[{"publication_identifier":{"issn":["1944-8244"],"eissn":["1944-8252"]},"tmp":{"short":"CC BY-NC-ND (4.0)","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"},"date_published":"2021-08-04T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"ACS Applied Materials and Interfaces","month":"08","date_created":"2021-08-08T22:01:28Z","pmid":1,"oa":1,"ec_funded":1,"abstract":[{"text":"Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science.","lang":"eng"}],"scopus_import":"1","page":"35545–35560","language":[{"iso":"eng"}],"intvolume":"        13","corr_author":"1","_id":"9822","citation":{"ama":"Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. <i>ACS Applied Materials and Interfaces</i>. 2021;13(30):35545–35560. doi:<a href=\"https://doi.org/10.1021/acsami.1c09850\">10.1021/acsami.1c09850</a>","ieee":"T. Zisis <i>et al.</i>, “Sequential and switchable patterning for studying cellular processes under spatiotemporal control,” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.","chicago":"Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” <i>ACS Applied Materials and Interfaces</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsami.1c09850\">https://doi.org/10.1021/acsami.1c09850</a>.","apa":"Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. <i>ACS Applied Materials and Interfaces</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsami.1c09850\">https://doi.org/10.1021/acsami.1c09850</a>","ista":"Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 13(30), 35545–35560.","mla":"Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:<a href=\"https://doi.org/10.1021/acsami.1c09850\">10.1021/acsami.1c09850</a>.","short":"T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560."},"oa_version":"Published Version","doi":"10.1021/acsami.1c09850","isi":1,"acknowledgement":"We would like to thank Charlott Leu for the production of our chromium wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim Rädler for his valuable scientific guidance.","volume":13,"year":"2021","day":"04","article_type":"original","project":[{"call_identifier":"H2020","grant_number":"724373","name":"Cellular Navigation Along Spatial Gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["34283577"],"isi":["000683741400026"]},"file_date_updated":"2021-08-09T09:44:03Z","ddc":["620","570"],"publisher":"American Chemical Society","quality_controlled":"1","author":[{"full_name":"Zisis, Themistoklis","first_name":"Themistoklis","last_name":"Zisis"},{"last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Schwarz, Jan"},{"full_name":"Balles, Miriam","first_name":"Miriam","last_name":"Balles"},{"last_name":"Kretschmer","first_name":"Maibritt","full_name":"Kretschmer, Maibritt"},{"id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","last_name":"Nemethova","full_name":"Nemethova, Maria","first_name":"Maria"},{"full_name":"Chait, Remy P","first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","last_name":"Chait","orcid":"0000-0003-0876-3187"},{"first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lange, Janina","first_name":"Janina","last_name":"Lange"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K","first_name":"Michael K"},{"first_name":"Stefan","full_name":"Zahler, Stefan","last_name":"Zahler"}],"department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","issue":"30","date_updated":"2025-07-10T12:02:02Z","type":"journal_article","publication_status":"published","file":[{"file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf","creator":"asandaue","content_type":"application/pdf","relation":"main_file","file_id":"9833","date_created":"2021-08-09T09:44:03Z","success":1,"file_size":7123293,"checksum":"b043a91d9f9200e467b970b692687ed3","access_level":"open_access","date_updated":"2021-08-09T09:44:03Z"}]},{"citation":{"chicago":"Chatterjee, Bapi, Ivan Walulya, and Philippas Tsigas. “Concurrent Linearizable Nearest Neighbour Search in LockFree-KD-Tree.” <i>Theoretical Computer Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.tcs.2021.06.041\">https://doi.org/10.1016/j.tcs.2021.06.041</a>.","ieee":"B. Chatterjee, I. Walulya, and P. Tsigas, “Concurrent linearizable nearest neighbour search in LockFree-kD-tree,” <i>Theoretical Computer Science</i>, vol. 886. Elsevier, pp. 27–48, 2021.","apa":"Chatterjee, B., Walulya, I., &#38; Tsigas, P. (2021). Concurrent linearizable nearest neighbour search in LockFree-kD-tree. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2021.06.041\">https://doi.org/10.1016/j.tcs.2021.06.041</a>","ama":"Chatterjee B, Walulya I, Tsigas P. Concurrent linearizable nearest neighbour search in LockFree-kD-tree. <i>Theoretical Computer Science</i>. 2021;886:27-48. doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.06.041\">10.1016/j.tcs.2021.06.041</a>","ista":"Chatterjee B, Walulya I, Tsigas P. 2021. Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. 886, 27–48.","mla":"Chatterjee, Bapi, et al. “Concurrent Linearizable Nearest Neighbour Search in LockFree-KD-Tree.” <i>Theoretical Computer Science</i>, vol. 886, Elsevier, 2021, pp. 27–48, doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.06.041\">10.1016/j.tcs.2021.06.041</a>.","short":"B. Chatterjee, I. Walulya, P. Tsigas, Theoretical Computer Science 886 (2021) 27–48."},"doi":"10.1016/j.tcs.2021.06.041","oa_version":"Submitted Version","intvolume":"       886","_id":"9827","corr_author":"1","language":[{"iso":"eng"}],"page":"27-48","scopus_import":"1","abstract":[{"lang":"eng","text":"The Nearest neighbour search (NNS) is a fundamental problem in many application domains dealing with multidimensional data. In a concurrent setting, where dynamic modifications are allowed, a linearizable implementation of the NNS is highly desirable.This paper introduces the LockFree-kD-tree (LFkD-tree ): a lock-free concurrent kD-tree, which implements an abstract data type (ADT) that provides the operations Add, Remove, Contains, and NNS. Our implementation is linearizable. The operations in the LFkD-tree use single-word read and compare-and-swap (Image 1 ) atomic primitives, which are readily supported on available multi-core processors. We experimentally evaluate the LFkD-tree using several benchmarks comprising real-world and synthetic datasets. The experiments show that the presented design is scalable and achieves significant speed-up compared to the implementations of an existing sequential kD-tree and a recently proposed multidimensional indexing structure, PH-tree."}],"oa":1,"publication":"Theoretical Computer Science","month":"09","date_created":"2021-08-08T22:01:31Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-09-13T00:00:00Z","publication_identifier":{"issn":["0304-3975"]},"type":"journal_article","publication_status":"published","date_updated":"2024-10-09T21:00:45Z","title":"Concurrent linearizable nearest neighbour search in LockFree-kD-tree","department":[{"_id":"DaAl"}],"article_processing_charge":"No","main_file_link":[{"url":"https://publications.lib.chalmers.se/records/fulltext/232185/232185.pdf","open_access":"1"}],"quality_controlled":"1","author":[{"full_name":"Chatterjee, Bapi","first_name":"Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2742-4028","last_name":"Chatterjee"},{"last_name":"Walulya","first_name":"Ivan","full_name":"Walulya, Ivan"},{"first_name":"Philippas","full_name":"Tsigas, Philippas","last_name":"Tsigas"}],"publisher":"Elsevier","keyword":["Concurrent data structure","kD-tree","Nearest neighbor search","Similarity search","Lock-free","Linearizability"],"external_id":{"isi":["000694718900004"]},"article_type":"original","day":"13","volume":886,"year":"2021","isi":1},{"external_id":{"isi":["000682123900002"],"arxiv":["2102.04832"]},"article_type":"original","acknowledgement":"The author thanks his colleagues K. Huszár and G. Tkačik for valuable discussions and comments on the manuscript.","isi":1,"day":"09","year":"2021","volume":69,"date_updated":"2024-10-09T21:00:43Z","article_processing_charge":"No","title":"Fast and accurate amplitude demodulation of wideband signals","department":[{"_id":"GaTk"}],"publication_status":"published","type":"journal_article","publisher":"Institute of Electrical and Electronics Engineers","author":[{"full_name":"Gabrielaitis, Mantas","first_name":"Mantas","id":"4D5B0CBC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7758-2016","last_name":"Gabrielaitis"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2102.04832","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_published":"2021-06-09T00:00:00Z","publication_identifier":{"eissn":["1941-0476"],"issn":["1053-587X"]},"arxiv":1,"language":[{"iso":"eng"}],"page":"4039 - 4054","oa_version":"Preprint","doi":"10.1109/TSP.2021.3087899","citation":{"ista":"Gabrielaitis M. 2021. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 69, 4039–4054.","mla":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” <i>IEEE Transactions on Signal Processing</i>, vol. 69, Institute of Electrical and Electronics Engineers, 2021, pp. 4039–54, doi:<a href=\"https://doi.org/10.1109/TSP.2021.3087899\">10.1109/TSP.2021.3087899</a>.","short":"M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054.","apa":"Gabrielaitis, M. (2021). Fast and accurate amplitude demodulation of wideband signals. <i>IEEE Transactions on Signal Processing</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/TSP.2021.3087899\">https://doi.org/10.1109/TSP.2021.3087899</a>","chicago":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” <i>IEEE Transactions on Signal Processing</i>. Institute of Electrical and Electronics Engineers, 2021. <a href=\"https://doi.org/10.1109/TSP.2021.3087899\">https://doi.org/10.1109/TSP.2021.3087899</a>.","ieee":"M. Gabrielaitis, “Fast and accurate amplitude demodulation of wideband signals,” <i>IEEE Transactions on Signal Processing</i>, vol. 69. Institute of Electrical and Electronics Engineers, pp. 4039–4054, 2021.","ama":"Gabrielaitis M. Fast and accurate amplitude demodulation of wideband signals. <i>IEEE Transactions on Signal Processing</i>. 2021;69:4039-4054. doi:<a href=\"https://doi.org/10.1109/TSP.2021.3087899\">10.1109/TSP.2021.3087899</a>"},"_id":"9828","corr_author":"1","intvolume":"        69","oa":1,"publication":"IEEE Transactions on Signal Processing","month":"06","date_created":"2021-08-08T22:01:31Z","abstract":[{"text":"Amplitude demodulation is a classical operation used in signal processing. For a long time, its effective applications in practice have been limited to narrowband signals. In this work, we generalize amplitude demodulation to wideband signals. We pose demodulation as a recovery problem of an oversampled corrupted signal and introduce special iterative schemes belonging to the family of alternating projection algorithms to solve it. Sensibly chosen structural assumptions on the demodulation outputs allow us to reveal the high inferential accuracy of the method over a rich set of relevant signals. This new approach surpasses current state-of-the-art demodulation techniques apt to wideband signals in computational efficiency by up to many orders of magnitude with no sacrifice in quality. Such performance opens the door for applications of the amplitude demodulation procedure in new contexts. In particular, the new method makes online and large-scale offline data processing feasible, including the calculation of modulator-carrier pairs in higher dimensions and poor sampling conditions, independent of the signal bandwidth. We illustrate the utility and specifics of applications of the new method in practice by using natural speech and synthetic signals.","lang":"eng"}],"scopus_import":"1"},{"date_published":"2021-07-06T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"intvolume":"        15","_id":"9829","citation":{"mla":"Baranov, Dmitry, et al. “News in Nanocrystals Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible Nanoscience.” <i>ACS Nano</i>, vol. 15, no. 7, American Chemical Society, 2021, pp. 10743–10747, doi:<a href=\"https://doi.org/10.1021/acsnano.1c03276\">10.1021/acsnano.1c03276</a>.","ista":"Baranov D, Šverko T, Moot T, Keller HR, Klein MD, Vishnu EK, Balazs D, Shulenberger KE. 2021. News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. ACS Nano. 15(7), 10743–10747.","short":"D. Baranov, T. Šverko, T. Moot, H.R. Keller, M.D. Klein, E.K. Vishnu, D. Balazs, K.E. Shulenberger, ACS Nano 15 (2021) 10743–10747.","ama":"Baranov D, Šverko T, Moot T, et al. News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. <i>ACS Nano</i>. 