[{"citation":{"chicago":"Clarke, Edmund M., Thomas A Henzinger, Helmut Veith, and Roderick Bloem. <i>Handbook of Model Checking</i>. 1st ed. Cham: Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-3-319-10575-8\">https://doi.org/10.1007/978-3-319-10575-8</a>.","short":"E.M. Clarke, T.A. Henzinger, H. Veith, R. Bloem, Handbook of Model Checking, 1st ed., Springer Nature, Cham, 2018.","ieee":"E. M. Clarke, T. A. Henzinger, H. Veith, and R. Bloem, <i>Handbook of Model Checking</i>, 1st ed. Cham: Springer Nature, 2018.","apa":"Clarke, E. M., Henzinger, T. A., Veith, H., &#38; Bloem, R. (2018). <i>Handbook of Model Checking</i> (1st ed.). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-10575-8\">https://doi.org/10.1007/978-3-319-10575-8</a>","mla":"Clarke, Edmund M., et al. <i>Handbook of Model Checking</i>. 1st ed., Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1007/978-3-319-10575-8\">10.1007/978-3-319-10575-8</a>.","ama":"Clarke EM, Henzinger TA, Veith H, Bloem R. <i>Handbook of Model Checking</i>. 1st ed. Cham: Springer Nature; 2018. doi:<a href=\"https://doi.org/10.1007/978-3-319-10575-8\">10.1007/978-3-319-10575-8</a>","ista":"Clarke EM, Henzinger TA, Veith H, Bloem R. 2018. Handbook of Model Checking 1st ed., Cham: Springer Nature, XLVIII, 1212p."},"page":"XLVIII, 1212","edition":"1","author":[{"first_name":"Edmund M.","full_name":"Clarke, Edmund M.","last_name":"Clarke"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Veith","first_name":"Helmut","full_name":"Veith, Helmut"},{"last_name":"Bloem","full_name":"Bloem, Roderick","first_name":"Roderick"}],"abstract":[{"lang":"eng","text":"This book first explores the origins of this idea, grounded in theoretical work on temporal logic and automata. The editors and authors are among the world's leading researchers in this domain, and they contributed 32 chapters representing a thorough view of the development and application of the technique. Topics covered include binary decision diagrams, symbolic model checking, satisfiability modulo theories, partial-order reduction, abstraction, interpolation, concurrency, security protocols, games, probabilistic model checking, and process algebra, and chapters on the transfer of theory to industrial practice, property specification languages for hardware, and verification of real-time systems and hybrid systems.\r\n\r\nThe book will be valuable for researchers and graduate students engaged with the development of formal methods and verification tools."}],"publist_id":"3340","date_updated":"2021-12-21T10:49:36Z","publication_identifier":{"eisbn":["978-3-319-10575-8"],"isbn":["978-3-319-10574-1"]},"publication_status":"published","day":"08","department":[{"_id":"ToHe"}],"fulldoi":"https://doi.org/10.1007/978-3-319-10575-8","doi":"10.1007/978-3-319-10575-8","publisher":"Springer Nature","article_processing_charge":"No","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:02:32Z","oa_version":"None","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","scopus_import":"1","title":"Handbook of Model Checking","quality_controlled":"1","type":"book","_id":"3300","status":"public","month":"06","date_published":"2018-06-08T00:00:00Z","year":"2018","place":"Cham"},{"publication_status":"published","department":[{"_id":"JiFr"}],"date_updated":"2023-09-19T10:00:46Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_updated":"2020-07-14T12:46:13Z","checksum":"34cb0a1611588b75bd6f4913fb4e30f1","relation":"main_file","file_id":"5741","file_name":"2018_JournalExperimBotany_Vu.pdf","content_type":"application/pdf","date_created":"2018-12-18T09:47:51Z","creator":"dernst","file_size":3359316,"access_level":"open_access"}],"quality_controlled":"1","intvolume":"        69","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2018-12-11T11:44:17Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-08-31T00:00:00Z","type":"journal_article","has_accepted_license":"1","issue":"19","citation":{"short":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624.","ieee":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet, “Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms,” <i>Journal of Experimental Botany</i>, vol. 69, no. 19. Oxford University Press, pp. 4609–4624, 2018.","mla":"Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” <i>Journal of Experimental Botany</i>, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:<a href=\"https://doi.org/10.1093/jxb/ery204\">10.1093/jxb/ery204</a>.","apa":"Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., &#38; De Smet, I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/ery204\">https://doi.org/10.1093/jxb/ery204</a>","ama":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. <i>Journal of Experimental Botany</i>. 2018;69(19):4609-4624. doi:<a href=\"https://doi.org/10.1093/jxb/ery204\">10.1093/jxb/ery204</a>","ista":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624.","chicago":"Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert, and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/jxb/ery204\">https://doi.org/10.1093/jxb/ery204</a>."},"page":"4609 - 4624","external_id":{"isi":["000443568700010"]},"volume":69,"acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","publist_id":"8019","day":"31","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:46:13Z","doi":"10.1093/jxb/ery204","publisher":"Oxford University Press","fulldoi":"https://doi.org/10.1093/jxb/ery204","ddc":["581"],"scopus_import":"1","title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms","article_processing_charge":"No","oa":1,"status":"public","_id":"36","month":"08","year":"2018","publication":"Journal of Experimental Botany","isi":1,"author":[{"first_name":"Lam","full_name":"Vu, Lam","last_name":"Vu"},{"first_name":"Tingting","full_name":"Zhu, Tingting","last_name":"Zhu"},{"last_name":"Verstraeten","orcid":"0000-0001-7241-2328","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge"},{"full_name":"Van De Cotte, Brigitte","first_name":"Brigitte","last_name":"Van De Cotte"},{"full_name":"Gevaert, Kris","first_name":"Kris","last_name":"Gevaert"},{"last_name":"De Smet","full_name":"De Smet, Ive","first_name":"Ive"}],"abstract":[{"lang":"eng","text":"Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity."}]},{"publist_id":"8018","volume":1863,"project":[{"call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord"}],"page":"47 - 63","citation":{"ieee":"M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube,” in <i>Morphogen Gradients </i>, vol. 1863, Springer Nature, 2018, pp. 47–63.","short":"M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63.","ista":"Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods in Molecular Biology, vol. 1863, 47–63.","ama":"Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: <i>Morphogen Gradients </i>. Vol 1863. MIMB. Springer Nature; 2018:47-63. doi:<a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">10.1007/978-1-4939-8772-6_4</a>","apa":"Zagórski, M. P., &#38; Kicheva, A. (2018). Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In <i>Morphogen Gradients </i> (Vol. 1863, pp. 47–63). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">https://doi.org/10.1007/978-1-4939-8772-6_4</a>","mla":"Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” <i>Morphogen Gradients </i>, vol. 1863, Springer Nature, 2018, pp. 47–63, doi:<a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">10.1007/978-1-4939-8772-6_4</a>.","chicago":"Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” In <i>Morphogen Gradients </i>, 1863:47–63. MIMB. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">https://doi.org/10.1007/978-1-4939-8772-6_4</a>."},"ec_funded":1,"has_accepted_license":"1","type":"book_chapter","date_published":"2018-10-16T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:17Z","oa_version":"Submitted Version","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"      1863","file":[{"success":1,"content_type":"application/pdf","file_name":"2018_MIMB_Zagorski.pdf","file_id":"8656","relation":"main_file","checksum":"2a97d0649fdcfcf1bdca7c8ad1dce71b","date_updated":"2020-10-13T14:20:37Z","access_level":"open_access","file_size":4906815,"creator":"dernst","date_created":"2020-10-13T14:20:37Z"}],"date_updated":"2025-04-14T07:27:29Z","department":[{"_id":"AnKi"}],"publication_status":"published","abstract":[{"text":"Developmental processes are inherently dynamic and understanding them requires quantitative measurements of gene and protein expression levels in space and time. While live imaging is a powerful approach for obtaining such data, it is still a challenge to apply it over long periods of time to large tissues, such as the embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression and signaling activity patterns in this organ can be studied by collecting tissue sections at different developmental stages. In combination with immunohistochemistry, this allows for measuring the levels of multiple developmental regulators in a quantitative manner with high spatiotemporal resolution. The mean protein expression levels over time, as well as embryo-to-embryo variability can be analyzed. A key aspect of the approach is the ability to compare protein levels across different samples. This requires a number of considerations in sample preparation, imaging and data analysis. Here we present a protocol for obtaining time course data of dorsoventral expression patterns from mouse and chick neural tube in the first 3 days of neural tube development. The described workflow starts from embryo dissection and ends with a processed dataset. Software scripts for data analysis are included. The protocol is adaptable and instructions that allow the user to modify different steps are provided. Thus, the procedure can be altered for analysis of time-lapse images and applied to systems other than the neural