[{"year":"2013","language":[{"iso":"eng"}],"intvolume":"        22","citation":{"ama":"Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . <i>Molecular Ecology</i>. 2013;22(4):987-1002. doi:<a href=\"https://doi.org/10.1111/mec.12165\">10.1111/mec.12165</a>","apa":"Aeschbacher, S., Futschik, A., &#38; Beaumont, M. (2013). Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mec.12165\">https://doi.org/10.1111/mec.12165</a>","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” <i>Molecular Ecology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/mec.12165\">https://doi.org/10.1111/mec.12165</a>.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002.","ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” <i>Molecular Ecology</i>, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002, 2013.","ista":"Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 22(4), 987–1002.","mla":"Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” <i>Molecular Ecology</i>, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:<a href=\"https://doi.org/10.1111/mec.12165\">10.1111/mec.12165</a>."},"doi":"10.1111/mec.12165","quality_controlled":"1","related_material":{"record":[{"relation":"research_data","status":"public","id":"9758"}]},"acknowledgement":"This study has made use of the computational resources provided by IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk). The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk). S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation, St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).","abstract":[{"lang":"eng","text":"We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction."}],"page":"987 - 1002","day":"01","volume":22,"title":"Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ","status":"public","date_created":"2018-12-11T12:00:28Z","oa_version":"None","issue":"4","type":"journal_article","_id":"2944","publication":"Molecular Ecology","acknowledged_ssus":[{"_id":"ScienComp"}],"author":[{"full_name":"Aeschbacher, Simon","id":"2D35326E-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Aeschbacher"},{"full_name":"Futschik, Andreas","first_name":"Andreas","last_name":"Futschik"},{"first_name":"Mark","last_name":"Beaumont","full_name":"Beaumont, Mark"}],"department":[{"_id":"NiBa"}],"date_published":"2013-02-01T00:00:00Z","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Wiley-Blackwell","publist_id":"3788","date_updated":"2023-02-23T14:07:19Z","scopus_import":1},{"has_accepted_license":"1","intvolume":"      7724","year":"2013","language":[{"iso":"eng"}],"conference":{"location":"Daejeon, Korea","start_date":"2012-11-05","end_date":"2012-11-09","name":"ACCV: Asian Conference on Computer Vision"},"acknowledgement":"This work was supported by the PASCAL 2 Network of Excellence (TT) and by the Newton International Fellowship (NQ)","citation":{"ama":"Tommasi T, Quadrianto N, Caputo B, Lampert C. Beyond dataset bias: Multi-task unaligned shared knowledge transfer. 2013;7724:1-15. doi:<a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">10.1007/978-3-642-37331-2_1</a>","chicago":"Tommasi, Tatiana, Novi Quadrianto, Barbara Caputo, and Christoph Lampert. “Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">https://doi.org/10.1007/978-3-642-37331-2_1</a>.","short":"T. Tommasi, N. Quadrianto, B. Caputo, C. Lampert, 7724 (2013) 1–15.","apa":"Tommasi, T., Quadrianto, N., Caputo, B., &#38; Lampert, C. (2013). Beyond dataset bias: Multi-task unaligned shared knowledge transfer. Presented at the ACCV: Asian Conference on Computer Vision, Daejeon, Korea: Springer. <a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">https://doi.org/10.1007/978-3-642-37331-2_1</a>","mla":"Tommasi, Tatiana, et al. <i>Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer</i>. Vol. 7724, Springer, 2013, pp. 1–15, doi:<a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">10.1007/978-3-642-37331-2_1</a>.","ieee":"T. Tommasi, N. Quadrianto, B. Caputo, and C. Lampert, “Beyond dataset bias: Multi-task unaligned shared knowledge transfer,” vol. 7724. Springer, pp. 1–15, 2013.","ista":"Tommasi T, Quadrianto N, Caputo B, Lampert C. 2013. Beyond dataset bias: Multi-task unaligned shared knowledge transfer. 7724, 1–15."},"doi":"10.1007/978-3-642-37331-2_1","quality_controlled":"1","oa":1,"ddc":["000"],"abstract":[{"text":"Many visual datasets are traditionally used to analyze the performance of different learning techniques. The evaluation is usually done within each dataset, therefore it is questionable if such results are a reliable indicator of true generalization ability. We propose here an algorithm to exploit the existing data resources when learning on a new multiclass problem. Our main idea is to identify an image representation that decomposes orthogonally into two subspaces: a part specific to each dataset, and a part generic to, and therefore shared between, all the considered source sets. This allows us to use the generic representation as un-biased reference knowledge for a novel classification task. By casting the method in the multi-view setting, we also make it possible to use different features for different databases. We call the algorithm MUST, Multitask Unaligned Shared knowledge Transfer. Through extensive experiments on five public datasets, we show that MUST consistently improves the cross-datasets generalization performance.","lang":"eng"}],"file":[{"file_name":"2012_ACCV_Tommasi.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_created":"2019-01-22T14:03:11Z","file_id":"5874","date_updated":"2020-07-14T12:45:55Z","creator":"dernst","file_size":1513620,"checksum":"a0a7234a89e2192af655b0d0ae3bf445"}],"alternative_title":["LNCS"],"page":"1 - 15","volume":7724,"title":"Beyond dataset bias: Multi-task unaligned shared knowledge transfer","status":"public","day":"04","author":[{"full_name":"Tommasi, Tatiana","first_name":"Tatiana","last_name":"Tommasi"},{"full_name":"Quadrianto, Novi","first_name":"Novi","last_name":"Quadrianto"},{"first_name":"Barbara","last_name":"Caputo","full_name":"Caputo, Barbara"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"}],"department":[{"_id":"ChLa"}],"date_created":"2018-12-11T12:00:30Z","oa_version":"Submitted Version","type":"conference","_id":"2948","file_date_updated":"2020-07-14T12:45:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Springer","date_updated":"2020-08-11T10:09:54Z","publist_id":"3784","month":"04","date_published":"2013-04-04T00:00:00Z","scopus_import":1,"series_title":"Lecture Notes in Computer Science"},{"day":"08","year":"2013","intvolume":"      7028","status":"public","title":"Bringing Zero-Knowledge Proofs of Knowledge to Practice","volume":7028,"_id":"2973","type":"conference","extern":1,"citation":{"apa":"Bangerter, E., Barzan, S., Krenn, S., Sadeghi, A., Schneider, T., &#38; Tsay, J. (2013). Bringing Zero-Knowledge Proofs of Knowledge to Practice. In B. Christianson, J. Malcolm, V. Matyas, &#38; M. Roe (Eds.) (Vol. 7028, pp. 51–62). Presented at the SPW: Security Protocols Workshop, Springer. <a href=\"https://doi.org/10.1007/978-3-642-36213-2_9\">https://doi.org/10.1007/978-3-642-36213-2_9</a>","chicago":"Bangerter, Endre, Stefania Barzan, Stephan Krenn, Ahmad Sadeghi, Thomas Schneider, and Joe Tsay. “Bringing Zero-Knowledge Proofs of Knowledge to Practice.” edited by Bruce Christianson, James Malcolm, Vashek Matyas, and Michael Roe, 7028:51–62. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36213-2_9\">https://doi.org/10.1007/978-3-642-36213-2_9</a>.","short":"E. Bangerter, S. Barzan, S. Krenn, A. Sadeghi, T. Schneider, J. Tsay, in:, B. Christianson, J. Malcolm, V. Matyas, M. Roe (Eds.), Springer, 2013, pp. 51–62.","ista":"Bangerter E, Barzan S, Krenn S, Sadeghi A, Schneider T, Tsay J. 2013. Bringing Zero-Knowledge Proofs of Knowledge to Practice. SPW: Security Protocols Workshop, LNCS, vol. 7028, 51–62.","ieee":"E. Bangerter, S. Barzan, S. Krenn, A. Sadeghi, T. Schneider, and J. Tsay, “Bringing Zero-Knowledge Proofs of Knowledge to Practice,” presented at the SPW: Security Protocols Workshop, 2013, vol. 7028, pp. 51–62.","mla":"Bangerter, Endre, et al. <i>Bringing Zero-Knowledge Proofs of Knowledge to Practice</i>. Edited by Bruce Christianson et al., vol. 7028, Springer, 2013, pp. 51–62, doi:<a href=\"https://doi.org/10.1007/978-3-642-36213-2_9\">10.1007/978-3-642-36213-2_9</a>.","ama":"Bangerter E, Barzan S, Krenn S, Sadeghi A, Schneider T, Tsay J. Bringing Zero-Knowledge Proofs of Knowledge to Practice. In: Christianson B, Malcolm J, Matyas V, Roe M, eds. Vol 7028. Springer; 2013:51-62. doi:<a href=\"https://doi.org/10.1007/978-3-642-36213-2_9\">10.1007/978-3-642-36213-2_9</a>"},"doi":"10.1007/978-3-642-36213-2_9","quality_controlled":0,"date_created":"2018-12-11T12:00:38Z","conference":{"name":"SPW: Security Protocols Workshop"},"acknowledgement":"This work is being performed within the FP7 EU project CACE (Computer Aided Cryptography Engineering).","author":[{"full_name":"Bangerter, Endre","last_name":"Bangerter","first_name":"Endre"},{"first_name":"Stefania","last_name":"Barzan","full_name":"Barzan, Stefania"},{"last_name":"Krenn","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan","orcid":"0000-0003-2835-9093","full_name":"Stephan Krenn"},{"full_name":"Sadeghi, Ahmad-Reza","first_name":"Ahmad","last_name":"Sadeghi"},{"last_name":"Schneider","first_name":"Thomas","full_name":"Schneider, Thomas"},{"full_name":"Tsay, Joe-Kai","last_name":"Tsay","first_name":"Joe"}],"date_published":"2013-01-08T00:00:00Z","month":"01","oa":1,"abstract":[{"text":"Efficient zero-knowledge proofs of knowledge (ZK-PoK) are basic building blocks of many practical cryptographic applications such as identification schemes, group signatures, and secure multiparty computation. Currently, first applications that critically rely on ZK-PoKs are being deployed in the real world. The most prominent example is Direct Anonymous Attestation (DAA), which was adopted by the Trusted Computing Group (TCG) and implemented as one of the functionalities of the cryptographic Trusted Platform Module (TPM) chip.\n\nImplementing systems using ZK-PoK turns out to be challenging, since ZK-PoK are, loosely speaking, significantly more complex than standard crypto primitives, such as encryption and signature schemes. As a result, implementation cycles of ZK-PoK are time-consuming and error-prone, in particular for developers with minor or no cryptographic skills. \n\nIn this paper we report on our ongoing and future research vision with the goal to bring ZK-PoK to practice by making them accessible to crypto and security engineers. To this end we are developing compilers and related tools that support and partially automate the design, implementation, verification and secure implementation of ZK-PoK protocols.","lang":"eng"}],"publisher":"Springer","publist_id":"3732","date_updated":"2021-01-12T07:40:10Z","publication_status":"published","main_file_link":[{"url":"http://eprint.iacr.org/2009/211.pdf","open_access":"1"}],"editor":[{"last_name":"Christianson","first_name":"Bruce","full_name":"Christianson, Bruce"},{"full_name":"Malcolm, James A.","last_name":"Malcolm","first_name":"James"},{"full_name":"Matyas, Vashek","first_name":"Vashek","last_name":"Matyas"},{"last_name":"Roe","first_name":"Michael","full_name":"Roe, Michael"}],"page":"51 - 62","alternative_title":["LNCS"]},{"publisher":"Springer","publist_id":"3583","date_updated":"2021-01-12T07:41:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_published":"2013-04-01T00:00:00Z","month":"04","abstract":[{"lang":"eng","text":"Multithreaded programs coordinate their interaction through synchronization primitives like mutexes and semaphores, which are managed by an OS-provided resource manager. We propose algorithms for the automatic construction of code-aware resource managers for multithreaded embedded applications. Such managers use knowledge about the structure and resource usage (mutex and semaphore usage) of the threads to guarantee deadlock freedom and progress while managing resources in an efficient way. Our algorithms compute managers as winning strategies in certain infinite games, and produce a compact code description of these strategies. We have implemented the algorithms in the tool Cynthesis. Given a multithreaded program in C, the tool produces C code implementing a code-aware resource manager. We show in experiments that Cynthesis produces compact resource managers within a few minutes on a set of embedded benchmarks with up to 6 threads. © 2012 Springer Science+Business Media, LLC."}],"page":"142 - 174","scopus_import":1,"status":"public","intvolume":"        42","volume":42,"title":"Code aware resource management","language":[{"iso":"eng"}],"year":"2013","day":"01","department":[{"_id":"KrCh"}],"acknowledgement":"This research was supported in part by the National Science Foundation CAREER award CCR-0132780, by the ONR grant N00014-02-1-0671, by the National Science Foundation grants CCR-0427202 and CCR-0234690, and by the ARP award TO.030.MM.D.","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"De Alfaro, Luca","first_name":"Luca","last_name":"De Alfaro"},{"full_name":"Faella, Marco","last_name":"Faella","first_name":"Marco"},{"full_name":"Majumdar, Ritankar","last_name":"Majumdar","first_name":"Ritankar"},{"first_name":"Vishwanath","last_name":"Raman","full_name":"Raman, Vishwanath"}],"_id":"3116","issue":"2","type":"journal_article","publication":"Formal Methods in System Design","citation":{"ama":"Chatterjee K, De Alfaro L, Faella M, Majumdar R, Raman V. Code aware resource management. <i>Formal Methods in System Design</i>. 