2021;15(7):10743–10747. doi:<a href=\"https://doi.org/10.1021/acsnano.1c03276\">10.1021/acsnano.1c03276</a>","chicago":"Baranov, Dmitry, Tara Šverko, Taylor Moot, Helena R. Keller, Megan D. Klein, E. K. Vishnu, Daniel Balazs, and Katherine E. Shulenberger. “News in Nanocrystals Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible Nanoscience.” <i>ACS Nano</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsnano.1c03276\">https://doi.org/10.1021/acsnano.1c03276</a>.","apa":"Baranov, D., Šverko, T., Moot, T., Keller, H. R., Klein, M. D., Vishnu, E. K., … Shulenberger, K. E. (2021). News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.1c03276\">https://doi.org/10.1021/acsnano.1c03276</a>","ieee":"D. Baranov <i>et al.</i>, “News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience,” <i>ACS Nano</i>, vol. 15, no. 7. American Chemical Society, pp. 10743–10747, 2021."},"oa_version":"Published Version","doi":"10.1021/acsnano.1c03276","page":"10743–10747","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"text":"In 2020, many in-person scientific events were canceled due to the COVID-19 pandemic, creating a vacuum in networking and knowledge exchange between scientists. To fill this void in scientific communication, a group of early career nanocrystal enthusiasts launched the virtual seminar series, News in Nanocrystals, in the summer of 2020. By the end of the year, the series had attracted over 850 participants from 46 countries. In this Nano Focus, we describe the process of organizing the News in Nanocrystals seminar series; discuss its growth, emphasizing what the organizers have learned in terms of diversity and accessibility; and provide an outlook for the next steps and future opportunities. This summary and analysis of experiences and learned lessons are intended to inform the broader scientific community, especially those who are looking for avenues to continue fostering discussion and scientific engagement virtually, both during the pandemic and after.","lang":"eng"}],"month":"07","date_created":"2021-08-08T22:01:31Z","publication":"ACS Nano","pmid":1,"oa":1,"article_type":"original","external_id":{"pmid":["34228432"],"isi":["000679406500002"]},"volume":15,"year":"2021","day":"06","isi":1,"acknowledgement":"K. E. Shulenberger, M. D. Klein, T. Šverko, and H. R. Keller would like to thank Professors Moungi Bawendi (MIT) and Gordana Dukovic (CU Boulder) for their feedback and support of the News in Nanocrystals initiative. The authors thank Madison Jilek (CU Boulder) and Dhananjeya Kumaar (ETH Zurich) for their help in the organization of the seminar, and Professors Brandi Cossairt (University of Washington) and Gordana Dukovic for their feedback on an earlier version of this manuscript. The authors thank all the seminar speakers and attendees for their interest and continuing participation in the seminar series.","type":"journal_article","publication_status":"published","department":[{"_id":"MaIb"}],"title":"News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience","article_processing_charge":"No","issue":"7","date_updated":"2025-07-10T12:02:03Z","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acsnano.1c03276"}],"author":[{"last_name":"Baranov","first_name":"Dmitry","full_name":"Baranov, Dmitry"},{"full_name":"Šverko, Tara","first_name":"Tara","last_name":"Šverko"},{"full_name":"Moot, Taylor","first_name":"Taylor","last_name":"Moot"},{"first_name":"Helena R.","full_name":"Keller, Helena R.","last_name":"Keller"},{"first_name":"Megan D.","full_name":"Klein, Megan D.","last_name":"Klein"},{"last_name":"Vishnu","full_name":"Vishnu, E. K.","first_name":"E. K."},{"id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X","last_name":"Balazs","full_name":"Balazs, Daniel","first_name":"Daniel"},{"first_name":"Katherine E.","full_name":"Shulenberger, Katherine E.","last_name":"Shulenberger"}],"publisher":"American Chemical Society"},{"article_number":"4808","genbank":["GSE178867"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-08-10T00:00:00Z","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-32785-0","relation":"erratum"}]},"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)"},"publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"citation":{"mla":"Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” <i>Nature Communications</i>, vol. 12, 4808, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-25211-4\">10.1038/s41467-021-25211-4</a>.","ista":"Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. 12, 4808.","short":"A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen, L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas, C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H. van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021).","ama":"Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-25211-4\">10.1038/s41467-021-25211-4</a>","apa":"Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen, D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-25211-4\">https://doi.org/10.1038/s41467-021-25211-4</a>","ieee":"A. Raso <i>et al.</i>, “A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021.","chicago":"Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-25211-4\">https://doi.org/10.1038/s41467-021-25211-4</a>."},"oa_version":"Published Version","doi":"10.1038/s41467-021-25211-4","intvolume":"        12","_id":"9874","oa":1,"publication":"Nature Communications","month":"08","date_created":"2021-08-10T11:49:20Z","pmid":1,"abstract":[{"text":"Myocardial regeneration is restricted to early postnatal life, when mammalian cardiomyocytes still retain the ability to proliferate. The molecular cues that induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster is higher expressed in the early postnatal myocardium and decreases in expression towards adulthood, especially under conditions of overload, and orchestrates the transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse heart provokes cardiomyocyte proliferation by targeting a network of negative cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated remodeling to overload by derepression of the prohypertrophic transcription factors Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25 provokes nearly complete regeneration of the adult myocardium after ischemic injury. Our data demonstrate that exploitation of conserved molecular programs can enhance the regenerative capacity of the injured heart.","lang":"eng"}],"scopus_import":"1","external_id":{"isi":["000683910200042"],"pmid":["34376683"]},"article_type":"original","file_date_updated":"2021-08-10T12:29:59Z","acknowledgement":"E.D. is supported by a VENI award 916-150-16 from the Netherlands Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship (EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number 627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência, Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART).","isi":1,"day":"10","volume":12,"year":"2021","has_accepted_license":"1","date_updated":"2023-08-11T10:27:03Z","department":[{"_id":"SaSi"}],"title":"A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration","article_processing_charge":"Yes","file":[{"access_level":"open_access","checksum":"48d8562e8229e4282f3f354b329722c5","date_updated":"2021-08-10T12:29:59Z","relation":"main_file","creator":"asandaue","content_type":"application/pdf","file_name":"2021_NatureCommunications_Raso.pdf","file_size":4364333,"success":1,"date_created":"2021-08-10T12:29:59Z","file_id":"9876"}],"type":"journal_article","publication_status":"published","publisher":"Springer Nature","ddc":["610","570"],"quality_controlled":"1","author":[{"last_name":"Raso","first_name":"Andrea","full_name":"Raso, Andrea"},{"last_name":"Dirkx","first_name":"Ellen","full_name":"Dirkx, Ellen"},{"last_name":"Sampaio-Pinto","first_name":"Vasco","full_name":"Sampaio-Pinto, Vasco"},{"last_name":"el Azzouzi","first_name":"Hamid","full_name":"el Azzouzi, Hamid"},{"id":"850B2E12-9CD4-11E9-837F-E719E6697425","last_name":"Cubero","orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J","first_name":"Ryan J"},{"last_name":"Sorensen","first_name":"Daniel W.","full_name":"Sorensen, Daniel W."},{"first_name":"Lara","full_name":"Ottaviani, Lara","last_name":"Ottaviani"},{"last_name":"Olieslagers","first_name":"Servé","full_name":"Olieslagers, Servé"},{"full_name":"Huibers, Manon M.","first_name":"Manon M.","last_name":"Huibers"},{"last_name":"de Weger","full_name":"de Weger, Roel","first_name":"Roel"},{"last_name":"Siddiqi","full_name":"Siddiqi, Sailay","first_name":"Sailay"},{"full_name":"Moimas, Silvia","first_name":"Silvia","last_name":"Moimas"},{"last_name":"Torrini","first_name":"Consuelo","full_name":"Torrini, Consuelo"},{"full_name":"Zentillin, Lorena","first_name":"Lorena","last_name":"Zentillin"},{"last_name":"Braga","first_name":"Luca","full_name":"Braga, Luca"},{"first_name":"Diana S.","full_name":"Nascimento, Diana S.","last_name":"Nascimento"},{"full_name":"da Costa Martins, Paula A.","first_name":"Paula A.","last_name":"da Costa Martins"},{"full_name":"van Berlo, Jop H.","first_name":"Jop H.","last_name":"van Berlo"},{"last_name":"Zacchigna","first_name":"Serena","full_name":"Zacchigna, Serena"},{"full_name":"Giacca, Mauro","first_name":"Mauro","last_name":"Giacca"},{"last_name":"De Windt","full_name":"De Windt, Leon J.","first_name":"Leon J."}]},{"abstract":[{"lang":"eng","text":"Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution."}],"scopus_import":"1","month":"07","date_created":"2021-08-10T19:30:41Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","pmid":1,"oa":1,"intvolume":"       118","_id":"9877","citation":{"short":"J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","mla":"Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2104445118\">10.1073/pnas.2104445118</a>.","ista":"Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences of the United States of America. 118(29), e2104445118.","chicago":"Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>.","ieee":"J. A. Rodrigues <i>et al.</i>, “Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 29. National Academy of Sciences, 2021.","apa":"Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma, R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>","ama":"Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(29). doi:<a href=\"https://doi.org/10.1073/pnas.2104445118\">10.1073/pnas.2104445118</a>"},"doi":"10.1073/pnas.2104445118","oa_version":"Published Version","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"tmp":{"short":"CC BY-NC-ND (4.0)","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"},"date_published":"2021-07-16T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e2104445118","quality_controlled":"1","author":[{"last_name":"Rodrigues","full_name":"Rodrigues, Jessica A.","first_name":"Jessica A."},{"last_name":"Hsieh","full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung"},{"last_name":"Ruan","first_name":"Deling","full_name":"Ruan, Deling"},{"full_name":"Nishimura, Toshiro","first_name":"Toshiro","last_name":"Nishimura"},{"full_name":"Sharma, Manoj K.","first_name":"Manoj K.","last_name":"Sharma"},{"last_name":"Sharma","first_name":"Rita","full_name":"Sharma, Rita"},{"first_name":"XinYi","full_name":"Ye, XinYi","last_name":"Ye"},{"first_name":"Nicholas D.","full_name":"Nguyen, Nicholas D.","last_name":"Nguyen"},{"last_name":"Nijjar","first_name":"Sukhranjan","full_name":"Nijjar, Sukhranjan"},{"full_name":"Ronald, Pamela C.","first_name":"Pamela C.","last_name":"Ronald"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."