tube.","lang":"eng"}],"author":[{"last_name":"Zagórski","orcid":"0000-0001-7896-7762","first_name":"Marcin P","full_name":"Zagórski, Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva"}],"alternative_title":["Methods in Molecular Biology"],"publication":"Morphogen Gradients ","year":"2018","_id":"37","month":"10","status":"public","oa":1,"article_processing_charge":"No","title":"Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube","scopus_import":"1","fulldoi":"https://doi.org/10.1007/978-1-4939-8772-6_4","ddc":["570"],"publisher":"Springer Nature","file_date_updated":"2020-10-13T14:20:37Z","doi":"10.1007/978-1-4939-8772-6_4","publication_identifier":{"isbn":["978-1-4939-8771-9"],"issn":["1064-3745"]},"day":"16","series_title":"MIMB"},{"isi":1,"abstract":[{"text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.","lang":"eng"}],"author":[{"full_name":"Tavares, Hugo","first_name":"Hugo","last_name":"Tavares"},{"last_name":"Whitley","full_name":"Whitley, Annabel","first_name":"Annabel"},{"last_name":"Field","orcid":"0000-0002-4014-8478","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"},{"full_name":"Bradley, Desmond","first_name":"Desmond","last_name":"Bradley"},{"last_name":"Couchman","full_name":"Couchman, Matthew","first_name":"Matthew"},{"last_name":"Copsey","full_name":"Copsey, Lucy","first_name":"Lucy"},{"first_name":"Joane","full_name":"Elleouet, Joane","last_name":"Elleouet"},{"first_name":"Monique","full_name":"Burrus, Monique","last_name":"Burrus"},{"first_name":"Christophe","full_name":"Andalo, Christophe","last_name":"Andalo"},{"last_name":"Li","full_name":"Li, Miaomiao","first_name":"Miaomiao"},{"last_name":"Li","first_name":"Qun","full_name":"Li, Qun"},{"first_name":"Yongbiao","full_name":"Xue, Yongbiao","last_name":"Xue"},{"last_name":"Rebocho","full_name":"Rebocho, Alexandra B","first_name":"Alexandra B"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"first_name":"Enrico","full_name":"Coen, Enrico","last_name":"Coen"}],"pmid":1,"publisher":"National Academy of Sciences","file_date_updated":"2020-07-14T12:46:16Z","doi":"10.1073/pnas.1801832115","fulldoi":"https://doi.org/10.1073/pnas.1801832115","ddc":["570"],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","day":"23","publication_identifier":{"issn":["0027-8424"]},"year":"2018","_id":"38","month":"10","status":"public","publication":"PNAS","title":"Selection and gene flow shape genomic islands that control floral guides","scopus_import":"1","oa":1,"article_processing_charge":"No","external_id":{"pmid":["30297406"],"isi":["000448040500065"]},"page":"11006 - 11011","citation":{"ieee":"H. Tavares <i>et al.</i>, “Selection and gene flow shape genomic islands that control floral guides,” <i>PNAS</i>, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. <i>PNAS</i>. 2018;115(43):11006-11011. doi:<a href=\"https://doi.org/10.1073/pnas.1801832115\">10.1073/pnas.1801832115</a>","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” <i>PNAS</i>, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:<a href=\"https://doi.org/10.1073/pnas.1801832115\">10.1073/pnas.1801832115</a>.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1801832115\">https://doi.org/10.1073/pnas.1801832115</a>","chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1801832115\">https://doi.org/10.1073/pnas.1801832115</a>."},"issue":"43","publist_id":"8017","volume":115,"acknowledgement":" ERC Grant 201252 (to N.H.B.)","file":[{"access_level":"open_access","date_created":"2018-12-17T08:44:03Z","file_size":1911302,"creator":"dernst","content_type":"application/pdf","file_name":"11006.full.pdf","date_updated":"2020-07-14T12:46:16Z","file_id":"5683","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","relation":"main_file"}],"tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"department":[{"_id":"NiBa"}],"publication_status":"published","date_updated":"2025-07-10T11:52:32Z","date_published":"2018-10-23T00:00:00Z","has_accepted_license":"1","type":"journal_article","intvolume":"       115","quality_controlled":"1","date_created":"2018-12-11T11:44:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","language":[{"iso":"eng"}]},{"pubrep_id":"999","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2018-12-11T11:46:10Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","intvolume":"        10","type":"journal_article","has_accepted_license":"1","date_published":"2018-03-01T00:00:00Z","date_updated":"2023-09-11T13:56:52Z","publication_status":"published","department":[{"_id":"FyKo"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"access_level":"open_access","date_created":"2018-12-12T10:08:07Z","creator":"system","file_size":691602,"file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:16Z","relation":"main_file","checksum":"458a7c2c2e79528567edfeb0f326cbe0","file_id":"4667"}],"volume":10,"acknowledgement":"his work was supported by the Deutsche Forschungsgemeinschaft  (grant  number  FR  1411/9-1).  This work  was  supported  by  the  German  Research  Foundation (DFG) and the Technical University of Munich within the fund- ing programme Open Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont status of the organisms and Michael Galperin for\r\nuseful comments. T","publist_id":"7445","issue":"3","citation":{"chicago":"Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/gbe/evy049\">https://doi.org/10.1093/gbe/evy049</a>.","short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 928–938.","ieee":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss,” <i>Genome Biology and Evolution</i>, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018.","mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” <i>Genome Biology and Evolution</i>, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:<a href=\"https://doi.org/10.1093/gbe/evy049\">10.1093/gbe/evy049</a>.","apa":"Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., &#38; Frishman, D. (2018). Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evy049\">https://doi.org/10.1093/gbe/evy049</a>","ista":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 10(3), 928–938.","ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. <i>Genome Biology and Evolution</i>. 2018;10(3):928-938. doi:<a href=\"https://doi.org/10.1093/gbe/evy049\">10.1093/gbe/evy049</a>"},"page":"928 - 938","external_id":{"isi":["000429483700022"]},"article_processing_charge":"No","oa":1,"scopus_import":"1","title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","publication":"Genome Biology and Evolution","_id":"384","status":"public","month":"03","year":"2018","day":"01","fulldoi":"https://doi.org/10.1093/gbe/evy049","ddc":["576"],"doi":"10.1093/gbe/evy049","file_date_updated":"2020-07-14T12:46:16Z","publisher":"Oxford University Press","author":[{"first_name":"Peter","full_name":"Hönigschmid, Peter","last_name":"Hönigschmid"},{"full_name":"Bykova, Nadya","first_name":"Nadya","last_name":"Bykova"},{"last_name":"Schneider","first_name":"René","full_name":"Schneider, René"},{"last_name":"Ivankov","full_name":"Ivankov, Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry"},{"first_name":"Dmitrij","full_name":"Frishman, Dmitrij","last_name":"Frishman"}],"abstract":[{"lang":"eng","text":"Can orthologous proteins differ in terms of their ability to be secreted? To answer this question, we investigated the distribution of signal peptides within the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons revealed a large number of signal peptide gain and loss events, in which signal peptides emerge or disappear in the course of evolution. Signal peptide losses prevail over gains, an effect which is especially pronounced in the transition from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate decline in the number of signal peptide-containing proteins in endosymbionts cannot be explained by the overall reduction of their genomes. Signal peptides can be gained and lost either by acquisition/elimination of the corresponding N-terminal regions or by gradual accumulation of mutations. The evolutionary dynamics of signal peptides in bacterial proteins represents a powerful mechanism of functional diversification."}],"isi":1},{"article_type":"original","publication_status":"published","department":[{"_id":"NiBa"}],"date_updated":"2025-07-10T11:52:33Z","date_published":"2018-12-04T00:00:00Z","type":"journal_article","intvolume":"       210","quality_controlled":"1","oa_version":"Preprint","date_created":"2018-12-11T11:44:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/379578v1"}],"external_id":{"isi":["000452315900021"]},"page":"1411-1427","citation":{"chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.301429\">https://doi.org/10.1534/genetics.118.301429</a>.","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.","ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” <i>Genetics</i>, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” <i>Genetics</i>, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:<a href=\"https://doi.org/10.1534/genetics.118.301429\">10.1534/genetics.118.301429</a>.","apa":"Sachdeva, H., &#38; Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.301429\">https://doi.org/10.1534/genetics.118.301429</a>","ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. <i>Genetics</i>. 2018;210(4):1411-1427. doi:<a href=\"https://doi.org/10.1534/genetics.118.301429\">10.1534/genetics.118.301429</a>"},"issue":"4","volume":210,"publisher":"Genetics Society of America","doi":"10.1534/genetics.118.301429","fulldoi":"https://doi.org/10.1534/genetics.118.301429","day":"04","publication_identifier":{"issn":["0016-6731"]},"year":"2018","_id":"39","status":"public","month":"12","publication":"Genetics","title":"Replicability of introgression under linked, polygenic selection","scopus_import":"1","oa":1,"article_processing_charge":"No","isi":1,"abstract":[{"lang":"eng","text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation."}],"author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}]},{"date_published":"2018-01-10T00:00:00Z","type":"journal_article","arxiv":1,"quality_controlled":"1","intvolume":"        18","language":[{"iso":"eng"}],"oa_version":"Submitted Version","date_created":"2018-12-11T11:46:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","extern":"1","date_updated":"2021-01-12T07:53:20Z","publist_id":"7435","volume":18,"main_file_link":[{"url":"https://arxiv.org/abs/1712.07925","open_access":"1"}],"page":"223 - 228","citation":{"chicago":"Mahmood, Fahad, Zhanybek Alpichshev, Yi Lee, Jing Kong, and Nuh Gedik. “Observation of Exciton-Exciton Interaction Mediated Valley Depolarization in Monolayer MoSe2.” <i>Nano Letters</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acs.nanolett.7b03953\">https://doi.org/10.1021/acs.nanolett.7b03953</a>.","ama":"Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. <i>Nano Letters</i>. 2018;18(1):223-228. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.7b03953\">10.1021/acs.nanolett.7b03953</a>","ista":"Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. 2018. Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. 18(1), 223–228.","apa":"Mahmood, F., Alpichshev, Z., Lee, Y., Kong, J., &#38; Gedik, N. (2018). Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.7b03953\">https://doi.org/10.1021/acs.nanolett.7b03953</a>","mla":"Mahmood, Fahad, et al. “Observation of Exciton-Exciton Interaction Mediated Valley Depolarization in Monolayer MoSe2.” <i>Nano Letters</i>, vol. 18, no. 1, American Chemical Society, 2018, pp. 223–28, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.7b03953\">10.1021/acs.nanolett.7b03953</a>.","ieee":"F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, and N. Gedik, “Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2,” <i>Nano Letters</i>, vol. 18, no. 1. American Chemical Society, pp. 223–228, 2018.","short":"F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, N. Gedik, Nano Letters 18 (2018) 223–228."},"external_id":{"arxiv":["1712.07925"]},"issue":"1","status":"public","month":"01","_id":"394","year":"2018","publication":"Nano Letters","title":"Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2","oa":1,"doi":"10.1021/acs.nanolett.7b03953","publisher":"American Chemical Society","fulldoi":"https://doi.org/10.1021/acs.nanolett.7b03953","day":"10","abstract":[{"text":"The valley pseudospin in monolayer transition metal dichalcogenides (TMDs) has been proposed as a new way to manipulate information in various optoelectronic devices. This relies on a large valley polarization that remains stable over long time scales (hundreds of nanoseconds). However, time-resolved measurements report valley lifetimes of only a few picoseconds. This has been attributed to mechanisms such as phonon-mediated intervalley scattering and a precession of the valley pseudospin through electron-hole exchange. Here we use transient spin grating to directly measure the valley depolarization lifetime in monolayer MoSe2. We find a fast valley decay rate that scales linearly with the excitation density at different temperatures. This establishes the presence of strong exciton-exciton Coulomb exchange interactions enhancing the valley depolarization. Our work highlights the microscopic processes inhibiting the efficient use of the exciton valley pseudospin in monolayer TMDs. ","lang":"eng"}],"author":[{"last_name":"Mahmood","first_name":"Fahad","full_name":"Mahmood, Fahad"},{"id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Alpichshev, Zhanybek","first_name":"Zhanybek","orcid":"0000-0002-7183-5203","last_name":"Alpichshev"},{"first_name":"Yi","full_name":"Lee, Yi","last_name":"Lee"},{"last_name":"Kong","full_name":"Kong, Jing","first_name":"Jing"},{"last_name":"Gedik","first_name":"Nuh","full_name":"Gedik, Nuh"}]},{"date_updated":"2023-09-11T14:10:25Z","publication_status":"published","department":[{"_id":"DaAl"}],"type":"conference","date_published":"2018-02-10T00:00:00Z","date_created":"2018-12-11T11:46:14Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","language":[{"iso":"eng"}],"intvolume":"        53","quality_controlled":"1","external_id":{"isi":["000446161100002"]},"citation":{"chicago":"Arbel Raviv, Maya, and Trevor A Brown. “Harnessing Epoch-Based Reclamation for Efficient Range Queries,” 53:14–27. ACM, 2018. <a href=\"https://doi.org/10.1145/3178487.3178489\">https://doi.org/10.1145/3178487.3178489</a>.","ieee":"M. Arbel Raviv and T. A. Brown, “Harnessing epoch-based reclamation for efficient range queries,” presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria, 2018, vol. 53, no. 1, pp. 14–27.","short":"M. Arbel Raviv, T.A. Brown, in:, ACM, 2018, pp. 14–27.","ista":"Arbel Raviv M, Brown TA. 2018. Harnessing epoch-based reclamation for efficient range queries. PPoPP: Principles and Practice of Parallel Programming, PPoPP, vol. 53, 14–27.","ama":"Arbel Raviv M, Brown TA. Harnessing epoch-based reclamation for efficient range queries. In: Vol 53. ACM; 2018:14-27. doi:<a href=\"https://doi.org/10.1145/3178487.3178489\">10.1145/3178487.3178489</a>","apa":"Arbel Raviv, M., &#38; Brown, T. A. (2018). Harnessing epoch-based reclamation for efficient range queries (Vol. 53, pp. 14–27). Presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria: ACM. <a href=\"https://doi.org/10.1145/3178487.3178489\">https://doi.org/10.1145/3178487.3178489</a>","mla":"Arbel Raviv, Maya, and Trevor A. Brown. <i>Harnessing Epoch-Based Reclamation for Efficient Range Queries</i>. Vol. 53, no. 1, ACM, 2018, pp. 14–27, doi:<a href=\"https://doi.org/10.1145/3178487.3178489\">10.1145/3178487.3178489</a>."},"page":"14 - 27","issue":"1","publist_id":"7430","volume":53,"fulldoi":"https://doi.org/10.1145/3178487.3178489","publisher":"ACM","doi":"10.1145/3178487.3178489","publication_identifier":{"isbn":["978-1-4503-4982-6"]},"day":"10","conference":{"start_date":"2018-02-24","location":"Vienna, Austria","name":"PPoPP: Principles and Practice of Parallel Programming","end_date":"2018-02-28"},"alternative_title":["PPoPP"],"year":"2018","month":"02","_id":"397","status":"public","article_processing_charge":"No","title":"Harnessing epoch-based reclamation for efficient range queries","scopus_import":"1","isi":1,"abstract":[{"text":"Concurrent sets with range query operations are highly desirable in applications such as in-memory databases. However, few set implementations offer range queries. Known techniques for augmenting data structures with range queries (or operations that can be used to build range queries) have numerous problems that limit their usefulness. For example, they impose high overhead or rely heavily on garbage collection. In this work, we show how to augment data structures with highly efficient range queries, without relying on garbage collection. We identify a property of epoch-based memory reclamation algorithms that makes them ideal for implementing range queries, and produce three algorithms, which use locks, transactional memory and lock-free techniques, respectively. Our algorithms are applicable to more data structures than previous work, and are shown to be highly efficient on a large scale Intel system. ","lang":"eng"}],"author":[{"last_name":"Arbel Raviv","first_name":"Maya","full_name":"Arbel Raviv, Maya"},{"first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A","last_name":"Brown"}]},{"page":"e568-e578","citation":{"short":"P. Dodier, J. Frischer, W. Wang, T. Auzinger, A. Mallouhi, W. Serles, A. Gruber, E. Knosp, G. Bavinzski, World Neurosurgery 13 (2018) e568–e578.","ieee":"P. Dodier <i>et al.</i>, “Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device,” <i>World Neurosurgery</i>, vol. 13. Elsevier, pp. e568–e578, 2018.","apa":"Dodier, P., Frischer, J., Wang, W., Auzinger, T., Mallouhi, A., Serles, W., … Bavinzski, G. (2018). Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. <i>World Neurosurgery</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.wneu.2018.02.096\">https://doi.org/10.1016/j.wneu.2018.02.096</a>","mla":"Dodier, Philippe, et al. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” <i>World Neurosurgery</i>, vol. 13, Elsevier, 2018, pp. e568–78, doi:<a href=\"https://doi.org/10.1016/j.wneu.2018.02.096\">10.1016/j.wneu.2018.02.096</a>.","ama":"Dodier P, Frischer J, Wang W, et al. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. <i>World Neurosurgery</i>. 2018;13:e568-e578. doi:<a href=\"https://doi.org/10.1016/j.wneu.2018.02.096\">10.1016/j.wneu.2018.02.096</a>","ista":"Dodier P, Frischer J, Wang W, Auzinger T, Mallouhi A, Serles W, Gruber A, Knosp E, Bavinzski G. 2018. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 13, e568–e578.","chicago":"Dodier, Philippe, Josa Frischer, Wei Wang, Thomas Auzinger, Ammar Mallouhi, Wolfgang Serles, Andreas Gruber, Engelbert Knosp, and Gerhard Bavinzski. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” <i>World Neurosurgery</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.wneu.2018.02.096\">https://doi.org/10.1016/j.wneu.2018.02.096</a>."