[{"article_number":"44","file_date_updated":"2021-08-09T11:41:50Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-10T14:25:08Z","doi":"10.1145/3450626.3459765","article_processing_charge":"Yes (in subscription journal)","author":[{"full_name":"Mallikarjun, B. R.","last_name":"Mallikarjun","first_name":"B. R."},{"first_name":"Ayush","last_name":"Tewari","full_name":"Tewari, Ayush"},{"full_name":"Dib, Abdallah","first_name":"Abdallah","last_name":"Dib"},{"full_name":"Weyrich, Tim","first_name":"Tim","last_name":"Weyrich"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385"},{"last_name":"Seidel","first_name":"Hans Peter","full_name":"Seidel, Hans Peter"},{"first_name":"Hanspeter","last_name":"Pfister","full_name":"Pfister, Hanspeter"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"first_name":"Louis","last_name":"Chevallier","full_name":"Chevallier, Louis"},{"last_name":"Elgharib","first_name":"Mohamed A.","full_name":"Elgharib, Mohamed A."},{"full_name":"Theobalt, Christian","first_name":"Christian","last_name":"Theobalt"}],"date_published":"2021-08-01T00:00:00Z","quality_controlled":"1","scopus_import":"1","publication_status":"published","file":[{"date_updated":"2021-08-09T11:41:50Z","file_id":"9834","checksum":"51b61b7e5c175e2d7ed8fa3b35f7525a","file_name":"2021_ACMTransactionsOnGraphics_Mallikarjun.pdf","file_size":49840741,"access_level":"open_access","creator":"asandaue","relation":"main_file","date_created":"2021-08-09T11:41:50Z","success":1,"content_type":"application/pdf"}],"intvolume":"        40","day":"01","ddc":["000"],"language":[{"iso":"eng"}],"month":"08","isi":1,"publisher":"Association for Computing Machinery","title":"PhotoApp: Photorealistic appearance editing of head portraits","department":[{"_id":"BeBi"}],"publication":"ACM Transactions on Graphics","oa_version":"Published Version","date_created":"2021-08-08T22:01:27Z","arxiv":1,"abstract":[{"lang":"eng","text":"Photorealistic editing of head portraits is a challenging task as humans are very sensitive to inconsistencies in faces. We present an approach for high-quality intuitive editing of the camera viewpoint and scene illumination (parameterised with an environment map) in a portrait image. This requires our method to capture and control the full reflectance field of the person in the image. Most editing approaches rely on supervised learning using training data captured with setups such as light and camera stages. Such datasets are expensive to acquire, not readily available and do not capture all the rich variations of in-the-wild portrait images. In addition, most supervised approaches only focus on relighting, and do not allow camera viewpoint editing. Thus, they only capture and control a subset of the reflectance field. Recently, portrait editing has been demonstrated by operating in the generative model space of StyleGAN. While such approaches do not require direct supervision, there is a significant loss of quality when compared to the supervised approaches. In this paper, we present a method which learns from limited supervised training data. The training images only include people in a fixed neutral expression with eyes closed, without much hair or background variations. Each person is captured under 150 one-light-at-a-time conditions and under 8 camera poses. Instead of training directly in the image space, we design a supervised problem which learns transformations in the latent space of StyleGAN. This combines the best of supervised learning and generative adversarial modeling. We show that the StyleGAN prior allows for generalisation to different expressions, hairstyles and backgrounds. This produces high-quality photorealistic results for in-the-wild images and significantly outperforms existing methods. Our approach can edit the illumination and pose simultaneously, and runs at interactive rates."}],"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":40,"year":"2021","has_accepted_license":"1","_id":"9819","external_id":{"arxiv":["2103.07658"],"isi":["000674930900011"]},"article_type":"original","issue":"4","acknowledgement":"This work was supported by the ERC Consolidator Grant 4DReply (770784). We also acknowledge support from Technicolor and InterDigital. We thank Tiancheng Sun for kindly helping us with the comparisons with Sun et al. [2019].","oa":1,"status":"public","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"citation":{"ama":"Mallikarjun BR, Tewari A, Dib A, et al. PhotoApp: Photorealistic appearance editing of head portraits. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459765\">10.1145/3450626.3459765</a>","mla":"Mallikarjun, B. R., et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 44, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459765\">10.1145/3450626.3459765</a>.","ista":"Mallikarjun BR, Tewari A, Dib A, Weyrich T, Bickel B, Seidel HP, Pfister H, Matusik W, Chevallier L, Elgharib MA, Theobalt C. 2021. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 40(4), 44.","short":"B.R. Mallikarjun, A. Tewari, A. Dib, T. Weyrich, B. Bickel, H.P. Seidel, H. Pfister, W. Matusik, L. Chevallier, M.A. Elgharib, C. Theobalt, ACM Transactions on Graphics 40 (2021).","ieee":"B. R. Mallikarjun <i>et al.</i>, “PhotoApp: Photorealistic appearance editing of head portraits,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","chicago":"Mallikarjun, B. R., Ayush Tewari, Abdallah Dib, Tim Weyrich, Bernd Bickel, Hans Peter Seidel, Hanspeter Pfister, et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459765\">https://doi.org/10.1145/3450626.3459765</a>.","apa":"Mallikarjun, B. R., Tewari, A., Dib, A., Weyrich, T., Bickel, B., Seidel, H. P., … Theobalt, C. (2021). PhotoApp: Photorealistic appearance editing of head portraits. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459765\">https://doi.org/10.1145/3450626.3459765</a>"}},{"day":"01","month":"08","isi":1,"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://zaguan.unizar.es/record/110704/files/texto_completo.pdf"}],"intvolume":"        40","publication_status":"published","date_published":"2021-08-01T00:00:00Z","author":[{"full_name":"Serrano, Ana","last_name":"Serrano","first_name":"Ana"},{"full_name":"Chen, Bin","first_name":"Bin","last_name":"Chen"},{"first_name":"Chao","last_name":"Wang","full_name":"Wang, Chao"},{"orcid":"0000-0002-5062-4474","last_name":"Piovarci","first_name":"Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","full_name":"Piovarci, Michael"},{"last_name":"Seidel","first_name":"Hans Peter","full_name":"Seidel, Hans Peter"},{"first_name":"Piotr","last_name":"Didyk","full_name":"Didyk, Piotr"},{"first_name":"Karol","last_name":"Myszkowski","full_name":"Myszkowski, Karol"}],"article_processing_charge":"No","doi":"10.1145/3450626.3459813","date_updated":"2023-08-10T14:20:10Z","scopus_import":"1","quality_controlled":"1","article_number":"125","oa":1,"status":"public","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie, grant agreement Nº 765911 (RealVision) and from the European Research Council (ERC), grant agreement Nº 804226 (PERDY).","issue":"4","article_type":"original","external_id":{"isi":["000674930900090"]},"citation":{"chicago":"Serrano, Ana, Bin Chen, Chao Wang, Michael Piovarci, Hans Peter Seidel, Piotr Didyk, and Karol Myszkowski. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459813\">https://doi.org/10.1145/3450626.3459813</a>.","ieee":"A. Serrano <i>et al.</i>, “The effect of shape and illumination on material perception: Model and applications,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","apa":"Serrano, A., Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., &#38; Myszkowski, K. (2021). The effect of shape and illumination on material perception: Model and applications. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459813\">https://doi.org/10.1145/3450626.3459813</a>","ama":"Serrano A, Chen B, Wang C, et al. The effect of shape and illumination on material perception: Model and applications. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459813\">10.1145/3450626.3459813</a>","ista":"Serrano A, Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K. 2021. The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. 40(4), 125.","mla":"Serrano, Ana, et al. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 125, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459813\">10.1145/3450626.3459813</a>.","short":"A. Serrano, B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, ACM Transactions on Graphics 40 (2021)."