2013;42(2):142-174. doi:<a href=\"https://doi.org/10.1007/s10703-012-0170-4\">10.1007/s10703-012-0170-4</a>","mla":"Chatterjee, Krishnendu, et al. “Code Aware Resource Management.” <i>Formal Methods in System Design</i>, vol. 42, no. 2, Springer, 2013, pp. 142–74, doi:<a href=\"https://doi.org/10.1007/s10703-012-0170-4\">10.1007/s10703-012-0170-4</a>.","ieee":"K. Chatterjee, L. De Alfaro, M. Faella, R. Majumdar, and V. Raman, “Code aware resource management,” <i>Formal Methods in System Design</i>, vol. 42, no. 2. Springer, pp. 142–174, 2013.","ista":"Chatterjee K, De Alfaro L, Faella M, Majumdar R, Raman V. 2013. Code aware resource management. Formal Methods in System Design. 42(2), 142–174.","short":"K. Chatterjee, L. De Alfaro, M. Faella, R. Majumdar, V. Raman, Formal Methods in System Design 42 (2013) 142–174.","chicago":"Chatterjee, Krishnendu, Luca De Alfaro, Marco Faella, Ritankar Majumdar, and Vishwanath Raman. “Code Aware Resource Management.” <i>Formal Methods in System Design</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s10703-012-0170-4\">https://doi.org/10.1007/s10703-012-0170-4</a>.","apa":"Chatterjee, K., De Alfaro, L., Faella, M., Majumdar, R., &#38; Raman, V. (2013). Code aware resource management. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-012-0170-4\">https://doi.org/10.1007/s10703-012-0170-4</a>"},"doi":"10.1007/s10703-012-0170-4","quality_controlled":"1","oa_version":"None","date_created":"2018-12-11T12:01:29Z"},{"date_created":"2018-12-11T12:02:19Z","oa_version":"Published Version","_id":"3261","issue":"41","type":"journal_article","file_date_updated":"2020-07-14T12:46:06Z","publication":"PNAS","author":[{"first_name":"Julien","last_name":"Dubuis","full_name":"Dubuis, Julien"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik"},{"full_name":"Wieschaus, Eric","last_name":"Wieschaus","first_name":"Eric"},{"full_name":"Gregor, Thomas","first_name":"Thomas","last_name":"Gregor"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"}],"department":[{"_id":"GaTk"}],"day":"08","title":"Positional information, in bits","volume":110,"status":"public","scopus_import":1,"date_published":"2013-10-08T00:00:00Z","month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"National Academy of Sciences","date_updated":"2021-01-12T07:42:13Z","publist_id":"3387","doi":"10.1073/pnas.1315642110","citation":{"ama":"Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. Positional information, in bits. <i>PNAS</i>. 2013;110(41):16301-16308. doi:<a href=\"https://doi.org/10.1073/pnas.1315642110\">10.1073/pnas.1315642110</a>","ieee":"J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, and W. Bialek, “Positional information, in bits,” <i>PNAS</i>, vol. 110, no. 41. National Academy of Sciences, pp. 16301–16308, 2013.","ista":"Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. 2013. Positional information, in bits. PNAS. 110(41), 16301–16308.","mla":"Dubuis, Julien, et al. “Positional Information, in Bits.” <i>PNAS</i>, vol. 110, no. 41, National Academy of Sciences, 2013, pp. 16301–08, doi:<a href=\"https://doi.org/10.1073/pnas.1315642110\">10.1073/pnas.1315642110</a>.","apa":"Dubuis, J., Tkačik, G., Wieschaus, E., Gregor, T., &#38; Bialek, W. (2013). Positional information, in bits. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1315642110\">https://doi.org/10.1073/pnas.1315642110</a>","short":"J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, W. Bialek, PNAS 110 (2013) 16301–16308.","chicago":"Dubuis, Julien, Gašper Tkačik, Eric Wieschaus, Thomas Gregor, and William Bialek. “Positional Information, in Bits.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1315642110\">https://doi.org/10.1073/pnas.1315642110</a>."},"quality_controlled":"1","year":"2013","language":[{"iso":"eng"}],"has_accepted_license":"1","pmid":1,"intvolume":"       110","page":"16301 - 16308","external_id":{"pmid":["24089448"]},"ddc":["570"],"oa":1,"abstract":[{"text":"Cells in a developing embryo have no direct way of &quot;measuring&quot; their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus form a code for &quot;positional information.&quot; We show how to measure this information, in bits, using the gap genes in the Drosophila embryo as an example. Individual genes carry nearly two bits of information, twice as much as expected if the expression patterns consisted only of on/off domains separated by sharp boundaries. Taken together, four gap genes carry enough information to define a cell's location with an error bar of ~1% along the anterior-posterior axis of the embryo. This precision is nearly enough for each cell to have a unique identity, which is the maximum information the system can use, and is nearly constant along the length of the embryo. We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network.","lang":"eng"}],"file":[{"file_size":1670548,"checksum":"ecd859fe52a562193027d428b5524a8d","creator":"dernst","date_updated":"2020-07-14T12:46:06Z","file_id":"5873","access_level":"open_access","date_created":"2019-01-22T13:53:23Z","content_type":"application/pdf","file_name":"2013_PNAS_Dubuis.pdf","relation":"main_file"}]},{"_id":"331","article_processing_charge":"No","type":"journal_article","issue":"19","extern":"1","publication":"Journal of the American Chemical Society","doi":"10.1021/ja401428e","citation":{"ama":"Li W, Zamani R, Rivera Gil P, et al. CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. <i>Journal of the American Chemical Society</i>. 2013;135(19):7098-7101. doi:<a href=\"https://doi.org/10.1021/ja401428e\">10.1021/ja401428e</a>","chicago":"Li, Wenhua, Reza Zamani, Pilar Rivera Gil, Beatriz Pelaz, Maria Ibáñez, Doris Cadavid, Alexey Shavel, et al. “CuTe Nanocrystals: Shape and Size Control, Plasmonic Properties, and Use as SERS Probes and Photothermal Agents.” <i>Journal of the American Chemical Society</i>. ACS, 2013. <a href=\"https://doi.org/10.1021/ja401428e\">https://doi.org/10.1021/ja401428e</a>.","short":"W. Li, R. Zamani, P. Rivera Gil, B. Pelaz, M. Ibáñez, D. Cadavid, A. Shavel, R. Alvarez Puebla, W. Parak, J. Arbiol, A. Cabot, Journal of the American Chemical Society 135 (2013) 7098–7101.","apa":"Li, W., Zamani, R., Rivera Gil, P., Pelaz, B., Ibáñez, M., Cadavid, D., … Cabot, A. (2013). CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. <i>Journal of the American Chemical Society</i>. ACS. <a href=\"https://doi.org/10.1021/ja401428e\">https://doi.org/10.1021/ja401428e</a>","mla":"Li, Wenhua, et al. “CuTe Nanocrystals: Shape and Size Control, Plasmonic Properties, and Use as SERS Probes and Photothermal Agents.” <i>Journal of the American Chemical Society</i>, vol. 135, no. 19, ACS, 2013, pp. 7098–101, doi:<a href=\"https://doi.org/10.1021/ja401428e\">10.1021/ja401428e</a>.","ista":"Li W, Zamani R, Rivera Gil P, Pelaz B, Ibáñez M, Cadavid D, Shavel A, Alvarez Puebla R, Parak W, Arbiol J, Cabot A. 2013. CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. Journal of the American Chemical Society. 