},"external_id":{"isi":["000432942700070"]},"publist_id":"7431","volume":13,"department":[{"_id":"BeBi"}],"publication_status":"published","date_updated":"2023-09-11T14:12:33Z","date_published":"2018-05-01T00:00:00Z","type":"journal_article","intvolume":"        13","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","date_created":"2018-12-11T11:46:15Z","isi":1,"abstract":[{"lang":"eng","text":"Objective: To report long-term results after Pipeline Embolization Device (PED) implantation, characterize complex and standard aneurysms comprehensively, and introduce a modified flow disruption scale. Methods: We retrospectively reviewed a consecutive series of 40 patients harboring 59 aneurysms treated with 54 PEDs. Aneurysm complexity was assessed using our proposed classification. Immediate angiographic results were analyzed using previously published grading scales and our novel flow disruption scale. Results: According to our new definition, 46 (78%) aneurysms were classified as complex. Most PED interventions were performed in the paraophthalmic and cavernous internal carotid artery segments. Excellent neurologic outcome (modified Rankin Scale 0 and 1) was observed in 94% of patients. Our data showed low permanent procedure-related mortality (0%) and morbidity (3%) rates. Long-term angiographic follow-up showed complete occlusion in 81% and near-total obliteration in a further 14%. Complete obliteration after deployment of a single PED was achieved in all standard aneurysms with 1-year follow-up. Our new scale was an independent predictor of aneurysm occlusion in a multivariable analysis. All aneurysms with a high flow disruption grade showed complete occlusion at follow-up regardless of PED number or aneurysm complexity. Conclusions: Treatment with the PED should be recognized as a primary management strategy for a highly selected cohort with predominantly complex intracranial aneurysms. We further show that a priori assessment of aneurysm complexity and our new postinterventional angiographic flow disruption scale predict occlusion probability and may help to determine the adequate number of per-aneurysm devices."}],"author":[{"last_name":"Dodier","full_name":"Dodier, Philippe","first_name":"Philippe"},{"full_name":"Frischer, Josa","first_name":"Josa","last_name":"Frischer"},{"full_name":"Wang, Wei","first_name":"Wei","last_name":"Wang"},{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","full_name":"Auzinger, Thomas","first_name":"Thomas","orcid":"0000-0002-1546-3265","last_name":"Auzinger"},{"last_name":"Mallouhi","first_name":"Ammar","full_name":"Mallouhi, Ammar"},{"first_name":"Wolfgang","full_name":"Serles, Wolfgang","last_name":"Serles"},{"last_name":"Gruber","full_name":"Gruber, Andreas","first_name":"Andreas"},{"first_name":"Engelbert","full_name":"Knosp, Engelbert","last_name":"Knosp"},{"last_name":"Bavinzski","first_name":"Gerhard","full_name":"Bavinzski, Gerhard"}],"doi":"10.1016/j.wneu.2018.02.096","publisher":"Elsevier","fulldoi":"https://doi.org/10.1016/j.wneu.2018.02.096","day":"01","status":"public","_id":"398","month":"05","year":"2018","publication":"World Neurosurgery","scopus_import":"1","title":"Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device","article_processing_charge":"No"},{"scopus_import":"1","title":"Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation","article_processing_charge":"No","oa":1,"_id":"399","status":"public","month":"01","year":"2018","publication":"EPL","day":"01","doi":"10.1209/0295-5075/121/10007","publisher":"IOP Publishing","fulldoi":"https://doi.org/10.1209/0295-5075/121/10007","author":[{"first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","full_name":"Napiórkowski, Marcin M","last_name":"Napiórkowski"},{"first_name":"Robin","full_name":"Reuvers, Robin","last_name":"Reuvers"},{"last_name":"Solovej","full_name":"Solovej, Jan","first_name":"Jan"}],"abstract":[{"text":"Following an earlier calculation in 3D, we calculate the 2D critical temperature of a dilute, translation-invariant Bose gas using a variational formulation of the Bogoliubov approximation introduced by Critchley and Solomon in 1976. This provides the first analytical calculation of the Kosterlitz-Thouless transition temperature that includes the constant in the logarithm.","lang":"eng"}],"isi":1,"article_number":"10007","arxiv":1,"quality_controlled":"1","intvolume":"       121","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:46:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_published":"2018-01-01T00:00:00Z","type":"journal_article","publication_status":"published","department":[{"_id":"RoSe"}],"date_updated":"2025-04-15T08:26:14Z","article_type":"original","project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"acknowledgement":"We thank Robert Seiringer and Daniel Ueltschi for bringing the issue of the change in critical temperature to our attention. We also thank the Erwin Schrödinger Institute (all authors) and the Department of Mathematics, University of Copenhagen (MN) for the hospitality during the period this work was carried out. We gratefully acknowledge the financial support by the European Unions Seventh Framework Programme under the ERC Grant Agreement Nos. 321029 (JPS and RR) and 337603 (RR) as well as support by the VIL-LUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059) (JPS and RR), by the National Science Center (NCN) under grant No. 2016/21/D/ST1/02430 and the Austrian Science Fund (FWF) through project No. P 27533-N27 (MN).","volume":121,"publist_id":"7432","issue":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.01822"}],"citation":{"chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” <i>EPL</i>. IOP Publishing, 2018. <a href=\"https://doi.org/10.1209/0295-5075/121/10007\">https://doi.org/10.1209/0295-5075/121/10007</a>.","mla":"Napiórkowski, Marcin M., et al. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” <i>EPL</i>, vol. 121, no. 1, 10007, IOP Publishing, 2018, doi:<a href=\"https://doi.org/10.1209/0295-5075/121/10007\">10.1209/0295-5075/121/10007</a>.","apa":"Napiórkowski, M. M., Reuvers, R., &#38; Solovej, J. (2018). Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. <i>EPL</i>. IOP Publishing. <a href=\"https://doi.org/10.1209/0295-5075/121/10007\">https://doi.org/10.1209/0295-5075/121/10007</a>","ama":"Napiórkowski MM, Reuvers R, Solovej J. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. <i>EPL</i>. 2018;121(1). doi:<a href=\"https://doi.org/10.1209/0295-5075/121/10007\">10.1209/0295-5075/121/10007</a>","ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 121(1), 10007.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, EPL 121 (2018).","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation,” <i>EPL</i>, vol. 121, no. 1. IOP Publishing, 2018."},"external_id":{"arxiv":["1706.01822"],"isi":["000460003000003"]}},{"related_material":{"record":[{"id":"9805","relation":"research_data","status":"public"}]},"abstract":[{"lang":"eng","text":"Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance."}],"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"pmid":1,"isi":1,"corr_author":"1","_id":"40","status":"public","month":"12","year":"2018","publication":"Molecular Ecology","scopus_import":"1","title":"The consequences of an introgression event","article_processing_charge":"Yes (via OA deal)","oa":1,"file_date_updated":"2020-07-14T12:46:22Z","doi":"10.1111/mec.14950","publisher":"Wiley","ddc":["576"],"fulldoi":"https://doi.org/10.1111/mec.14950","day":"31","publication_identifier":{"issn":["1365-294X"]},"publist_id":"8014","volume":27,"citation":{"chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” <i>Molecular Ecology</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/mec.14950\">https://doi.org/10.1111/mec.14950</a>.","short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975.","ieee":"N. H. Barton, “The consequences of an introgression event,” <i>Molecular Ecology</i>, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.","apa":"Barton, N. H. (2018). The consequences of an introgression event. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.14950\">https://doi.org/10.1111/mec.14950</a>","mla":"Barton, Nicholas H. “The Consequences of an Introgression Event.” <i>Molecular Ecology</i>, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:<a href=\"https://doi.org/10.1111/mec.14950\">10.1111/mec.14950</a>.","ama":"Barton NH. The consequences of an introgression event. <i>Molecular Ecology</i>. 2018;27(24):4973-4975. doi:<a href=\"https://doi.org/10.1111/mec.14950\">10.1111/mec.14950</a>","ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975."},"page":"4973-4975","external_id":{"isi":["000454600500001"],"pmid":["30599087"]},"issue":"24","date_published":"2018-12-31T00:00:00Z","type":"journal_article","has_accepted_license":"1","quality_controlled":"1","intvolume":"        27","language":[{"iso":"eng"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:18Z","article_type":"letter_note","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_name":"2018_MolecularEcology_BartonNick.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:22Z","relation":"main_file","file_id":"6652","access_level":"open_access","date_created":"2019-07-19T06:54:46Z","creator":"apreinsp","file_size":295452}],"publication_status":"published","department":[{"_id":"NiBa"}],"date_updated":"2025-07-10T11:52:34Z"},{"intvolume":"        19","quality_controlled":"1","date_created":"2018-12-11T11:46:15Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","pubrep_id":"1011","language":[{"iso":"eng"}],"date_published":"2018-05-01T00:00:00Z","has_accepted_license":"1","type":"journal_article","publication_status":"published","department":[{"_id":"RoSe"}],"date_updated":"2025-04-14T07:26:53Z","file":[{"creator":"system","file_size":582680,"date_created":"2018-12-12T10:12:47Z","access_level":"open_access","relation":"main_file","checksum":"04d2c9bd7cbf3ca1d7acaaf4e7dca3e5","file_id":"4966","date_updated":"2020-07-14T12:46:22Z","file_name":"IST-2018-1011-v1+1_2018_Deuchert_Persistence.pdf","content_type":"application/pdf"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"volume":19,"publist_id":"7429","ec_funded":1,"issue":"5","external_id":{"isi":["000429799900008"]},"citation":{"chicago":"Deuchert, Andreas, Alissa Geisinge, Christian Hainzl, and Michael Loss. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” <i>Annales Henri Poincare</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00023-018-0665-7\">https://doi.org/10.1007/s00023-018-0665-7</a>.","mla":"Deuchert, Andreas, et al. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” <i>Annales Henri Poincare</i>, vol. 19, no. 5, Springer, 2018, pp. 1507–27, doi:<a href=\"https://doi.org/10.1007/s00023-018-0665-7\">10.1007/s00023-018-0665-7</a>.","apa":"Deuchert, A., Geisinge, A., Hainzl, C., &#38; Loss, M. (2018). Persistence of translational symmetry in the BCS model with radial pair interaction. <i>Annales Henri Poincare</i>. Springer. <a href=\"https://doi.org/10.1007/s00023-018-0665-7\">https://doi.org/10.1007/s00023-018-0665-7</a>","ama":"Deuchert A, Geisinge A, Hainzl C, Loss M. Persistence of translational symmetry in the BCS model with radial pair interaction. <i>Annales Henri Poincare</i>. 2018;19(5):1507-1527. doi:<a href=\"https://doi.org/10.1007/s00023-018-0665-7\">10.1007/s00023-018-0665-7</a>","ista":"Deuchert A, Geisinge A, Hainzl C, Loss M. 2018. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 19(5), 1507–1527.","short":"A. Deuchert, A. Geisinge, C. Hainzl, M. Loss, Annales Henri Poincare 19 (2018) 1507–1527.","ieee":"A. Deuchert, A. Geisinge, C. Hainzl, and M. Loss, “Persistence of translational symmetry in the BCS model with radial pair interaction,” <i>Annales Henri Poincare</i>, vol. 19, no. 5. Springer, pp. 1507–1527, 2018."},"page":"1507 - 1527","title":"Persistence of translational symmetry in the BCS model with radial pair interaction","scopus_import":"1","oa":1,"article_processing_charge":"Yes (via OA deal)","year":"2018","status":"public","_id":"400","month":"05","publication":"Annales Henri Poincare","day":"01","publisher":"Springer","file_date_updated":"2020-07-14T12:46:22Z","doi":"10.1007/s00023-018-0665-7","ddc":["510"],"fulldoi":"https://doi.org/10.1007/s00023-018-0665-7","author":[{"last_name":"Deuchert","full_name":"Deuchert, Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3146-6746","first_name":"Andreas"},{"full_name":"Geisinge, Alissa","first_name":"Alissa","last_name":"Geisinge"},{"last_name":"Hainzl","full_name":"Hainzl, Christian","first_name":"Christian"},{"full_name":"Loss, Michael","first_name":"Michael","last_name":"Loss"}],"abstract":[{"text":"We consider the two-dimensional BCS functional with a radial pair interaction. We show that the translational symmetry is not broken in a certain temperature interval below the critical temperature. In the case of vanishing angular momentum, our results carry over to the three-dimensional case.","lang":"eng"}],"corr_author":"1","isi":1},{"publist_id":"7427","volume":9,"citation":{"ama":"Qin X, Hannezo EB, Mangeat T, et al. A biochemical network controlling basal myosin oscillation. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-018-03574-5\">10.1038/s41467-018-03574-5</a>","ista":"Qin X, Hannezo EB, Mangeat T, Liu C, Majumder P, Liu J, Choesmel Cadamuro V, Mcdonald J, Liu Y, Yi B, Wang X. 2018. A biochemical network controlling basal myosin oscillation. Nature Communications. 9(1), 1210.","apa":"Qin, X., Hannezo, E. B., Mangeat, T., Liu, C., Majumder, P., Liu, J., … Wang, X. (2018). A biochemical network controlling basal myosin oscillation. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-018-03574-5\">https://doi.org/10.1038/s41467-018-03574-5</a>","mla":"Qin, Xiang, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” <i>Nature Communications</i>, vol. 9, no. 1, 1210, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-03574-5\">10.1038/s41467-018-03574-5</a>.","ieee":"X. Qin <i>et al.</i>, “A biochemical network controlling basal myosin oscillation,” <i>Nature Communications</i>, vol. 9, no. 1. Nature Publishing Group, 2018.","short":"X. Qin, E.B. Hannezo, T. Mangeat, C. Liu, P. Majumder, J. Liu, V. Choesmel Cadamuro, J. Mcdonald, Y. Liu, B. Yi, X. Wang, Nature Communications 9 (2018).","chicago":"Qin, Xiang, Edouard B Hannezo, Thomas Mangeat, Chang Liu, Pralay Majumder, Jjiaying Liu, Valerie Choesmel Cadamuro, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” <i>Nature Communications</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41467-018-03574-5\">https://doi.org/10.1038/s41467-018-03574-5</a>."},"external_id":{"isi":["000428165400009"]},"issue":"1","type":"journal_article","has_accepted_license":"1","date_published":"2018-03-23T00:00:00Z","language":[{"iso":"eng"}],"pubrep_id":"996","oa_version":"Published Version","date_created":"2018-12-11T11:46:16Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"         9","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_id":"4902","checksum":"87a427bc2e8724be3dd22a4efdd21a33","relation":"main_file","date_updated":"2020-07-14T12:46:22Z","content_type":"application/pdf","file_name":"IST-2018-996-v1+1_2018_Hannezo_A-biochemical.pdf","file_size":3780491,"creator":"system","date_created":"2018-12-12T10:11:45Z","access_level":"open_access"}],"date_updated":"2023-09-08T11:41:45Z","publication_status":"published","department":[{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"The actomyosin cytoskeleton, a key stress-producing unit in epithelial cells, oscillates spontaneously in a wide variety of systems. Although much of the signal cascade regulating myosin activity has been characterized, the origin of such oscillatory behavior is still unclear. Here, we show that basal myosin II oscillation in Drosophila ovarian epithelium is not controlled by actomyosin cortical tension, but instead relies on a biochemical oscillator involving ROCK and myosin phosphatase. Key to this oscillation is a diffusive ROCK flow, linking junctional Rho1 to medial actomyosin cortex, and dynamically maintained by a self-activation loop reliant on ROCK kinase activity. In response to the resulting myosin II recruitment, myosin phosphatase is locally enriched and shuts off ROCK and myosin II signals. Coupling Drosophila genetics, live imaging, modeling, and optogenetics, we uncover an intrinsic biochemical oscillator at the core of myosin II regulatory network, shedding light on the spatio-temporal dynamics of force generation."}],"author":[{"last_name":"Qin","first_name":"Xiang","full_name":"Qin, Xiang"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","full_name":"Mangeat, Thomas","last_name":"Mangeat"},{"first_name":"Chang","full_name":"Liu, Chang","last_name":"Liu"},{"last_name":"Majumder","first_name":"Pralay","full_name":"Majumder, Pralay"},{"first_name":"Jjiaying","full_name":"Liu, Jjiaying","last_name":"Liu"},{"last_name":"Choesmel Cadamuro","full_name":"Choesmel Cadamuro, Valerie","first_name":"Valerie"},{"last_name":"Mcdonald","first_name":"Jocelyn","full_name":"Mcdonald, Jocelyn"},{"last_name":"Liu","first_name":"Yinyao","full_name":"Liu, Yinyao"},{"last_name":"Yi","first_name":"Bin","full_name":"Yi, Bin"},{"first_name":"Xiaobo","full_name":"Wang, Xiaobo","last_name":"Wang"}],"isi":1,"article_number":"1210","publication":"Nature Communications","_id":"401","month":"03","status":"public","year":"2018","article_processing_charge":"No","oa":1,"scopus_import":"1","title":"A biochemical network controlling basal myosin oscillation","fulldoi":"https://doi.org/10.1038/s41467-018-03574-5","ddc":["539","570"],"file_date_updated":"2020-07-14T12:46:22Z","doi":"10.1038/s41467-018-03574-5","publisher":"Nature Publishing Group","day":"23"},{"page":"1010 - 1022","citation":{"chicago":"Cavallari, Nicola, Candida Nibau, Armin Fuchs, Despoina Dadarou, Andrea Barta, and John Doonan. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” <i>The Plant Journal</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/tpj.13914\">https://doi.org/10.1111/tpj.13914</a>.","apa":"Cavallari, N., Nibau, C., Fuchs, A., Dadarou, D., Barta, A., &#38; Doonan, J. (2018). The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. <i>The Plant Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/tpj.13914\">https://doi.org/10.1111/tpj.13914</a>","mla":"Cavallari, Nicola, et al. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” <i>The Plant Journal</i>, vol. 94, no. 6, Wiley, 2018, pp. 1010–22, doi:<a href=\"https://doi.org/10.1111/tpj.13914\">10.1111/tpj.13914</a>.","ama":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. <i>The Plant Journal</i>. 2018;94(6):1010-1022. doi:<a href=\"https://doi.org/10.1111/tpj.13914\">10.1111/tpj.13914</a>","ista":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. 2018. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 94(6), 1010–1022.","short":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, J. Doonan, The Plant Journal 94 (2018) 1010–1022.","ieee":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, and J. Doonan, “The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A,” <i>The Plant Journal</i>, vol. 94, no. 6. Wiley, pp. 1010–1022, 2018."