[{"abstract":[{"lang":"eng","text":"This document is created as a part of the project “Repository for Research Data on IST Austria”. It summarises the actual state of research data at IST Austria, based on survey results. It supports the choice of appropriate software, which would best fit the requirements of their users, the researchers."}],"file_date_updated":"2020-07-14T12:46:44Z","type":"report","file":[{"file_name":"IST-2012-103-v1+1_Actual_state_of_research_data_@_IST_Austria.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":238544,"file_id":"5472","relation":"main_file","date_updated":"2020-07-14T12:46:44Z","date_created":"2018-12-12T11:53:11Z","checksum":"e0a7c041eea1ca4b70ab6f9ec5177f4e"}],"oa_version":"Published Version","date_updated":"2020-07-14T23:04:49Z","date_created":"2018-12-12T11:39:06Z","pubrep_id":"103","author":[{"full_name":"Porsche, Jana","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87","first_name":"Jana","last_name":"Porsche"}],"publisher":"IST Austria","department":[{"_id":"E-Lib"}],"ddc":["020"],"title":"Actual state of research data @ ISTAustria","status":"public","publication_status":"published","_id":"5398","year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","month":"11","day":"12","language":[{"iso":"eng"}],"date_published":"2012-11-12T00:00:00Z","oa":1,"citation":{"ama":"Porsche J. Actual State of Research Data @ ISTAustria. IST Austria; 2012.","ista":"Porsche J. 2012. Actual state of research data @ ISTAustria, IST Austria,p.","apa":"Porsche, J. (2012). Actual state of research data @ ISTAustria. IST Austria.","ieee":"J. Porsche, Actual state of research data @ ISTAustria. IST Austria, 2012.","mla":"Porsche, Jana. Actual State of Research Data @ ISTAustria. IST Austria, 2012.","short":"J. Porsche, Actual State of Research Data @ ISTAustria, IST Austria, 2012.","chicago":"Porsche, Jana. Actual State of Research Data @ ISTAustria. IST Austria, 2012."}},{"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.protcy.2012.05.134","month":"05","publication_identifier":{"issn":["2212-0173"]},"publication_status":"published","publisher":"Elsevier","year":"2012","date_updated":"2021-01-12T08:03:43Z","date_created":"2019-01-17T11:54:21Z","volume":4,"author":[{"full_name":"Biswas, Ranita","orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas","first_name":"Ranita"},{"last_name":"Sil","first_name":"Jaya","full_name":"Sil, Jaya"}],"extern":"1","file_date_updated":"2020-07-14T12:47:12Z","page":"820-824","publication":"Procedia Technology","citation":{"ama":"Biswas R, Sil J. An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. Procedia Technology. 2012;4:820-824. doi:10.1016/j.protcy.2012.05.134","ista":"Biswas R, Sil J. 2012. An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. Procedia Technology. 4, 820–824.","apa":"Biswas, R., & Sil, J. (2012). An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets. Procedia Technology. Elsevier. https://doi.org/10.1016/j.protcy.2012.05.134","ieee":"R. Biswas and J. Sil, “An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets,” Procedia Technology, vol. 4. Elsevier, pp. 820–824, 2012.","mla":"Biswas, Ranita, and Jaya Sil. “An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets.” Procedia Technology, vol. 4, Elsevier, 2012, pp. 820–24, doi:10.1016/j.protcy.2012.05.134.","short":"R. Biswas, J. Sil, Procedia Technology 4 (2012) 820–824.","chicago":"Biswas, Ranita, and Jaya Sil. “An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets.” Procedia Technology. Elsevier, 2012. https://doi.org/10.1016/j.protcy.2012.05.134."},"date_published":"2012-05-01T00:00:00Z","day":"01","has_accepted_license":"1","status":"public","title":"An Improved Canny Edge Detection Algorithm Based on Type-2 Fuzzy Sets","ddc":["000"],"intvolume":" 4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5839","file":[{"access_level":"open_access","file_name":"2012_Procedia_Biswas.pdf","creator":"dernst","content_type":"application/pdf","file_size":305426,"file_id":"5863","relation":"main_file","checksum":"ba0185986b151d8c11201f48cd505ceb","date_created":"2019-01-21T07:28:06Z","date_updated":"2020-07-14T12:47:12Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Canny's edge detection algorithm is a classical and robust method for edge detection in gray-scale images. The two \r\nsignificant features of this method are introduction of NMS (Non-Maximum Suppression) and double thresholding of \r\nthe gradient image. Due to poor illumination, the region boundaries in an image may become vague, creating \r\nuncertainties in the gradient image. In this paper, we have proposed an algorithm based on the concept of type-2 fuzzy sets to handle uncertainties that automatically selects the threshold values needed to segment the gradient image using classical Canny’s edge detection algorithm. The results show that our algorithm works significantly well on different benchmark images as well as medical images (hand radiography images). ","lang":"eng"}]},{"language":[{"iso":"eng"}],"doi":"10.1016/j.jmb.2012.02.014","date_published":"2012-04-13T00:00:00Z","page":"387 - 394","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4582759/"}],"oa":1,"citation":{"mla":"Bernecky, Carrie, and Dylan Taatjes. “Activator-Mediator Binding Stabilizes RNA Polymerase II Orientation within the Human Mediator-RNA Polymerase II-TFIIF Assembly.” Journal of Molecular Biology, vol. 417, no. 5, Elsevier, 2012, pp. 387–94, doi:10.1016/j.jmb.2012.02.014.","short":"C. Bernecky, D. Taatjes, Journal of Molecular Biology 417 (2012) 387–394.","chicago":"Bernecky, Carrie, and Dylan Taatjes. “Activator-Mediator Binding Stabilizes RNA Polymerase II Orientation within the Human Mediator-RNA Polymerase II-TFIIF Assembly.” Journal of Molecular Biology. Elsevier, 2012. https://doi.org/10.1016/j.jmb.2012.02.014.","ama":"Bernecky C, Taatjes D. Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. Journal of Molecular Biology. 2012;417(5):387-394. doi:10.1016/j.jmb.2012.02.014","ista":"Bernecky C, Taatjes D. 2012. Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. Journal of Molecular Biology. 417(5), 387–394.","ieee":"C. Bernecky and D. Taatjes, “Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly,” Journal of Molecular Biology, vol. 417, no. 5. Elsevier, pp. 387–394, 2012.","apa":"Bernecky, C., & Taatjes, D. (2012). Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2012.02.014"},"publication":"Journal of Molecular Biology","article_processing_charge":"No","day":"13","month":"04","oa_version":"None","volume":417,"date_updated":"2021-01-12T08:05:21Z","date_created":"2018-12-11T11:47:24Z","author":[{"first_name":"Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A"},{"full_name":"Taatjes, Dylan","first_name":"Dylan","last_name":"Taatjes"}],"intvolume":" 417","publisher":"Elsevier","status":"public","publication_status":"published","title":"Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly","_id":"596","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","extern":"1","issue":"5","publist_id":"7208","abstract":[{"text":"The human Mediator complex controls RNA polymerase II (pol II) function in ways that remain incompletely understood. Activator-Mediator binding alters Mediator structure, and these activator-induced structural shifts appear to play key roles in regulating transcription. A recent cryo-electron microscopy (EM) analysis revealed that pol II adopted a stable orientation within a Mediator-pol II-TFIIF assembly in which Mediator was bound to the activation domain of viral protein 16 (VP16). Whereas TFIIF was shown to be important for orienting pol II within this assembly, the potential role of the activator was not assessed. To determine how activator binding might affect pol II orientation, we isolated human Mediator-pol II-TFIIF complexes in which Mediator was not bound to an activator. Cryo-EM analysis of this assembly, coupled with pol II crystal structure docking, revealed that pol II binds Mediator at the same general location; however, in contrast to VP16-bound Mediator, pol II does not appear to stably orient in the absence of an activator. Variability in pol II orientation might be important mechanistically, perhaps to enable sense and antisense transcription at human promoters. Because Mediator interacts extensively with pol II, these results suggest that Mediator structural shifts induced by activator binding help stably orient pol II prior to transcription initiation.","lang":"eng"}],"type":"journal_article"},{"month":"03","publication_identifier":{"issn":["1097-6256","1546-1726"]},"language":[{"iso":"eng"}],"doi":"10.1038/nn.3061","quality_controlled":"1","external_id":{"pmid":["22388961"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564487/","open_access":"1"}],"oa":1,"extern":"1","date_created":"2019-03-20T14:23:30Z","date_updated":"2021-01-12T08:06:17Z","volume":15,"author":[{"first_name":"Karl Emanuel","last_name":"Busch","full_name":"Busch, Karl Emanuel"},{"first_name":"Patrick","last_name":"Laurent","full_name":"Laurent, Patrick"},{"full_name":"Soltesz, Zoltan","first_name":"Zoltan","last_name":"Soltesz"},{"last_name":"Murphy","first_name":"Robin Joseph","full_name":"Murphy, Robin Joseph"},{"full_name":"Faivre, Olivier","last_name":"Faivre","first_name":"Olivier"},{"last_name":"Hedwig","first_name":"Berthold","full_name":"Hedwig, Berthold"},{"last_name":"Thomas","first_name":"Martin","full_name":"Thomas, Martin"},{"first_name":"Heather L","last_name":"Smith","full_name":"Smith, Heather L"},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario","full_name":"de Bono, Mario"}],"publication_status":"published","publisher":"Springer Nature","year":"2012","pmid":1,"day":"04","date_published":"2012-03-04T00:00:00Z","page":"581-591","publication":"Nature Neuroscience","citation":{"mla":"Busch, Karl Emanuel, et al. “Tonic Signaling from O2 Sensors Sets Neural Circuit Activity and Behavioral State.” Nature Neuroscience, vol. 15, no. 4, Springer Nature, 2012, pp. 581–91, doi:10.1038/nn.3061.","short":"K.E. Busch, P. Laurent, Z. Soltesz, R.J. Murphy, O. Faivre, B. Hedwig, M. Thomas, H.L. Smith, M. de Bono, Nature Neuroscience 15 (2012) 581–591.","chicago":"Busch, Karl Emanuel, Patrick Laurent, Zoltan Soltesz, Robin Joseph Murphy, Olivier Faivre, Berthold Hedwig, Martin Thomas, Heather L Smith, and Mario de Bono. “Tonic Signaling from O2 Sensors Sets Neural Circuit Activity and Behavioral State.” Nature Neuroscience. Springer Nature, 2012. https://doi.org/10.1038/nn.3061.","ama":"Busch KE, Laurent P, Soltesz Z, et al. Tonic signaling from O2 sensors sets neural circuit activity and behavioral state. Nature Neuroscience. 2012;15(4):581-591. doi:10.1038/nn.3061","ista":"Busch KE, Laurent P, Soltesz Z, Murphy RJ, Faivre O, Hedwig B, Thomas M, Smith HL, de Bono M. 2012. Tonic signaling from O2 sensors sets neural circuit activity and behavioral state. Nature Neuroscience. 15(4), 581–591.","apa":"Busch, K. E., Laurent, P., Soltesz, Z., Murphy, R. J., Faivre, O., Hedwig, B., … de Bono, M. (2012). Tonic signaling from O2 sensors sets neural circuit activity and behavioral state. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/nn.3061","ieee":"K. E. Busch et al., “Tonic signaling from O2 sensors sets neural circuit activity and behavioral state,” Nature Neuroscience, vol. 15, no. 4. Springer Nature, pp. 581–591, 2012."},"abstract":[{"lang":"eng","text":"Tonic receptors convey stimulus duration and intensity and are implicated in homeostatic control. However, how tonic homeostatic signals are generated and how they reconfigure neural circuits and modify animal behavior is poorly understood. Here we show that Caenorhabditis elegans O2-sensing neurons are tonic receptors that continuously signal ambient [O2] to set the animal's behavioral state. Sustained signaling relied on a Ca2+ relay involving L-type voltage-gated Ca2+ channels, the ryanodine and the inositol-1,4,5-trisphosphate receptors. Tonic activity evoked continuous neuropeptide release, which helps elicit the enduring behavioral state associated with high [O2]. Sustained O2 receptor signaling was propagated to downstream neural circuits, including the hub interneuron RMG. O2 receptors evoked similar locomotory states at particular O2 concentrations, regardless of previous d[O2]/dt. However, a phasic component of the URX receptors' response to high d[O2]/dt, as well as tonic-to-phasic transformations in downstream interneurons, enabled transient reorientation movements shaped by d[O2]/dt. Our results highlight how tonic homeostatic signals can generate both transient and enduring behavioral change."}],"issue":"4","type":"journal_article","oa_version":"Submitted Version","title":"Tonic signaling from O2 sensors sets neural circuit activity and behavioral state","status":"public","intvolume":" 15","_id":"6136","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"lang":"eng","text":"This paper proposes a novel cooperative approach for two-hop amplify-and-forward (A&F) relaying that exploits both the signal forwarded by the relay and the one directly transmitted by the source in impulse-radio ultra-wideband (IR-UWB) systems. Specifically, we focus on a non-coherent setup employing a double-differential encoding scheme at the source node and a single differential demodulation at the relay and destination. The log-likelihood ratio based decision rule is derived at the destination node. A semi-analytical power allocation strategy is presented by evaluating a closed-form expression for the effective signal to noise ratio (SNR) at the destination, which is maximized by exhaustive search. Numerical simulations show that the proposed system outperforms both the direct transmission with single differential encoding and the non-cooperative multi-hop approach in different scenarios."}],"extern":"1","type":"conference","author":[{"first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"full_name":"Zhou, Qi","last_name":"Zhou","first_name":"Qi"},{"first_name":"Xiaoli","last_name":"Ma","full_name":"Ma, Xiaoli"},{"first_name":"Vincenzo","last_name":"Lottici","full_name":"Lottici, Vincenzo"}],"oa_version":"None","date_created":"2019-07-31T09:14:48Z","date_updated":"2021-01-12T08:08:49Z","_id":"6746","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","publisher":"IEEE","publication_status":"published","status":"public","title":"A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems","publication_identifier":{"issn":["1520-6149"]},"day":"31","month":"07","date_published":"2012-07-31T00:00:00Z","doi":"10.1109/icassp.2012.6288524","conference":{"end_date":"2012-03-30","start_date":"2012-03-25","location":"Kyoto, Japan","name":"ICASSP: International Conference on Acoustics, Speech and Signal Processing"},"language":[{"iso":"eng"}],"citation":{"mla":"Mondelli, Marco, et al. “A Cooperative Approach for Amplify-and-Forward Differential Transmitted Reference IR-UWB Relay Systems.” 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), IEEE, 2012, pp. 2905–08, doi:10.1109/icassp.2012.6288524.","short":"M. Mondelli, Q. Zhou, X. Ma, V. Lottici, in:, 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), IEEE, 2012, pp. 2905–2908.","chicago":"Mondelli, Marco, Qi Zhou, Xiaoli Ma, and Vincenzo Lottici. “A Cooperative Approach for Amplify-and-Forward Differential Transmitted Reference IR-UWB Relay Systems.” In 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2905–8. IEEE, 2012. https://doi.org/10.1109/icassp.2012.6288524.","ama":"Mondelli M, Zhou Q, Ma X, Lottici V. A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems. In: 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). IEEE; 2012:2905-2908. doi:10.1109/icassp.2012.6288524","ista":"Mondelli M, Zhou Q, Ma X, Lottici V. 2012. A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems. 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). ICASSP: International Conference on Acoustics, Speech and Signal Processing, 2905–2908.","apa":"Mondelli, M., Zhou, Q., Ma, X., & Lottici, V. (2012). A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems. In 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) (pp. 2905–2908). Kyoto, Japan: IEEE. https://doi.org/10.1109/icassp.2012.6288524","ieee":"M. Mondelli, Q. Zhou, X. Ma, and V. Lottici, “A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems,” in 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Kyoto, Japan, 2012, pp. 2905–2908."},"publication":"2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)","page":"2905-2908","quality_controlled":"1"},{"publication_identifier":{"issn":["0022-2461"],"eissn":["1573-4803"]},"article_processing_charge":"No","month":"08","day":"01","citation":{"ista":"Lukas KC, Joshi G, Modic KA, Ren ZF, Opeil CP. 2012. Thermoelectric properties of Ho-doped Bi0.88Sb0.12. Journal of Materials Science. 47(15), 5729–5734.","ieee":"K. C. Lukas, G. Joshi, K. A. Modic, Z. F. Ren, and C. P. Opeil, “Thermoelectric properties of Ho-doped Bi0.88Sb0.12,” Journal of Materials Science, vol. 47, no. 15. Springer Nature, pp. 5729–5734, 2012.","apa":"Lukas, K. C., Joshi, G., Modic, K. A., Ren, Z. F., & Opeil, C. P. (2012). Thermoelectric properties of Ho-doped Bi0.88Sb0.12. Journal of Materials Science. Springer Nature. https://doi.org/10.1007/s10853-012-6463-6","ama":"Lukas KC, Joshi G, Modic KA, Ren ZF, Opeil CP. Thermoelectric properties of Ho-doped Bi0.88Sb0.12. Journal of Materials Science. 2012;47(15):5729-5734. doi:10.1007/s10853-012-6463-6","chicago":"Lukas, K. C., G. Joshi, Kimberly A Modic, Z. F. Ren, and C. P. Opeil. “Thermoelectric Properties of Ho-Doped Bi0.88Sb0.12.” Journal of Materials Science. Springer Nature, 2012. https://doi.org/10.1007/s10853-012-6463-6.","mla":"Lukas, K. C., et al. “Thermoelectric Properties of Ho-Doped Bi0.88Sb0.12.” Journal of Materials Science, vol. 47, no. 15, Springer Nature, 2012, pp. 5729–34, doi:10.1007/s10853-012-6463-6.","short":"K.C. Lukas, G. Joshi, K.A. Modic, Z.F. Ren, C.P. Opeil, Journal of Materials Science 47 (2012) 5729–5734."},"publication":"Journal of Materials Science","page":"5729-5734","article_type":"original","quality_controlled":"1","doi":"10.1007/s10853-012-6463-6","date_published":"2012-08-01T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","issue":"15","abstract":[{"lang":"eng","text":"The Seebeck coefficients, electrical resistivities, total thermal conductivities, and magnetization are reported for temperatures between 5 and 350 K for n-type Bi0.88Sb0.12 nano-composite alloys made by Ho-doping at the 0, 1, and 3 % atomic levels. The alloys were prepared using a dc hot-pressing method, and are shown to be single phase for both Ho contents with grain sizes on the average of 900 nm. We find the parent compound has a maximum of ZT = 0.28 at 231 K, while doping 1 % Ho increases the maximum ZT to 0.31 at 221 K and the 3 % doped sample suppresses the maximum ZT = 0.24 at a temperature of 260 K."}],"extern":"1","_id":"7074","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","intvolume":" 47","publisher":"Springer Nature","status":"public","title":"Thermoelectric properties of Ho-doped Bi0.88Sb0.12","publication_status":"published","author":[{"first_name":"K. C.","last_name":"Lukas","full_name":"Lukas, K. C."},{"first_name":"G.","last_name":"Joshi","full_name":"Joshi, G."},{"full_name":"Modic, Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","orcid":"0000-0001-9760-3147","first_name":"Kimberly A","last_name":"Modic"},{"first_name":"Z. F.","last_name":"Ren","full_name":"Ren, Z. F."},{"last_name":"Opeil","first_name":"C. P.","full_name":"Opeil, C. P."}],"volume":47,"oa_version":"None","date_created":"2019-11-19T13:36:54Z","date_updated":"2021-01-12T08:11:43Z"},{"article_type":"original","quality_controlled":"1","page":"494-500","publication":"Journal of the American Chemical Society","citation":{"chicago":"Ottakam Thotiyl, Muhammed M., Stefan Alexander Freunberger, Zhangquan Peng, and Peter G. Bruce. “The Carbon Electrode in Nonaqueous Li–O2 Cells.” Journal of the American Chemical Society. ACS, 2012. https://doi.org/10.1021/ja310258x.","mla":"Ottakam Thotiyl, Muhammed M., et al. “The Carbon Electrode in Nonaqueous Li–O2 Cells.” Journal of the American Chemical Society, vol. 135, no. 1, ACS, 2012, pp. 494–500, doi:10.1021/ja310258x.","short":"M.M. Ottakam Thotiyl, S.A. Freunberger, Z. Peng, P.G. Bruce, Journal of the American Chemical Society 135 (2012) 494–500.","ista":"Ottakam Thotiyl MM, Freunberger SA, Peng Z, Bruce PG. 2012. The carbon electrode in nonaqueous Li–O2 cells. Journal of the American Chemical Society. 135(1), 494–500.","ieee":"M. M. Ottakam Thotiyl, S. A. Freunberger, Z. Peng, and P. G. Bruce, “The carbon electrode in nonaqueous Li–O2 cells,” Journal of the American Chemical Society, vol. 135, no. 1. ACS, pp. 494–500, 2012.","apa":"Ottakam Thotiyl, M. M., Freunberger, S. A., Peng, Z., & Bruce, P. G. (2012). The carbon electrode in nonaqueous Li–O2 cells. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja310258x","ama":"Ottakam Thotiyl MM, Freunberger SA, Peng Z, Bruce PG. The carbon electrode in nonaqueous Li–O2 cells. Journal of the American Chemical Society. 