135(19), 7098–7101.","ieee":"W. Li <i>et al.</i>, “CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents,” <i>Journal of the American Chemical Society</i>, vol. 135, no. 19. ACS, pp. 7098–7101, 2013."},"date_created":"2018-12-11T11:45:51Z","oa_version":"None","quality_controlled":"1","author":[{"first_name":"Wenhua","last_name":"Li","full_name":"Li, Wenhua"},{"full_name":"Zamani, Reza","first_name":"Reza","last_name":"Zamani"},{"full_name":"Rivera Gil, Pilar","first_name":"Pilar","last_name":"Rivera Gil"},{"full_name":"Pelaz, Beatriz","last_name":"Pelaz","first_name":"Beatriz"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"},{"last_name":"Cadavid","first_name":"Doris","full_name":"Cadavid, Doris"},{"full_name":"Shavel, Alexey","first_name":"Alexey","last_name":"Shavel"},{"last_name":"Alvarez Puebla","first_name":"Ramon","full_name":"Alvarez Puebla, Ramon"},{"last_name":"Parak","first_name":"Wolfgang","full_name":"Parak, Wolfgang"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"language":[{"iso":"eng"}],"day":"30","year":"2013","intvolume":"       135","status":"public","volume":135,"title":"CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents","page":"7098 - 7101","date_published":"2013-04-30T00:00:00Z","month":"04","article_type":"original","abstract":[{"lang":"eng","text":"We report a procedure to prepare highly monodisperse copper telluride nanocubes, nanoplates, and nanorods. The procedure is based on the reaction of a copper salt with trioctylphosphine telluride in the presence of lithium bis(trimethylsilyl)amide and oleylamine. CuTe nanocrystals display a strong near-infrared optical absorption associated with localized surface plasmon resonances. We exploit this plasmon resonance for the design of surface-enhanced Raman scattering sensors for unconventional optical probes. Furthermore, we also report here our preliminary analysis of the use of CuTe nanocrystals as cytotoxic and photothermal agents."}],"publisher":"ACS","date_updated":"2021-01-12T07:42:33Z","publist_id":"7521","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"MDPI","date_updated":"2022-03-21T12:15:29Z","month":"10","date_published":"2013-10-21T00:00:00Z","article_type":"original","scopus_import":"1","title":"Calcium: The missing link in auxin action","tmp":{"image":"/images/cc_by.png","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"volume":2,"status":"public","day":"21","author":[{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"department":[{"_id":"JiFr"}],"oa_version":"Published Version","date_created":"2022-03-21T07:13:49Z","_id":"10895","article_processing_charge":"No","issue":"4","type":"journal_article","publication":"Plants","file_date_updated":"2022-03-21T12:12:56Z","ddc":["580"],"oa":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. "}],"keyword":["Plant Science","Ecology","Ecology","Evolution","Behavior and Systematics"],"file":[{"creator":"dernst","checksum":"fb4ff2e820e344e253c9197544610be6","file_size":670188,"date_updated":"2022-03-21T12:12:56Z","date_created":"2022-03-21T12:12:56Z","access_level":"open_access","file_id":"10916","relation":"main_file","file_name":"2013_Plants_Vanneste.pdf","success":1,"content_type":"application/pdf"}],"page":"650-675","license":"https://creativecommons.org/licenses/by/3.0/","external_id":{"pmid":["27137397"]},"has_accepted_license":"1","pmid":1,"intvolume":"         2","year":"2013","publication_identifier":{"issn":["2223-7747"]},"language":[{"iso":"eng"}],"doi":"10.3390/plants2040650","citation":{"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>","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>.","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.","ista":"Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants. 2(4), 650–675.","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>.","short":"S. Vanneste, J. Friml, Plants 2 (2013) 650–675.","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>"},"quality_controlled":"1"},{"date_published":"2013-06-01T00:00:00Z","month":"06","date_updated":"2023-09-05T15:10:20Z","publisher":"Springer Nature","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","series_title":"LNCS","scopus_import":"1","day":"01","status":"public","title":"Persistent homology in image processing","volume":7877,"publication":"Graph-Based Representations in Pattern Recognition","article_processing_charge":"No","_id":"10897","type":"conference","oa_version":"None","date_created":"2022-03-21T07:30:33Z","project":[{"name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493","call_identifier":"FP7"}],"department":[{"_id":"HeEd"}],"author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","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."}],"place":"Berlin, Heidelberg","page":"182-183","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783642382208"],"eisbn":["9783642382215"],"issn":["0302-9743"]},"year":"2013","intvolume":"      7877","quality_controlled":"1","ec_funded":1,"doi":"10.1007/978-3-642-38221-5_19","citation":{"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>","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.","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.","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>.","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>","short":"H. Edelsbrunner, in:, Graph-Based Representations in Pattern Recognition, Springer Nature, Berlin, Heidelberg, 2013, pp. 182–183.","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>."