},"publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"volume":40,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"9820","year":"2021","abstract":[{"lang":"eng","text":"Material appearance hinges on material reflectance properties but also surface geometry and illumination. The unlimited number of potential combinations between these factors makes understanding and predicting material appearance a very challenging task. In this work, we collect a large-scale dataset of perceptual ratings of appearance attributes with more than 215,680 responses for 42,120 distinct combinations of material, shape, and illumination. The goal of this dataset is twofold. First, we analyze for the first time the effects of illumination and geometry in material perception across such a large collection of varied appearances. We connect our findings to those of the literature, discussing how previous knowledge generalizes across very diverse materials, shapes, and illuminations. Second, we use the collected dataset to train a deep learning architecture for predicting perceptual attributes that correlate with human judgments. We demonstrate the consistent and robust behavior of our predictor in various challenging scenarios, which, for the first time, enables estimating perceived material attributes from general 2D images. Since our predictor relies on the final appearance in an image, it can compare appearance properties across different geometries and illumination conditions. Finally, we demonstrate several applications that use our predictor, including appearance reproduction using 3D printing, BRDF editing by integrating our predictor in a differentiable renderer, illumination design, or material recommendations for scene design."}],"publication":"ACM Transactions on Graphics","department":[{"_id":"BeBi"}],"title":"The effect of shape and illumination on material perception: Model and applications","publisher":"Association for Computing Machinery","date_created":"2021-08-08T22:01:28Z","oa_version":"Submitted Version"},{"isi":1,"month":"07","language":[{"iso":"eng"}],"pmid":1,"ddc":["006"],"day":"01","intvolume":"        16","file":[{"file_name":"2021_PLoSONE_Graff.pdf","checksum":"0277aa155d5db1febd2cb384768bba5f","file_size":2706919,"file_id":"9832","date_updated":"2021-08-09T09:25:41Z","success":1,"date_created":"2021-08-09T09:25:41Z","content_type":"application/pdf","creator":"asandaue","access_level":"open_access","relation":"main_file"}],"publication_status":"published","scopus_import":"1","quality_controlled":"1","author":[{"full_name":"Graff, Grzegorz","last_name":"Graff","first_name":"Grzegorz"},{"first_name":"Beata","last_name":"Graff","full_name":"Graff, Beata"},{"id":"3768D56A-F248-11E8-B48F-1D18A9856A87","full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk","first_name":"Pawel"},{"first_name":"Grzegorz","last_name":"Jablonski","orcid":"0000-0002-3536-9866","full_name":"Jablonski, Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dariusz","last_name":"Gąsecki","full_name":"Gąsecki, Dariusz"},{"first_name":"Krzysztof","last_name":"Narkiewicz","full_name":"Narkiewicz, Krzysztof"}],"date_published":"2021-07-01T00:00:00Z","article_processing_charge":"Yes","date_updated":"2023-08-10T14:21:42Z","doi":"10.1371/journal.pone.0253851","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2021-08-09T09:25:41Z","article_number":"e0253851","citation":{"ista":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 16(7), e0253851.","short":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz, PLoS ONE 16 (2021).","mla":"Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” <i>PLoS ONE</i>, vol. 16, no. 7, e0253851, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0253851\">10.1371/journal.pone.0253851</a>.","ama":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent homology as a new method of the assessment of heart rate variability. <i>PLoS ONE</i>. 2021;16(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0253851\">10.1371/journal.pone.0253851</a>","apa":"Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., &#38; Narkiewicz, K. (2021). Persistent homology as a new method of the assessment of heart rate variability. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0253851\">https://doi.org/10.1371/journal.pone.0253851</a>","chicago":"Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0253851\">https://doi.org/10.1371/journal.pone.0253851</a>.","ieee":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz, “Persistent homology as a new method of the assessment of heart rate variability,” <i>PLoS ONE</i>, vol. 16, no. 7. Public Library of Science, 2021."},"publication_identifier":{"eissn":["19326203"]},"acknowledgement":"We express our gratitude to the anonymous referees who provided constructive comments that helped us improve the quality of the paper.","status":"public","oa":1,"issue":"7","external_id":{"pmid":["34292957"],"isi":["000678124900050"]},"article_type":"original","_id":"9821","year":"2021","has_accepted_license":"1","volume":16,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","abstract":[{"lang":"eng","text":"Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. However, attempts are still being made to define new and more effective hrv assessment tools. Persistent homology is a novel data analysis tool developed in the recent decades that is rooted at algebraic topology. The Topological Data Analysis (TDA) approach focuses on examining the shape of the data in terms of connectedness and holes, and has recently proved to be very effective in various fields of research. In this paper we propose the use of persistent homology to the hrv analysis. We recall selected topological descriptors used in the literature and we introduce some new topological descriptors that reflect the specificity of hrv, and we discuss their relation to the standard hrv measures. In particular, we show that this novel approach provides a collection of indices that might be at least as useful as the classical parameters in differentiating between series of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering from a stroke episode."}],"date_created":"2021-08-08T22:01:28Z","oa_version":"Published Version","publication":"PLoS ONE","title":"Persistent homology as a new method of the assessment of heart rate variability","department":[{"_id":"HeEd"}],"publisher":"Public Library of Science"},{"file_date_updated":"2021-08-09T09:44:03Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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)"},"author":[{"full_name":"Zisis, Themistoklis","first_name":"Themistoklis","last_name":"Zisis"},{"last_name":"Schwarz","first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan"},{"last_name":"Balles","first_name":"Miriam","full_name":"Balles, Miriam"},{"full_name":"Kretschmer, Maibritt","last_name":"Kretschmer","first_name":"Maibritt"},{"id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Nemethova, Maria","last_name":"Nemethova","first_name":"Maria"},{"full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P","last_name":"Chait","orcid":"0000-0003-0876-3187"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"full_name":"Lange, Janina","first_name":"Janina","last_name":"Lange"},{"orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"last_name":"Sixt","orcid":"0000-0002-4561-241X","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"first_name":"Stefan","last_name":"Zahler","full_name":"Zahler, Stefan"}],"date_published":"2021-08-04T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","date_updated":"2023-08-10T14:22:48Z","doi":"10.1021/acsami.1c09850","scopus_import":"1","quality_controlled":"1","intvolume":"        13","file":[{"relation":"main_file","creator":"asandaue","access_level":"open_access","content_type":"application/pdf","date_created":"2021-08-09T09:44:03Z","success":1,"file_id":"9833","date_updated":"2021-08-09T09:44:03Z","file_size":7123293,"checksum":"b043a91d9f9200e467b970b692687ed3","file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf"}],"publication_status":"published","pmid":1,"ddc":["620","570"],"day":"04","isi":1,"month":"08","language":[{"iso":"eng"}],"project":[{"name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication":"ACS Applied Materials and Interfaces","title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"publisher":"American Chemical Society","ec_funded":1,"date_created":"2021-08-08T22:01:28Z","oa_version":"Published Version","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"}],"volume":13,"page":"35545–35560","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"9822","has_accepted_license":"1","year":"2021","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.","status":"public","oa":1,"issue":"30","article_type":"original","external_id":{"isi":["000683741400026"],"pmid":["34283577"]},"citation":{"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>","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>.","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.","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.","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.","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>.","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>"},"publication_identifier":{"issn":["19448244"],"eissn":["19448252"]}},{"article_processing_charge":"No","date_updated":"2023-02-23T14:09:49Z","alternative_title":["LNCS"],"doi":"10.1007/978-3-030-79527-6_6","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Ellen, Faith","first_name":"Faith","last_name":"Ellen"},{"first_name":"Joel","last_name":"Rybicki","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2021-06-20T00:00:00Z","quality_controlled":"1","scopus_import":"1","conference":{"location":"Wrocław, Poland","start_date":"2021-06-28","name":"SIROCCO: Structural Information and Communication Complexity","end_date":"2021-07-01"},"day":"20","month":"06","language":[{"iso":"eng"}],"publication_status":"published","intvolume":"     12810","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.08949"}],"arxiv":1,"abstract":[{"lang":"eng","text":"Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a vertex of the graph as input and, if non-faulty, must output a vertex such that\r\nall the outputs are within distance 1 of one another, and\r\n\r\neach output value lies on a shortest path between two input values.