[{"keyword":["Cell Biology","Molecular Biology","Physiology"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","external_id":{"pmid":["31178361"]},"pmid":1,"author":[{"full_name":"Arrojo e Drigo, Rafael","last_name":"Arrojo e Drigo","first_name":"Rafael"},{"first_name":"Varda","last_name":"Lev-Ram","full_name":"Lev-Ram, Varda"},{"full_name":"Tyagi, Swati","first_name":"Swati","last_name":"Tyagi"},{"first_name":"Ranjan","last_name":"Ramachandra","full_name":"Ramachandra, Ranjan"},{"first_name":"Thomas","last_name":"Deerinck","full_name":"Deerinck, Thomas"},{"last_name":"Bushong","first_name":"Eric","full_name":"Bushong, Eric"},{"last_name":"Phan","first_name":"Sebastien","full_name":"Phan, Sebastien"},{"full_name":"Orphan, Victoria","last_name":"Orphan","first_name":"Victoria"},{"first_name":"Claude","last_name":"Lechene","full_name":"Lechene, Claude"},{"last_name":"Ellisman","first_name":"Mark H.","full_name":"Ellisman, Mark H."},{"first_name":"Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"}],"_id":"11062","publication_identifier":{"issn":["1550-4131"]},"issue":"2","intvolume":"        30","quality_controlled":"1","date_published":"2019-08-06T00:00:00Z","month":"08","status":"public","page":"343-351.e3","department":[{"_id":"MaHe"}],"date_created":"2022-04-07T07:45:21Z","publisher":"Elsevier","citation":{"chicago":"Arrojo e Drigo, Rafael, Varda Lev-Ram, Swati Tyagi, Ranjan Ramachandra, Thomas Deerinck, Eric Bushong, Sebastien Phan, et al. “Age Mosaicism across Multiple Scales in Adult Tissues.” <i>Cell Metabolism</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cmet.2019.05.010\">https://doi.org/10.1016/j.cmet.2019.05.010</a>.","ista":"Arrojo e Drigo R, Lev-Ram V, Tyagi S, Ramachandra R, Deerinck T, Bushong E, Phan S, Orphan V, Lechene C, Ellisman MH, Hetzer M. 2019. Age mosaicism across multiple scales in adult tissues. Cell Metabolism. 30(2), 343–351.e3.","short":"R. Arrojo e Drigo, V. Lev-Ram, S. Tyagi, R. Ramachandra, T. Deerinck, E. Bushong, S. Phan, V. Orphan, C. Lechene, M.H. Ellisman, M. Hetzer, Cell Metabolism 30 (2019) 343–351.e3.","mla":"Arrojo e Drigo, Rafael, et al. “Age Mosaicism across Multiple Scales in Adult Tissues.” <i>Cell Metabolism</i>, vol. 30, no. 2, Elsevier, 2019, p. 343–351.e3, doi:<a href=\"https://doi.org/10.1016/j.cmet.2019.05.010\">10.1016/j.cmet.2019.05.010</a>.","ama":"Arrojo e Drigo R, Lev-Ram V, Tyagi S, et al. Age mosaicism across multiple scales in adult tissues. <i>Cell Metabolism</i>. 2019;30(2):343-351.e3. doi:<a href=\"https://doi.org/10.1016/j.cmet.2019.05.010\">10.1016/j.cmet.2019.05.010</a>","ieee":"R. Arrojo e Drigo <i>et al.</i>, “Age mosaicism across multiple scales in adult tissues,” <i>Cell Metabolism</i>, vol. 30, no. 2. Elsevier, p. 343–351.e3, 2019.","apa":"Arrojo e Drigo, R., Lev-Ram, V., Tyagi, S., Ramachandra, R., Deerinck, T., Bushong, E., … Hetzer, M. (2019). Age mosaicism across multiple scales in adult tissues. <i>Cell Metabolism</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cmet.2019.05.010\">https://doi.org/10.1016/j.cmet.2019.05.010</a>"},"language":[{"iso":"eng"}],"abstract":[{"text":"Most neurons are not replaced during an animal’s lifetime. This nondividing state is characterized by extreme longevity and age-dependent decline of key regulatory proteins. To study the lifespans of cells and proteins in adult tissues, we combined isotope labeling of mice with a hybrid imaging method (MIMS-EM). Using 15N mapping, we show that liver and pancreas are composed of cells with vastly different ages, many as old as the animal. Strikingly, we also found that a subset of fibroblasts and endothelial cells, both known for their replicative potential, are characterized by the absence of cell division during adulthood. In addition, we show that the primary cilia of beta cells and neurons contains different structural regions with vastly different lifespans. Based on these results, we propose that age mosaicism across multiple scales is a fundamental principle of adult tissue, cell, and protein complex organization.","lang":"eng"}],"extern":"1","oa":1,"day":"06","year":"2019","title":"Age mosaicism across multiple scales in adult tissues","volume":30,"doi":"10.1016/j.cmet.2019.05.010","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cmet.2019.05.010"}],"scopus_import":"1","publication":"Cell Metabolism","type":"journal_article","date_updated":"2025-12-15T10:02:11Z","article_processing_charge":"No","article_type":"original"},{"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Marsh, Ashley","last_name":"Marsh","first_name":"Ashley"},{"first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Paul","last_name":"Lockhart","full_name":"Lockhart, Paul"},{"last_name":"Leventer","first_name":"Richard","full_name":"Leventer, Richard"}],"pmid":1,"external_id":{"isi":["000454111500019"],"pmid":["30089829"]},"isi":1,"acknowledgement":"This work was supported by EuroGentest2 (Unit 2: “Genetic testing as part of health care”), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics. We acknowledge the participation of the patients and their families in these studies, as well as the generous financial support of the Lefroy and Handbury families. APLM was supported by an Australian Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364). RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.","page":"161-166","status":"public","month":"01","citation":{"apa":"Marsh, A., Novarino, G., Lockhart, P., &#38; Leventer, R. (2019). CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. <i>European Journal of Human Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41431-018-0231-2\">https://doi.org/10.1038/s41431-018-0231-2</a>","ama":"Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. <i>European Journal of Human Genetics</i>. 2019;27:161-166. doi:<a href=\"https://doi.org/10.1038/s41431-018-0231-2\">10.1038/s41431-018-0231-2</a>","ieee":"A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63,” <i>European Journal of Human Genetics</i>, vol. 27. Springer Nature, pp. 161–166, 2019.","ista":"Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 27, 161–166.","mla":"Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” <i>European Journal of Human Genetics</i>, vol. 27, Springer Nature, 2019, pp. 161–66, doi:<a href=\"https://doi.org/10.1038/s41431-018-0231-2\">10.1038/s41431-018-0231-2</a>.","short":"A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166.","chicago":"Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” <i>European Journal of Human Genetics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41431-018-0231-2\">https://doi.org/10.1038/s41431-018-0231-2</a>."},"publisher":"Springer Nature","department":[{"_id":"GaNo"}],"date_created":"2018-12-11T11:44:39Z","intvolume":"        27","_id":"105","date_published":"2019-01-01T00:00:00Z","quality_controlled":"1","publication_status":"published","doi":"10.1038/s41431-018-0231-2","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41431-018-0231-2"}],"abstract":[{"lang":"eng","text":"Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease: 615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2 at 1p13.3. 4. OMIM# of the Gene(s): 102771."}],"language":[{"iso":"eng"}],"publist_id":"7949","volume":27,"title":"CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63","year":"2019","day":"01","oa":1,"article_type":"original","article_processing_charge":"No","scopus_import":"1","date_updated":"2023-08-24T14:28:24Z","publication":"European Journal of Human Genetics","type":"journal_article"},{"publisher":"American Mathematical Society","citation":{"chicago":"Browning, Timothy D, and Daniel Loughran. “Sieving Rational Points on Varieties.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2019. <a href=\"https://doi.org/10.1090/tran/7514\">https://doi.org/10.1090/tran/7514</a>.","ista":"Browning TD, Loughran D. 2019. Sieving rational points on varieties. Transactions of the American Mathematical Society. 371(8), 5757–5785.","short":"T.D. Browning, D. Loughran, Transactions of the American Mathematical Society 371 (2019) 5757–5785.","mla":"Browning, Timothy D., and Daniel Loughran. “Sieving Rational Points on Varieties.” <i>Transactions of the American Mathematical Society</i>, vol. 371, no. 8, American Mathematical Society, 2019, pp. 5757–85, doi:<a href=\"https://doi.org/10.1090/tran/7514\">10.1090/tran/7514</a>.","apa":"Browning, T. D., &#38; Loughran, D. (2019). Sieving rational points on varieties. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/7514\">https://doi.org/10.1090/tran/7514</a>","ieee":"T. D. Browning and D. Loughran, “Sieving rational points on varieties,” <i>Transactions of the American Mathematical Society</i>, vol. 371, no. 8. American Mathematical Society, pp. 5757–5785, 2019.","ama":"Browning TD, Loughran D. Sieving rational points on varieties. <i>Transactions of the American Mathematical Society</i>. 2019;371(8):5757-5785. doi:<a href=\"https://doi.org/10.1090/tran/7514\">10.1090/tran/7514</a>"},"department":[{"_id":"TiBr"}],"date_created":"2018-12-11T11:45:01Z","page":"5757-5785","month":"04","status":"public","date_published":"2019-04-15T00:00:00Z","quality_controlled":"1","_id":"175","intvolume":"       371","issue":"8","publication_identifier":{"eissn":["1088-6850"],"issn":["0002-9947"]},"arxiv":1,"external_id":{"isi":["000464034200019"],"arxiv":["1705.01999"]},"author":[{"last_name":"Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177"},{"last_name":"Loughran","first_name":"Daniel","full_name":"Loughran, Daniel"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","article_processing_charge":"No","publication":"Transactions of the American Mathematical Society","type":"journal_article","date_updated":"2025-07-10T11:51:20Z","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1705.01999","open_access":"1"}],"publication_status":"published","doi":"10.1090/tran/7514","year":"2019","volume":371,"title":"Sieving rational points on varieties","oa":1,"day":"15","abstract":[{"lang":"eng","text":"An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points."}],"publist_id":"7746","language":[{"iso":"eng"}]},{"page":"238-255","status":"public","month":"01","publisher":"Society for Neuroscience","citation":{"apa":"Trébuchet, G., Cattenoz, P. B., Zsámboki, J., Mazaud, D., Siekhaus, D. E., Fanto, M., &#38; Giangrande, A. (2019). The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.1059-18.2018\">https://doi.org/10.1523/JNEUROSCI.1059-18.2018</a>","ama":"Trébuchet G, Cattenoz PB, Zsámboki J, et al. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. <i>Journal of Neuroscience</i>. 2019;39(2):238-255. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1059-18.2018\">10.1523/JNEUROSCI.1059-18.2018</a>","ieee":"G. Trébuchet <i>et al.</i>, “The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate,” <i>Journal of Neuroscience</i>, vol. 39, no. 2. Society for Neuroscience, pp. 238–255, 2019.","mla":"Trébuchet, Guillaume, et al. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” <i>Journal of Neuroscience</i>, vol. 39, no. 2, Society for Neuroscience, 2019, pp. 238–55, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1059-18.2018\">10.1523/JNEUROSCI.1059-18.2018</a>.","short":"G. Trébuchet, P.B. Cattenoz, J. Zsámboki, D. Mazaud, D.E. Siekhaus, M. Fanto, A. Giangrande, Journal of Neuroscience 39 (2019) 238–255.","ista":"Trébuchet G, Cattenoz PB, Zsámboki J, Mazaud D, Siekhaus DE, Fanto M, Giangrande A. 2019. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. 39(2), 238–255.","chicago":"Trébuchet, Guillaume, Pierre B Cattenoz, János Zsámboki, David Mazaud, Daria E Siekhaus, Manolis Fanto, and Angela Giangrande. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2019. <a href=\"https://doi.org/10.1523/JNEUROSCI.1059-18.2018\">https://doi.org/10.1523/JNEUROSCI.1059-18.2018</a>."},"date_created":"2018-12-11T11:44:07Z","department":[{"_id":"DaSi"}],"issue":"2","intvolume":"        39","_id":"8","date_published":"2019-01-09T00:00:00Z","project":[{"grant_number":"334077","call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions"}],"quality_controlled":"1","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pmid":1,"author":[{"last_name":"Trébuchet","first_name":"Guillaume","full_name":"Trébuchet, Guillaume"},{"last_name":"Cattenoz","first_name":"Pierre B","full_name":"Cattenoz, Pierre B"},{"first_name":"János","last_name":"Zsámboki","full_name":"Zsámboki, János"},{"full_name":"Mazaud, David","last_name":"Mazaud","first_name":"David"},{"orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E"},{"last_name":"Fanto","first_name":"Manolis","full_name":"Fanto, Manolis"},{"full_name":"Giangrande, Angela","last_name":"Giangrande","first_name":"Angela"}],"external_id":{"isi":["000455189900006"],"pmid":["30504274"]},"isi":1,"acknowledgement":"This work was supported by INSERM, CNRS, UDS, Ligue Régionale contre le Cancer, Hôpital de Strasbourg, Association pour la Recherche sur le Cancer (ARC) and Agence Nationale de la Recherche (ANR) grants. P.B.C. was funded by the ANR and by the ARSEP (Fondation pour l'Aide à la Recherche sur la Sclérose en Plaques), and G.T. by governmental and ARC fellowships. This work was also supported by grants from the Ataxia UK (2491) and the NC3R (NC/L000199/1) awarded to M.F. The Institut de Génétique et de Biologie Moléculaire et Cellulaire was also supported by a French state fund through the ANR labex. D.E.S. was funded by Marie Curie Grant CIG 334077/IRTIM. We thank B. Altenhein, K. Brückner, M. Crozatier, L. Waltzer, M. Logan, E. Kurant, R. Reuter, E. Kurucz, J.L Dimarcq, J. Hoffmann, C. Goodman, the DHSB, and the BDSC for reagents and flies. We also thank all of the laboratory members for comments on the manuscript; C. Diebold, C. Delaporte, M. Pezze, the fly, and imaging and antibody facilities for technical assistance; and D. Dembele for help with statistics. In addition, we thank Alison Brewer for help with Luciferase assays.","has_accepted_license":"1","file":[{"file_id":"8596","date_updated":"2020-10-02T09:33:28Z","creator":"dernst","content_type":"application/pdf","date_created":"2020-10-02T09:33:28Z","access_level":"open_access","relation":"main_file","file_name":"2019_JournNeuroscience_Trebuchet.pdf","success":1,"file_size":9455414,"checksum":"8f6925eb4cd1e8747d8ea25929c68de6"}],"article_type":"original","article_processing_charge":"No","ddc":["570"],"scopus_import":"1","date_updated":"2025-04-15T06:52:10Z","publication":"Journal of Neuroscience","type":"journal_article","publication_status":"published","doi":"10.1523/JNEUROSCI.1059-18.2018","ec_funded":1,"file_date_updated":"2020-10-02T09:33:28Z","abstract":[{"lang":"eng","text":"Despite their different origins, Drosophila glia and hemocytes are related cell populations that provide an immune function. Drosophila hemocytes patrol the body cavity and act as macrophages outside the nervous system whereas glia originate from the neuroepithelium and provide the scavenger population of the nervous system. Drosophila glia are hence the functional orthologs of vertebrate microglia, even though the latter are cells of immune origin that subsequently move into the brain during development. Interestingly, the Drosophila immune cells within (glia) and outside the nervous system (hemocytes) require the same transcription factor Glide/Gcm for their development. This raises the issue of how do glia specifically differentiate in the nervous system and hemocytes in the procephalic mesoderm. The Repo homeodomain transcription factor and pan-glial direct target of Glide/Gcm is known to ensure glial terminal differentiation. Here we show that Repo also takes center stage in the process that discriminates between glia and hemocytes. First, Repo expression is repressed in the hemocyte anlagen by mesoderm-specific factors. Second, Repo ectopic activation in the procephalic mesoderm is sufficient to repress the expression of hemocyte-specific genes. Third, the lack of Repo triggers the expression of hemocyte markers in glia. Thus, a complex network of tissue-specific cues biases the potential of Glide/Gcm. These data allow us to revise the concept of fate determinants and help us understand the bases of cell specification. Both sexes were analyzed.SIGNIFICANCE STATEMENTDistinct cell types often require the same pioneer transcription factor, raising the issue of how does one factor trigger different fates. In Drosophila, glia and hemocytes provide a scavenger activity within and outside the nervous system, respectively. While they both require the Glide/Gcm transcription factor, glia originate from the ectoderm, hemocytes from the mesoderm. Here we show that tissue-specific factors inhibit the gliogenic potential of Glide/Gcm in the mesoderm by repressing the expression of the homeodomain protein Repo, a major glial-specific target of Glide/Gcm. Repo expression in turn inhibits the expression of hemocyte-specific genes in the nervous system. These cell-specific networks secure the establishment of the glial fate only in the nervous system and allow cell diversification."