[{"scopus_import":"1","day":"09","article_processing_charge":"No","publication":"IEEE Transactions on Signal Processing","citation":{"mla":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing, vol. 69, Institute of Electrical and Electronics Engineers, 2021, pp. 4039–54, doi:10.1109/TSP.2021.3087899.","short":"M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054.","chicago":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/TSP.2021.3087899.","ama":"Gabrielaitis M. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 2021;69:4039-4054. doi:10.1109/TSP.2021.3087899","ista":"Gabrielaitis M. 2021. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 69, 4039–4054.","apa":"Gabrielaitis, M. (2021). Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/TSP.2021.3087899","ieee":"M. Gabrielaitis, “Fast and accurate amplitude demodulation of wideband signals,” IEEE Transactions on Signal Processing, vol. 69. Institute of Electrical and Electronics Engineers, pp. 4039–4054, 2021."},"article_type":"original","page":"4039 - 4054","date_published":"2021-06-09T00:00:00Z","type":"journal_article","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"}],"_id":"9828","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Fast and accurate amplitude demodulation of wideband signals","status":"public","intvolume":" 69","oa_version":"Preprint","month":"06","publication_identifier":{"issn":["1053-587X"],"eissn":["1941-0476"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.04832"}],"oa":1,"external_id":{"arxiv":["2102.04832"],"isi":["000682123900002"]},"quality_controlled":"1","isi":1,"doi":"10.1109/TSP.2021.3087899","language":[{"iso":"eng"}],"acknowledgement":"The author thanks his colleagues K. Huszár and G. Tkačik for valuable discussions and comments on the manuscript.","year":"2021","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Institute of Electrical and Electronics Engineers","author":[{"full_name":"Gabrielaitis, Mantas","orcid":"0000-0002-7758-2016","id":"4D5B0CBC-F248-11E8-B48F-1D18A9856A87","last_name":"Gabrielaitis","first_name":"Mantas"}],"date_created":"2021-08-08T22:01:31Z","date_updated":"2023-08-10T14:19:33Z","volume":69},{"file_date_updated":"2021-04-26T09:33:44Z","abstract":[{"text":"This archive contains the missing sweater mesh animations and displacement models for the code of \"Mechanics-Aware Deformation of Yarn Pattern Geometry\"\r\n\r\nCode Repository: https://git.ist.ac.at/gsperl/MADYPG","lang":"eng"}],"license":"https://opensource.org/licenses/MIT","type":"software","gitlab_commit_id":"6a77e7e22769230ae5f5edaa090fb4b828e57573","gitlab_url":"https://git.ist.ac.at/gsperl/MADYPG","author":[{"full_name":"Sperl, Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","last_name":"Sperl","first_name":"Georg"},{"full_name":"Narain, Rahul","first_name":"Rahul","last_name":"Narain"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan"}],"related_material":{"record":[{"id":"9818","status":"public","relation":"used_for_analysis_in"}]},"date_created":"2021-04-16T14:26:19Z","date_updated":"2023-08-10T14:24:36Z","file":[{"file_id":"9328","relation":"main_file","date_updated":"2021-04-16T14:15:12Z","date_created":"2021-04-16T14:15:12Z","success":1,"checksum":"0324cb519273371708743f3282e7c081","file_name":"MADYPG_extra_data.zip","access_level":"open_access","creator":"gsperl","content_type":"application/zip","file_size":802586232},{"date_updated":"2021-04-26T09:33:44Z","date_created":"2021-04-26T09:33:44Z","checksum":"4c224551adf852b136ec21a4e13f0c1b","file_id":"9353","relation":"main_file","creator":"pub-gitlab-bot","content_type":"application/gzip","file_size":64962865,"file_name":"MADYPG.zip","access_level":"open_access"}],"_id":"9327","year":"2021","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data)","ddc":["005"],"status":"public","publisher":"IST Austria","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"month":"05","has_accepted_license":"1","date_published":"2021-05-01T00:00:00Z","doi":"10.15479/AT:ISTA:9327","tmp":{"name":"The MIT License","legal_code_url":"https://opensource.org/licenses/MIT","short":"MIT"},"oa":1,"citation":{"chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9327.","short":"G. Sperl, R. Narain, C. Wojtan, (2021).","mla":"Sperl, Georg, et al. Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data). IST Austria, 2021, doi:10.15479/AT:ISTA:9327.","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021.","apa":"Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data). IST Austria. https://doi.org/10.15479/AT:ISTA:9327","ista":"Sperl G, Narain R, Wojtan C. 2021. Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data), IST Austria, 10.15479/AT:ISTA:9327.","ama":"Sperl G, Narain R, Wojtan C. Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data). 2021. doi:10.15479/AT:ISTA:9327"}},{"article_type":"original","publication":"Physical Review B","citation":{"short":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, A. Ghazaryan, Physical Review B 104 (2021).","mla":"Volosniev, Artem, et al. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” Physical Review B, vol. 104, no. 2, 024430, American Physical Society, 2021, doi:10.1103/physrevb.104.024430.","chicago":"Volosniev, Artem, Hen Alpern, Yossi Paltiel, Oded Millo, Mikhail Lemeshko, and Areg Ghazaryan. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/physrevb.104.024430.","ama":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. 2021;104(2). doi:10.1103/physrevb.104.024430","apa":"Volosniev, A., Alpern, H., Paltiel, Y., Millo, O., Lemeshko, M., & Ghazaryan, A. (2021). Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.104.024430","ieee":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, and A. Ghazaryan, “Interplay between friction and spin-orbit coupling as a source of spin polarization,” Physical Review B, vol. 104, no. 2. American Physical Society, 2021.","ista":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. 2021. Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. 104(2), 024430."},"date_published":"2021-07-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Interplay between friction and spin-orbit coupling as a source of spin polarization","intvolume":" 104","_id":"9770","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We study an effective one-dimensional quantum model that includes friction and spin-orbit coupling (SOC), and show that the model exhibits spin polarization when both terms are finite. Most important, strong spin polarization can be observed even for moderate SOC, provided that the friction is strong. Our findings might help to explain the pronounced effect of chirality on spin distribution and transport in chiral molecules. In particular, our model implies static magnetic properties of a chiral molecule, which lead to Shiba-like states when a molecule is placed on a superconductor, in accordance with recent experimental data."}],"issue":"2","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"main_file_link":[{"url":"https://arxiv.org/abs/2101.05173","open_access":"1"}],"external_id":{"arxiv":["2101.05173"],"isi":["000678780800003"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.104.024430","month":"07","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"acknowledgement":"We thank Rafael Barfknecht for useful discussions. This work has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.\r\nand A.G.V.). M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). Y.P. and O.M. acknowledge funding from the Nidersachsen Ministry of Science and Culture, and from the\r\nAcademia Sinica Research Program. O.M. is thankful for support through the Harry de Jur Chair in Applied Science.","year":"2021","date_created":"2021-08-04T15:05:32Z","date_updated":"2023-08-10T14:27:07Z","volume":104,"author":[{"last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"},{"full_name":"Alpern, Hen","first_name":"Hen","last_name":"Alpern"},{"last_name":"Paltiel","first_name":"Yossi","full_name":"Paltiel, Yossi"},{"full_name":"Millo, Oded","last_name":"Millo","first_name":"Oded"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan"}],"article_number":"024430","ec_funded":1},{"month":"09","publication_identifier":{"issn":["0304-3975"]},"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://publications.lib.chalmers.se/records/fulltext/232185/232185.pdf"}],"external_id":{"isi":["000694718900004"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.tcs.2021.06.041","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Elsevier","year":"2021","date_updated":"2023-08-10T14:27:43Z","date_created":"2021-08-08T22:01:31Z","volume":886,"author":[{"full_name":"Chatterjee, Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2742-4028","first_name":"Bapi","last_name":"Chatterjee"},{"full_name":"Walulya, Ivan","last_name":"Walulya","first_name":"Ivan"},{"full_name":"Tsigas, Philippas","first_name":"Philippas","last_name":"Tsigas"}],"keyword":["Concurrent data structure","kD-tree","Nearest neighbor search","Similarity search","Lock-free","Linearizability"],"scopus_import":"1","day":"13","article_processing_charge":"No","article_type":"original","page":"27-48","publication":"Theoretical Computer Science","citation":{"ieee":"B. Chatterjee, I. Walulya, and P. Tsigas, “Concurrent linearizable nearest neighbour search in LockFree-kD-tree,” Theoretical Computer Science, vol. 886. Elsevier, pp. 27–48, 2021.","apa":"Chatterjee, B., Walulya, I., & Tsigas, P. (2021). Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2021.06.041","ista":"Chatterjee B, Walulya I, Tsigas P. 2021. Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. 886, 27–48.","ama":"Chatterjee B, Walulya I, Tsigas P. Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. 2021;886:27-48. doi:10.1016/j.tcs.2021.06.041","chicago":"Chatterjee, Bapi, Ivan Walulya, and Philippas Tsigas. “Concurrent Linearizable Nearest Neighbour Search in LockFree-KD-Tree.” Theoretical Computer Science. Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.06.041.","short":"B. Chatterjee, I. Walulya, P. Tsigas, Theoretical Computer Science 886 (2021) 27–48.","mla":"Chatterjee, Bapi, et al. “Concurrent Linearizable Nearest Neighbour Search in LockFree-KD-Tree.” Theoretical Computer Science, vol. 886, Elsevier, 2021, pp. 27–48, doi:10.1016/j.tcs.2021.06.041."},"date_published":"2021-09-13T00:00:00Z","type":"journal_article","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."}],"status":"public","title":"Concurrent linearizable nearest neighbour search in LockFree-kD-tree","intvolume":" 886","_id":"9827","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version"},{"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2104445118","quality_controlled":"1","isi":1,"external_id":{"isi":["000685037700012"],"pmid":["34272287"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"07","volume":118,"date_updated":"2023-08-11T10:28:10Z","date_created":"2021-08-10T19:30:41Z","author":[{"first_name":"Jessica A.","last_name":"Rodrigues","full_name":"Rodrigues, Jessica A."},{"full_name":"Hsieh, Ping-Hung","last_name":"Hsieh","first_name":"Ping-Hung"},{"first_name":"Deling","last_name":"Ruan","full_name":"Ruan, Deling"},{"full_name":"Nishimura, Toshiro","last_name":"Nishimura","first_name":"Toshiro"},{"first_name":"Manoj K.","last_name":"Sharma","full_name":"Sharma, Manoj K."},{"last_name":"Sharma","first_name":"Rita","full_name":"Sharma, Rita"},{"full_name":"Ye, XinYi","last_name":"Ye","first_name":"XinYi"},{"first_name":"Nicholas D.","last_name":"Nguyen","full_name":"Nguyen, Nicholas D."},{"last_name":"Nijjar","first_name":"Sukhranjan","full_name":"Nijjar, Sukhranjan"},{"first_name":"Pamela C.","last_name":"Ronald","full_name":"Ronald, Pamela C."},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"}],"department":[{"_id":"DaZi"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":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.","year":"2021","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2021-08-11T09:31:41Z","article_number":"e2104445118","date_published":"2021-07-16T00:00:00Z","article_type":"original","citation":{"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. Proceedings of the National Academy of Sciences. 2021;118(29). doi:10.1073/pnas.2104445118","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. 118(29), e2104445118.","ieee":"J. A. Rodrigues et al., “Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting,” Proceedings of the National Academy of Sciences, 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. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2104445118","mla":"Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” Proceedings of the National Academy of Sciences, vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:10.1073/pnas.2104445118.","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 118 (2021).","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.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118."},"publication":"Proceedings of the National Academy of Sciences","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"16","scopus_import":"1","file":[{"file_name":"2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf","access_level":"open_access","creator":"asandaue","content_type":"application/pdf","file_size":1898360,"file_id":"9879","relation":"main_file","date_updated":"2021-08-11T09:31:41Z","date_created":"2021-08-11T09:31:41Z","success":1,"checksum":"19e84ad8c03c60222744ee8e16cd6998"}],"oa_version":"Published Version","intvolume":" 118","status":"public","title":"Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting","ddc":["580","570"],"_id":"9877","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"29","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."