},"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.","conference":{"location":"Vienna, Austria","start_date":"2013-05-15","end_date":"2013-05-17","name":"GbRPR: Graph-based Representations in Pattern Recognition"}},{"_id":"10898","article_processing_charge":"No","issue":"5","type":"conference","publication":"Proceedings of the ACM International Conference on Computing Frontiers - CF '13","citation":{"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 Press. <a href=\"https://doi.org/10.1145/2482767.2482789\">https://doi.org/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 Press, 2013. <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 Press, 2013.","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.","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.","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 Press, 2013, doi:<a href=\"https://doi.org/10.1145/2482767.2482789\">10.1145/2482767.2482789</a>.","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 Press; 2013. doi:<a href=\"https://doi.org/10.1145/2482767.2482789\">10.1145/2482767.2482789</a>"},"doi":"10.1145/2482767.2482789","quality_controlled":"1","date_created":"2022-03-21T07:33:22Z","oa_version":"None","conference":{"location":"Ischia, Italy","end_date":"2013-05-16","start_date":"2013-05-14","name":"CF: Conference on Computing Frontiers"},"department":[{"_id":"ToHe"}],"author":[{"full_name":"Haas, Andreas","last_name":"Haas","first_name":"Andreas"},{"full_name":"Lippautz, Michael","last_name":"Lippautz","first_name":"Michael"},{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Payer, Hannes","last_name":"Payer","first_name":"Hannes"},{"last_name":"Sokolova","first_name":"Ana","full_name":"Sokolova, Ana"},{"full_name":"Kirsch, Christoph M.","last_name":"Kirsch","first_name":"Christoph M."},{"full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali","last_name":"Sezgin"}],"publication_identifier":{"isbn":["978-145032053-5"]},"language":[{"iso":"eng"}],"year":"2013","day":"01","article_number":"17","status":"public","title":"Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation","scopus_import":"1","month":"05","date_published":"2013-05-01T00:00:00Z","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."}],"publisher":"ACM Press","date_updated":"2022-06-21T08:01:19Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published"},{"scopus_import":"1","page":"508-515","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Elsevier","date_updated":"2022-06-20T09:18:06Z","keyword":["Adaptive landscape","Cline","Coalescent process","Gene flow","Hybrid zone","Local adaptation","Natural selection","Neutral theory","Population structure","Speciation"],"date_published":"2013-01-01T00:00:00Z","month":"01","author":[{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"department":[{"_id":"NiBa"}],"doi":"10.1016/b978-0-12-384719-5.00031-9","citation":{"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.","ieee":"N. H. Barton, “Differentiation,” in <i>Encyclopedia of Biodiversity</i>, 2nd ed., Elsevier, 2013, pp. 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>.","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>.","short":"N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515."},"quality_controlled":"1","oa_version":"None","date_created":"2022-03-21T07:46:22Z","article_processing_charge":"No","_id":"10899","type":"book_chapter","publication":"Encyclopedia of Biodiversity","title":"Differentiation","status":"public","year":"2013","edition":"2","day":"01","publication_identifier":{"isbn":["978-0-12-384720-1"]},"language":[{"iso":"eng"}]},{"scopus_import":"1","series_title":"MIMB","date_updated":"2023-09-05T13:15:33Z","publisher":"Humana Press","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"04","date_published":"2013-04-03T00:00:00Z","department":[{"_id":"MiSi"}],"author":[{"full_name":"Weber, Michele","last_name":"Weber","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","first_name":"Michele"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"publication":"Chemokines","article_processing_charge":"No","_id":"10900","type":"book_chapter","date_created":"2022-03-21T07:47:41Z","oa_version":"None","status":"public","volume":1013,"title":"Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations","day":"03","external_id":{"pmid":["23625502"]},"alternative_title":["Methods in Molecular Biology"],"page":"215-226","editor":[{"last_name":"Cardona","first_name":"Astrid","full_name":"Cardona, Astrid"},{"full_name":"Ubogu, Eroboghene","last_name":"Ubogu","first_name":"Eroboghene"}],"place":"Totowa, NJ","abstract":[{"lang":"eng","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."}],"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.","quality_controlled":"1","citation":{"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.","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.","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>","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>.","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","intvolume":"      1013","pmid":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1064-3745"],"eisbn":["9781627034265"],"isbn":["9781627034258"],"eissn":["1940-6029"]},"year":"2013"},{"day":"15","volume":7810,"title":"How to travel between languages","status":"public","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"oa_version":"None","date_created":"2022-03-21T07:56:21Z","type":"conference","_id":"10902","article_processing_charge":"No","publication":"7th International Conference on Language and Automata Theory and Applications","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Siddhesh","last_name":"Chaubal","full_name":"Chaubal, Siddhesh"},{"last_name":"Rubin","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha","full_name":"Rubin, Sasha"}],"department":[{"_id":"KrCh"}],"month":"04","date_published":"2013-04-15T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","publisher":"Springer Nature","date_updated":"2023-09-05T15:10:38Z","scopus_import":"1","series_title":"LNCS","year":"2013","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"isbn":["9783642370632"],"eisbn":["9783642370649"],"eissn":["1611-3349"]},"intvolume":"      7810","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>","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.","ista":"Chatterjee K, Chaubal S, Rubin S. 2013. How to travel between languages. 7th International Conference on Language and Automata Theory and Applications. LATA: Conference on Language and Automata Theory and ApplicationsLNCS, LNCS, vol. 7810, 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.","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>."},"doi":"10.1007/978-3-642-37064-9_20","quality_controlled":"1","ec_funded":1,"conference":{"name":"LATA: Conference on Language and Automata Theory and Applications","location":"Bilbao, Spain","start_date":"2013-04-02","end_date":"2013-04-05"},"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.","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."}],"place":"Berlin, Heidelberg","page":"214-225","alternative_title":["LNCS"]},{"publisher":"Elsevier","date_updated":"2022-07-18T08:45:34Z","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","publication_status":"published","date_published":"2013-03-01T00:00:00Z","month":"03","article_type":"letter_note","scopus_import":"1","status":"public","volume":23,"title":"The role of Nup98 in transcription regulation in healthy and diseased cells","day":"01","author":[{"first_name":"Tobias M.","last_name":"Franks","full_name":"Franks, Tobias M."