovsky"},{"full_name":"Sejnowski, Terrence J.","first_name":"Terrence J.","last_name":"Sejnowski"}],"publisher":"Elsevier","article_processing_charge":"No","language":[{"iso":"eng"}]},{"volume":111,"oa":1,"date_updated":"2021-11-29T14:05:19Z","article_type":"original","intvolume":"       111","title":"Living clusters and crystals from low-density suspensions of active colloids","external_id":{"arxiv":["1311.4681"],"pmid":["24483677"]},"status":"public","publication":"Physical Review Letters","citation":{"short":"B.M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, D. Frenkel, Physical Review Letters 111 (2013).","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>","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.","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>","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>.","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>."},"doi":"10.1103/physrevlett.111.245702","oa_version":"Preprint","pmid":1,"arxiv":1,"keyword":["general physics and astronomy"],"publication_status":"published","year":"2013","month":"12","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"11","quality_controlled":"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"}],"type":"journal_article","publisher":"American Physical Society","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2013-12-11T00:00:00Z","author":[{"first_name":"B. M.","full_name":"Mognetti, B. M.","last_name":"Mognetti"},{"first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Angioletti-Uberti","full_name":"Angioletti-Uberti, S.","first_name":"S."},{"last_name":"Cacciuto","full_name":"Cacciuto, A.","first_name":"A."},{"first_name":"C.","full_name":"Valeriani, C.","last_name":"Valeriani"},{"last_name":"Frenkel","first_name":"D.","full_name":"Frenkel, D."}],"scopus_import":"1","article_number":"245702","_id":"10384","issue":"24","extern":"1","date_created":"2021-11-29T13:29:31Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.4681"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"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."},{"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Royal Society of Chemistry","author":[{"last_name":"Napoli","first_name":"Joseph A.","full_name":"Napoli, Joseph A."},{"first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Angelo","full_name":"Cacciuto, Angelo","last_name":"Cacciuto"}],"page":"8881-8886","date_published":"2013-08-08T00:00:00Z","scopus_import":"1","_id":"10385","extern":"1","issue":"37","date_created":"2021-11-29T13:31:24Z","acknowledgement":"This work was supported by the National Science Foundation under Career Grant no. DMR-0846426.","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"article_type":"original","date_updated":"2021-11-29T14:05:23Z","volume":9,"intvolume":"         9","status":"public","title":"Collapsing nanoparticle-laden nanotubes","citation":{"short":"J.A. Napoli, A. Šarić, A. Cacciuto, Soft Matter 9 (2013) 8881–8886.","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.","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>","ista":"Napoli JA, Šarić A, Cacciuto A. 2013. Collapsing nanoparticle-laden nanotubes. Soft Matter. 9(37), 8881–8886.","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>","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>.","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>."},"doi":"10.1039/c3sm51495a","publication":"Soft Matter","oa_version":"None","month":"08","year":"2013","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","keyword":["condensed matter physics","general chemistry"],"type":"journal_article","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"}],"quality_controlled":"1","day":"08"},{"main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2013/sm/c3sm50188d"}],"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"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.","issue":"29","extern":"1","date_created":"2021-11-29T14:06:32Z","scopus_import":"1","article_number":"6677","_id":"10386","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Royal Society of Chemistry","author":[{"first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Cacciuto, Angelo","first_name":"Angelo","last_name":"Cacciuto"}],"date_published":"2013-05-03T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2013","month":"05","publication_status":"published","keyword":["condensed matter physics","general chemistry"],"quality_controlled":"1","day":"03","type":"journal_article","abstract":[{"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.","lang":"eng"}],"oa_version":"None","status":"public","title":"Self-assembly of nanoparticles adsorbed on fluid and elastic membranes","doi":"10.1039/c3sm50188d","citation":{"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>","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>.","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).","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.","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>","ista":"Šarić A, Cacciuto A. 2013. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. Soft Matter. 9(29), 6677."},"publication":"Soft Matter","date_updated":"2021-11-29T14:29:31Z","volume":9,"article_type":"original","intvolume":"         9"},{"publication_identifier":{"issn":["0013-5585"],"eissn":["1862-278X"]},"isi":1,"issue":"SI-1-Track-G","file_date_updated":"2021-12-01T14:38:08Z","ddc":["005","610"],"date_created":"2021-12-01T14:35:35Z","_id":"10396","article_number":"000010151520134181","publisher":"De Gruyter","article_processing_charge":"No","language":[{"iso":"eng"}],"has_accepted_license":"1","date_published":"2013-08-01T00:00:00Z","author":[{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","first_name":"Alois"},{"full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas"},{"full_name":"Schmidt-Hieber, C.","first_name":"C.","last_name":"Schmidt-Hieber"},{"last_name":"Guzman","full_name":"Guzman, S. J.","first_name":"S. J."}],"conference":{"name":"BMT: Biomedizinische Technik ","location":"Graz, Austria","start_date":"2013-09-19","end_date":"2013-09-21"},"publication_status":"published","keyword":["biomedical engineering","data analysis","free software"],"year":"2013","month":"08","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"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.","lang":"eng"}],"type":"journal_article","day":"01","quality_controlled":"1","corr_author":"1","pmid":1,"oa_version":"Submitted Version","external_id":{"isi":["000497714000034"],"pmid":["24042795"]},"title":"Stimfit: A fast visualization and analysis environment for cellular neurophysiology","status":"public","department":[{"_id":"PeJo"}],"publication":"Biomedical Engineering / Biomedizinische Technik","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>.","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>.","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>","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.","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>","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.","short":"A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering / Biomedizinische Technik 58 (2013)."},"doi":"10.1515/bmt-2013-4181","article_type":"original","oa":1,"volume":58,"date_updated":"2025-09-30T07:31:23Z","intvolume":"        58","file":[{"file_id":"10397","checksum":"cdfc5339b530a25d6079f7223f0b1f16","success":1,"relation":"main_file","creator":"schloegl","file_size":149825,"access_level":"open_access","content_type":"application/pdf","date_created":"2021-12-01T14:38:08Z","file_name":"Schloegl_Abstract-BMT2013.pdf","date_updated":"2021-12-01T14:38:08Z"}]},{"title":"Computational design of actuated deformable characters","status":"public","article_number":"82","publication":"ACM Transactions on Graphics","_id":"2107","doi":"10.1145/2461912.2461979","citation":{"short":"M. Skouras, B. Thomaszewski, S. Coros, B. Bickel, M. Groß, ACM Transactions on Graphics 32 (2013).","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.","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>","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.","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>","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>.","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>."},"publist_id":"4926","volume":32,"date_updated":"2025-10-01T08:08:25Z","publisher":"ACM","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2013-07-01T00:00:00Z","author":[{"last_name":"Skouras","first_name":"Mélina","full_name":"Skouras, Mélina"},{"last_name":"Thomaszewski","full_name":"Thomaszewski, Bernhard","first_name":"Bernhard"},{"first_name":"Stelian","full_name":"Coros, Stelian","last_name":"Coros"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bickel, Bernd"},{"last_name":"Groß","full_name":"Groß, Markus","first_name":"Markus"}],"intvolume":"        32","publication_status":"published","month":"07","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","acknowledgement":"This work was partly funded by the NCCR Co-Me of the Swiss NSF","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."