2012;135(1):494-500. doi:10.1021/ja310258x"},"language":[{"iso":"eng"}],"doi":"10.1021/ja310258x","date_published":"2012-11-28T00:00:00Z","day":"28","month":"11","article_processing_charge":"No","publication_identifier":{"issn":["0002-7863","1520-5126"]},"title":"The carbon electrode in nonaqueous Li–O2 cells","publication_status":"published","status":"public","publisher":"ACS","intvolume":" 135","_id":"7308","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","date_updated":"2021-01-12T08:12:56Z","date_created":"2020-01-15T12:18:57Z","oa_version":"None","volume":135,"author":[{"full_name":"Ottakam Thotiyl, Muhammed M.","first_name":"Muhammed M.","last_name":"Ottakam Thotiyl"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Peng, Zhangquan","first_name":"Zhangquan","last_name":"Peng"},{"full_name":"Bruce, Peter G.","last_name":"Bruce","first_name":"Peter G."}],"type":"journal_article","extern":"1","abstract":[{"text":"Carbon has been used widely as the basis of porous cathodes for nonaqueous Li–O2 cells. However, the stability of carbon and the effect of carbon on electrolyte decomposition in such cells are complex and depend on the hydrophobicity/hydrophilicity of the carbon surface. Analyzing carbon cathodes, cycled in Li–O2 cells between 2 and 4 V, using acid treatment and Fenton’s reagent, and combined with differential electrochemical mass spectrometry and FTIR, demonstrates the following: Carbon is relatively stable below 3.5 V (vs Li/Li+) on discharge or charge, especially so for hydrophobic carbon, but is unstable on charging above 3.5 V (in the presence of Li2O2), oxidatively decomposing to form Li2CO3. Direct chemical reaction with Li2O2 accounts for only a small proportion of the total carbon decomposition on cycling. Carbon promotes electrolyte decomposition during discharge and charge in a Li–O2 cell, giving rise to Li2CO3 and Li carboxylates (DMSO and tetraglyme electrolytes). The Li2CO3 and Li carboxylates present at the end of discharge and those that form on charge result in polarization on the subsequent charge. Li2CO3 (derived from carbon and from the electrolyte) as well as the Li carboxylates (derived from the electrolyte) decompose and form on charging. Oxidation of Li2CO3 on charging to ∼4 V is incomplete; Li2CO3 accumulates on cycling resulting in electrode passivation and capacity fading. Hydrophilic carbon is less stable and more catalytically active toward electrolyte decomposition than carbon with a hydrophobic surface. If the Li–O2 cell could be charged at or below 3.5 V, then carbon may be relatively stable, however, its ability to promote electrolyte decomposition, presenting problems for its use in a practical Li–O2 battery. The results emphasize that stable cycling of Li2O2 at the cathode in a Li–O2 cell depends on the synergy between electrolyte and electrode; the stability of the electrode and the electrolyte cannot be considered in isolation.","lang":"eng"}],"issue":"1"},{"citation":{"ama":"Choi N-S, Chen Z, Freunberger SA, et al. Challenges facing Lithium batteries and electrical double-layer capacitors. Angewandte Chemie International Edition. 2012;51(40):9994-10024. doi:10.1002/anie.201201429","ista":"Choi N-S, Chen Z, Freunberger SA, Ji X, Sun Y-K, Amine K, Yushin G, Nazar LF, Cho J, Bruce PG. 2012. Challenges facing Lithium batteries and electrical double-layer capacitors. Angewandte Chemie International Edition. 51(40), 9994–10024.","apa":"Choi, N.-S., Chen, Z., Freunberger, S. A., Ji, X., Sun, Y.-K., Amine, K., … Bruce, P. G. (2012). Challenges facing Lithium batteries and electrical double-layer capacitors. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201201429","ieee":"N.-S. Choi et al., “Challenges facing Lithium batteries and electrical double-layer capacitors,” Angewandte Chemie International Edition, vol. 51, no. 40. Wiley, pp. 9994–10024, 2012.","mla":"Choi, Nam-Soon, et al. “Challenges Facing Lithium Batteries and Electrical Double-Layer Capacitors.” Angewandte Chemie International Edition, vol. 51, no. 40, Wiley, 2012, pp. 9994–10024, doi:10.1002/anie.201201429.","short":"N.-S. Choi, Z. Chen, S.A. Freunberger, X. Ji, Y.-K. Sun, K. Amine, G. Yushin, L.F. Nazar, J. Cho, P.G. Bruce, Angewandte Chemie International Edition 51 (2012) 9994–10024.","chicago":"Choi, Nam-Soon, Zonghai Chen, Stefan Alexander Freunberger, Xiulei Ji, Yang-Kook Sun, Khalil Amine, Gleb Yushin, Linda F. Nazar, Jaephil Cho, and Peter G. Bruce. “Challenges Facing Lithium Batteries and Electrical Double-Layer Capacitors.” Angewandte Chemie International Edition. Wiley, 2012. https://doi.org/10.1002/anie.201201429."},"publication":"Angewandte Chemie International Edition","page":"9994-10024","article_type":"original","quality_controlled":"1","date_published":"2012-10-01T00:00:00Z","doi":"10.1002/anie.201201429","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["1433-7851"]},"day":"01","month":"10","year":"2012","_id":"7309","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 51","publisher":"Wiley","title":"Challenges facing Lithium batteries and electrical double-layer capacitors","status":"public","publication_status":"published","author":[{"first_name":"Nam-Soon","last_name":"Choi","full_name":"Choi, Nam-Soon"},{"full_name":"Chen, Zonghai","last_name":"Chen","first_name":"Zonghai"},{"full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger"},{"last_name":"Ji","first_name":"Xiulei","full_name":"Ji, Xiulei"},{"first_name":"Yang-Kook","last_name":"Sun","full_name":"Sun, Yang-Kook"},{"full_name":"Amine, Khalil","first_name":"Khalil","last_name":"Amine"},{"last_name":"Yushin","first_name":"Gleb","full_name":"Yushin, Gleb"},{"first_name":"Linda F.","last_name":"Nazar","full_name":"Nazar, Linda F."},{"last_name":"Cho","first_name":"Jaephil","full_name":"Cho, Jaephil"},{"full_name":"Bruce, Peter G.","first_name":"Peter G.","last_name":"Bruce"}],"volume":51,"oa_version":"None","date_created":"2020-01-15T12:19:11Z","date_updated":"2021-01-12T08:12:56Z","type":"journal_article","issue":"40","abstract":[{"lang":"eng","text":"Energy‐storage technologies, including electrical double‐layer capacitors and rechargeable batteries, have attracted significant attention for applications in portable electronic devices, electric vehicles, bulk electricity storage at power stations, and “load leveling” of renewable sources, such as solar energy and wind power. Transforming lithium batteries and electric double‐layer capacitors requires a step change in the science underpinning these devices, including the discovery of new materials, new electrochemistry, and an increased understanding of the processes on which the devices depend. The Review will consider some of the current scientific issues underpinning lithium batteries and electric double‐layer capacitors."}],"extern":"1"},{"language":[{"iso":"eng"}],"doi":"10.1126/science.1223985","date_published":"2012-08-03T00:00:00Z","quality_controlled":"1","article_type":"original","page":"563-566","publication":"Science","citation":{"mla":"Peng, Z., et al. “A Reversible and Higher-Rate Li-O2 Battery.” Science, vol. 337, no. 6094, AAAS, 2012, pp. 563–66, doi:10.1126/science.1223985.","short":"Z. Peng, S.A. Freunberger, Y. Chen, P.G. Bruce, Science 337 (2012) 563–566.","chicago":"Peng, Z., Stefan Alexander Freunberger, Y. Chen, and P. G. Bruce. “A Reversible and Higher-Rate Li-O2 Battery.” Science. AAAS, 2012. https://doi.org/10.1126/science.1223985.","ama":"Peng Z, Freunberger SA, Chen Y, Bruce PG. A reversible and higher-rate Li-O2 battery. Science. 2012;337(6094):563-566. doi:10.1126/science.1223985","ista":"Peng Z, Freunberger SA, Chen Y, Bruce PG. 2012. A reversible and higher-rate Li-O2 battery. Science. 337(6094), 563–566.","ieee":"Z. Peng, S. A. Freunberger, Y. Chen, and P. G. Bruce, “A reversible and higher-rate Li-O2 battery,” Science, vol. 337, no. 6094. AAAS, pp. 563–566, 2012.","apa":"Peng, Z., Freunberger, S. A., Chen, Y., & Bruce, P. G. (2012). A reversible and higher-rate Li-O2 battery. Science. AAAS. https://doi.org/10.1126/science.1223985"},"day":"03","month":"08","publication_identifier":{"issn":["0036-8075","1095-9203"]},"article_processing_charge":"No","date_created":"2020-01-15T12:19:23Z","date_updated":"2021-01-12T08:12:57Z","volume":337,"oa_version":"None","author":[{"first_name":"Z.","last_name":"Peng","full_name":"Peng, Z."},{"full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319"},{"full_name":"Chen, Y.","last_name":"Chen","first_name":"Y."},{"full_name":"Bruce, P. G.","first_name":"P. G.","last_name":"Bruce"}],"status":"public","title":"A reversible and higher-rate Li-O2 battery","publication_status":"published","intvolume":" 337","publisher":"AAAS","_id":"7310","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","extern":"1","abstract":[{"lang":"eng","text":"The rechargeable nonaqueous lithium-air (Li-O2) battery is receiving a great deal of interest because, theoretically, its specific energy far exceeds the best that can be achieved with lithium-ion cells. Operation of the rechargeable Li-O2 battery depends critically on repeated and highly reversible formation/decomposition of lithium peroxide (Li2O2) at the cathode upon cycling. Here, we show that this process is possible with the use of a dimethyl sulfoxide electrolyte and a porous gold electrode (95% capacity retention from cycles 1 to 100), whereas previously only partial Li2O2 formation/decomposition and limited cycling could occur. Furthermore, we present data indicating that the kinetics of Li2O2 oxidation on charge is approximately 10 times faster than on carbon electrodes."}],"issue":"6094","type":"journal_article"},{"doi":"10.1021/ja302178w","date_published":"2012-04-19T00:00:00Z","language":[{"iso":"eng"}],"citation":{"short":"Y. Chen, S.A. Freunberger, Z. Peng, F. Bardé, P.G. Bruce, Journal of the American Chemical Society 134 (2012) 7952–7957.","mla":"Chen, Yuhui, et al. “Li–O2 Battery with a Dimethylformamide Electrolyte.” Journal of the American Chemical Society, vol. 134, no. 18, ACS, 2012, pp. 7952–57, doi:10.1021/ja302178w.","chicago":"Chen, Yuhui, Stefan Alexander Freunberger, Zhangquan Peng, Fanny Bardé, and Peter G. Bruce. “Li–O2 Battery with a Dimethylformamide Electrolyte.” Journal of the American Chemical Society. ACS, 2012. https://doi.org/10.1021/ja302178w.","ama":"Chen Y, Freunberger SA, Peng Z, Bardé F, Bruce PG. Li–O2 battery with a dimethylformamide electrolyte. Journal of the American Chemical Society. 2012;134(18):7952-7957. doi:10.1021/ja302178w","ieee":"Y. Chen, S. A. Freunberger, Z. Peng, F. Bardé, and P. G. Bruce, “Li–O2 battery with a dimethylformamide electrolyte,” Journal of the American Chemical Society, vol. 134, no. 18. ACS, pp. 7952–7957, 2012.","apa":"Chen, Y., Freunberger, S. A., Peng, Z., Bardé, F., & Bruce, P. G. (2012). Li–O2 battery with a dimethylformamide electrolyte. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja302178w","ista":"Chen Y, Freunberger SA, Peng Z, Bardé F, Bruce PG. 2012. Li–O2 battery with a dimethylformamide electrolyte. Journal of the American Chemical Society. 134(18), 7952–7957."},"publication":"Journal of the American Chemical Society","page":"7952-7957","quality_controlled":"1","article_type":"original","publication_identifier":{"issn":["0002-7863","1520-5126"]},"article_processing_charge":"No","month":"04","day":"19","author":[{"last_name":"Chen","first_name":"Yuhui","full_name":"Chen, Yuhui"},{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"},{"first_name":"Zhangquan","last_name":"Peng","full_name":"Peng, Zhangquan"},{"full_name":"Bardé, Fanny","last_name":"Bardé","first_name":"Fanny"},{"last_name":"Bruce","first_name":"Peter G.","full_name":"Bruce, Peter G."}],"oa_version":"None","volume":134,"date_created":"2020-01-15T12:19:36Z","date_updated":"2021-01-12T08:12:58Z","year":"2012","_id":"7311","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 134","publisher":"ACS","title":"Li–O2 battery with a dimethylformamide electrolyte","status":"public","publication_status":"published","issue":"18","abstract":[{"text":"Stability of the electrolyte toward reduced oxygen species generated at the cathode is a crucial challenge for the rechargeable nonaqueous Li–O2 battery. Here, we investigate dimethylformamide as the basis of an electrolyte. Although reactions at the O2 cathode on the first discharge–charge cycle are dominated by reversible Li2O2 formation/decomposition, there is also electrolyte decomposition, which increases on cycling. The products of decomposition at the cathode on discharge are Li2O2, Li2CO3, HCO2Li, CH3CO2Li, NO, H2O, and CO2. Li2CO3 accumulates in the electrode with cycling. The stability of dimethylformamide toward reduced oxygen species is insufficient for its use in the rechargeable nonaqueous Li–O2 battery.","lang":"eng"}],"extern":"1","type":"journal_article"},{"type":"conference","abstract":[{"lang":"eng","text":"Decades of research in distributed computing have led to a variety of perspectives on what it means for a concurrent algorithm to be efficient, depending on model assumptions, progress guarantees, and complexity metrics. It is therefore natural to ask whether one could compose algorithms that perform efficiently under different conditions, so that the composition preserves the performance of the original components when their conditions are met. In this paper, we evaluate the cost of composing shared-memory algorithms. First, we formally define the notion of safely composable algorithms and we show that every sequential type has a safely composable implementation, as long as enough state is transferred between modules. Since such generic implementations are inherently expensive, we present a more general light-weight specification that allows the designer to transfer very little state between modules, by taking advantage of the semantics of the implemented object. Using this framework, we implement a composed longlived test-and-set object, with the property that each of its modules is asymptotically optimal with respect to the progress condition it ensures, while the entire implementation only uses objects with consensus number at most two. Thus, we show that the overhead of composition can be negligible in the case of some important shared-memory abstractions."}],"publist_id":"6892","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"762","year":"2012","publication_status":"published","status":"public","title":"On the cost of composing shared-memory algorithms","publisher":"ACM","author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"full_name":"Guerraoui, Rachid","last_name":"Guerraoui","first_name":"Rachid"},{"first_name":"Petr","last_name":"Kuznetsov","full_name":"Kuznetsov, Petr"},{"last_name":"Losa","first_name":"Giuliano","full_name":"Losa, Giuliano"}],"date_updated":"2023-02-23T13:12:27Z","date_created":"2018-12-11T11:48:22Z","oa_version":"None","day":"01","month":"01","article_processing_charge":"No","citation":{"ista":"Alistarh D-A, Guerraoui R, Kuznetsov P, Losa G. 2012. On the cost of composing shared-memory algorithms. SPAA: Symposium on Parallelism in Algorithms and Architectures, 298–307.","apa":"Alistarh, D.-A., Guerraoui, R., Kuznetsov, P., & Losa, G. (2012). On the cost of composing shared-memory algorithms (pp. 298–307). Presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, ACM. https://doi.org/10.1145/2312005.2312057","ieee":"D.-A. Alistarh, R. Guerraoui, P. Kuznetsov, and G. Losa, “On the cost of composing shared-memory algorithms,” presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, 2012, pp. 298–307.","ama":"Alistarh D-A, Guerraoui R, Kuznetsov P, Losa G. On the cost of composing shared-memory algorithms. In: ACM; 2012:298-307. doi:10.1145/2312005.2312057","chicago":"Alistarh, Dan-Adrian, Rachid Guerraoui, Petr Kuznetsov, and Giuliano Losa. “On the Cost of Composing Shared-Memory Algorithms,” 298–307. ACM, 2012. https://doi.org/10.1145/2312005.2312057.","mla":"Alistarh, Dan-Adrian, et al. On the Cost of Composing Shared-Memory Algorithms. ACM, 2012, pp. 298–307, doi:10.1145/2312005.2312057.","short":"D.-A. Alistarh, R. Guerraoui, P. Kuznetsov, G. Losa, in:, ACM, 2012, pp. 298–307."},"page":"298 - 307","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"doi":"10.1145/2312005.2312057","date_published":"2012-01-01T00:00:00Z","language":[{"iso":"eng"}]},{"type":"conference","alternative_title":["LNCS"],"publist_id":"6893","abstract":[{"text":"Renaming is a fundamental problem in distributed computing, in which a set of n processes need to pick unique names from a namespace of limited size. In this paper, we present the first early-deciding upper bounds for synchronous renaming, in which the running time adapts to the actual number of failures f in the execution. We show that, surprisingly, renaming can be solved in constant time if the number of failures f is limited to O(√n), while for general f ≤ n - 1 renaming can always be solved in O(log f) communication rounds. In the wait-free case, i.e. for f = n - 1, our upper bounds match the Ω(log n) lower bound of Chaudhuri et al. [13].","lang":"eng"}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"763","year":"2012","acknowledgement":"Hagit Attiya - Supported in party by Israel Science Foundation (grant number 1227/10).\r\nCorentin Travers - Additional supports from the ANR projects ALADDIN and DISPLEXITY\r\n","publisher":"Springer","publication_status":"published","status":"public","title":"Early deciding synchronous renaming in O(log f) rounds or less","author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"last_name":"Attiya","first_name":"Hagit","full_name":"Attiya, Hagit"},{"full_name":"Guerraoui, Rachid","first_name":"Rachid","last_name":"Guerraoui"},{"first_name":"Corentin","last_name":"Travers","full_name":"Travers, Corentin"}],"volume":"7355 LNCS","oa_version":"None","date_created":"2018-12-11T11:48:22Z","date_updated":"2023-02-23T13:12:41Z","article_processing_charge":"No","day":"01","month":"01","citation":{"ama":"Alistarh D-A, Attiya H, Guerraoui R, Travers C. Early deciding synchronous renaming in O(log f) rounds or less. In: Vol 7355 LNCS. Springer; 2012:195-206. doi:10.1007/978-3-642-31104-8_17","ista":"Alistarh D-A, Attiya H, Guerraoui R, Travers C. 2012. Early deciding synchronous renaming in O(log f) rounds or less. SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 7355 LNCS, 195–206.","apa":"Alistarh, D.-A., Attiya, H., Guerraoui, R., & Travers, C. (2012). Early deciding synchronous renaming in O(log f) rounds or less (Vol. 7355 LNCS, pp. 195–206). Presented at the SIROCCO: Structural Information and Communication Complexity, Springer. https://doi.org/10.1007/978-3-642-31104-8_17","ieee":"D.-A. Alistarh, H. Attiya, R. Guerraoui, and C. Travers, “Early deciding synchronous renaming in O(log f) rounds or less,” presented at the SIROCCO: Structural Information and Communication Complexity, 2012, vol. 7355 LNCS, pp. 195–206.","mla":"Alistarh, Dan-Adrian, et al. Early Deciding Synchronous Renaming in O(Log f) Rounds or Less. Vol. 7355 LNCS, Springer, 2012, pp. 195–206, doi:10.1007/978-3-642-31104-8_17.","short":"D.-A. Alistarh, H. Attiya, R. Guerraoui, C. Travers, in:, Springer, 2012, pp. 195–206.","chicago":"Alistarh, Dan-Adrian, Hagit Attiya, Rachid Guerraoui, and Corentin Travers. “Early Deciding Synchronous Renaming in O(Log f) Rounds or Less,” 7355 LNCS:195–206. Springer, 2012. https://doi.org/10.1007/978-3-642-31104-8_17."},"page":"195 - 206","date_published":"2012-01-01T00:00:00Z","doi":"10.1007/978-3-642-31104-8_17","conference":{"name":"SIROCCO: Structural Information and Communication Complexity"},"language":[{"iso":"eng"}]},{"article_processing_charge":"No","month":"02","day":"01","doi":"10.1007/s00453-011-9581-7","date_published":"2012-02-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Of choices, failures and asynchrony: the many faces of set agreement. Algorithmica (New York). 2012;62(1-2):595-629. doi:10.1007/s00453-011-9581-7","apa":"Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2012). Of choices, failures and asynchrony: the many faces of set agreement. Algorithmica (New York). Springer. https://doi.org/10.1007/s00453-011-9581-7","ieee":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Of choices, failures and asynchrony: the many faces of set agreement,” Algorithmica (New York), vol. 62, no. 1–2. Springer, pp. 595–629, 2012.","ista":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2012. Of choices, failures and asynchrony: the many faces of set agreement. Algorithmica (New York). 62(1–2), 595–629.","short":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, Algorithmica (New York) 62 (2012) 595–629.","mla":"Alistarh, Dan-Adrian, et al. “Of Choices, Failures and Asynchrony: The Many Faces of Set Agreement.” Algorithmica (New York), vol. 62, no. 1–2, Springer, 2012, pp. 595–629, doi:10.1007/s00453-011-9581-7.","chicago":"Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers. “Of Choices, Failures and Asynchrony: The Many Faces of Set Agreement.” Algorithmica (New York). Springer, 2012. https://doi.org/10.1007/s00453-011-9581-7."