},"external_id":{"isi":["000434365500008"]},"issue":"6","publist_id":"7426","acknowledgement":"CN, DD and JHD were funded by the BBSRC (grant number BB/M009459/1). NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna. AB and AF were supported by the Austrian Science Fund (FWF) [DK W1207; SFB RNAreg F43-P10]","volume":94,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"content_type":"application/pdf","file_name":"2018_PlantJourn_Cavallari.pdf","date_updated":"2020-07-14T12:46:22Z","file_id":"5934","relation":"main_file","checksum":"d9d3ad3215ac0e581731443fca312266","access_level":"open_access","date_created":"2019-02-06T11:40:54Z","file_size":1543354,"creator":"dernst"}],"publication_status":"published","department":[{"_id":"EvBe"}],"date_updated":"2024-10-09T20:58:42Z","date_published":"2018-06-01T00:00:00Z","type":"journal_article","has_accepted_license":"1","quality_controlled":"1","intvolume":"        94","language":[{"iso":"eng"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:17Z","isi":1,"corr_author":"1","abstract":[{"text":"The ability to adapt growth and development to temperature variations is crucial to generate plant varieties resilient to predicted temperature changes. However, the mechanisms underlying plant response to progressive increases in temperature have just started to be elucidated. Here, we report that the Cyclin-dependent Kinase G1 (CDKG1) is a central element in a thermo-sensitive mRNA splicing cascade that transduces changes in ambient temperature into differential expression of the fundamental spliceosome component, ATU2AF65A. CDKG1 is alternatively spliced in a temperature-dependent manner. We found that this process is partly dependent on both the Cyclin-dependent Kinase G2 (CDKG2) and the interacting co-factor CYCLIN L1 resulting in two distinct messenger RNAs. Relative abundance of both CDKG1 transcripts correlates with ambient temperature and possibly with different expression levels of the associated protein isoforms. Both CDKG1 alternative transcripts are necessary to fully complement the expression of ATU2AF65A across the temperature range. Our data support a previously unidentified temperature-dependent mechanism based on the alternative splicing of CDKG1 and regulated by CDKG2 and CYCLIN L1. We propose that changes in ambient temperature affect the relative abundance of CDKG1 transcripts and this in turn translates into differential CDKG1 protein expression coordinating the alternative splicing of ATU2AF65A. This article is protected by copyright. All rights reserved.","lang":"eng"}],"author":[{"last_name":"Cavallari","first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","full_name":"Cavallari, Nicola"},{"last_name":"Nibau","first_name":"Candida","full_name":"Nibau, Candida"},{"last_name":"Fuchs","first_name":"Armin","full_name":"Fuchs, Armin"},{"first_name":"Despoina","full_name":"Dadarou, Despoina","last_name":"Dadarou"},{"first_name":"Andrea","full_name":"Barta, Andrea","last_name":"Barta"},{"first_name":"John","full_name":"Doonan, John","last_name":"Doonan"}],"doi":"10.1111/tpj.13914","file_date_updated":"2020-07-14T12:46:22Z","publisher":"Wiley","ddc":["580"],"fulldoi":"https://doi.org/10.1111/tpj.13914","day":"01","month":"06","_id":"403","status":"public","year":"2018","publication":"The Plant Journal","scopus_import":"1","title":"The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A","article_processing_charge":"No","oa":1},{"corr_author":"1","isi":1,"related_material":{"record":[{"relation":"research_data","id":"9831","status":"public"}]},"abstract":[{"text":"Recent developments in automated tracking allow uninterrupted, high-resolution recording of animal trajectories, sometimes coupled with the identification of stereotyped changes of body pose or other behaviors of interest. Analysis and interpretation of such data represents a challenge: the timing of animal behaviors may be stochastic and modulated by kinematic variables, by the interaction with the environment or with the conspecifics within the animal group, and dependent on internal cognitive or behavioral state of the individual. Existing models for collective motion typically fail to incorporate the discrete, stochastic, and internal-state-dependent aspects of behavior, while models focusing on individual animal behavior typically ignore the spatial aspects of the problem. Here we propose a probabilistic modeling framework to address this gap. Each animal can switch stochastically between different behavioral states, with each state resulting in a possibly different law of motion through space. Switching rates for behavioral transitions can depend in a very general way, which we seek to identify from data, on the effects of the environment as well as the interaction between the animals. We represent the switching dynamics as a Generalized Linear Model and show that: (i) forward simulation of multiple interacting animals is possible using a variant of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly, the maximum likelihood inference of switching rate functions is tractably solvable by gradient descent; (iii) model selection can be used to identify factors that modulate behavioral state switching and to appropriately adjust model complexity to data. To illustrate our framework, we apply it to two synthetic models of animal motion and to real zebrafish tracking data. ","lang":"eng"}],"author":[{"last_name":"Bod’Ová","first_name":"Katarína","full_name":"Bod’Ová, Katarína"},{"first_name":"Gabriel","full_name":"Mitchell, Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","last_name":"Mitchell"},{"last_name":"Harpaz","full_name":"Harpaz, Roy","first_name":"Roy"},{"last_name":"Schneidman","full_name":"Schneidman, Elad","first_name":"Elad"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"publisher":"Public Library of Science","doi":"10.1371/journal.pone.0193049","file_date_updated":"2020-07-14T12:46:22Z","fulldoi":"https://doi.org/10.1371/journal.pone.0193049","ddc":["530","571"],"day":"07","year":"2018","_id":"406","status":"public","month":"03","publication":"PLoS One","title":"Probabilistic models of individual and collective animal behavior","scopus_import":"1","oa":1,"article_processing_charge":"Yes","external_id":{"isi":["000426896800032"]},"citation":{"chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” <i>PLoS One</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pone.0193049\">https://doi.org/10.1371/journal.pone.0193049</a>.","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic models of individual and collective animal behavior. PLoS One. 13(3).","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models of individual and collective animal behavior. <i>PLoS One</i>. 2018;13(3). doi:<a href=\"https://doi.org/10.1371/journal.pone.0193049\">10.1371/journal.pone.0193049</a>","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., &#38; Tkačik, G. (2018). Probabilistic models of individual and collective animal behavior. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0193049\">https://doi.org/10.1371/journal.pone.0193049</a>","mla":"Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” <i>PLoS One</i>, vol. 13, no. 3, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pone.0193049\">10.1371/journal.pone.0193049</a>.","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic models of individual and collective animal behavior,” <i>PLoS One</i>, vol. 13, no. 3. Public Library of Science, 2018.","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018)."},"issue":"3","publist_id":"7423","project":[{"name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"This work was supported by the Human Frontier Science Program RGP0065/2012 (GT, ES).","volume":13,"file":[{"date_updated":"2020-07-14T12:46:22Z","checksum":"684229493db75b43e98a46cd922da497","relation":"main_file","file_id":"5165","file_name":"IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:15:43Z","creator":"system","file_size":6887358,"access_level":"open_access"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","department":[{"_id":"GaTk"}],"date_updated":"2025-04-15T06:44:30Z","date_published":"2018-03-07T00:00:00Z","has_accepted_license":"1","type":"journal_article","quality_controlled":"1","intvolume":"        13","date_created":"2018-12-11T11:46:18Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","pubrep_id":"995","language":[{"iso":"eng"}]},{"publist_id":"7422","acknowledgement":"This work was supported by the Ministry of Education Youth and Sports, Czech Republic (grant LO1204 from the National Program of Sustainability I and Agricultural Research ) and by Czech Science Foundation grants 16-04184S , 501/10/1450 and 13-39982S and by IGA projects IGA_PrF_2018_033 and IGA_PrF_2018_023 . We would like to thank Jarmila Balonová, Olga Hustáková and Miroslava Šubová for their skillful technical assistance and Mgr. Tomáš Pospíšil, Ph.D. for his measurement of 1 H NMR and analysis of some 2D NMR spectral data. \r\n","volume":150,"citation":{"ama":"Kubiasová K, Mik V, Nisler J, et al. Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. <i>Phytochemistry</i>. 2018;150:1-11. doi:<a href=\"https://doi.org/10.1016/j.phytochem.2018.02.015\">10.1016/j.phytochem.2018.02.015</a>","ista":"Kubiasová K, Mik V, Nisler J, Hönig M, Husičková A, Spíchal L, Pěkná Z, Šamajová O, Doležal K, Plíhal O, Benková E, Strnad M, Plíhalová L. 2018. Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. 150, 1–11.","apa":"Kubiasová, K., Mik, V., Nisler, J., Hönig, M., Husičková, A., Spíchal, L., … Plíhalová, L. (2018). Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. <i>Phytochemistry</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.phytochem.2018.02.015\">https://doi.org/10.1016/j.phytochem.2018.02.015</a>","mla":"Kubiasová, Karolina, et al. “Design, Synthesis and Perception of Fluorescently Labeled Isoprenoid Cytokinins.” <i>Phytochemistry</i>, vol. 150, Elsevier, 2018, pp. 1–11, doi:<a href=\"https://doi.org/10.1016/j.phytochem.2018.02.015\">10.1016/j.phytochem.2018.02.015</a>.","ieee":"K. Kubiasová <i>et al.</i>, “Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins,” <i>Phytochemistry</i>, vol. 150. Elsevier, pp. 1–11, 2018.","short":"K. Kubiasová, V. Mik, J. Nisler, M. Hönig, A. Husičková, L. Spíchal, Z. Pěkná, O. Šamajová, K. Doležal, O. Plíhal, E. Benková, M. Strnad, L. Plíhalová, Phytochemistry 150 (2018) 1–11.","chicago":"Kubiasová, Karolina, Václav Mik, Jaroslav Nisler, Martin Hönig, Alexandra Husičková, Lukáš Spíchal, Zuzana Pěkná, et al. “Design, Synthesis and Perception of Fluorescently Labeled Isoprenoid Cytokinins.” <i>Phytochemistry</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.phytochem.2018.02.015\">https://doi.org/10.1016/j.phytochem.2018.02.015</a>."