}],"type":"journal_article"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000683910200042"],"pmid":["34376683"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41467-021-25211-4","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"month":"08","pmid":1,"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).","year":"2021","publisher":"Springer Nature","department":[{"_id":"SaSi"}],"publication_status":"published","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-32785-0"}]},"author":[{"last_name":"Raso","first_name":"Andrea","full_name":"Raso, Andrea"},{"full_name":"Dirkx, Ellen","first_name":"Ellen","last_name":"Dirkx"},{"first_name":"Vasco","last_name":"Sampaio-Pinto","full_name":"Sampaio-Pinto, Vasco"},{"last_name":"el Azzouzi","first_name":"Hamid","full_name":"el Azzouzi, Hamid"},{"last_name":"Cubero","first_name":"Ryan J","orcid":"0000-0003-0002-1867","id":"850B2E12-9CD4-11E9-837F-E719E6697425","full_name":"Cubero, Ryan J"},{"first_name":"Daniel W.","last_name":"Sorensen","full_name":"Sorensen, Daniel W."},{"last_name":"Ottaviani","first_name":"Lara","full_name":"Ottaviani, Lara"},{"full_name":"Olieslagers, Servé","last_name":"Olieslagers","first_name":"Servé"},{"last_name":"Huibers","first_name":"Manon M.","full_name":"Huibers, Manon M."},{"full_name":"de Weger, Roel","last_name":"de Weger","first_name":"Roel"},{"last_name":"Siddiqi","first_name":"Sailay","full_name":"Siddiqi, Sailay"},{"last_name":"Moimas","first_name":"Silvia","full_name":"Moimas, Silvia"},{"first_name":"Consuelo","last_name":"Torrini","full_name":"Torrini, Consuelo"},{"full_name":"Zentillin, Lorena","first_name":"Lorena","last_name":"Zentillin"},{"full_name":"Braga, Luca","last_name":"Braga","first_name":"Luca"},{"last_name":"Nascimento","first_name":"Diana S.","full_name":"Nascimento, Diana S."},{"full_name":"da Costa Martins, Paula A.","first_name":"Paula A.","last_name":"da Costa Martins"},{"last_name":"van Berlo","first_name":"Jop H.","full_name":"van Berlo, Jop H."},{"last_name":"Zacchigna","first_name":"Serena","full_name":"Zacchigna, Serena"},{"full_name":"Giacca, Mauro","first_name":"Mauro","last_name":"Giacca"},{"first_name":"Leon J.","last_name":"De Windt","full_name":"De Windt, Leon J."}],"volume":12,"date_created":"2021-08-10T11:49:20Z","date_updated":"2023-08-11T10:27:03Z","article_number":"4808","file_date_updated":"2021-08-10T12:29:59Z","license":"https://creativecommons.org/licenses/by/4.0/","citation":{"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.","ieee":"A. Raso et al., “A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration,” Nature Communications, vol. 12. Springer Nature, 2021.","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. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-25211-4","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. Nature Communications. 2021;12. doi:10.1038/s41467-021-25211-4","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.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-25211-4.","mla":"Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” Nature Communications, vol. 12, 4808, Springer Nature, 2021, doi:10.1038/s41467-021-25211-4.","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)."},"publication":"Nature Communications","article_type":"original","date_published":"2021-08-10T00:00:00Z","scopus_import":"1","genbank":["GSE178867"],"article_processing_charge":"Yes","has_accepted_license":"1","day":"10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9874","intvolume":" 12","ddc":["610","570"],"title":"A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration","status":"public","file":[{"access_level":"open_access","file_name":"2021_NatureCommunications_Raso.pdf","creator":"asandaue","file_size":4364333,"content_type":"application/pdf","file_id":"9876","relation":"main_file","success":1,"checksum":"48d8562e8229e4282f3f354b329722c5","date_created":"2021-08-10T12:29:59Z","date_updated":"2021-08-10T12:29:59Z"}],"oa_version":"Published Version","type":"journal_article","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"}]},{"file":[{"creator":"asandaue","content_type":"application/pdf","file_size":1085300,"access_level":"open_access","file_name":"2021_SciPostPhysics_Brauneis.pdf","success":1,"checksum":"eaa847346b1a023d97bbb291779610ed","date_updated":"2021-08-10T11:44:59Z","date_created":"2021-08-10T11:44:59Z","file_id":"9875","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9769","ddc":["530"],"title":"Impurities in a one-dimensional Bose gas: The flow equation approach","status":"public","intvolume":" 11","abstract":[{"text":"A few years ago, flow equations were introduced as a technique for calculating the ground-state energies of cold Bose gases with and without impurities. In this paper, we extend this approach to compute observables other