\r\n\r\nFrom prior work, it is known that there is no wait-free algorithm among   𝑛≥3  processes for this problem on any cycle of length   𝑐≥4 , by reduction from 2-set agreement (Castañeda et al. 2018).\r\n\r\nIn this work, we investigate the solvability and complexity of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length   𝑐≥4 , via a generalisation of Sperner’s Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a class of graphs that properly contains the class of chordal graphs."}],"publisher":"Springer Nature","publication":"Structural Information and Communication Complexity","department":[{"_id":"DaAl"}],"title":"Wait-free approximate agreement on graphs","date_created":"2021-08-08T22:01:29Z","oa_version":"Preprint","external_id":{"arxiv":["2103.08949"]},"status":"public","oa":1,"publication_identifier":{"issn":["03029743"],"eissn":["16113349"],"isbn":["9783030795269"]},"citation":{"chicago":"Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate Agreement on Graphs.” In <i>Structural Information and Communication Complexity</i>, 12810:87–105. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-79527-6_6\">https://doi.org/10.1007/978-3-030-79527-6_6</a>.","ieee":"D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement on graphs,” in <i>Structural Information and Communication Complexity</i>, Wrocław, Poland, 2021, vol. 12810, pp. 87–105.","apa":"Alistarh, D.-A., Ellen, F., &#38; Rybicki, J. (2021). Wait-free approximate agreement on graphs. In <i>Structural Information and Communication Complexity</i> (Vol. 12810, pp. 87–105). Wrocław, Poland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-79527-6_6\">https://doi.org/10.1007/978-3-030-79527-6_6</a>","ama":"Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs. In: <i>Structural Information and Communication Complexity</i>. Vol 12810. Springer Nature; 2021:87-105. doi:<a href=\"https://doi.org/10.1007/978-3-030-79527-6_6\">10.1007/978-3-030-79527-6_6</a>","mla":"Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” <i>Structural Information and Communication Complexity</i>, vol. 12810, Springer Nature, 2021, pp. 87–105, doi:<a href=\"https://doi.org/10.1007/978-3-030-79527-6_6\">10.1007/978-3-030-79527-6_6</a>.","ista":"Alistarh D-A, Ellen F, Rybicki J. 2021. Wait-free approximate agreement on graphs. Structural Information and Communication Complexity. SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 12810, 87–105.","short":"D.-A. Alistarh, F. Ellen, J. Rybicki, in:, Structural Information and Communication Complexity, Springer Nature, 2021, pp. 87–105."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"conference","volume":12810,"page":"87-105","year":"2021","_id":"9823"},{"abstract":[{"lang":"eng","text":"We define a new compact coordinate system in which each integer triplet addresses a voxel in the BCC grid, and we investigate some of its properties. We propose a characterization of 3D discrete analytical planes with their topological features (in the Cartesian and in the new coordinate system) such as the interrelation between the thickness of the plane and the separability constraint we aim to obtain."}],"department":[{"_id":"HeEd"}],"title":"Body centered cubic grid - coordinate system and discrete analytical plane definition","publication":"Discrete Geometry and Mathematical Morphology","publisher":"Springer Nature","oa_version":"None","date_created":"2021-08-08T22:01:29Z","ec_funded":1,"acknowledgement":"This work has been partially supported by the Ministry of Education, Science and Technological Development of the Republic of Serbia through the project no. 451-03-68/2020-14/200156: “Innovative scientific and artistic research from the FTS (activity) domain” (LČ), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183 (RB), and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35 (RB).","status":"public","citation":{"apa":"Čomić, L., Zrour, R., Largeteau-Skapin, G., Biswas, R., &#38; Andres, E. (2021). Body centered cubic grid - coordinate system and discrete analytical plane definition. In <i>Discrete Geometry and Mathematical Morphology</i> (Vol. 12708, pp. 152–163). Uppsala, Sweden: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-76657-3_10\">https://doi.org/10.1007/978-3-030-76657-3_10</a>","ieee":"L. Čomić, R. Zrour, G. Largeteau-Skapin, R. Biswas, and E. Andres, “Body centered cubic grid - coordinate system and discrete analytical plane definition,” in <i>Discrete Geometry and Mathematical Morphology</i>, Uppsala, Sweden, 2021, vol. 12708, pp. 152–163.","chicago":"Čomić, Lidija, Rita Zrour, Gaëlle Largeteau-Skapin, Ranita Biswas, and Eric Andres. “Body Centered Cubic Grid - Coordinate System and Discrete Analytical Plane Definition.” In <i>Discrete Geometry and Mathematical Morphology</i>, 12708:152–63. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-76657-3_10\">https://doi.org/10.1007/978-3-030-76657-3_10</a>.","mla":"Čomić, Lidija, et al. “Body Centered Cubic Grid - Coordinate System and Discrete Analytical Plane Definition.” <i>Discrete Geometry and Mathematical Morphology</i>, vol. 12708, Springer Nature, 2021, pp. 152–63, doi:<a href=\"https://doi.org/10.1007/978-3-030-76657-3_10\">10.1007/978-3-030-76657-3_10</a>.","ista":"Čomić L, Zrour R, Largeteau-Skapin G, Biswas R, Andres E. 2021. Body centered cubic grid - coordinate system and discrete analytical plane definition. Discrete Geometry and Mathematical Morphology. DGMM: International Conference on Discrete Geometry and Mathematical Morphology, LNCS, vol. 12708, 152–163.","short":"L. Čomić, R. Zrour, G. Largeteau-Skapin, R. Biswas, E. Andres, in:, Discrete Geometry and Mathematical Morphology, Springer Nature, 2021, pp. 152–163.","ama":"Čomić L, Zrour R, Largeteau-Skapin G, Biswas R, Andres E. Body centered cubic grid - coordinate system and discrete analytical plane definition. In: <i>Discrete Geometry and Mathematical Morphology</i>. Vol 12708. Springer Nature; 2021:152-163. doi:<a href=\"https://doi.org/10.1007/978-3-030-76657-3_10\">10.1007/978-3-030-76657-3_10</a>"},"publication_identifier":{"issn":["03029743"],"eissn":["16113349"],"isbn":["9783030766566"]},"page":"152-163","volume":12708,"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9824","year":"2021","date_published":"2021-05-16T00:00:00Z","author":[{"full_name":"Čomić, Lidija","first_name":"Lidija","last_name":"Čomić"},{"last_name":"Zrour","first_name":"Rita","full_name":"Zrour, Rita"},{"first_name":"Gaëlle","last_name":"Largeteau-Skapin","full_name":"Largeteau-Skapin, Gaëlle"},{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","orcid":"0000-0002-5372-7890","last_name":"Biswas"},{"first_name":"Eric","last_name":"Andres","full_name":"Andres, Eric"}],"doi":"10.1007/978-3-030-76657-3_10","alternative_title":["LNCS"],"date_updated":"2022-05-31T06:58:21Z","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","conference":{"location":"Uppsala, Sweden","start_date":"2021-05-24","name":"DGMM: International Conference on Discrete Geometry and Mathematical Morphology","end_date":"2021-05-27"},"day":"16","language":[{"iso":"eng"}],"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"month":"05","intvolume":"     12708","publication_status":"published"},{"year":"2021","_id":"9825","type":"conference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","page":"478-502","volume":12704,"publication_identifier":{"isbn":["9783030755386"],"eissn":["16113349"],"issn":["03029743"]},"citation":{"ama":"Laarhoven T, Walter M. Dual lattice attacks for closest vector problems (with preprocessing). In: <i>Topics in Cryptology – CT-RSA 2021</i>. Vol 12704. Springer Nature; 2021:478-502. doi:<a href=\"https://doi.org/10.1007/978-3-030-75539-3_20\">10.1007/978-3-030-75539-3_20</a>","short":"T. Laarhoven, M. Walter, in:, Topics in Cryptology – CT-RSA 2021, Springer Nature, 2021, pp. 478–502.","ista":"Laarhoven T, Walter M. 2021. Dual lattice attacks for closest vector problems (with preprocessing). Topics in Cryptology – CT-RSA 2021. CT-RSA: Cryptographers’ Track at the RSA Conference, LNCS, vol. 12704, 478–502.","mla":"Laarhoven, Thijs, and Michael Walter. “Dual Lattice Attacks for Closest Vector Problems (with Preprocessing).” <i>Topics in Cryptology – CT-RSA 2021</i>, vol. 12704, Springer Nature, 2021, pp. 478–502, doi:<a href=\"https://doi.org/10.1007/978-3-030-75539-3_20\">10.1007/978-3-030-75539-3_20</a>.","chicago":"Laarhoven, Thijs, and Michael Walter. “Dual Lattice Attacks for Closest Vector Problems (with Preprocessing).” In <i>Topics in Cryptology – CT-RSA 2021</i>, 12704:478–502. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-75539-3_20\">https://doi.org/10.1007/978-3-030-75539-3_20</a>.","ieee":"T. Laarhoven and M. Walter, “Dual lattice attacks for closest vector problems (with preprocessing),” in <i>Topics in Cryptology – CT-RSA 2021</i>, Virtual Event, 2021, vol. 12704, pp. 478–502.","apa":"Laarhoven, T., &#38; Walter, M. (2021). Dual lattice attacks for closest vector problems (with preprocessing). In <i>Topics in Cryptology – CT-RSA 2021</i> (Vol. 12704, pp. 478–502). Virtual Event: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-75539-3_20\">https://doi.org/10.1007/978-3-030-75539-3_20</a>"},"oa":1,"acknowledgement":"The authors thank Sauvik Bhattacharya, L´eo Ducas, Rachel Player, and Christine van Vredendaal for early discussions on this topic and on preliminary results. The authors further thank the reviewers of CT-RSA 2021 for their valuable feedback.","status":"public","oa_version":"Preprint","date_created":"2021-08-08T22:01:30Z","publisher":"Springer Nature","title":"Dual lattice attacks for closest vector problems (with preprocessing)","department":[{"_id":"KrPi"}],"publication":"Topics in Cryptology – CT-RSA 2021","abstract":[{"lang":"eng","text":"The dual attack has long been considered a relevant attack on lattice-based cryptographic schemes relying on the hardness of learning with errors (LWE) and its structured variants. As solving LWE corresponds to finding a nearest point on a lattice, one may naturally wonder how efficient this dual approach is for solving more general closest vector problems, such as the classical closest vector problem (CVP), the variants bounded distance decoding (BDD) and approximate CVP, and preprocessing versions of these problems. While primal, sieving-based solutions to these problems (with preprocessing) were recently studied in a series of works on approximate Voronoi cells [Laa16b, DLdW19, Laa20, DLvW20], for the dual attack no such overview exists, especially for problems with preprocessing. With one of the take-away messages of the approximate Voronoi cell line of work being that primal attacks work well for approximate CVP(P) but scale poorly for BDD(P), one may further wonder if the dual attack suffers the same drawbacks, or if it is perhaps a better solution when trying to solve BDD(P).\r\n\r\nIn this work we provide an overview of cost estimates for dual algorithms for solving these “classical” closest lattice vector problems. Heuristically we expect to solve the search version of average-case CVPP in time and space   20.293𝑑+𝑜(𝑑)  in the single-target model. The distinguishing version of average-case CVPP, where we wish to distinguish between random targets and targets planted at distance (say)   0.99⋅𝑔𝑑  from the lattice, has the same complexity in the single-target model, but can be solved in time and space   20.195𝑑+𝑜(𝑑)  in the multi-target setting, when given a large number of targets from either target distribution. This suggests an inequivalence between distinguishing and searching, as we do not expect a similar improvement in the multi-target setting to hold for search-CVPP. We analyze three slightly different decoders, both for distinguishing and searching, and experimentally obtain concrete cost estimates for the dual attack in dimensions 50 to 80, which confirm our heuristic assumptions, and show that the hidden order terms in the asymptotic estimates are quite small.\r\n\r\nOur main take-away message is that the dual attack appears to mirror the approximate Voronoi cell line of work – whereas using approximate Voronoi cells works well for approximate CVP(P) but scales poorly for BDD(P), the dual approach scales well for BDD(P) instances but performs poorly on approximate CVP(P)."}],"publication_status":"published","intvolume":"     12704","main_file_link":[{"url":"https://eprint.iacr.org/2021/557","open_access":"1"}],"language":[{"iso":"eng"}],"month":"05","day":"11","conference":{"location":"Virtual Event","start_date":"2021-05-17","name":"CT-RSA: Cryptographers’ Track at the RSA Conference","end_date":"2021-05-20"},"quality_controlled":"1","scopus_import":"1","alternative_title":["LNCS"],"doi":"10.1007/978-3-030-75539-3_20","date_updated":"2023-02-23T14:09:54Z","article_processing_charge":"No","date_published":"2021-05-11T00:00:00Z","author":[{"last_name":"Laarhoven","first_name":"Thijs","full_name":"Laarhoven, Thijs"},{"first_name":"Michael","orcid":"0000-0003-3186-2482","last_name":"Walter","full_name":"Walter, Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87"}]},{"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2020/670"}],"intvolume":"     12704","day":"11","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"language":[{"iso":"eng"}],"month":"05","conference":{"name":"CT-RSA: Cryptographers’ Track at the RSA Conference","end_date":"2021-05-20","location":"Virtual Event","start_date":"2021-05-17"},"doi":"10.1007/978-3-030-75539-3_17","date_updated":"2023-02-23T14:09:56Z","alternative_title":["LNCS"],"article_processing_charge":"No","author":[{"id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","full_name":"Auerbach, Benedikt","orcid":"0000-0002-7553-6606","last_name":"Auerbach","first_name":"Benedikt"},{"id":"B9CD0494-D033-11E9-B219-A439E6697425","full_name":"Chakraborty, Suvradip","last_name":"Chakraborty","first_name":"Suvradip"},{"id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen","last_name":"Klein","first_name":"Karen"},{"last_name":"Pascual Perez","first_name":"Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","full_name":"Pascual Perez, Guillermo"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z"},{"full_name":"Walter, Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","orcid":"0000-0003-3186-2482","last_name":"Walter"},{"first_name":"Michelle X","last_name":"Yeo","full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2021-05-11T00:00:00Z","quality_controlled":"1","scopus_import":"1","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"399-421","volume":12704,"year":"2021","_id":"9826","oa":1,"acknowledgement":"Guillermo Pascual-Perez and Michelle Yeo were funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska–Curie Grant Agreement No. 665385; the remaining contributors to this project have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","status":"public","publication_identifier":{"isbn":["9783030755386"],"issn":["03029743"],"eissn":["16113349"]},"citation":{"apa":"Auerbach, B., Chakraborty, S., Klein, K., Pascual Perez, G., Pietrzak, K. Z., Walter, M., &#38; Yeo, M. X. (2021). Inverse-Sybil attacks in automated contact tracing. In <i>Topics in Cryptology – CT-RSA 2021</i> (Vol. 12704, pp. 399–421). Virtual Event: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-75539-3_17\">https://doi.org/10.1007/978-3-030-75539-3_17</a>","ieee":"B. Auerbach <i>et al.</i>, “Inverse-Sybil attacks in automated contact tracing,” in <i>Topics in Cryptology – CT-RSA 2021</i>, Virtual Event, 2021, vol. 12704, pp. 399–421.","chicago":"Auerbach, Benedikt, Suvradip Chakraborty, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, Michael Walter, and Michelle X Yeo. “Inverse-Sybil Attacks in Automated Contact Tracing.” In <i>Topics in Cryptology – CT-RSA 2021</i>, 12704:399–421. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-75539-3_17\">https://doi.org/10.1007/978-3-030-75539-3_17</a>.","ista":"Auerbach B, Chakraborty S, Klein K, Pascual Perez G, Pietrzak KZ, Walter M, Yeo MX. 2021. Inverse-Sybil attacks in automated contact tracing. Topics in Cryptology – CT-RSA 2021. CT-RSA: Cryptographers’ Track at the RSA Conference, LNCS, vol. 12704, 399–421.","mla":"Auerbach, Benedikt, et al. “Inverse-Sybil Attacks in Automated Contact Tracing.” <i>Topics in Cryptology – CT-RSA 2021</i>, vol. 12704, Springer Nature, 2021, pp. 399–421, doi:<a href=\"https://doi.org/10.1007/978-3-030-75539-3_17\">10.1007/978-3-030-75539-3_17</a>.","short":"B. Auerbach, S. Chakraborty, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, M.X. Yeo, in:, Topics in Cryptology – CT-RSA 2021, Springer Nature, 2021, pp. 399–421.","ama":"Auerbach B, Chakraborty S, Klein K, et al. Inverse-Sybil attacks in automated contact tracing. In: <i>Topics in Cryptology – CT-RSA 2021</i>. Vol 12704. Springer Nature; 2021:399-421. doi:<a href=\"https://doi.org/10.1007/978-3-030-75539-3_17\">10.1007/978-3-030-75539-3_17</a>"},"publisher":"Springer Nature","title":"Inverse-Sybil attacks in automated contact tracing","department":[{"_id":"KrPi"},{"_id":"GradSch"}],"publication":"Topics in Cryptology – CT-RSA 2021","oa_version":"Submitted Version","date_created":"2021-08-08T22:01:30Z","ec_funded":1,"abstract":[{"lang":"eng","text":"Automated contract tracing aims at supporting manual contact tracing during pandemics by alerting users of encounters with infected people. There are currently many proposals for protocols (like the “decentralized” DP-3T and PACT or the “centralized” ROBERT and DESIRE) to be run on mobile phones, where the basic idea is to regularly broadcast (using low energy Bluetooth) some values, and at the same time store (a function of) incoming messages broadcasted by users in their proximity. In the existing proposals one can trigger false positives on a massive scale by an “inverse-Sybil” attack, where a large number of devices (malicious users or hacked phones) pretend to be the same user, such that later, just a single person needs to be diagnosed (and allowed to upload) to trigger an alert for all users who were in proximity to any of this large group of devices.