},{"first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"ddc":["580","570"],"publisher":"National Academy of Sciences","type":"journal_article","publication_status":"published","file":[{"date_updated":"2021-08-11T09:31:41Z","checksum":"19e84ad8c03c60222744ee8e16cd6998","access_level":"open_access","date_created":"2021-08-11T09:31:41Z","file_id":"9879","success":1,"file_size":1898360,"creator":"asandaue","content_type":"application/pdf","file_name":"2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf","relation":"main_file"}],"department":[{"_id":"DaZi"}],"title":"Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting","article_processing_charge":"Yes (in subscription journal)","issue":"29","has_accepted_license":"1","date_updated":"2025-05-14T10:59:43Z","volume":118,"year":"2021","day":"16","isi":1,"acknowledgement":"We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing team for generating the IR64 genome sequence and initial analysis; L. Bartley and E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University of California (UC), Berkeley Sanger sequencing team for technical advice and service. This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.","file_date_updated":"2021-08-11T09:31:41Z","article_type":"original","external_id":{"pmid":["34272287"],"isi":["000685037700012"]}},{"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"title":"Floating Wigner crystal and periodic jellium configurations","article_processing_charge":"No","issue":"8","has_accepted_license":"1","date_updated":"2024-10-09T21:00:48Z","type":"journal_article","publication_status":"published","file":[{"file_size":4352640,"success":1,"file_id":"10188","date_created":"2021-10-27T12:57:06Z","relation":"main_file","file_name":"2021_JMathPhy_Lauritsen.pdf","content_type":"application/pdf","creator":"cziletti","date_updated":"2021-10-27T12:57:06Z","access_level":"open_access","checksum":"d035be2b894c4d50d90ac5ce252e27cd"}],"publisher":"AIP Publishing","ddc":["530"],"quality_controlled":"1","author":[{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen","orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard","first_name":"Asbjørn Bækgaard"}],"article_type":"original","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"external_id":{"arxiv":["2103.07975"],"isi":["000683960800003"]},"file_date_updated":"2021-10-27T12:57:06Z","isi":1,"acknowledgement":"The author would like to thank Robert Seiringer for guidance and many helpful comments on this project. The author would also like to thank Mathieu Lewin for his comments on the manuscript and Lorenzo Portinale for providing his lecture notes for the course “Mathematics of quantum many-body systems” in spring 2020, taught by Robert Seiringer. The Proof of Theorem III.1 is inspired by these lecture notes.","volume":62,"year":"2021","day":"01","language":[{"iso":"eng"}],"intvolume":"        62","corr_author":"1","_id":"9891","citation":{"mla":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” <i>Journal of Mathematical Physics</i>, vol. 62, no. 8, 083305, AIP Publishing, 2021, doi:<a href=\"https://doi.org/10.1063/5.0053494\">10.1063/5.0053494</a>.","ista":"Lauritsen AB. 2021. Floating Wigner crystal and periodic jellium configurations. Journal of Mathematical Physics. 62(8), 083305.","short":"A.B. Lauritsen, Journal of Mathematical Physics 62 (2021).","ama":"Lauritsen AB. Floating Wigner crystal and periodic jellium configurations. <i>Journal of Mathematical Physics</i>. 2021;62(8). doi:<a href=\"https://doi.org/10.1063/5.0053494\">10.1063/5.0053494</a>","chicago":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2021. <a href=\"https://doi.org/10.1063/5.0053494\">https://doi.org/10.1063/5.0053494</a>.","apa":"Lauritsen, A. B. (2021). Floating Wigner crystal and periodic jellium configurations. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0053494\">https://doi.org/10.1063/5.0053494</a>","ieee":"A. B. Lauritsen, “Floating Wigner crystal and periodic jellium configurations,” <i>Journal of Mathematical Physics</i>, vol. 62, no. 8. AIP Publishing, 2021."},"oa_version":"Published Version","doi":"10.1063/5.0053494","date_created":"2021-08-12T07:08:36Z","month":"08","publication":"Journal of Mathematical Physics","oa":1,"abstract":[{"lang":"eng","text":"Extending on ideas of Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)], we present a modified “floating crystal” trial state for jellium (also known as the classical homogeneous electron gas) with density equal to a characteristic function. This allows us to show that three definitions of the jellium energy coincide in dimensions d ≥ 2, thus extending the result of Cotar and Petrache [“Equality of the Jellium and uniform electron gas next-order asymptotic terms for Coulomb and Riesz potentials,” arXiv: 1707.07664 (2019)] and Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)] that the three definitions coincide in dimension d ≥ 3. We show that the jellium energy is also equivalent to a “renormalized energy” studied in a series of papers by Serfaty and others, and thus, by the work of Bétermin and Sandier [Constr. Approximation 47, 39–74 (2018)], we relate the jellium energy to the order n term in the logarithmic energy of n points on the unit 2-sphere. We improve upon known lower bounds for this renormalized energy. Additionally, we derive formulas for the jellium energy of periodic configurations."}],"scopus_import":"1","article_number":"083305","date_published":"2021-08-01T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","arxiv":1,"publication_identifier":{"eissn":["1089-7658"],"issn":["0022-2488"]},"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)"}},{"publisher":"MDPI","ddc":["570"],"quality_controlled":"1","author":[{"last_name":"Yotova","full_name":"Yotova, Iveta","first_name":"Iveta"},{"full_name":"Hudson, Quanah J.","first_name":"Quanah J.","last_name":"Hudson"},{"first_name":"Florian","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Proestling","first_name":"Katharina","full_name":"Proestling, Katharina"},{"full_name":"Haslinger, Isabella","first_name":"Isabella","last_name":"Haslinger"},{"first_name":"Lorenz","full_name":"Kuessel, Lorenz","last_name":"Kuessel"},{"last_name":"Perricos","first_name":"Alexandra","full_name":"Perricos, Alexandra"},{"full_name":"Husslein, Heinrich","first_name":"Heinrich","last_name":"Husslein"},{"full_name":"Wenzl, René","first_name":"René","last_name":"Wenzl"}],"issue":"16","has_accepted_license":"1","date_updated":"2025-06-12T06:29:07Z","department":[{"_id":"SiHi"}],"title":"LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line","article_processing_charge":"Yes","file":[{"file_id":"9922","date_created":"2021-08-16T09:29:17Z","file_size":2646018,"success":1,"file_name":"2021_InternationalJournalOfMolecularSciences_Yotova.pdf","content_type":"application/pdf","creator":"asandaue","relation":"main_file","date_updated":"2021-08-16T09:29:17Z","checksum":"be7f0042607ca60549cb27513c19c6af","access_level":"open_access"}],"type":"journal_article","publication_status":"published","acknowledgement":"Open access funding provided by Medical University of Vienna. The authors would like to thank all the participants and health professionals involved in the present study. We want to thank our technical assistants Barbara Widmar and Matthias Witzmann-Stern for their diligent work and constant assistance. We would like to thank Simon Hippenmeyer for access to\r\nbioinformatic infrastructure and resources.","isi":1,"day":"04","volume":22,"year":"2021","external_id":{"isi":["000689147400001"],"pmid":["34445100"]},"article_type":"original","file_date_updated":"2021-08-16T09:29:17Z","oa":1,"date_created":"2021-08-15T22:01:27Z","publication":"International Journal of Molecular Sciences","month":"08","pmid":1,"abstract":[{"text":"Endometriosis is a common gynecological disorder characterized by ectopic growth of endometrium outside the uterus and is associated with chronic pain and infertility. We investigated the role of the long intergenic noncoding RNA 01133 (LINC01133) in endometriosis, an lncRNA that has been implicated in several types of cancer. We found that LINC01133 is upregulated in ectopic endometriotic lesions. As expression appeared higher in the epithelial endometrial layer, we performed a siRNA knockdown of LINC01133 in an endometriosis epithelial cell line. Phenotypic assays indicated that LINC01133 may promote proliferation and suppress cellular migration, and affect the cytoskeleton and morphology of the cells. Gene ontology analysis of differentially expressed genes indicated that cell proliferation and migration pathways were affected in line with the observed phenotype. We validated upregulation of p21 and downregulation of Cyclin A at the protein level, which together with the quantification of the DNA content using fluorescence-activated cell sorting (FACS) analysis indicated that the observed effects on cellular proliferation may be due to changes in cell cycle. Further, we found testis-specific protein kinase 1 (TESK1) kinase upregulation corresponding with phosphorylation and inactivation of actin severing protein Cofilin, which could explain changes in the cytoskeleton and cellular migration. These results indicate that endometriosis is associated with LINC01133 upregulation, which may affect pathogenesis via the cellular proliferation and migration pathways.","lang":"eng"}],"scopus_import":"1","language":[{"iso":"eng"}],"citation":{"ama":"Yotova I, Hudson QJ, Pauler F, et al. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. <i>International Journal of Molecular Sciences</i>. 2021;22(16). doi:<a href=\"https://doi.org/10.3390/ijms22168385\">10.3390/ijms22168385</a>","apa":"Yotova, I., Hudson, Q. J., Pauler, F., Proestling, K., Haslinger, I., Kuessel, L., … Wenzl, R. (2021). LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22168385\">https://doi.org/10.3390/ijms22168385</a>","chicago":"Yotova, Iveta, Quanah J. Hudson, Florian Pauler, Katharina Proestling, Isabella Haslinger, Lorenz Kuessel, Alexandra Perricos, Heinrich Husslein, and René Wenzl. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22168385\">https://doi.org/10.3390/ijms22168385</a>.","ieee":"I. Yotova <i>et al.</i>, “LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 16. MDPI, 2021.","mla":"Yotova, Iveta, et al. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 16, 8385, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22168385\">10.3390/ijms22168385</a>.","ista":"Yotova I, Hudson QJ, Pauler F, Proestling K, Haslinger I, Kuessel L, Perricos A, Husslein H, Wenzl R. 2021. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. International Journal of Molecular Sciences. 22(16), 8385.","short":"I. Yotova, Q.J. Hudson, F. Pauler, K. Proestling, I. Haslinger, L. Kuessel, A. Perricos, H. Husslein, R. Wenzl, International Journal of Molecular Sciences 22 (2021)."},"oa_version":"Published Version","doi":"10.3390/ijms22168385","intvolume":"        22","_id":"9906","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)"},"publication_identifier":{"eissn":["1422-0067"],"issn":["1661-6596"]},"article_number":"8385","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-08-04T00:00:00Z"},{"date_published":"2021-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","article_number":"8350","publication_identifier":{"issn":["1661-6596"],"eissn":["1422-0067"]},"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)"},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"_id":"9907","intvolume":"        22","doi":"10.3390/ijms22158350","oa_version":"Published Version","citation":{"short":"N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International Journal of Molecular Sciences 22 (2021).","ista":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. 22(15), 8350.","mla":"Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15, 8350, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>.","ama":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. 