},"publication":"Algorithmica (New York)","page":"595 - 629","publist_id":"6894","issue":"1-2","abstract":[{"lang":"eng","text":"Set agreement is a fundamental problem in distributed computing in which processes collectively choose a small subset of values from a larger set of proposals. The impossibility of fault-tolerant set agreement in asynchronous networks is one of the seminal results in distributed computing. In synchronous networks, too, the complexity of set agreement has been a significant research challenge that has now been resolved. Real systems, however, are neither purely synchronous nor purely asynchronous. Rather, they tend to alternate between periods of synchrony and periods of asynchrony. Nothing specific is known about the complexity of set agreement in such a "partially synchronous" setting. In this paper, we address this challenge, presenting the first (asymptotically) tight bound on the complexity of set agreement in such systems. We introduce a novel technique for simulating, in a fault-prone asynchronous shared memory, executions of an asynchronous and failure-prone message-passing system in which some fragments appear synchronous to some processes. We use this simulation technique to derive a lower bound on the round complexity of set agreement in a partially synchronous system by a reduction from asynchronous wait-free set agreement. Specifically, we show that every set agreement protocol requires at least $\\lfloor\\frac t k \\rfloor + 2$ synchronous rounds to decide. We present an (asymptotically) matching algorithm that relies on a distributed asynchrony detection mechanism to decide as soon as possible during periods of synchrony. From these two results, we derive the size of the minimal window of synchrony needed to solve set agreement. By relating synchronous, asynchronous and partially synchronous environments, our simulation technique is of independent interest. In particular, it allows us to obtain a new lower bound on the complexity of early deciding k-set agreement complementary to that of Gafni et al. (in SIAM J. Comput. 40(1):63-78, 2011), and to re-derive the combinatorial topology lower bound of Guerraoui et al. (in Theor. Comput. Sci. 410(6-7):570-580, 2009) in an algorithmic way."}],"extern":"1","type":"journal_article","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Seth","last_name":"Gilbert","full_name":"Gilbert, Seth"},{"full_name":"Guerraoui, Rachid","last_name":"Guerraoui","first_name":"Rachid"},{"full_name":"Travers, Corentin","last_name":"Travers","first_name":"Corentin"}],"oa_version":"None","volume":62,"date_updated":"2023-02-23T13:13:02Z","date_created":"2018-12-11T11:48:23Z","year":"2012","_id":"764","acknowledgement":"We would like to thank Hagit Attiya, Keren Censor-Hillel, and the anonymous\r\nreviewers for their feedback on drafts of this paper.\r\nPart of the work was performed as C. Travers was a Post-Doctoral Fellow at the Technion, Haifa,\r\nsupported by the “Sam & Cecilia Neaman” Fellowship. Part of the work was performed as S. Gilbert was\r\na Post-Doctoral Fellow at the Swiss Federal Institute of Technology, Lausanne, Switzerland.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 62","publisher":"Springer","status":"public","publication_status":"published","title":"Of choices, failures and asynchrony: the many faces of set agreement"},{"type":"conference","publist_id":"6890","abstract":[{"text":"Asynchronous task allocation is a fundamental problem in distributed computing in which p asynchronous processes must execute a set of m tasks. Also known as write-all or do-all, this problem been studied extensively, both independently and as a key building block for various distributed algorithms. In this paper, we break new ground on this classic problem: we introduce the To-Do Tree concurrent data structure, which improves on the best known randomized and deterministic upper bounds. In the presence of an adaptive adversary, the randomized To-Do Tree algorithm has O(m + p log p log2 m) work complexity. We then show that there exists a deterministic variant of the To-Do Tree algorithm with work complexity O(m + p log5 m log2 max(m, p)). For all values of m and p, our algorithms are within log factors of the Ω(m + p log p) lower bound for this problem. The key technical ingredient in our results is a new approach for analyzing concurrent executions against a strong adaptive scheduler. This technique allows us to handle the complex dependencies between the processes' coin flips and their scheduling, and to tightly bound the work needed to perform subsets of the tasks.","lang":"eng"}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"766","year":"2012","publisher":"IEEE","title":"How to allocate tasks asynchronously","status":"public","publication_status":"published","author":[{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bender, Michael","first_name":"Michael","last_name":"Bender"},{"full_name":"Gilbert, Seth","first_name":"Seth","last_name":"Gilbert"},{"full_name":"Guerraoui, Rachid","last_name":"Guerraoui","first_name":"Rachid"}],"oa_version":"None","date_created":"2018-12-11T11:48:23Z","date_updated":"2023-02-23T13:13:27Z","article_processing_charge":"No","month":"01","day":"01","citation":{"chicago":"Alistarh, Dan-Adrian, Michael Bender, Seth Gilbert, and Rachid Guerraoui. “How to Allocate Tasks Asynchronously,” 331–40. IEEE, 2012. https://doi.org/10.1109/FOCS.2012.41.","mla":"Alistarh, Dan-Adrian, et al. How to Allocate Tasks Asynchronously. IEEE, 2012, pp. 331–40, doi:10.1109/FOCS.2012.41.","short":"D.-A. Alistarh, M. Bender, S. Gilbert, R. Guerraoui, in:, IEEE, 2012, pp. 331–340.","ista":"Alistarh D-A, Bender M, Gilbert S, Guerraoui R. 2012. How to allocate tasks asynchronously. FOCS: Foundations of Computer Science, 331–340.","apa":"Alistarh, D.-A., Bender, M., Gilbert, S., & Guerraoui, R. (2012). How to allocate tasks asynchronously (pp. 331–340). Presented at the FOCS: Foundations of Computer Science, IEEE. https://doi.org/10.1109/FOCS.2012.41","ieee":"D.-A. Alistarh, M. Bender, S. Gilbert, and R. Guerraoui, “How to allocate tasks asynchronously,” presented at the FOCS: Foundations of Computer Science, 2012, pp. 331–340.","ama":"Alistarh D-A, Bender M, Gilbert S, Guerraoui R. How to allocate tasks asynchronously. In: IEEE; 2012:331-340. doi:10.1109/FOCS.2012.41"},"page":"331 - 340","date_published":"2012-01-01T00:00:00Z","doi":"10.1109/FOCS.2012.41","conference":{"name":"FOCS: Foundations of Computer Science"},"language":[{"iso":"eng"}]},{"issue":"4","publist_id":"6891","abstract":[{"text":"Synchronous distributed algorithms are easier to design and prove correct than algorithms that tolerate asynchrony. Yet, in the real world, networks experience asynchrony and other timing anomalies. In this paper, we address the question of how to efficiently transform an algorithm that relies on synchronous timing into an algorithm that tolerates asynchronous executions. We introduce a transformation technique from synchronous algorithms to indulgent algorithms (Guerraoui, in PODC, pp. 289-297, 2000), which induces only a constant overhead in terms of time complexity in well-behaved executions. Our technique is based on a new abstraction we call an asynchrony detector, which the participating processes implement collectively. The resulting transformation works for the class of colorless distributed tasks, including consensus and set agreement. Interestingly, we also show that our technique is relevant for colored tasks, by applying it to the renaming problem, to obtain the first indulgent renaming algorithm.","lang":"eng"}],"extern":"1","type":"journal_article","author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"full_name":"Gilbert, Seth","first_name":"Seth","last_name":"Gilbert"},{"first_name":"Rachid","last_name":"Guerraoui","full_name":"Guerraoui, Rachid"},{"first_name":"Corentin","last_name":"Travers","full_name":"Travers, Corentin"}],"volume":51,"oa_version":"None","date_created":"2018-12-11T11:48:23Z","date_updated":"2023-02-23T13:13:40Z","_id":"767","year":"2012","acknowledgement":"Dan Alistarh was supported by the NCCR MICS Project. Corentin Travers had additional support from INRIA team REGAL and ANR project SPREADS.\r\nThe authors would like to thank Hagit Attiya and Nikola Kneževi\r\n ́\r\nc for their feed-\r\nback on previous drafts of this paper, and the anonymous reviewers for their useful comments.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","intvolume":" 51","publication_status":"published","title":"Generating Fast Indulgent Algorithms","status":"public","article_processing_charge":"No","month":"01","day":"01","date_published":"2012-01-01T00:00:00Z","doi":"10.1007/s00224-012-9407-2","language":[{"iso":"eng"}],"citation":{"chicago":"Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers. “Generating Fast Indulgent Algorithms.” Theory of Computing Systems. Elsevier, 2012. https://doi.org/10.1007/s00224-012-9407-2.","short":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, Theory of Computing Systems 51 (2012) 404–424.","mla":"Alistarh, Dan-Adrian, et al. “Generating Fast Indulgent Algorithms.” Theory of Computing Systems, vol. 51, no. 4, Elsevier, 2012, pp. 404–24, doi:10.1007/s00224-012-9407-2.","ieee":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Generating Fast Indulgent Algorithms,” Theory of Computing Systems, vol. 51, no. 4. Elsevier, pp. 404–424, 2012.","apa":"Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2012). Generating Fast Indulgent Algorithms. Theory of Computing Systems. Elsevier. https://doi.org/10.1007/s00224-012-9407-2","ista":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2012. Generating Fast Indulgent Algorithms. Theory of Computing Systems. 51(4), 404–424.","ama":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Generating Fast Indulgent Algorithms. Theory of Computing Systems. 2012;51(4):404-424. doi:10.1007/s00224-012-9407-2"},"publication":"Theory of Computing Systems","page":"404 - 424"},{"type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"Although studies on laboratory species and natural populations of vertebrates have shown reproduction to impair later performance, little is known of the age‐specific associations between reproduction and survival, and how such findings apply to the ageing of large, long‐lived species. Herein we develop a framework to examine population‐level patterns of reproduction and survival across lifespan in long‐lived organisms, and decompose those changes into individual‐level effects, and the effects of age‐specific trade‐offs between fitness components. We apply this to an extensive longitudinal dataset on female semi‐captive Asian timber elephants (Elephas maximus) and report the first evidence of age‐specific fitness declines that are driven by age‐specific associations between fitness components in a long‐lived mammal. Associations between reproduction and survival are positive in early life, but negative in later life with up to 71% of later‐life survival declines associated with investing in the production of offspring within this population of this critically endangered species."}],"issue":"3","title":"Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants","status":"public","publication_status":"published","intvolume":" 15","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7749","year":"2012","date_updated":"2021-01-12T08:15:16Z","date_created":"2020-04-30T11:01:26Z","volume":15,"oa_version":"None","author":[{"full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"first_name":"Khyne U","last_name":"Mar","full_name":"Mar, Khyne U"},{"full_name":"Lummaa, Virpi","first_name":"Virpi","last_name":"Lummaa"}],"month":"03","day":"01","publication_identifier":{"issn":["1461-023X"]},"article_processing_charge":"No","article_type":"original","quality_controlled":"1","page":"260-266","publication":"Ecology Letters","citation":{"ista":"Robinson MR, Mar KU, Lummaa V. 2012. Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants. Ecology Letters. 15(3), 260–266.","apa":"Robinson, M. R., Mar, K. U., & Lummaa, V. (2012). Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants. Ecology Letters. Wiley. https://doi.org/10.1111/j.1461-0248.2011.01735.x","ieee":"M. R. Robinson, K. U. Mar, and V. Lummaa, “Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants,” Ecology Letters, vol. 15, no. 3. Wiley, pp. 260–266, 2012.","ama":"Robinson MR, Mar KU, Lummaa V. Senescence and age-specific trade-offs between reproduction and survival in female Asian elephants. Ecology Letters. 2012;15(3):260-266. doi:10.1111/j.1461-0248.2011.01735.x","chicago":"Robinson, Matthew Richard, Khyne U Mar, and Virpi Lummaa. “Senescence and Age-Specific Trade-Offs between Reproduction and Survival in Female Asian Elephants.” Ecology Letters. Wiley, 2012. https://doi.org/10.1111/j.1461-0248.2011.01735.x.","mla":"Robinson, Matthew Richard, et al. “Senescence and Age-Specific Trade-Offs between Reproduction and Survival in Female Asian Elephants.” Ecology Letters, vol. 15, no. 3, Wiley, 2012, pp. 260–66, doi:10.1111/j.1461-0248.2011.01735.x.","short":"M.R. Robinson, K.U. Mar, V. Lummaa, Ecology Letters 15 (2012) 260–266."},"language":[{"iso":"eng"}],"doi":"10.1111/j.1461-0248.2011.01735.x","date_published":"2012-03-01T00:00:00Z"},{"quality_controlled":"1","article_type":"original","page":"611-618","publication":"Ecology Letters","citation":{"ama":"Robinson MR, Sander van Doorn G, Gustafsson L, Qvarnström A. Environment-dependent selection on mate choice in a natural population of birds. Ecology Letters. 2012;15(6):611-618. doi:10.1111/j.1461-0248.2012.01780.x","ieee":"M. R. Robinson, G. Sander van Doorn, L. Gustafsson, and A. Qvarnström, “Environment-dependent selection on mate choice in a natural population of birds,” Ecology Letters, vol. 15, no. 6. Wiley, pp. 611–618, 2012.","apa":"Robinson, M. R., Sander van Doorn, G., Gustafsson, L., & Qvarnström, A. (2012). Environment-dependent selection on mate choice in a natural population of birds. Ecology Letters. Wiley. https://doi.org/10.1111/j.1461-0248.2012.01780.x","ista":"Robinson MR, Sander van Doorn G, Gustafsson L, Qvarnström A. 2012. Environment-dependent selection on mate choice in a natural population of birds. Ecology Letters. 15(6), 611–618.","short":"M.R. Robinson, G. Sander van Doorn, L. Gustafsson, A. Qvarnström, Ecology Letters 15 (2012) 611–618.","mla":"Robinson, Matthew Richard, et al. “Environment-Dependent Selection on Mate Choice in a Natural Population of Birds.” Ecology Letters, vol. 15, no. 6, Wiley, 2012, pp. 611–18, doi:10.1111/j.1461-0248.2012.01780.x.","chicago":"Robinson, Matthew Richard, G. Sander van Doorn, Lars Gustafsson, and Anna Qvarnström. “Environment-Dependent Selection on Mate Choice in a Natural Population of Birds.” Ecology Letters. Wiley, 2012. https://doi.org/10.1111/j.1461-0248.2012.01780.x."},"language":[{"iso":"eng"}],"date_published":"2012-06-01T00:00:00Z","doi":"10.1111/j.1461-0248.2012.01780.x","day":"01","month":"06","article_processing_charge":"No","publication_identifier":{"issn":["1461-023X"]},"status":"public","title":"Environment-dependent selection on mate choice in a natural population of birds","publication_status":"published","intvolume":" 15","publisher":"Wiley","_id":"7748","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","date_created":"2020-04-30T11:01:07Z","date_updated":"2021-01-12T08:15:15Z","oa_version":"None","volume":15,"author":[{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson"},{"first_name":"G.","last_name":"Sander van Doorn","full_name":"Sander van Doorn, G."},{"first_name":"Lars","last_name":"Gustafsson","full_name":"Gustafsson, Lars"},{"first_name":"Anna","last_name":"Qvarnström","full_name":"Qvarnström, Anna"}],"type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"Female mate choice acts as an important evolutionary force, yet the influence of the environment on both its expression and the selective pressures acting upon it remains unknown. We found consistent heritable differences between females in their choice of mate based on ornament size during a 25‐year study of a population of collared flycatchers. However, the fitness consequences of mate choice were dependent on environmental conditions experienced whilst breeding. Females breeding with highly ornamented males experienced high relative fitness during dry summer conditions, but low relative fitness during wetter years. Our results imply that sexual selection within a population can be highly variable and dependent upon the prevailing weather conditions experienced by individuals."}],"issue":"6"},{"article_number":"095704","type":"journal_article","abstract":[{"lang":"eng","text":"We present an analysis of finite-size effects in jammed packings of N soft, frictionless spheres at zero temperature. There is a 1/N correction to the discrete jump in the contact number at the transition so that jammed packings exist only above isostaticity. As a result, the canonical power-law scalings of the contact number and elastic moduli break down at low pressure. These quantities exhibit scaling collapse with a nontrivial scaling function, demonstrating that the jamming transition can be considered a phase transition. Scaling is achieved as a function of N in both two and three dimensions, indicating an upper critical dimension of 2."}],"issue":"9","extern":"1","_id":"7776","year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Finite-size scaling at the jamming transition","publication_status":"published","publisher":"American Physical Society","intvolume":" 109","author":[{"full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074"},{"full_name":"Liu, Andrea J.","last_name":"Liu","first_name":"Andrea J."},{"first_name":"Sidney R.","last_name":"Nagel","full_name":"Nagel, Sidney R."}],"date_updated":"2021-01-12T08:15:27Z","date_created":"2020-04-30T11:44:12Z","volume":109,"oa_version":"None","month":"08","day":"27","publication_identifier":{"issn":["0031-9007","1079-7114"]},"article_processing_charge":"No","publication":"Physical Review Letters","citation":{"mla":"Goodrich, Carl Peter, et al. “Finite-Size Scaling at the Jamming Transition.” Physical Review Letters, vol. 109, no. 9, 095704, American Physical Society, 2012, doi:10.1103/physrevlett.109.095704.","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 109 (2012).","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Finite-Size Scaling at the Jamming Transition.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/physrevlett.109.095704.","ama":"Goodrich CP, Liu AJ, Nagel SR. Finite-size scaling at the jamming transition. Physical Review Letters. 2012;109(9). doi:10.1103/physrevlett.109.095704","ista":"Goodrich CP, Liu AJ, Nagel SR. 2012. Finite-size scaling at the jamming transition. Physical Review Letters. 109(9), 095704.","apa":"Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2012). Finite-size scaling at the jamming transition. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.109.095704","ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Finite-size scaling at the jamming transition,” Physical Review Letters, vol. 109, no. 9. American Physical Society, 2012."},"quality_controlled":"1","article_type":"original","doi":"10.1103/physrevlett.109.095704","date_published":"2012-08-27T00:00:00Z","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"Fungal cell walls frequently contain a polymer of mannose and galactose called galactomannan. In the pathogenic filamentous fungus Aspergillus fumigatus, this polysaccharide is made of a linear mannan backbone with side chains of galactofuran and is anchored to the plasma membrane via a glycosylphosphatidylinositol or is covalently linked to the cell wall. To date, the biosynthesis and significance of this polysaccharide are unknown. The present data demonstrate that deletion of the Golgi UDP-galactofuranose transporter GlfB or the GDP-mannose transporter GmtA leads to the absence of galactofuran or galactomannan, respectively. This indicates that the biosynthesis of galactomannan probably occurs in the lumen of the Golgi apparatus and thus contrasts with the biosynthesis of other fungal cell wall polysaccharides studied to date that takes place at the plasma membrane. Transglycosylation of galactomannan from the membrane to the cell wall is hypothesized because both the cell wall-bound and membrane-bound polysaccharide forms are affected in the generated mutants. Considering the severe growth defect of the A. fumigatus GmtA-deficient mutant, proving this paradigm might provide new targets for antifungal therapy."}],"issue":"53","type":"journal_article","oa_version":"None","status":"public","title":"Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose","intvolume":" 287","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"801","day":"28","article_processing_charge":"No","scopus_import":"1","date_published":"2012-12-28T00:00:00Z","article_type":"original","page":"44418 - 44424","publication":"Journal of Biological Chemistry","citation":{"ama":"Engel J, Schmalhorst PS, Routier F. Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose. Journal of Biological Chemistry. 2012;287(53):44418-44424. doi:10.1074/jbc.M112.398321","apa":"Engel, J., Schmalhorst, P. S., & Routier, F. (2012). Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M112.398321","ieee":"J. Engel, P. S. Schmalhorst, and F. Routier, “Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose,” Journal of Biological Chemistry, vol. 287, no. 53. American Society for Biochemistry and Molecular Biology, pp. 44418–44424, 2012.","ista":"Engel J, Schmalhorst PS, Routier F. 2012. Biosynthesis of the fungal cell wall polysaccharide galactomannan requires intraluminal GDP-mannose. Journal of Biological Chemistry. 287(53), 44418–44424.","short":"J. Engel, P.S. Schmalhorst, F. Routier, Journal of Biological Chemistry 287 (2012) 44418–44424.","mla":"Engel, Jakob, et al. “Biosynthesis of the Fungal Cell Wall Polysaccharide Galactomannan Requires Intraluminal GDP-Mannose.” Journal of Biological Chemistry, vol. 287, no. 53, American Society for Biochemistry and Molecular Biology, 2012, pp. 44418–24, doi:10.1074/jbc.M112.398321.","chicago":"Engel, Jakob, Philipp S Schmalhorst, and Françoise Routier. “Biosynthesis of the Fungal Cell Wall Polysaccharide Galactomannan Requires Intraluminal GDP-Mannose.