\r\n\r\nWe propose the first protocols that do not succumb to such attacks assuming the devices involved in the attack do not constantly communicate, which we observe is a necessary assumption. The high level idea of the protocols is to derive the values to be broadcasted by a hash chain, so that two (or more) devices who want to launch an inverse-Sybil attack will not be able to connect their respective chains and thus only one of them will be able to upload. Our protocols also achieve security against replay, belated replay, and one of them even against relay attacks."}]},{"external_id":{"isi":["000694718900004"]},"article_type":"original","oa":1,"status":"public","publication_identifier":{"issn":["0304-3975"]},"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>","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.","ista":"Chatterjee B, Walulya I, Tsigas P. 2021. Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. 886, 27–48."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":886,"page":"27-48","year":"2021","_id":"9827","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."}],"publisher":"Elsevier","publication":"Theoretical Computer Science","title":"Concurrent linearizable nearest neighbour search in LockFree-kD-tree","department":[{"_id":"DaAl"}],"date_created":"2021-08-08T22:01:31Z","oa_version":"Submitted Version","day":"13","isi":1,"month":"09","language":[{"iso":"eng"}],"publication_status":"published","main_file_link":[{"url":"https://publications.lib.chalmers.se/records/fulltext/232185/232185.pdf","open_access":"1"}],"intvolume":"       886","article_processing_charge":"No","doi":"10.1016/j.tcs.2021.06.041","date_updated":"2023-08-10T14:27:43Z","date_published":"2021-09-13T00:00:00Z","author":[{"full_name":"Chatterjee, Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","first_name":"Bapi","last_name":"Chatterjee","orcid":"0000-0002-2742-4028"},{"first_name":"Ivan","last_name":"Walulya","full_name":"Walulya, Ivan"},{"first_name":"Philippas","last_name":"Tsigas","full_name":"Tsigas, Philippas"}],"quality_controlled":"1","keyword":["Concurrent data structure","kD-tree","Nearest neighbor search","Similarity search","Lock-free","Linearizability"],"scopus_import":"1"},{"quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","doi":"10.1109/TSP.2021.3087899","date_updated":"2023-08-10T14:19:33Z","date_published":"2021-06-09T00:00:00Z","author":[{"orcid":"0000-0002-7758-2016","last_name":"Gabrielaitis","first_name":"Mantas","id":"4D5B0CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Gabrielaitis, Mantas"}],"isi":1,"month":"06","language":[{"iso":"eng"}],"day":"09","publication_status":"published","intvolume":"        69","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.04832"}],"abstract":[{"lang":"eng","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."}],"arxiv":1,"date_created":"2021-08-08T22:01:31Z","oa_version":"Preprint","publisher":"Institute of Electrical and Electronics Engineers","publication":"IEEE Transactions on Signal Processing","title":"Fast and accurate amplitude demodulation of wideband signals","department":[{"_id":"GaTk"}],"publication_identifier":{"issn":["1053-587X"],"eissn":["1941-0476"]},"citation":{"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.","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>.","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>","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>","ista":"Gabrielaitis M. 2021. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 69, 4039–4054.","short":"M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 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>."},"external_id":{"arxiv":["2102.04832"],"isi":["000682123900002"]},"article_type":"original","acknowledgement":"The author thanks his colleagues K. Huszár and G. Tkačik for valuable discussions and comments on the manuscript.","status":"public","oa":1,"year":"2021","_id":"9828","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":69,"page":"4039 - 4054"},{"title":"News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience","department":[{"_id":"MaIb"}],"publication":"ACS Nano","publisher":"American Chemical Society","oa_version":"Published Version","date_created":"2021-08-08T22:01:31Z","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"}],"page":"10743–10747","volume":15,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9829","year":"2021","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.","status":"public","oa":1,"external_id":{"isi":["000679406500002"],"pmid":["34228432"]},"article_type":"original","issue":"7","citation":{"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>","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>.","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.","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.","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.","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>.","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>"},"publication_identifier":{"eissn":["1936086X"],"issn":["19360851"]},"author":[{"full_name":"Baranov, Dmitry","first_name":"Dmitry","last_name":"Baranov"},{"full_name":"Šverko, Tara","first_name":"Tara","last_name":"Šverko"},{"last_name":"Moot","first_name":"Taylor","full_name":"Moot, Taylor"},{"full_name":"Keller, Helena R.","first_name":"Helena R.","last_name":"Keller"},{"full_name":"Klein, Megan D.","last_name":"Klein","first_name":"Megan D."},{"full_name":"Vishnu, E. K.","first_name":"E. K.","last_name":"Vishnu"},{"first_name":"Daniel","last_name":"Balazs","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"first_name":"Katherine E.","last_name":"Shulenberger","full_name":"Shulenberger, Katherine E."}],"date_published":"2021-07-06T00:00:00Z","doi":"10.1021/acsnano.1c03276","date_updated":"2023-08-11T10:55:08Z","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1021/acsnano.1c03276","open_access":"1"}],"intvolume":"        15","publication_status":"published","pmid":1,"day":"06","language":[{"iso":"eng"}],"isi":1,"month":"07"},{"pmid":1,"ddc":["610","570"],"day":"10","month":"08","isi":1,"genbank":["GSE178867"],"language":[{"iso":"eng"}],"intvolume":"        12","file":[{"file_id":"9876","date_updated":"2021-08-10T12:29:59Z","file_name":"2021_NatureCommunications_Raso.pdf","checksum":"48d8562e8229e4282f3f354b329722c5","file_size":4364333,"creator":"asandaue","access_level":"open_access","relation":"main_file","success":1,"date_created":"2021-08-10T12:29:59Z","content_type":"application/pdf"}],"publication_status":"published","date_published":"2021-08-10T00:00:00Z","author":[{"last_name":"Raso","first_name":"Andrea","full_name":"Raso, Andrea"},{"last_name":"Dirkx","first_name":"Ellen","full_name":"Dirkx, Ellen"},{"full_name":"Sampaio-Pinto, Vasco","last_name":"Sampaio-Pinto","first_name":"Vasco"},{"first_name":"Hamid","last_name":"el Azzouzi","full_name":"el Azzouzi, Hamid"},{"first_name":"Ryan J","last_name":"Cubero","orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425"},{"full_name":"Sorensen, Daniel W.","last_name":"Sorensen","first_name":"Daniel W."},{"full_name":"Ottaviani, Lara","first_name":"Lara","last_name":"Ottaviani"},{"full_name":"Olieslagers, Servé","first_name":"Servé","last_name":"Olieslagers"},{"first_name":"Manon M.","last_name":"Huibers","full_name":"Huibers, Manon M."},{"full_name":"de Weger, Roel","first_name":"Roel","last_name":"de Weger"},{"last_name":"Siddiqi","first_name":"Sailay","full_name":"Siddiqi, Sailay"},{"first_name":"Silvia","last_name":"Moimas","full_name":"Moimas, Silvia"},{"full_name":"Torrini, Consuelo","last_name":"Torrini","first_name":"Consuelo"},{"full_name":"Zentillin, Lorena","first_name":"Lorena","last_name":"Zentillin"},{"full_name":"Braga, Luca","first_name":"Luca","last_name":"Braga"},{"full_name":"Nascimento, Diana S.","first_name":"Diana S.","last_name":"Nascimento"},{"full_name":"da Costa Martins, Paula A.","last_name":"da Costa Martins","first_name":"Paula A."},{"first_name":"Jop H.","last_name":"van Berlo","full_name":"van Berlo, Jop H."},{"full_name":"Zacchigna, Serena","first_name":"Serena","last_name":"Zacchigna"},{"first_name":"Mauro","last_name":"Giacca","full_name":"Giacca, Mauro"},{"last_name":"De Windt","first_name":"Leon J.","full_name":"De Windt, Leon J."