},"page":"1-11","external_id":{"isi":["000435623400001"]},"date_published":"2018-06-01T00:00:00Z","type":"journal_article","quality_controlled":"1","intvolume":"       150","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","date_created":"2018-12-11T11:46:18Z","department":[{"_id":"EvBe"}],"publication_status":"published","date_updated":"2023-09-11T12:53:11Z","abstract":[{"lang":"eng","text":"Isoprenoid cytokinins play a number of crucial roles in the regulation of plant growth and development. To study cytokinin receptor properties in plants, we designed and prepared fluorescent derivatives of 6-[(3-methylbut-2-en-1-yl)amino]purine (N6-isopentenyladenine, iP) with several fluorescent labels attached to the C2 or N9 atom of the purine moiety via a 2- or 6-carbon linker. The fluorescent labels included dansyl (DS), fluorescein (FC), 7-nitrobenzofurazan (NBD), rhodamine B (RhoB), coumarin (Cou), 7-(diethylamino)coumarin (DEAC) and cyanine 5 dye (Cy5). All prepared compounds were screened for affinity for the Arabidopsis thaliana cytokinin receptor (CRE1/AHK4). Although the attachment of the fluorescent labels to iP via the linkers mostly disrupted binding to the receptor, several fluorescent derivatives interacted well. For this reason, three derivatives, two rhodamine B and one 4-chloro-7-nitrobenzofurazan labeled iP were tested for their interaction with CRE1/AHK4 and Zea mays cytokinin receptors in detail. We further showed that the three derivatives were able to activate transcription of cytokinin response regulator ARR5 in Arabidopsis seedlings. The activity of fluorescently labeled cytokinins was compared with corresponding 6-dimethylaminopurine fluorescently labeled negative controls. Selected rhodamine B C2-labeled compounds 17, 18 and 4-chloro-7-nitrobenzofurazan N9-labeled compound 28 and their respective negative controls (19, 20 and 29, respectively) were used for in planta staining experiments in Arabidopsis thaliana cell suspension culture using live cell confocal microscopy."}],"author":[{"first_name":"Karolina","full_name":"Kubiasová, Karolina","last_name":"Kubiasová"},{"full_name":"Mik, Václav","first_name":"Václav","last_name":"Mik"},{"first_name":"Jaroslav","full_name":"Nisler, Jaroslav","last_name":"Nisler"},{"last_name":"Hönig","first_name":"Martin","full_name":"Hönig, Martin"},{"last_name":"Husičková","first_name":"Alexandra","full_name":"Husičková, Alexandra"},{"full_name":"Spíchal, Lukáš","first_name":"Lukáš","last_name":"Spíchal"},{"full_name":"Pěkná, Zuzana","first_name":"Zuzana","last_name":"Pěkná"},{"first_name":"Olga","full_name":"Šamajová, Olga","last_name":"Šamajová"},{"last_name":"Doležal","full_name":"Doležal, Karel","first_name":"Karel"},{"full_name":"Plíhal, Ondřej","first_name":"Ondřej","last_name":"Plíhal"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"},{"last_name":"Strnad","first_name":"Miroslav","full_name":"Strnad, Miroslav"},{"last_name":"Plíhalová","first_name":"Lucie","full_name":"Plíhalová, Lucie"}],"isi":1,"_id":"407","status":"public","month":"06","year":"2018","publication":"Phytochemistry","scopus_import":"1","title":"Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins","article_processing_charge":"No","doi":"10.1016/j.phytochem.2018.02.015","publisher":"Elsevier","fulldoi":"https://doi.org/10.1016/j.phytochem.2018.02.015","day":"01"},{"publication_identifier":{"issn":["1064-3745"]},"day":"01","fulldoi":"https://doi.org/10.1007/978-1-4939-7747-5_7","doi":"10.1007/978-1-4939-7747-5_7","publisher":"Springer Nature","article_processing_charge":"No","scopus_import":"1","title":"In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls","publication":"Root Development ","alternative_title":["MIMB"],"_id":"408","status":"public","month":"03","year":"2018","pmid":1,"author":[{"full_name":"Trinh, Hoang","first_name":"Hoang","last_name":"Trinh"},{"full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","first_name":"Inge","last_name":"Verstraeten"},{"first_name":"Danny","full_name":"Geelen, Danny","last_name":"Geelen"}],"abstract":[{"text":"Adventitious roots (AR) are de novo formed roots that emerge from any part of the plant or from callus in tissue culture, except root tissue. The plant tissue origin and the method by which they are induced determine the physiological properties of emerged ARs. Hence, a standard method encompassing all types of AR does not exist. Here we describe a method for the induction and analysis of AR that emerge from the etiolated hypocotyl of dicot plants. The hypocotyl is formed during embryogenesis and shows a determined developmental pattern which usually does not involve AR formation. However, the hypocotyl shows propensity to form de novo roots under specific circumstances such as removal of the root system, high humidity or flooding, or during de-etiolation. The hypocotyl AR emerge from a pericycle-like cell layer surrounding the vascular tissue of the central cylinder, which is reminiscent to the developmental program of lateral roots. Here we propose an easy protocol for in vitro hypocotyl AR induction from etiolated Arabidopsis seedlings.","lang":"eng"}],"date_updated":"2021-01-12T07:54:21Z","department":[{"_id":"JiFr"}],"publication_status":"published","language":[{"iso":"eng"}],"oa_version":"None","date_created":"2018-12-11T11:46:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"      1761","quality_controlled":"1","type":"book_chapter","date_published":"2018-03-01T00:00:00Z","page":"95 - 102","citation":{"chicago":"Trinh, Hoang, Inge Verstraeten, and Danny Geelen. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” In <i>Root Development </i>, 1761:95–102. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-1-4939-7747-5_7\">https://doi.org/10.1007/978-1-4939-7747-5_7</a>.","ista":"Trinh H, Verstraeten I, Geelen D. 2018.In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . MIMB, vol. 1761, 95–102.","ama":"Trinh H, Verstraeten I, Geelen D. In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: <i>Root Development </i>. Vol 1761. Springer Nature; 2018:95-102. doi:<a href=\"https://doi.org/10.1007/978-1-4939-7747-5_7\">10.1007/978-1-4939-7747-5_7</a>","apa":"Trinh, H., Verstraeten, I., &#38; Geelen, D. (2018). In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In <i>Root Development </i> (Vol. 1761, pp. 95–102). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-7747-5_7\">https://doi.org/10.1007/978-1-4939-7747-5_7</a>","mla":"Trinh, Hoang, et al. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” <i>Root Development </i>, vol. 1761, Springer Nature, 2018, pp. 95–102, doi:<a href=\"https://doi.org/10.1007/978-1-4939-7747-5_7\">10.1007/978-1-4939-7747-5_7</a>.","ieee":"H. Trinh, I. Verstraeten, and D. Geelen, “In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls,” in <i>Root Development </i>, vol. 1761, Springer Nature, 2018, pp. 95–102.","short":"H. Trinh, I. Verstraeten, D. Geelen, in:, Root Development , Springer Nature, 2018, pp. 95–102."},"external_id":{"pmid":["29525951"]},"volume":1761,"publist_id":"7421"},{"volume":356,"publist_id":"7420","issue":"4","external_id":{"isi":["000430402700009"],"arxiv":["1805.01652"]},"citation":{"chicago":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” <i>Comptes Rendus Mathematique</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.crma.2018.03.005\">https://doi.org/10.1016/j.crma.2018.03.005</a>.","ieee":"A. Akopyan, “On the number of non-hexagons in a planar tiling,” <i>Comptes Rendus Mathematique</i>, vol. 356, no. 4. Elsevier, pp. 412–414, 2018.","short":"A. Akopyan, Comptes Rendus Mathematique 356 (2018) 412–414.","ama":"Akopyan A. On the number of non-hexagons in a planar tiling. <i>Comptes Rendus Mathematique</i>. 2018;356(4):412-414. doi:<a href=\"https://doi.org/10.1016/j.crma.2018.03.005\">10.1016/j.crma.2018.03.005</a>","ista":"Akopyan A. 2018. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 356(4), 412–414.","apa":"Akopyan, A. (2018). On the number of non-hexagons in a planar tiling. <i>Comptes Rendus Mathematique</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.crma.2018.03.005\">https://doi.org/10.1016/j.crma.2018.03.005</a>","mla":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” <i>Comptes Rendus Mathematique</i>, vol. 356, no. 4, Elsevier, 2018, pp. 412–14, doi:<a href=\"https://doi.org/10.1016/j.crma.2018.03.005\">10.1016/j.crma.2018.03.005</a>."},"page":"412-414","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.01652"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_created":"2018-12-11T11:46:19Z","language":[{"iso":"eng"}],"intvolume":"       356","arxiv":1,"quality_controlled":"1","type":"journal_article","date_published":"2018-04-01T00:00:00Z","date_updated":"2025-07-10T11:52:35Z","department":[{"_id":"HeEd"}],"publication_status":"published","article_type":"original","author":[{"last_name":"Akopyan","orcid":"0000-0002-2548-617X","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy"}],"abstract":[{"lang":"eng","text":"We give a simple proof of T. Stehling's result [4], whereby in any normal tiling of the plane with convex polygons with number of sides not less than six, all tiles except a finite number are hexagons."