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2012. https://doi.org/10.1074/jbc.M112.398321."},"extern":"1","publist_id":"6852","date_created":"2018-12-11T11:48:34Z","date_updated":"2022-03-21T07:57:14Z","volume":287,"author":[{"full_name":"Engel, Jakob","last_name":"Engel","first_name":"Jakob"},{"full_name":"Schmalhorst, Philipp S","last_name":"Schmalhorst","first_name":"Philipp S","orcid":"0000-0002-5795-0133","id":"309D50DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Routier","first_name":"Françoise","full_name":"Routier, Françoise"}],"publication_status":"published","publisher":"American Society for Biochemistry and Molecular Biology","year":"2012","acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft.","pmid":1,"month":"12","language":[{"iso":"eng"}],"doi":"10.1074/jbc.M112.398321","quality_controlled":"1","external_id":{"pmid":["23139423"]}},{"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"In dynamical models of cortical networks, the recurrent connectivity can amplify the input given to the network in two distinct ways. One is induced by the presence of near-critical eigenvalues in the connectivity matrix W, producing large but slow activity fluctuations along the corresponding eigenvectors (dynamical slowing). The other relies on W not being normal, which allows the network activity to make large but fast excursions along specific directions. Here we investigate the trade-off between non-normal amplification and dynamical slowing in the spontaneous activity of large random neuronal networks composed of excitatory and inhibitory neurons. We use a Schur decomposition of W to separate the two amplification mechanisms. Assuming linear stochastic dynamics, we derive an exact expression for the expected amount of purely non-normal amplification. We find that amplification is very limited if dynamical slowing must be kept weak. We conclude that, to achieve strong transient amplification with little slowing, the connectivity must be structured. We show that unidirectional connections between neurons of the same type together with reciprocal connections between neurons of different types, allow for amplification already in the fast dynamical regime. Finally, our results also shed light on the differences between balanced networks in which inhibition exactly cancels excitation and those where inhibition dominates."}],"_id":"8024","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","intvolume":" 86","title":"Non-normal amplification in random balanced neuronal networks","status":"public","oa_version":"None","article_processing_charge":"No","day":"11","citation":{"ieee":"G. Hennequin, T. P. Vogels, and W. Gerstner, “Non-normal amplification in random balanced neuronal networks,” Physical Review E, vol. 86, no. 1. American Physical Society, 2012.","apa":"Hennequin, G., Vogels, T. P., & Gerstner, W. (2012). Non-normal amplification in random balanced neuronal networks. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.86.011909","ista":"Hennequin G, Vogels TP, Gerstner W. 2012. Non-normal amplification in random balanced neuronal networks. Physical Review E. 86(1), 011909.","ama":"Hennequin G, Vogels TP, Gerstner W. Non-normal amplification in random balanced neuronal networks. Physical Review E. 2012;86(1). doi:10.1103/physreve.86.011909","chicago":"Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Non-Normal Amplification in Random Balanced Neuronal Networks.” Physical Review E. American Physical Society, 2012. https://doi.org/10.1103/physreve.86.011909.","short":"G. Hennequin, T.P. Vogels, W. Gerstner, Physical Review E 86 (2012).","mla":"Hennequin, Guillaume, et al. “Non-Normal Amplification in Random Balanced Neuronal Networks.” Physical Review E, vol. 86, no. 1, 011909, American Physical Society, 2012, doi:10.1103/physreve.86.011909."},"publication":"Physical Review E","article_type":"original","date_published":"2012-06-11T00:00:00Z","article_number":"011909","extern":"1","pmid":1,"year":"2012","publisher":"American Physical Society","publication_status":"published","author":[{"last_name":"Hennequin","first_name":"Guillaume","full_name":"Hennequin, Guillaume"},{"last_name":"Vogels","first_name":"Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P"},{"last_name":"Gerstner","first_name":"Wulfram","full_name":"Gerstner, Wulfram"}],"volume":86,"date_created":"2020-06-25T13:09:06Z","date_updated":"2021-01-12T08:16:35Z","publication_identifier":{"issn":["1539-3755"],"eisbn":["1550-2376"]},"month":"06","external_id":{"pmid":["23005454"]},"quality_controlled":"1","doi":"10.1103/physreve.86.011909","language":[{"iso":"eng"}]},{"type":"journal_article","abstract":[{"lang":"eng","text":"Using correlated live-cell imaging and electron tomography we found that actin branch junctions in protruding and treadmilling lamellipodia are not concentrated at the front as previously supposed, but link actin filament subsets in which there is a continuum of distances from a junction to the filament plus ends, for up to at least 1 mm. When branch sites were observed closely spaced on the same filament their separation was commonly a multiple of the actin helical repeat of 36 nm. Image averaging of branch junctions in the tomograms yielded a model for the in vivo branch at 2.9 nm resolution, which was comparable with that derived for the in vitro actin- Arp2/3 complex. Lamellipodium initiation was monitored in an intracellular wound-healing model and was found to involve branching from the sides of actin filaments oriented parallel to the plasmalemma. Many filament plus ends, presumably capped, terminated behind the lamellipodium tip and localized on the dorsal and ventral surfaces of the actin network. These findings reveal how branching events initiate and maintain a network of actin filaments of variable length, and provide the first structural model of the branch junction in vivo. A possible role of filament capping in generating the lamellipodium leaflet is discussed and a mathematical model of protrusion is also presented."}],"issue":"11","_id":"808","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"Actin branching in the initiation and maintenance of lamellipodia","intvolume":" 125","file":[{"access_level":"open_access","file_name":"2012_Biologists_Vinzenz.pdf","creator":"kschuh","content_type":"application/pdf","file_size":3326073,"file_id":"5956","relation":"main_file","checksum":"2f59e15cc3a85bb500a9887cef2aab67","date_created":"2019-02-12T08:54:51Z","date_updated":"2020-07-14T12:48:09Z"}],"oa_version":"None","day":"01","has_accepted_license":"1","publication":"Journal of Cell Science","citation":{"ama":"Vinzenz M, Nemethova M, Schur FK, et al. Actin branching in the initiation and maintenance of lamellipodia. Journal of Cell Science. 2012;125(11):2775-2785. doi:10.1242/jcs.107623","ista":"Vinzenz M, Nemethova M, Schur FK, Mueller J, Narita A, Urban E, Winkler C, Schmeiser C, Koestler S, Rottner K, Resch G, Maéda Y, Small J. 2012. Actin branching in the initiation and maintenance of lamellipodia. Journal of Cell Science. 125(11), 2775–2785.","apa":"Vinzenz, M., Nemethova, M., Schur, F. K., Mueller, J., Narita, A., Urban, E., … Small, J. (2012). Actin branching in the initiation and maintenance of lamellipodia. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.107623","ieee":"M. Vinzenz et al., “Actin branching in the initiation and maintenance of lamellipodia,” Journal of Cell Science, vol. 125, no. 11. Company of Biologists, pp. 2775–2785, 2012.","mla":"Vinzenz, Marlene, et al. “Actin Branching in the Initiation and Maintenance of Lamellipodia.” Journal of Cell Science, vol. 125, no. 11, Company of Biologists, 2012, pp. 2775–85, doi:10.1242/jcs.107623.","short":"M. Vinzenz, M. Nemethova, F.K. Schur, J. Mueller, A. Narita, E. Urban, C. Winkler, C. Schmeiser, S. Koestler, K. Rottner, G. Resch, Y. Maéda, J. Small, Journal of Cell Science 125 (2012) 2775–2785.","chicago":"Vinzenz, Marlene, Maria Nemethova, Florian KM Schur, Jan Mueller, Akihiro Narita, Edit Urban, Christoph Winkler, et al. “Actin Branching in the Initiation and Maintenance of Lamellipodia.” Journal of Cell Science. Company of Biologists, 2012. https://doi.org/10.1242/jcs.107623."},"page":"2775 - 2785","date_published":"2012-06-01T00:00:00Z","file_date_updated":"2020-07-14T12:48:09Z","publist_id":"6842","extern":"1","acknowledgement":"This work was supported by the Austrian Science Fund [projects FWF I516-B09 and FWF P21292-B09 to J.V.S.]; the Vienna Science and Technology Fund [WWTF-grant numbers MA 09-004 to J.V.S. and C.S], ZIT - The Technology Agency of the City of Vienna [VSOE, CMCN to J.V.S. and G.P.R.]; the Deutsche Forschungsgemeinschaft [grant number RO 2414/1-2 to K.R.]; the Daiko research foundation [grant number 9134 to A.N.]; and a Grant-in-Aid for Scientific Research [S, grant number 20227008 to Y.M.] and a Grant-in-Aid for Young Scientists [B, grant number 22770145 to A.N.] (B) from The Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government. Deposited in PMC for immediate release. We thank Tibor Kulcsar for assistance with graphics.","year":"2012","publication_status":"published","publisher":"Company of Biologists","author":[{"full_name":"Vinzenz, Marlene","first_name":"Marlene","last_name":"Vinzenz"},{"id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","last_name":"Nemethova","first_name":"Maria","full_name":"Nemethova, Maria"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian","full_name":"Schur, Florian"},{"first_name":"Jan","last_name":"Mueller","full_name":"Mueller, Jan"},{"last_name":"Narita","first_name":"Akihiro","full_name":"Narita, Akihiro"},{"full_name":"Urban, Edit","last_name":"Urban","first_name":"Edit"},{"first_name":"Christoph","last_name":"Winkler","full_name":"Winkler, Christoph"},{"last_name":"Schmeiser","first_name":"Christian","full_name":"Schmeiser, Christian"},{"full_name":"Koestler, Stefan","first_name":"Stefan","last_name":"Koestler"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"first_name":"Guenter","last_name":"Resch","full_name":"Resch, Guenter"},{"last_name":"Maéda","first_name":"Yuichiro","full_name":"Maéda, Yuichiro"},{"last_name":"Small","first_name":"John","full_name":"Small, John"}],"date_created":"2018-12-11T11:48:37Z","date_updated":"2021-01-12T08:16:47Z","volume":125,"month":"06","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"quality_controlled":"1","doi":"10.1242/jcs.107623","language":[{"iso":"eng"}]},{"month":"08","publication_identifier":{"issn":["0378-1097"]},"external_id":{"pmid":["22640011"]},"quality_controlled":"1","doi":"10.1111/j.1574-6968.2012.02603.x","language":[{"iso":"eng"}],"extern":"1","year":"2012","pmid":1,"publication_status":"published","publisher":"Oxford University Press","author":[{"full_name":"Dengler, Vanina","first_name":"Vanina","last_name":"Dengler"},{"full_name":"Meier, Patricia Stutzmann","first_name":"Patricia Stutzmann","last_name":"Meier"},{"full_name":"Heusser, Ronald","first_name":"Ronald","last_name":"Heusser"},{"last_name":"Kupferschmied","first_name":"Peter","full_name":"Kupferschmied, Peter"},{"full_name":"Fazekas, Judit","first_name":"Judit","last_name":"Fazekas","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502"},{"first_name":"Sarah","last_name":"Friebe","full_name":"Friebe, Sarah"},{"full_name":"Staufer, Sibylle Burger","last_name":"Staufer","first_name":"Sibylle Burger"},{"last_name":"Majcherczyk","first_name":"Paul A.","full_name":"Majcherczyk, Paul A."},{"last_name":"Moreillon","first_name":"Philippe","full_name":"Moreillon, Philippe"},{"full_name":"Berger-Bächi, Brigitte","first_name":"Brigitte","last_name":"Berger-Bächi"},{"full_name":"McCallum, Nadine","last_name":"McCallum","first_name":"Nadine"}],"date_updated":"2021-01-12T08:17:43Z","date_created":"2020-08-10T11:54:47Z","volume":333,"day":"01","article_processing_charge":"No","publication":"FEMS Microbiology Letters","citation":{"ieee":"V. Dengler et al., “Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response,” FEMS Microbiology Letters, vol. 333, no. 2. Oxford University Press, pp. 109–120, 2012.","apa":"Dengler, V., Meier, P. S., Heusser, R., Kupferschmied, P., Singer, J., Friebe, S., … McCallum, N. (2012). Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response. FEMS Microbiology Letters. Oxford University Press. https://doi.org/10.1111/j.1574-6968.2012.02603.x","ista":"Dengler V, Meier PS, Heusser R, Kupferschmied P, Singer J, Friebe S, Staufer SB, Majcherczyk PA, Moreillon P, Berger-Bächi B, McCallum N. 2012. Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response. FEMS Microbiology Letters. 333(2), 109–120.","ama":"Dengler V, Meier PS, Heusser R, et al. Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response. FEMS Microbiology Letters. 2012;333(2):109-120. doi:10.1111/j.1574-6968.2012.02603.x","chicago":"Dengler, Vanina, Patricia Stutzmann Meier, Ronald Heusser, Peter Kupferschmied, Judit Singer, Sarah Friebe, Sibylle Burger Staufer, et al. “Deletion of Hypothetical Wall Teichoic Acid Ligases in Staphylococcus Aureus Activates the Cell Wall Stress Response.” FEMS Microbiology Letters. Oxford University Press, 2012. https://doi.org/10.1111/j.1574-6968.2012.02603.x.","short":"V. Dengler, P.S. Meier, R. Heusser, P. Kupferschmied, J. Singer, S. Friebe, S.B. Staufer, P.A. Majcherczyk, P. Moreillon, B. Berger-Bächi, N. McCallum, FEMS Microbiology Letters 333 (2012) 109–120.","mla":"Dengler, Vanina, et al. “Deletion of Hypothetical Wall Teichoic Acid Ligases in Staphylococcus Aureus Activates the Cell Wall Stress Response.” FEMS Microbiology Letters, vol. 333, no. 2, Oxford University Press, 2012, pp. 109–20, doi:10.1111/j.1574-6968.2012.02603.x."},"article_type":"original","page":"109-120","date_published":"2012-08-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The Staphylococcus aureus cell wall stress stimulon (CWSS) is activated by cell envelope-targeting antibiotics or depletion of essential cell wall biosynthesis enzymes. The functionally uncharacterized S. aureus LytR-CpsA-Psr (LCP) proteins, MsrR, SA0908 and SA2103, all belong to the CWSS. Although not essential, deletion of all three LCP proteins severely impairs cell division. We show here that VraSR-dependent CWSS expression was up to 250-fold higher in single, double and triple LCP mutants than in wild type S. aureus in the absence of external stress. The LCP triple mutant was virtually depleted of wall teichoic acids (WTA), which could be restored to different degrees by any of the single LCP proteins. Subinhibitory concentrations of tunicamycin, which inhibits the first WTA synthesis enzyme TarO (TagO), could partially complement the severe growth defect of the LCP triple mutant. Both of the latter findings support a role for S. aureus LCP proteins in late WTA synthesis, as in Bacillus subtilis where LCP proteins were recently proposed to transfer WTA from lipid carriers to the cell wall peptidoglycan. Intrinsic activation of the CWSS upon LCP deletion and the fact that LCP proteins were essential for WTA-loading of the cell wall, highlight their important role(s) in S. aureus cell envelope biogenesis."}],"issue":"2","_id":"8246","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the cell wall stress response","status":"public","intvolume":" 333","oa_version":"None"},{"author":[{"full_name":"Vanstraelen, Marleen","last_name":"Vanstraelen","first_name":"Marleen"},{"full_name":"Eva Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"}],"volume":28,"date_updated":"2021-01-12T08:17:46Z","date_created":"2018-12-11T11:48:43Z","acknowledgement":"We would like to thank Annick Bleys for help in preparing the manuscript. This work was supported by the European Research Council with a Starting Independent Research grant (ERC-2007-Stg-207362-HCPO) and the project CZ.1.07/2.3.00/20.0043 (to the Central European Institute of Technology, CEITEC) to E.B. M.V. is a postdoctoral fellow of the Research Foundation Flanders. We apologize that, because of space restrictions, the scientific contributions of only a limited number of original articles could be cited and discussed.","_id":"826","year":"2012","publisher":"Annual Reviews","intvolume":" 28","status":"public","publication_status":"published","title":"Hormonal interactions in the regulation of plant development","publist_id":"6822","abstract":[{"lang":"eng","text":"Plants exhibit a unique developmental flexibility to ever-changing environmental conditions. To achieve their profound adaptability, plants are able to maintain permanent stem cell populations and form new organs during the entire plant life cycle. Signaling substances, called plant hormones, such as auxin, cytokinin, abscisic acid, brassinosteroid, ethylene, gibberellin, jasmonic acid, and strigolactone, govern and coordinate these developmental processes. Physiological and genetic studies have dissected the molecular components of signal perception and transduction of the individual hormonal pathways. However, over recent years it has become evident that hormones do not act only in a linear pathway. Hormonal pathways are interconnected by a complex network of interactions and feedback circuits that determines the final outcome of the individual hormone actions. This raises questions about the molecular mechanisms underlying hormonal cross talk and about how these hormonal networks are established, maintained, and modulated throughout plant development."}],"extern":1,"type":"journal_article","date_published":"2012-11-01T00:00:00Z","doi":"10.1146/annurev-cellbio-101011-155741","citation":{"mla":"Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation of Plant Development.” Annual Review of Cell and Developmental Biology, vol. 28, Annual Reviews, 2012, pp. 463–87, doi:10.1146/annurev-cellbio-101011-155741.","short":"M. Vanstraelen, E. Benková, Annual Review of Cell and Developmental Biology 28 (2012) 463–487.","chicago":"Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation of Plant Development.” Annual Review of Cell and Developmental Biology. Annual Reviews, 2012. https://doi.org/10.1146/annurev-cellbio-101011-155741.","ama":"Vanstraelen M, Benková E. Hormonal interactions in the regulation of plant development. Annual Review of Cell and Developmental Biology. 2012;28:463-487. doi:10.1146/annurev-cellbio-101011-155741","ista":"Vanstraelen M, Benková E. 2012. Hormonal interactions in the regulation of plant development. Annual Review of Cell and Developmental Biology. 28, 463–487.","ieee":"M. Vanstraelen and E. Benková, “Hormonal interactions in the regulation of plant development,” Annual Review of Cell and Developmental Biology, vol. 28. Annual Reviews, pp. 463–487, 2012.","apa":"Vanstraelen, M., & Benková, E. (2012). Hormonal interactions in the regulation of plant development. Annual Review of Cell and Developmental Biology. Annual Reviews. https://doi.org/10.1146/annurev-cellbio-101011-155741"},"publication":"Annual Review of Cell and Developmental Biology","page":"463 - 487","quality_controlled":0,"day":"01","month":"11"},{"type":"journal_article","extern":1,"abstract":[{"text":"The architecture of a plant's root system, established postembryonically, results from both coordinated root growth and lateral root branching. The plant hormones auxin and cytokinin are central endogenous signaling molecules that regulate lateral root organogenesis positively and negatively, respectively. Tight control and mutual balance of their antagonistic activities are particularly important during the early phases of lateral root organogenesis to ensure continuous lateral root initiation (LRI) and proper development of lateral root primordia (LRP). Here, we show that the early phases of lateral root organogenesis, including priming and initiation, take place in root zones with a repressed cytokinin response. Accordingly, ectopic overproduction of cytokinin in the root basal meristem most efficiently inhibits LRI. Enhanced cytokinin responses in pericycle cells between existing LRP might restrict LRI near existing LRP and, when compromised, ectopic LRI occurs. Furthermore, our results demonstrate that young LRP are more sensitive to perturbations in the cytokinin activity than are developmentally more advanced primordia. We hypothesize that the effect of cytokinin on the development of primordia possibly depends on the robustness and stability of the auxin gradient.","lang":"eng"}],"publist_id":"6819","issue":"10","status":"public","title":"Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin","publication_status":"published","intvolume":" 24","publisher":"American Society of Plant Biologists","_id":"829","year":"2012","acknowledgement":"We thank Jen Sheen, Dolf Weijers, Tatsuo Kakimoto, Stephen Depuydt, and Laurent Laplaze for sharing published material, Jiri Friml for discussions, and Martine De Cock and Annick Bleys for help in preparing the manuscript. This work was supported by a Starting Independent Research grant from the European Research Council (ERC-2007-Stg-207362-HCPO) and the project CZ.1.07/2.3.00/20.0043 to the Central European Institute of Technology to E.B. and grants from the Ministry of Education, Youth, and Sports of the Czech Republic (MSM 6198959216) and the Centre of the Region Haná for Biotechnological and Agricultural Research (ED0007/01/01) to P.T.","date_created":"2018-12-11T11:48:43Z","date_updated":"2021-01-12T08:17:55Z","volume":24,"author":[{"last_name":"Bielach","first_name":"Agnieszka","full_name":"Bielach, Agnieszka"},{"full_name":"Podlesakova, Katerina","first_name":"Katerina","last_name":"Podlesakova"},{"full_name":"Peter Marhavy","last_name":"Marhavy","first_name":"Peter","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Duclercq, Jérôme","last_name":"Duclercq","first_name":"Jérôme"},{"full_name":"Candela Cuesta","orcid":"0000-0003-1923-2410","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","last_name":"Cuesta","first_name":"Candela"},{"first_name":"Bruno","last_name":"Muller","full_name":"Muller, Bruno"},{"first_name":"Wim","last_name":"Grunewald","full_name":"Grunewald, Wim"},{"first_name":"Petr","last_name":"Tarkowski","full_name":"Tarkowski, Petr"},{"full_name":"Eva Benková","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"day":"01","month":"10","quality_controlled":0,"page":"3967 - 3981","publication":"The Plant Cell","citation":{"ista":"Bielach A, Podlesakova K, Marhavý P, Duclercq J, Cuesta C, Muller B, Grunewald W, Tarkowski P, Benková E. 2012. Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin. The Plant Cell. 24(10), 3967–3981.","apa":"Bielach, A., Podlesakova, K., Marhavý, P., Duclercq, J., Cuesta, C., Muller, B., … Benková, E. (2012). Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.112.103044","ieee":"A. Bielach et al., “Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin,” The Plant Cell, vol. 24, no. 10. American Society of Plant Biologists, pp. 3967–3981, 2012.","ama":"Bielach A, Podlesakova K, Marhavý P, et al. Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin. The Plant Cell. 2012;24(10):3967-3981. doi:10.1105/tpc.112.103044","chicago":"Bielach, Agnieszka, Katerina Podlesakova, Peter Marhavý, Jérôme Duclercq, Candela Cuesta, Bruno Muller, Wim Grunewald, Petr Tarkowski, and Eva Benková. “Spatiotemporal Regulation of Lateral Root Organogenesis in Arabidopsis by Cytokinin.” The Plant Cell. American Society of Plant Biologists, 2012. https://doi.org/10.1105/tpc.112.103044.","mla":"Bielach, Agnieszka, et al. “Spatiotemporal Regulation of Lateral Root Organogenesis in Arabidopsis by Cytokinin.” The Plant Cell, vol. 24, no. 10, American Society of Plant Biologists, 2012, pp. 3967–81, doi:10.1105/tpc.112.103044.","short":"A. Bielach, K. Podlesakova, P. Marhavý, J. Duclercq, C. Cuesta, B. Muller, W. Grunewald, P. Tarkowski, E. Benková, The Plant Cell 24 (2012) 3967–3981."},"date_published":"2012-10-01T00:00:00Z","doi":"10.1105/tpc.112.103044"},{"author":[{"last_name":"Soylemez","first_name":"Onuralp","full_name":"Soylemez, Onuralp"},{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov"}],"volume":4,"date_created":"2018-12-11T11:48:49Z","date_updated":"2021-01-12T08:19:25Z","acknowledgement":"This work was supported by Plan Nacional grant BFU2009-09271 from the Spanish Ministry of Science and Innovation and by FPU (Formación del Profesorado Universitario) program grant AP2008-01888 from the Spanish Ministry of Education to O.S. F.A.K. is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist.","_id":"846","year":"2012","intvolume":" 4","publisher":"Oxford University Press","status":"public","title":"Estimating the rate of irreversibility in protein evolution","publication_status":"published","issue":"12","publist_id":"6802","abstract":[{"text":"Whether or not evolutionary change is inherently irreversible remains a controversial topic. Some examples of evolutionary irreversibility are known; however, this question has not been comprehensively addressed at the molecular level. Here, we use data from 221 human genes with known pathogenic mutations to estimate the rate of irreversibility in protein evolution. For these genes, we reconstruct ancestral amino acid sequences along the mammalian phylogeny and identify ancestral amino acid states that match known pathogenic mutations. Such cases represent inherent evolutionary irreversibility because, at the present moment, reversals to these ancestral amino acid states are impossible for the human lineage. We estimate that approximately 10% of all amino acid substitutions along the mammalian phylogeny are irreversible, such that a return to the ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes with high rates of irreversibility, as much as 40% of all amino acid evolution was estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes, the molecular nature of the high rate of irreversibility in proteins is best explained by evolution with a high prevalence of compensatory, epistatic interactions between amino acid sites. Under such mode of protein evolution, once an amino acid substitution is fixed, the probability of its reversal declines as the protein sequence accumulates changes that affect the phenotypic manifestation of the ancestral state. The prevalence of epistasis in evolution indicates that the observed high rate of irreversibility in protein evolution is an inherent property of protein structure and function.","lang":"eng"}],"extern":1,"type":"journal_article","date_published":"2012-01-01T00:00:00Z","doi":"10.1093/gbe/evs096","citation":{"ama":"Soylemez O, Kondrashov F. Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. 2012;4(12):1213-1222. doi:10.1093/gbe/evs096","ista":"Soylemez O, Kondrashov F. 2012. Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. 4(12), 1213–1222.","ieee":"O. Soylemez and F. Kondrashov, “Estimating the rate of irreversibility in protein evolution,” Genome Biology and Evolution, vol. 4, no. 12. Oxford University Press, pp. 1213–1222, 2012.","apa":"Soylemez, O., & Kondrashov, F. (2012). Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evs096","mla":"Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility in Protein Evolution.” Genome Biology and Evolution, vol. 4, no. 12, Oxford University Press, 2012, pp. 1213–22, doi:10.1093/gbe/evs096.","short":"O. Soylemez, F. Kondrashov, Genome Biology and Evolution 4 (2012) 1213–1222.","chicago":"Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility in Protein Evolution.” Genome Biology and Evolution. Oxford University Press, 2012. https://doi.org/10.1093/gbe/evs096."},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"publication":"Genome Biology and Evolution","page":"1213 - 1222","quality_controlled":0,"day":"01","month":"01"},{"extern":"1","issue":"2","abstract":[{"text":"The 1H dipolar network, which is the major obstacle for applying proton detection in the solid-state, can be reduced by deuteration, employing the RAP (Reduced Adjoining Protonation) labeling scheme, which yields random protonation at non-exchangeable sites. We present here a systematic study on the optimal degree of random sidechain protonation in RAP samples as a function of the MAS (magic angle spinning) frequency. In particular, we compare 1H sensitivity and linewidth of a microcrystalline protein, the SH3 domain of chicken α-spectrin, for samples, prepared with 5–25 % H2O in the E. coli growth medium, in the MAS frequency range of 20–60 kHz. At an external field of 19.96 T (850 MHz), we find that using a proton concentration between 15 and 25 % in the M9 medium yields the best compromise in terms of sensitivity and resolution, with an achievable average 1H linewidth on the order of 40–50 Hz. Comparing sensitivities at a MAS frequency of 60 versus 20 kHz, a gain in sensitivity by a factor of 4–4.5 is observed in INEPT-based 1H detected 1D 1H,13C correlation experiments. In total, we find that spectra recorded with a 1.3 mm rotor at 60 kHz have almost the same sensitivity as spectra recorded with a fully packed 3.2 mm rotor at 20 kHz, even though ~20× less material is employed. The improved sensitivity is attributed to 1H line narrowing due to fast MAS and to the increased efficiency of the 1.3 mm coil.","lang":"eng"}],"type":"journal_article","volume":54,"oa_version":"None","date_created":"2020-09-18T10:09:18Z","date_updated":"2021-01-12T08:19:27Z","author":[{"last_name":"Asami","first_name":"Sam","full_name":"Asami, Sam"},{"full_name":"Szekely, Kathrin","last_name":"Szekely","first_name":"Kathrin"},{"first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"last_name":"Meier","first_name":"Beat H.","full_name":"Meier, Beat H."},{"full_name":"Reif, Bernd","last_name":"Reif","first_name":"Bernd"}],"publisher":"Springer Nature","intvolume":" 54","status":"public","publication_status":"published","title":"Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency","_id":"8463","year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publication_identifier":{"issn":["0925-2738","1573-5001"]},"day":"23","month":"08","language":[{"iso":"eng"}],"doi":"10.1007/s10858-012-9659-9","date_published":"2012-08-23T00:00:00Z","page":"155-168","quality_controlled":"1","article_type":"original","citation":{"ama":"Asami S, Szekely K, Schanda P, Meier BH, Reif B. Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency. Journal of Biomolecular NMR. 2012;54(2):155-168. doi:10.1007/s10858-012-9659-9","ista":"Asami S, Szekely K, Schanda P, Meier BH, Reif B. 2012. Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency. Journal of Biomolecular NMR. 54(2), 155–168.","ieee":"S. Asami, K. Szekely, P. Schanda, B. H. Meier, and B. Reif, “Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency,” Journal of Biomolecular NMR, vol. 54, no. 2. Springer Nature, pp. 155–168, 2012.","apa":"Asami, S., Szekely, K., Schanda, P., Meier, B. H., & Reif, B. (2012). Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-012-9659-9","mla":"Asami, Sam, et al. “Optimal Degree of Protonation for 1H Detection of Aliphatic Sites in Randomly Deuterated Proteins as a Function of the MAS Frequency.” Journal of Biomolecular NMR, vol. 54, no. 2, Springer Nature, 2012, pp. 155–68, doi:10.1007/s10858-012-9659-9.","short":"S. Asami, K. Szekely, P. Schanda, B.H. Meier, B. Reif, Journal of Biomolecular NMR 54 (2012) 155–168.","chicago":"Asami, Sam, Kathrin Szekely, Paul Schanda, Beat H. Meier, and Bernd Reif. “Optimal Degree of Protonation for 1H Detection of Aliphatic Sites in Randomly Deuterated Proteins as a Function of the MAS Frequency.” Journal of Biomolecular NMR. Springer Nature, 2012. https://doi.org/10.1007/s10858-012-9659-9."},"publication":"Journal of Biomolecular NMR"},{"date_created":"2020-09-18T10:10:20Z","date_updated":"2021-01-12T08:19:27Z","oa_version":"None","volume":134,"author":[{"first_name":"Martin","last_name":"Tollinger","full_name":"Tollinger, Martin"},{"full_name":"Sivertsen, Astrid C.","last_name":"Sivertsen","first_name":"Astrid C."},{"last_name":"Meier","first_name":"Beat H.","full_name":"Meier, Beat H."},{"full_name":"Ernst, Matthias","last_name":"Ernst","first_name":"Matthias"},{"last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}],"status":"public","title":"Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy","publication_status":"published","publisher":"American Chemical Society","intvolume":" 134","_id":"8465","year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","abstract":[{"lang":"eng","text":"We demonstrate that conformational exchange processes in proteins on microsecond-to-millisecond time scales can be detected and quantified by solid-state NMR spectroscopy. We show two independent approaches that measure the effect of conformational exchange on transverse relaxation parameters, namely Carr–Purcell–Meiboom–Gill relaxation-dispersion experiments and measurement of differential multiple-quantum coherence decay. Long coherence lifetimes, as required for these experiments, are achieved by the use of highly deuterated samples and fast magic-angle spinning. The usefulness of the approaches is demonstrated by application to microcrystalline ubiquitin. We detect a conformational exchange process in a region of the protein for which dynamics have also been observed in solution. Interestingly, quantitative analysis of the data reveals that the exchange process is more than 1 order of magnitude slower than in solution, and this points to the impact of the crystalline environment on free energy barriers."}],"issue":"36","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2012-08-21T00:00:00Z","doi":"10.1021/ja303591y","article_type":"original","quality_controlled":"1","page":"14800-14807","publication":"Journal of the American Chemical Society","citation":{"chicago":"Tollinger, Martin, Astrid C. Sivertsen, Beat H. Meier, Matthias Ernst, and Paul Schanda. “Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy.” Journal of the American Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja303591y.","mla":"Tollinger, Martin, et al. “Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy.” Journal of the American Chemical Society, vol. 134, no. 36, American Chemical Society, 2012, pp. 14800–07, doi:10.1021/ja303591y.","short":"M. Tollinger, A.C. Sivertsen, B.H. Meier, M. Ernst, P. Schanda, Journal of the American Chemical Society 134 (2012) 14800–14807.","ista":"Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. 2012. Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. Journal of the American Chemical Society. 134(36), 14800–14807.","ieee":"M. Tollinger, A. C. Sivertsen, B. H. Meier, M. Ernst, and P. Schanda, “Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy,” Journal of the American Chemical Society, vol. 134, no. 36. American Chemical Society, pp. 14800–14807, 2012.","apa":"Tollinger, M., Sivertsen, A. C., Meier, B. H., Ernst, M., & Schanda, P. (2012). Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja303591y","ama":"Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. Journal of the American Chemical Society. 2012;134(36):14800-14807. doi:10.1021/ja303591y"},"month":"08","day":"21","publication_identifier":{"issn":["0002-7863","1520-5126"]},"article_processing_charge":"No"},{"author":[{"full_name":"Rennella, Enrico","last_name":"Rennella","first_name":"Enrico"},{"last_name":"Cutuil","first_name":"Thomas","full_name":"Cutuil, Thomas"},{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"full_name":"Forge, Vincent","first_name":"Vincent","last_name":"Forge"},{"first_name":"Bernhard","last_name":"Brutscher","full_name":"Brutscher, Bernhard"}],"date_updated":"2021-01-12T08:19:28Z","date_created":"2020-09-18T10:10:28Z","volume":134,"oa_version":"None","_id":"8466","year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate","publication_status":"published","status":"public","intvolume":" 134","publisher":"American Chemical Society","abstract":[{"lang":"eng","text":"Recent advances in NMR spectroscopy and the availability of high magnetic field strengths now offer the possibility to record real-time 3D NMR spectra of short-lived protein states, e.g., states that become transiently populated during protein folding. Here we present a strategy for obtaining sequential NMR assignments as well as atom-resolved information on structural and dynamic features within a folding intermediate of the amyloidogenic protein β2-microglobulin that has a half-lifetime of only 20 min."}],"issue":"19","extern":"1","type":"journal_article","doi":"10.1021/ja302598j","date_published":"2012-05-03T00:00:00Z","language":[{"iso":"eng"}],"publication":"Journal of the American Chemical Society","citation":{"mla":"Rennella, Enrico, et al. “Real-Time NMR Characterization of Structure and Dynamics in a Transiently Populated Protein Folding Intermediate.” Journal of the American Chemical Society, vol. 134, no. 19, American Chemical Society, 2012, pp. 8066–69, doi:10.1021/ja302598j.","short":"E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, B. Brutscher, Journal of the American Chemical Society 134 (2012) 8066–8069.","chicago":"Rennella, Enrico, Thomas Cutuil, Paul Schanda, Isabel Ayala, Vincent Forge, and Bernhard Brutscher. “Real-Time NMR Characterization of Structure and Dynamics in a Transiently Populated Protein Folding Intermediate.” Journal of the American Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja302598j.","ama":"Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. Journal of the American Chemical Society. 2012;134(19):8066-8069. doi:10.1021/ja302598j","ista":"Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. 2012. Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. Journal of the American Chemical Society. 134(19), 8066–8069.","apa":"Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Forge, V., & Brutscher, B. (2012). Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja302598j","ieee":"E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, and B. Brutscher, “Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate,” Journal of the American Chemical Society, vol. 134, no. 19. American Chemical Society, pp. 8066–8069, 2012."},"article_type":"original","quality_controlled":"1","page":"8066-8069","month":"05","day":"03","publication_identifier":{"issn":["0002-7863","1520-5126"]},"article_processing_charge":"No"},{"abstract":[{"lang":"eng","text":"Partial deuteration is a powerful tool to increase coherence life times and spectral resolution in proton solid-state NMR. The J coupling to deuterium needs, however, to be decoupled to maintain the good resolution in the (usually indirect) 13C dimension(s). We present a simple and reversible way to expand a commercial 1.3 mm HCN MAS probe with a 2H channel with sufficient field strength for J-decoupling of deuterium, namely 2–3 kHz. The coil is placed at the outside of the stator and requires no significant modifications to the probe. The performance and the realizable gains in sensitivity and resolution are demonstrated using perdeuterated ubiquitin, with selectively CHD2-labeled methyl groups."}],"extern":"1","type":"journal_article","author":[{"last_name":"Huber","first_name":"Matthias","full_name":"Huber, Matthias"},{"full_name":"With, Oliver","first_name":"Oliver","last_name":"With"},{"full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"},{"last_name":"Verel","first_name":"René","full_name":"Verel, René"},{"full_name":"Ernst, Matthias","last_name":"Ernst","first_name":"Matthias"},{"last_name":"Meier","first_name":"Beat H.","full_name":"Meier, Beat H."}],"date_created":"2020-09-18T10:10:36Z","date_updated":"2021-01-12T08:19:28Z","oa_version":"None","volume":214,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8467","year":"2012","title":"A supplementary coil for 2H decoupling with commercial HCN MAS probes","status":"public","publication_status":"published","intvolume":" 214","publisher":"Elsevier","month":"01","day":"01","publication_identifier":{"issn":["1090-7807"]},"article_processing_charge":"No","doi":"10.1016/j.jmr.2011.10.010","date_published":"2012-01-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Journal of Magnetic Resonance","citation":{"chicago":"Huber, Matthias, Oliver With, Paul Schanda, René Verel, Matthias Ernst, and Beat H. Meier. “A Supplementary Coil for 2H Decoupling with Commercial HCN MAS Probes.” Journal of Magnetic Resonance. Elsevier, 2012. https://doi.org/10.1016/j.jmr.2011.10.010.","mla":"Huber, Matthias, et al. “A Supplementary Coil for 2H Decoupling with Commercial HCN MAS Probes.” Journal of Magnetic Resonance, vol. 214, Elsevier, 2012, pp. 76–80, doi:10.1016/j.jmr.2011.10.010.","short":"M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, B.H. Meier, Journal of Magnetic Resonance 214 (2012) 76–80.","ista":"Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. 2012. A supplementary coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance. 214, 76–80.","ieee":"M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, and B. H. Meier, “A supplementary coil for 2H decoupling with commercial HCN MAS probes,” Journal of Magnetic Resonance, vol. 214. Elsevier, pp. 76–80, 2012.","apa":"Huber, M., With, O., Schanda, P., Verel, R., Ernst, M., & Meier, B. H. (2012). A supplementary coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2011.10.010","ama":"Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. A supplementary coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance. 2012;214:76-80. doi:10.1016/j.jmr.2011.10.010"},"article_type":"original","quality_controlled":"1","page":"76-80"},{"type":"journal_article","issue":"3","abstract":[{"text":"The famous ergodic hypothesis suggests that for a typical Hamiltonian on a typical energy surface nearly all trajectories are dense. KAM theory disproves it. Ehrenfest (The Conceptual Foundations of the Statistical Approach in Mechanics. Ithaca, NY: Cornell University Press, 1959) and Birkhoff (Collected Math Papers. Vol 2, New York: Dover, pp 462–465, 1968) stated the quasi-ergodic hypothesis claiming that a typical Hamiltonian on a typical energy surface has a dense orbit. This question is wide open. Herman (Proceedings of the International Congress of Mathematicians, Vol II (Berlin, 1998). Doc Math 1998, Extra Vol II, Berlin: Int Math Union, pp 797–808, 1998) proposed to look for an example of a Hamiltonian near H0(I)=⟨I,I⟩2 with a dense orbit on the unit energy surface. In this paper we construct a Hamiltonian H0(I)+εH1(θ,I,ε) which has an orbit dense in a set of maximal Hausdorff dimension equal to 5 on the unit energy surface.","lang":"eng"}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8502","year":"2012","publisher":"Springer Nature","intvolume":" 315","status":"public","title":"An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension","publication_status":"published","author":[{"full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim"},{"full_name":"Saprykina, Maria","last_name":"Saprykina","first_name":"Maria"}],"volume":315,"oa_version":"None","date_updated":"2021-01-12T08:19:44Z","date_created":"2020-09-18T10:47:16Z","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"article_processing_charge":"No","publication_identifier":{"issn":["0010-3616","1432-0916"]},"day":"01","month":"11","citation":{"ista":"Kaloshin V, Saprykina M. 2012. An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. Communications in Mathematical Physics. 