}],"type":"journal_article","oa_version":"None","issue":"4","extern":"1","date_created":"2018-12-11T11:55:45Z"},{"issue":"4","extern":1,"date_created":"2018-12-11T11:55:46Z","publication_status":"published","year":"2013","month":"07","day":"01","quality_controlled":0,"abstract":[{"text":"We present an interactive design system that allows non-expert users to create animated mechanical characters. Given an articulated character as input, the user iteratively creates an animation by sketching motion curves indicating how different parts of the character should move. For each motion curve, our framework creates an optimized mechanism that reproduces it as closely as possible. The resulting mechanisms are attached to the character and then connected to each other using gear trains, which are created in a semi-automated fashion. The mechanical assemblies generated with our system can be driven with a single input driver, such as a hand-operated crank or an electric motor, and they can be fabricated using rapid prototyping devices. We demonstrate the versatility of our approach by designing a wide range of mechanical characters, several of which we manufactured using 3D printing. While our pipeline is designed for characters driven by planar mechanisms, significant parts of it extend directly to non-planar mechanisms, allowing us to create characters with compelling 3D motions. ","lang":"eng"}],"type":"journal_article","publist_id":"4927","volume":32,"date_updated":"2021-01-12T06:55:21Z","publisher":"ACM","date_published":"2013-07-01T00:00:00Z","author":[{"full_name":"Coros, Stelian","first_name":"Stelian","last_name":"Coros"},{"last_name":"Thomaszewski","first_name":"Bernhard","full_name":"Thomaszewski, Bernhard"},{"last_name":"Noris","full_name":"Noris, Gioacchino","first_name":"Gioacchino"},{"first_name":"Shinjiro","full_name":"Sueda, Shinjiro","last_name":"Sueda"},{"first_name":"Moira","full_name":"Forberg, Moira","last_name":"Forberg"},{"full_name":"Sumner, Robert W","first_name":"Robert","last_name":"Sumner"},{"last_name":"Matusik","full_name":"Matusik, Wojciech","first_name":"Wojciech"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","last_name":"Bickel","full_name":"Bernd Bickel","first_name":"Bernd"}],"intvolume":"        32","title":"Computational design of mechanical characters","status":"public","publication":"ACM Transactions on Graphics","_id":"2108","citation":{"apa":"Coros, S., Thomaszewski, B., Noris, G., Sueda, S., Forberg, M., Sumner, R., … Bickel, B. (2013). Computational design of mechanical characters. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461953\">https://doi.org/10.1145/2461912.2461953</a>","mla":"Coros, Stelian, et al. “Computational Design of Mechanical Characters.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461953\">10.1145/2461912.2461953</a>.","chicago":"Coros, Stelian, Bernhard Thomaszewski, Gioacchino Noris, Shinjiro Sueda, Moira Forberg, Robert Sumner, Wojciech Matusik, and Bernd Bickel. “Computational Design of Mechanical Characters.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461953\">https://doi.org/10.1145/2461912.2461953</a>.","ama":"Coros S, Thomaszewski B, Noris G, et al. Computational design of mechanical characters. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461953\">10.1145/2461912.2461953</a>","ista":"Coros S, Thomaszewski B, Noris G, Sueda S, Forberg M, Sumner R, Matusik W, Bickel B. 2013. Computational design of mechanical characters. ACM Transactions on Graphics. 32(4).","short":"S. Coros, B. Thomaszewski, G. Noris, S. Sueda, M. Forberg, R. Sumner, W. Matusik, B. Bickel, ACM Transactions on Graphics 32 (2013).","ieee":"S. Coros <i>et al.</i>, “Computational design of mechanical characters,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013."},"doi":"10.1145/2461912.2461953"},{"publisher":"Elsevier","volume":37,"publist_id":"4924","date_updated":"2021-01-12T06:55:22Z","intvolume":"        37","date_published":"2013-10-01T00:00:00Z","page":"669 - 675","author":[{"last_name":"Hildebrand","first_name":"Kristian","full_name":"Hildebrand, Kristian"},{"full_name":"Bernd Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","orcid":"0000-0001-6511-9385"},{"last_name":"Alexa","full_name":"Alexa, Marc","first_name":"Marc"}],"title":"Orthogonal slicing for additive manufacturing","status":"public","publication":"Computers and Graphics (Pergamon)","_id":"2109","citation":{"chicago":"Hildebrand, Kristian, Bernd Bickel, and Marc Alexa. “Orthogonal Slicing for Additive Manufacturing.” <i>Computers and Graphics (Pergamon)</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cag.2013.05.011\">https://doi.org/10.1016/j.cag.2013.05.011</a>.","mla":"Hildebrand, Kristian, et al. “Orthogonal Slicing for Additive Manufacturing.” <i>Computers and Graphics (Pergamon)</i>, vol. 37, no. 6, Elsevier, 2013, pp. 669–75, doi:<a href=\"https://doi.org/10.1016/j.cag.2013.05.011\">10.1016/j.cag.2013.05.011</a>.","apa":"Hildebrand, K., Bickel, B., &#38; Alexa, M. (2013). Orthogonal slicing for additive manufacturing. <i>Computers and Graphics (Pergamon)</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cag.2013.05.011\">https://doi.org/10.1016/j.cag.2013.05.011</a>","ista":"Hildebrand K, Bickel B, Alexa M. 2013. Orthogonal slicing for additive manufacturing. Computers and Graphics (Pergamon). 