}],"corr_author":"1","isi":1,"oa":1,"article_processing_charge":"No","title":"On the number of non-hexagons in a planar tiling","scopus_import":"1","publication":"Comptes Rendus Mathematique","year":"2018","status":"public","_id":"409","month":"04","publication_identifier":{"issn":["1631-073X"]},"day":"01","fulldoi":"https://doi.org/10.1016/j.crma.2018.03.005","publisher":"Elsevier","doi":"10.1016/j.crma.2018.03.005"},{"article_processing_charge":"No","oa":1,"scopus_import":"1","title":"Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells","publication":"Frontiers in Cellular Neuroscience","status":"public","_id":"41","month":"09","year":"2018","publication_identifier":{"issn":["1662-5102"]},"day":"19","ddc":["570"],"fulldoi":"https://doi.org/10.3389/fncel.2018.00311","file_date_updated":"2020-07-14T12:46:23Z","doi":"10.3389/fncel.2018.00311","publisher":"Frontiers Media","author":[{"last_name":"Luján","full_name":"Luján, Rafæl","first_name":"Rafæl"},{"last_name":"Aguado","full_name":"Aguado, Carolina","first_name":"Carolina"},{"full_name":"Ciruela, Francisco","first_name":"Francisco","last_name":"Ciruela"},{"full_name":"Arus, Xavier","first_name":"Xavier","last_name":"Arus"},{"first_name":"Alejandro","full_name":"Martín Belmonte, Alejandro","last_name":"Martín Belmonte"},{"last_name":"Alfaro Ruiz","full_name":"Alfaro Ruiz, Rocío","first_name":"Rocío"},{"last_name":"Martinez Gomez","first_name":"Jesus","full_name":"Martinez Gomez, Jesus"},{"first_name":"Luis","full_name":"De La Ossa, Luis","last_name":"De La Ossa"},{"last_name":"Watanabe","first_name":"Masahiko","full_name":"Watanabe, Masahiko"},{"last_name":"Adelman","first_name":"John","full_name":"Adelman, John"},{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"}],"abstract":[{"lang":"eng","text":"The small-conductance, Ca2+-activated K+ (SK) channel subtype SK2 regulates the spike rate and firing frequency, as well as Ca2+ transients in Purkinje cells (PCs). To understand the molecular basis by which SK2 channels mediate these functions, we analyzed the exact location and densities of SK2 channels along the neuronal surface of the mouse cerebellar PCs using SDS-digested freeze-fracture replica labeling (SDS-FRL) of high sensitivity combined with quantitative analyses. Immunogold particles for SK2 were observed on post- and pre-synaptic compartments showing both scattered and clustered distribution patterns. We found an axo-somato-dendritic gradient of the SK2 particle density increasing 12-fold from soma to dendritic spines. Using two different immunogold approaches, we also found that SK2 immunoparticles were frequently adjacent to, but never overlap with, the postsynaptic density of excitatory synapses in PC spines. Co-immunoprecipitation analysis demonstrated that SK2 channels form macromolecular complexes with two types of proteins that mobilize Ca2+: CaV2.1 channels and mGlu1α receptors in the cerebellum. Freeze-fracture replica double-labeling showed significant co-clustering of particles for SK2 with those for CaV2.1 channels and mGlu1α receptors. SK2 channels were also detected at presynaptic sites, mostly at the presynaptic active zone (AZ), where they are close to CaV2.1 channels, though they are not significantly co-clustered. These data demonstrate that SK2 channels located in different neuronal compartments can associate with distinct proteins mobilizing Ca2+, and suggest that the ultrastructural association of SK2 with CaV2.1 and mGlu1α provides the mechanism that ensures voltage (excitability) regulation by distinct intracellular Ca2+ transients in PCs."}],"isi":1,"article_number":"311","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:19Z","oa_version":"Published Version","quality_controlled":"1","intvolume":"        12","type":"journal_article","has_accepted_license":"1","date_published":"2018-09-19T00:00:00Z","date_updated":"2025-07-10T11:52:35Z","department":[{"_id":"RySh"}],"publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"content_type":"application/pdf","file_name":"fncel-12-00311.pdf","file_id":"5684","checksum":"0bcaec8d596162af0b7fe3f31325d480","relation":"main_file","date_updated":"2020-07-14T12:46:23Z","access_level":"open_access","file_size":6834251,"creator":"dernst","date_created":"2018-12-17T08:49:03Z"}],"article_type":"original","volume":12,"project":[{"grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1","_id":"25CBA828-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publist_id":"8013","ec_funded":1,"citation":{"chicago":"Luján, Rafæl, Carolina Aguado, Francisco Ciruela, Xavier Arus, Alejandro Martín Belmonte, Rocío Alfaro Ruiz, Jesus Martinez Gomez, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” <i>Frontiers in Cellular Neuroscience</i>. Frontiers Media, 2018. <a href=\"https://doi.org/10.3389/fncel.2018.00311\">https://doi.org/10.3389/fncel.2018.00311</a>.","short":"R. Luján, C. Aguado, F. Ciruela, X. Arus, A. Martín Belmonte, R. Alfaro Ruiz, J. Martinez Gomez, L. De La Ossa, M. Watanabe, J. Adelman, R. Shigemoto, Y. Fukazawa, Frontiers in Cellular Neuroscience 12 (2018).","ieee":"R. Luján <i>et al.</i>, “Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells,” <i>Frontiers in Cellular Neuroscience</i>, vol. 12. Frontiers Media, 2018.","mla":"Luján, Rafæl, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” <i>Frontiers in Cellular Neuroscience</i>, vol. 12, 311, Frontiers Media, 2018, doi:<a href=\"https://doi.org/10.3389/fncel.2018.00311\">10.3389/fncel.2018.00311</a>.","apa":"Luján, R., Aguado, C., Ciruela, F., Arus, X., Martín Belmonte, A., Alfaro Ruiz, R., … Fukazawa, Y. (2018). Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. <i>Frontiers in Cellular Neuroscience</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fncel.2018.00311\">https://doi.org/10.3389/fncel.2018.00311</a>","ista":"Luján R, Aguado C, Ciruela F, Arus X, Martín Belmonte A, Alfaro Ruiz R, Martinez Gomez J, De La Ossa L, Watanabe M, Adelman J, Shigemoto R, Fukazawa Y. 2018. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 12, 311.","ama":"Luján R, Aguado C, Ciruela F, et al. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. <i>Frontiers in Cellular Neuroscience</i>. 2018;12. doi:<a href=\"https://doi.org/10.3389/fncel.2018.00311\">10.3389/fncel.2018.00311</a>"},"external_id":{"isi":["000445090100002"]}},{"file":[{"file_name":"IST-2018-994-v1+1_2018_Joesch_A-micro-CT-based.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:23Z","relation":"main_file","checksum":"653fcb852f899c75b00ceee2a670d738","file_id":"4831","access_level":"open_access","date_created":"2018-12-12T10:10:42Z","creator":"system","file_size":2359430}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2023-09-08T11:48:39Z","publication_status":"published","department":[{"_id":"MaJö"}],"has_accepted_license":"1","type":"journal_article","date_published":"2018-03-26T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","date_created":"2018-12-11T11:46:19Z","language":[{"iso":"eng"}],"pubrep_id":"994","intvolume":"         8","quality_controlled":"1","external_id":{"isi":["000428234100005"]},"citation":{"ama":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. <i>Scientific Reports</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-23247-z\">10.1038/s41598-018-23247-z</a>","ista":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 8(1), 5184.","apa":"Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., &#38; Cox, D. (2018). A micro-CT-based method for quantitative brain lesion characterization and electrode localization. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-018-23247-z\">https://doi.org/10.1038/s41598-018-23247-z</a>","mla":"Masís, Javier, et al. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” <i>Scientific Reports</i>, vol. 8, no. 1, 5184, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-23247-z\">10.1038/s41598-018-23247-z</a>.","ieee":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A micro-CT-based method for quantitative brain lesion characterization and electrode localization,” <i>Scientific Reports</i>, vol. 8, no. 1. Nature Publishing Group, 2018.","short":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Scientific Reports 8 (2018).","chicago":"Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian A Jösch, and David Cox. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” <i>Scientific Reports</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41598-018-23247-z\">https://doi.org/10.1038/s41598-018-23247-z</a>."},"issue":"1","publist_id":"7419","volume":8,"fulldoi":"https://doi.org/10.1038/s41598-018-23247-z","ddc":["571","572"],"publisher":"Nature Publishing Group","doi":"10.1038/s41598-018-23247-z","file_date_updated":"2020-07-14T12:46:23Z","day":"26","publication":"Scientific Reports","year":"2018","_id":"410","month":"03","status":"public","oa":1,"article_processing_charge":"No","title":"A micro-CT-based method for quantitative brain lesion characterization and electrode localization","scopus_import":"1","article_number":"5184","isi":1,"abstract":[{"lang":"eng","text":"Lesion verification and quantification is traditionally done via histological examination of sectioned brains, a time-consuming process that relies heavily on manual estimation. Such methods are particularly problematic in posterior cortical regions (e.g. visual cortex), where sectioning leads to significant damage and distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes, which relies on the same techniques, suffers from similar drawbacks and requires even higher precision. Here, we propose a new, simple method for quantitative lesion characterization and electrode localization that is less labor-intensive and yields more detailed results than conventional methods. We leverage staining techniques standard in electron microscopy with the use of commodity micro-CT imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed these in resin and scan entire brains in a micro-CT machine. The scans result in 3D reconstructions of the brains with section thickness dependent on sample size (12–15 and 5–6 microns for rat and zebra finch respectively) that can be segmented manually or automatically. Because the method captures the entire intact brain volume, comparisons within and across studies are more tractable, and the extent of lesions and electrodes may be studied with higher accuracy than with current methods."}],"author":[{"full_name":"Masís, Javier","first_name":"Javier","last_name":"Masís"},{"last_name":"Mankus","first_name":"David","full_name":"Mankus, David"},{"last_name":"Wolff","full_name":"Wolff, Steffen","first_name":"Steffen"},{"full_name":"Guitchounts, Grigori","first_name":"Grigori","last_name":"Guitchounts"},{"full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch"},{"last_name":"Cox","first_name":"David","full_name":"Cox, David"}]}]