}],"article_processing_charge":"Yes","date_updated":"2023-08-11T10:27:03Z","doi":"10.1038/s41467-021-25211-4","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-32785-0"}]},"scopus_import":"1","quality_controlled":"1","file_date_updated":"2021-08-10T12:29:59Z","article_number":"4808","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":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).","status":"public","article_type":"original","external_id":{"pmid":["34376683"],"isi":["000683910200042"]},"citation":{"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>","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>.","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.","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.","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>.","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>"},"publication_identifier":{"eissn":["2041-1723"]},"volume":12,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"9874","has_accepted_license":"1","year":"2021","abstract":[{"lang":"eng","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."}],"publication":"Nature Communications","department":[{"_id":"SaSi"}],"title":"A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration","publisher":"Springer Nature","date_created":"2021-08-10T11:49:20Z","oa_version":"Published Version"},{"day":"16","ddc":["580","570"],"pmid":1,"language":[{"iso":"eng"}],"isi":1,"month":"07","publication_status":"published","file":[{"file_size":1898360,"file_name":"2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf","checksum":"19e84ad8c03c60222744ee8e16cd6998","file_id":"9879","date_updated":"2021-08-11T09:31:41Z","content_type":"application/pdf","success":1,"date_created":"2021-08-11T09:31:41Z","relation":"main_file","creator":"asandaue","access_level":"open_access"}],"intvolume":"       118","date_updated":"2023-08-11T10:28:10Z","doi":"10.1073/pnas.2104445118","article_processing_charge":"Yes (in subscription journal)","author":[{"full_name":"Rodrigues, Jessica A.","first_name":"Jessica A.","last_name":"Rodrigues"},{"last_name":"Hsieh","first_name":"Ping-Hung","full_name":"Hsieh, Ping-Hung"},{"last_name":"Ruan","first_name":"Deling","full_name":"Ruan, Deling"},{"last_name":"Nishimura","first_name":"Toshiro","full_name":"Nishimura, Toshiro"},{"full_name":"Sharma, Manoj K.","first_name":"Manoj K.","last_name":"Sharma"},{"full_name":"Sharma, Rita","first_name":"Rita","last_name":"Sharma"},{"first_name":"XinYi","last_name":"Ye","full_name":"Ye, XinYi"},{"last_name":"Nguyen","first_name":"Nicholas D.","full_name":"Nguyen, Nicholas D."},{"full_name":"Nijjar, Sukhranjan","last_name":"Nijjar","first_name":"Sukhranjan"},{"full_name":"Ronald, Pamela C.","first_name":"Pamela C.","last_name":"Ronald"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","first_name":"Daniel"}],"date_published":"2021-07-16T00:00:00Z","quality_controlled":"1","scopus_import":"1","article_number":"e2104445118","file_date_updated":"2021-08-11T09:31:41Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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)"},"external_id":{"isi":["000685037700012"],"pmid":["34272287"]},"article_type":"original","issue":"29","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.","oa":1,"status":"public","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"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. <i>Proceedings of the National Academy of Sciences</i>. 2021;118(29). doi:<a href=\"https://doi.org/10.1073/pnas.2104445118\">10.1073/pnas.2104445118</a>","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).","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.","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</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>.","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</i>, vol. 118, no. 29. National Academy of Sciences, 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.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>.","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</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>"},"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":118,"has_accepted_license":"1","year":"2021","_id":"9877","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."}],"publisher":"National Academy of Sciences","department":[{"_id":"DaZi"}],"title":"Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting","publication":"Proceedings of the National Academy of Sciences","oa_version":"Published Version","date_created":"2021-08-10T19:30:41Z"},{"file_date_updated":"2021-12-15T08:59:40Z","article_number":"e2113046118","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"author":[{"orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"full_name":"Dahhan, Dana A","first_name":"Dana A","last_name":"Dahhan"},{"orcid":"0000-0002-2198-0509","last_name":"Gnyliukh","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","full_name":"Gnyliukh, Nataliia"},{"orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"full_name":"Zheden, Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","last_name":"Zheden","orcid":"0000-0002-9438-4783"},{"orcid":"0000-0001-9732-3815","last_name":"Costanzo","first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso"},{"first_name":"Pierre","last_name":"Mahou","full_name":"Mahou, Pierre"},{"first_name":"Mónika","last_name":"Hrtyan","full_name":"Hrtyan, Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wang, Jie","first_name":"Jie","last_name":"Wang"},{"orcid":"0000-0002-2862-8372","last_name":"Aguilera Servin","first_name":"Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","full_name":"Aguilera Servin, Juan L"},{"full_name":"van Damme, Daniël","last_name":"van Damme","first_name":"Daniël"},{"full_name":"Beaurepaire, Emmanuel","first_name":"Emmanuel","last_name":"Beaurepaire"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin"},{"first_name":"Sebastian Y","last_name":"Bednarek","full_name":"Bednarek, Sebastian Y"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"date_published":"2021-12-14T00:00:00Z","article_processing_charge":"No","date_updated":"2024-02-19T11:06:09Z","doi":"10.1073/pnas.2113046118","related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2021.04.26.441441"}],"record":[{"relation":"dissertation_contains","status":"public","id":"14510"},{"relation":"research_data","status":"public","id":"14988"}]},"quality_controlled":"1","intvolume":"       118","file":[{"success":1,"date_created":"2021-12-15T08:59:40Z","content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","relation":"main_file","file_name":"2021_PNAS_Johnson.pdf","checksum":"8d01e72e22c4fb1584e72d8601947069","file_size":2757340,"file_id":"10546","date_updated":"2021-12-15T08:59:40Z"}],"publication_status":"published","pmid":1,"ddc":["580"],"day":"14","month":"12","isi":1,"project":[{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"publisher":"National Academy of Sciences","date_created":"2021-08-11T14:11:43Z","oa_version":"Published Version","abstract":[{"text":"Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells.","lang":"eng"}],"volume":118,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"9887","year":"2021","has_accepted_license":"1","acknowledgement":"We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).","oa":1,"status":"public","issue":"51","article_type":"original","external_id":{"isi":["000736417600043"],"pmid":["34907016"]},"citation":{"ama":"Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences</i>. 2021;118(51). doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>","mla":"Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 51, e2113046118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>.","ista":"Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M, Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. 118(51), e2113046118.","short":"A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences 118 (2021).","ieee":"A. J. Johnson <i>et al.</i>, “The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 51. National Academy of Sciences, 2021.","chicago":"Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann, Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>.","apa":"Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo, T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>"},"publication_identifier":{"eissn":["1091-6490"]}},{"isi":1,"month":"08","language":[{"iso":"eng"}],"ddc":["530"],"day":"01","intvolume":"        62","file":[{"date_updated":"2021-10-27T12:57:06Z","file_id":"10188","file_size":4352640,"file_name":"2021_JMathPhy_Lauritsen.pdf","checksum":"d035be2b894c4d50d90ac5ce252e27cd","relation":"main_file","creator":"cziletti","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2021-10-27T12:57:06Z"}],"publication_status":"published","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"scopus_import":"1","quality_controlled":"1","author":[{"orcid":"0000-0003-4476-2288","last_name":"Lauritsen","first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard"}],"date_published":"2021-08-01T00:00:00Z","article_processing_charge":"No","date_updated":"2023-08-11T10:29:48Z","doi":"10.1063/5.0053494","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2021-10-27T12:57:06Z","article_number":"083305","citation":{"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>","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>.","ieee":"A. B. Lauritsen, “Floating Wigner crystal and periodic jellium configurations,” <i>Journal of Mathematical Physics</i>, vol. 62, no. 8. AIP Publishing, 2021.","ista":"Lauritsen AB. 2021. Floating Wigner crystal and periodic jellium configurations. Journal of Mathematical Physics. 