2021;22(15). doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>","ieee":"N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák, “Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15. MDPI, 2021.","chicago":"Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>.","apa":"Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., &#38; Barák, I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>"},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"DivIVA is a protein initially identified as a spatial regulator of cell division in the model organism Bacillus subtilis, but its homologues are present in many other Gram-positive bacteria, including Clostridia species. Besides its role as topological regulator of the Min system during bacterial cell division, DivIVA is involved in chromosome segregation during sporulation, genetic competence, and cell wall synthesis. DivIVA localizes to regions of high membrane curvature, such as the cell poles and cell division site, where it recruits distinct binding partners. Previously, it was suggested that negative curvature sensing is the main mechanism by which DivIVA binds to these specific regions. Here, we show that Clostridioides difficile DivIVA binds preferably to membranes containing negatively charged phospholipids, especially cardiolipin. Strikingly, we observed that upon binding, DivIVA modifies the lipid distribution and induces changes to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA might play a more complex and so far unknown active role during the formation of the cell division septal membrane. "}],"scopus_import":"1","ec_funded":1,"pmid":1,"date_created":"2021-08-15T22:01:27Z","month":"08","publication":"International Journal of Molecular Sciences","oa":1,"file_date_updated":"2021-08-16T09:35:56Z","article_type":"original","external_id":{"isi":["000681815400001"],"pmid":["34361115"]},"project":[{"grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell"}],"year":"2021","volume":22,"day":"01","isi":1,"acknowledgement":"We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova and other members of Barák’s laboratory for useful discussions, suggestions and help. Special thanks also to Emília Chovancová for technical support. We are grateful to Juraj Labaj for drawing the model and for help with graphics. Many thanks to all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp Radler, and other members of the Loose’s laboratory for sharing their knowledge of SLB preparation and TIRF experiment chambers, for sharing coverslips and for help with the TIRF microscope and data analysis. We also thank the members of the Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J. Bauer for critically reading the manuscript.","publication_status":"published","type":"journal_article","file":[{"date_updated":"2021-08-16T09:35:56Z","checksum":"a4bc06e9a2c803ceff5a91f10b174054","access_level":"open_access","file_id":"9923","date_created":"2021-08-16T09:35:56Z","success":1,"file_size":6132410,"file_name":"2021_InternationalJournalOfMolecularSciences_Labajová .pdf","content_type":"application/pdf","creator":"asandaue","relation":"main_file"}],"article_processing_charge":"Yes","title":"Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva","department":[{"_id":"MaLo"}],"date_updated":"2025-07-10T12:02:05Z","has_accepted_license":"1","issue":"15","author":[{"last_name":"Labajová","full_name":"Labajová, Naďa","first_name":"Naďa"},{"id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S.","first_name":"Natalia S."},{"first_name":"Miroslav","full_name":"Jurásek, Miroslav","last_name":"Jurásek"},{"first_name":"Robert","full_name":"Vácha, Robert","last_name":"Vácha"},{"first_name":"Martin","full_name":"Loose, Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Imrich","full_name":"Barák, Imrich","last_name":"Barák"}],"quality_controlled":"1","publisher":"MDPI","ddc":["570"]},{"date_published":"2021-07-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_identifier":{"eissn":["1476-5438"],"issn":["1018-4813"]},"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)"},"_id":"9910","intvolume":"        29","oa_version":"Published Version","doi":"10.1038/s41431-021-00836-7","citation":{"short":"S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich, F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.","ista":"Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European Journal of Human Genetics. 29(7), 1082–1091.","mla":"Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.” <i>European Journal of Human Genetics</i>, vol. 29, no. 7, Springer Nature, 2021, pp. 1082–91, doi:<a href=\"https://doi.org/10.1038/s41431-021-00836-7\">10.1038/s41431-021-00836-7</a>.","ieee":"S. A. Slavskii <i>et al.</i>, “The limits of normal approximation for adult height,” <i>European Journal of Human Genetics</i>, vol. 29, no. 7. Springer Nature, pp. 1082–1091, 2021.","chicago":"Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A. Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The Limits of Normal Approximation for Adult Height.” <i>European Journal of Human Genetics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41431-021-00836-7\">https://doi.org/10.1038/s41431-021-00836-7</a>.","apa":"Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich, T. I., Kondrashov, F., &#38; Aulchenko, Y. S. (2021). The limits of normal approximation for adult height. <i>European Journal of Human Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41431-021-00836-7\">https://doi.org/10.1038/s41431-021-00836-7</a>","ama":"Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation for adult height. <i>European Journal of Human Genetics</i>. 2021;29(7):1082-1091. doi:<a href=\"https://doi.org/10.1038/s41431-021-00836-7\">10.1038/s41431-021-00836-7</a>"},"page":"1082-1091","language":[{"iso":"eng"}],"abstract":[{"text":"Adult height inspired the first biometrical and quantitative genetic studies and is a test-case trait for understanding heritability. The studies of height led to formulation of the classical polygenic model, that has a profound influence on the way we view and analyse complex traits. An essential part of the classical model is an assumption of additivity of effects and normality of the distribution of the residuals. However, it may be expected that the normal approximation will become insufficient in bigger studies. Here, we demonstrate that when the height of hundreds of thousands of individuals is analysed, the model complexity needs to be increased to include non-additive interactions between sex, environment and genes. Alternatively, the use of log-normal approximation allowed us to still use the additive effects model. These findings are important for future genetic and methodologic studies that make use of adult height as an exemplar trait.","lang":"eng"}],"ec_funded":1,"scopus_import":"1","pmid":1,"publication":"European Journal of Human Genetics","month":"07","date_created":"2021-08-15T22:01:28Z","oa":1,"file_date_updated":"2021-08-16T09:14:36Z","article_type":"original","external_id":{"pmid":["33664501"],"isi":["000625853200001"]},"project":[{"name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209","call_identifier":"H2020"}],"year":"2021","volume":29,"day":"01","isi":1,"acknowledgement":"We are grateful to Marianna Bevova and Pavel Borodin for fruitful discussion and help with conceptualising our findings and to Lennart C. Karssen for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects in control of complex human traits”). The work of SAS, IAK, and TIS were supported by Russian Ministry of Science and Education under the 5–100 Excellence Programme. The work of YSA and TIA was supported by the Ministry of Education and Science of the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4). FAK is supported by the ERC Consolidator Grant (ChrFL: 771209).","publication_status":"published","type":"journal_article","file":[{"relation":"main_file","content_type":"application/pdf","creator":"asandaue","file_name":"2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf","success":1,"file_size":1079395,"date_created":"2021-08-16T09:14:36Z","file_id":"9921","access_level":"open_access","checksum":"a676d76f91b0dbe0504c63e469129c2a","date_updated":"2021-08-16T09:14:36Z"}],"article_processing_charge":"Yes (in subscription journal)","title":"The limits of normal approximation for adult height","department":[{"_id":"FyKo"}],"date_updated":"2025-07-10T12:02:05Z","issue":"7","has_accepted_license":"1","author":[{"last_name":"Slavskii","first_name":"Sergei A.","full_name":"Slavskii, Sergei A."},{"full_name":"Kuznetsov, Ivan A.","first_name":"Ivan A.","last_name":"Kuznetsov"},{"last_name":"Shashkova","full_name":"Shashkova, Tatiana I.","first_name":"Tatiana I."},{"last_name":"Bazykin","full_name":"Bazykin, Georgii A.","first_name":"Georgii A."},{"first_name":"Tatiana I.","full_name":"Axenovich, Tatiana I.","last_name":"Axenovich"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","first_name":"Fyodor"},{"first_name":"Yurii S.","full_name":"Aulchenko, Yurii S.","last_name":"Aulchenko"}],"quality_controlled":"1","ddc":["576"],"publisher":"Springer Nature"},{"isi":1,"acknowledgement":"We thank https://www.somersault1824.com/somersault18:24 BV (Leuven, Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122, in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg.","year":"2021","volume":284,"day":"11","article_type":"original","external_id":{"pmid":["34214188"],"isi":["000683702700001"]},"publisher":"Wiley","author":[{"full_name":"Nelson, Glyn","first_name":"Glyn","last_name":"Nelson"},{"full_name":"Boehm, Ulrike","first_name":"Ulrike","last_name":"Boehm"},{"first_name":"Steve","full_name":"Bagley, Steve","last_name":"Bagley"},{"first_name":"Peter","full_name":"Bajcsy, Peter","last_name":"Bajcsy"},{"full_name":"Bischof, Johanna","first_name":"Johanna","last_name":"Bischof"},{"full_name":"Brown, Claire M.","first_name":"Claire M.","last_name":"Brown"},{"first_name":"Aurélien","full_name":"Dauphin, Aurélien","last_name":"Dauphin"},{"full_name":"Dobbie, Ian M.","first_name":"Ian M.","last_name":"Dobbie"},{"first_name":"John E.","full_name":"Eriksson, John E.","last_name":"Eriksson"},{"full_name":"Faklaris, Orestis","first_name":"Orestis","last_name":"Faklaris"},{"last_name":"Fernandez-Rodriguez","full_name":"Fernandez-Rodriguez, Julia","first_name":"Julia"},{"first_name":"Alexia","full_name":"Ferrand, Alexia","last_name":"Ferrand"},{"full_name":"Gelman, Laurent","first_name":"Laurent","last_name":"Gelman"},{"full_name":"Gheisari, Ali","first_name":"Ali","last_name":"Gheisari"},{"last_name":"Hartmann","full_name":"Hartmann, Hella","first_name":"Hella"},{"full_name":"Kukat, Christian","first_name":"Christian","last_name":"Kukat"},{"full_name":"Laude, Alex","first_name":"Alex","last_name":"Laude"},{"last_name":"Mitkovski","full_name":"Mitkovski, Miso","first_name":"Miso"},{"first_name":"Sebastian","full_name":"Munck, Sebastian","last_name":"Munck"},{"full_name":"North, Alison J.","first_name":"Alison J.","last_name":"North"},{"first_name":"Tobias M.","full_name":"Rasse, Tobias M.","last_name":"Rasse"},{"last_name":"Resch-Genger","first_name":"Ute","full_name":"Resch-Genger, Ute"},{"full_name":"Schuetz, Lucas C.","first_name":"Lucas C.","last_name":"Schuetz"},{"last_name":"Seitz","first_name":"Arne","full_name":"Seitz, Arne"},{"last_name":"Strambio-De-Castillia","full_name":"Strambio-De-Castillia, Caterina","first_name":"Caterina"},{"last_name":"Swedlow","first_name":"Jason R.","full_name":"Swedlow, Jason R."},{"last_name":"Alexopoulos","full_name":"Alexopoulos, Ioannis","first_name":"Ioannis"},{"full_name":"Aumayr, Karin","first_name":"Karin","last_name":"Aumayr"},{"full_name":"Avilov, Sergiy","first_name":"Sergiy","last_name":"Avilov"},{"last_name":"Bakker","full_name":"Bakker, Gert Jan","first_name":"Gert Jan"},{"last_name":"Bammann","first_name":"Rodrigo R.","full_name":"Bammann, Rodrigo R."},{"last_name":"Bassi","full_name":"Bassi, Andrea","first_name":"Andrea"},{"last_name":"Beckert","first_name":"Hannes","full_name":"Beckert, Hannes"},{"last_name":"Beer","full_name":"Beer, Sebastian","first_name":"Sebastian"},{"last_name":"Belyaev","first_name":"Yury","full_name":"Belyaev, Yury"},{"full_name":"Bierwagen, Jakob","first_name":"Jakob","last_name":"Bierwagen"},{"first_name":"Konstantin A.","full_name":"Birngruber, Konstantin A.","last_name":"Birngruber"},{"first_name":"Manel","full_name":"Bosch, Manel","last_name":"Bosch"},{"last_name":"Breitlow","first_name":"Juergen","full_name":"Breitlow, Juergen"},{"last_name":"Cameron","first_name":"Lisa A.","full_name":"Cameron, Lisa A."},{"last_name":"Chalfoun","first_name":"Joe","full_name":"Chalfoun, Joe"},{"first_name":"James J.","full_name":"Chambers, James J.","last_name":"Chambers"},{"full_name":"Chen, Chieh Li","first_name":"Chieh Li","last_name":"Chen"},{"first_name":"Eduardo","full_name":"Conde-Sousa, Eduardo","last_name":"Conde-Sousa"},{"first_name":"Alexander D.","full_name":"Corbett, Alexander D.","last_name":"Corbett"},{"full_name":"Cordelieres, Fabrice P.","first_name":"Fabrice P.","last_name":"Cordelieres"},{"last_name":"Nery","first_name":"Elaine Del","full_name":"Nery, Elaine Del"},{"last_name":"Dietzel","full_name":"Dietzel, Ralf","first_name":"Ralf"},{"last_name":"Eismann","first_name":"Frank","full_name":"Eismann, Frank"},{"first_name":"Elnaz","full_name":"Fazeli, Elnaz","last_name":"Fazeli"},{"last_name":"Felscher","full_name":"Felscher, Andreas","first_name":"Andreas"},{"full_name":"Fried, Hans","first_name":"Hans","last_name":"Fried"},{"last_name":"Gaudreault","first_name":"Nathalie","full_name":"Gaudreault, Nathalie"},{"full_name":"Goh, Wah Ing","first_name":"Wah Ing","last_name":"Goh"},{"last_name":"Guilbert","first_name":"Thomas","full_name":"Guilbert, Thomas"},{"first_name":"Roland","full_name":"Hadleigh, Roland","last_name":"Hadleigh"},{"first_name":"Peter","full_name":"Hemmerich, Peter","last_name":"Hemmerich"},{"last_name":"Holst","full_name":"Holst, Gerhard A.","first_name":"Gerhard A."