},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W"}],"issue":"3","_id":"11083","article_processing_charge":"No","type":"journal_article","publication":"Trends in Cell Biology","date_created":"2022-04-07T07:50:33Z","oa_version":"None","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"}],"keyword":["Cell Biology"],"external_id":{"pmid":["23246429"]},"page":"112-117","pmid":1,"intvolume":"        23","publication_identifier":{"issn":["0962-8924"]},"language":[{"iso":"eng"}],"year":"2013","extern":"1","citation":{"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>","short":"T.M. Franks, M. Hetzer, Trends in Cell Biology 23 (2013) 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>.","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>.","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.","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."},"doi":"10.1016/j.tcb.2012.10.013","quality_controlled":"1"},{"status":"public","volume":14,"title":"Protein homeostasis: Live long, won't prosper","day":"01","author":[{"last_name":"Toyama","first_name":"Brandon H.","full_name":"Toyama, Brandon H."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}],"publication":"Nature Reviews Molecular Cell Biology","_id":"11084","type":"journal_article","article_processing_charge":"No","date_created":"2022-04-07T07:50:43Z","oa_version":"None","date_updated":"2022-07-18T08:37:53Z","publisher":"Springer Nature","publication_status":"published","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","article_type":"original","month":"01","date_published":"2013-01-01T00:00:00Z","scopus_import":"1","intvolume":"        14","pmid":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1471-0072","1471-0080"]},"year":"2013","extern":"1","quality_controlled":"1","doi":"10.1038/nrm3496","citation":{"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>.","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.","ista":"Toyama BH, Hetzer M. 2013. Protein homeostasis: Live long, won’t prosper. Nature Reviews Molecular Cell Biology. 14, 55–61.","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>.","short":"B.H. Toyama, M. Hetzer, Nature Reviews Molecular Cell Biology 14 (2013) 55–61.","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>"},"keyword":["Cell Biology","Molecular Biology"],"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."}],"external_id":{"pmid":["23258296"]},"page":"55-61"},{"keyword":["General Biochemistry","Genetics and Molecular Biology"],"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."}],"oa":1,"external_id":{"pmid":["23827674"]},"page":"47-60","publication_identifier":{"issn":["0092-8674"]},"language":[{"iso":"eng"}],"year":"2013","intvolume":"       154","pmid":1,"extern":"1","quality_controlled":"1","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>","short":"E.M. Hatch, A.H. Fischer, T.J. Deerinck, M. Hetzer, Cell 154 (2013) 47–60.","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.","ista":"Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. 2013. Catastrophic nuclear envelope collapse in cancer cell micronuclei. Cell. 154(1), 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>.","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>"},"doi":"10.1016/j.cell.2013.06.007","article_type":"original","month":"07","date_published":"2013-07-03T00:00:00Z","date_updated":"2022-07-18T08:45:47Z","publisher":"Elsevier","publication_status":"published","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2013.06.007","open_access":"1"}],"scopus_import":"1","day":"03","status":"public","volume":154,"title":"Catastrophic nuclear envelope collapse in cancer cell micronuclei","publication":"Cell","_id":"11085","issue":"1","article_processing_charge":"No","type":"journal_article","date_created":"2022-04-07T07:50:51Z","oa_version":"Published Version","author":[{"full_name":"Hatch, Emily M.","first_name":"Emily M.","last_name":"Hatch"},{"full_name":"Fischer, Andrew H.","last_name":"Fischer","first_name":"Andrew H."},{"full_name":"Deerinck, Thomas J.","first_name":"Thomas J.","last_name":"Deerinck"},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER"}]},{"pmid":1,"intvolume":"         9","publication_identifier":{"issn":["1553-7404"]},"language":[{"iso":"eng"}],"year":"2013","extern":"1","citation":{"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>","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>.","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.","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).","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>.","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>"},"doi":"10.1371/journal.pgen.1003308","quality_controlled":"1","oa":1,"keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"abstract":[{"lang":"eng","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."}],"external_id":{"pmid":["23468646"]},"article_number":"e1003308","status":"public","title":"Dynamic association of NUP98 with the human genome","volume":9,"day":"28","author":[{"last_name":"Liang","first_name":"Yun","full_name":"Liang, Yun"},{"last_name":"Franks","first_name":"Tobias M.","full_name":"Franks, Tobias M."},{"full_name":"Marchetto, Maria C.","first_name":"Maria C.","last_name":"Marchetto"},{"last_name":"Gage","first_name":"Fred H.","full_name":"Gage, Fred H."},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W"}],"article_processing_charge":"No","_id":"11086","issue":"2","type":"journal_article","publication":"PLoS Genetics","date_created":"2022-04-07T07:50:59Z","oa_version":"Published Version","publisher":"Public Library of Science","date_updated":"2022-07-18T08:45:58Z","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","publication_status":"published","month":"02","date_published":"2013-02-28T00:00:00Z","article_type":"original","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1371/journal.pgen.1003308","open_access":"1"}]},{"external_id":{"pmid":["23993091"]},"page":"971-982","oa":1,"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"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"extern":"1","doi":"10.1016/j.cell.2013.07.037","citation":{"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>","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>","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>.","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.","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.","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>."