than the energy. As an example, we calculate the densities, and phase fluctuations of one-dimensional Bose gases with one and two impurities. For a single mobile impurity, we use flow equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation. We show that the mean-field approximation is accurate for all values of the boson-impurity interaction strength as long as the phase coherence length is much larger than the healing length of the condensate. For two static impurities, we calculate impurity-impurity interactions induced by the Bose gas. We find that leading order perturbation theory fails when boson-impurity interactions are stronger than boson-boson interactions. The mean-field approximation reproduces the flow equation results for all values of the boson-impurity interaction strength as long as boson-boson interactions are weak.","lang":"eng"}],"issue":"1","type":"journal_article","date_published":"2021-07-13T00:00:00Z","publication":"SciPost Physics","citation":{"ista":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 11(1), 008.","apa":"Brauneis, F., Hammer, H.-W., Lemeshko, M., & Volosniev, A. (2021). Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. SciPost. https://doi.org/10.21468/scipostphys.11.1.008","ieee":"F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in a one-dimensional Bose gas: The flow equation approach,” SciPost Physics, vol. 11, no. 1. SciPost, 2021.","ama":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 2021;11(1). doi:10.21468/scipostphys.11.1.008","chicago":"Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.1.008.","mla":"Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost Physics, vol. 11, no. 1, 008, SciPost, 2021, doi:10.21468/scipostphys.11.1.008.","short":"F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11 (2021)."},"article_type":"original","day":"13","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","author":[{"full_name":"Brauneis, Fabian","last_name":"Brauneis","first_name":"Fabian"},{"full_name":"Hammer, Hans-Werner","first_name":"Hans-Werner","last_name":"Hammer"},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"},{"full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem"}],"date_created":"2021-08-04T15:00:55Z","date_updated":"2023-08-11T10:25:44Z","volume":11,"acknowledgement":"We thank Matthias Heinz and Volker Karle for helpful comments on the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing with us the data for the densities presented in Ref. [14]. This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G. V.) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). H.-W.H. thanks the ECT* for hospitality during the workshop “Universal physics in Many-Body Quantum Systems – From Atoms to Quarks\". This infrastructure is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824093. H.-W.H. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 279384907 - SFB 1245.","year":"2021","publication_status":"published","publisher":"SciPost","department":[{"_id":"MiLe"}],"file_date_updated":"2021-08-10T11:44:59Z","ec_funded":1,"article_number":"008","doi":"10.21468/scipostphys.11.1.008","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2101.10958"],"isi":["000680039500013"]},"quality_controlled":"1","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"month":"07","publication_identifier":{"eissn":["2542-4653"]}},{"author":[{"full_name":"Batra, Aditi","first_name":"Aditi","last_name":"Batra"},{"last_name":"Römhild","first_name":"Roderich","orcid":"0000-0001-9480-5261","id":"68E56E44-62B0-11EA-B963-444F3DDC885E","full_name":"Römhild, Roderich"},{"last_name":"Rousseau","first_name":"Emilie","full_name":"Rousseau, Emilie"},{"full_name":"Franzenburg, Sören","first_name":"Sören","last_name":"Franzenburg"},{"last_name":"Niemann","first_name":"Stefan","full_name":"Niemann, Stefan"},{"full_name":"Schulenburg, Hinrich","last_name":"Schulenburg","first_name":"Hinrich"}],"date_created":"2021-07-28T13:36:57Z","date_updated":"2023-08-11T10:26:29Z","volume":10,"year":"2021","acknowledgement":"We would like to thank Leif Tueffers and João Botelho for discussions and suggestions as well as Kira Haas and Julia Bunk for technical support. We acknowledge financial support from the German Science Foundation (grant SCHU 1415/12-2 to HS, and funding under Germany’s Excellence Strategy EXC 2167–390884018 as well as the Research Training Group 2501 TransEvo to HS and SN), the Max Planck Society (IMPRS scholarship to AB; Max-Planck fellowship to HS), and the Leibniz Science Campus Evolutionary Medicine of the Lung (EvoLUNG, to HS and SN). This work was further supported by the German Science Foundation