},{"first_name":"Michelle S.","full_name":"Itano, Michelle S.","last_name":"Itano"},{"full_name":"Jaffe, Claudia B.","first_name":"Claudia B.","last_name":"Jaffe"},{"full_name":"Jambor, Helena K.","first_name":"Helena K.","last_name":"Jambor"},{"first_name":"Stuart C.","full_name":"Jarvis, Stuart C.","last_name":"Jarvis"},{"first_name":"Antje","full_name":"Keppler, Antje","last_name":"Keppler"},{"first_name":"David","full_name":"Kirchenbuechler, David","last_name":"Kirchenbuechler"},{"first_name":"Marcel","full_name":"Kirchner, Marcel","last_name":"Kirchner"},{"last_name":"Kobayashi","full_name":"Kobayashi, Norio","first_name":"Norio"},{"first_name":"Gabriel","full_name":"Krens, Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Susanne","full_name":"Kunis, Susanne","last_name":"Kunis"},{"last_name":"Lacoste","full_name":"Lacoste, Judith","first_name":"Judith"},{"first_name":"Marco","full_name":"Marcello, Marco","last_name":"Marcello"},{"last_name":"Martins","first_name":"Gabriel G.","full_name":"Martins, Gabriel G."},{"last_name":"Metcalf","first_name":"Daniel J.","full_name":"Metcalf, Daniel J."},{"first_name":"Claire A.","full_name":"Mitchell, Claire A.","last_name":"Mitchell"},{"last_name":"Moore","first_name":"Joshua","full_name":"Moore, Joshua"},{"last_name":"Mueller","full_name":"Mueller, Tobias","first_name":"Tobias"},{"full_name":"Nelson, Michael S.","first_name":"Michael S.","last_name":"Nelson"},{"full_name":"Ogg, Stephen","first_name":"Stephen","last_name":"Ogg"},{"last_name":"Onami","full_name":"Onami, Shuichi","first_name":"Shuichi"},{"last_name":"Palmer","full_name":"Palmer, Alexandra L.","first_name":"Alexandra L."},{"last_name":"Paul-Gilloteaux","first_name":"Perrine","full_name":"Paul-Gilloteaux, Perrine"},{"last_name":"Pimentel","first_name":"Jaime A.","full_name":"Pimentel, Jaime A."},{"last_name":"Plantard","first_name":"Laure","full_name":"Plantard, Laure"},{"last_name":"Podder","first_name":"Santosh","full_name":"Podder, Santosh"},{"last_name":"Rexhepaj","full_name":"Rexhepaj, Elton","first_name":"Elton"},{"first_name":"Arnaud","full_name":"Royon, Arnaud","last_name":"Royon"},{"first_name":"Markku A.","full_name":"Saari, Markku A.","last_name":"Saari"},{"last_name":"Schapman","full_name":"Schapman, Damien","first_name":"Damien"},{"first_name":"Vincent","full_name":"Schoonderwoert, Vincent","last_name":"Schoonderwoert"},{"last_name":"Schroth-Diez","first_name":"Britta","full_name":"Schroth-Diez, Britta"},{"full_name":"Schwartz, Stanley","first_name":"Stanley","last_name":"Schwartz"},{"first_name":"Michael","full_name":"Shaw, Michael","last_name":"Shaw"},{"first_name":"Martin","full_name":"Spitaler, Martin","last_name":"Spitaler"},{"full_name":"Stoeckl, Martin T.","first_name":"Martin T.","last_name":"Stoeckl"},{"full_name":"Sudar, Damir","first_name":"Damir","last_name":"Sudar"},{"full_name":"Teillon, Jeremie","first_name":"Jeremie","last_name":"Teillon"},{"first_name":"Stefan","full_name":"Terjung, Stefan","last_name":"Terjung"},{"last_name":"Thuenauer","full_name":"Thuenauer, Roland","first_name":"Roland"},{"first_name":"Christian D.","full_name":"Wilms, Christian D.","last_name":"Wilms"},{"first_name":"Graham D.","full_name":"Wright, Graham D.","last_name":"Wright"},{"last_name":"Nitschke","first_name":"Roland","full_name":"Nitschke, Roland"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jmi.13041"}],"article_processing_charge":"Yes","department":[{"_id":"Bio"}],"title":"QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy","date_updated":"2025-06-12T06:29:47Z","issue":"1","publication_status":"published","type":"journal_article","publication_identifier":{"eissn":["1365-2818"],"issn":["0022-2720"]},"date_published":"2021-08-11T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","pmid":1,"month":"08","date_created":"2021-08-15T22:01:29Z","publication":"Journal of Microscopy","oa":1,"abstract":[{"text":"A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.","lang":"eng"}],"scopus_import":"1","page":"56-73","language":[{"iso":"eng"}],"_id":"9911","intvolume":"       284","doi":"10.1111/jmi.13041","oa_version":"Published Version","citation":{"apa":"Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M., … Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. <i>Journal of Microscopy</i>. Wiley. <a href=\"https://doi.org/10.1111/jmi.13041\">https://doi.org/10.1111/jmi.13041</a>","ieee":"G. Nelson <i>et al.</i>, “QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy,” <i>Journal of Microscopy</i>, vol. 284, no. 1. Wiley, pp. 56–73, 2021.","chicago":"Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” <i>Journal of Microscopy</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jmi.13041\">https://doi.org/10.1111/jmi.13041</a>.","ama":"Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. <i>Journal of Microscopy</i>. 2021;284(1):56-73. doi:<a href=\"https://doi.org/10.1111/jmi.13041\">10.1111/jmi.13041</a>","ista":"Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 284(1), 56–73.","mla":"Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” <i>Journal of Microscopy</i>, vol. 284, no. 1, Wiley, 2021, pp. 56–73, doi:<a href=\"https://doi.org/10.1111/jmi.13041\">10.1111/jmi.13041</a>.","short":"G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin, I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L. Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck, A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia, J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann, A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch, J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa, A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli, A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich, G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler, M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins, D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami, A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj, A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz, M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer, C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73."}},{"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)"},"arxiv":1,"publication_identifier":{"eissn":["1424-0661"],"issn":["1424-0637"]},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-12-01T00:00:00Z","oa":1,"month":"12","publication":"Annales Henri Poincaré ","date_created":"2021-08-15T22:01:29Z","scopus_import":"1","ec_funded":1,"abstract":[{"text":"In the customary random matrix model for transport in quantum dots with M internal degrees of freedom coupled to a chaotic environment via 𝑁≪𝑀 channels, the density 𝜌 of transmission eigenvalues is computed from a specific invariant ensemble for which explicit formula for the joint probability density of all eigenvalues is available. We revisit this problem in the large N regime allowing for (i) arbitrary ratio 𝜙:=𝑁/𝑀≤1; and (ii) general distributions for the matrix elements of the Hamiltonian of the quantum dot. In the limit 𝜙→0, we recover the formula for the density 𝜌 that Beenakker (Rev Mod Phys 69:731–808, 1997) has derived for a special matrix ensemble. We also prove that the inverse square root singularity of the density at zero and full transmission in Beenakker’s formula persists for any 𝜙<1 but in the borderline case 𝜙=1 an anomalous 𝜆−2/3 singularity arises at zero. To access this level of generality, we develop the theory of global and local laws on the spectral density of a large class of noncommutative rational expressions in large random matrices with i.i.d. entries.","lang":"eng"}],"language":[{"iso":"eng"}],"page":"4205–4269","citation":{"short":"L. Erdös, T.H. Krüger, Y. Nemish, Annales Henri Poincaré  22 (2021) 4205–4269.","ista":"Erdös L, Krüger TH, Nemish Y. 2021. Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . 22, 4205–4269.","mla":"Erdös, László, et al. “Scattering in Quantum Dots via Noncommutative Rational Functions.” <i>Annales Henri Poincaré </i>, vol. 22, Springer Nature, 2021, pp. 4205–4269, doi:<a href=\"https://doi.org/10.1007/s00023-021-01085-6\">10.1007/s00023-021-01085-6</a>.","ieee":"L. Erdös, T. H. Krüger, and Y. Nemish, “Scattering in quantum dots via noncommutative rational functions,” <i>Annales Henri Poincaré </i>, vol. 22. Springer Nature, pp. 4205–4269, 2021.","chicago":"Erdös, László, Torben H Krüger, and Yuriy Nemish. “Scattering in Quantum Dots via Noncommutative Rational Functions.” <i>Annales Henri Poincaré </i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00023-021-01085-6\">https://doi.org/10.1007/s00023-021-01085-6</a>.","apa":"Erdös, L., Krüger, T. H., &#38; Nemish, Y. (2021). Scattering in quantum dots via noncommutative rational functions. <i>Annales Henri Poincaré </i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-021-01085-6\">https://doi.org/10.1007/s00023-021-01085-6</a>","ama":"Erdös L, Krüger TH, Nemish Y. Scattering in quantum dots via noncommutative rational functions. <i>Annales Henri Poincaré </i>. 2021;22:4205–4269. doi:<a href=\"https://doi.org/10.1007/s00023-021-01085-6\">10.1007/s00023-021-01085-6</a>"},"oa_version":"Published Version","doi":"10.1007/s00023-021-01085-6","intvolume":"        22","_id":"9912","acknowledgement":"The authors are very grateful to Yan Fyodorov for discussions on the physical background and for providing references, and to the anonymous referee for numerous valuable remarks.","isi":1,"day":"01","volume":22,"year":"2021","project":[{"grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems"}],"external_id":{"isi":["000681531500001"],"arxiv":["1911.05112"]},"article_type":"original","file_date_updated":"2022-05-12T12:50:27Z","ddc":["510"],"publisher":"Springer Nature","quality_controlled":"1","author":[{"last_name":"Erdös","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","first_name":"Torben H"},{"id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7327-856X","last_name":"Nemish","full_name":"Nemish, Yuriy","first_name":"Yuriy"}],"has_accepted_license":"1","date_updated":"2025-04-15T08:04:59Z","department":[{"_id":"LaEr"}],"title":"Scattering in quantum dots via noncommutative rational functions","article_processing_charge":"Yes (in subscription journal)","file":[{"date_updated":"2022-05-12T12:50:27Z","access_level":"open_access","checksum":"8d6bac0e2b0a28539608b0538a8e3b38","file_size":1162454,"success":1,"file_id":"11365","date_created":"2022-05-12T12:50:27Z","relation":"main_file","file_name":"2021_AnnHenriPoincare_Erdoes.pdf","creator":"dernst","content_type":"application/pdf"}],"type":"journal_article","publication_status":"published"},{"_id":"9933","oa_version":"Submitted Version","doi":"10.1145/3465084.3467903","citation":{"ama":"Czumaj A, Davies P, Parter M. Component stability in low-space massively parallel computation. In: <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2021:481–491. doi:<a href=\"https://doi.org/10.1145/3465084.3467903\">10.1145/3465084.3467903</a>","apa":"Czumaj, A., Davies, P., &#38; Parter, M. (2021). Component stability in low-space massively parallel computation. In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i> (pp. 481–491). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3465084.3467903\">https://doi.org/10.1145/3465084.3467903</a>","ieee":"A. Czumaj, P. Davies, and M. Parter, “Component stability in low-space massively parallel computation,” in <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2021, pp. 481–491.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Component Stability in Low-Space Massively Parallel Computation.” In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, 481–491. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3465084.3467903\">https://doi.org/10.1145/3465084.3467903</a>.","ista":"Czumaj A, Davies P, Parter M. 2021. Component stability in low-space massively parallel computation. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 481–491.","mla":"Czumaj, Artur, et al. “Component Stability in Low-Space Massively Parallel Computation.” <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2021, pp. 481–491, doi:<a href=\"https://doi.org/10.1145/3465084.3467903\">10.1145/3465084.3467903</a>.","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 481–491."