37(6), 669–675.","ama":"Hildebrand K, Bickel B, Alexa M. Orthogonal slicing for additive manufacturing. <i>Computers and Graphics (Pergamon)</i>. 2013;37(6):669-675. doi:<a href=\"https://doi.org/10.1016/j.cag.2013.05.011\">10.1016/j.cag.2013.05.011</a>","ieee":"K. Hildebrand, B. Bickel, and M. Alexa, “Orthogonal slicing for additive manufacturing,” <i>Computers and Graphics (Pergamon)</i>, vol. 37, no. 6. Elsevier, pp. 669–675, 2013.","short":"K. Hildebrand, B. Bickel, M. Alexa, Computers and Graphics (Pergamon) 37 (2013) 669–675."},"doi":"10.1016/j.cag.2013.05.011","extern":1,"issue":"6","date_created":"2018-12-11T11:55:46Z","publication_status":"published","month":"10","year":"2013","abstract":[{"text":"Most additive manufacturing technologies work by layering, i.e. slicing the shape and then generating each slice independently. This introduces an anisotropy into the process, often as different accuracies in the tangential and normal directions, but also in terms of other parameters such as build speed or tensile strength and strain. We model this as an anisotropic cubic element. Our approach then finds a compromise between modeling each part of the shape individually in the best possible direction and using one direction for the whole shape part. In particular, we compute an orthogonal basis and consider only the three basis vectors as slice normals (i.e. fabrication directions). Then we optimize a decomposition of the shape along this basis so that each part can be consistently sliced along one of the basis vectors. In simulation, we show that this approach is superior to slicing the whole shape in one direction, only. It also has clear benefits if the shape is larger than the build volume of the available equipment.","lang":"eng"}],"type":"journal_article","day":"01","quality_controlled":0},{"citation":{"apa":"Papas, M., Regg, C., Jarosz, W., Bickel, B., Jackson, P., Matusik, W., … Groß, M. (2013). Fabricating translucent materials using continuous pigment mixtures. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461974\">https://doi.org/10.1145/2461912.2461974</a>","mla":"Papas, Marios, et al. “Fabricating Translucent Materials Using Continuous Pigment Mixtures.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461974\">10.1145/2461912.2461974</a>.","chicago":"Papas, Marios, Christian Regg, Wojciech Jarosz, Bernd Bickel, Philip Jackson, Wojciech Matusik, Steve Marschner, and Markus Groß. “Fabricating Translucent Materials Using Continuous Pigment Mixtures.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461974\">https://doi.org/10.1145/2461912.2461974</a>.","ama":"Papas M, Regg C, Jarosz W, et al. Fabricating translucent materials using continuous pigment mixtures. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461974\">10.1145/2461912.2461974</a>","ista":"Papas M, Regg C, Jarosz W, Bickel B, Jackson P, Matusik W, Marschner S, Groß M. 2013. Fabricating translucent materials using continuous pigment mixtures. ACM Transactions on Graphics. 32(4).","short":"M. Papas, C. Regg, W. Jarosz, B. Bickel, P. Jackson, W. Matusik, S. Marschner, M. Groß, ACM Transactions on Graphics 32 (2013).","ieee":"M. Papas <i>et al.</i>, “Fabricating translucent materials using continuous pigment mixtures,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013."