},"quality_controlled":"1","pmid":1,"intvolume":"       154","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0092-8674"]},"year":"2013","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2013.07.037","open_access":"1"}],"publisher":"Elsevier","date_updated":"2022-07-18T08:50:47Z","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","publication_status":"published","date_published":"2013-08-29T00:00:00Z","month":"08","article_type":"original","author":[{"full_name":"Toyama, Brandon H.","last_name":"Toyama","first_name":"Brandon H."},{"first_name":"Jeffrey N.","last_name":"Savas","full_name":"Savas, Jeffrey N."},{"first_name":"Sung Kyu","last_name":"Park","full_name":"Park, Sung Kyu"},{"full_name":"Harris, Michael S.","last_name":"Harris","first_name":"Michael S."},{"last_name":"Ingolia","first_name":"Nicholas T.","full_name":"Ingolia, Nicholas T."},{"first_name":"John R.","last_name":"Yates","full_name":"Yates, John R."},{"last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}],"type":"journal_article","_id":"11087","article_processing_charge":"No","issue":"5","publication":"Cell","date_created":"2022-04-07T07:51:08Z","oa_version":"Published Version","status":"public","title":"Identification of long-lived proteins reveals exceptional stability of essential cellular structures","volume":154,"day":"29"},{"extern":"1","citation":{"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>","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.","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.","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>","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>.","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."},"doi":"10.1016/j.bpj.2013.01.049","quality_controlled":"1","publication_identifier":{"issn":["0006-3495"]},"language":[{"iso":"eng"}],"year":"2013","pmid":1,"intvolume":"       104","external_id":{"pmid":["23601312"]},"page":"1652-1660","oa":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"}],"keyword":["Biophysics"],"_id":"11088","article_processing_charge":"No","issue":"8","type":"journal_article","publication":"Biophysical Journal","date_created":"2022-04-07T07:51:26Z","oa_version":"Published Version","author":[{"last_name":"Regner","first_name":"Benjamin M.","full_name":"Regner, Benjamin M."},{"full_name":"Vučinić, Dejan","last_name":"Vučinić","first_name":"Dejan"},{"full_name":"Domnisoru, Cristina","first_name":"Cristina","last_name":"Domnisoru"},{"first_name":"Thomas M.","last_name":"Bartol","full_name":"Bartol, Thomas M."},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W"},{"full_name":"Tartakovsky, Daniel M.","last_name":"Tartakovsky","first_name":"Daniel M."},{"full_name":"Sejnowski, Terrence J.","last_name":"Sejnowski","first_name":"Terrence J."}],"day":"16","status":"public","volume":104,"title":"Anomalous diffusion of single particles in cytoplasm","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.bpj.2013.01.049"}],"scopus_import":"1","month":"04","date_published":"2013-04-16T00:00:00Z","article_type":"original","publisher":"Elsevier","date_updated":"2022-07-18T08:51:01Z","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","publication_status":"published"},{"language":[{"iso":"eng"}],"day":"07","year":"2013","status":"public","intvolume":"        84","article_number":"025104","volume":84,"title":"In situ granular charge measurement by free-fall videography","extern":"1","publication":"Review of Scientific Instruments","_id":"115","type":"journal_article","issue":"2","date_created":"2018-12-11T11:44:42Z","quality_controlled":"1","oa_version":"None","citation":{"short":"S.R. Waitukaitis, H. Jaeger, Review of Scientific Instruments 84 (2013).","chicago":"Waitukaitis, Scott R, and Heinrich Jaeger. “In Situ Granular Charge Measurement by Free-Fall Videography.” <i>Review of Scientific Instruments</i>. AIP, 2013. <a href=\"https://doi.org/10.1063/1.4789496\">https://doi.org/10.1063/1.4789496</a>.","apa":"Waitukaitis, S. R., &#38; Jaeger, H. (2013). In situ granular charge measurement by free-fall videography. <i>Review of Scientific Instruments</i>. AIP. <a href=\"https://doi.org/10.1063/1.4789496\">https://doi.org/10.1063/1.4789496</a>","mla":"Waitukaitis, Scott R., and Heinrich Jaeger. “In Situ Granular Charge Measurement by Free-Fall Videography.” <i>Review of Scientific Instruments</i>, vol. 84, no. 2, 025104, AIP, 2013, doi:<a href=\"https://doi.org/10.1063/1.4789496\">10.1063/1.4789496</a>.","ista":"Waitukaitis SR, Jaeger H. 2013. In situ granular charge measurement by free-fall videography. Review of Scientific Instruments. 84(2), 025104.","ieee":"S. R. Waitukaitis and H. Jaeger, “In situ granular charge measurement by free-fall videography,” <i>Review of Scientific Instruments</i>, vol. 84, no. 2. AIP, 2013.","ama":"Waitukaitis SR, Jaeger H. In situ granular charge measurement by free-fall videography. <i>Review of Scientific Instruments</i>. 2013;84(2). doi:<a href=\"https://doi.org/10.1063/1.4789496\">10.1063/1.4789496</a>"},"doi":"10.1063/1.4789496","acknowledgement":"This work was supported financially by the National Science Foundation (NSF) through its Materials Research Science and Engineering Center (MRSEC) program (DMR-0820054) and by the US Army Research Office through Grant No. W911NF-12-1-0182. S.R.W. acknowledges support from a University of Chicago Millikan Fellowship.","author":[{"first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176"},{"full_name":"Jaeger, Heinrich","last_name":"Jaeger","first_name":"Heinrich"}],"date_published":"2013-02-07T00:00:00Z","month":"02","abstract":[{"text":"We present the design and performance characterization of a new experimental technique for measuring individual particle charges in large ensembles of macroscopic grains. The measurement principle is qualitatively similar to that used in determining the elementary charge by Millikan in that it follows individual particle trajectories. However, by taking advantage of new technology we are able to work with macroscopic grains and achieve several orders of magnitude better resolution in charge to mass ratios. By observing freely falling grains accelerated in a horizontal electric field with a co-falling, high-speed video camera, we dramatically increase particle tracking time and measurement precision. Keeping the granular medium under vacuum, we eliminate air drag, leaving the electrostatic force as the primary source of particle accelerations in the co-moving frame. Because the technique is based on direct imaging, we can distinguish between different particle types during the experiment, opening up the possibility of studying charge transfer processes between different particle species. For the ∼300 μm diameter grains reported here, we achieve an average acceleration resolution of ∼0.008 m/s2, a force resolution of ∼500 