}],"language":[{"iso":"eng"}],"publist_id":"8048","title":"The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate","volume":39,"year":"2019","day":"09","oa":1},{"_id":"80","intvolume":"       368","issue":"2","date_published":"2019-06-01T00:00:00Z","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"723-776","month":"06","status":"public","publisher":"Springer","citation":{"ieee":"A. Deuchert, R. Seiringer, and J. Yngvason, “Bose–Einstein condensation in a dilute, trapped gas at positive temperature,” <i>Communications in Mathematical Physics</i>, vol. 368, no. 2. Springer, pp. 723–776, 2019.","apa":"Deuchert, A., Seiringer, R., &#38; Yngvason, J. (2019). Bose–Einstein condensation in a dilute, trapped gas at positive temperature. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-018-3239-0\">https://doi.org/10.1007/s00220-018-3239-0</a>","ama":"Deuchert A, Seiringer R, Yngvason J. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. <i>Communications in Mathematical Physics</i>. 2019;368(2):723-776. doi:<a href=\"https://doi.org/10.1007/s00220-018-3239-0\">10.1007/s00220-018-3239-0</a>","short":"A. Deuchert, R. Seiringer, J. Yngvason, Communications in Mathematical Physics 368 (2019) 723–776.","mla":"Deuchert, Andreas, et al. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” <i>Communications in Mathematical Physics</i>, vol. 368, no. 2, Springer, 2019, pp. 723–76, doi:<a href=\"https://doi.org/10.1007/s00220-018-3239-0\">10.1007/s00220-018-3239-0</a>.","ista":"Deuchert A, Seiringer R, Yngvason J. 2019. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 368(2), 723–776.","chicago":"Deuchert, Andreas, Robert Seiringer, and Jakob Yngvason. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” <i>Communications in Mathematical Physics</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s00220-018-3239-0\">https://doi.org/10.1007/s00220-018-3239-0</a>."},"date_created":"2018-12-11T11:44:31Z","department":[{"_id":"RoSe"}],"file":[{"date_created":"2018-12-17T10:34:06Z","relation":"main_file","access_level":"open_access","checksum":"c7e9880b43ac726712c1365e9f2f73a6","file_size":893902,"file_name":"2018_CommunMathPhys_Deuchert.pdf","file_id":"5688","date_updated":"2020-07-14T12:48:07Z","creator":"dernst","content_type":"application/pdf"}],"has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","external_id":{"isi":["000467796800007"]},"author":[{"full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Deuchert"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert"},{"full_name":"Yngvason, Jakob","first_name":"Jakob","last_name":"Yngvason"}],"isi":1,"scopus_import":"1","ddc":["530"],"license":"https://creativecommons.org/licenses/by/4.0/","type":"journal_article","publication":"Communications in Mathematical Physics","date_updated":"2025-04-14T07:27:00Z","article_type":"original","article_processing_charge":"Yes (via OA deal)","abstract":[{"lang":"eng","text":"We consider an interacting, dilute Bose gas trapped in a harmonic potential at a positive temperature. The system is analyzed in a combination of a thermodynamic and a Gross–Pitaevskii (GP) limit where the trap frequency ω, the temperature T, and the particle number N are related by N∼ (T/ ω) 3→ ∞ while the scattering length is so small that the interaction energy per particle around the center of the trap is of the same order of magnitude as the spectral gap in the trap. We prove that the difference between the canonical free energy of the interacting gas and the one of the noninteracting system can be obtained by minimizing the GP energy functional. We also prove Bose–Einstein condensation in the following sense: The one-particle density matrix of any approximate minimizer of the canonical free energy functional is to leading order given by that of the noninteracting gas but with the free condensate wavefunction replaced by the GP minimizer."}],"publist_id":"7974","language":[{"iso":"eng"}],"year":"2019","title":"Bose–Einstein condensation in a dilute, trapped gas at positive temperature","volume":368,"oa":1,"day":"01","publication_status":"published","doi":"10.1007/s00220-018-3239-0","ec_funded":1,"file_date_updated":"2020-07-14T12:48:07Z"},{"publication":"Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics","type":"conference","date_updated":"2021-01-12T08:17:18Z","scopus_import":"1","article_processing_charge":"No","oa":1,"conference":{"start_date":"2019-07-01","location":"Ljubljana, Slovenia","end_date":"2019-07-05","name":"FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics"},"day":"01","year":"2019","title":"New edge asymptotics of skew Young diagrams via free boundaries","article_number":"34","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We study edge asymptotics of poissonized Plancherel-type measures on skew Young diagrams (integer partitions). These measures can be seen as generalizations of those studied by Baik--Deift--Johansson and Baik--Rains in resolving Ulam's problem on longest increasing subsequences of random permutations and the last passage percolation (corner growth) discrete versions thereof. Moreover they interpolate between said measures and the uniform measure on partitions. In the new KPZ-like 1/3 exponent edge scaling limit with logarithmic corrections, we find new probability distributions generalizing the classical Tracy--Widom GUE, GOE and GSE distributions from the theory of random matrices."}],"ec_funded":1,"main_file_link":[{"url":"https://arxiv.org/abs/1902.08750","open_access":"1"}],"publication_status":"published","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"},{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"}],"quality_controlled":"1","date_published":"2019-07-01T00:00:00Z","_id":"8175","department":[{"_id":"LaEr"}],"date_created":"2020-07-26T22:01:04Z","citation":{"chicago":"Betea, Dan, Jérémie Bouttier, Peter Nejjar, and Mirjana Vuletíc. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” In <i>Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics</i>. Formal Power Series and Algebraic Combinatorics, 2019.","mla":"Betea, Dan, et al. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” <i>Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics</i>, 34, Formal Power Series and Algebraic Combinatorics, 2019.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletíc, in:, Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Formal Power Series and Algebraic Combinatorics, 2019.","ista":"Betea D, Bouttier J, Nejjar P, Vuletíc M. 2019. New edge asymptotics of skew Young diagrams via free boundaries. Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics, 34.","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletíc, “New edge asymptotics of skew Young diagrams via free boundaries,” in <i>Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics</i>, Ljubljana, Slovenia, 2019.","apa":"Betea, D., Bouttier, J., Nejjar, P., &#38; Vuletíc, M. (2019). New edge asymptotics of skew Young diagrams via free boundaries. In <i>Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics</i>. Ljubljana, Slovenia: Formal Power Series and Algebraic Combinatorics.","ama":"Betea D, Bouttier J, Nejjar P, Vuletíc M. New edge asymptotics of skew Young diagrams via free boundaries. In: <i>Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics</i>. Formal Power Series and Algebraic Combinatorics; 2019."},"publisher":"Formal Power Series and Algebraic Combinatorics","month":"07","status":"public","acknowledgement":"D.B. is especially grateful to Patrik Ferrari for suggesting simplifications in Section 3 and\r\nto Alessandra Occelli for suggesting the name for the models of Section 2.