},"doi":"10.1145/2461912.2461974","publication":"ACM Transactions on Graphics","_id":"2110","status":"public","title":"Fabricating translucent materials using continuous pigment mixtures","author":[{"last_name":"Papas","first_name":"Marios","full_name":"Papas, Marios"},{"full_name":"Regg, Christian","first_name":"Christian","last_name":"Regg"},{"last_name":"Jarosz","full_name":"Jarosz, Wojciech","first_name":"Wojciech"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bernd Bickel","first_name":"Bernd"},{"first_name":"Philip","full_name":"Jackson, Philip V","last_name":"Jackson"},{"last_name":"Matusik","full_name":"Matusik, Wojciech","first_name":"Wojciech"},{"last_name":"Marschner","first_name":"Steve","full_name":"Marschner, Steve"},{"last_name":"Groß","first_name":"Markus","full_name":"Groß, Markus S"}],"date_published":"2013-07-01T00:00:00Z","intvolume":"        32","date_updated":"2021-01-12T06:55:22Z","volume":32,"publist_id":"4925","publisher":"ACM","quality_controlled":0,"day":"01","type":"journal_article","abstract":[{"lang":"eng","text":"We present a method for practical physical reproduction and design of homogeneous materials with desired subsurface scattering. Our process uses a collection of different pigments that can be suspended in a clear base material. Our goal is to determine pigment concentrations that best reproduce the appearance and subsurface scattering of a given target material. In order to achieve this task we first fabricate a collection of material samples composed of known mixtures of the available pigments with the base material. We then acquire their reflectance profiles using a custom-built measurement device. We use the same device to measure the reflectance profile of a target material. Based on the database of mappings from pigment concentrations to reflectance profiles, we use an optimization process to compute the concentration of pigments to best replicate the target material appearance. We demonstrate the practicality of our method by reproducing a variety of different translucent materials. We also present a tool that allows the user to explore the range of achievable appearances for a given set of pigments. "}],"month":"07","year":"2013","publication_status":"published","date_created":"2018-12-11T11:55:46Z","issue":"4","extern":1},{"date_updated":"2021-01-12T06:55:23Z","volume":32,"publist_id":"4922","publisher":"ACM","author":[{"last_name":"Bermano","full_name":"Bermano, Amit H","first_name":"Amit"},{"first_name":"Philipp","full_name":"Bruschweiler, Philipp","last_name":"Bruschweiler"},{"full_name":"Grundhöfer, Anselm","first_name":"Anselm","last_name":"Grundhöfer"},{"full_name":"Iwai, Daisuke","first_name":"Daisuke","last_name":"Iwai"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bernd Bickel"},{"last_name":"Groß","first_name":"Markus","full_name":"Groß, Markus S"}],"date_published":"2013-11-01T00:00:00Z","intvolume":"        32","status":"public","title":"Augmenting physical avatars using projector-based illumination","doi":"10.1145/2508363.2508416","citation":{"ista":"Bermano A, Bruschweiler P, Grundhöfer A, Iwai D, Bickel B, Groß M. 2013. Augmenting physical avatars using projector-based illumination. ACM Transactions on Graphics. 32(6).","ama":"Bermano A, Bruschweiler P, Grundhöfer A, Iwai D, Bickel B, Groß M. Augmenting physical avatars using projector-based illumination. <i>ACM Transactions on Graphics</i>. 2013;32(6). doi:<a href=\"https://doi.org/10.1145/2508363.2508416\">10.1145/2508363.2508416</a>","ieee":"A. Bermano, P. Bruschweiler, A. Grundhöfer, D. Iwai, B. Bickel, and M. Groß, “Augmenting physical avatars using projector-based illumination,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 6. ACM, 2013.","short":"A. Bermano, P. Bruschweiler, A. Grundhöfer, D. Iwai, B. Bickel, M. Groß, ACM Transactions on Graphics 32 (2013).","mla":"Bermano, Amit, et al. “Augmenting Physical Avatars Using Projector-Based Illumination.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 6, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2508363.2508416\">10.1145/2508363.2508416</a>.","chicago":"Bermano, Amit, Philipp Bruschweiler, Anselm Grundhöfer, Daisuke Iwai, Bernd Bickel, and Markus Groß. “Augmenting Physical Avatars Using Projector-Based Illumination.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2508363.2508416\">https://doi.org/10.1145/2508363.2508416</a>.","apa":"Bermano, A., Bruschweiler, P., Grundhöfer, A., Iwai, D., Bickel, B., &#38; Groß, M. (2013). Augmenting physical avatars using projector-based illumination. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2508363.2508416\">https://doi.org/10.1145/2508363.2508416</a>"},"_id":"2111","publication":"ACM Transactions on Graphics","issue":"6","extern":1,"date_created":"2018-12-11T11:55:47Z","month":"11","year":"2013","publication_status":"published","quality_controlled":0,"day":"01","type":"journal_article","abstract":[{"text":"Animated animatronic figures are a unique way to give physical presence to a character. However, their movement and expressions are often limited due to mechanical constraints. In this paper, we propose a complete process for augmenting physical avatars using projector-based illumination, significantly increasing their expressiveness. Given an input animation, the system decomposes the motion into low-frequency motion that can be physically reproduced by the animatronic head and high-frequency details that are added using projected shading. At the core is a spatio-temporal optimization process that compresses the motion in gradient space, ensuring faithful motion replay while respecting the physical limitations of the system. We also propose a complete multi-camera and projection system, including a novel defocused projection and subsurface scattering compensation scheme. The result of our system is a highly expressive physical avatar that features facial details and motion otherwise unattainable due to physical constraints.","lang":"eng"}]},{"intvolume":"        69","date_updated":"2026-02-23T08:56:25Z","volume":69,"article_type":"original","OA_type":"closed access","doi":"10.1107/s1744309113003667","citation":{"apa":"Aggarwal, N., Mandal, P. K., Gautham, N., &#38; Chadha, A. (2013). Expression, purification, crystallization and preliminary X-ray diffraction analysis of carbonyl reductase from Candida parapsilosis ATCC 7330. <i>Acta Crystallographica Section F Structural Biology Communications</i>. International Union of Crystallography. <a href=\"https://doi.org/10.1107/s1744309113003667\">https://doi.org/10.1107/s1744309113003667</a>","chicago":"Aggarwal, Nidhi, Pradeep K Mandal, Namasivayam Gautham, and Anju Chadha. “Expression, Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of Carbonyl Reductase from Candida Parapsilosis ATCC 7330.” <i>Acta Crystallographica Section F Structural Biology Communications</i>. International Union of Crystallography, 2013. <a href=\"https://doi.org/10.1107/s1744309113003667\">https://doi.org/10.1107/s1744309113003667</a>.","mla":"Aggarwal, Nidhi, et al. “Expression, Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of Carbonyl Reductase from Candida Parapsilosis ATCC 7330.” <i>Acta Crystallographica Section F Structural Biology Communications</i>, vol. 69, no. 3, International Union of Crystallography, 2013, pp. 313–15, doi:<a href=\"https://doi.org/10.1107/s1744309113003667\">10.1107/s1744309113003667</a>.","short":"N. Aggarwal, P.K. Mandal, N. Gautham, A. Chadha, Acta Crystallographica Section F Structural Biology Communications 69 (2013) 313–315.","ieee":"N. Aggarwal, P. K. Mandal, N. Gautham, and A. Chadha, “Expression, purification, crystallization and preliminary X-ray diffraction analysis of carbonyl reductase from Candida parapsilosis ATCC 7330,” <i>Acta Crystallographica Section F Structural Biology Communications</i>, vol. 69, no. 3. International Union of Crystallography, pp. 313–315, 2013.","ama":"Aggarwal N, Mandal PK, Gautham N, Chadha A. Expression, purification, crystallization and preliminary X-ray diffraction analysis of carbonyl reductase from Candida parapsilosis ATCC 7330. <i>Acta Crystallographica Section F Structural Biology Communications</i>. 2013;69(3):313-315. doi:<a href=\"https://doi.org/10.1107/s1744309113003667\">10.1107/s1744309113003667</a>","ista":"Aggarwal N, Mandal PK, Gautham N, Chadha A. 2013. Expression, purification, crystallization and preliminary X-ray diffraction analysis of carbonyl reductase from Candida parapsilosis ATCC 7330. Acta Crystallographica Section F Structural Biology Communications. 69(3), 313–315."},"publication":"Acta Crystallographica Section F Structural Biology Communications","status":"public","title":"Expression, purification, crystallization and preliminary X-ray diffraction analysis of carbonyl reductase from Candida parapsilosis ATCC 7330","oa_version":"None","quality_controlled":"1","day":"01","type":"journal_article","abstract":[{"text":"The NAD(P)H-dependent carbonyl reductase from Candida parapsilosis ATCC 7330 catalyses the asymmetric reduction of ethyl 4-phenyl-2-oxobutanoate to ethyl (R)-4-phenyl-2-hydroxybutanoate, a precursor of angiotensin-converting enzyme inhibitors such as Cilazapril and Benazepril. The carbonyl reductase was expressed in Escherichia coli and purified by GST-affinity and size-exclusion chromatography. Crystals were obtained by the hanging-drop vapour-diffusion method and diffracted to 1.86 Å resolution. The asymmetric unit contained two molecules of carbonyl reductase, with a solvent content of 48%. The structure was solved by molecular replacement using cinnamyl alcohol dehydrogenase from Saccharomyces cerevisiae as a search model.","lang":"eng"}],"month":"03","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","author":[{"last_name":"Aggarwal","first_name":"Nidhi","full_name":"Aggarwal, Nidhi"},{"last_name":"Mandal","orcid":"0000-0001-5996-956X","id":"6a3def15-d4b4-11ef-9fa9-a24c1f545ec3","first_name":"Pradeep