Research Infrastructure NGS_CC (project 407495230) as part of the Next Generation Sequencing Competence Network (project 423957469). NGS analyses were carried out at the Competence Centre for Genomic Analysis Kiel (CCGA Kiel).","pmid":1,"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"CaGu"}],"article_number":"e68876","doi":"10.7554/elife.68876","language":[{"iso":"eng"}],"external_id":{"pmid":["34318749"],"isi":["000692027800001"]},"main_file_link":[{"url":"https://doi.org/10.7554/eLife.68876","open_access":"1"}],"oa":1,"isi":1,"quality_controlled":"1","month":"07","publication_identifier":{"eissn":["2050-084X"]},"oa_version":"Published Version","_id":"9746","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"High potency of sequential therapy with only beta-lactam antibiotics","intvolume":" 10","abstract":[{"lang":"eng","text":"Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution-informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only β-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross-resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs."}],"type":"journal_article","date_published":"2021-07-28T00:00:00Z","publication":"eLife","citation":{"short":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, H. Schulenburg, ELife 10 (2021).","mla":"Batra, Aditi, et al. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” ELife, vol. 10, e68876, eLife Sciences Publications, 2021, doi:10.7554/elife.68876.","chicago":"Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.68876.","ama":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 2021;10. doi:10.7554/elife.68876","ieee":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, and H. Schulenburg, “High potency of sequential therapy with only beta-lactam antibiotics,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., & Schulenburg, H. (2021). High potency of sequential therapy with only beta-lactam antibiotics. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68876","ista":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. 2021. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 10, e68876."},"article_type":"original","day":"28","article_processing_charge":"No","scopus_import":"1"},{"day":"11","article_processing_charge":"Yes","scopus_import":"1","date_published":"2021-08-11T00:00:00Z","article_type":"original","page":"56-73","publication":"Journal of Microscopy","citation":{"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.” Journal of Microscopy. Wiley, 2021. https://doi.org/10.1111/jmi.13041.","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.” Journal of Microscopy, vol. 284, no. 1, Wiley, 2021, pp. 56–73, doi:10.1111/jmi.13041.","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.","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.","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. Journal of Microscopy. Wiley. https://doi.org/10.1111/jmi.13041","ieee":"G. Nelson et al., “QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy,” Journal of Microscopy, vol. 284, no. 1. Wiley, pp. 56–73, 2021.","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. Journal of Microscopy. 2021;284(1):56-73. doi:10.1111/jmi.13041"},"abstract":[{"lang":"eng","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."}],"issue":"1","type":"journal_article","oa_version":"Published Version","status":"public","title":"QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy","intvolume":" 284","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9911","month":"08","publication_identifier":{"eissn":["1365-2818"],"issn":["0022-2720"]},"language":[{"iso":"eng"}],"doi":"10.1111/jmi.13041","quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jmi.13041"}],"oa":1,"external_id":{"isi":["000683702700001"]},"date_created":"2021-08-15T22:01:29Z","date_updated":"2023-08-11T10:30:40Z","volume":284,"author":[{"last_name":"Nelson","first_name":"Glyn","full_name":"Nelson, Glyn"},{"full_name":"Boehm, Ulrike","last_name":"Boehm","first_name":"Ulrike"},{"full_name":"Bagley, Steve","last_name":"Bagley","first_name":"Steve"},{"first_name":"Peter","last_name":"Bajcsy","full_name":"Bajcsy, Peter"},{"full_name":"Bischof, Johanna","first_name":"Johanna","last_name":"Bischof"},{"last_name":"Brown","first_name":"Claire M.","full_name":"Brown, Claire M."},{"full_name":"Dauphin, 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Alexandra L.","last_name":"Palmer","first_name":"Alexandra L."},{"last_name":"Paul-Gilloteaux","first_name":"Perrine","full_name":"Paul-Gilloteaux, Perrine"},{"full_name":"Pimentel, Jaime A.","last_name":"Pimentel","first_name":"Jaime A."