\r\n","arxiv":1,"external_id":{"arxiv":["1902.08750"]},"author":[{"first_name":"Dan","last_name":"Betea","full_name":"Betea, Dan"},{"full_name":"Bouttier, Jérémie","last_name":"Bouttier","first_name":"Jérémie"},{"full_name":"Nejjar, Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Nejjar"},{"last_name":"Vuletíc","first_name":"Mirjana","full_name":"Vuletíc, Mirjana"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"},{"article_processing_charge":"No","editor":[{"full_name":"Balding, David","first_name":"David","last_name":"Balding"},{"last_name":"Moltke","first_name":"Ida","full_name":"Moltke, Ida"},{"last_name":"Marioni","first_name":"John","full_name":"Marioni, John"}],"scopus_import":"1","ddc":["576"],"publication":"Handbook of statistical genomics","type":"book_chapter","date_updated":"2024-10-21T06:02:39Z","doi":"10.1002/9781119487845.ch4","publication_status":"published","edition":"4","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We review the history of population genetics, starting with its origins a century ago from the synthesis between Mendel and Darwin's ideas, through to the recent development of sophisticated schemes of inference from sequence data, based on the coalescent. We explain the close relation between the coalescent and a diffusion process, which we illustrate by their application to understand spatial structure. We summarise the powerful methods available for analysis of multiple loci, when linkage equilibrium can be assumed, and then discuss approaches to the more challenging case, where associations between alleles require that we follow genotype, rather than allele, frequencies. Though we can hardly cover the whole of population genetics, we give an overview of the current state of the subject, and future challenges to it."}],"day":"29","year":"2019","title":"Mathematical models in population genetics","month":"07","status":"public","page":"115-144","department":[{"_id":"NiBa"}],"date_created":"2020-08-21T04:25:39Z","publisher":"Wiley","citation":{"ieee":"N. H. Barton and A. Etheridge, “Mathematical models in population genetics,” in <i>Handbook of statistical genomics</i>, 4th ed., D. Balding, I. Moltke, and J. Marioni, Eds. Wiley, 2019, pp. 115–144.","apa":"Barton, N. H., &#38; Etheridge, A. (2019). Mathematical models in population genetics. In D. Balding, I. Moltke, &#38; J. Marioni (Eds.), <i>Handbook of statistical genomics</i> (4th ed., pp. 115–144). Wiley. <a href=\"https://doi.org/10.1002/9781119487845.ch4\">https://doi.org/10.1002/9781119487845.ch4</a>","ama":"Barton NH, Etheridge A. Mathematical models in population genetics. In: Balding D, Moltke I, Marioni J, eds. <i>Handbook of Statistical Genomics</i>. 4th ed. Wiley; 2019:115-144. doi:<a href=\"https://doi.org/10.1002/9781119487845.ch4\">10.1002/9781119487845.ch4</a>","chicago":"Barton, Nicholas H, and Alison Etheridge. “Mathematical Models in Population Genetics.” In <i>Handbook of Statistical Genomics</i>, edited by David Balding, Ida Moltke, and John Marioni, 4th ed., 115–44. Wiley, 2019. <a href=\"https://doi.org/10.1002/9781119487845.ch4\">https://doi.org/10.1002/9781119487845.ch4</a>.","ista":"Barton NH, Etheridge A. 2019.Mathematical models in population genetics. In: Handbook of statistical genomics. , 115–144.","short":"N.H. Barton, A. Etheridge, in:, D. Balding, I. Moltke, J. Marioni (Eds.), Handbook of Statistical Genomics, 4th ed., Wiley, 2019, pp. 115–144.","mla":"Barton, Nicholas H., and Alison Etheridge. “Mathematical Models in Population Genetics.” <i>Handbook of Statistical Genomics</i>, edited by David Balding et al., 4th ed., Wiley, 2019, pp. 115–44, doi:<a href=\"https://doi.org/10.1002/9781119487845.ch4\">10.1002/9781119487845.ch4</a>."},"_id":"8281","publication_identifier":{"isbn":["9781119429142"]},"quality_controlled":"1","date_published":"2019-07-29T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","isi":1,"external_id":{"isi":["000261343000003"]},"author":[{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"}]},{"publication_status":"submitted","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/1015"}],"author":[{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"KOKORIS KOGIAS, Eleftherios","last_name":"KOKORIS KOGIAS","first_name":"Eleftherios"},{"first_name":"Alexander","last_name":"Spiegelman","full_name":"Spiegelman, Alexander"},{"full_name":"Malkhi, Dahlia","last_name":"Malkhi","first_name":"Dahlia"},{"full_name":"Abraham, Ittai","first_name":"Ittai","last_name":"Abraham"}],"abstract":[{"lang":"eng","text":"In this paper, we present the first fully asynchronous distributed key generation (ADKG) algorithm as well as the first distributed key generation algorithm that can create keys with a dual (f,2f+1)−threshold that are necessary for scalable consensus (which so far needs a trusted dealer assumption). In order to create a DKG with a dual (f,2f+1)− threshold we first answer in the affirmative the open question posed by Cachin et al. how to create an AVSS protocol with recovery thresholds f+1<k≤2f+1, which is of independent interest. Our High-threshold-AVSS (HAVSS) uses an asymmetric bi-variate polynomial, where the secret shared is hidden from any set of k nodes but an honest node that did not participate in the sharing phase can still recover his share with only n−2f shares, hence be able to contribute in the secret reconstruction. Another building block for ADKG is a novel Eventually Perfect Common Coin (EPCC) abstraction and protocol that enables the participants to create a common coin that might fail to agree at most f+1 times (even if invoked a polynomial number of times). Using EPCC we implement an Eventually Efficient Asynchronous Binary Agreement (EEABA) in which each instance takes O(n2) bits and O(1) rounds in expectation, except for at most f+1 instances which may take O(n4) bits and O(n) rounds in total. Using EEABA we construct the first fully Asynchronous Distributed Key Generation (ADKG) which has the same overhead and expected runtime as the best partially-synchronous DKG (O(n4) words, O(n) rounds). As a corollary of our ADKG we can also create the first Validated Asynchronous Byzantine Agreement (VABA) in the authenticated setting that does not need a trusted dealer to setup threshold signatures of degree n−f. Our VABA has an overhead of expected O(n2) words and O(1) time per instance after an initial O(n4) words and O(n) time bootstrap via ADKG."}],"article_number":"2019/1015","language":[{"iso":"eng"}],"year":"2019","title":"Bootstrapping consensus without trusted setup: Fully asynchronous distributed key generation","oa":1,"day":"10","article_processing_charge":"No","month":"09","status":"public","citation":{"short":"E. Kokoris Kogias, A. Spiegelman, D. Malkhi, I. Abraham, Cryptology EPrint Archive (n.d.).","mla":"Kokoris Kogias, Eleftherios, et al. “Bootstrapping Consensus without Trusted Setup: Fully Asynchronous Distributed Key Generation.” <i>Cryptology EPrint Archive</i>, 2019/1015.","ista":"Kokoris Kogias E, Spiegelman A, Malkhi D, Abraham I. Bootstrapping consensus without trusted setup: Fully asynchronous distributed key generation. Cryptology ePrint Archive, 2019/1015.","chicago":"Kokoris Kogias, Eleftherios, Alexander Spiegelman, Dahlia Malkhi, and Ittai Abraham. “Bootstrapping Consensus without Trusted Setup: Fully Asynchronous Distributed Key Generation.” <i>Cryptology EPrint Archive</i>, n.d.","apa":"Kokoris Kogias, E., Spiegelman, A., Malkhi, D., &#38; Abraham, I. (n.d.). Bootstrapping consensus without trusted setup: Fully asynchronous distributed key generation. <i>Cryptology ePrint Archive</i>.","ieee":"E. Kokoris Kogias, A. Spiegelman, D. Malkhi, and I. Abraham, “Bootstrapping consensus without trusted setup: Fully asynchronous distributed key generation,” <i>Cryptology ePrint Archive</i>. .","ama":"Kokoris Kogias E, Spiegelman A, Malkhi D, Abraham I. Bootstrapping consensus without trusted setup: Fully asynchronous distributed key generation. <i>Cryptology ePrint Archive</i>."