},"page":"481–491","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"In this paper, we study the power and limitations of component-stable algorithms in the low-space model of Massively Parallel Computation (MPC). Recently Ghaffari, Kuhn and Uitto (FOCS 2019) introduced the class of component-stable low-space MPC algorithms, which are, informally, defined as algorithms for which the outputs reported by the nodes in different connected components are required to be independent. This very natural notion was introduced to capture most (if not all) of the known efficient MPC algorithms to date, and it was the first general class of MPC algorithms for which one can show non-trivial conditional lower bounds. In this paper we enhance the framework of component-stable algorithms and investigate its effect on the complexity of randomized and deterministic low-space MPC. Our key contributions include: 1) We revise and formalize the lifting approach of Ghaffari, Kuhn and Uitto. This requires a very delicate amendment of the notion of component stability, which allows us to fill in gaps in the earlier arguments. 2) We also extend the framework to obtain conditional lower bounds for deterministic algorithms and fine-grained lower bounds that depend on the maximum degree Δ. 3) We demonstrate a collection of natural graph problems for which non-component-stable algorithms break the conditional lower bound obtained for component-stable algorithms. This implies that, for both deterministic and randomized algorithms, component-stable algorithms are conditionally weaker than the non-component-stable ones.\r\n\r\nAltogether our results imply that component-stability might limit the computational power of the low-space MPC model, paving the way for improved upper bounds that escape the conditional lower bound setting of Ghaffari, Kuhn, and Uitto."}],"ec_funded":1,"date_created":"2021-08-17T18:11:16Z","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","month":"07","oa":1,"date_published":"2021-07-21T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"isbn":["9781450385480"]},"arxiv":1,"publication_status":"published","type":"conference","article_processing_charge":"No","title":"Component stability in low-space massively parallel computation","department":[{"_id":"DaAl"}],"date_updated":"2025-04-14T07:43:49Z","author":[{"last_name":"Czumaj","full_name":"Czumaj, Artur","first_name":"Artur"},{"id":"11396234-BB50-11E9-B24C-90FCE5697425","last_name":"Davies","orcid":"0000-0002-5646-9524","full_name":"Davies, Peter","first_name":"Peter"},{"full_name":"Parter, Merav","first_name":"Merav","last_name":"Parter"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2106.01880"}],"quality_controlled":"1","publisher":"Association for Computing Machinery","conference":{"end_date":"2021-07-30","start_date":"2021-07-26","name":"PODC: Principles of Distributed Computing","location":"Virtual, Italy"},"external_id":{"arxiv":["2106.01880"],"isi":["000744439800049"]},"project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"year":"2021","day":"21","isi":1,"acknowledgement":"This work is partially supported by a Weizmann-UK Making Connections Grant, the Centre for Discrete Mathematics and its Applications (DIMAP), IBM Faculty Award, EPSRC award EP/V01305X/1, European Research Council (ERC) Grant No. 949083, the Minerva foundation with funding from the Federal German Ministry for Education and Research No. 713238, and the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No 754411."},{"_id":"9935","oa_version":"Submitted Version","doi":"10.1145/3465084.3467937","citation":{"ama":"Czumaj A, Davies P, Parter M. Improved deterministic (Δ+1) coloring in low-space MPC. In: <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2021:469–479. doi:<a href=\"https://doi.org/10.1145/3465084.3467937\">10.1145/3465084.3467937</a>","ieee":"A. Czumaj, P. Davies, and M. Parter, “Improved deterministic (Δ+1) coloring in low-space MPC,” in <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2021, pp. 469–479.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Improved Deterministic (Δ+1) Coloring in Low-Space MPC.” In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, 469–479. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3465084.3467937\">https://doi.org/10.1145/3465084.3467937</a>.","apa":"Czumaj, A., Davies, P., &#38; Parter, M. (2021). Improved deterministic (Δ+1) coloring in low-space MPC. In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i> (pp. 469–479). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3465084.3467937\">https://doi.org/10.1145/3465084.3467937</a>","ista":"Czumaj A, Davies P, Parter M. 2021. Improved deterministic (Δ+1) coloring in low-space MPC. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 469–479.","mla":"Czumaj, Artur, et al. “Improved Deterministic (Δ+1) Coloring in Low-Space MPC.” <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2021, pp. 469–479, doi:<a href=\"https://doi.org/10.1145/3465084.3467937\">10.1145/3465084.3467937</a>.","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 469–479."},"page":"469–479","language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"We present a deterministic O(log log log n)-round low-space Massively Parallel Computation (MPC) algorithm for the classical problem of (Δ+1)-coloring on n-vertex graphs. In this model, every machine has sublinear local space of size n^φ for any arbitrary constant φ \\in (0,1). Our algorithm works under the relaxed setting where each machine is allowed to perform exponential local computations, while respecting the n^φ space and bandwidth limitations.\r\n\r\nOur key technical contribution is a novel derandomization of the ingenious (Δ+1)-coloring local algorithm by Chang-Li-Pettie (STOC 2018, SIAM J. Comput. 2020). The Chang-Li-Pettie algorithm runs in T_local =poly(loglog n) rounds, which sets the state-of-the-art randomized round complexity for the problem in the local model. Our derandomization employs a combination of tools, notably pseudorandom generators (PRG) and bounded-independence hash functions.\r\n\r\nThe achieved round complexity of O(logloglog n) rounds matches the bound of log(T_local ), which currently serves an upper bound barrier for all known randomized algorithms for locally-checkable problems in this model. Furthermore, no deterministic sublogarithmic low-space MPC algorithms for the (Δ+1)-coloring problem have been known before."}],"scopus_import":"1","month":"07","date_created":"2021-08-17T18:14:15Z","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","oa":1,"date_published":"2021-07-21T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"isbn":["978-1-4503-8548-0"]},"publication_status":"published","type":"conference","article_processing_charge":"No","department":[{"_id":"DaAl"}],"title":"Improved deterministic (Δ+1) coloring in low-space MPC","date_updated":"2025-04-14T07:43:49Z","author":[{"full_name":"Czumaj, Artur","first_name":"Artur","last_name":"Czumaj"},{"id":"11396234-BB50-11E9-B24C-90FCE5697425","last_name":"Davies","orcid":"0000-0002-5646-9524","full_name":"Davies, Peter","first_name":"Peter"},{"last_name":"Parter","full_name":"Parter, Merav","first_name":"Merav"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://wrap.warwick.ac.uk/153753"}],"publisher":"Association for Computing Machinery","conference":{"end_date":"2021-07-30","name":"PODC: Symposium on Principles of Distributed Computing","start_date":"2021-07-26","location":"Virtual, Italy"},"external_id":{"isi":["000744439800048"]},"project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"year":"2021","day":"21","isi":1,"acknowledgement":"This work is partially supported by a Weizmann-UK Making Connections Grant, the Centre for Discrete Mathematics and its Applications (DIMAP), IBM Faculty Award, EPSRC award EP/V01305X/1, European Research Council (ERC) Grant No. 949083, the Minerva foundation with funding from the Federal German Ministry for Education and Research No. 713238, and the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No 754411."},{"file":[{"date_updated":"2021-09-03T12:34:28Z","access_level":"open_access","checksum":"0f9aafd59444cb6bdca6925d163ab946","file_size":"320453","date_created":"2021-08-20T19:59:44Z","file_id":"9948","relation":"main_file","creator":"fmuehlbo","content_type":"application/pdf","file_name":"differentialmonitoring-techreport.pdf"}],"type":"technical_report","publication_status":"published","has_accepted_license":"1","date_updated":"2025-04-15T06:55:00Z","title":"Differential monitoring","department":[{"_id":"ToHe"}],"article_processing_charge":"No","author":[{"first_name":"Fabian","full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177","last_name":"Mühlböck","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"ddc":["005"],"publisher":"IST Austria","file_date_updated":"2021-09-03T12:34:28Z","keyword":["run-time verification","software engineering","implicit specification"],"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","grant_number":"Z211"}],"day":"01","year":"2021","alternative_title":["IST Austria Technical Report"],"acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Matthew Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","citation":{"ama":"Mühlböck F, Henzinger TA. <i>Differential Monitoring</i>. IST Austria; 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9946\">10.15479/AT:ISTA:9946</a>","ieee":"F. Mühlböck and T. A. Henzinger, <i>Differential monitoring</i>. IST Austria, 2021.","chicago":"Mühlböck, Fabian, and Thomas A Henzinger. <i>Differential Monitoring</i>. IST Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9946\">https://doi.org/10.15479/AT:ISTA:9946</a>.","apa":"Mühlböck, F., &#38; Henzinger, T. A. (2021). <i>Differential monitoring</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9946\">https://doi.org/10.15479/AT:ISTA:9946</a>","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. <i>Differential Monitoring</i>. IST Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9946\">10.15479/AT:ISTA:9946</a>.","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring, IST Austria, 17p.","short":"F. Mühlböck, T.A. Henzinger, Differential Monitoring, IST Austria, 2021."},"oa_version":"Published Version","doi":"10.15479/AT:ISTA:9946","_id":"9946","language":[{"iso":"eng"}],"page":"17","abstract":[{"lang":"eng","text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs."}],"oa":1,"date_created":"2021-08-20T20:00:37Z","month":"09","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"relation":"shorter_version","status":"public","id":"10108"},{"relation":"other","status":"public","id":"9281"}]},"date_published":"2021-09-01T00:00:00Z","publication_identifier":{"issn":["2664-1690"]}},{"citation":{"short":"B. Vicoso, (2021).","mla":"Vicoso, Beatriz. <i>Data from Hyulmans et Al 2021, “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9949\">10.15479/AT:ISTA:9949</a>.","ista":"Vicoso B. 2021. Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:9949\">10.15479/AT:ISTA:9949</a>.","chicago":"Vicoso, Beatriz. “Data from Hyulmans et Al 2021, ‘Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9949\">https://doi.org/10.15479/AT:ISTA:9949</a>.","ieee":"B. Vicoso, “Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2021.","apa":"Vicoso, B. (2021). Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9949\">https://doi.org/10.15479/AT:ISTA:9949</a>","ama":"Vicoso B. Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9949\">10.15479/AT:ISTA:9949</a>"},"file":[{"file_size":139188306,"success":1,"file_id":"9950","date_created":"2021-08-21T13:43:59Z","relation":"main_file","file_name":"Data.zip","content_type":"application/zip","creator":"bvicoso","date_updated":"2021-08-21T13:43:59Z","access_level":"open_access","checksum":"90461837eed66beac6fa302993cf0ca9"}],"doi":"10.15479/AT:ISTA:9949","oa_version":"None","type":"research_data","_id":"9949","has_accepted_license":"1","date_updated":"2025-04-15T07:49:47Z","department":[{"_id":"BeVi"}],"title":"Data from Hyulmans et al 2021, \"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp\"","article_processing_charge":"No","author":[{"first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"date_created":"2021-08-21T13:44:22Z","month":"08","publisher":"Institute of Science and Technology Austria","status":"public","file_date_updated":"2021-08-21T13:43:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"10166","relation":"used_in_publication","status":"public"}]},"date_published":"2021-08-24T00:00:00Z","day":"24","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)"},"year":"2021"},{"quality_controlled":"1","abstract":[{"lang":"eng","text":"There has recently been a surge of interest in the computational and complexity properties of the population model, which assumes n anonymous, computationally-bounded nodes, interacting at random, with the goal of jointly computing global predicates. Significant work has gone towards investigating majority or consensus dynamics in this model: that is, assuming that every node is initially in one of two states X or Y, determine which state had higher initial count.