K","full_name":"Mandal, Pradeep K"},{"last_name":"Gautham","first_name":"Namasivayam","full_name":"Gautham, Namasivayam"},{"last_name":"Chadha","full_name":"Chadha, Anju","first_name":"Anju"}],"page":"313-315","date_published":"2013-03-01T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"International Union of Crystallography","_id":"21110","date_created":"2026-01-29T22:11:18Z","issue":"3","extern":"1","publication_identifier":{"issn":["1744-3091"]}},{"volume":32,"publist_id":"4923","date_updated":"2021-01-12T06:55:23Z","publisher":"ACM","date_published":"2013-11-01T00:00:00Z","author":[{"last_name":"Miguel","full_name":"Miguel, Eder","first_name":"Eder"},{"first_name":"Rasmus","full_name":"Tamstorf, Rasmus","last_name":"Tamstorf"},{"last_name":"Bradley","full_name":"Bradley, Derek J","first_name":"Derek"},{"last_name":"Schvartzman","full_name":"Schvartzman, Sara C","first_name":"Sara"},{"last_name":"Thomaszewski","full_name":"Thomaszewski, Bernhard","first_name":"Bernhard"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","last_name":"Bickel","full_name":"Bernd Bickel","first_name":"Bernd"},{"last_name":"Matusik","full_name":"Matusik, Wojciech","first_name":"Wojciech"},{"last_name":"Marschner","first_name":"Steve","full_name":"Marschner, Steve"},{"first_name":"Miguel","full_name":"Otaduy, Miguel A","last_name":"Otaduy"}],"intvolume":"        32","title":"Modeling and estimation of internal friction in cloth","status":"public","publication":"ACM Transactions on Graphics","_id":"2112","doi":"10.1145/2508363.2508389 ","citation":{"short":"E. Miguel, R. Tamstorf, D. Bradley, S. Schvartzman, B. Thomaszewski, B. Bickel, W. Matusik, S. Marschner, M. Otaduy, ACM Transactions on Graphics 32 (2013).","ieee":"E. Miguel <i>et al.</i>, “Modeling and estimation of internal friction in cloth,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 6. ACM, 2013.","ama":"Miguel E, Tamstorf R, Bradley D, et al. Modeling and estimation of internal friction in cloth. <i>ACM Transactions on Graphics</i>. 2013;32(6). doi:<a href=\"https://doi.org/10.1145/2508363.2508389 \">10.1145/2508363.2508389 </a>","ista":"Miguel E, Tamstorf R, Bradley D, Schvartzman S, Thomaszewski B, Bickel B, Matusik W, Marschner S, Otaduy M. 2013. Modeling and estimation of internal friction in cloth. ACM Transactions on Graphics. 32(6).","apa":"Miguel, E., Tamstorf, R., Bradley, D., Schvartzman, S., Thomaszewski, B., Bickel, B., … Otaduy, M. (2013). Modeling and estimation of internal friction in cloth. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2508363.2508389 \">https://doi.org/10.1145/2508363.2508389 </a>","mla":"Miguel, Eder, et al. “Modeling and Estimation of Internal Friction in Cloth.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 6, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2508363.2508389 \">10.1145/2508363.2508389 </a>.","chicago":"Miguel, Eder, Rasmus Tamstorf, Derek Bradley, Sara Schvartzman, Bernhard Thomaszewski, Bernd Bickel, Wojciech Matusik, Steve Marschner, and Miguel Otaduy. “Modeling and Estimation of Internal Friction in Cloth.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2508363.2508389 \">https://doi.org/10.1145/2508363.2508389 </a>."},"issue":"6","extern":1,"date_created":"2018-12-11T11:55:47Z","publication_status":"published","month":"11","year":"2013","day":"01","quality_controlled":0,"acknowledgement":"This work was supported in part by the European Research Council (ERC-2011-StG-280135 Animetrics) and the Spanish Ministry of Economy (TIN2012-35840).","abstract":[{"text":"Force-deformation measurements of cloth exhibit significant hysteresis, and many researchers have identified internal friction as the source of this effect. However, it has not been incorporated into computer animation models of cloth. In this paper, we propose a model of internal friction based on an augmented reparameterization of Dahl's model, and we show that this model provides a good match to several important features of cloth hysteresis even with a minimal set of parameters. We also propose novel parameter estimation procedures that are based on simple and inexpensive setups and need only sparse data, as opposed to the complex hardware and dense data acquisition of previous methods. Finally, we provide an algorithm for the efficient simulation of internal friction, and we demonstrate it on simulation examples that show disparate behavior with and without internal friction.","lang":"eng"}],"type":"journal_article"}]