},"department":[{"_id":"ElKo"}],"date_created":"2020-08-26T12:18:00Z","_id":"8305","date_published":"2019-09-10T00:00:00Z","type":"preprint","publication":"Cryptology ePrint Archive","date_updated":"2025-01-20T14:08:03Z"},{"language":[{"iso":"eng"}],"abstract":[{"text":"Bending-active structures are able to efficiently produce complex curved shapes starting from flat panels. The desired deformation of the panels derives from the proper selection of their elastic properties. Optimized panels, called FlexMaps, are designed such that, once they are bent and assembled, the resulting static equilibrium configuration matches a desired input 3D shape. The FlexMaps elastic properties are controlled by locally varying spiraling geometric mesostructures, which are optimized in size and shape to match the global curvature (i.e., bending requests) of the target shape. The design pipeline starts from a quad mesh representing the input 3D shape, which defines the edge size and the total amount of spirals: every quad will embed one spiral. Then, an optimization algorithm tunes the geometry of the spirals by using a simplified pre-computed rod model. This rod model is derived from a non-linear regression algorithm which approximates the non-linear behavior of solid FEM spiral models subject to hundreds of load combinations. This innovative pipeline has been applied to the project of a lightweight plywood pavilion named FlexMaps Pavilion, which is a single-layer piecewise twisted arc that fits a bounding box of 3.90x3.96x3.25 meters.","lang":"eng"}],"day":"10","conference":{"location":"Barcelona, Spain","end_date":"2019-10-10","name":"IASS: International Association for Shell and Spatial Structures","start_date":"2019-10-07"},"year":"2019","title":"FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","publication_status":"published","isi":1,"external_id":{"isi":["000563497600059"]},"author":[{"full_name":"Laccone, Francesco","first_name":"Francesco","last_name":"Laccone"},{"full_name":"Malomo, Luigi","last_name":"Malomo","first_name":"Luigi"},{"id":"2DC83906-F248-11E8-B48F-1D18A9856A87","full_name":"Perez Rodriguez, Jesus","first_name":"Jesus","last_name":"Perez Rodriguez"},{"last_name":"Pietroni","first_name":"Nico","full_name":"Pietroni, Nico"},{"full_name":"Ponchio, Federico","last_name":"Ponchio","first_name":"Federico"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd"},{"last_name":"Cignoni","first_name":"Paolo","full_name":"Cignoni, Paolo"}],"_id":"9261","publication_identifier":{"issn":["2518-6582"],"isbn":["9788412110104"]},"scopus_import":"1","publication":"IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE","type":"conference","quality_controlled":"1","date_updated":"2023-09-08T11:21:54Z","date_published":"2019-10-10T00:00:00Z","month":"10","article_processing_charge":"No","status":"public","page":"509-515","date_created":"2021-03-21T23:01:21Z","department":[{"_id":"BeBi"}],"publisher":"International Center for Numerical Methods in Engineering","citation":{"chicago":"Laccone, Francesco, Luigi Malomo, Jesus Perez Rodriguez, Nico Pietroni, Federico Ponchio, Bernd Bickel, and Paolo Cignoni. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” In <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>, 509–15. International Center for Numerical Methods in Engineering, 2019.","ista":"Laccone F, Malomo L, Perez Rodriguez J, Pietroni N, Ponchio F, Bickel B, Cignoni P. 2019. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE. IASS: International Association for Shell and Spatial Structures, 509–515.","short":"F. Laccone, L. Malomo, J. Perez Rodriguez, N. Pietroni, F. Ponchio, B. Bickel, P. Cignoni, in:, IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, International Center for Numerical Methods in Engineering, 2019, pp. 509–515.","mla":"Laccone, Francesco, et al. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>, International Center for Numerical Methods in Engineering, 2019, pp. 509–15.","ieee":"F. Laccone <i>et al.</i>, “FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels,” in <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>, Barcelona, Spain, 2019, pp. 509–515.","ama":"Laccone F, Malomo L, Perez Rodriguez J, et al. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In: <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>. International Center for Numerical Methods in Engineering; 2019:509-515.","apa":"Laccone, F., Malomo, L., Perez Rodriguez, J., Pietroni, N., Ponchio, F., Bickel, B., &#38; Cignoni, P. (2019). FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i> (pp. 509–515). Barcelona, Spain: International Center for Numerical Methods in Engineering."}},{"file_date_updated":"2021-06-04T12:50:47Z","publication_status":"published","doi":"10.1073/pnas.1821435116","year":"2019","volume":116,"title":"DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm","extern":"1","oa":1,"day":"07","abstract":[{"lang":"eng","text":"Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion."}],"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication":"Proceedings of the National Academy of Sciences","type":"journal_article","date_updated":"2021-12-14T07:52:30Z","scopus_import":"1","ddc":["580"],"external_id":{"pmid":["31000601"]},"pmid":1,"author":[{"full_name":"Kim, M. Yvonne","first_name":"M. Yvonne","last_name":"Kim"},{"first_name":"Akemi","last_name":"Ono","full_name":"Ono, Akemi"},{"full_name":"Scholten, Stefan","last_name":"Scholten","first_name":"Stefan"},{"full_name":"Kinoshita, Tetsu","last_name":"Kinoshita","first_name":"Tetsu"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel"},{"first_name":"Takashi","last_name":"Okamoto","full_name":"Okamoto, Takashi"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","file":[{"creator":"asandaue","content_type":"application/pdf","date_updated":"2021-06-04T12:50:47Z","file_id":"9461","file_name":"2019_PNAS_Kim.pdf","file_size":1142540,"success":1,"checksum":"5b0ae3779b8b21b5223bd2d3cceede3a","date_created":"2021-06-04T12:50:47Z","access_level":"open_access","relation":"main_file"}],"has_accepted_license":"1","keyword":["Multidisciplinary"],"publisher":"National Academy of Sciences","citation":{"ieee":"M. Y. Kim <i>et al.</i>, “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.","ama":"Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. <i>Proceedings of the National Academy of Sciences</i>. 2019;116(19):9652-9657. doi:<a href=\"https://doi.org/10.1073/pnas.1821435116\">10.1073/pnas.1821435116</a>","apa":"Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., &#38; Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1821435116\">https://doi.org/10.1073/pnas.1821435116</a>","chicago":"Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1821435116\">https://doi.org/10.1073/pnas.1821435116</a>.","ista":"Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. 2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.","mla":"Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:<a href=\"https://doi.org/10.1073/pnas.1821435116\">10.1073/pnas.1821435116</a>.","short":"M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657."},"department":[{"_id":"DaZi"}],"date_created":"2021-06-04T12:38:20Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"page":"9652-9657","month":"05","status":"public","date_published":"2019-05-07T00:00:00Z","quality_controlled":"1","_id":"9460","intvolume":"       116","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"issue":"19"},{"date_published":"2019-10-10T00:00:00Z","quality_controlled":"1","_id":"9530","publication_identifier":{"eissn":["1756-8935"]},"intvolume":"        12","citation":{"ama":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. <i>Epigenetics and Chromatin</i>. 2019;12. doi:<a href=\"https://doi.org/10.1186/s13072-019-0307-4\">10.1186/s13072-019-0307-4</a>","ieee":"K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development,” <i>Epigenetics and Chromatin</i>, vol. 12. Springer Nature, 2019.","apa":"Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., &#38; Zemach, A. (2019). DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. <i>Epigenetics and Chromatin</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13072-019-0307-4\">https://doi.org/10.1186/s13072-019-0307-4</a>","short":"K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019).","mla":"Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” <i>Epigenetics and Chromatin</i>, vol. 12, 62, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1186/s13072-019-0307-4\">10.1186/s13072-019-0307-4</a>.","ista":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 12, 62.","chicago":"Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” <i>Epigenetics and Chromatin</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1186/s13072-019-0307-4\">https://doi.org/10.1186/s13072-019-0307-4</a>."