315(3), 643–697.","apa":"Kaloshin, V., & Saprykina, M. (2012). An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-012-1532-x","ieee":"V. Kaloshin and M. Saprykina, “An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension,” Communications in Mathematical Physics, vol. 315, no. 3. Springer Nature, pp. 643–697, 2012.","ama":"Kaloshin V, Saprykina M. An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension. Communications in Mathematical Physics. 2012;315(3):643-697. doi:10.1007/s00220-012-1532-x","chicago":"Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable Hamiltonian System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.” Communications in Mathematical Physics. Springer Nature, 2012. https://doi.org/10.1007/s00220-012-1532-x.","mla":"Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable Hamiltonian System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.” Communications in Mathematical Physics, vol. 315, no. 3, Springer Nature, 2012, pp. 643–97, doi:10.1007/s00220-012-1532-x.","short":"V. Kaloshin, M. Saprykina, Communications in Mathematical Physics 315 (2012) 643–697."},"publication":"Communications in Mathematical Physics","page":"643-697","quality_controlled":"1","article_type":"original","doi":"10.1007/s00220-012-1532-x","date_published":"2012-11-01T00:00:00Z","language":[{"iso":"eng"}]},{"publist_id":"6792","abstract":[{"lang":"eng","text":"ackground: The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of stop codons in bacterial genomes.Results: We show that in bacteria stop codons evolve slower than synonymous sites, suggesting the action of weak negative selection. However, the frequency of stop codons relative to genomic nucleotide content indicated that this selection regime is not straightforward. The frequency of TAA and TGA stop codons is GC-content dependent, with TAA decreasing and TGA increasing with GC-content, while TAG frequency is independent of GC-content. Applying a formal, analytical model to these data we found that the relationship between stop codon frequencies and nucleotide content cannot be explained by mutational biases or selection on nucleotide content. However, with weak nucleotide content-dependent selection on TAG, -0.5 < Nes < 1.5, the model fits all of the data and recapitulates the relationship between TAG and nucleotide content. For biologically plausible rates of mutations we show that, in bacteria, TAG stop codon is universally associated with lower fitness, with TAA being the optimal for G-content < 16% while for G-content > 16% TGA has a higher fitness than TAG.Conclusions: Our data indicate that TAG codon is universally suboptimal in the bacterial lineage, such that TAA is likely to be the preferred stop codon for low GC content while the TGA is the preferred stop codon for high GC content. The optimization of stop codon usage may therefore be useful in genome engineering or gene expression optimization applications.Reviewers: This article was reviewed by Michail Gelfand, Arcady Mushegian and Shamil Sunyaev. For the full reviews, please go to the Reviewers' Comments section."}],"extern":1,"type":"journal_article","author":[{"first_name":"Inna","last_name":"Povolotskaya","full_name":"Povolotskaya, Inna"},{"full_name":"Fyodor Kondrashov","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"first_name":"Alice","last_name":"Ledda","full_name":"Ledda, Alice"},{"first_name":"Peter","last_name":"Vlasov","full_name":"Vlasov, Peter K"}],"volume":7,"date_created":"2018-12-11T11:48:52Z","date_updated":"2021-01-12T08:20:08Z","acknowledgement":"We thank Elena Alkalaeva and Peter Kolosov for insightful discussion and Brian Charlesworth for a critical reading of our manuscript. The work has been supported by a Plan Nacional grant from the Spanish Ministry of Science and Innovation, EMBO Young Investigator and Howard Hughes Medical Institute International Early Career Scientist awards.\n","_id":"858","year":"2012","intvolume":" 7","publisher":"BioMed Central","status":"public","title":"Stop codons in bacteria are not selectively equivalent","publication_status":"published","day":"01","month":"09","date_published":"2012-09-01T00:00:00Z","doi":"10.1186/1745-6150-7-30","citation":{"mla":"Povolotskaya, Inna, et al. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct, vol. 7, BioMed Central, 2012, doi:10.1186/1745-6150-7-30.","short":"I. Povolotskaya, F. Kondrashov, A. Ledda, P. Vlasov, Biology Direct 7 (2012).","chicago":"Povolotskaya, Inna, Fyodor Kondrashov, Alice Ledda, and Peter Vlasov. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-30.","ama":"Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. Stop codons in bacteria are not selectively equivalent. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-30","ista":"Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. 2012. Stop codons in bacteria are not selectively equivalent. Biology Direct. 7.","ieee":"I. Povolotskaya, F. Kondrashov, A. Ledda, and P. Vlasov, “Stop codons in bacteria are not selectively equivalent,” Biology Direct, vol. 7. BioMed Central, 2012.","apa":"Povolotskaya, I., Kondrashov, F., Ledda, A., & Vlasov, P. (2012). Stop codons in bacteria are not selectively equivalent. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-30"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication":"Biology Direct","quality_controlled":0},{"citation":{"ieee":"M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Epistasis as the primary factor in molecular evolution,” Nature, vol. 490, no. 7421. Nature Publishing Group, pp. 535–538, 2012.","apa":"Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2012). Epistasis as the primary factor in molecular evolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11510","ista":"Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2012. Epistasis as the primary factor in molecular evolution. Nature. 490(7421), 535–538.","ama":"Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Epistasis as the primary factor in molecular evolution. Nature. 2012;490(7421):535-538. doi:10.1038/nature11510","chicago":"Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Epistasis as the Primary Factor in Molecular Evolution.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11510.","short":"M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 490 (2012) 535–538.","mla":"Breen, Michael, et al. “Epistasis as the Primary Factor in Molecular Evolution.” Nature, vol. 490, no. 7421, Nature Publishing Group, 2012, pp. 535–38, doi:10.1038/nature11510."},"publication":"Nature","page":"535 - 538","quality_controlled":0,"date_published":"2012-10-25T00:00:00Z","doi":"10.1038/nature11510","day":"25","month":"10","_id":"900","acknowledgement":"The work was supported by Plan Nacional grants from the Spanish Ministry of Science and Innovation, to F.A.K. and C.N. C.K. was supported by the European Union FP7 project Quantomics (KBBE2A222664). F.A.K. is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist. We thank B. Lehner and T. Warnecke for input and a critical reading of the manuscript.\n","year":"2012","publisher":"Nature Publishing Group","intvolume":" 490","publication_status":"published","title":"Epistasis as the primary factor in molecular evolution","status":"public","author":[{"full_name":"Breen, Michael S","last_name":"Breen","first_name":"Michael"},{"full_name":"Kemena, Carsten","last_name":"Kemena","first_name":"Carsten"},{"full_name":"Vlasov, Peter K","first_name":"Peter","last_name":"Vlasov"},{"first_name":"Cédric","last_name":"Notredame","full_name":"Notredame, Cédric"},{"full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"}],"volume":490,"date_updated":"2021-01-12T08:21:45Z","date_created":"2018-12-11T11:49:06Z","type":"journal_article","issue":"7421","publist_id":"6748","abstract":[{"lang":"eng","text":"The main forces directing long-term molecular evolution remain obscure. A sizable fraction of amino-acid substitutions seem to be fixed by positive selection, but it is unclear to what degree long-term protein evolution is constrained by epistasis, that is, instances when substitutions that are accepted in one genotype are deleterious in another. Here we obtain a quantitative estimate of the prevalence of epistasis in long-term protein evolution by relating data on amino-acid usage in 14 organelle proteins and 2 nuclear-encoded proteins to their rates of short-term evolution. We studied multiple alignments of at least 1,000 orthologues for each of these 16 proteins from species from a diverse phylogenetic background and found that an average site contained approximately eight different amino acids. Thus, without epistasis an average site should accept two-fifths of all possible amino acids, and the average rate of amino-acid substitutions should therefore be about three-fifths lower than the rate of neutral evolution. However, we found that the measured rate of amino-acid substitution in recent evolution is 20 times lower than the rate of neutral evolution and an order of magnitude lower than that expected in the absence of epistasis. These data indicate that epistasis is pervasive throughout protein evolution: about 90 per cent of all amino-acid substitutions have a neutral or beneficial impact only in the genetic backgrounds in which they occur, and must therefore be deleterious in a different background of other species. Our findings show that most amino-acid substitutions have different fitness effects in different species and that epistasis provides the primary conceptual framework to describe the tempo and mode of long-term protein evolution."}],"extern":1},{"article_type":"letter_note","publication":"Physical Review Letters","citation":{"ama":"Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. 2012;108(26). doi:10.1103/physrevlett.108.268303","ieee":"I. Theurkauff, C. Cottin-Bizonne, J. A. Palacci, C. Ybert, and L. Bocquet, “Dynamic clustering in active colloidal suspensions with chemical signaling,” Physical Review Letters, vol. 108, no. 26. American Physical Society , 2012.","apa":"Theurkauff, I., Cottin-Bizonne, C., Palacci, J. A., Ybert, C., & Bocquet, L. (2012). Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. American Physical Society . https://doi.org/10.1103/physrevlett.108.268303","ista":"Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. 2012. Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. 108(26), 268303.","short":"I. Theurkauff, C. Cottin-Bizonne, J.A. Palacci, C. Ybert, L. Bocquet, Physical Review Letters 108 (2012).","mla":"Theurkauff, I., et al. “Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling.” Physical Review Letters, vol. 108, no. 26, 268303, American Physical Society , 2012, doi:10.1103/physrevlett.108.268303.","chicago":"Theurkauff, I., C. Cottin-Bizonne, Jérémie A Palacci, C. Ybert, and L. Bocquet. “Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling.” Physical Review Letters. American Physical Society , 2012. https://doi.org/10.1103/physrevlett.108.268303."},"date_published":"2012-06-29T00:00:00Z","scopus_import":"1","day":"29","article_processing_charge":"No","title":"Dynamic clustering in active colloidal suspensions with chemical signaling","status":"public","intvolume":" 108","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"9014","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"In this Letter, we explore experimentally the phase behavior of a dense active suspension of self-propelled colloids. In addition to a solidlike and gaslike phase observed for high and low densities, a novel cluster phase is reported at intermediate densities. This takes the form of a stationary assembly of dense aggregates—resulting from a permanent dynamical merging and separation of active colloids—whose average size grows with activity as a linear function of the self-propelling velocity. While different possible scenarios can be considered to account for these observations—such as a generic velocity weakening instability recently put forward—we show that the experimental results are reproduced mathematically by a chemotactic aggregation mechanism, originally introduced to account for bacterial aggregation and accounting here for diffusiophoretic chemical interaction between colloidal swimmers.","lang":"eng"}],"issue":"26","quality_controlled":"1","external_id":{"arxiv":["1202.6264"],"pmid":["23005020"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1202.6264"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.108.268303","month":"06","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"publication_status":"published","publisher":"American Physical Society ","year":"2012","pmid":1,"date_updated":"2023-02-23T13:46:45Z","date_created":"2021-01-19T10:26:59Z","volume":108,"author":[{"last_name":"Theurkauff","first_name":"I.","full_name":"Theurkauff, I."},{"full_name":"Cottin-Bizonne, C.","last_name":"Cottin-Bizonne","first_name":"C."},{"full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","first_name":"Jérémie A"},{"first_name":"C.","last_name":"Ybert","full_name":"Ybert, C."},{"last_name":"Bocquet","first_name":"L.","full_name":"Bocquet, L."}],"article_number":"268303","extern":"1"},{"month":"02","day":"07","language":[{"iso":"eng"}],"doi":"10.1063/1.3678593","date_published":"2012-02-07T00:00:00Z","quality_controlled":"1","publication":"Journal of Applied Physics","citation":{"mla":"Higginbotham, Andrew P., et al. “Identifying and Evaluating Organic Nonlinear Optical Materials via Molecular Moments.” Journal of Applied Physics, vol. 111, no. 3, 033512, American Institute of Physics, 2012, doi:10.1063/1.3678593.","short":"A.P. Higginbotham, J. Cole, M. Blood Forsythe, D. Hickstein, Journal of Applied Physics 111 (2012).","chicago":"Higginbotham, Andrew P, Jacqueline Cole, Martin Blood Forsythe, and Daniel Hickstein. “Identifying and Evaluating Organic Nonlinear Optical Materials via Molecular Moments.” Journal of Applied Physics. American Institute of Physics, 2012. https://doi.org/10.1063/1.3678593.","ama":"Higginbotham AP, Cole J, Blood Forsythe M, Hickstein D. Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. 2012;111(3). doi:10.1063/1.3678593","ista":"Higginbotham AP, Cole J, Blood Forsythe M, Hickstein D. 2012. Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. 111(3), 033512.","apa":"Higginbotham, A. P., Cole, J., Blood Forsythe, M., & Hickstein, D. (2012). Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. American Institute of Physics. https://doi.org/10.1063/1.3678593","ieee":"A. P. Higginbotham, J. Cole, M. Blood Forsythe, and D. Hickstein, “Identifying and evaluating organic nonlinear optical materials via molecular moments,” Journal of Applied Physics, vol. 111, no. 3. American Institute of Physics, 2012."},"extern":"1","abstract":[{"text":"We demonstrate how to appropriately estimate the zero-frequency (static) hyperpolarizability of an organic molecule from its charge distribution, and we explore applications of these estimates for identifying and evaluating new organic nonlinear optical (NLO) materials. First, we calculate hyperpolarizabilities from Hartree-Fock-derived charge distributions and find order-of-magnitude agreement with experimental values. We show that these simple arithmetic calculations will enable systematic searches for new organic NLO molecules. Second, we derive hyperpolarizabilities from crystallographic data using a multipolar charge-density analysis and find good agreement with empirical calculations. This demonstrates an experimental determination of the full static hyperpolarizability tensor in a solid-state sample. ","lang":"eng"}],"publist_id":"7963","issue":"3","article_number":"033512","type":"journal_article","date_created":"2018-12-11T11:44:35Z","date_updated":"2021-01-12T08:21:50Z","oa_version":"None","volume":111,"author":[{"full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","first_name":"Andrew P","last_name":"Higginbotham"},{"full_name":"Cole, Jacqueline","last_name":"Cole","first_name":"Jacqueline"},{"full_name":"Blood Forsythe, Martin","last_name":"Blood Forsythe","first_name":"Martin"},{"first_name":"Daniel","last_name":"Hickstein","full_name":"Hickstein, Daniel"}],"status":"public","publication_status":"published","title":"Identifying and evaluating organic nonlinear optical materials via molecular moments","publisher":"American Institute of Physics","intvolume":" 111","_id":"91","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by The Winston Churchill Foundation of the United States (A.P.H., M.A.B.F., D.D.H.), The Royal Society via a University Research Fellowship (J.M.C.), and the University of New Brunswick via The Vice-Chancellor’s Research Chair (J.M.C.)."},{"abstract":[{"text":"In models of radiative–convective equilibrium it is known that convection can spontaneously aggregate into one single localized moist region if the domain is large enough. The large changes in the mean climate state and radiative fluxes accompanying this self-aggregation raise questions as to what simulations at lower resolutions with parameterized convection, in similar homogeneous geometries, should be expected to produce to be considered successful in mimicking a cloud-resolving model.\r\nThe authors investigate this self-aggregation in a nonrotating, three-dimensional cloud-resolving model on a square domain without large-scale forcing. It is found that self-aggregation is sensitive not only to the domain size, but also to the horizontal resolution. With horizontally homogeneous initial conditions, convective aggregation only occurs on domains larger than about 200km and with resolutions coarser than about 2km in the model examined. The system exhibits hysteresis, so that with aggregated initial conditions, convection remains aggregated even at our finest resolution, 500m, as long as the domain is greater than 200–300km.\r\nThe sensitivity of self-aggregation to resolution and domain size in this model is due to the sensitivity of the distribution of low clouds to these two parameters. Indeed, the mechanism responsible for the aggregation of convection is the dynamical response to the longwave radiative cooling from low clouds. Strong longwave cooling near cloud top in dry regions forces downward motion, which by continuity generates inflow near cloud top and near-surface outflow from dry regions. This circulation results in the net export of moist static energy from regions with low moist static energy, yielding a positive feedback.","lang":"eng"}],"issue":"8","type":"journal_article","oa_version":"Published Version","status":"public","title":"Detailed investigation of the self-aggregation of convection in cloud-resolving simulations","intvolume":" 69","_id":"9142","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","article_processing_charge":"No","keyword":["Atmospheric Science"],"date_published":"2012-08-01T00:00:00Z","article_type":"original","page":"2551-2565","publication":"Journal of the Atmospheric Sciences","citation":{"ama":"Muller CJ, Held IM. Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. 2012;69(8):2551-2565. doi:10.1175/jas-d-11-0257.1","ieee":"C. J. Muller and I. M. Held, “Detailed investigation of the self-aggregation of convection in cloud-resolving simulations,” Journal of the Atmospheric Sciences, vol. 69, no. 8. American Meteorological Society, pp. 2551–2565, 2012.","apa":"Muller, C. J., & Held, I. M. (2012). Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. American Meteorological Society. https://doi.org/10.1175/jas-d-11-0257.1","ista":"Muller CJ, Held IM. 2012. Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. 69(8), 2551–2565.","short":"C.J. Muller, I.M. Held, Journal of the Atmospheric Sciences 69 (2012) 2551–2565.","mla":"Muller, Caroline J., and Isaac M. Held. “Detailed Investigation of the Self-Aggregation of Convection in Cloud-Resolving Simulations.” Journal of the Atmospheric Sciences, vol. 69, no. 8, American Meteorological Society, 2012, pp. 2551–65, doi:10.1175/jas-d-11-0257.1.","chicago":"Muller, Caroline J, and Isaac M. Held. “Detailed Investigation of the Self-Aggregation of Convection in Cloud-Resolving Simulations.” Journal of the Atmospheric Sciences. American Meteorological Society, 2012. https://doi.org/10.1175/jas-d-11-0257.1."},"extern":"1","date_created":"2021-02-15T14:39:03Z","date_updated":"2022-01-24T13:49:41Z","volume":69,"author":[{"first_name":"Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J"},{"full_name":"Held, Isaac M.","first_name":"Isaac M.","last_name":"Held"}],"publication_status":"published","publisher":"American Meteorological Society","year":"2012","month":"08","publication_identifier":{"issn":["0022-4928","1520-0469"]},"language":[{"iso":"eng"}],"doi":"10.1175/jas-d-11-0257.1","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1175/JAS-D-11-0257.1","open_access":"1"}],"oa":1},{"extern":"1","year":"2012","pmid":1,"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"DaZi"}],"author":[{"full_name":"Ibarra, Christian A.","last_name":"Ibarra","first_name":"Christian A."},{"full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi"},{"first_name":"Vera K.","last_name":"Schoft","full_name":"Schoft, Vera K."