pN, and a median charge resolution ∼6× 104 elementary charges per grain (corresponding to surface charge densities ∼1 elementary charges per μm2). The primary source of error is indeterminacy in the grain mass, but with higher resolution cameras and better optics this can be further improved. The high degree of resolution and the ability to visually identify particles of different species or sizes with direct imaging make this a powerful new tool to characterize charging processes in granular media.","lang":"eng"}],"date_updated":"2021-01-12T06:48:39Z","publist_id":"7939","publisher":"AIP","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"arxiv":1,"intvolume":"       779","year":"2013","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"language":[{"iso":"eng"}],"acknowledgement":"We thank the referee for many helpful comments and suggestions which greatly improved the clarity and quality of this work. D.S. acknowledges financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship and also funding from the European Community Seventh Framework Programme (FP7/2007-2013) under grant agreement number RG226604 (OPTICON) which allowed access to CFHT time (proposals: 11BO29 & 12AO19). A.M.S. gratefully acknowledges an STFC Advanced Fellowship through grant number ST/H005234/1. I.R.S., J.P.S., and R.G.B. acknowledge support from the UK Science and Technology Facilities Council (STFC) under ST/I001573/1. I.R.S. acknowledges STFC (ST/J001422/1), the ERC Advanced Investigator program DUSTYGAL and a Royal Society/Wolfson Merit Award. P.N.B. acknowledges support from STFC. R.M.S. acknowledges support from the grant ST/1001573/1. The data presented here are based on observations with the KMOS spectrograph on the ESO/VLT under program 60.A-9460 and can be accessed through the ESO data archive. The authors also wish to acknowledge the help from Michael Hilker in preparing the KMOS observations.","quality_controlled":"1","doi":"10.1088/0004-637x/779/2/139","citation":{"ama":"Sobral D, Swinbank AM, Stott JP, et al. The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS. <i>The Astrophysical Journal</i>. 2013;779(2). doi:<a href=\"https://doi.org/10.1088/0004-637x/779/2/139\">10.1088/0004-637x/779/2/139</a>","apa":"Sobral, D., Swinbank, A. M., Stott, J. P., Matthee, J. J., Bower, R. G., Smail, I., … Sharples, R. M. (2013). The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/0004-637x/779/2/139\">https://doi.org/10.1088/0004-637x/779/2/139</a>","chicago":"Sobral, D., A. M. Swinbank, J. P. Stott, Jorryt J Matthee, R. G. Bower, Ian Smail, P. Best, J. E. Geach, and R. M. Sharples. “The Dynamics of Z=0.8 H-Alpha-Selected Star-Forming Galaxies from KMOS/CF-HiZELS.” <i>The Astrophysical Journal</i>. IOP Publishing, 2013. <a href=\"https://doi.org/10.1088/0004-637x/779/2/139\">https://doi.org/10.1088/0004-637x/779/2/139</a>.","short":"D. Sobral, A.M. Swinbank, J.P. Stott, J.J. Matthee, R.G. Bower, I. Smail, P. Best, J.E. Geach, R.M. Sharples, The Astrophysical Journal 779 (2013).","ista":"Sobral D, Swinbank AM, Stott JP, Matthee JJ, Bower RG, Smail I, Best P, Geach JE, Sharples RM. 2013. The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS. The Astrophysical Journal. 779(2), 139.","ieee":"D. Sobral <i>et al.</i>, “The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS,” <i>The Astrophysical Journal</i>, vol. 779, no. 2. IOP Publishing, 2013.","mla":"Sobral, D., et al. “The Dynamics of Z=0.8 H-Alpha-Selected Star-Forming Galaxies from KMOS/CF-HiZELS.” <i>The Astrophysical Journal</i>, vol. 779, no. 2, 139, IOP Publishing, 2013, doi:<a href=\"https://doi.org/10.1088/0004-637x/779/2/139\">10.1088/0004-637x/779/2/139</a>."},"extern":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution – galaxies","high-redshift – galaxies","starburst"],"abstract":[{"text":"We present the spatially resolved Hα dynamics of 16 star-forming galaxies at z ∼ 0.81 using the new KMOS multi-object integral field spectrograph on the ESO Very Large Telescope. These galaxies, selected using 1.18 μm narrowband imaging from the 10 deg2 CFHT-HiZELS survey of the SA 22 hr field, are found in a ∼4 Mpc overdensity of Hα emitters and likely reside in a group/intermediate environment, but not a cluster. We confirm and identify a rich group of star-forming galaxies at z = 0.813 ± 0.003, with 13 galaxies within 1000 km s−1 of each other, and seven within a diameter of 3 Mpc. All of our galaxies are “typical” star-forming galaxies at their redshift, 0.8 ± 0.4 SFR$^*_{z = 0.8}$, spanning a range of specific star formation rates (sSFRs) of 0.2–1.1 Gyr−1 and have a median metallicity very close to solar of 12 + log(O/H) = 8.62 ± 0.06. We measure the spatially resolved Hα dynamics of the galaxies in our sample and show that 13 out of 16 galaxies can be described by rotating disks and use the data to derive inclination corrected rotation speeds of 50–275 km s−1. The fraction of disks within our sample is 75% ± 8%, consistent with previous results based on Hubble Space Telescope morphologies of Hα-selected galaxies at z ∼ 1 and confirming that disks dominate the SFR density at z ∼ 1. Our Hα galaxies are well fitted by the z ∼ 1–2 Tully–Fisher (TF) relation, confirming the evolution seen in the zero point. Apart from having, on average, higher stellar masses and lower sSFRs, our group galaxies at z = 0.81 present the same mass–metallicity and TF relation as z ∼ 1 field galaxies and are all disk galaxies.","lang":"eng"}],"oa":1,"external_id":{"arxiv":["1310.3822"]},"title":"The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS","volume":779,"status":"public","article_number":"139","day":"03","author":[{"full_name":"Sobral, D.","first_name":"D.","last_name":"Sobral"},{"full_name":"Swinbank, A. M.","first_name":"A. M.","last_name":"Swinbank"},{"full_name":"Stott, J. P.","first_name":"J. P.","last_name":"Stott"},{"last_name":"Matthee","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J"},{"full_name":"Bower, R. G.","first_name":"R. G.","last_name":"Bower"},{"full_name":"Smail, Ian","first_name":"Ian","last_name":"Smail"},{"last_name":"Best","first_name":"P.","full_name":"Best, P."},{"last_name":"Geach","first_name":"J. E.","full_name":"Geach, J. E."},{"full_name":"Sharples, R. M.","last_name":"Sharples","first_name":"R. M."}],"oa_version":"Preprint","date_created":"2022-07-07T09:14:48Z","publication":"The Astrophysical Journal","_id":"11520","type":"journal_article","article_processing_charge":"No","issue":"2","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2022-08-18T10:43:07Z","publisher":"IOP Publishing","article_type":"original","date_published":"2013-12-03T00:00:00Z","month":"12","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1310.3822"}]}]