[{"oa":1,"external_id":{"isi":["000487184200024"],"pmid":["31111487"]},"quality_controlled":"1","isi":1,"doi":"10.1111/nph.15932","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"month":"10","pmid":1,"year":"2019","department":[{"_id":"JiFr"}],"publisher":"Wiley","publication_status":"published","author":[{"full_name":"Zhang, Yuzhou","first_name":"Yuzhou","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956"},{"first_name":"P","last_name":"He","full_name":"He, P"},{"first_name":"X","last_name":"Ma","full_name":"Ma, X"},{"full_name":"Yang, Z","last_name":"Yang","first_name":"Z"},{"first_name":"C","last_name":"Pang","full_name":"Pang, C"},{"full_name":"Yu, J","last_name":"Yu","first_name":"J"},{"last_name":"Wang","first_name":"G","full_name":"Wang, G"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"first_name":"G","last_name":"Xiao","full_name":"Xiao, G"}],"volume":224,"date_created":"2019-05-28T14:33:26Z","date_updated":"2023-08-28T08:40:13Z","file_date_updated":"2020-10-14T08:59:33Z","citation":{"chicago":"Zhang, Yuzhou, P He, X Ma, Z Yang, C Pang, J Yu, G Wang, Jiří Friml, and G Xiao. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.15932.","mla":"Zhang, Yuzhou, et al. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist, vol. 224, no. 2, Wiley, 2019, pp. 761–74, doi:10.1111/nph.15932.","short":"Y. Zhang, P. He, X. Ma, Z. Yang, C. Pang, J. Yu, G. Wang, J. Friml, G. Xiao, New Phytologist 224 (2019) 761–774.","ista":"Zhang Y, He P, Ma X, Yang Z, Pang C, Yu J, Wang G, Friml J, Xiao G. 2019. Auxin-mediated statolith production for root gravitropism. New Phytologist. 224(2), 761–774.","ieee":"Y. Zhang et al., “Auxin-mediated statolith production for root gravitropism,” New Phytologist, vol. 224, no. 2. Wiley, pp. 761–774, 2019.","apa":"Zhang, Y., He, P., Ma, X., Yang, Z., Pang, C., Yu, J., … Xiao, G. (2019). Auxin-mediated statolith production for root gravitropism. New Phytologist. Wiley. https://doi.org/10.1111/nph.15932","ama":"Zhang Y, He P, Ma X, et al. Auxin-mediated statolith production for root gravitropism. New Phytologist. 2019;224(2):761-774. doi:10.1111/nph.15932"},"publication":"New Phytologist","page":"761-774","article_type":"original","date_published":"2019-10-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6504","intvolume":" 224","status":"public","ddc":["580"],"title":"Auxin-mediated statolith production for root gravitropism","oa_version":"Submitted Version","file":[{"file_id":"8661","relation":"main_file","date_created":"2020-10-14T08:59:33Z","date_updated":"2020-10-14T08:59:33Z","success":1,"checksum":"6488243334538f5c39099a701cbf76b9","file_name":"2019_NewPhytologist_Zhang_accepted.pdf","access_level":"open_access","creator":"dernst","file_size":1099061,"content_type":"application/pdf"}],"type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Root gravitropism is one of the most important processes allowing plant adaptation to the land environment. Auxin plays a central role in mediating root gravitropism, but how auxin contributes to gravitational perception and the subsequent response is still unclear.\r\n\r\nHere, we showed that the local auxin maximum/gradient within the root apex, which is generated by the PIN directional auxin transporters, regulates the expression of three key starch granule synthesis genes, SS4, PGM and ADG1, which in turn influence the accumulation of starch granules that serve as a statolith perceiving gravity.\r\n\r\nMoreover, using the cvxIAA‐ccvTIR1 system, we also showed that TIR1‐mediated auxin signaling is required for starch granule formation and gravitropic response within root tips. In addition, axr3 mutants showed reduced auxin‐mediated starch granule accumulation and disruption of gravitropism within the root apex.\r\n\r\nOur results indicate that auxin‐mediated statolith production relies on the TIR1/AFB‐AXR3‐mediated auxin signaling pathway. In summary, we propose a dual role for auxin in gravitropism: the regulation of both gravity perception and response."}]},{"scopus_import":"1","article_processing_charge":"No","day":"01","page":"1221–1230","article_type":"original","citation":{"apa":"Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni, A., & Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0412-y","ieee":"L. Noda-García et al., “Chance and pleiotropy dominate genetic diversity in complex bacterial environments,” Nature Microbiology, vol. 4, no. 7. Springer Nature, pp. 1221–1230, 2019.","ista":"Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik DS. 2019. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 4(7), 1221–1230.","ama":"Noda-García L, Davidi D, Korenblum E, et al. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 2019;4(7):1221–1230. doi:10.1038/s41564-019-0412-y","chicago":"Noda-García, Lianet, Dan Davidi, Elisa Korenblum, Assaf Elazar, Ekaterina Putintseva, Asaph Aharoni, and Dan S. Tawfik. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology. Springer Nature, 2019. https://doi.org/10.1038/s41564-019-0412-y.","short":"L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni, D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230.","mla":"Noda-García, Lianet, et al. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology, vol. 4, no. 7, Springer Nature, 2019, pp. 1221–1230, doi:10.1038/s41564-019-0412-y."},"publication":"Nature Microbiology","date_published":"2019-07-01T00:00:00Z","type":"journal_article","issue":"7","abstract":[{"text":"How does environmental complexity affect the evolution of single genes? Here, we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase mutants across 19 different environments—from phenotypically homogeneous single-cell populations in liquid media to heterogeneous biofilms, plant roots and soil populations. The effects of individual gene mutations on organismal fitness were highly reproducible in liquid cultures. However, 84% of the tested alleles showed opposing fitness effects under different growth conditions (sign environmental pleiotropy). In colony biofilms and soil samples, different alleles dominated in parallel replica experiments. Accordingly, we found that in these heterogeneous cell populations the fate of mutations was dictated by a combination of selection and drift. The latter relates to programmed prophage excisions that occurred during biofilm development. Overall, for each condition, a wide range of glutamate dehydrogenase mutations persisted and sometimes fixated as a result of the combined action of selection, pleiotropy and chance. However, over longer periods and in multiple environments, nearly all of this diversity would be lost—across all the environments and conditions that we tested, the wild type was the fittest allele.","lang":"eng"}],"intvolume":" 4","status":"public","title":"Chance and pleiotropy dominate genetic diversity in complex bacterial environments","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6506","oa_version":"Preprint","publication_identifier":{"issn":["2058-5276"]},"month":"07","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/340828v2","open_access":"1"}],"external_id":{"isi":["000480348200017"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41564-019-0412-y","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"publication_status":"published","year":"2019","volume":4,"date_updated":"2023-08-28T08:39:47Z","date_created":"2019-05-29T13:03:30Z","author":[{"full_name":"Noda-García, Lianet","first_name":"Lianet","last_name":"Noda-García"},{"full_name":"Davidi, Dan","first_name":"Dan","last_name":"Davidi"},{"last_name":"Korenblum","first_name":"Elisa","full_name":"Korenblum, Elisa"},{"last_name":"Elazar","first_name":"Assaf","full_name":"Elazar, Assaf"},{"last_name":"Putintseva","first_name":"Ekaterina","id":"2EF67C84-F248-11E8-B48F-1D18A9856A87","full_name":"Putintseva, Ekaterina"},{"full_name":"Aharoni, Asaph","first_name":"Asaph","last_name":"Aharoni"},{"full_name":"Tawfik, Dan S.","last_name":"Tawfik","first_name":"Dan S."}]},{"month":"08","publication_identifier":{"issn":["0304-3940"]},"doi":"10.1016/j.neulet.2019.134310","language":[{"iso":"eng"}],"external_id":{"isi":["000486094600037"],"pmid":["31158432"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020","grant_number":"715571","_id":"25D4A630-B435-11E9-9278-68D0E5697425"},{"_id":"267F75D8-B435-11E9-9278-68D0E5697425","name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling"}],"file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"article_number":"134310","author":[{"full_name":"Maes, Margaret E","first_name":"Margaret E","last_name":"Maes","id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085"},{"first_name":"Gloria","last_name":"Colombo","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria"},{"full_name":"Schulz, Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5297-733X","first_name":"Rouven","last_name":"Schulz"},{"full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra"}],"date_updated":"2023-08-28T09:30:57Z","date_created":"2019-06-05T13:16:24Z","volume":707,"year":"2019","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"SaSi"}],"day":"10","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-08-10T00:00:00Z","publication":"Neuroscience Letters","citation":{"ista":"Maes ME, Colombo G, Schulz R, Siegert S. 2019. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 707, 134310.","apa":"Maes, M. E., Colombo, G., Schulz, R., & Siegert, S. (2019). Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. Elsevier. https://doi.org/10.1016/j.neulet.2019.134310","ieee":"M. E. Maes, G. Colombo, R. Schulz, and S. Siegert, “Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges,” Neuroscience Letters, vol. 707. Elsevier, 2019.","ama":"Maes ME, Colombo G, Schulz R, Siegert S. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 2019;707. doi:10.1016/j.neulet.2019.134310","chicago":"Maes, Margaret E, Gloria Colombo, Rouven Schulz, and Sandra Siegert. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” Neuroscience Letters. Elsevier, 2019. https://doi.org/10.1016/j.neulet.2019.134310.","mla":"Maes, Margaret E., et al. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” Neuroscience Letters, vol. 707, 134310, Elsevier, 2019, doi:10.1016/j.neulet.2019.134310.","short":"M.E. Maes, G. Colombo, R. Schulz, S. Siegert, Neuroscience Letters 707 (2019)."},"article_type":"original","abstract":[{"text":"Microglia have emerged as a critical component of neurodegenerative diseases. Genetic manipulation of microglia can elucidate their functional impact in disease. In neuroscience, recombinant viruses such as lentiviruses and adeno-associated viruses (AAVs) have been successfully used to target various cell types in the brain, although effective transduction of microglia is rare. In this review, we provide a short background of lentiviruses and AAVs, and strategies for designing recombinant viral vectors. Then, we will summarize recent literature on successful microglial transductions in vitro and in vivo, and discuss the current challenges. Finally, we provide guidelines for reporting the efficiency and specificity of viral targeting in microglia, which will enable the microglial research community to assess and improve methodologies for future studies.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2019_Neuroscience_Maes.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1779287,"file_id":"6551","relation":"main_file","date_created":"2019-06-08T11:44:20Z","date_updated":"2020-07-14T12:47:33Z","checksum":"553c9dbd39727fbed55ee991c51ca4d1"}],"_id":"6521","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges","intvolume":" 707"},{"publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"month":"06","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986928","open_access":"1"}],"external_id":{"isi":["000470149000048"],"pmid":["31092921"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41586-019-1212-5","department":[{"_id":"EdHa"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2019","volume":570,"date_updated":"2023-08-28T09:30:23Z","date_created":"2019-06-02T21:59:14Z","author":[{"full_name":"Guiu, Jordi","last_name":"Guiu","first_name":"Jordi"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"first_name":"Shiro","last_name":"Yui","full_name":"Yui, Shiro"},{"first_name":"Samuel","last_name":"Demharter","full_name":"Demharter, Samuel"},{"first_name":"Svetlana","last_name":"Ulyanchenko","full_name":"Ulyanchenko, Svetlana"},{"full_name":"Maimets, Martti","last_name":"Maimets","first_name":"Martti"},{"full_name":"Jørgensen, Anne","first_name":"Anne","last_name":"Jørgensen"},{"full_name":"Perlman, Signe","last_name":"Perlman","first_name":"Signe"},{"full_name":"Lundvall, Lene","last_name":"Lundvall","first_name":"Lene"},{"full_name":"Mamsen, Linn Salto","first_name":"Linn Salto","last_name":"Mamsen"},{"first_name":"Agnete","last_name":"Larsen","full_name":"Larsen, Agnete"},{"last_name":"Olesen","first_name":"Rasmus H.","full_name":"Olesen, Rasmus H."},{"full_name":"Andersen, Claus Yding","last_name":"Andersen","first_name":"Claus Yding"},{"full_name":"Thuesen, Lea Langhoff","last_name":"Thuesen","first_name":"Lea Langhoff"},{"full_name":"Hare, Kristine Juul","last_name":"Hare","first_name":"Kristine Juul"},{"full_name":"Pers, Tune H.","first_name":"Tune H.","last_name":"Pers"},{"full_name":"Khodosevich, Konstantin","last_name":"Khodosevich","first_name":"Konstantin"},{"full_name":"Simons, Benjamin D.","first_name":"Benjamin D.","last_name":"Simons"},{"full_name":"Jensen, Kim B.","last_name":"Jensen","first_name":"Kim B."}],"scopus_import":"1","article_processing_charge":"No","day":"06","page":"107-111","article_type":"original","citation":{"ista":"Guiu J, Hannezo EB, Yui S, Demharter S, Ulyanchenko S, Maimets M, Jørgensen A, Perlman S, Lundvall L, Mamsen LS, Larsen A, Olesen RH, Andersen CY, Thuesen LL, Hare KJ, Pers TH, Khodosevich K, Simons BD, Jensen KB. 2019. Tracing the origin of adult intestinal stem cells. Nature. 570, 107–111.","ieee":"J. Guiu et al., “Tracing the origin of adult intestinal stem cells,” Nature, vol. 570. Springer Nature, pp. 107–111, 2019.","apa":"Guiu, J., Hannezo, E. B., Yui, S., Demharter, S., Ulyanchenko, S., Maimets, M., … Jensen, K. B. (2019). Tracing the origin of adult intestinal stem cells. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1212-5","ama":"Guiu J, Hannezo EB, Yui S, et al. Tracing the origin of adult intestinal stem cells. Nature. 