},{"full_name":"Hsieh, Tzung-Fu","first_name":"Tzung-Fu","last_name":"Hsieh"},{"full_name":"Uzawa, Rie","first_name":"Rie","last_name":"Uzawa"},{"full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues","first_name":"Jessica A."},{"first_name":"Assaf","last_name":"Zemach","full_name":"Zemach, Assaf"},{"last_name":"Chumak","first_name":"Nina","full_name":"Chumak, Nina"},{"full_name":"Machlicova, Adriana","first_name":"Adriana","last_name":"Machlicova"},{"full_name":"Nishimura, Toshiro","first_name":"Toshiro","last_name":"Nishimura"},{"full_name":"Rojas, Denisse","first_name":"Denisse","last_name":"Rojas"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."},{"first_name":"Hisashi","last_name":"Tamaru","full_name":"Tamaru, Hisashi"},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"}],"date_updated":"2021-12-14T08:28:51Z","date_created":"2021-06-04T07:51:31Z","volume":337,"month":"09","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"oa":1,"external_id":{"pmid":["22984074"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/","open_access":"1"}],"quality_controlled":"1","doi":"10.1126/science.1224839","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations."}],"issue":"6100","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9451","title":"Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes","status":"public","ddc":["580"],"intvolume":" 337","oa_version":"Published Version","scopus_import":"1","day":"14","has_accepted_license":"1","article_processing_charge":"No","publication":"Science","citation":{"ieee":"C. A. Ibarra et al., “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100. American Association for the Advancement of Science, pp. 1360–1364, 2012.","apa":"Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1224839","ista":"Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 337(6100), 1360–1364.","ama":"Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364. doi:10.1126/science.1224839","chicago":"Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839.","short":"C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H. Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.","mla":"Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science, vol. 337, no. 6100, American Association for the Advancement of Science, 2012, pp. 1360–64, doi:10.1126/science.1224839."},"article_type":"original","page":"1360-1364","date_published":"2012-09-14T00:00:00Z"},{"publication_status":"published","department":[{"_id":"DaZi"}],"publisher":"Cold Spring Harbor Laboratory Press","year":"2012","pmid":1,"date_created":"2021-06-08T13:01:23Z","date_updated":"2021-12-14T08:33:09Z","volume":77,"author":[{"last_name":"Coleman-Derr","first_name":"D.","full_name":"Coleman-Derr, D."},{"first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"extern":"1","quality_controlled":"1","external_id":{"pmid":["23250988"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/sqb.2012.77.014944"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1101/sqb.2012.77.014944","month":"12","publication_identifier":{"eissn":["1943-4456"],"issn":["0091-7451"]},"title":"DNA methylation, H2A.Z, and the regulation of constitutive expression","status":"public","intvolume":" 77","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9535","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The most well-studied function of DNA methylation in eukaryotic cells is the transcriptional silencing of genes and transposons. More recent results showed that many eukaryotes methylate the bodies of genes as well and that this methylation correlates with transcriptional activity rather than repression. The purpose of gene body methylation remains mysterious, but is potentially related to the histone variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and other investigators have shown that this relationship is likely to be the result of an ancient but unknown mechanism by which DNA methylation prevents the incorporation of H2A.Z. Recently, we discovered strong correlations between the presence of H2A.Z within gene bodies, the degree to which a gene's expression varies across tissue types or environmental conditions, and transcriptional misregulation in an h2a.z mutant. We propose that one basal function of gene body methylation is the establishment of constitutive expression patterns within housekeeping genes by excluding H2A.Z from their bodies."}],"article_type":"review","page":"147-154","publication":"Cold Spring Harbor Symposia on Quantitative Biology","citation":{"apa":"Coleman-Derr, D., & Zilberman, D. (2012). DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/sqb.2012.77.014944","ieee":"D. Coleman-Derr and D. Zilberman, “DNA methylation, H2A.Z, and the regulation of constitutive expression,” Cold Spring Harbor Symposia on Quantitative Biology, vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012.","ista":"Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 77, 147–154.","ama":"Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 2012;77:147-154. doi:10.1101/sqb.2012.77.014944","chicago":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Laboratory Press, 2012. https://doi.org/10.1101/sqb.2012.77.014944.","short":"D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative Biology 77 (2012) 147–154.","mla":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology, vol. 77, Cold Spring Harbor Laboratory Press, 2012, pp. 147–54, doi:10.1101/sqb.2012.77.014944."},"date_published":"2012-12-18T00:00:00Z","scopus_import":"1","day":"18","article_processing_charge":"No"},{"has_accepted_license":"1","day":"03","scopus_import":1,"date_published":"2012-04-03T00:00:00Z","citation":{"ista":"Konrad M, Vyleta M, Theis F, Stock M, Tragust S, Klatt M, Drescher V, Marr C, Ugelvig LV, Cremer S. 2012. Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biology. 10(4), e1001300.","ieee":"M. Konrad et al., “Social transfer of pathogenic fungus promotes active immunisation in ant colonies,” PLoS Biology, vol. 10, no. 4. Public Library of Science, 2012.","apa":"Konrad, M., Vyleta, M., Theis, F., Stock, M., Tragust, S., Klatt, M., … Cremer, S. (2012). Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1001300","ama":"Konrad M, Vyleta M, Theis F, et al. Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biology. 2012;10(4). doi:10.1371/journal.pbio.1001300","chicago":"Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Simon Tragust, Martina Klatt, Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer. “Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” PLoS Biology. Public Library of Science, 2012. https://doi.org/10.1371/journal.pbio.1001300.","mla":"Konrad, Matthias, et al. “Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” PLoS Biology, vol. 10, no. 4, e1001300, Public Library of Science, 2012, doi:10.1371/journal.pbio.1001300.","short":"M. Konrad, M. Vyleta, F. Theis, M. Stock, S. Tragust, M. Klatt, V. Drescher, C. Marr, L.V. Ugelvig, S. Cremer, PLoS Biology 10 (2012)."},"publication":"PLoS Biology","issue":"4","abstract":[{"lang":"eng","text":"Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”)."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"IST-2012-96-v1+1_journal.pbio.1001300.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":674228,"file_id":"4689","relation":"main_file","date_updated":"2020-07-14T12:46:04Z","date_created":"2018-12-12T10:08:28Z","checksum":"4ebacefd9fbab5c68adf829124115fd1"}],"pubrep_id":"96","intvolume":" 10","ddc":["570","579"],"status":"public","title":"Social transfer of pathogenic fungus promotes active immunisation in ant colonies","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3242","month":"04","language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.1001300","project":[{"grant_number":"CR-118/3-1","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution"},{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7","grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425"},{"_id":"25E0E184-B435-11E9-9278-68D0E5697425","name":"Antnet"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publist_id":"3434","ec_funded":1,"file_date_updated":"2020-07-14T12:46:04Z","article_number":"e1001300","volume":10,"date_updated":"2023-02-23T14:07:11Z","date_created":"2018-12-11T12:02:13Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9755"}]},"author":[{"last_name":"Konrad","first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","full_name":"Konrad, Matthias"},{"full_name":"Vyleta, Meghan","last_name":"Vyleta","first_name":"Meghan","id":"418901AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Theis, Fabian","last_name":"Theis","first_name":"Fabian"},{"full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","last_name":"Stock","first_name":"Miriam"},{"full_name":"Tragust, Simon","last_name":"Tragust","first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"id":"E60F29C6-E9AE-11E9-AF6E-D190C7302F38","first_name":"Martina","last_name":"Klatt","full_name":"Klatt, Martina"},{"full_name":"Drescher, Verena","first_name":"Verena","last_name":"Drescher"},{"full_name":"Marr, Carsten","first_name":"Carsten","last_name":"Marr"},{"full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","first_name":"Line V"},{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia"}],"publisher":"Public Library of Science","department":[{"_id":"SyCr"}],"publication_status":"published","year":"2012","acknowledgement":"Funding for this project was obtained by the German Research Foundation DFG (http://www.dfg.de/en/index.jsp) as an Individual Research Grant (CR118/2-1 to SC) and the European Research Council (http://erc.europa.eu/) in form of two ERC Starting Grants (ERC-2009-StG240371-SocialVaccines to SC and ERC-2010-StG259294-LatentCauses to FJT). In addition, the Junge Akademie (Young Academy of the Berlin-Brandenburg Academy of Sciences and Humanities and the National Academy of Sciences Leopoldina (http://www.diejungeakademie.de/english/index.html) funded this joint Antnet project of SC and FJT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."},{"doi":"10.5061/dryad.sv37s","date_published":"2012-09-27T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.sv37s"}],"oa":1,"citation":{"chicago":"Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Martina Klatt, Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer. “Data from: Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” Dryad, 2012. https://doi.org/10.5061/dryad.sv37s.","short":"M. Konrad, M. Vyleta, F. Theis, M. Stock, M. Klatt, V. Drescher, C. Marr, L.V. Ugelvig, S. Cremer, (2012).","mla":"Konrad, Matthias, et al. Data from: Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies. Dryad, 2012, doi:10.5061/dryad.sv37s.","ieee":"M. Konrad et al., “Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies.” Dryad, 2012.","apa":"Konrad, M., Vyleta, M., Theis, F., Stock, M., Klatt, M., Drescher, V., … Cremer, S. (2012). Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. Dryad. https://doi.org/10.5061/dryad.sv37s","ista":"Konrad M, Vyleta M, Theis F, Stock M, Klatt M, Drescher V, Marr C, Ugelvig LV, Cremer S. 2012. Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies, Dryad, 10.5061/dryad.sv37s.","ama":"Konrad M, Vyleta M, Theis F, et al. Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. 2012. doi:10.5061/dryad.sv37s"},"article_processing_charge":"No","month":"09","day":"27","oa_version":"Published Version","date_created":"2021-07-30T08:39:13Z","date_updated":"2023-02-23T11:18:41Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"3242"}]},"author":[{"full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad","first_name":"Matthias"},{"full_name":"Vyleta, Meghan","id":"418901AA-F248-11E8-B48F-1D18A9856A87","first_name":"Meghan","last_name":"Vyleta"},{"full_name":"Theis, Fabian","last_name":"Theis","first_name":"Fabian"},{"id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam","last_name":"Stock","full_name":"Stock, Miriam"},{"last_name":"Klatt","first_name":"Martina","id":"E60F29C6-E9AE-11E9-AF6E-D190C7302F38","full_name":"Klatt, Martina"},{"first_name":"Verena","last_name":"Drescher","full_name":"Drescher, Verena"},{"last_name":"Marr","first_name":"Carsten","full_name":"Marr, Carsten"},{"full_name":"Ugelvig, Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","first_name":"Line V","last_name":"Ugelvig"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"}],"publisher":"Dryad","department":[{"_id":"SyCr"}],"title":"Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies","status":"public","_id":"9755","year":"2012","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”)."}],"type":"research_data_reference"},{"article_processing_charge":"No","day":"14","month":"11","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.274b1","open_access":"1"}],"citation":{"mla":"Aeschbacher, Simon, et al. Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. Dryad, 2012, doi:10.5061/dryad.274b1.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, (2012).","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates.” Dryad, 2012. https://doi.org/10.5061/dryad.274b1.","ama":"Aeschbacher S, Futschik A, Beaumont M. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. 2012. doi:10.5061/dryad.274b1","ista":"Aeschbacher S, Futschik A, Beaumont M. 2012. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates, Dryad, 10.5061/dryad.274b1.","ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates.” Dryad, 2012.","apa":"Aeschbacher, S., Futschik, A., & Beaumont, M. (2012). Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. Dryad. https://doi.org/10.5061/dryad.274b1"},"date_published":"2012-11-14T00:00:00Z","doi":"10.5061/dryad.274b1","type":"research_data_reference","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"NiBa"}],"publisher":"Dryad","status":"public","title":"Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates","year":"2012","_id":"9758","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_updated":"2023-02-23T11:05:19Z","date_created":"2021-07-30T12:36:39Z","related_material":{"record":[{"id":"2944","status":"public","relation":"used_in_publication"}]},"author":[{"first_name":"Simon","last_name":"Aeschbacher","id":"2D35326E-F248-11E8-B48F-1D18A9856A87","full_name":"Aeschbacher, Simon"},{"last_name":"Futschik","first_name":"Andreas","full_name":"Futschik, Andreas"},{"last_name":"Beaumont","first_name":"Mark","full_name":"Beaumont, Mark"}]},{"abstract":[{"lang":"eng","text":"To fight infectious diseases, host immune defences are employed at multiple levels. Sanitary behaviour, such as pathogen avoidance and removal, acts as a first line of defence to prevent infection [1] before activation of the physiological immune system. Insect societies have evolved a wide range of collective hygiene measures and intensive health care towards pathogen-exposed group members [2]. One of the most common behaviours is allogrooming, in which nestmates remove infectious particles from the body surfaces of exposed individuals [3]. Here we show that, in invasive garden ants, grooming of fungus-exposed brood is effective beyond the sheer mechanical removal of fungal conidiospores as it also includes chemical disinfection through the application of poison produced by the ants themselves. Formic acid is the main active component of the poison. It inhibits fungal growth of conidiospores remaining on the brood surface after grooming and also those collected in the mouth of the grooming ant. This dual function is achieved by uptake of the poison droplet into the mouth through acidopore self-grooming and subsequent application onto the infectious brood via brood grooming. This extraordinary behaviour extends current understanding of grooming and the establishment of social immunity in insect societies."}],"type":"research_data_reference","date_updated":"2023-02-23T11:04:28Z","date_created":"2021-07-30T12:31:31Z","oa_version":"Published Version","author":[{"full_name":"Tragust, Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","last_name":"Tragust","first_name":"Simon"},{"full_name":"Mitteregger, Barbara","last_name":"Mitteregger","first_name":"Barbara","id":"479DDAAC-E9CD-11E9-9B5F-82450873F7A1"},{"last_name":"Barone","first_name":"Vanessa","orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","full_name":"Barone, Vanessa"},{"first_name":"Matthias","last_name":"Konrad","id":"46528076-F248-11E8-B48F-1D18A9856A87","full_name":"Konrad, Matthias"},{"full_name":"Ugelvig, Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","first_name":"Line V","last_name":"Ugelvig"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"related_material":{"record":[{"id":"2926","relation":"used_in_publication","status":"public"}]},"title":"Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison","status":"public","publisher":"Dryad","department":[{"_id":"SyCr"}],"year":"2012","_id":"9757","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"12","day":"14","article_processing_charge":"No","doi":"10.5061/dryad.61649","date_published":"2012-12-14T00:00:00Z","citation":{"short":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer, (2012).","mla":"Tragust, Simon, et al. Data from: Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison. Dryad, 2012, doi:10.5061/dryad.61649.","chicago":"Tragust, Simon, Barbara Mitteregger, Vanessa Barone, Matthias Konrad, Line V Ugelvig, and Sylvia Cremer. “Data from: Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” Dryad, 2012. https://doi.org/10.5061/dryad.61649.","ama":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. 2012. doi:10.5061/dryad.61649","apa":"Tragust, S., Mitteregger, B., Barone, V., Konrad, M., Ugelvig, L. V., & Cremer, S. (2012). Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Dryad. https://doi.org/10.5061/dryad.61649","ieee":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer, “Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison.” Dryad, 2012.","ista":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. 2012. Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison, Dryad, 10.5061/dryad.61649."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.61649","open_access":"1"}]},{"publication_identifier":{"issn":["0143-3857","1469-4417"]},"article_processing_charge":"No","month":"02","day":"01","keyword":["Applied Mathematics","General Mathematics"],"language":[{"iso":"eng"}],"date_published":"2012-02-01T00:00:00Z","doi":"10.1017/s0143385710000817","page":"159-165","article_type":"original","quality_controlled":"1","citation":{"ista":"Kaloshin V, KOZLOVSKI OS. 2012. A Cr unimodal map with an arbitrary fast growth of the number of periodic points. Ergodic Theory and Dynamical Systems. 32(1), 159–165.","ieee":"V. Kaloshin and O. S. KOZLOVSKI, “A Cr unimodal map with an arbitrary fast growth of the number of periodic points,” Ergodic Theory and Dynamical Systems, vol. 32, no. 1. Cambridge University Press, pp. 159–165, 2012.","apa":"Kaloshin, V., & KOZLOVSKI, O. S. (2012). A Cr unimodal map with an arbitrary fast growth of the number of periodic points. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/s0143385710000817","ama":"Kaloshin V, KOZLOVSKI OS. A Cr unimodal map with an arbitrary fast growth of the number of periodic points. Ergodic Theory and Dynamical Systems. 2012;32(1):159-165. doi:10.1017/s0143385710000817","chicago":"Kaloshin, Vadim, and O. S. KOZLOVSKI. “A Cr Unimodal Map with an Arbitrary Fast Growth of the Number of Periodic Points.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2012. https://doi.org/10.1017/s0143385710000817.","mla":"Kaloshin, Vadim, and O. S. KOZLOVSKI. “A Cr Unimodal Map with an Arbitrary Fast Growth of the Number of Periodic Points.” Ergodic Theory and Dynamical Systems, vol. 32, no. 1, Cambridge University Press, 2012, pp. 159–65, doi:10.1017/s0143385710000817.","short":"V. Kaloshin, O.S. KOZLOVSKI, Ergodic Theory and Dynamical Systems 32 (2012) 159–165."},"publication":"Ergodic Theory and Dynamical Systems","extern":"1","issue":"1","abstract":[{"text":"In this paper we present a surprising example of a Cr unimodal map of an interval f:I→I whose number of periodic points Pn(f)=∣{x∈I:fnx=x}∣ grows faster than any ahead given sequence along a subsequence nk=3k. This example also shows that ‘non-flatness’ of critical points is necessary for the Martens–de Melo–van Strien theorem [M. Martens, W. de Melo and S. van Strien. Julia–Fatou–Sullivan theory for real one-dimensional dynamics. Acta Math.168(3–4) (1992), 273–318] to hold.","lang":"eng"}],"type":"journal_article","oa_version":"None","volume":32,"date_updated":"2021-01-12T08:19:44Z","date_created":"2020-09-18T10:47:33Z","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","first_name":"Vadim","last_name":"Kaloshin","full_name":"Kaloshin, Vadim"},{"full_name":"KOZLOVSKI, O. S.","first_name":"O. S.","last_name":"KOZLOVSKI"}],"publisher":"Cambridge University Press","intvolume":" 32","status":"public","title":"A Cr unimodal map with an arbitrary fast growth of the number of periodic points","publication_status":"published","_id":"8504","year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","extern":"1","issue":"1","abstract":[{"lang":"eng","text":"We prove there are finitely many isometry classes of planar central configurations (also called relative equilibria) in the Newtonian 5-body problem, except perhaps if the 5-tuple of positive masses belongs to a given codimension 2 subvariety of the mass space."