},{"full_name":"Plantard, Laure","last_name":"Plantard","first_name":"Laure"},{"last_name":"Podder","first_name":"Santosh","full_name":"Podder, Santosh"},{"full_name":"Rexhepaj, Elton","last_name":"Rexhepaj","first_name":"Elton"},{"full_name":"Royon, Arnaud","first_name":"Arnaud","last_name":"Royon"},{"full_name":"Saari, Markku A.","last_name":"Saari","first_name":"Markku A."},{"last_name":"Schapman","first_name":"Damien","full_name":"Schapman, Damien"},{"full_name":"Schoonderwoert, Vincent","first_name":"Vincent","last_name":"Schoonderwoert"},{"full_name":"Schroth-Diez, Britta","first_name":"Britta","last_name":"Schroth-Diez"},{"full_name":"Schwartz, Stanley","first_name":"Stanley","last_name":"Schwartz"},{"last_name":"Shaw","first_name":"Michael","full_name":"Shaw, Michael"},{"full_name":"Spitaler, Martin","last_name":"Spitaler","first_name":"Martin"},{"last_name":"Stoeckl","first_name":"Martin T.","full_name":"Stoeckl, Martin T."},{"full_name":"Sudar, Damir","last_name":"Sudar","first_name":"Damir"},{"last_name":"Teillon","first_name":"Jeremie","full_name":"Teillon, Jeremie"},{"full_name":"Terjung, Stefan","first_name":"Stefan","last_name":"Terjung"},{"last_name":"Thuenauer","first_name":"Roland","full_name":"Thuenauer, Roland"},{"full_name":"Wilms, Christian D.","first_name":"Christian D.","last_name":"Wilms"},{"first_name":"Graham D.","last_name":"Wright","full_name":"Wright, Graham D."},{"full_name":"Nitschke, Roland","last_name":"Nitschke","first_name":"Roland"}],"publication_status":"published","department":[{"_id":"Bio"}],"publisher":"Wiley","year":"2021","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."},{"type":"journal_article","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"}],"issue":"16","_id":"9906","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","title":"LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line","intvolume":" 22","file":[{"success":1,"checksum":"be7f0042607ca60549cb27513c19c6af","date_updated":"2021-08-16T09:29:17Z","date_created":"2021-08-16T09:29:17Z","file_id":"9922","relation":"main_file","creator":"asandaue","content_type":"application/pdf","file_size":2646018,"access_level":"open_access","file_name":"2021_InternationalJournalOfMolecularSciences_Yotova.pdf"}],"oa_version":"Published Version","scopus_import":"1","day":"04","has_accepted_license":"1","article_processing_charge":"Yes","publication":"International Journal of Molecular Sciences","citation":{"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.","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. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22168385","ieee":"I. Yotova et al., “LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line,” International Journal of Molecular Sciences, vol. 22, no. 16. MDPI, 2021.","ama":"Yotova I, Hudson QJ, Pauler F, et al. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. International Journal of Molecular Sciences. 2021;22(16). doi:10.3390/ijms22168385","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.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22168385.","mla":"Yotova, Iveta, et al. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” International Journal of Molecular Sciences, vol. 22, no. 16, 8385, MDPI, 2021, doi:10.3390/ijms22168385.","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)."},"article_type":"original","date_published":"2021-08-04T00:00:00Z","article_number":"8385","file_date_updated":"2021-08-16T09:29:17Z","year":"2021","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.","publication_status":"published","publisher":"MDPI","department":[{"_id":"SiHi"}],"author":[{"first_name":"Iveta","last_name":"Yotova","full_name":"Yotova, Iveta"},{"full_name":"Hudson, Quanah J.","first_name":"Quanah J.","last_name":"Hudson"},{"full_name":"Pauler, Florian","last_name":"Pauler","first_name":"Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Proestling, Katharina","first_name":"Katharina","last_name":"Proestling"},{"first_name":"Isabella","last_name":"Haslinger","full_name":"Haslinger, Isabella"},{"full_name":"Kuessel, Lorenz","first_name":"Lorenz","last_name":"Kuessel"},{"last_name":"Perricos","first_name":"Alexandra","full_name":"Perricos, Alexandra"},{"first_name":"Heinrich","last_name":"Husslein","full_name":"Husslein, Heinrich"},{"full_name":"Wenzl, René","first_name":"René","last_name":"Wenzl"}],"date_created":"2021-08-15T22:01:27Z","date_updated":"2023-08-11T10:34:13Z","volume":22,"month":"08","publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"external_id":{"isi":["000689147400001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.3390/ijms22168385","language":[{"iso":"eng"}]}]