2019;570:107-111. doi:10.1038/s41586-019-1212-5","chicago":"Guiu, Jordi, Edouard B Hannezo, Shiro Yui, Samuel Demharter, Svetlana Ulyanchenko, Martti Maimets, Anne Jørgensen, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1212-5.","mla":"Guiu, Jordi, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature, vol. 570, Springer Nature, 2019, pp. 107–11, doi:10.1038/s41586-019-1212-5.","short":"J. Guiu, E.B. Hannezo, S. Yui, S. Demharter, S. Ulyanchenko, M. Maimets, A. Jørgensen, S. Perlman, L. Lundvall, L.S. Mamsen, A. Larsen, R.H. Olesen, C.Y. Andersen, L.L. Thuesen, K.J. Hare, T.H. Pers, K. Khodosevich, B.D. Simons, K.B. Jensen, Nature 570 (2019) 107–111."},"publication":"Nature","date_published":"2019-06-06T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Adult intestinal stem cells are located at the bottom of crypts of Lieberkühn, where they express markers such as LGR5 1,2 and fuel the constant replenishment of the intestinal epithelium1. Although fetal LGR5-expressing cells can give rise to adult intestinal stem cells3,4, it remains unclear whether this population in the patterned epithelium represents unique intestinal stem-cell precursors. Here we show, using unbiased quantitative lineage-tracing approaches, biophysical modelling and intestinal transplantation, that all cells of the mouse intestinal epithelium—irrespective of their location and pattern of LGR5 expression in the fetal gut tube—contribute actively to the adult intestinal stem cell pool. Using 3D imaging, we find that during fetal development the villus undergoes gross remodelling and fission. This brings epithelial cells from the non-proliferative villus into the proliferative intervillus region, which enables them to contribute to the adult stem-cell niche. Our results demonstrate that large-scale remodelling of the intestinal wall and cell-fate specification are closely linked. Moreover, these findings provide a direct link between the observed plasticity and cellular reprogramming of differentiating cells in adult tissues following damage5,6,7,8,9, revealing that stem-cell identity is an induced rather than a hardwired property."}],"intvolume":" 570","status":"public","title":"Tracing the origin of adult intestinal stem cells","_id":"6513","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version"},{"_id":"6564","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions","status":"public","intvolume":" 431","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Optogenetics enables the spatio-temporally precise control of cell and animal behavior. Many optogenetic tools are driven by light-controlled protein–protein interactions (PPIs) that are repurposed from natural light-sensitive domains (LSDs). Applying light-controlled PPIs to new target proteins is challenging because it is difficult to predict which of the many available LSDs, if any, will yield robust light regulation. As a consequence, fusion protein libraries need to be prepared and tested, but methods and platforms to facilitate this process are currently not available. Here, we developed a genetic engineering strategy and vector library for the rapid generation of light-controlled PPIs. The strategy permits fusing a target protein to multiple LSDs efficiently and in two orientations. The public and expandable library contains 29 vectors with blue, green or red light-responsive LSDs, many of which have been previously applied ex vivo and in vivo. We demonstrate the versatility of the approach and the necessity for sampling LSDs by generating light-activated caspase-9 (casp9) enzymes. Collectively, this work provides a new resource for optical regulation of a broad range of target proteins in cell and developmental biology.","lang":"eng"}],"issue":"17","publication":"Journal of Molecular Biology","citation":{"short":"A.-M. Tichy, E.J. Gerrard, J.M.D. Legrand, R.M. Hobbs, H.L. Janovjak, Journal of Molecular Biology 431 (2019) 3046–3055.","mla":"Tichy, Alexandra-Madelaine, et al. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” Journal of Molecular Biology, vol. 431, no. 17, Elsevier, 2019, pp. 3046–55, doi:10.1016/j.jmb.2019.05.033.","chicago":"Tichy, Alexandra-Madelaine, Elliot J. Gerrard, Julien M.D. Legrand, Robin M. Hobbs, and Harald L Janovjak. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” Journal of Molecular Biology. Elsevier, 2019. https://doi.org/10.1016/j.jmb.2019.05.033.","ama":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. 2019;431(17):3046-3055. doi:10.1016/j.jmb.2019.05.033","apa":"Tichy, A.-M., Gerrard, E. J., Legrand, J. M. D., Hobbs, R. M., & Janovjak, H. L. (2019). Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2019.05.033","ieee":"A.-M. Tichy, E. J. Gerrard, J. M. D. Legrand, R. M. Hobbs, and H. L. Janovjak, “Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions,” Journal of Molecular Biology, vol. 431, no. 17. Elsevier, pp. 3046–3055, 2019.","ista":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. 2019. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. 431(17), 3046–3055."},"article_type":"original","page":"3046-3055","date_published":"2019-08-09T00:00:00Z","scopus_import":"1","day":"09","article_processing_charge":"No","year":"2019","publication_status":"published","department":[{"_id":"HaJa"}],"publisher":"Elsevier","author":[{"full_name":"Tichy, Alexandra-Madelaine","last_name":"Tichy","first_name":"Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gerrard, Elliot J.","first_name":"Elliot J.","last_name":"Gerrard"},{"full_name":"Legrand, Julien M.D.","last_name":"Legrand","first_name":"Julien M.D."},{"last_name":"Hobbs","first_name":"Robin M.","full_name":"Hobbs, Robin M."},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"date_created":"2019-06-16T21:59:14Z","date_updated":"2023-08-28T09:39:22Z","volume":431,"main_file_link":[{"open_access":"1","url":"http://www.biorxiv.org/content/10.1101/583369v1"}],"external_id":{"isi":["000482872100002"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1016/j.jmb.2019.05.033","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["00222836"],"eissn":["10898638"]}},{"author":[{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"volume":29,"date_updated":"2023-08-28T09:38:00Z","date_created":"2019-06-09T21:59:10Z","pmid":1,"year":"2019","publisher":"Elsevier","department":[{"_id":"SyCr"}],"publication_status":"published","publication_identifier":{"issn":["09609822"]},"month":"06","doi":"10.1016/j.cub.2019.03.035","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2019.03.035","open_access":"1"}],"oa":1,"external_id":{"pmid":["31163158"],"isi":["000470902000023"]},"isi":1,"quality_controlled":"1","issue":"11","abstract":[{"text":"When animals become sick, infected cells and an armada of activated immune cells attempt to eliminate the pathogen from the body. Once infectious particles have breached the body's physical barriers of the skin or gut lining, an initially local response quickly escalates into a systemic response, attracting mobile immune cells to the site of infection. These cells complement the initial, unspecific defense with a more specialized, targeted response. This can also provide long-term immune memory and protection against future infection. The cell-autonomous defenses of the infected cells are thus aided by the actions of recruited immune cells. These specialized cells are the most mobile cells in the body, constantly patrolling through the otherwise static tissue to detect incoming pathogens. Such constant immune surveillance means infections are noticed immediately and can be rapidly cleared from the body. Some immune cells also remove infected cells that have succumbed to infection. All this prevents pathogen replication and spread to healthy tissues. Although this may involve the sacrifice of some somatic tissue, this is typically replaced quickly. Particular care is, however, given to the reproductive organs, which should always remain disease free (immune privilege). ","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6552","intvolume":" 29","title":"Social immunity in insects","status":"public","article_processing_charge":"No","day":"03","scopus_import":"1","date_published":"2019-06-03T00:00:00Z","citation":{"chicago":"Cremer, Sylvia. “Social Immunity in Insects.” Current Biology. Elsevier, 2019. https://doi.org/10.1016/j.cub.2019.03.035.","short":"S. Cremer, Current Biology 29 (2019) R458–R463.","mla":"Cremer, Sylvia. “Social Immunity in Insects.” Current Biology, vol. 29, no. 11, Elsevier, 2019, pp. R458–63, doi:10.1016/j.cub.2019.03.035.","ieee":"S. Cremer, “Social immunity in insects,” Current Biology, vol. 29, no. 11. Elsevier, pp. R458–R463, 2019.","apa":"Cremer, S. (2019). Social immunity in insects. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2019.03.035","ista":"Cremer S. 2019. Social immunity in insects. Current Biology. 29(11), R458–R463.","ama":"Cremer S. Social immunity in insects. Current Biology. 2019;29(11):R458-R463. doi:10.1016/j.cub.2019.03.035"},"publication":"Current Biology","page":"R458-R463","article_type":"original"},{"month":"05","publication_identifier":{"issn":["00911798"]},"doi":"10.1214/18-AOP1284","language":[{"iso":"eng"}],"external_id":{"isi":["000466616100003"],"arxiv":["1612.05920"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.05920"}],"quality_controlled":"1","isi":1,"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"ec_funded":1,"author":[{"full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao","first_name":"Zhigang"},{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"last_name":"Schnelli","first_name":"Kevin","orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin"}],"date_updated":"2023-08-28T09:32:29Z","date_created":"2019-06-02T21:59:13Z","volume":47,"year":"2019","publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-05-01T00:00:00Z","publication":"Annals of Probability","citation":{"apa":"Bao, Z., Erdös, L., & Schnelli, K. (2019). Local single ring theorem on optimal scale. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AOP1284","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local single ring theorem on optimal scale,” Annals of Probability, vol. 47, no. 3. Institute of Mathematical Statistics, pp. 1270–1334, 2019.","ista":"Bao Z, Erdös L, Schnelli K. 2019. Local single ring theorem on optimal scale. Annals of Probability. 47(3), 1270–1334.","ama":"Bao Z, Erdös L, Schnelli K. Local single ring theorem on optimal scale. Annals of Probability. 2019;47(3):1270-1334. doi:10.1214/18-AOP1284","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Single Ring Theorem on Optimal Scale.” Annals of Probability. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AOP1284.","short":"Z. Bao, L. Erdös, K. Schnelli, Annals of Probability 47 (2019) 1270–1334.","mla":"Bao, Zhigang, et al. “Local Single Ring Theorem on Optimal Scale.” Annals of Probability, vol. 47, no. 3, Institute of Mathematical Statistics, 2019, pp. 1270–334, doi:10.1214/18-AOP1284."},"page":"1270-1334","abstract":[{"text":"Let U and V be two independent N by N random matrices that are distributed according to Haar measure on U(N). Let Σ be a nonnegative deterministic N by N matrix. The single ring theorem [Ann. of Math. (2) 174 (2011) 1189–1217] asserts that the empirical eigenvalue distribution of the matrix X:=UΣV∗ converges weakly, in the limit of large N, to a deterministic measure which is supported on a single ring centered at the origin in ℂ. Within the bulk regime, that is, in the interior of the single ring, we establish the convergence of the empirical eigenvalue distribution on the optimal local scale of order N−1/2+ε and establish the optimal convergence rate. The same results hold true when U and V are Haar distributed on O(N).","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6511","title":"Local single ring theorem on optimal scale","status":"public","intvolume":" 47"},{"publication_identifier":{"eissn":["18790410"],"issn":["09550674"]},"month":"10","quality_controlled":"1","isi":1,"external_id":{"pmid":["31181348"],"isi":["000486545800014"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.ceb.2019.04.008","publisher":"Elsevier","department":[{"_id":"EdHa"}],"publication_status":"published","pmid":1,"year":"2019","volume":60,"date_updated":"2023-08-28T09:38:57Z","date_created":"2019-06-16T21:59:12Z","author":[{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"last_name":"Simons","first_name":"Benjamin D.","full_name":"Simons, Benjamin D."}],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"99-105","article_type":"original","citation":{"ista":"Hannezo EB, Simons BD. 2019. Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. 60, 99–105.","ieee":"E. B. Hannezo and B. D. Simons, “Multiscale dynamics of branching morphogenesis,” Current Opinion in Cell Biology, vol. 60. Elsevier, pp. 99–105, 2019.","apa":"Hannezo, E. B., & Simons, B. D. (2019). Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2019.04.008","ama":"Hannezo EB, Simons BD. Multiscale dynamics of branching morphogenesis. Current Opinion in Cell Biology. 2019;60:99-105. doi:10.1016/j.ceb.2019.04.008","chicago":"Hannezo, Edouard B, and Benjamin D. Simons. “Multiscale Dynamics of Branching Morphogenesis.” Current Opinion in Cell Biology. Elsevier, 2019. https://doi.org/10.1016/j.ceb.2019.04.008.","mla":"Hannezo, Edouard B., and Benjamin D. Simons. “Multiscale Dynamics of Branching Morphogenesis.” Current Opinion in Cell Biology, vol. 60, Elsevier, 2019, pp. 99–105, doi:10.1016/j.ceb.2019.04.008.","short":"E.B. Hannezo, B.D. Simons, Current Opinion in Cell Biology 60 (2019) 99–105."},"publication":"Current Opinion in Cell Biology","date_published":"2019-10-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Branching morphogenesis is a prototypical example of complex three-dimensional organ sculpting, required in multiple developmental settings to maximize the area of exchange surfaces. It requires, in particular, the coordinated growth of different cell types together with complex patterning to lead to robust macroscopic outputs. In recent years, novel multiscale quantitative biology approaches, together with biophysical modelling, have begun to shed new light of this topic. Here, we wish to review some of these recent developments, highlighting the generic design principles that can be abstracted across different branched organs, as well as the implications for the broader fields of stem cell, developmental and systems biology.","lang":"eng"}],"intvolume":" 60","status":"public","title":"Multiscale dynamics of branching