\r\n\r\nIn this paper, we consider a natural generalization of majority/consensus, which we call comparison : in its simplest formulation, we are given two baseline states, X and Y, present in any initial configuration in fixed, but possibly small counts. One of these states has higher count than the other: we will assume |X_0| > C |Y_0| for some constant C > 1. The challenge is to design a protocol by which nodes can quickly and reliably decide on which of the baseline states X_0 and Y_0 has higher initial count. We begin by analyzing a simple and general dynamics solving the above comparison problem, which uses O( log n ) states per node, and converges in O(log n) (parallel) time, with high probability, to a state where the whole population votes on opinions X or Y at rates proportional to the initial concentrations of |X_0| vs. |Y_0|. We then describe how this procedure can be bootstrapped to solve comparison, i.e. have every node in the population reach the \"correct'' decision, with probability 1 - o(1), at the cost of O (log log n) additional states. Further, we prove that this dynamics is self-stabilizing, in the sense that it converges to the correct decision from arbitrary initial states, and leak-robust, in the sense that it can withstand spurious faulty reactions, which are known to occur in practical implementations of population protocols. Our analysis is based on a new martingale concentration result relating the discrete-time evolution of a population protocol to its expected (steady-state) analysis, which should be a useful tool when analyzing opinion dynamics and epidemic dissemination in the population model."}],"scopus_import":"1","author":[{"orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"id":"4B865388-F248-11E8-B48F-1D18A9856A87","last_name":"Töpfer","full_name":"Töpfer, Martin","first_name":"Martin"},{"full_name":"Uznański, Przemysław","first_name":"Przemysław","last_name":"Uznański"}],"date_created":"2021-08-22T22:01:20Z","month":"07","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","publisher":"Association for Computing Machinery","citation":{"ista":"Alistarh D-A, Töpfer M, Uznański P. 2021. Comparison dynamics in population protocols. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 55–65.","mla":"Alistarh, Dan-Adrian, et al. “Comparison Dynamics in Population Protocols.” <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2021, pp. 55–65, doi:<a href=\"https://doi.org/10.1145/3465084.3467915\">10.1145/3465084.3467915</a>.","short":"D.-A. Alistarh, M. Töpfer, P. Uznański, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 55–65.","ieee":"D.-A. Alistarh, M. Töpfer, and P. Uznański, “Comparison dynamics in population protocols,” in <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2021, pp. 55–65.","apa":"Alistarh, D.-A., Töpfer, M., &#38; Uznański, P. (2021). Comparison dynamics in population protocols. In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i> (pp. 55–65). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3465084.3467915\">https://doi.org/10.1145/3465084.3467915</a>","chicago":"Alistarh, Dan-Adrian, Martin Töpfer, and Przemysław Uznański. “Comparison Dynamics in Population Protocols.” In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, 55–65. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3465084.3467915\">https://doi.org/10.1145/3465084.3467915</a>.","ama":"Alistarh D-A, Töpfer M, Uznański P. Comparison dynamics in population protocols. In: <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2021:55-65. doi:<a href=\"https://doi.org/10.1145/3465084.3467915\">10.1145/3465084.3467915</a>"},"doi":"10.1145/3465084.3467915","oa_version":"None","type":"conference","_id":"9951","publication_status":"published","language":[{"iso":"eng"}],"date_updated":"2023-08-11T10:56:04Z","page":"55-65","department":[{"_id":"DaAl"}],"title":"Comparison dynamics in population protocols","article_processing_charge":"No","day":"21","publication_identifier":{"isbn":["9781450385480"]},"year":"2021","acknowledgement":"We would like to thank Rati Gelashvili for very useful discussions, and the PODC anonymous reviewers for their careful reading of our paper, and for their useful remarks. This work is partially supported by the Polish National Science Center (NCN) grant UMO2017/25/B/ST6/02010.","isi":1,"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-07-21T00:00:00Z","external_id":{"isi":["000744439800005"]},"conference":{"name":"PODC: Symposium on Principles of Distributed Computing","start_date":"2021-07-26","end_date":"2021-07-30","location":"Virtual, Italy"}},{"day":"01","year":"2021","volume":134,"acknowledgement":"We would like to thank the entire Paluch and Baum laboratories at the MRC-LMCB and the Chalut lab at the Cambridge SCI for discussions and feedback throughout the project, and the MRC-LMCB microscopy platform, in particular Andrew Vaughan, for technical support.","isi":1,"file_date_updated":"2021-08-23T07:32:20Z","external_id":{"isi":["000681395800008"]},"article_type":"original","author":[{"last_name":"Chaigne","full_name":"Chaigne, Agathe","first_name":"Agathe"},{"last_name":"Smith","full_name":"Smith, Matthew B.","first_name":"Matthew B."},{"first_name":"R. L.","full_name":"Cavestany, R. L.","last_name":"Cavestany"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"first_name":"Kevin J.","full_name":"Chalut, Kevin J.","last_name":"Chalut"},{"last_name":"Paluch","first_name":"Ewa K.","full_name":"Paluch, Ewa K."}],"quality_controlled":"1","ddc":["570"],"publisher":"The Company of Biologists","file":[{"access_level":"open_access","checksum":"f086f9d7cb63b2474c01921cb060c513","date_updated":"2021-08-23T07:32:20Z","relation":"main_file","content_type":"application/pdf","creator":"asandaue","file_name":"2021_JournalOfCellScience_Chaigne.pdf","success":1,"file_size":8651724,"date_created":"2021-08-23T07:32:20Z","file_id":"9954"}],"publication_status":"published","type":"journal_article","date_updated":"2025-07-10T12:02:07Z","has_accepted_license":"1","issue":"14","article_processing_charge":"Yes (in subscription journal)","title":"Three-dimensional geometry controls division symmetry in stem cell colonies","department":[{"_id":"EdHa"}],"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)"},"publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2021-07-01T00:00:00Z","article_number":"jcs255018","scopus_import":"1","abstract":[{"lang":"eng","text":"Proper control of division orientation and symmetry, largely determined by spindle positioning, is essential to development and homeostasis. Spindle positioning has been extensively studied in cells dividing in two-dimensional (2D) environments and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient division along the interphase long axis of the cell. However, little is known about how cells control spindle positioning in three-dimensional (3D) environments, such as early mammalian embryos and a variety of adult tissues. Here, we use mouse embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate division in 3D. We observe that, at the periphery of 3D colonies, ESCs display high spindle mobility and divide asymmetrically. Our data suggest that enhanced spindle movements are due to unequal distribution of the cell–cell junction protein E-cadherin between future daughter cells. Interestingly, when cells progress towards differentiation, division becomes more symmetric, with more elongated shapes in metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this study suggests that in 3D contexts, the geometry of the cell and its contacts with neighbors control division orientation and symmetry."}],"oa":1,"date_created":"2021-08-22T22:01:20Z","publication":"Journal of Cell Science","month":"07","oa_version":"Published Version","doi":"10.1242/jcs.255018","citation":{"short":"A. Chaigne, M.B. Smith, R.L. Cavestany, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Journal of Cell Science 134 (2021).","ista":"Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. 2021. Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. 134(14), jcs255018.","mla":"Chaigne, Agathe, et al. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” <i>Journal of Cell Science</i>, vol. 134, no. 14, jcs255018, The Company of Biologists, 2021, doi:<a href=\"https://doi.org/10.1242/jcs.255018\">10.1242/jcs.255018</a>.","chicago":"Chaigne, Agathe, Matthew B. Smith, R. L. Cavestany, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” <i>Journal of Cell Science</i>. The Company of Biologists, 2021. <a href=\"https://doi.org/10.1242/jcs.255018\">https://doi.org/10.1242/jcs.255018</a>.","ieee":"A. Chaigne, M. B. Smith, R. L. Cavestany, E. B. Hannezo, K. J. Chalut, and E. K. Paluch, “Three-dimensional geometry controls division symmetry in stem cell colonies,” <i>Journal of Cell Science</i>, vol. 134, no. 14. The Company of Biologists, 2021.","apa":"Chaigne, A., Smith, M. B., Cavestany, R. L., Hannezo, E. B., Chalut, K. J., &#38; Paluch, E. K. (2021). Three-dimensional geometry controls division symmetry in stem cell colonies. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.255018\">https://doi.org/10.1242/jcs.255018</a>","ama":"Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. Three-dimensional geometry controls division symmetry in stem cell colonies. <i>Journal of Cell Science</i>. 2021;134(14). doi:<a href=\"https://doi.org/10.1242/jcs.255018\">10.1242/jcs.255018</a>"},"_id":"9952","intvolume":"       134","language":[{"iso":"eng"}]},{"publication_identifier":{"issn":["0889-1591"]},"date_published":"2021-10-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","abstract":[{"lang":"eng","text":"Chronic psychological stress is one of the most important triggers and environmental risk factors for neuropsychiatric disorders. Chronic stress can influence all organs via the secretion of stress hormones, including glucocorticoids by the adrenal glands, which coordinate the stress response across the body. In the brain, glucocorticoid receptors (GR) are expressed by various cell types including microglia, which are its resident immune cells regulating stress-induced inflammatory processes. To study the roles of microglial GR under normal homeostatic conditions and following chronic stress, we generated a mouse model in which the GR gene is depleted in microglia specifically at adulthood to prevent developmental confounds. We first confirmed that microglia were depleted in GR in our model in males and females among the cingulate cortex and the hippocampus, both stress-sensitive brain regions. Then, cohorts of microglial-GR depleted and wild-type (WT) adult female mice were housed for 3 weeks in a standard or stressful condition, using a chronic unpredictable mild stress (CUMS) paradigm. CUMS induced stress-related behavior in both microglial-GR depleted and WT animals as demonstrated by a decrease of both saccharine preference and progressive ratio breakpoint. Nevertheless, the hippocampal microglial and neural mechanisms underlying the adaptation to stress occurred differently between the two genotypes. Upon CUMS exposure, microglial morphology was altered in the WT controls, without any apparent effect in microglial-GR depleted mice. Furthermore, in the standard environment condition, GR depleted-microglia showed increased expression of pro-inflammatory genes, and genes involved in microglial homeostatic functions (such as Trem2, Cx3cr1 and Mertk). On the contrary, in CUMS condition, GR depleted-microglia showed reduced expression levels of pro-inflammatory genes and increased neuroprotective as well as anti-inflammatory genes compared to WT-microglia. Moreover, in microglial-GR depleted mice, but not in WT mice, CUMS led to a significant reduction of CA1 long-term potentiation and paired-pulse ratio. Lastly, differences in adult hippocampal neurogenesis were observed between the genotypes during normal homeostatic conditions, with microglial-GR deficiency increasing the formation of newborn neurons in the dentate gyrus subgranular zone independently from stress exposure. Together, these findings indicate that, although the deletion of microglial GR did not prevent the animal’s ability to respond to stress, it contributed to modulating hippocampal functions in both standard and stressful conditions, notably by shaping the microglial response to chronic stress."