}],"intvolume":" 176","publisher":"Princeton University Press","publication_status":"published","title":"Finiteness of central configurations of five bodies in the plane","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8503","year":"2012","volume":176,"oa_version":"None","date_updated":"2021-01-12T08:19:44Z","date_created":"2020-09-18T10:47:24Z","author":[{"first_name":"Alain","last_name":"Albouy","full_name":"Albouy, Alain"},{"full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim"}],"publication_identifier":{"issn":["0003-486X"]},"article_processing_charge":"No","day":"01","month":"07","page":"535-588","quality_controlled":"1","article_type":"original","citation":{"chicago":"Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations of Five Bodies in the Plane.” Annals of Mathematics. Princeton University Press, 2012. https://doi.org/10.4007/annals.2012.176.1.10.","mla":"Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations of Five Bodies in the Plane.” Annals of Mathematics, vol. 176, no. 1, Princeton University Press, 2012, pp. 535–88, doi:10.4007/annals.2012.176.1.10.","short":"A. Albouy, V. Kaloshin, Annals of Mathematics 176 (2012) 535–588.","ista":"Albouy A, Kaloshin V. 2012. Finiteness of central configurations of five bodies in the plane. Annals of Mathematics. 176(1), 535–588.","apa":"Albouy, A., & Kaloshin, V. (2012). Finiteness of central configurations of five bodies in the plane. Annals of Mathematics. Princeton University Press. https://doi.org/10.4007/annals.2012.176.1.10","ieee":"A. Albouy and V. Kaloshin, “Finiteness of central configurations of five bodies in the plane,” Annals of Mathematics, vol. 176, no. 1. Princeton University Press, pp. 535–588, 2012.","ama":"Albouy A, Kaloshin V. Finiteness of central configurations of five bodies in the plane. Annals of Mathematics. 2012;176(1):535-588. doi:10.4007/annals.2012.176.1.10"},"publication":"Annals of Mathematics","language":[{"iso":"eng"}],"date_published":"2012-07-01T00:00:00Z","doi":"10.4007/annals.2012.176.1.10"},{"extern":1,"abstract":[{"lang":"eng","text":"A subject of extensive study in evolutionary theory has been the issue of how neutral, redundant copies can be maintained in the genome for long periods of time. Concurrently, examples of adaptive gene duplications to various environmental conditions in different species have been described. At this point, it is too early to tell whether or not a substantial fraction of gene copies have initially achieved fixation by positive selection for increased dosage. Nevertheless, enough examples have accumulated in the literature that such a possibility should be considered. Here, I review the recent examples of adaptive gene duplications and make an attempt to draw generalizations on what types of genes may be particularly prone to be selected for under certain environmental conditions. The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve our understanding of gene duplications as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications."}],"issue":"1749","publist_id":"6765","type":"journal_article","date_updated":"2021-01-12T08:21:16Z","date_created":"2018-12-11T11:49:01Z","volume":279,"author":[{"full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"}],"status":"public","publication_status":"published","title":"Gene duplication as a mechanism of genomic adaptation to a changing environment","publisher":"Royal Society, The","intvolume":" 279","_id":"887","year":"2012","acknowledgement":"The work was supported by a Plan Nacional grant no. BFU2009-09271 from the Spanish Ministry of Science and Innovation. The author is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist.","day":"01","month":"01","doi":"10.1098/rspb.2012.1108","date_published":"2012-01-01T00:00:00Z","quality_controlled":0,"page":"5048 - 5057","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"chicago":"Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation to a Changing Environment.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2012. https://doi.org/10.1098/rspb.2012.1108.","short":"F. Kondrashov, Proceedings of the Royal Society of London Series B Biological Sciences 279 (2012) 5048–5057.","mla":"Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation to a Changing Environment.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 279, no. 1749, Royal Society, The, 2012, pp. 5048–57, doi:10.1098/rspb.2012.1108.","apa":"Kondrashov, F. (2012). Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.1108","ieee":"F. Kondrashov, “Gene duplication as a mechanism of genomic adaptation to a changing environment,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 279, no. 1749. Royal Society, The, pp. 5048–5057, 2012.","ista":"Kondrashov F. 2012. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. 279(1749), 5048–5057.","ama":"Kondrashov F. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. 2012;279(1749):5048-5057. doi:10.1098/rspb.2012.1108"}},{"year":"2012","_id":"9049","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","status":"public","publication_status":"published","title":"Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis","intvolume":" 8","publisher":"Royal Society of Chemistry","author":[{"last_name":"Palacci","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A"},{"first_name":"Cécile","last_name":"Cottin-Bizonne","full_name":"Cottin-Bizonne, Cécile"},{"last_name":"Ybert","first_name":"Christophe","full_name":"Ybert, Christophe"},{"full_name":"Bocquet, Lydéric","last_name":"Bocquet","first_name":"Lydéric"}],"date_created":"2021-02-01T13:43:10Z","date_updated":"2023-02-23T13:47:31Z","oa_version":"None","volume":8,"type":"journal_article","abstract":[{"text":"Diffusiophoretic motion of colloids and macromolecules under salt gradients exhibits a logarithmic-sensing, i.e. the particle velocity is proportional to the spatial gradient of the logarithm of the salt concentration, as VDP = DDP∇logc. Here we explore experimentally the implications of this log-sensing behavior, on the basis of a hydrogel microfluidic device allowing to build spatially and temporally controlled gradients. We first demonstrate that the non-linearity of the salt-taxis leads to a trapping of particles under concentration gradient oscillations via a rectification of the motion. As an alternative, we make use of the high sensitivity of diffusiophoretic migration to vanishing salt concentration due to the log-sensing: in a counter-intuitive way, a vanishing gradient can lead to measurable velocity provided that the solute concentration is low enough, thus keeping ∇c/c finite. We show that this leads to a strong segregation of particles in osmotic shock configuration, resulting from a step change of the salt concentration at the boundaries. These various phenomena are rationalized on the basis of a theoretical description for the time-dependent Smoluchowski equation for the colloidal density.","lang":"eng"}],"issue":"4","extern":"1","publication":"Soft Matter","citation":{"apa":"Palacci, J. A., Cottin-Bizonne, C., Ybert, C., & Bocquet, L. (2012). Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c1sm06395b","ieee":"J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis,” Soft Matter, vol. 8, no. 4. Royal Society of Chemistry, pp. 980–994, 2012.","ista":"Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2012. Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. 8(4), 980–994.","ama":"Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. 2012;8(4):980-994. doi:10.1039/c1sm06395b","chicago":"Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Osmotic Traps for Colloids and Macromolecules Based on Logarithmic Sensing in Salt Taxis.” Soft Matter. Royal Society of Chemistry, 2012. https://doi.org/10.1039/c1sm06395b.","short":"J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Soft Matter 8 (2012) 980–994.","mla":"Palacci, Jérémie A., et al. “Osmotic Traps for Colloids and Macromolecules Based on Logarithmic Sensing in Salt Taxis.” Soft Matter, vol. 8, no. 4, Royal Society of Chemistry, 2012, pp. 980–94, doi:10.1039/c1sm06395b."},"quality_controlled":"1","article_type":"original","page":"980-994","date_published":"2012-01-28T00:00:00Z","doi":"10.1039/c1sm06395b","language":[{"iso":"eng"}],"scopus_import":"1","day":"28","month":"01","article_processing_charge":"No","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]}},{"publication":"Physical Review Letters","oa":1,"citation":{"ista":"Hannezo EB, Prost J, Joanny J. 2012. Mechanical instabilities of biological tubes. Physical Review Letters. 109(1).","apa":"Hannezo, E. B., Prost, J., & Joanny, J. (2012). Mechanical instabilities of biological tubes. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.109.018101","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Mechanical instabilities of biological tubes,” Physical Review Letters, vol. 109, no. 1. American Physical Society, 2012.","ama":"Hannezo EB, Prost J, Joanny J. Mechanical instabilities of biological tubes. Physical Review Letters. 2012;109(1). doi:10.1103/PhysRevLett.109.018101","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Mechanical Instabilities of Biological Tubes.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.109.018101.","mla":"Hannezo, Edouard B., et al. “Mechanical Instabilities of Biological Tubes.” Physical Review Letters, vol. 109, no. 1, American Physical Society, 2012, doi:10.1103/PhysRevLett.109.018101.","short":"E.B. Hannezo, J. Prost, J. Joanny, Physical Review Letters 109 (2012)."},"external_id":{"arxiv":["1207.1516"]},"main_file_link":[{"url":"https://arxiv.org/abs/1207.1516","open_access":"1"}],"date_published":"2012-07-03T00:00:00Z","doi":"10.1103/PhysRevLett.109.018101","language":[{"iso":"eng"}],"month":"07","day":"03","article_processing_charge":"No","_id":"922","year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Mechanical instabilities of biological tubes","publication_status":"published","intvolume":" 109","publisher":"American Physical Society","author":[{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"last_name":"Prost","first_name":"Jacques","full_name":"Prost, Jacques"},{"last_name":"Joanny","first_name":"Jean","full_name":"Joanny, Jean"}],"date_created":"2018-12-11T11:49:13Z","date_updated":"2021-01-12T08:21:56Z","oa_version":"Preprint","volume":109,"type":"journal_article","abstract":[{"lang":"eng","text":"We study theoretically the morphologies of biological tubes affected by various pathologies. When epithelial cells grow, the negative tension produced by their division provokes a buckling instability. Several shapes are investigated: varicose, dilated, sinuous, or sausagelike. They are all found in pathologies of tracheal, renal tubes, or arteries. The final shape depends crucially on the mechanical parameters of the tissues: Young's modulus, wall-to-lumen ratio, homeostatic pressure. We argue that since tissues must be in quasistatic mechanical equilibrium, abnormal shapes convey information as to what causes the pathology. We calculate a phase diagram of tubular instabilities which could be a helpful guide for investigating the underlying genetic regulation."}],"publist_id":"6519","issue":"1","extern":"1"},{"type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination. Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment levels of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying cell fates during growth and differentiation. H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism."}],"_id":"9499","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 8","title":"EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development","status":"public","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"22","citation":{"ista":"Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. 2012. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 8(3), e1002512.","ieee":"S. Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, and Z. R. Sung, “EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development,” PLoS Genetics, vol. 8, no. 3. Public Library of Science, 2012.","apa":"Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., & Sung, Z. R. (2012). EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002512","ama":"Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 2012;8(3). doi:10.1371/journal.pgen.1002512","chicago":"Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002512.","mla":"Kim, Sang Yeol, et al. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” PLoS Genetics, vol. 8, no. 3, e1002512, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002512.","short":"S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012)."},"publication":"PLoS Genetics","article_type":"original","date_published":"2012-03-22T00:00:00Z","article_number":"e1002512","extern":"1","pmid":1,"year":"2012","publisher":"Public Library of Science","department":[{"_id":"DaZi"}],"publication_status":"published","author":[{"full_name":"Kim, Sang Yeol","last_name":"Kim","first_name":"Sang Yeol"},{"full_name":"Lee, Jungeun","first_name":"Jungeun","last_name":"Lee"},{"first_name":"Leor","last_name":"Eshed-Williams","full_name":"Eshed-Williams, Leor"},{"full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"},{"full_name":"Sung, Z. Renee","last_name":"Sung","first_name":"Z. Renee"}],"volume":8,"date_created":"2021-06-07T11:07:56Z","date_updated":"2021-12-14T08:31:14Z","publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"month":"03","external_id":{"pmid":["22457632"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pgen.1002512"}],"quality_controlled":"1","doi":"10.1371/journal.pgen.1002512","language":[{"iso":"eng"}]},{"article_number":"e1002988","extern":"1","year":"2012","pmid":1,"publication_status":"published","department":[{"_id":"DaZi"}],"publisher":"Public Library of Science","author":[{"first_name":"Devin","last_name":"Coleman-Derr","full_name":"Coleman-Derr, Devin"},{"first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"date_updated":"2021-12-14T08:29:57Z","date_created":"2021-06-07T10:55:27Z","volume":8,"month":"10","publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"external_id":{"pmid":["23071449"]},"main_file_link":[{"url":"https://doi.org/10.1371/journal.pgen.1002988","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.1371/journal.pgen.1002988","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes."}],"issue":"10","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9497","status":"public","title":"Deposition of histone variant H2A.Z within gene bodies regulates responsive genes","intvolume":" 8","oa_version":"Published Version","scopus_import":"1","day":"11","article_processing_charge":"No","publication":"PLoS Genetics","citation":{"chicago":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002988.","mla":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics, vol. 8, no. 10, e1002988, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002988.","short":"D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012).","ista":"Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988.","ieee":"D. Coleman-Derr and D. Zilberman, “Deposition of histone variant H2A.Z within gene bodies regulates responsive genes,” PLoS Genetics, vol. 8, no. 10. Public Library of Science, 2012.","apa":"Coleman-Derr, D., & Zilberman, D. (2012). Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002988","ama":"Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 2012;8(10). doi:10.1371/journal.pgen.1002988"},"article_type":"original","date_published":"2012-10-11T00:00:00Z"},{"publication_identifier":{"issn":["0959-437X"]},"month":"04","doi":"10.1016/j.gde.2012.01.007","language":[{"iso":"eng"}],"external_id":{"pmid":["22336527"]},"quality_controlled":"1","extern":"1","author":[{"last_name":"Huff","first_name":"Jason T.","full_name":"Huff, Jason T."},{"full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"volume":22,"date_updated":"2021-12-14T08:32:38Z","date_created":"2021-06-08T08:58:52Z","pmid":1,"year":"2012","publisher":"Elsevier","department":[{"_id":"DaZi"}],"publication_status":"published","article_processing_charge":"No","scopus_import":"1","date_published":"2012-04-01T00:00:00Z","citation":{"ista":"Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 22(2), 132–138.","ieee":"J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision, and memory by plant chromatin organization,” Current Opinion in Genetics and Development, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.","apa":"Huff, J. T., & Zilberman, D. (2012). Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2012.01.007","ama":"Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 2012;22(2):132-138. doi:10.1016/j.gde.2012.01.007","chicago":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.01.007.","mla":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and Development, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:10.1016/j.gde.2012.01.007.","short":"J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138."},"publication":"Current Opinion in Genetics and Development","page":"132-138","article_type":"review","issue":"2","abstract":[{"text":"Accumulating evidence points toward diverse functions for plant chromatin. Remarkable progress has been made over the last few years in elucidating the mechanisms for a number of these functions. Activity of the histone demethylase IBM1 accurately targets DNA methylation to silent repeats and transposable elements, not to genes. A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes in sensing precise differences in ambient temperature and consequent gene regulation. Precise maintenance of chromosome number is assured by a histone modification that suppresses inappropriate DNA replication and by centromeric histone H3 regulation of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS C, the expression of which quantitatively measures the duration of cold exposure, functioning as memory of winter. These findings are a testament to the power of using plants to research chromatin organization, and demonstrate examples of how chromatin functions to achieve biological accuracy, precision, and memory.","lang":"eng"}],"type":"journal_article","oa_version":"None","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9528","intvolume":" 22","status":"public","title":"Regulation of biological accuracy, precision, and memory by plant chromatin organization"},{"month":"12","day":"13","doi":"10.1103/PhysRevB.86.224409","date_published":"2012-12-13T00:00:00Z","citation":{"mla":"Bieri, Samuel, et al. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics, vol. 86, no. 22, American Physical Society, 2012, doi:10.1103/PhysRevB.86.224409.","short":"S. Bieri, M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 86 (2012).","chicago":"Bieri, Samuel, Maksym Serbyn, Todadri Senthil, and Patrick Lee. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2012. https://doi.org/10.1103/PhysRevB.86.224409.","ama":"Bieri S, Serbyn M, Senthil T, Lee P. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 2012;86(22). doi:10.1103/PhysRevB.86.224409","ista":"Bieri S, Serbyn M, Senthil T, Lee P. 2012. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 86(22).","ieee":"S. Bieri, M. Serbyn, T. Senthil, and P. Lee, “Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice,” Physical Review B - Condensed Matter and Materials Physics, vol. 86, no. 22. American Physical Society, 2012.","apa":"Bieri, S., Serbyn, M., Senthil, T., & Lee, P. (2012). Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.86.224409"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1208.3231"}],"oa":1,"publication":"Physical Review B - Condensed Matter and Materials Physics","quality_controlled":0,"issue":"22","publist_id":"6431","abstract":[{"lang":"eng","text":"Motivated by recent experiments on Ba3NiSb2O 9, we investigate possible quantum spin liquid ground states for spin S=1 Heisenberg models on the triangular lattice. We use variational Monte Carlo techniques to calculate the energies of microscopic spin liquid wave functions where spin is represented by three flavors of fermionic spinon operators. These energies are compared with the energies of various competing three-sublattice ordered states. Our approach shows that the antiferromagnetic Heisenberg model with biquadratic term and single-ion anisotropy does not have a low-temperature spin liquid phase. However, for an SU(3)-invariant model with sufficiently strong ring-exchange terms, we find a paired chiral quantum spin liquid with a Fermi surface of deconfined spinons that is stable against all types of ordering patterns we considered. We discuss the physics of this exotic spin liquid state in relation to the recent experiment and suggest new ways to test this scenario."}],"extern":1,"type":"journal_article","author":[{"first_name":"Samuel","last_name":"Bieri","full_name":"Bieri, Samuel"},{"full_name":"Maksym Serbyn","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"full_name":"Senthil, Todadri S","last_name":"Senthil","first_name":"Todadri"},{"first_name":"Patrick","last_name":"Lee","full_name":"Lee, Patrick"}],"volume":86,"date_created":"2018-12-11T11:49:27Z","date_updated":"2021-01-12T08:22:18Z","_id":"966","acknowledgement":"We thank Kuang-Ting Chen, Rebecca Flint, Dmitri Ivanov, Z.-X. Liu, Tai-Kai Ng, Lara Thompson, Tamás Tóth, and Fa Wang for helpful discussions. T.S. is supported by NSF DMR 1005434. P.A.L. is supported by NSF DMR 1104498. S.B. acknowledges support from the Swiss National Science Foundation (SNSF).","year":"2012","publisher":"American Physical Society","intvolume":" 86","title":"Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice","publication_status":"published","status":"public"}]