morphogenesis","_id":"6559","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None"},{"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6644","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-07-16T14:17:09Z","file_name":"2019_ACSNano_Ibanez.pdf","access_level":"open_access","content_type":"application/pdf","file_size":8628690,"creator":"dernst"}],"ddc":["540"],"title":"Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks","status":"public","intvolume":" 13","_id":"6566","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Methodologies that involve the use of nanoparticles as “artificial atoms” to rationally build materials in a bottom-up fashion are particularly well-suited to control the matter at the nanoscale. Colloidal synthetic routes allow for an exquisite control over such “artificial atoms” in terms of size, shape, and crystal phase as well as core and surface compositions. We present here a bottom-up approach to produce Pb–Ag–K–S–Te nanocomposites, which is a highly promising system for thermoelectric energy conversion. First, we developed a high-yield and scalable colloidal synthesis route to uniform lead sulfide (PbS) nanorods, whose tips are made of silver sulfide (Ag2S). We then took advantage of the large surface-to-volume ratio to introduce a p-type dopant (K) by replacing native organic ligands with K2Te. Upon thermal consolidation, K2Te-surface modified PbS–Ag2S nanorods yield p-type doped nanocomposites with PbTe and PbS as major phases and Ag2S and Ag2Te as embedded nanoinclusions. Thermoelectric characterization of such consolidated nanosolids showed a high thermoelectric figure-of-merit of 1 at 620 K."}],"issue":"6","type":"journal_article","date_published":"2019-06-25T00:00:00Z","article_type":"original","page":"6572-6580","publication":"ACS Nano","citation":{"short":"M. Ibáñez, A. Genç, R. Hasler, Y. Liu, O. Dobrozhan, O. Nazarenko, M. de la Mata, J. Arbiol, A. Cabot, M.V. Kovalenko, ACS Nano 13 (2019) 6572–6580.","mla":"Ibáñez, Maria, et al. “Tuning Transport Properties in Thermoelectric Nanocomposites through Inorganic Ligands and Heterostructured Building Blocks.” ACS Nano, vol. 13, no. 6, American Chemical Society, 2019, pp. 6572–80, doi:10.1021/acsnano.9b00346.","chicago":"Ibáñez, Maria, Aziz Genç, Roger Hasler, Yu Liu, Oleksandr Dobrozhan, Olga Nazarenko, María de la Mata, Jordi Arbiol, Andreu Cabot, and Maksym V. Kovalenko. “Tuning Transport Properties in Thermoelectric Nanocomposites through Inorganic Ligands and Heterostructured Building Blocks.” ACS Nano. American Chemical Society, 2019. https://doi.org/10.1021/acsnano.9b00346.","ama":"Ibáñez M, Genç A, Hasler R, et al. Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks. ACS Nano. 2019;13(6):6572-6580. doi:10.1021/acsnano.9b00346","ieee":"M. Ibáñez et al., “Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks,” ACS Nano, vol. 13, no. 6. American Chemical Society, pp. 6572–6580, 2019.","apa":"Ibáñez, M., Genç, A., Hasler, R., Liu, Y., Dobrozhan, O., Nazarenko, O., … Kovalenko, M. V. (2019). Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.9b00346","ista":"Ibáñez M, Genç A, Hasler R, Liu Y, Dobrozhan O, Nazarenko O, Mata M de la, Arbiol J, Cabot A, Kovalenko MV. 2019. Tuning transport properties in thermoelectric nanocomposites through inorganic ligands and heterostructured building blocks. ACS Nano. 13(6), 6572–6580."},"day":"25","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","keyword":["colloidal nanoparticles","asymmetric nanoparticles","inorganic ligands","heterostructures","catalyst assisted growth","nanocomposites","thermoelectrics"],"scopus_import":"1","date_created":"2019-06-18T13:54:34Z","date_updated":"2023-08-28T12:20:53Z","volume":13,"author":[{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria"},{"full_name":"Genç, Aziz","last_name":"Genç","first_name":"Aziz"},{"full_name":"Hasler, Roger","first_name":"Roger","last_name":"Hasler"},{"last_name":"Liu","first_name":"Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu"},{"full_name":"Dobrozhan, Oleksandr","last_name":"Dobrozhan","first_name":"Oleksandr"},{"full_name":"Nazarenko, Olga","last_name":"Nazarenko","first_name":"Olga"},{"first_name":"María de la","last_name":"Mata","full_name":"Mata, María de la"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"},{"full_name":"Kovalenko, Maksym V.","last_name":"Kovalenko","first_name":"Maksym V."