}],"scopus_import":"1","pmid":1,"date_created":"2021-08-22T22:01:21Z","publication":"Brain, Behavior, and Immunity","month":"10","oa":1,"_id":"9953","intvolume":"        97","oa_version":"Submitted Version","doi":"10.1016/j.bbi.2021.07.022","citation":{"mla":"Picard, Katherine, et al. “Microglial-Glucocorticoid Receptor Depletion Alters the Response of Hippocampal Microglia and Neurons in a Chronic Unpredictable Mild Stress Paradigm in Female Mice.” <i>Brain, Behavior, and Immunity</i>, vol. 97, Elsevier, 2021, pp. 423–39, doi:<a href=\"https://doi.org/10.1016/j.bbi.2021.07.022\">10.1016/j.bbi.2021.07.022</a>.","ista":"Picard K, Bisht K, Poggini S, Garofalo S, Golia MT, Basilico B, Abdallah F, Ciano Albanese N, Amrein I, Vernoux N, Sharma K, Hui CW, C. Savage J, Limatola C, Ragozzino D, Maggi L, Branchi I, Tremblay MÈ. 2021. Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice. Brain, Behavior, and Immunity. 97, 423–439.","short":"K. Picard, K. Bisht, S. Poggini, S. Garofalo, M.T. Golia, B. Basilico, F. Abdallah, N. Ciano Albanese, I. Amrein, N. Vernoux, K. Sharma, C.W. Hui, J. C. Savage, C. Limatola, D. Ragozzino, L. Maggi, I. Branchi, M.È. Tremblay, Brain, Behavior, and Immunity 97 (2021) 423–439.","ama":"Picard K, Bisht K, Poggini S, et al. Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice. <i>Brain, Behavior, and Immunity</i>. 2021;97:423-439. doi:<a href=\"https://doi.org/10.1016/j.bbi.2021.07.022\">10.1016/j.bbi.2021.07.022</a>","chicago":"Picard, Katherine, Kanchan Bisht, Silvia Poggini, Stefano Garofalo, Maria Teresa Golia, Bernadette Basilico, Fatima Abdallah, et al. “Microglial-Glucocorticoid Receptor Depletion Alters the Response of Hippocampal Microglia and Neurons in a Chronic Unpredictable Mild Stress Paradigm in Female Mice.” <i>Brain, Behavior, and Immunity</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.bbi.2021.07.022\">https://doi.org/10.1016/j.bbi.2021.07.022</a>.","ieee":"K. Picard <i>et al.</i>, “Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice,” <i>Brain, Behavior, and Immunity</i>, vol. 97. Elsevier, pp. 423–439, 2021.","apa":"Picard, K., Bisht, K., Poggini, S., Garofalo, S., Golia, M. T., Basilico, B., … Tremblay, M. È. (2021). Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice. <i>Brain, Behavior, and Immunity</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbi.2021.07.022\">https://doi.org/10.1016/j.bbi.2021.07.022</a>"},"page":"423-439","language":[{"iso":"eng"}],"year":"2021","volume":97,"day":"01","isi":1,"acknowledgement":"We acknowledge that Université Laval stands on the traditional and unceded land of the Huron-Wendat peoples; and that the University of Victoria exists on the territory of the Lekwungen peoples and that the Songhees, Esquimalt and WSÁNEÆ peoples have relationships to this land. We thank Emmanuel Planel for the access to the epifluorescence microscope and Julie-Christine Lévesque at the Bioimaging Platform of CRCHU de Québec-Université Laval for technical assistance. We also thank the Centre for Advanced Materials and Related Technology for the access to the confocal microscope with Airyscan. K.P. was supported by a doctoral scholarship from Fonds de Recherche du Québec – Santé (FRQS), an excellence award from Fondation du CHU de Québec, as well as from Centre Thématique de Recherche en Neurosciences and from Fondation Famille-Choquette. K.B. was supported by excellence scholarships from Université Laval and Fondation du CHU de Québec. S.G. is supported by FIRC-AIRC fellowship for Italy 22329/2018 and by Pilot ARISLA NKINALS 2019. C.W.H. and J.C.S. were supported by postdoctoral fellowships from FRQS. This study was funded by a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery grant (RGPIN-2014-05308) awarded to M.E.T., by ERANET neuron 2017 MicroSynDep to M.E.T. and I.B., and by the Italian Ministry of Health, grant RF-2018-12367249 to I.B, by PRIN 2017, AIRC 2019 and Ministero della Salute RF2018 to C.L. M.E.T. is a Tier II Canada Research Chair in Neurobiology of Aging and Cognition.","article_type":"original","external_id":{"pmid":["34343616"],"isi":["000702878400007"]},"author":[{"last_name":"Picard","first_name":"Katherine","full_name":"Picard, Katherine"},{"last_name":"Bisht","first_name":"Kanchan","full_name":"Bisht, Kanchan"},{"last_name":"Poggini","full_name":"Poggini, Silvia","first_name":"Silvia"},{"first_name":"Stefano","full_name":"Garofalo, Stefano","last_name":"Garofalo"},{"first_name":"Maria Teresa","full_name":"Golia, Maria Teresa","last_name":"Golia"},{"first_name":"Bernadette","full_name":"Basilico, Bernadette","last_name":"Basilico","orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425"},{"full_name":"Abdallah, Fatima","first_name":"Fatima","last_name":"Abdallah"},{"last_name":"Ciano Albanese","first_name":"Naomi","full_name":"Ciano Albanese, Naomi"},{"last_name":"Amrein","full_name":"Amrein, Irmgard","first_name":"Irmgard"},{"first_name":"Nathalie","full_name":"Vernoux, Nathalie","last_name":"Vernoux"},{"first_name":"Kaushik","full_name":"Sharma, Kaushik","last_name":"Sharma"},{"first_name":"Chin Wai","full_name":"Hui, Chin Wai","last_name":"Hui"},{"last_name":"C. Savage","full_name":"C. Savage, Julie","first_name":"Julie"},{"first_name":"Cristina","full_name":"Limatola, Cristina","last_name":"Limatola"},{"full_name":"Ragozzino, Davide","first_name":"Davide","last_name":"Ragozzino"},{"full_name":"Maggi, Laura","first_name":"Laura","last_name":"Maggi"},{"last_name":"Branchi","first_name":"Igor","full_name":"Branchi, Igor"},{"last_name":"Tremblay","full_name":"Tremblay, Marie Ève","first_name":"Marie Ève"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.zora.uzh.ch/id/eprint/208855/1/ZORA208855.pdf"}],"publisher":"Elsevier","publication_status":"published","type":"journal_article","article_processing_charge":"No","department":[{"_id":"GaNo"}],"title":"Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice","date_updated":"2023-10-03T09:49:18Z"},{"citation":{"short":"M. B R, A. Tewari, T.-H. Oh, T. Weyrich, B. Bickel, H.-P. Seidel, H. Pfister, W. Matusik, M. Elgharib, C. Theobalt, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2021, pp. 4791–4800.","mla":"B R, Mallikarjun, et al. “Monocular Reconstruction of Neural Face Reflectance Fields.” <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2021, pp. 4791–800, doi:<a href=\"https://doi.org/10.1109/CVPR46437.2021.00476\">10.1109/CVPR46437.2021.00476</a>.","ista":"B R M, Tewari A, Oh T-H, Weyrich T, Bickel B, Seidel H-P, Pfister H, Matusik W, Elgharib M, Theobalt C. 2021. Monocular reconstruction of neural face reflectance fields. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 4791–4800.","apa":"B R, M., Tewari, A., Oh, T.-H., Weyrich, T., Bickel, B., Seidel, H.-P., … Theobalt, C. (2021). Monocular reconstruction of neural face reflectance fields. In <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i> (pp. 4791–4800). Nashville, TN, United States; Virtual: IEEE. <a href=\"https://doi.org/10.1109/CVPR46437.2021.00476\">https://doi.org/10.1109/CVPR46437.2021.00476</a>","chicago":"B R, Mallikarjun, Ayush Tewari, Tae-Hyun Oh, Tim Weyrich, Bernd Bickel, Hans-Peter Seidel, Hanspeter Pfister, Wojciech Matusik, Mohamed Elgharib, and Christian Theobalt. “Monocular Reconstruction of Neural Face Reflectance Fields.” In <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>, 4791–4800. IEEE, 2021. <a href=\"https://doi.org/10.1109/CVPR46437.2021.00476\">https://doi.org/10.1109/CVPR46437.2021.00476</a>.","ieee":"M. B R <i>et al.</i>, “Monocular reconstruction of neural face reflectance fields,” in <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>, Nashville, TN, United States; Virtual, 2021, pp. 4791–4800.","ama":"B R M, Tewari A, Oh T-H, et al. Monocular reconstruction of neural face reflectance fields. In: <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2021:4791-4800. doi:<a href=\"https://doi.org/10.1109/CVPR46437.2021.00476\">10.1109/CVPR46437.2021.00476</a>"},"doi":"10.1109/CVPR46437.2021.00476","oa_version":"Preprint","_id":"9957","language":[{"iso":"eng"}],"page":"4791-4800","scopus_import":"1","abstract":[{"lang":"eng","text":"The reflectance field of a face describes the reflectance properties responsible for complex lighting effects including diffuse, specular, inter-reflection and self shadowing. Most existing methods for estimating the face reflectance from a monocular image assume faces to be diffuse with very few approaches adding a specular component. This still leaves out important perceptual aspects of reflectance as higher-order global illumination effects and self-shadowing are not modeled. We present a new neural representation for face reflectance where we can estimate all components of the reflectance responsible for the final appearance from a single monocular image. Instead of modeling each component of the reflectance separately using parametric models, our neural representation allows us to generate a basis set of faces in a geometric deformation-invariant space, parameterized by the input light direction, viewpoint and face geometry. We learn to reconstruct this reflectance field of a face just from a monocular image, which can be used to render the face from any viewpoint in any light condition. Our method is trained on a light-stage training dataset, which captures 300 people illuminated with 150 light conditions from 8 viewpoints. We show that our method outperforms existing monocular reflectance reconstruction methods, in terms of photorealism due to better capturing of physical premitives, such as sub-surface scattering, specularities, self-shadows and other higher-order effects."}],"oa":1,"date_created":"2021-08-24T06:03:00Z","publication":"Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition","month":"09","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-09-01T00:00:00Z","arxiv":1,"publication_identifier":{"isbn":["978-166544509-2"],"issn":["1063-6919"]},"file":[{"access_level":"open_access","checksum":"961db0bde76dd87cf833930080bb9f38","date_updated":"2021-08-24T06:02:15Z","relation":"main_file","creator":"bbickel","content_type":"application/pdf","file_name":"R_Monocular_Reconstruction_of_Neural_Face_Reflectance_Fields_CVPR_2021_paper[1].pdf","file_size":4746649,"date_created":"2021-08-24T06:02:15Z","file_id":"9958"}],"type":"conference","publication_status":"published","has_accepted_license":"1","date_updated":"2023-08-11T11:08:35Z","department":[{"_id":"BeBi"}],"title":"Monocular reconstruction of neural face reflectance fields","article_processing_charge":"No","quality_controlled":"1","author":[{"first_name":"Mallikarjun","full_name":"B R, Mallikarjun","last_name":"B R"},{"full_name":"Tewari, Ayush","first_name":"Ayush","last_name":"Tewari"},{"full_name":"Oh, Tae-Hyun","first_name":"Tae-Hyun","last_name":"Oh"},{"first_name":"Tim","full_name":"Weyrich, Tim","last_name":"Weyrich"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bickel, Bernd"},{"first_name":"Hans-Peter","full_name":"Seidel, Hans-Peter","last_name":"Seidel"},{"full_name":"Pfister, Hanspeter","first_name":"Hanspeter","last_name":"Pfister"},{"first_name":"Wojciech","full_name":"Matusik, Wojciech","last_name":"Matusik"},{"last_name":"Elgharib","full_name":"Elgharib, Mohamed","first_name":"Mohamed"},{"last_name":"Theobalt","first_name":"Christian","full_name":"Theobalt, Christian"}],"publisher":"IEEE","ddc":["000"],"file_date_updated":"2021-08-24T06:02:15Z","external_id":{"arxiv":["2008.10247"],"isi":["000739917304096"]},"conference":{"name":"CVPR: Conference on Computer Vision and Pattern Recognition","start_date":"2021-06-20","end_date":"2021-06-25","location":"Nashville, TN, United States; Virtual"},"day":"01","year":"2021","acknowledgement":"We thank Tarun Yenamandra and Duarte David for helping us with the comparisons. This work was supported by the\r\nERC Consolidator Grant 4DReply (770784). We also acknowledge support from InterDigital.","isi":1}]