},"publisher":"Springer Nature","department":[{"_id":"DaZi"}],"date_created":"2021-06-08T09:21:51Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"month":"10","status":"public","file":[{"file_id":"9531","date_updated":"2021-06-08T09:29:19Z","content_type":"application/pdf","creator":"asandaue","relation":"main_file","access_level":"open_access","date_created":"2021-06-08T09:29:19Z","checksum":"86ff50a7517891511af2733c76c81b67","file_size":3221067,"success":1,"file_name":"2019_EpigeneticsAndChromatin_Harris.pdf"}],"has_accepted_license":"1","external_id":{"pmid":["31601251"]},"pmid":1,"author":[{"last_name":"Harris","first_name":"Keith D.","full_name":"Harris, Keith D."},{"full_name":"Lloyd, James P. B.","last_name":"Lloyd","first_name":"James P. B."},{"full_name":"Domb, Katherine","first_name":"Katherine","last_name":"Domb"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel"},{"last_name":"Zemach","first_name":"Assaf","full_name":"Zemach, Assaf"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","publication":"Epigenetics and Chromatin","type":"journal_article","date_updated":"2021-12-14T07:53:00Z","scopus_import":"1","ddc":["570"],"article_type":"original","article_processing_charge":"No","year":"2019","title":"DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development","volume":12,"oa":1,"extern":"1","day":"10","abstract":[{"lang":"eng","text":"Background\r\nDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems."}],"language":[{"iso":"eng"}],"article_number":"62","file_date_updated":"2021-06-08T09:29:19Z","publication_status":"published","doi":"10.1186/s13072-019-0307-4"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.1021/acs.nanolett.9b04445.s001","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7166"}]},"oa_version":"Published Version","author":[{"last_name":"Ucar","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217"},{"last_name":"Lipowsky","first_name":"Reinhard","full_name":"Lipowsky, Reinhard"}],"abstract":[{"text":"A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF)","lang":"eng"}],"year":"2019","title":"Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding","day":"19","month":"12","article_processing_charge":"No","status":"public","publisher":"American Chemical Society ","citation":{"chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” American Chemical Society , 2019. <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">https://doi.org/10.1021/acs.nanolett.9b04445.s001</a>.","ista":"Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding, American Chemical Society , <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">10.1021/acs.nanolett.9b04445.s001</a>.","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. <i>Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding</i>. American Chemical Society , 2019, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">10.1021/acs.nanolett.9b04445.s001</a>.","short":"M.C. Ucar, R. Lipowsky, (2019).","ieee":"M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding.” American Chemical Society , 2019.","apa":"Ucar, M. C., &#38; Lipowsky, R. (2019). Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. American Chemical Society . <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">https://doi.org/10.1021/acs.nanolett.9b04445.s001</a>","ama":"Ucar MC, Lipowsky R. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. 2019. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s001\">10.1021/acs.nanolett.9b04445.s001</a>"},"date_created":"2021-07-27T09:51:46Z","department":[{"_id":"EdHa"}],"_id":"9726","date_published":"2019-12-19T00:00:00Z","type":"research_data_reference","date_updated":"2024-10-09T20:59:07Z"},{"title":"Supporting text and results","year":"2019","day":"02","related_material":{"record":[{"status":"public","id":"6784","relation":"used_in_publication"}]},"oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.1371/journal.pcbi.1007168.s001","author":[{"last_name":"Ruess","first_name":"Jakob","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob"},{"orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros","last_name":"Pleska"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"_id":"9786","date_published":"2019-07-02T00:00:00Z","date_updated":"2025-04-15T07:33:55Z","type":"research_data_reference","status":"public","month":"07","article_processing_charge":"No","citation":{"apa":"Ruess, J., Pleska, M., Guet, C. C., &#38; Tkačik, G. (2019). Supporting text and results. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007168.s001\">https://doi.org/10.1371/journal.pcbi.1007168.s001</a>","ieee":"J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Supporting text and results.” Public Library of Science, 2019.","ama":"Ruess J, Pleska M, Guet CC, Tkačik G. Supporting text and results. 2019. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007168.s001\">10.1371/journal.pcbi.1007168.s001</a>","short":"J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, (2019).","mla":"Ruess, Jakob, et al. <i>Supporting Text and Results</i>. Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007168.s001\">10.1371/journal.pcbi.1007168.s001</a>.","ista":"Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Supporting text and results, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1007168.s001\">10.1371/journal.pcbi.1007168.s001</a>.","chicago":"Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Supporting Text and Results.” Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pcbi.1007168.s001\">https://doi.org/10.1371/journal.pcbi.1007168.s001</a>."},"publisher":"Public Library of Science","date_created":"2021-08-06T08:23:43Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}]},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.1371/journal.pbio.2005902.s006","oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6022"}]},"author":[{"first_name":"Richard M.","last_name":"Merrill","full_name":"Merrill, Richard M."},{"last_name":"Rastas","first_name":"Pasi","full_name":"Rastas, Pasi"},{"full_name":"Martin, Simon H.","first_name":"Simon H.","last_name":"Martin"},{"full_name":"Melo Hurtado, Maria C","id":"386D7308-F248-11E8-B48F-1D18A9856A87","first_name":"Maria C","last_name":"Melo Hurtado"},{"full_name":"Barker, Sarah","first_name":"Sarah","last_name":"Barker"},{"last_name":"Davey","first_name":"John","full_name":"Davey, John"},{"full_name":"Mcmillan, W. Owen","last_name":"Mcmillan","first_name":"W. Owen"},{"full_name":"Jiggins, Chris D.","first_name":"Chris D.","last_name":"Jiggins"}],"day":"07","year":"2019","title":"Raw behavioral data","article_processing_charge":"No","month":"02","status":"public","department":[{"_id":"NiBa"}],"date_created":"2021-08-06T11:34:56Z","publisher":"Public Library of Science","citation":{"ieee":"R. M. Merrill <i>et al.</i>, “Raw behavioral data.” Public Library of Science, 2019.","apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Raw behavioral data. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005902.s006\">https://doi.org/10.1371/journal.pbio.2005902.s006</a>","ama":"Merrill RM, Rastas P, Martin SH, et al. Raw behavioral data. 2019. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005902.s006\">10.1371/journal.pbio.2005902.s006</a>","ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Raw behavioral data, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2005902.s006\">10.1371/journal.pbio.2005902.s006</a>.","mla":"Merrill, Richard M., et al. <i>Raw Behavioral Data</i>. Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005902.s006\">10.1371/journal.pbio.2005902.s006</a>.","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, (2019).","chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Raw Behavioral Data.” Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pbio.2005902.s006\">https://doi.org/10.1371/journal.pbio.2005902.s006</a>."},"_id":"9801","type":"research_data_reference","date_updated":"2023-08-24T14:46:23Z","date_published":"2019-02-07T00:00:00Z"},{"date_published":"2019-07-16T00:00:00Z","date_updated":"2024-10-09T20:58:56Z","type":"research_data_reference","_id":"9802","citation":{"short":"H. Sachdeva, (2019).","mla":"Sachdeva, Himani. <i>Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat</i>. Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/dryad.8tp0900\">10.5061/dryad.8tp0900</a>.","ista":"Sachdeva H. 2019. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat, Dryad, <a href=\"https://doi.org/10.5061/dryad.8tp0900\">10.5061/dryad.8tp0900</a>.","chicago":"Sachdeva, Himani. “Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Dryad, 2019. <a href=\"https://doi.org/10.5061/dryad.8tp0900\">https://doi.org/10.5061/dryad.8tp0900</a>.","apa":"Sachdeva, H. (2019). Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. Dryad. <a href=\"https://doi.org/10.5061/dryad.8tp0900\">https://doi.org/10.5061/dryad.8tp0900</a>","ama":"Sachdeva H. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. 2019. doi:<a href=\"https://doi.org/10.5061/dryad.8tp0900\">10.5061/dryad.8tp0900</a>","ieee":"H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat.” Dryad, 2019."},"publisher":"Dryad","department":[{"_id":"NiBa"}],"date_created":"2021-08-06T11:45:11Z","status":"public","article_processing_charge":"No","month":"07","title":"Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat","year":"2019","day":"16","oa":1,"abstract":[{"lang":"eng","text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation-selection balance in a large, partially selfing source population under selection involving multiple non-identical loci. I then use individual-based simulations to study the eco-evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long-term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed."}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.8tp0900","open_access":"1"}],"author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6680"}]},"oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.5061/dryad.8tp0900"},{"_id":"9804","date_updated":"2023-08-29T06:41:51Z","type":"research_data_reference","date_published":"2019-06-06T00:00:00Z","status":"public","article_processing_charge":"No","month":"06","department":[{"_id":"NiBa"}],"date_created":"2021-08-06T11:52:54Z","publisher":"Dryad","citation":{"chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” Dryad, 2019. <a href=\"https://doi.org/10.5061/dryad.0q2h6tk\">https://doi.org/10.5061/dryad.0q2h6tk</a>.","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice, Dryad, <a href=\"https://doi.org/10.5061/dryad.0q2h6tk\">10.5061/dryad.0q2h6tk</a>.","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, (2019).","mla":"Castro, João Pl, et al. <i>Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice</i>. Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/dryad.0q2h6tk\">10.5061/dryad.0q2h6tk</a>.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. Dryad. <a href=\"https://doi.org/10.5061/dryad.0q2h6tk\">https://doi.org/10.5061/dryad.0q2h6tk</a>","ieee":"J. P. Castro <i>et al.</i>, “Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice.” Dryad, 2019.","ama":"Castro JP, Yancoskie MN, Marchini M, et al. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. 2019. doi:<a href=\"https://doi.org/10.5061/dryad.0q2h6tk\">10.5061/dryad.0q2h6tk</a>"},"abstract":[{"lang":"eng","text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response."}],"day":"06","oa":1,"title":"Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","year":"2019","oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6713"}]},"doi":"10.5061/dryad.0q2h6tk","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"url":"https://doi.org/10.5061/dryad.0q2h6tk","open_access":"1"}],"author":[{"full_name":"Castro, João Pl","last_name":"Castro","first_name":"João Pl"},{"full_name":"Yancoskie, Michelle N.","first_name":"Michelle N.","last_name":"Yancoskie"},{"last_name":"Marchini","first_name":"Marta","full_name":"Marchini, Marta"},{"first_name":"Stefanie","last_name":"Belohlavy","full_name":"Belohlavy, Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9849-498X"},{"first_name":"Layla","last_name":"Hiramatsu","full_name":"Hiramatsu, Layla"},{"full_name":"Kučka, Marek","first_name":"Marek","last_name":"Kučka"},{"full_name":"Beluch, William H.","last_name":"Beluch","first_name":"William H."},{"last_name":"Naumann","first_name":"Ronald","full_name":"Naumann, Ronald"},{"full_name":"Skuplik, Isabella","last_name":"Skuplik","first_name":"Isabella"},{"last_name":"Cobb","first_name":"John","full_name":"Cobb, John"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Rolian","first_name":"Campbell","full_name":"Rolian, Campbell"},{"last_name":"Chan","first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank"}]},{"department":[{"_id":"NiBa"}],"date_created":"2021-08-06T12:03:50Z","publisher":"Dryad","citation":{"chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. <a href=\"https://doi.org/10.5061/dryad.2kb6fh4\">https://doi.org/10.5061/dryad.2kb6fh4</a>.","mla":"Barton, Nicholas H. <i>Data from: The Consequences of an Introgression Event</i>. Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/dryad.2kb6fh4\">10.5061/dryad.2kb6fh4</a>.","short":"N.H. Barton, (2019).","ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, <a href=\"https://doi.org/10.5061/dryad.2kb6fh4\">10.5061/dryad.2kb6fh4</a>.","ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:<a href=\"https://doi.org/10.5061/dryad.2kb6fh4\">10.5061/dryad.2kb6fh4</a>","ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. <a href=\"https://doi.org/10.5061/dryad.2kb6fh4\">https://doi.org/10.5061/dryad.2kb6fh4</a>"},"month":"01","article_processing_charge":"No","status":"public","type":"research_data_reference","date_updated":"2025-07-10T11:52:34Z","date_published":"2019-01-09T00:00:00Z","_id":"9805","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.2kb6fh4"}],"doi":"10.5061/dryad.2kb6fh4","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"relation":"used_in_publication","id":"40","status":"public"}]},"oa_version":"Published Version","oa":1,"day":"09","year":"2019","title":"Data from: The consequences of an introgression event","abstract":[{"lang":"eng","text":"The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?"}]},{"doi":"10.5061/dryad.9kj41f0","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6105"}]},"oa_version":"Published Version","author":[{"orcid":"0000-0002-8696-6978","full_name":"Kutzer, Megan","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","last_name":"Kutzer","first_name":"Megan"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"},{"full_name":"Armitage, Sophie A.O.","last_name":"Armitage","first_name":"Sophie A.O."}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.9kj41f0","open_access":"1"}],"abstract":[{"lang":"eng","text":"1. Hosts can alter their strategy towards pathogens during their lifetime, i.e., they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e. resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fitness consequences that result from a high pathogen load. Finally, previous exposure may also lead to life history adjustments, such as terminal investment into reproduction. 2. Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested if previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute-phase infection (one day post-challenge). We then asked if previous pathogen exposure affects chronic-phase pathogen persistence and longer-term survival (28 days post-challenge). 3. We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long-term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses. 4. We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection. 5. To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi-faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host-pathogen system and that infection persistence may be bacterium-specific."}],"oa":1,"day":"05","year":"2019","title":"Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance","month":"02","article_processing_charge":"No","status":"public","date_created":"2021-08-06T12:06:40Z","department":[{"_id":"SyCr"}],"publisher":"Dryad","citation":{"ieee":"M. Kutzer, J. Kurtz, and S. A. O. Armitage, “Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance.” Dryad, 2019.","ama":"Kutzer M, Kurtz J, Armitage SAO. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. 2019. doi:<a href=\"https://doi.org/10.5061/dryad.9kj41f0\">10.5061/dryad.9kj41f0</a>","apa":"Kutzer, M., Kurtz, J., &#38; Armitage, S. A. O. (2019). Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Dryad. <a href=\"https://doi.org/10.5061/dryad.9kj41f0\">https://doi.org/10.5061/dryad.9kj41f0</a>","ista":"Kutzer M, Kurtz J, Armitage SAO. 2019. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance, Dryad, <a href=\"https://doi.org/10.5061/dryad.9kj41f0\">10.5061/dryad.9kj41f0</a>.","mla":"Kutzer, Megan, et al. <i>Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance</i>. Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/dryad.9kj41f0\">10.5061/dryad.9kj41f0</a>.","short":"M. Kutzer, J. Kurtz, S.A.O. Armitage, (2019).","chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie A.O. Armitage. “Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Dryad, 2019. <a href=\"https://doi.org/10.5061/dryad.9kj41f0\">https://doi.org/10.5061/dryad.9kj41f0</a>."},"_id":"9806","type":"research_data_reference","date_updated":"2025-07-10T11:53:11Z","date_published":"2019-02-05T00:00:00Z"},{"date_updated":"2023-09-19T10:13:08Z","type":"journal_article","publication":"Journal of the London Mathematical Society","ddc":["510"],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","day":"01","oa":1,"title":"The wonderful compactification for quantum groups","volume":99,"year":"2019","language":[{"iso":"eng"}],"publist_id":"8052","abstract":[{"lang":"eng","text":"In this paper, we introduce a quantum version of the wonderful compactification of a group as a certain noncommutative projective scheme. Our approach stems from the fact that the wonderful compactification encodes the asymptotics of matrix coefficients, and from its realization as a GIT quotient of the Vinberg semigroup. In order to define the wonderful compactification for a quantum group, we adopt a generalized formalism of Proj categories in the spirit of Artin and Zhang. Key to our construction is a quantum version of the Vinberg semigroup, which we define as a q-deformation of a certain Rees algebra, compatible with a standard Poisson structure. Furthermore, we discuss quantum analogues of the stratification of the wonderful compactification by orbits for a certain group action, and provide explicit computations in the case of SL2."}],"file_date_updated":"2020-07-14T12:46:35Z","doi":"10.1112/jlms.12193","publication_status":"published","quality_controlled":"1","date_published":"2019-06-01T00:00:00Z","issue":"3","intvolume":"        99","_id":"5","department":[{"_id":"TaHa"}],"date_created":"2018-12-11T11:44:06Z","citation":{"chicago":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” <i>Journal of the London Mathematical Society</i>. Wiley, 2019. <a href=\"https://doi.org/10.1112/jlms.12193\">https://doi.org/10.1112/jlms.12193</a>.","ista":"Ganev IV. 2019. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 99(3), 778–806.","short":"I.V. Ganev, Journal of the London Mathematical Society 99 (2019) 778–806.","mla":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” <i>Journal of the London Mathematical Society</i>, vol. 99, no. 3, Wiley, 2019, pp. 778–806, doi:<a href=\"https://doi.org/10.1112/jlms.12193\">10.1112/jlms.12193</a>.","apa":"Ganev, I. V. (2019). The wonderful compactification for quantum groups. <i>Journal of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/jlms.12193\">https://doi.org/10.1112/jlms.12193</a>","ieee":"I. V. Ganev, “The wonderful compactification for quantum groups,” <i>Journal of the London Mathematical Society</i>, vol. 99, no. 3. Wiley, pp. 778–806, 2019.","ama":"Ganev IV. The wonderful compactification for quantum groups. <i>Journal of the London Mathematical Society</i>. 2019;99(3):778-806. doi:<a href=\"https://doi.org/10.1112/jlms.12193\">10.1112/jlms.12193</a>"},"publisher":"Wiley","status":"public","month":"06","page":"778-806","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","file":[{"creator":"kschuh","content_type":"application/pdf","file_id":"7238","date_updated":"2020-07-14T12:46:35Z","file_size":431754,"checksum":"1be56239b2cd740a0e9a084f773c22f6","file_name":"2019_Wiley_Ganev.pdf","date_created":"2020-01-07T13:31:53Z","relation":"main_file","access_level":"open_access"}],"isi":1,"author":[{"full_name":"Ganev, Iordan V","id":"447491B8-F248-11E8-B48F-1D18A9856A87","last_name":"Ganev","first_name":"Iordan V"}],"external_id":{"isi":["000470025900008"]},"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"day":"01","volume":166,"title":"Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone","year":"2019","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Pollinators display a remarkable diversity of foraging strategies with flowering plants, from primarily mutualistic interactions to cheating through nectar robbery. Despite numerous studies on the effect of nectar robbing on components of plant fitness, its contribution to reproductive isolation is unclear. We experimentally tested the impact of different pollinator strategies in a natural hybrid zone between two subspecies of Antirrhinum majus with alternate flower colour guides. On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus (magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral visitors at different time points during the flowering season. Using long-run camera surveys, we quantify the impact of nectar robbing on the number of flowers visited per inflorescence and the flower probing time. We further experimentally tested the effect of nectar robbing on female reproductive success by manipulating the intensity of robbing. While robbing increased over time the number of legitimate visitors tended to decrease concomitantly. We found that the number of flowers pollinated on a focal inflorescence decreased with the number of prior robbing events. However, in the manipulative experiment, fruit set and fruit volume did not vary significantly between low robbing and control treatments. Our findings challenge the idea that robbers have a negative impact on plant fitness through female function. This study also adds to our understanding of the components of pollinator-mediated reproductive isolation and the maintenance of Antirrhinum hybrid zones."}],"doi":"10.1080/23818107.2018.1545142","publication_status":"published","date_updated":"2025-07-10T11:52:54Z","publication":"Botany Letters","type":"journal_article","scopus_import":"1","article_processing_charge":"No","isi":1,"author":[{"last_name":"Andalo","first_name":"Christophe","full_name":"Andalo, Christophe"},{"full_name":"Burrus, Monique","last_name":"Burrus","first_name":"Monique"},{"full_name":"Paute, Sandrine","last_name":"Paute","first_name":"Sandrine"},{"first_name":"Christine","last_name":"Lauzeral","full_name":"Lauzeral, Christine"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field"}],"external_id":{"isi":["000463802800009"]},"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","date_published":"2019-01-01T00:00:00Z","issue":"1","intvolume":"       166","publication_identifier":{"issn":["2381-8107"],"eissn":["2381-8115"]},"_id":"5680","date_created":"2018-12-16T22:59:20Z","department":[{"_id":"NiBa"}],"publisher":"Taylor and Francis","citation":{"ieee":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, and D. Field, “Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone,” <i>Botany Letters</i>, vol. 166, no. 1. Taylor and Francis, pp. 80–92, 2019.","ama":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. <i>Botany Letters</i>. 2019;166(1):80-92. doi:<a href=\"https://doi.org/10.1080/23818107.2018.1545142\">10.1080/23818107.2018.1545142</a>","apa":"Andalo, C., Burrus, M., Paute, S., Lauzeral, C., &#38; Field, D. (2019). Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. <i>Botany Letters</i>. Taylor and Francis. <a href=\"https://doi.org/10.1080/23818107.2018.1545142\">https://doi.org/10.1080/23818107.2018.1545142</a>","chicago":"Andalo, Christophe, Monique Burrus, Sandrine Paute, Christine Lauzeral, and David Field. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” <i>Botany Letters</i>. Taylor and Francis, 2019. <a href=\"https://doi.org/10.1080/23818107.2018.1545142\">https://doi.org/10.1080/23818107.2018.1545142</a>.","ista":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. 2019. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 166(1), 80–92.","mla":"Andalo, Christophe, et al. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” <i>Botany Letters</i>, vol. 166, no. 1, Taylor and Francis, 2019, pp. 80–92, doi:<a href=\"https://doi.org/10.1080/23818107.2018.1545142\">10.1080/23818107.2018.1545142</a>.","short":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, D. Field, Botany Letters 166 (2019) 80–92."},"status":"public","month":"01","page":"80-92"}]