}],"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"MaIb"}],"year":"2019","pmid":1,"file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1021/acsnano.9b00346","isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"pmid":["31185159"],"isi":["000473248300043"]},"month":"06","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]}},{"abstract":[{"text":"Acute myeloid leukemia (AML) is a heterogeneous disease with respect to its genetic and molecular basis and to patients´ outcome. Clinical, cytogenetic, and mutational data are used to classify patients into risk groups with different survival, however, within-group heterogeneity is still an issue. Here, we used a robust likelihood-based survival modeling approach and publicly available gene expression data to identify a minimal number of genes whose combined expression values were prognostic of overall survival. The resulting gene expression signature (4-GES) consisted of 4 genes (SOCS2, IL2RA, NPDC1, PHGDH), predicted patient survival as an independent prognostic parameter in several cohorts of AML patients (total, 1272 patients), and further refined prognostication based on the European Leukemia Net classification. An oncogenic role of the top scoring gene in this signature, SOCS2, was investigated using MLL-AF9 and Flt3-ITD/NPM1c driven mouse models of AML. SOCS2 promoted leukemogenesis as well as the abundance, quiescence, and activity of AML stem cells. Overall, the 4-GES represents a highly discriminating prognostic parameter in AML, whose clinical applicability is greatly enhanced by its small number of genes. The newly established role of SOCS2 in leukemia aggressiveness and stemness raises the possibility that the signature might even be exploitable therapeutically.","lang":"eng"}],"issue":"1","type":"journal_article","file":[{"file_size":2017352,"content_type":"application/pdf","creator":"kschuh","file_name":"nature_2019_Nguyen.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:34Z","date_created":"2019-07-08T15:15:28Z","checksum":"3283522fffadf4b5fc8c7adfe3ba4564","relation":"main_file","file_id":"6623"}],"oa_version":"Published Version","status":"public","title":"SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness","ddc":["576"],"intvolume":" 9","_id":"6607","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"24","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-06-24T00:00:00Z","publication":"Scientific Reports","citation":{"apa":"Nguyen, C. H., Glüxam, T., Schlerka, A., Bauer, K., Grandits, A. M., Hackl, H., … Heller, G. (2019). SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-019-45579-0","ieee":"C. H. Nguyen et al., “SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness,” Scientific Reports, vol. 9, no. 1. Nature Publishing Group, 2019.","ista":"Nguyen CH, Glüxam T, Schlerka A, Bauer K, Grandits AM, Hackl H, Dovey O, Zöchbauer-Müller S, Cooper JL, Vassiliou GS, Stoiber D, Wieser R, Heller G. 2019. SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. 9(1), 9139.","ama":"Nguyen CH, Glüxam T, Schlerka A, et al. SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. 2019;9(1). doi:10.1038/s41598-019-45579-0","chicago":"Nguyen, Chi Huu, Tobias Glüxam, Angela Schlerka, Katharina Bauer, Alexander M. Grandits, Hubert Hackl, Oliver Dovey, et al. “SOCS2 Is Part of a Highly Prognostic 4-Gene Signature in AML and Promotes Disease Aggressiveness.” Scientific Reports. Nature Publishing Group, 2019. https://doi.org/10.1038/s41598-019-45579-0.","short":"C.H. Nguyen, T. Glüxam, A. Schlerka, K. Bauer, A.M. Grandits, H. Hackl, O. Dovey, S. Zöchbauer-Müller, J.L. Cooper, G.S. Vassiliou, D. Stoiber, R. Wieser, G. Heller, Scientific Reports 9 (2019).","mla":"Nguyen, Chi Huu, et al. “SOCS2 Is Part of a Highly Prognostic 4-Gene Signature in AML and Promotes Disease Aggressiveness.” Scientific Reports, vol. 9, no. 1, 9139, Nature Publishing Group, 2019, doi:10.1038/s41598-019-45579-0."},"file_date_updated":"2020-07-14T12:47:34Z","article_number":"9139","date_created":"2019-07-07T21:59:19Z","date_updated":"2023-08-28T12:26:51Z","volume":9,"author":[{"full_name":"Nguyen, Chi Huu","first_name":"Chi Huu","last_name":"Nguyen"},{"full_name":"Glüxam, Tobias","first_name":"Tobias","last_name":"Glüxam"},{"first_name":"Angela","last_name":"Schlerka","full_name":"Schlerka, Angela"},{"full_name":"Bauer, Katharina","first_name":"Katharina","last_name":"Bauer","id":"2ED6B14C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grandits, Alexander M.","last_name":"Grandits","first_name":"Alexander M."},{"full_name":"Hackl, Hubert","first_name":"Hubert","last_name":"Hackl"},{"full_name":"Dovey, Oliver","last_name":"Dovey","first_name":"Oliver"},{"full_name":"Zöchbauer-Müller, Sabine","first_name":"Sabine","last_name":"Zöchbauer-Müller"},{"first_name":"Jonathan L.","last_name":"Cooper","full_name":"Cooper, Jonathan L."},{"full_name":"Vassiliou, George S.","first_name":"George S.","last_name":"Vassiliou"},{"full_name":"Stoiber, Dagmar","last_name":"Stoiber","first_name":"Dagmar"},{"first_name":"Rotraud","last_name":"Wieser","full_name":"Wieser, Rotraud"},{"last_name":"Heller","first_name":"Gerwin","full_name":"Heller, Gerwin"}],"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"PreCl"}],"year":"2019","month":"06","language":[{"iso":"eng"}],"doi":"10.1038/s41598-019-45579-0","isi":1,"quality_controlled":"1","external_id":{"isi":["000472597400042"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1}]