62(8), 083305.","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>.","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>"},"publication_identifier":{"issn":["0022-2488"],"eissn":["1089-7658"]},"status":"public","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.","oa":1,"issue":"8","article_type":"original","external_id":{"arxiv":["2103.07975"],"isi":["000683960800003"]},"_id":"9891","has_accepted_license":"1","year":"2021","volume":62,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","abstract":[{"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.","lang":"eng"}],"arxiv":1,"date_created":"2021-08-12T07:08:36Z","oa_version":"Published Version","publication":"Journal of Mathematical Physics","title":"Floating Wigner crystal and periodic jellium configurations","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"publisher":"AIP Publishing"},{"oa_version":"Published Version","ec_funded":1,"date_created":"2021-08-13T09:27:39Z","department":[{"_id":"MaSe"},{"_id":"GradSch"},{"_id":"MiLe"}],"title":"Area-law entangled eigenstates from nullspaces of local Hamiltonians","publication":"Physical Review Letters","publisher":"American Physical Society","abstract":[{"text":"Eigenstate thermalization in quantum many-body systems implies that eigenstates at high energy are similar to random vectors. Identifying systems where at least some eigenstates are nonthermal is an outstanding question. In this Letter we show that interacting quantum models that have a nullspace—a degenerate subspace of eigenstates at zero energy (zero modes), which corresponds to infinite temperature, provide a route to nonthermal eigenstates. We analytically show the existence of a zero mode which can be represented as a matrix product state for a certain class of local Hamiltonians. In the more general case we use a subspace disentangling algorithm to generate an orthogonal basis of zero modes characterized by increasing entanglement entropy. We show evidence for an area-law entanglement scaling of the least-entangled zero mode in the broad parameter regime, leading to a conjecture that all local Hamiltonians with the nullspace feature zero modes with area-law entanglement scaling and, as such, break the strong thermalization hypothesis. Finally, we find zero modes in constrained models and propose a setup for observing their experimental signatures.","lang":"eng"}],"arxiv":1,"_id":"9903","has_accepted_license":"1","year":"2021","volume":127,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Karle V, Serbyn M, Michailidis A. 2021. Area-law entangled eigenstates from nullspaces of local Hamiltonians. Physical Review Letters. 127(6), 060602.","mla":"Karle, Volker, et al. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” <i>Physical Review Letters</i>, vol. 127, no. 6, 060602, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.127.060602\">10.1103/physrevlett.127.060602</a>.","short":"V. Karle, M. Serbyn, A. Michailidis, Physical Review Letters 127 (2021).","ama":"Karle V, Serbyn M, Michailidis A. Area-law entangled eigenstates from nullspaces of local Hamiltonians. <i>Physical Review Letters</i>. 2021;127(6). doi:<a href=\"https://doi.org/10.1103/physrevlett.127.060602\">10.1103/physrevlett.127.060602</a>","apa":"Karle, V., Serbyn, M., &#38; Michailidis, A. (2021). Area-law entangled eigenstates from nullspaces of local Hamiltonians. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.127.060602\">https://doi.org/10.1103/physrevlett.127.060602</a>","ieee":"V. Karle, M. Serbyn, and A. Michailidis, “Area-law entangled eigenstates from nullspaces of local Hamiltonians,” <i>Physical Review Letters</i>, vol. 127, no. 6. American Physical Society, 2021.","chicago":"Karle, Volker, Maksym Serbyn, and Alexios Michailidis. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevlett.127.060602\">https://doi.org/10.1103/physrevlett.127.060602</a>."},"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"oa":1,"status":"public","acknowledgement":"We acknowledge useful discussions with V. Gritsev and A. Garkun and suggestions on implementation of the\r\nPPXPP model by D. Bluvstein. A. M. and M. S. were supported by the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899)","article_type":"letter_note","external_id":{"arxiv":["2102.13633"],"isi":["000684276000002"]},"issue":"6","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2021-08-13T09:28:08Z","article_number":"060602","quality_controlled":"1","date_published":"2021-08-06T00:00:00Z","author":[{"first_name":"Volker","orcid":"0000-0002-6963-0129","last_name":"Karle","full_name":"Karle, Volker","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425"},{"first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Michailidis, Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios","orcid":"0000-0002-8443-1064","last_name":"Michailidis"}],"doi":"10.1103/physrevlett.127.060602","date_updated":"2023-08-11T10:43:27Z","article_processing_charge":"Yes (in subscription journal)","intvolume":"       127","publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","creator":"mserbyn","content_type":"application/pdf","date_created":"2021-08-13T09:28:08Z","success":1,"date_updated":"2021-08-13T09:28:08Z","file_id":"9904","file_size":5064231,"checksum":"51218f302dcef99d90d1209809fcc874","file_name":"PhysRevLett.127.060602_SOM.pdf"}],"project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"month":"08","isi":1,"day":"06","ddc":["539"]},{"pmid":1,"day":"30","ddc":["570","610"],"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"month":"07","isi":1,"intvolume":"        11","publication_status":"published","file":[{"date_created":"2021-08-16T11:36:49Z","success":1,"content_type":"application/pdf","creator":"asandaue","access_level":"open_access","relation":"main_file","checksum":"ac86892ed17e6724c7251844da5cef5c","file_name":"2021_ScientificReports_Rella.pdf","file_size":3432001,"file_id":"9927","date_updated":"2021-08-16T11:36:49Z"}],"author":[{"last_name":"Rella","first_name":"Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","full_name":"Rella, Simon"},{"full_name":"Kulikova, Yuliya A.","first_name":"Yuliya A.","last_name":"Kulikova"},{"last_name":"Dermitzakis","first_name":"Emmanouil T.","full_name":"Dermitzakis, Emmanouil T."},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"}],"date_published":"2021-07-30T00:00:00Z","doi":"10.1038/s41598-021-95025-3","related_material":{"link":[{"url":"https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/","relation":"press_release","description":"News on IST Website"}]},"date_updated":"2023-08-11T10:42:58Z","article_processing_charge":"Yes","scopus_import":"1","quality_controlled":"1","file_date_updated":"2021-08-16T11:36:49Z","article_number":"15729","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"status":"public","acknowledgement":"We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta, Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España for useful comments. The opinions expressed in this document are exclusively of the authors and, therefore, do not necessarily coincide with those of the Banco de España or the Eurosystem. ETD is supported by the Swiss National Science and Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator Grant (771209-CharFL).","external_id":{"isi":["000683329100001"],"pmid":["34330988"]},"article_type":"original","issue":"1","citation":{"apa":"Rella, S., Kulikova, Y. A., Dermitzakis, E. T., &#38; Kondrashov, F. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-021-95025-3\">https://doi.org/10.1038/s41598-021-95025-3</a>","ieee":"S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,” <i>Scientific Reports</i>, vol. 11, no. 1. Springer Nature, 2021.","chicago":"Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-021-95025-3\">https://doi.org/10.1038/s41598-021-95025-3</a>.","mla":"Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” <i>Scientific Reports</i>, vol. 11, no. 1, 15729, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-021-95025-3\">10.1038/s41598-021-95025-3</a>.","ista":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 11(1), 15729.","short":"S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports 11 (2021).","ama":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. <i>Scientific Reports</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.1038/s41598-021-95025-3\">10.1038/s41598-021-95025-3</a>"},"publication_identifier":{"eissn":["20452322"]},"volume":11,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9905","has_accepted_license":"1","year":"2021","abstract":[{"lang":"eng","text":"Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions and transmission-reducing behaviours throughout the entire vaccination period."}],"title":"Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains","department":[{"_id":"FyKo"}],"publication":"Scientific Reports","publisher":"Springer Nature","oa_version":"Published Version","date_created":"2021-08-15T22:01:26Z","ec_funded":1},{"date_created":"2021-08-15T22:01:27Z","oa_version":"Published Version","publication":"International Journal of Molecular Sciences","department":[{"_id":"SiHi"}],"title":"LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line","publisher":"MDPI","abstract":[{"lang":"eng","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."}],"_id":"9906","year":"2021","has_accepted_license":"1","volume":22,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","citation":{"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.","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>.","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>","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>","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).","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."},"publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"status":"public","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.","oa":1,"issue":"16","external_id":{"isi":["000689147400001"]},"article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2021-08-16T09:29:17Z","article_number":"8385","scopus_import":"1","quality_controlled":"1","author":[{"full_name":"Yotova, Iveta","last_name":"Yotova","first_name":"Iveta"},{"full_name":"Hudson, Quanah J.","first_name":"Quanah J.","last_name":"Hudson"},{"last_name":"Pauler","orcid":"0000-0002-7462-0048","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian"},{"full_name":"Proestling, Katharina","last_name":"Proestling","first_name":"Katharina"},{"first_name":"Isabella","last_name":"Haslinger","full_name":"Haslinger, Isabella"},{"full_name":"Kuessel, Lorenz","last_name":"Kuessel","first_name":"Lorenz"},{"first_name":"Alexandra","last_name":"Perricos","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_published":"2021-08-04T00:00:00Z","article_processing_charge":"Yes","date_updated":"2023-08-11T10:34:13Z","doi":"10.3390/ijms22168385","intvolume":"        22","file":[{"content_type":"application/pdf","success":1,"date_created":"2021-08-16T09:29:17Z","relation":"main_file","access_level":"open_access","creator":"asandaue","file_size":2646018,"file_name":"2021_InternationalJournalOfMolecularSciences_Yotova.pdf","checksum":"be7f0042607ca60549cb27513c19c6af","file_id":"9922","date_updated":"2021-08-16T09:29:17Z"}],"publication_status":"published","month":"08","isi":1,"language":[{"iso":"eng"}],"ddc":["570"],"day":"04"},{"publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"citation":{"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>.","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.","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>","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>","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>.","short":"N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International Journal of Molecular Sciences 22 (2021)."},"external_id":{"pmid":["34361115"],"isi":["000681815400001"]},"article_type":"original","issue":"15","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.","oa":1,"status":"public","year":"2021","has_accepted_license":"1","_id":"9907","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":22,"abstract":[{"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. ","lang":"eng"}],"oa_version":"Published Version","date_created":"2021-08-15T22:01:27Z","ec_funded":1,"publisher":"MDPI","title":"Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva","department":[{"_id":"MaLo"}],"publication":"International Journal of Molecular Sciences","language":[{"iso":"eng"}],"project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020"}],"month":"08","isi":1,"day":"01","ddc":["570"],"pmid":1,"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","creator":"asandaue","content_type":"application/pdf","date_created":"2021-08-16T09:35:56Z","success":1,"date_updated":"2021-08-16T09:35:56Z","file_id":"9923","file_size":6132410,"checksum":"a4bc06e9a2c803ceff5a91f10b174054","file_name":"2021_InternationalJournalOfMolecularSciences_Labajová .pdf"}],"intvolume":"        22","quality_controlled":"1","scopus_import":"1","date_updated":"2023-08-11T10:34:44Z","doi":"10.3390/ijms22158350","article_processing_charge":"Yes","author":[{"full_name":"Labajová, Naďa","last_name":"Labajová","first_name":"Naďa"},{"full_name":"Baranova, Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S.","last_name":"Baranova","orcid":"0000-0002-3086-9124"},{"last_name":"Jurásek","first_name":"Miroslav","full_name":"Jurásek, Miroslav"},{"last_name":"Vácha","first_name":"Robert","full_name":"Vácha, Robert"},{"orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"},{"full_name":"Barák, Imrich","first_name":"Imrich","last_name":"Barák"}],"date_published":"2021-08-01T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"8350","file_date_updated":"2021-08-16T09:35:56Z"},{"day":"01","ddc":["570"],"project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"language":[{"iso":"eng"}],"month":"08","isi":1,"publication_status":"published","file":[{"content_type":"application/pdf","success":1,"date_created":"2021-08-16T09:49:35Z","relation":"main_file","access_level":"open_access","creator":"asandaue","file_size":2297655,"file_name":"2021_Genes_Picard.pdf","checksum":"744e60e56d290a96da3c91a9779f886f","file_id":"9926","date_updated":"2021-08-16T09:49:35Z"}],"intvolume":"        12","doi":"10.3390/genes12081136","date_updated":"2023-08-11T10:42:32Z","article_processing_charge":"Yes","author":[{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","full_name":"Picard, Marion A L","last_name":"Picard","orcid":"0000-0002-8101-2518","first_name":"Marion A L"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"},{"last_name":"Bertrand","first_name":"Stéphanie","full_name":"Bertrand, Stéphanie"},{"first_name":"Hector","last_name":"Escriva","full_name":"Escriva, Hector"}],"date_published":"2021-08-01T00:00:00Z","quality_controlled":"1","scopus_import":"1","article_number":"1136","file_date_updated":"2021-08-16T09:49:35Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"review","external_id":{"isi":["000690475900001"]},"issue":"8","status":"public","oa":1,"publication_identifier":{"eissn":["20734425"]},"citation":{"apa":"Picard, M. A. L., Vicoso, B., Bertrand, S., &#38; Escriva, H. (2021). Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12081136\">https://doi.org/10.3390/genes12081136</a>","ieee":"M. A. L. Picard, B. Vicoso, S. Bertrand, and H. Escriva, “Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict,” <i>Genes</i>, vol. 12, no. 8. MDPI, 2021.","chicago":"Picard, Marion A L, Beatriz Vicoso, Stéphanie Bertrand, and Hector Escriva. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12081136\">https://doi.org/10.3390/genes12081136</a>.","ista":"Picard MAL, Vicoso B, Bertrand S, Escriva H. 2021. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. Genes. 12(8), 1136.","mla":"Picard, Marion A. L., et al. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” <i>Genes</i>, vol. 12, no. 8, 1136, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12081136\">10.3390/genes12081136</a>.","short":"M.A.L. Picard, B. Vicoso, S. Bertrand, H. Escriva, Genes 12 (2021).","ama":"Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. <i>Genes</i>. 2021;12(8). doi:<a href=\"https://doi.org/10.3390/genes12081136\">10.3390/genes12081136</a>"},"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":12,"has_accepted_license":"1","year":"2021","_id":"9908","abstract":[{"lang":"eng","text":"About eight million animal species are estimated to live on Earth, and all except those belonging to one subphylum are invertebrates. Invertebrates are incredibly diverse in their morphologies, life histories, and in the range of the ecological niches that they occupy. A great variety of modes of reproduction and sex determination systems is also observed among them, and their mosaic-distribution across the phylogeny shows that transitions between them occur frequently and rapidly. Genetic conflict in its various forms is a long-standing theory to explain what drives those evolutionary transitions. Here, we review (1) the different modes of reproduction among invertebrate species, highlighting sexual reproduction as the probable ancestral state; (2) the paradoxical diversity of sex determination systems; (3) the different types of genetic conflicts that could drive the evolution of such different systems."}],"publisher":"MDPI","title":"Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict","department":[{"_id":"BeVi"}],"publication":"Genes","oa_version":"Published Version","ec_funded":1,"date_created":"2021-08-15T22:01:27Z"}]